@article {719916,
	title = {BlastAssist: a deep learning pipeline to measure interpretable features of human embryos},
	journal = {Human Reproduction},
	year = {2024},
	abstract = {
	STUDY QUESTION: Can the BlastAssist deep learning pipeline perform comparably to or outperform human experts and embryologists at measuring interpretable, clinically relevant features of human embryos in IVF?



	SUMMARY ANSWER: The BlastAssist pipeline can measure a comprehensive set of interpretable features of human embryos and either outperform or perform comparably to embryologists and human experts in measuring these features,



	WHAT IS KNOWN ALREADY: Some studies have applied deep learning and developed {\textquoteleft}black-box{\textquoteright} algorithms to predict embryo viability directly from microscope images and videos but these lack interpretability and generalizability. Other studies have developed deep learning networks to measure individual features of embryos but fail to conduct careful comparisons to embryologists{\textquoteright} performance, which are fundamental to demonstrate the network{\textquoteright}s effectiveness.



	STUDY DESIGN, SIZE, DURATION: We applied the BlastAssist pipeline to 67 043 973 images (32 939 embryos) recorded in the IVF lab from 2012 to 2017 in Tel Aviv Sourasky Medical Center. We first compared the pipeline measurements of individual images/embryos to manual measurements by human experts for sets of features, including: (i) fertilization status (n = 207 embryos), (ii) cell symmetry (n = 109 embryos), (iii) degree of fragmentation (n = 6664 images), and (iv) developmental timing (n = 21 036 images). We then conducted detailed comparisons between pipeline outputs and annotations made by embryologists during routine treatments for features, including: (i) fertilization status (n = 18 922 embryos), (ii) pronuclei (PN) fade time (n = 13 781 embryos), (iii) degree of fragmentation on Day 2 (n = 11 582 embryos), and (iv) time of blastulation (n = 3266 embryos). In addition, we compared the pipeline outputs to the implantation results of 723 single embryo transfer (SET) cycles, and to the live birth results of 3421 embryos transferred in 1801 cycles.



	PARTICIPANTS/MATERIALS, SETTING, METHODS: In addition to EmbryoScope{\texttrademark} image data, manual embryo grading and annotations, and electronic health record (EHR) data on treatment outcomes were also included. We integrated the deep learning networks we developed for individual features to construct the BlastAssist pipeline. Pearson{\textquoteright}s\&nbsp;χ2\&nbsp;test was used to evaluate the statistical independence of individual features and implantation success. Bayesian statistics was used to evaluate the association of the probability of an embryo resulting in live birth to BlastAssist inputs.



	MAIN RESULTS AND THE ROLE OF CHANCE: The BlastAssist pipeline integrates five deep learning networks and measures comprehensive, interpretable, and quantitative features in clinical IVF. The pipeline performs similarly or better than manual measurements. For fertilization status, the network performs with very good parameters of specificity and sensitivity (area under the receiver operating characteristics (AUROC) 0.84{\textendash}0.94). For symmetry score, the pipeline performs comparably to the human expert at both 2-cell (r = 0.71 {\textpm} 0.06) and 4-cell stages (r = 0.77 {\textpm} 0.07). For degree of fragmentation, the pipeline (acc = 69.4\%) slightly under-performs compared to human experts (acc = 73.8\%). For developmental timing, the pipeline (acc = 90.0\%) performs similarly to human experts (acc = 91.4\%). There is also strong agreement between pipeline outputs and annotations made by embryologists during routine treatments. For fertilization status, the pipeline and embryologists strongly agree (acc = 79.6\%), and there is strong correlation between the two measurements (r = 0.683). For degree of fragmentation, the pipeline and embryologists mostly agree (acc = 55.4\%), and there is also strong correlation between the two measurements (r = 0.648). For both PN fade time (r = 0.787) and time of blastulation (r = 0.887), there{\textquoteright}s strong correlation between the pipeline and embryologists. For SET cycles, 2-cell time (P \&lt; 0.01) and 2-cell symmetry (P \&lt; 0.03) are significantly correlated with implantation success rate, while other features showed correlations with implantation success without statistical significance. In addition, 2-cell time (P \&lt; 5 {\texttimes} 10-11), PN fade time (P \&lt; 5 {\texttimes} 10-10), degree of fragmentation on Day 3 (P \&lt; 5 {\texttimes} 10-4), and 2-cell symmetry (P \&lt; 5 {\texttimes} 10-3) showed statistically significant correlation with the probability of the transferred embryo resulting in live birth.



	LIMITATIONS, REASONS FOR CAUTION: We have not tested the BlastAssist pipeline on data from other clinics or other time-lapse microscopy (TLM) systems. The association study we conducted with live birth results do not take into account confounding variables, which will be necessary to construct an embryo selection algorithm. Randomized controlled trials (RCT) will be necessary to determine whether the pipeline can improve success rates in clinical IVF.



	WIDER IMPLICATIONS OF THE FINDINGS: BlastAssist provides a comprehensive and holistic means of evaluating human embryos. Instead of using a black-box algorithm, BlastAssist outputs meaningful measurements of embryos that can be interpreted and corroborated by embryologists, which is crucial in clinical decision making. Furthermore, the unprecedentedly large dataset generated by BlastAssist measurements can be used as a powerful resource for further research in human embryology and IVF.



	STUDY FUNDING/COMPETING INTEREST(S): This work was supported by Harvard Quantitative Biology Initiative, the NSF-Simons Center for Mathematical and Statistical Analysis of Biology at Harvard (award number 1764269), the National Institute of Heath (award number R01HD104969), the Perelson Fund, and the Sagol fund for embryos and stem cells as part of the Sagol Network. The authors declare no competing interests.



	TRIAL REGISTRATION NUMBER: Not applicable.

},
	author = {Helen Y. Yang and Brian D. Leahy and Jang, Won-Dong and Donglai Wei and Kalma, Yael and Roni Rahav and Ariella Carmon and Rotem Kopel and Foad Azem and Marta Venturas and Colm P. Kelleher and Liz Cam and Pfister, Hanspeter and Daniel J. Needleman and Dalit Ben-Yosef}
}
@article {710906,
	title = {Laser ablation and fluid flows reveal the mechanism behind spindle and centrosome positioning},
	journal = {Nature Physics},
	year = {2023},
	abstract = {
	Few techniques are available for studying the nature of forces that drive subcellular dynamics. Here we develop two complementary ones. The first is femtosecond stereotactic laser ablation, which rapidly creates complex cuts of subcellular structures and enables precise dissection of when, where and in what direction forces are generated. The second is an assessmentof subcellular fluid flows by comparison of direct flow measurementsusing microinjected fluorescent nanodiamonds with large-scale fluid-structure simulations of different force transduction models. We apply these techniques to study spindle and centrosome positioning in early Caenorhabditis elegans embryos and to probe the contributionsof microtubule pushing, cytoplasmic pulling and cortical pulling upon centrosomal microtubules. Based on our results, we construct a biophysical model to explain the dynamics of centrosomes. We demonstrate that cortical pulling forces provide a general explanation for many behaviours mediated by centrosomes, including pronuclear migration and centration, rotation, metaphase spindle positioning, asymmetric spindle elongation and spindle oscillations. This work establishes methodologies for disentangling the forces responsible for cell biological phenomena.



	\&nbsp;

},
	author = {Wu, Hai-Yin and G{\"o}kberk Kabacao{\u g}lu and Nazockdast, Ehssan and Huan-Cheng Chang and Shelley, Michael J. and Daniel J. Needleman}
}
@article {708966,
	title = {Multi-Task Curriculum Learning for Partially Labeled Data},
	journal = {IEEE 20th International Symposium on Biomedical Imaging (ISBI)},
	year = {2023},
	abstract = {Incomplete labels are common in multi-task learning for biomedical applications due to several practical difficulties, e.g., expensive annotation efforts by experts, limit of data collection, different sources of data. A naive approach to enable joint learning for partially labeled data is adding self-supervised learning for tasks without ground truths by augmenting an input image and forcing the multi-task model to return the same outputs for both the input and augmented images. However, the partially labeled setting can result in imbalanced learning of tasks since not all tasks are trainable with ground truth supervisions for each data sample. In this work, we propose a multi-task curriculum learning method tailored for partially labeled data. For balanced learning of tasks, our multitask curriculum prioritizes less performing tasks during training by setting different supervised learning frequencies for each task. We demonstrate that our method outperforms standard approaches on one biomedical and two natural image datasets. Furthermore, our learning method with partially labeled data performs better than the standard multi-task learning methods with fully labeled data for the same number of annotations.},
	author = {Jang, Won-Dong and Stanislav Lukyanenko and Donglai Wei and Jiancheng Yang and Brian Leahy and Helen Yang and Dalit Ben-Yosef and Needleman, Daniel and Pfister, Hanspeter}
}
@article {708961,
	title = {Learning Vector Quantized Shape Code for Amodal Blastomere Instance Segmentation},
	journal = {IEEE 20th International Symposium on Biomedical Imaging (ISBI)},
	year = {2023},
	abstract = {Blastomere instance segmentation is important for analyzing embryos{\textquoteright} abnormality. To measure the accurate shapes and sizes of blastomeres, their amodal segmentation is necessary. Amodal instance segmentation aims to recover an object{\textquoteright}s complete silhouette even when the object is not fully visible. For each detected object, previous methods directly regress the target mask from input features. However, images of an object under different amounts of occlusion should have the same amodal mask output, making it harder to train the regression model. To alleviate the problem, we propose to classify input features into intermediate shape codes and recover complete object shapes. First, we pre-train the Vector Quantized Variational Autoencoder (VQ-VAE) model to learn these discrete shape codes from ground truth amodal masks. Then, we incorporate the VQ-VAE model into the amodal instance segmentation pipeline with an additional refinement module. We also detect an occlusion map to integrate occlusion information with a backbone feature. As such, our network faithfully detects bounding boxes of amodal objects. On an internal embryo cell image benchmark, the proposed method outperforms previous state-of-the-art methods. To show generalizability, we show segmentation results on the public KINS natural image benchmark. Our method would enable accurate measurement of blastomeres in In Vitro Fertilization (IVF) clinics, potentially increasing the IVF success rate.},
	author = {Jang, Won-Dong and Donglai Wei and Xingxuan Zhang and Brian Leahy and Helen Yang and James Tompkin and Dalit Ben-Yosef and Needleman, Daniel and Pfister, Hanspeter}
}
@article {699826,
	title = {Noninvasive metabolic profiling of cumulus cells, oocytes, and embryos via fluorescence lifetime imaging microscopy: a mini-review},
	journal = {Human Reproduction},
	year = {2023},
	abstract = {
	A major challenge in ART is to select high-quality oocytes and embryos. The metabolism of oocytes and embryos has long been linked to their viability, suggesting the potential utility of metabolic measurements to aid in selection. Here, we review recent work on noninvasive metabolic imaging of cumulus cells, oocytes, and embryos. We focus our discussion on fluorescence lifetime imaging microscopy (FLIM) of the autofluorescent coenzymes NAD(P)H and flavine adenine dinucleotide (FAD{\th}), which play central roles in many metabolic pathways. FLIM measurements provide quantitative information on NAD(P)H and FAD{\th}\&nbsp;concentrations and engagement with enzymes, leading to a robust means of characterizing the metabolic state of cells. We argue that FLIM is a promising approach to aid in oocyte and embryo selection.

},
	author = {Marta Venturas and Xingbo Yang and Sakkas, Denny and Needleman, Dan}
}
@article {699681,
	title = {Dissipation and energy propagation across scales in an active cytoskeletal material},
	journal = {PNAS},
	volume = {120},
	number = {14},
	year = {2023},
	abstract = {
	Living systems are intrinsically nonequilibrium: They use metabolically derived chemical energy to power their emergent dynamics and self-organization. A crucial driver of these dynamics is the cellular cytoskeleton, a defining example of an active material where the energy injected by molecular motors cascades across length scales, allowing the material to break the constraints of thermodynamic equilibrium and display emergent nonequilibrium dynamics only possible due to the constant influx of energy. Notwithstanding recent experimental advances in the use of local probes to quantify entropy production and the breaking of detailed balance, little is known about the energetics of active materials or how energy propagates from the molecular to emergent length scales. Here, we use a recently developed picowatt calorimeter to experimentally measure the energetics of an active microtubule gel that displays emergent large-scale flows. We find that only approximately one-billionth of the system{\textquoteright}s total energy consumption contributes to these emergent flows. We develop a chemical kinetics model that quantitatively captures how the system{\textquoteright}s total thermal dissipation varies with ATP and microtubule concentrations but that breaks down at high motor concentration, signaling an interference between motors. Finally, we estimate how energy losses accumulate across scales. Taken together, these results highlight energetic efficiency as a key consideration for the engineering of active materials and are a powerful step toward developing a nonequilibrium thermody- namics of living systems.

},
	author = {Peter J. Foster and Jinhye Bae and Bezia Lemma and Juanjuan Zheng and William Ireland and Pooja Chandrakar and R{\'e}mi Boros and Zvonimir Dogic and Daniel J. Needleman and Joost J. Vlassak}
}
@article {696196,
	title = {Dissecting Flux Balances to Measure Energetic Costs in Cell Biology: Techniques and Challenges},
	journal = {Annual Review of Condensed Matter Physics},
	year = {2022},
	abstract = {Life is a nonequilibrium phenomenon: Metabolism provides a continuous supply of energy that drives nearly all cellular processes. However, very little is known about how much energy different cellular processes use, i.e., their energetic costs. The most direct experimental measurements of these costs involve modulating the activity of cellular processes and determining the resulting changes in energetic fluxes. In this review, we present a flux balance framework to aid in the design and interpretation of such experiments and discuss the challenges associated with measuring the relevant metabolic fluxes. We then describe selected techniques that enable measurement of these fluxes. Finally, we review prior experimental and theoretical work that has employed techniques from biochemistry and nonequilibrium physics to determine the energetic costs of cellular processes.},
	author = {Easun Arunachalam and William Ireland and Xingbo Yang and Needleman, Daniel}
}
@article {693124,
	title = {Self-organization of kinetochore-fibers in human mitotic spindles},
	journal = {eLife},
	year = {2022},
	abstract = {
	During eukaryotic cell division, chromosomes are linked to microtubules (MTs) in the spindle by a macromolecular complex called the kinetochore. The bound kinetochore microtubules (KMTs) are crucial to ensuring accurate chromosome segregation. Recent reconstructions by electron tomography (Kiewisz et al., 2022) captured the positions and configurations of every MT in human mitotic spindles, revealing that roughly half the KMTs in these spindles do not reach the pole. Here, we investigate the processes that give rise to this distribution of KMTs using a combination of anal- ysis of large-scale electron tomography, photoconversion experiments, quantitative polarized light microscopy, and biophysical modeling. Our results indicate that in metaphase, KMTs grow away from the kinetochores along well-defined trajectories, with the speed of the KMT minus ends contin- ually decreasing as the minus ends approach the pole, implying that longer KMTs grow more slowly than shorter KMTs. The locations of KMT minus ends, and the turnover and movements of tubulin



	in KMTs, are consistent with models in which KMTs predominately nucleate de novo at kinetochores in metaphase and are inconsistent with substantial numbers of non-KMTs being recruited to the kinetochore in metaphase. Taken together, this work leads to a mathematical model of the self- organization of kinetochore-fibers in human mitotic spindles.

},
	author = {Conway, William and Robert Kiewisz and Gunar Fabig and Colm P Kelleher and Wu, Hai-Yin and Maya Anjur-Dietrich and M{\"u}ller-Reichert, Thomas and Needleman, Daniel J}
}
@article {692706,
	title = {Three-dimensional structure of kinetochore-fibers in human mitotic spindles},
	journal = {eLife},
	year = {2022},
	abstract = {
	During cell division, kinetochore microtubules (KMTs) provide a physical linkage between the chromosomes and the rest of the spindle. KMTs in mammalian cells are organized into bundles, so-called kinetochore-fibers (k-fibers), but the ultrastructure of these fibers is currently not well characterized. Here, we show by large-scale electron tomography that each k-fiber in HeLa cells in metaphase is composed of approximately nine KMTs, only half of which reach the spindle pole. Our comprehensive reconstructions allowed us to analyze the three-dimensional (3D) morphology of k-fibers and their surrounding MTs in detail. We found that k-fibers exhibit remarkable variationin circumference and KMT density along their length, with the pole-proximal side showing a broad- ening. Extending our structural analysis then to other MTs in the spindle, we further observed that the association of KMTs with non-KMTs predominantly occurs in the spindle pole regions. Our 3D reconstructions have implications for KMT growth and k-fiber self-organization models as coveredin a parallel publication applying complementary live-cell imaging in combination with biophysical modeling (Conway et al., 2022). Finally, we also introduce a new visualization tool allowing an inter- active display of our 3D spindle data that will serve as a resource for further structural studies on mitosis in human cells.

},
	author = {Robert Kiewisz and Gunar Fabig and Conway, William and Daniel Baum and Needleman, Daniel and M{\"u}ller-Reichert, Thomas}
}
@article {691857,
	title = {Active Microphase Separation in Mixtures of Microtubules and Tip-Accumulating Molecular Motors},
	journal = {Physical Review X},
	volume = {12},
	year = {2022},
	abstract = {
	Mixtures of filaments and molecular motors form active materials with diverse dynamical behaviors that vary based on their constituents{\textquoteright}\&nbsp;molecular properties. To develop a multiscale of these materials, we map the nonequilibrium phase diagram of microtubules and tip-accumulating kinesin-4 molecular motors. We find that kinesin-4 can drive either global contractions or turbulentlike extensile dynamics, depending on the concentrations of both microtubules and a bundling agent. We also observe a range of spatially heterogeneous nonequilibrium phases, including finite-sized radial asters, 1D wormlike chains, extended 2D bilayers, and system-spanning 3D active foams. Finally, we describe intricate kinetic pathways that yield microphase separated structures and arise from the inherent frustration between the orientational order of filamentous microtubules and the positional order of tip-accumulating molecular motors. Our work reveals a range of novel active states. It also shows that the form of active stresses is not solely dictated by the properties of individual motors and filaments, but is also contingent on the constituent concentrations and spatial arrangement of motors on the filaments.

},
	author = {Bezia Lemma and Noah P. Mitchell and Radhika Subramanian and Daniel J. Needleman and Zvonimir Dogic}
}
@article {688056,
	title = {A coarse-grained NADH redox model enables inference of subcellular metabolic fluxes from fluorescence lifetime imaging},
	journal = {eLife},
	year = {2022},
	abstract = {Mitochondrial metabolism is of central importance to diverse aspects of cell and developmental biology. Defects in mitochondria are associated with many diseases, including cancer, neuropathology, and infertility. Our understanding of mitochondrial metabolism in situ and dysfunction in diseases are limited by the lack of techniques to measure mitochondrial metabolic fluxes with sufficient spatiotemporal resolution. Herein, we developed a new method to infer mitochondrial metabolic fluxes in living cells with subcellular resolution from fluorescence lifetime imaging of NADH. This result is based on the use of a generic coarse-grained NADH redox model. We tested the model in mouse oocytes and human tissue culture cells subject to a wide variety of perturbations by comparing predicted fluxes through the electron transport chain (ETC) to direct measurements of oxygen consumption rate. Interpreting the fluorescence lifetime imaging microscopy measurements of NADH using this model, we discovered a homeostasis of ETC flux in mouse oocytes: perturbations of nutrient supply and energy demand of the cell do not change ETC flux despite significantly impacting NADH metabolic state. Furthermore, we observed a subcellular spatial gradient of ETC flux in mouse oocytes and found that this gradient is primarily a result of a spatially heterogeneous mitochondrial proton leak. We concluded from these observations that ETC flux in mouse oocytes is not controlled by energy demand or supply, but by the intrinsic rates of mitochondrial respiration},
	author = {Xingbo Yang and Gloria Ha and Daniel J. Needleman}
}
@article {687257,
	title = {Engineering stability, longevity, and miscibility of microtubule-based active fluids},
	journal = {Soft Matter},
	year = {2022},
	abstract = {Microtubule-based active matter provides insight into the self-organization of motile interacting constituents. We describe several formulations of microtubule-based 3D active isotropic fluids. Dynamics of these fluids is powered by three types of kinesin motors: a processive motor, a nonprocessive motor, and a motor which is permanently linked to a microtubule backbone. Another modification uses a specific microtubule crosslinker to induce bundle formation instead of a nonspecific polymer depletant. In comparison to the already established system, each formulation exhibits distinct properties. These developments reveal the temporal stability of microtubule-based active fluids while extending their reach and the applicability},
	author = {Pooja Chandrakar and John Berezney and Bezia Lemma and Bernard Hishamunda and Angela Berry and Kun-Ta Wu and Radhika Subramanian and Johnson Chung and Needleman, Daniel and Jeff Gelles and Zvonimir Dogic}
}
@article {686615,
	title = {Fluorescence lifetime imaging microscopy (FLIM) detects differences in metabolic signatures between euploid and aneuploid human blastocysts},
	journal = {Human Reproduction},
	year = {2022},
	abstract = {STUDY QUESTION: Can non-invasive imaging with fluorescence lifetime imaging microscopy (FLIM) detect metabolic differences in euploid versus aneuploid human blastocysts?SUMMARY ANSWER: FLIM has identified significant metabolic differences between euploid and aneuploid blastocysts. WHAT IS KNOWN ALREADY: Prior studies have demonstrated that FLIM can detect metabolic differences in mouse oocytes and embryos and in discarded human blastocysts. STUDY DESIGN, SIZE, DURATION: This was a prospective observational study from August 2019 to February 2020. Embryo metabolic state was assessed using FLIM to measure the autofluorescence metabolic factors nicotinamide adenine dinucleotide dehydrogenase together with nicotinamide adenine phosphate dinucleotide dehydrogenase (NAD(P)H) and flavin adenine dinucleotide (FAD). Eight metabolic FLIM parameters were obtained from each blastocyst (four for NAD(P)H and four for FAD): short (T1) and long (T2) fluorescence lifetime, fluorescence intensity (I) and fraction of the molecules engaged with enzymes (F). The redox ratio (NAD(P)H-I)/(FAD-I) was also calculated for each image.PARTICIPANTS/MATERIALS, SETTING, METHODS: This study was performed at a single academically affiliated centre where there were 156 discarded frozen blastocysts (n {\textonequarter} 17 euploids; 139 aneuploids) included. Ploidy status was determined by pre-implantation genetic testing for aneuploidy (PGT-A). Discarded human blastocysts were compared using single FLIM parameters. Additionally, inner cell mass (ICM) and trophectoderm (TE) were also evaluated. Multilevel models were used for analysis. A post-hoc correction used Benjamini{\textendash}Hochberg{\textquoteright}s false discovery rate, at a q-value of 0.05.MAIN RESULTS AND THE ROLE OF CHANCE: Comparing euploid (n {\textonequarter} 17) versus aneuploid (n {\textonequarter} 139) embryos, a significant difference was seen in NAD(P)H-F (P \&lt; 0.04), FAD-I (P \&lt; 0.04) and redox ratio (P \&lt; 0.05). Euploid ICM (n {\textonequarter} 15) versus aneuploid ICM (n {\textonequarter} 119) also demonstrated significantly different signatures in NAD(P)H-F (P \&lt; 0.009), FAD-I (P \&lt; 0.03) and redox ratio (P \&lt; 0.03). Similarly, euploid TE (n {\textonequarter} 15) versus aneuploid TE (n {\textonequarter} 119) had significant differences in NAD(P)H-F (P \&lt; 0.0001) and FAD-I (P \&lt; 0.04).LIMITATIONS, REASONS FOR CAUTION: This study utilized discarded human blastocysts, and these embryos may differ metabolically from non-discarded human embryos. The blastocysts analysed were vitrified after PGT-A biopsy and it is unclear how the vitrification process may affect the metabolic profile of blastocysts. Our study was also limited by the small number of rare donated euploid embryos\&nbsp;\&nbsp;Euploid embryos are very rarely discarded due to their value to patients trying to conceive, which limits their use for research purposes. However, we controlled for the imbalance with the bootstrap resampling analysis.WIDER IMPLICATIONS OF THE FINDINGS: These findings provide preliminary evidence that FLIM may be a useful non-invasive clinical tool to assist in identifying the ploidy status of embryos.STUDY FUNDING/COMPETING INTEREST(S): The study was supported by the Blavatnik Biomedical Accelerator Grant at Harvard University. Becker and Hickl GmbH and Boston Electronics sponsored research with the loaning of equipment for FLIM. D.J.N. is an inventor on patent US20170039415A1. There are no other conflicts of interest to declare.TRIAL REGISTRATION NUMBER: N/A Key words: fluorescence lifetime imaging microscopy / FLIM / mitochondria / euploid / aneuploid},
	author = {Jaimin S. Shah and Marta Venturas and Tim H. Sanchez and Alan S. Penzias and Daniel J. Needleman and Sakkas, Denny}
}
@article {685907,
	title = {Metabolic state of human blastocysts measured by fluorescence lifetime imaging microscopy},
	journal = {Human Reproduction},
	year = {2022},
	abstract = {
	STUDY QUESTION: Can non-invasive metabolic imaging via fluorescence lifetime imaging microscopy (FLIM) detect variations in metabolic profiles between discarded human blastocysts?



	SUMMARY ANSWER: FLIM revealed extensive variations in the metabolic state of discarded human blastocysts associated with blastocyst development over 36 h, the day after fertilization and blastocyst developmental stage, as well as metabolic heterogeneity within individual blastocysts.



	WHAT IS KNOWN ALREADY: Mammalian embryos undergo large changes in metabolism over the course of preimplantation development. Embryo metabolism has long been linked to embryo viability, suggesting its potential utility in ART to aid in selecting high quality embryos. However, the metabolism of human embryos remains poorly characterized due to a lack of non-invasive methods to measure their metabolic state. STUDY DESIGN, SIZE, DURATION: We conducted a prospective observational study. We used 215 morphologically normal human embryos from 137 patients that were discarded and donated for research under an approved institutional review board protocol. These embryos were imaged using metabolic imaging via FLIM to measure the autofluorescence of two central coenzymes, nicotinamide adenine (phosphate) dinucleotide (NAD(P)H) and flavine adenine dinucleotide (FAD{\th}), which are essential for cellular respiration and glycolysis.



	PARTICIPANTS/MATERIALS, SETTING, METHODS: Here, we used non-invasive FLIM to measure the metabolic state of human blastocysts. We first studied spatial patterns in the metabolic state within human blastocysts and the association of the metabolic state of the whole blastocysts with stage of expansion, day of development since fertilization and morphology. We explored the sensitivity of this technique in detecting metabolic variations between blastocysts from the same patient and between patients. Next, we explored whether FLIM can quantitatively measure metabolic changes through human blastocyst expansion and hatching via time-lapse imaging. For all test conditions, the level of significance was set at P \&lt; 0.05 after correction for multiple comparisons using Benjamini{\textendash}Hochberg{\textquoteright}s false discovery rate.



	MAIN RESULTS AND THE ROLE OF CHANCE: We found that FLIM is sensitive enough to detect significant metabolic differences between blastocysts. We found that metabolic variations between blastocyst are partially explained by both the time since fertilization and their developmental expansion stage (P\&lt; 0.05), but not their morphological grade. Substantial metabolic variations between blastocysts from the same patients remain, even after controlling for these factors. We also observe significant metabolic heterogeneity within individual blastocysts, including between the inner cell mass and the trophectoderm, and between the portions of hatching blastocysts within and without the zona pellucida (P\&lt; 0.05). And finally, we observed that the metabolic state of human blastocysts continuously varies over time.



	LIMITATIONS, REASONS FOR CAUTION: Although we observed significant variations in metabolic parameters, our data are taken from human blastocysts that were discarded and donated for research and we do not know their clinical outcome. Moreover, the embryos used in this study are a mixture of aneuploid, euploid and embryos of unknown ploidy.



	WIDER IMPLICATIONS OF THE FINDINGS: This work reveals novel aspects of the metabolism of human blastocysts and suggests that FLIM is a promising approach to assess embryo viability through non-invasive, quantitative measurements of their metabolism. These results further demonstrate that FLIM can provide biologically relevant information that may be valuable for the assessment of embryo quality.



	STUDY FUNDING/COMPETING INTEREST(S): Supported by the Blavatnik Biomedical Accelerator Grant at Harvard University. Becker and Hickl GmbH and Boston Electronics sponsored research with the loaning of equipment for FLIM. D.J.N. is an inventor on patent US20170039415A1.



	TRIAL REGISTRATION NUMBER: N/A

},
	author = {Marta Venturas and Jaimin S. Shah and Xingbo Yang and Tim H. Sanchez and Conway, William and Sakkas, Denny and Dan J. Needleman}
}
@article {684453,
	title = {Cell cycle regulation of ER membrane biogenesis protects against chromosome missegregation},
	journal = {Developmental Cell},
	volume = {56},
	year = {2021},
	abstract = {Failure to reorganize the endoplasmic reticulum (ER) in mitosis results in chromosome missegregation. Here, we show that accurate chromosome segregation in human cells requires cell cycle-regulated ER membrane production. Excess ER membranes increase the viscosity of the mitotic cytoplasm to physically restrict chromosome movements, which impedes the correction of mitotic errors leading to the formation of micronuclei. Mechanistically, we demonstrate that the protein phosphatase CTDNEP1 counteracts mTOR kinase to establish a dephosphorylated pool of the phosphatidic acid phosphatase lipin 1 in interphase. CTDNEP1 control of lipin 1 limits the synthesis of fatty acids for ER membrane biogenesis in interphase that then protects against chromosome missegregation in mitosis. Thus, regulation of ER size can dictate the biophysical properties of mitotic cells, providing an explanation for why ER reorganization is necessary for mitotic fidelity. Our data further suggest that dysregulated lipid metabolism is a potential source of aneuploidy in cancer cells.},
	author = {Holly Merta and Jake W. Carrasquillo Rodr{\i}guez and Maya I. Anjur-Dietrich and Tevis Vitale and Mitchell E. Granade and Thurl E. Harris and Daniel J. Needleman and Bahmanyar, Shirin}
}
@article {684185,
	title = {Extensive analysis of mitochondrial DNA quantity and sequence variation in human cumulus cells and assisted reproduction outcomes},
	journal = {Human Reproduction},
	year = {2021},
	abstract = {STUDY QUESTION: Are relative mitochondrial DNA (mtDNA) content and mitochondrial genome (mtGenome) variants in human cumulus cells (CCs) associated with oocyte reproductive potential and assisted reproductive technology (ART) outcomes? SUMMARY ANSWER: Neither the CC mtDNA quantity nor the presence of specific mtDNA genetic variants was associated with ART outcomes, although associations with patient body mass index (BMI) were detected, and the total number of oocytes retrieved differed between major mitochondrial haplogroups. WHAT IS KNOWN ALREADY: CCs fulfil a vital role in the support of oocyte developmental competence. As with other cell types, appropriate cellular function is likely to rely upon adequate energy production, which in turn depends on the quantity and genetic competence of the mitochondria. mtDNA mutations can be inherited or they can accumulate in somatic cells over time, potentially contributing to aging. Such mutations may be homoplasmic (affecting all mtDNA in a cell) or they may display varying levels of heteroplasmy (affecting a proportion of the mtDNA). Currently, little is known concerning variation in CC mitochondrial genetics and how this might influence the reproductive potential of the associated oocyte. STUDY DESIGN, SIZE, DURATION: This was a prospective observational study involving human CCs collected with 541 oocytes from 177 IVF patients. mtDNA quantity was measured in all the samples with a validated quantitative PCR method and the entire mtGenome was sequenced in a subset of 138 samples using a high-depth massively parallel sequencing approach. Associations between relative mtDNA quantity and mtGenome variants in CCs and patient age, BMI (kg/m2 ), infertility diagnosis and ART outcomes were investigated. PARTICIPANTS/MATERIALS, SETTING, METHODS: Massively parallel sequencing permitted not only the accurate detection of mutations but also the precise quantification of levels of mutations in cases of heteroplasmy. Sequence variants in the mtDNA were evaluated using Mitomaster and HmtVar to predict their potential impact. MAIN RESULTS AND THE ROLE OF CHANCE: The relative mtDNA CC content was significantly associated with BMI. No significant associations were observed between CC mtDNA quantity and patient age, female infertility diagnosis or any ART outcome variable. mtGenome sequencing revealed 4181 genetic variants with respect to a reference genome. The COXI locus contained the least number of coding sequence variants, whereas ATPase8 had the most. The number of variants predicted to affect the ATP production differed significantly between mitochondrial macrohaplogroups. The total number of retrieved oocytes was different between the H-V and J-T as well as the U-K and J-T macrohaplogroups. There was a non-significant increase in mtDNA levels in CCs with heteroplasmic mitochondrial mutations. LARGE SCALE DATA: N/A.LIMITATIONS, REASONS FOR CAUTION: Although a large number of samples were analysed in this study, it was not possible to analyse all the CCs from every patient. Also, the results obtained with respect to specific clinical outcomes and macrohaplogroups should be interpreted with caution due to the smaller sample sizes when subdividing the dataset. WIDER IMPLICATIONS OF THE FINDINGS: These findings suggest that the analysis of mtDNA in CCs is unlikely to provide an advantage in terms of improved embryo selection during assisted reproduction cycles. Nonetheless, our data raise interesting biological questions, particularly regarding the interplay of metabolism and BMI and the association of mtDNA haplogroup with oocyte yield in ovarian stimulation cycles. STUDY FUNDING/COMPETING INTEREST(S): This study was funded by National Institutes of Health grant 5R01HD092550-02. D.J.N. and C.R. co-hold patent US20150346100A1 and D.J.N. holds US20170039415A1, both for metabolic imaging methods. D.W},
	author = {Kishlay Kumar and Marta Venturas and Daniel J. Needleman and Racowsky, Catherine and Racowsky, Catherine}
}
@article {680873,
	title = {Inferring simple but precise quantitative models of human oocyte and early embryo development},
	journal = {Interface},
	volume = {18},
	number = {20210475},
	year = {2021},
	abstract = {Macroscopic, phenomenological models are useful as concise framings of our understandings in fields from statistical physics to finance to biology. Constructing a phenomenological model for development would provide a framework for understanding the complicated, regulatory nature of oogenesis and embryogenesis. Here, we use a data-driven approach to infer quantitative, precise models of human oocyte maturation and pre-implantation embryo development, by analysing clinical in-vitro fertilization (IVF) data on 7399 IVF cycles resulting in 57 827 embryos. Surprisingly, we find that both oocyte maturation and early embryo development are quantitatively described by simple models with minimal interactions. This simplicity suggests that oogenesis and embryogenesis are composed of modular processes that are relatively siloed from one another. In particular, our analysis provides strong evidence that (i) preantral follicles produce anti-M{\"u}llerian hormone independently of effects from other follicles, (ii) oocytes mature to metaphase-II independently of the woman{\textquoteright}s age, her BMI and other factors, (iii) early embryo development is memoryless for the variables assessed here, in that the probability of an embryo transitioning from its current developmental stage to the next is independent of its previous stage. Our results both provide insight into the fundamentals of oogenesis and embryogenesis and have implications for the clinical IVF.},
	author = {Brian Leahy and Racowsky, Catherine and Daniel J. Needleman}
}
@article {680695,
	title = {Metabolic imaging of human cumulus cells reveals associations among metabolic profiles of cumulus cells, patient clinical factors, and oocyte maturity},
	journal = {Fertility and Sterility},
	year = {2021},
	abstract = {Objective: To determine whether fluorescence lifetime imaging microscopy (FLIM) detects differences in metabolic state among cumulus cell samples and whether their metabolic state is associated with patient age, body mass index (BMI), and antimullerian hor- {\texteuro} mone (AMH) level and maturity of the oocyte. Design: Prospective observational study. Setting: Academic laboratory. Patient(s): Cumulus cell (CC) clusters from cumulus-oocyte complexes were collected from patients undergoing assisted reproductive technology treatment after oocyte retrieval and vitrified. Intervention(s): Cumulus cell metabolism was assessed using FLIM to measure autofluorescence of nicotinamide adenine (phosphate) dinucleotide and flavine adenine dinucleotide, endogenous coenzymes essential for cellular respiration and glycolysis. Patient age, BMI, and AMH level and the maturity of the corresponding oocytes were recorded. Main Outcome Measure(s): Quantitative information from FLIM was obtained regarding metabolite concentrations from fluorescence intensity and metabolite enzyme engagement from fluorescence lifetimes. Associations were investigated between each FLIM parameter and oocyte maturity and patient age, BMI, and AMH. Variance between CC clusters within and between patients was determined. Result(s): Of 619 CC clusters from 193 patients, 90 were associated with immature oocytes and 505 with metaphase II oocytes. FLIM enabled quantitative measurements of the metabolic state of CC clusters. These parameters were significantly correlated with patient age and AMH independently, but not with BMI. Cumulus cell nicotinamide adenine (phosphate) dinucleotide FLIM parameters and redox ratio were significantly associated with maturity of the enclosed oocyte. Conclusion(s): FLIM detects variations in the metabolic state of CCs, showing a greater variance among clusters from each patient than between patients. Fluorescence lifetime imaging microscopy can detect CC metabolic associations with patient age and AMH and variations between mature and immature oocytes, suggesting the potential utility of this technique to help identify superior oocytes. (Fertil Steril 2021;-:-{\textendash}-. 2021 by American Society for Reproductive Medicine.) Key Words: Cumulus cells, cumulus-oocyte complexes, fluorescence lifetime imaging microscopy, human oocytes, maturity, metabolism},
	author = {Marta Venturas and Xingbo Yang and Kishlay Kumar and Dagan Wells and Catherine Rancowsky and Daniel J. Needleman}
}
@article {678437,
	title = {Developmental Stage Classification of Embryos Using Two-Stream Neural Network with Linear-Chain Conditional Random Field},
	journal = {arXiv},
	year = {2021},
	abstract = {The developmental process of embryos follows a monotonic order. An embryo can progressively cleave from one cell to multiple cells and finally transform to morula and blastocyst. For time-lapse videos of embryos, most existing developmental stage classification methods conduct per-frame predictions using an image frame at each time step. However, classification using only images suffers from overlapping between cells and imbalance between stages. Temporal information can be valuable in addressing this problem by capturing movements between neighboring frames. In this work, we propose a two-stream model for developmental stage classification. Unlike previous methods, our twostream model accepts both temporal and image information. We develop a linear-chain conditional random field (CRF) on top of neural network features extracted from the temporal and image streams to make use of both modalities. The linear-chain CRF formulation enables tractable training of global sequential models over multiple frames while also making it possible to inject monotonic development order constraints into the learning process explicitly. We demonstrate our algorithm on two timelapse embryo video datasets: i) mouse and ii) human embryo datasets. Our method achieves 98.1\% and 80.6\% for mouse and human embryo stage classification, respectively. Our approach will enable more profound clinical and biological studies and suggests a new direction for developmental stage classification by utilizing temporal information.},
	url = {https://arxiv.org/pdf/2107.06360.pdf},
	author = {Stanislav Lukyanenko and Jang, Won-Dong and Donglai Wei and Robbert Struyven and Yoon Kim and Brian Leahy and Helen Yang and Rush, Alexander and Dalit Ben-Yose and Needleman, Daniel and Hanspeter Pfiser}
}
@article {677495,
	title = {Physical bioenergetics: Energy fluxes, budgets, and constraints in cells},
	journal = {PNAS},
	volume = {118},
	number = {28},
	year = {2021},
	abstract = {Cells are the basic units of all living matter which harness the flow of energy to drive the processes of life. While the biochemical networks involved in energy transduction are well-characterized, the energetic costs and constraints for specific cellular processes remain largely unknown. In particular, what are the energy budgets of cells? What are the constraints and limits energy flows impose on cellular processes? Do cells operate near these limits, and if so how do energetic constraints impact cellular functions? Physics has provided many tools to study nonequilibrium systems and to define physical limits, but applying these tools to cell biology remains a challenge. Physical bioenergetics, which resides at the interface of nonequilibrium physics, energy metabolism, and cell biology, seeks to understand how much energy cells are using, how they partition this energy between different cellular processes, and the associated energetic constraints. Here we review recent advances and discuss open questions and challenges in physical bioenergetics.},
	author = {Xingbo Yang and Matthias Heminemannc and Howard, Jonathon and Greg Hubere and Srividya Iyer-Biswasf and Guillaume Le Treut and Lynch, Michael and Kristi L. Montooth and Daniel J. Needleman and Simone Pigolotti and Rodenfels, Jonathan and Pierre Ronceray and Sadasivan Shankar and Iman Tavassoly and hashi Thutupalli and Titov, Denis V. and Wang, Jin and Peter J. Foster}
}
@article {671406,
	title = {Mechanical Mechanisms of Chromosome Segregation },
	journal = {Cells},
	volume = {10},
	number = {465},
	year = {2021},
	author = {Maya I. Anjur-Dietrich and Colm P. Kelleher and Daniel J. Needleman}
}
@article {669164,
	title = {A Micromachined Picocalorimeter Sensor for Liquid Samples with Application to Chemical Reactions and Biochemistry},
	journal = {Advanced Science News},
	number = {2003415},
	year = {2021},
	abstract = {Calorimetry has long been used to probe the physical state of a system by measuring the heat exchanged with the environment as a result of chemical reactions or phase transitions. Application of calorimetry to microscale biological samples, however, is hampered by insufficient sensitivity and the difficulty of handling liquid samples at this scale. Here, a micromachined calorimeter sensor that is capable of resolving picowatt levels of power is described. The sensor consists of low-noise thermopiles on a thin silicon nitride membrane that allow direct differential temperature measurements between a sample and four coplanar references, which significantly reduces thermal drift. The partial pressure of water in the ambient around the sample is maintained at saturation level using a small hydrogel-lined enclosure. The materials used in the sensor and its geometry are optimized to minimize the noise equivalent power generated by the sensor in response to the temperature field that develops around a typical sample. The experimental response of the sensor is characterized as a function of thermopile dimensions and sample volume, and its capability is demonstrated by measuring the heat dissipated during an enzymatically catalyzed biochemical reaction in a microliter-sized liquid droplet. The sensor offers particular promise for quantitative measurements on biological systems},
	author = {Jinhye Bae and Juanjuan Zheng and Haitao Zhang and Peter J. Foster and Daniel J. Needleman and Joost J. Vlassak}
}
@article {669137,
	title = {A design framework for actively crosslinked filament networks},
	journal = {New Journal of Physics},
	number = {23},
	year = {2021},
	abstract = {Living matter moves, deforms, and organizes itself. In cells this is made possible by networks ofpolymer filaments and crosslinking molecules that connect filaments to each other and that act asmotors to do mechanical work on the network. For the case of highly cross-linked filamentnetworks, we discuss how the material properties of assemblies emerge from the forces exerted bymicroscopic agents. First, we introduce a phenomenological model that characterizes the forcesthat crosslink populations exert between filaments. Second, we derive a theory that predicts thematerial properties of highly crosslinked filament networks, given the crosslinks present. Third, wediscuss which properties of crosslinks set the material properties and behavior of highlycrosslinked cytoskeletal networks. The work presented here, will enable the better understandingof cytoskeletal mechanics and its molecular underpinnings. This theory is also a first step toward atheory of how molecular perturbations impact cytoskeletal organization, and provides aframework for designing cytoskeletal networks with desirable properties in the lab.},
	author = {F{\"u}rthauer, Sebastian and Daniel J. Needleman and Michael J. Shelly}
}
@article {667641,
	title = {A mechanical model of blastocyst hatching},
	journal = {Extreme Mechanics Letters},
	volume = {42},
	year = {2021},
	abstract = {We develop a continuum mechanics model of blastocyst hatching. The blastocyst and the zona pellucida are modeled as concentric thick-walled initially spherical shells embedded in a viscous medium. Each shell is characterized by a nonlinear elastic{\textendash}viscous{\textendash}constitutive relation. The stiffer outer shell (the zona pellucida) contains an opening. The softer inner shell (the blastocyst) is subject to a continually increasing pressure, which can eventually drive the escape of the inner shell from the outer shell ({\textquoteleft}{\textquoteleft}hatching{\textquoteright}{\textquoteright}). The focus is on the continuum mechanics modeling framework and illustrating the sort of quantitative predictions that can be made. Numerical examples are presented for the predicted dependence of the evolution of the escape process on values of parameters characterizing the constitutive response of the shells, on the viscosity of the external medium and on the size of the opening in the zona pellucida.},
	author = {Viggo Tvergaard and Needleman, Daniel and Alan Needleman}
}
@article {663513,
	title = {Stoichiometric interactions explain spindle dynamics and scaling across 100 million years of nematode evolution},
	journal = {eLife},
	year = {2020},
	abstract = {The spindle shows remarkable diversity, and changes in an integrated fashion, as cells vary over evolution. Here, we provide a mechanistic explanation for variations in the first mitotic spindle in nematodes. We used a combination of quantitative genetics and biophysics to rule out broad classes of models of the regulation of spindle length and dynamics, and to establish the importance of a balance of cortical pulling forces acting in different directions. These experiments led us to construct a model of cortical pulling forces in which the stoichiometric interactions of microtubules and force generators (each force generator can bind only one microtubule), is key to explaining the dynamics of spindle positioning and elongation, and spindle final length and scaling with cell size. This model accounts for variations in all the spindle traits we studied here, both within species and across nematode species spanning over 100 million years of evolution.},
	author = {Farhadifar, Reza and Yu, Che-Hang and Gunar Fabig and Wu, Hai-Yin and David B Stein and Matthew Rockman and M{\"u}ller-Reichert, Thomas and Shelley, Michael J and Needleman, Daniel J}
}
@article {662443,
	title = {Non-invasive imaging of mouse embryo metabolism in response to induced hypoxia},
	journal = {Journal of Assisted Reproduction and Genetics},
	year = {2020},
	abstract = {
	Purpose



	This study used noninvasive, fluorescence lifetime imaging microscopy (FLIM)-based imaging of NADH and FAD to characterize the metabolic response of mouse embryos to short-term oxygen deprivation. We investigated the response to hypoxia at various preimplantation stages.



	Methods



	Mouse oocytes and embryos were exposed to transient hypoxia by dropping the oxygen concentration in media from 5{\textendash}0\% over the course of ~1.5 h, then 5\% O2\&nbsp;was restored. During this time, FLIM-based metabolic imaging measurements of oocyte/embryo cohorts were taken every 3 minutes. Experiments were performed in triplicate for oocytes and embryos at the 1- to 8-cell, morula, and blastocyst stages. Maximum hypoxia response for each of eight measured quantitative FLIM parameters was taken from the time points immediately before oxygen restoration.



	Results



	Metabolic profiles showed significant changes in response to hypoxia for all stages of embryo development. The response of the eight measured FLIM parameters to hypoxia was highly stage-dependent. Of the eight FLIM parameters measured, NADH and FAD intensity showed the most dramatic metabolic responses in early developmental stages. At later stages, however, other parameters, such as NADH fraction engaged and FAD lifetimes, showed greater changes. Metabolic parameter values generally returned to baseline with the restoration of 5\% oxygen.



	Conclusions



	Quantitative FLIM-based metabolic imaging was highly sensitive to metabolic changes induced by hypoxia. Metabolic response profiles to oxygen deprivation were distinct at different stages, reflecting differences in metabolic plasticity as preimplantation embryos develop.

},
	url = {https://link.springer.com/article/10.1007/s10815-020-01872-w?wt_mc=Internal.Event.1.SEM.ArticleAuthorOnlineFirst},
	author = {Emily A. Seidler and Sanchez, Tim and Marta Venturas and Sakkas, Denny and Daniel J. Needleman}
}
@article {655138,
	title = {Automated Measurements of Key Morphological Features of Human Embryos for IVF},
	journal = {arXiv},
	year = {2020},
	abstract = {A major challenge in clinical In-Vitro Fertilization (IVF) is selecting the highest quality embryo to transfer to the patient in the hopes of achieving a pregnancy. Time-lapse microscopy provides clinicians with a wealth of information for selecting embryos. However, the resulting movies of embryos are currently analyzed manually, which is time consuming and subjective. Here, we automate feature extraction of timelapse microscopy of human embryos with a machine-learning pipeline of five convolutional neural networks (CNNs). Our pipeline consists of (1) semantic segmentation of the regions of the embryo, (2) regression predictions of fragment severity, (3) classification of the developmental stage, and object instance segmentation of (4) cells and (5) pronuclei. Our approach greatly speeds up the measurement of quantitative, biologically relevant features that may aid in embryo selection. Please see here for more information:\&nbsp;https://wdjang.github.io/miccai2020-ivf.github.io/\&nbsp;},
	url = {https://arxiv.org/pdf/2006.00067.pdf},
	author = {B.D. Leahy and W-D. Jang and H.Y. Yang and R. Struyven and D. Wei and Sun, Z and K. R. Lee and C. Royston and L. Cam and Y. Kalma and F. Azem and D. Ben-Yosef and H. Pfister and D. Needleman}
}
@article {654726,
	title = {Probing and manipulating embryogenesis via nanoscale thermometry and temperature control},
	journal = {PNAS},
	year = {2020},
	url = {https://www.pnas.org/content/early/2020/06/12/1922730117},
	author = {Joonhee Choi and Hengyun Zhou and Renate Landig and Wu, Hai-Yin and Xiaofei Yu and Stephen E. Von Stetina and Georg Kucsko and Susan E. Mango and Daniel J. Needleman and Aravinthan D. T. Samuel and Peter C. Maurer and Park, Hongkun and Mikhail D. Lukin}
}
@article {645249,
	title = {Combined noninvasive metabolic and spindle imaging as potential tools for embryo and oocyte assessment},
	journal = {Human Reproduction},
	year = {2019},
	pages = {1-13},
	author = {Sanchez, Tim and Marta Venturas and A Sli Aghvami and Xingbo Yang and Seth Fraden and Sakkas, Denny and Needleman, Daniel}
}
@article {644144,
	title = {Electrical control of interlayer exciton dynamics in atomically thin heterostructures},
	journal = {Science},
	volume = {336},
	number = {6467},
	year = {2019},
	pages = {870-875},
	abstract = {A van der Waals heterostructure built from atomically thin semiconducting transition metal dichalcogenides (TMDs) enables the formation of excitons from electrons and holes in distinct layers, producing interlayer excitons with large binding energy and a long lifetime. By employing heterostructures of monolayer TMDs, we realize optical and electrical generation of long-lived neutral and charged interlayer excitons. We demonstrate that neutral interlayer excitons can propagate across the entire sample and that their propagation can be controlled by excitation power and gate electrodes. We also use devices with ohmic contacts to facilitate the drift motion of charged interlayer excitons. The electrical generation and control of excitons provide a route for achieving quantum manipulation of bosonic composite particles with complete electrical tunability.},
	url = {https://science.sciencemag.org/content/366/6467/870},
	author = {Jauregui, Luis A. and Andrew Y. Joe and Pistunova, Kateryna and Dominik S. Wild and Alexander A. High and Zhou, You and Scuri, Giovanni and De Greve, Kristiaan and Sushko, Andrey and Yu, Che-Hang and Takashi Taniguchi and Kenji Watanabe and Daniel J. Needleman and Mikhail D. Lukin and Park, Hongkun and Philip Kim}
}
@article {641089,
	title = {Self-straining of actively crosslinked microtubule networks},
	journal = {Nature Physics},
	year = {2019},
	abstract = {Cytoskeletal networks are foundational examples of active matter and central to self-organized structures in the cell. In vivo, these networks are active and densely crosslinked. Relating their large-scale dynamics to the properties of their constituents remains an unsolved problem. Here, we study an in vitro active gel made from aligned microtubules and XCTK2 kinesin motors. Using photobleaching, we demonstrate that the gel{\textquoteright}s aligned microtubules, driven by motors, continually slide past each other at a speed independent of the local microtubule polarity and motor concentration. This phenomenon is also observed, and remains unexplained, in spindles. We derive a general framework for coarse graining microtubule gels crosslinked by molecular motors from microscopic considerations. Using microtubule{\textendash}microtubule coupling through a force{\textendash}velocity relationship for kinesin, this theory naturally explains the experimental results: motors generate an active strain rate in regions of changing polarity, which allows microtubules of opposite polarities to slide past each other without stressing the material.},
	author = {F{\"u}rthauer, Sebastian and Bezia Lemma  and Peter J. Foster and Stephanie C. Ems-McClung and Che-Hang Yu7 and Claire E. Walczak and Zvonimir Dogic and Daniel J. Needleman and Shelley, Michael J.}
}
@article {640861,
	title = {The stormy fluid dynamics of the living cell},
	journal = {Physics Today},
	volume = {72},
	number = {9},
	year = {2019},
	abstract = {Cell biology has its beginnings in the first observations of cells through primitive microscopes and in the formulation of cell theory, which postulates that cells are the fundamental building blocks of life. Light microscopes showed that the insides of cells contained complex structures, such as nuclei, spindles, and chromosomes. The advent of electron microscopy in the mid 20th century brought the first truly detailed views of cell innards. Images revealed complexity at all observable scales, including cell-spanning networks of polymers, intricate organelles made of membranes, and a variety of micron- to nanometer-sized sacs and granules such as vesicles, lipid droplets, and ribosomes. (For a glossary of cellular components, see the Quick Study by Ned Wingreen, PHYSICS TODAY, September 2006, page 80.) Those structures are immersed in or part of the aqueous cytoplasm{\textemdash}the cell{\textquoteright}s fluidic medium.},
	url = {https://physicstoday.scitation.org/doi/pdf/10.1063/PT.3.4292},
	author = {Needleman, Daniel and Shelley, Michael}
}
@article {640683,
	title = {Central-spindle microtubules are strongly coupled to chromosomes during both anaphase A and anaphase B},
	journal = {Molecular Biology of the Cell},
	volume = {30},
	year = {2019},
	pages = {2503-2514},
	abstract = {
	Spindle microtubules, whose dynamics vary over time and at different locations, cooperatively drive chromosome segregation. Measurements of microtubule dynamics and spindle ultrastructure can provide insight into the behaviors of microtubules, helping elucidate the mechanism of chromosome segregation. Much work has focused on the dynamics and organization of kinetochore microtubules, that is, on the region between chromosomes and poles. In comparison, microtubules in the central-spindle region, between segregating chromosomes, have been less thoroughly characterized. Here, we report measurements of the movement of central-spindle microtubules during chromosome segregation in human mitotic spindles and\&nbsp;Caenorhabditis elegans\&nbsp;mitotic and female meiotic spindles. We found that these central-spindle microtubules slide apart at the same speed as chromosomes, even as chromosomes move toward spindle poles. In these systems, damaging central-spindle microtubules by laser ablation caused an immediate and complete cessation of chromosome motion, suggesting a strong coupling between central-spindle microtubules and chromosomes. Electron tomographic reconstruction revealed that the analyzed anaphase spindles all contain microtubules with both ends between segregating chromosomes. Our results provide new dynamical, functional, and ultrastructural characterizations of central-spindle microtubules during chromosome segregation in diverse spindles and suggest that central-spindle microtubules and chromosomes are strongly coupled in anaphase.

},
	url = {https://www.molbiolcell.org/doi/full/10.1091/mbc.E19-01-0074},
	author = {MBoC Paper of the Year Award Winner: Yu, Che-Hang* and Stefanie Redemann* and Wu, Hai-Yin and Robert Kiewisz and Yoo, Tae Yeon and Conway, William and Farhadifar, Reza and M{\"u}ller-Reichert, Thomas and Needleman, Daniel}
}
@article {SANCHEZ2019212,
	title = {Metabolic imaging via fluorescence lifetime imaging microscopy for egg and embryo assessment},
	journal = {Fertility and Sterility},
	volume = {111},
	number = {2},
	year = {2019},
	pages = {212 - 218},
	abstract = {Current strategies for embryo assessment in the assisted reproductive technology laboratories rely primarily on morphologic parameters that have limited accuracy for determining embryo viability. Even with the addition of invasive diagnostic interventions such as preimplantation genetic testing for aneuploidy alone or in combination with mitochondrial DNA copy number assessment, at least one third of embryos fail to implant. Therefore, at a time when the clinical benefits of single ET are widely accepted, improving viability assessment of embryos is ever more important. Building on the previous work demonstrating the importance of metabolic state in oocytes and embryos, metabolic imaging via fluorescence lifetime imaging microscopy offers new and potentially useful diagnostic method by detecting natural fluorescence of FAD and NADH, the two electron transporters that play a central role in oxidative phosphorylation. Recent studies demonstrate that fluorescence lifetime imaging microscopy can detect oocyte and embryo metabolic function and dysfunction in a multitude of experimental models and provide encouraging evidence for use in scientific investigation and possibly for clinical application.},
	keywords = {embryo assessment, FAD, Metabolism, Mitochondria, NADH, non-invasive, viability},
	issn = {0015-0282},
	doi = {https://doi.org/10.1016/j.fertnstert.2018.12.014},
	url = {http://www.sciencedirect.com/science/article/pii/S0015028218323008},
	author = {Sanchez, Tim and Zhang, Man and Needleman, Dan and Seli, Emre}
}
@article {foster2019cytoskeletal,
	title = {From cytoskeletal assemblies to living materials},
	journal = {Current Opinion in Cell Biology},
	volume = {56},
	year = {2019},
	pages = {109{\textendash}114},
	publisher = {Elsevier},
	author = {Foster, Peter J and F{\"u}rthauer, Sebastian and Shelley, Michael J and Needleman, Daniel J}
}
@article {sanchez2018metabolic,
	title = {Metabolic imaging with the use of fluorescence lifetime imaging microscopy (FLIM) accurately detects mitochondrial dysfunction in mouse oocytes},
	journal = {Fertility and sterility},
	volume = {110},
	number = {7},
	year = {2018},
	pages = {1271},
	publisher = {Elsevier},
	author = {Sanchez, Tim and Wang, Tianren and Pedro, Marta Venturas and Zhang, Man and Esencan, Ecem and Sakkas, Denny and Needleman, Dan and Seli, Emre}
}
@article {yoo2018measuring,
	title = {Measuring NDC80 binding reveals the molecular basis of tension-dependent kinetochore-microtubule attachments},
	journal = {eLife},
	year = {2018},
	pages = {7:e36392},
	publisher = {Cold Spring Harbor Laboratory},
	url = {https://elifesciences.org/articles/36392},
	author = {Yoo, Tae Yeon and Choi, Jeong-Mo and Conway, William and Yu, Che-Hang and Pappu, Rohit V and Needleman, Daniel J}
}
@article {oriola2018physics,
	title = {The Physics of the Metaphase Spindle.},
	journal = {Annual review of biophysics},
	volume = {47},
	year = {2018},
	pages = {655{\textendash}673},
	author = {Oriola, D and Needleman, D. J. and Brugu{\'e}s, J}
}
@article {kaye2018measuring,
	title = {Measuring and modeling polymer concentration profiles near spindle boundaries argues that spindle microtubules regulate their own nucleation},
	journal = {New Journal of Physics},
	year = {2018},
	publisher = {IOP Publishing},
	author = {Bryan Kaye and Stiehl, Olivia and Foster, Peter J and Shelley, M and Needleman, Daniel J and F{\"u}rthauer, Sebastian}
}
@article {penfield2018dynein,
	title = {Dynein pulling forces counteract lamin-mediated nuclear stability during nuclear envelope repair},
	journal = {Molecular biology of the cell},
	volume = {29},
	number = {7},
	year = {2018},
	pages = {852{\textendash}868},
	publisher = {Am Soc Cell Biol},
	author = {Penfield, Lauren and Wysolmerski, Brian and Mauro, Michael and Farhadifar, Reza and Martinez, Michael A and Biggs, Ronald and Wu, Hai-Yin and Broberg, Curtis and Needleman, Daniel and Bahmanyar, Shirin}
}
@booklet {racowsky2018cumulus,
	title = {Cumulus cell gene expression as a potential biomarker for oocyte quality},
	journal = {Fertility and Sterility},
	year = {2018},
	pages = {109(3):438-439},
	publisher = {Elsevier},
	author = {Racowsky, Catherine and Needleman, Daniel J}
}
@article {Sherman798,
	title = {Lipopolysaccharide is transported to the cell surface by a membrane-to-membrane protein bridge},
	journal = {Science},
	volume = {359},
	number = {6377},
	year = {2018},
	pages = {798{\textendash}801},
	publisher = {American Association for the Advancement of Science},
	abstract = {The outer membrane of Gram-negative bacteria is composed of lipopolysaccharide, a large glycolipid that prevents drugs from entering the cells. Disrupting lipopolysaccharide assembly hypersensitizes bacteria to antibiotics. Sherman et al. used biochemical tools to observe lipopolysaccharide transport. Seven proteins, which are conserved in all Gram-negative bacteria, appear to form a protein bridge that uses adenosine triphosphate to power transport of lipopolysaccharide from one membrane to another. The ability to monitor intermembrane transport of lipopolysaccharide will help in efforts to develop and characterize inhibitors.Science, this issue p. 798Gram-negative bacteria have an outer membrane that serves as a barrier to noxious agents in the environment. This protective function is dependent on lipopolysaccharide, a large glycolipid located in the outer leaflet of the outer membrane. Lipopolysaccharide is synthesized at the cytoplasmic membrane and must be transported to the cell surface. To understand this transport process, we reconstituted membrane-to-membrane movement of lipopolysaccharide by incorporating purified inner and outer membrane transport complexes into separate proteoliposomes. Transport involved stable association between the inner and outer membrane proteoliposomes. Our results support a model in which lipopolysaccharide molecules are pushed one after the other in a PEZ dispenser{\textendash}like manner across a protein bridge that connects the inner and outer membranes.},
	issn = {0036-8075},
	doi = {10.1126/science.aar1886},
	url = {http://science.sciencemag.org/content/359/6377/798},
	author = {Sherman, David J. and Xie, Ran and Taylor, Rebecca J. and George, Alexander H. and Okuda, Suguru and Peter J. Foster and Daniel J. Needleman and Kahne, Daniel}
}
@article {tan2018cooperative,
	title = {Cooperative accumulation of dynein-dynactin at microtubule minus-ends drives microtubule network reorganization},
	journal = {Developmental Cell},
	volume = {44},
	number = {2},
	year = {2018},
	pages = {233{\textendash}247},
	publisher = {Elsevier},
	author = {Tan, Ruensern and Foster, Peter J and Needleman, Daniel J and McKenney, Richard J}
}
@article {foster2017connecting,
	title = {Connecting macroscopic dynamics with microscopic properties in active microtubule network contraction},
	journal = {New Journal of Physics},
	year = {2017},
	publisher = {IOP Publishing},
	author = {Foster, Peter J and Yan, Wen and F{\"u}rthauer, Sebastian and Shelley, M and Needleman, Daniel J}
}
@article {sanchez2017will,
	title = {Will noninvasive methods surpass invasive for assessing gametes and embryos?},
	journal = {Fertility and Sterility},
	volume = {108},
	number = {5},
	year = {2017},
	pages = {730{\textendash}737},
	publisher = {Elsevier},
	author = {Sanchez, Tim and Seidler, Emily A and Gardner, David K and Needleman, Daniel and Sakkas, Denny}
}
@article {nazockdast2017cytoplasmic,
	title = {Cytoplasmic flows as signatures for the mechanics of mitotic positioning},
	journal = {Molecular Biology of the Cell},
	year = {2017},
	pages = {mbc{\textendash}E16},
	publisher = {Am Soc Cell Biol},
	author = {Nazockdast, Ehssan and Rahimian, Abtin and Needleman, Daniel and Shelley, Michael}
}
@article {Needleman2017,
	title = {Active matter at the interface between materials science and cell biology},
	journal = {Nature Reviews Materials},
	volume = {2},
	year = {2017},
	note = {Review Article},
	month = {Jul},
	pages = {17048 EP -},
	publisher = {Macmillan Publishers Limited SN -},
	url = {http://dx.doi.org/10.1038/natrevmats.2017.48},
	author = {Needleman, Daniel and Zvonimir Dogic}
}
@article {545896,
	title = {Use of imaging software for assessment of the associations among zona pellucida thickness variation, assisted hatching, and implantation of day 3 embryos},
	journal = {Journal of Assisted Reproduction and Genetics},
	year = {2017},
	pages = {1-9},
	author = {Erin Lewis and Farhadifar, Reza and Farland, Leslie V and Needleman, Daniel J and Missmer, Stacey A and Racowsky, Catherine}
}
@article {hanley2017chromosomal,
	title = {Chromosomal passenger complex hydrodynamics suggests chaperoning of the inactive state by nucleoplasmin/nucleophosmin},
	journal = {Molecular Biology of the Cell},
	year = {2017},
	pages = {mbc{\textendash}E16},
	publisher = {Am Soc Cell Biol},
	author = {Hanley, Mariah L and Yoo, Tae Yeon and Sonnett, Matthew and Needleman, Daniel J and Mitchison, Timothy J}
}
@article {529756,
	title = {Bridging length scales to measure polymer assembly},
	journal = {Mol. Biol. Cell},
	volume = {28},
	year = {2017},
	pages = {1379-1388},
	author = {Bryan Kaye and Yoo, Tae Yeon and Peter J. Foster and Yu, Che-Hang and Daniel J. Needleman}
}
@article {483826,
	title = {Developing and Testing a Bayesian Analysis of Fluorescence Lifetime Measurements},
	journal = {PLoS ONE},
	volume = {12},
	number = {1},
	year = {2017},
	month = {6 Jan 2017},
	pages = {e0169337. doi:10.1371/journal.pone.0169337},
	author = {Bryan Kaye and Peter J. Foster and Yoo, Tae Yeon and Daniel J. Needleman}
}
@article {BIES:BIES201600212,
	title = {Forces positioning the mitotic spindle: Theories, and now experiments},
	journal = {BioEssays},
	year = {2016},
	note = {1600212},
	month = {Dec 2016},
	pages = {1600212{\textendash}n/a},
	keywords = {force measurement, magnetic tweezers, microtubule, pronuclear migration and rotation, spindle, spindle positioning},
	issn = {1521-1878},
	doi = {10.1002/bies.201600212},
	url = {http://dx.doi.org/10.1002/bies.201600212},
	author = {Wu, Hai-Yin and Nazockdast, Ehssan and Shelley, Michael J. and Daniel J. Needleman}
}
@article {424511,
	title = {Spatial organization of the Ran pathway by microtubules in mitosis},
	journal = {Proceedings of the National Academy of Sciences},
	year = {2016},
	pages = {113 (31) 8729-8734},
	author = {Oh, Doogie and Yu, Che-Hang and Needleman, Daniel}
}
@article {Farhadifargenetics.115.185736,
	title = {Mutation Is a Sufficient and Robust Predictor of Genetic Variation for Mitotic Spindle Traits in Caenorhabditis elegans},
	journal = {Genetics},
	volume = {203},
	number = {4},
	year = {2016},
	pages = {1859-1870},
	publisher = {Genetics},
	abstract = {Different types of phenotypic traits consistently exhibit different levels of genetic variation in natural populations. There are two potential explanations: either mutation produces genetic variation at different rates, or natural selection removes or promotes genetic variation at different rates. Whether mutation or selection is of greater general importance is a longstanding unresolved question in evolutionary genetics. We report mutational variances (VM) for 19 traits related to the first mitotic cell division in C. elegans, and compare them to the standing genetic variances (VG) for the same suite of traits in a worldwide collection C. elegans. Two robust conclusions emerge. First, the mutational process is highly repeatable: the correlation between VM in two independent sets of mutation accumulation lines is \&nbsp;0.9. Second, VM for a trait is a good predictor of VG for that trait: the correlation between VM and VG is \&nbsp;0.9. This result is predicted for a population at mutation-selection balance; it is not predicted if balancing selection plays a primary role in maintaining genetic variation.},
	issn = {0016-6731},
	doi = {10.1534/genetics.115.185736},
	url = {http://www.genetics.org/content/early/2016/06/20/genetics.115.185736},
	author = {Farhadifar, Reza and Ponciano, Jos{\'e} Miguel and Andersen, Erik C. and Daniel J. Needleman and Baer, Charles F.}
}
@article {yoo2016studying,
	title = {Studying Kinetochores In Vivo Using FLIM-FRET},
	journal = {The Mitotic Spindle: Methods and Protocols},
	number = {1413},
	year = {2016},
	pages = {169{\textendash}186},
	publisher = {Springer},
	author = {Yoo, Tae Yeon and Needleman, Daniel J}
}
@article {366301,
	title = {Phosphoinositide 3-Kinase Regulates Glycolysis through Mobilization of Aldolase from the Actin Cytoskeleton},
	journal = {Cell},
	volume = {164},
	year = {2016},
	pages = {433-446},
	author = {Hai Hu and Ashish Juvekar and Costas A. Lyssiotis and Evan C. Lien and John G. Albeck and Oh, Doogie and Gopal Varma and Yin Pun Hung and Soumya Ullas and Josh Lauring and Pankaj Seth and Mark R. Lundquist and Dean R. Tolan and Aaron K. Grant and Daniel J. Needleman and John M. Asara and Lewis C. Cantley and Gerburg M. Wulf}
}
@article {358521,
	title = {Active contraction of microtubule networks},
	journal = {eLife},
	year = {2015},
	pages = {10.7554/eLife.10837},
	author = {PJ Foster and S F{\"u}rthauer and MJ Shelley and Needleman, D. J.}
}
@article {needleman2015material,
	title = {The Material Basis of Life},
	journal = {Trends in cell biology},
	year = {2015},
	publisher = {Elsevier},
	author = {Needleman, Daniel}
}
@article {farhadifar2015scaling,
	title = {Scaling, selection, and evolutionary dynamics of the mitotic spindle},
	journal = {Current Biology},
	volume = {25},
	year = {2015},
	pages = {732{\textendash}740},
	publisher = {Elsevier},
	author = {Farhadifar, Reza and Baer, Charles F and Valfort, Aurore-C{\'e}cile and Andersen, Erik C and M{\"u}ller-Reichert, Thomas and Delattre, Marie and Needleman, Daniel J}
}
@article {sazer2014deciphering,
	title = {Deciphering the Evolutionary History of Open and Closed Mitosis},
	journal = {Current Biology},
	volume = {24},
	year = {2014},
	pages = {R1099{\textendash}R1103},
	publisher = {Elsevier},
	author = {Sazer, Shelley and Lynch, Michael and Needleman, Daniel}
}
@article {needleman2014determining,
	title = {Determining physical principles of subcellular organization},
	journal = {Developmental cell},
	volume = {29},
	year = {2014},
	pages = {135{\textendash}138},
	publisher = {Elsevier},
	author = {Needleman, Dan and Brugues, Jan}
}
@article {brugues2014physical,
	title = {Physical basis of spindle self-organization},
	journal = {Proceedings of the National Academy of Sciences},
	volume = {111},
	year = {2014},
	pages = {18496{\textendash}18500},
	publisher = {National Acad Sciences},
	author = {Brugu{\'e}s, Jan and Needleman, Daniel}
}
@inbook {farhadifar2014automated,
	title = {Automated segmentation of the first mitotic spindle in differential interference contrast microcopy images of C. elegans embryos},
	booktitle = {Mitosis},
	year = {2014},
	pages = {41{\textendash}45},
	publisher = {Springer},
	organization = {Springer},
	author = {Farhadifar, Reza and Needleman, Daniel}
}
@article {yu2013measuring,
	title = {Measuring Microtubule Polarity in Spindles with Second-Harmonic-Generation Microscopy},
	journal = {Biophysical Journal},
	volume = {106},
	year = {2014},
	pages = {1578-1587},
	publisher = {Elsevier},
	author = {Yu, Che-Hang and Langowitz, Noah and Wu, Hai-Yin and Brugues, Jan and Needleman, Daniel}
}
@article {ojeda2014transformation,
	title = {Transformation of taxol-stabilized microtubules into inverted tubulin tubules triggered by a tubulin conformation switch},
	journal = {Nature materials},
	volume = {13},
	year = {2014},
	pages = {195{\textendash}203},
	publisher = {Nature Publishing Group},
	author = {Ojeda-Lopez, Miguel A and Needleman, Daniel J and Chaeyeon Song and Ginsburg, Avi and Kohl, Phillip A and Li, Youli and Miller, Herbert P and Wilson, Leslie and Raviv, Uri and Myung Chul Choi and others}
}
@article {needleman2013developing,
	title = {Developing cell biology},
	journal = {eLife},
	volume = {2},
	year = {2013},
	pages = {e00571},
	publisher = {eLife Sciences Publications Limited},
	author = {Needleman, Daniel}
}
@article {needleman2013ion,
	title = {Ion specific effects in bundling and depolymerization of taxol-stabilized microtubules},
	journal = {Faraday discussions},
	volume = {166},
	year = {2013},
	pages = {31{\textendash}45},
	publisher = {Royal Society of Chemistry},
	author = {Needleman, Daniel J and Ojeda-Lopez, Miguel A and Raviv, Uri and Miller, Herbert P and Li, Youli and Chaeyeon Song and Feinstein, Stuart C and Wilson, Leslie and Myung Chul Choi and Safinya, Cyrus R}
}
@article {brugues2012nucleation,
	title = {Nucleation and transport organize microtubules in metaphase spindles},
	journal = {Cell},
	volume = {149},
	year = {2012},
	pages = {554{\textendash}564},
	publisher = {Elsevier},
	author = {Brugu{\'e}s, Jan and Nuzzo, Valeria and Eric Mazur and Needleman, Daniel J}
}
@article {oh2011development,
	title = {Development of time-integrated multipoint moment analysis for spatially resolved fluctuation spectroscopy with high time resolution},
	journal = {Biophysical journal},
	volume = {101},
	year = {2011},
	pages = {1546{\textendash}1554},
	publisher = {Elsevier},
	author = {Oh, Doogie and Zidovska, Alexandra and Xu, Yangqing and Needleman, Daniel J}
}
@article {safinya2011nanoscale,
	title = {Nanoscale assembly in biological systems: from neuronal cytoskeletal proteins to curvature stabilizing lipids},
	journal = {Advanced Materials},
	volume = {23},
	year = {2011},
	pages = {2260{\textendash}2270},
	publisher = {Wiley Online Library},
	author = {Safinya, Cyrus R and Raviv, Uri and Needleman, Daniel J and Zidovska, Alexandra and Myung Chul Choi and Ojeda-Lopez, Miguel A and Ewert, Kai K and Li, Youli and Miller, Herbert P and Quispe, Joel and others}
}
@article {needleman2010mitosis,
	title = {Mitosis: Taking the Measure of Spindle Length},
	journal = {Current Biology},
	volume = {20},
	year = {2010},
	pages = {R359{\textendash}R360},
	publisher = {Elsevier},
	author = {Needleman, Daniel J and Farhadifar, Reza}
}
@conference {brugues2010nonequilibrium,
	title = {Nonequilibrium fluctuations in metaphase spindles: Polarized light microscopy, image registration, and correlation functions},
	booktitle = {OPTO},
	year = {2010},
	pages = {76180L{\textendash}76180L},
	publisher = {International Society for Optics and Photonics},
	organization = {International Society for Optics and Photonics},
	author = {Brugu{\'e}s, Jan and Needleman, Daniel J}
}
@article {mirny2010quantitative,
	title = {Quantitative characterization of filament dynamics by single-molecule lifetime measurements},
	journal = {Methods in cell biology},
	volume = {95},
	year = {2010},
	pages = {582{\textendash}600},
	publisher = {Elsevier},
	author = {Mirny, Leonid A and Needleman, Daniel J}
}
@article {nurgaliev2010automated,
	title = {Automated identification of microtubules in cellular electron tomography},
	journal = {Methods in cell biology},
	volume = {97},
	year = {2010},
	pages = {475{\textendash}495},
	publisher = {Elsevier},
	author = {Nurgaliev, Daniyar and Gatanov, Timur and Needleman, Daniel J}
}
@article {needleman2010fast,
	title = {Fast microtubule dynamics in meiotic spindles measured by single molecule imaging: evidence that the spindle environment does not stabilize microtubules},
	journal = {Molecular biology of the cell},
	volume = {21},
	year = {2010},
	pages = {323{\textendash}333},
	publisher = {Am Soc Cell Biol},
	author = {Needleman, Daniel J and Groen, Aaron and Ohi, Ryoma and Maresca, Tom and Mirny, Leonid and Mitchison, Tim}
}
@article {choi2009human,
	title = {Human microtubule-associated-protein tau regulates the number of protofilaments in microtubules: a synchrotron x-ray scattering study},
	journal = {Biophysical journal},
	volume = {97},
	year = {2009},
	pages = {519{\textendash}527},
	publisher = {Elsevier},
	author = {Choi, MC and Raviv, U and Miller, HP and Gaylord, MR and Kiris, E and Ventimiglia, D and Needleman, D. J. and Kim, MW and Wilson, L. and Feinstein, SC and others}
}
@article {needleman2009cellular,
	title = {Cellular allometry: the spindle in development and inheritance},
	journal = {Current Biology},
	volume = {19},
	year = {2009},
	pages = {R846{\textendash}R847},
	publisher = {Elsevier},
	author = {Needleman, Daniel J}
}
@article {schier2009developmental,
	title = {Developmental biology: Rise of the source{\textendash}sink model},
	journal = {Nature},
	volume = {461},
	year = {2009},
	pages = {480{\textendash}481},
	publisher = {Nature Publishing Group},
	author = {Schier, Alexander F and Needleman, Daniel}
}
@article {wühr2009does,
	title = {How does a millimeter-sized cell find its center?},
	journal = {Cell cycle},
	volume = {8},
	year = {2009},
	pages = {1115{\textendash}1121},
	publisher = {Taylor \& Francis},
	author = {Wühr, Martin and Dumont, Sophie and Groen, Aaron C and Needleman, Daniel J and Mitchison, Timothy J}
}
@article {needleman2009pin,
	title = {Pin-hole array correlation imaging: highly parallel fluorescence correlation spectroscopy},
	journal = {Biophysical journal},
	volume = {96},
	year = {2009},
	pages = {5050{\textendash}5059},
	publisher = {Elsevier},
	author = {Needleman, Daniel J and Xu, Yangqing and Mitchison, Timothy J}
}
@article {gatlin2009spindle,
	title = {Spindle fusion requires dynein-mediated sliding of oppositely oriented microtubules},
	journal = {Current Biology},
	volume = {19},
	year = {2009},
	pages = {287{\textendash}296},
	publisher = {Elsevier},
	author = {Gatlin, Jesse C and Matov, Alexandre and Groen, Aaron C and Needleman, Daniel J and Maresca, Thomas J and Gaudenz Danuser and Mitchison, Timothy J and Salmon, ED}
}
@article {wuhr2008evidence,
	title = {Evidence for an upper limit to mitotic spindle length},
	journal = {Current Biology},
	volume = {18},
	year = {2008},
	pages = {1256{\textendash}1261},
	publisher = {Elsevier},
	author = {Martin W{\"u}hr and Chen, Yao and Dumont, Sophie and Groen, Aaron C and Needleman, Daniel J and Salic, Adrian and Mitchison, Timothy J}
}
@article {groen2008novel,
	title = {A novel small-molecule inhibitor reveals a possible role of kinesin-5 in anastral spindle-pole assembly},
	journal = {Journal of cell science},
	volume = {121},
	year = {2008},
	pages = {2293{\textendash}2300},
	publisher = {The Company of Biologists Ltd},
	author = {Groen, Aaron C and Needleman, Daniel and Brangwynne, Clifford and Gradinaru, Christain and Fowler, Brandon and Mazitschek, Ralph and Mitchison, Timothy J}
}
@article {needleman2008plasmid,
	title = {Plasmid segregation: is a total understanding within reach?},
	journal = {Current Biology},
	volume = {18},
	year = {2008},
	pages = {R212{\textendash}R214},
	publisher = {Elsevier},
	author = {Needleman, Daniel J}
}
@article {raviv2007hierarchical,
	title = {Hierarchical bionanotubes formed by the self assembly of microtubules with cationic membranes or polypeptides},
	journal = {Journal of Applied Crystallography},
	volume = {40},
	year = {2007},
	pages = {s83{\textendash}s87},
	publisher = {International Union of Crystallography},
	author = {Raviv, Uri and Needleman, Daniel J and Ewert, Kai K and Safinya, Cyrus R}
}
@article {raviv2007microtubule,
	title = {Microtubule protofilament number is modulated in a stepwise fashion by the charge density of an enveloping layer},
	journal = {Biophysical journal},
	volume = {92},
	year = {2007},
	pages = {278{\textendash}287},
	publisher = {Elsevier},
	author = {Raviv, Uri and Nguyen, Toan and Ghafouri, Rouzbeh and Needleman, Daniel J and Li, Youli and Miller, Herbert P and Wilson, Leslie and Bruinsma, Robijn F and Safinya, Cyrus R}
}
@article {safinya2006cationic,
	title = {Cationic liposome{\textendash}DNA complexes: from liquid crystal science to gene delivery applications},
	journal = {Philosophical Transactions of the Royal Society of London A: Mathematical, Physical and Engineering Sciences},
	volume = {364},
	year = {2006},
	pages = {2573{\textendash}2596},
	publisher = {The Royal Society},
	author = {Safinya, Cyrus R and Ewert, Kai and Ahmad, Ayesha and Evans, Heather M and Raviv, Uri and Needleman, Daniel J and Lin, Alison J and Slack, Nelle L and George, Cyril and Samuel, Charles E}
}
@article {raviv2006cationic,
	title = {Cationic membranes complexed with oppositely charged microtubules: hierarchical self-assembly leading to bio-nanotubes},
	journal = {Journal of Physics: Condensed Matter},
	volume = {18},
	year = {2006},
	pages = {S1271},
	publisher = {IOP Publishing},
	author = {Raviv, Uri and Needleman, Daniel J and Safinya, Cyrus R}
}
@article {raviv2005cationic,
	title = {Cationic liposome{\textendash}microtubule complexes: Pathways to the formation of two-state lipid{\textendash}protein nanotubes with open or closed ends},
	journal = {Proceedings of the National Academy of Sciences of the United States of America},
	volume = {102},
	year = {2005},
	pages = {11167{\textendash}11172},
	publisher = {National Acad Sciences},
	author = {Raviv, Uri and Needleman, Daniel J and Li, Youli and Miller, Herbert P and Wilson, Leslie and Safinya, Cyrus R}
}
@article {needleman2005radial,
	title = {Radial compression of microtubules and the mechanism of action of taxol and associated proteins},
	journal = {Biophysical journal},
	volume = {89},
	year = {2005},
	pages = {3410{\textendash}3423},
	publisher = {Elsevier},
	author = {Needleman, Daniel J and Ojeda-Lopez, Miguel A and Raviv, Uri and Ewert, Kai and Miller, Herbert P and Wilson, Leslie and Safinya, Cyrus R}
}
@article {needleman2005supramolecular,
	title = {Supramolecular assembly of biological molecules purified from bovine nerve cells: from microtubule bundles and necklaces to neurofilament networks},
	journal = {Journal of Physics: Condensed Matter},
	volume = {17},
	year = {2005},
	pages = {S3225},
	publisher = {IOP Publishing},
	author = {Needleman, Daniel J and Jones, Jayna B and Raviv, Uri and Ojeda-Lopez, Miguel A and Miller, HP and Li, Y. and Wilson, L. and Safinya, CR}
}
@article {needleman2004higher,
	title = {Higher-order assembly of microtubules by counterions: From hexagonal bundles to living necklaces},
	journal = {Proceedings of the National Academy of Sciences of the United States of America},
	volume = {101},
	year = {2004},
	pages = {16099{\textendash}16103},
	publisher = {National Acad Sciences},
	author = {Needleman, Daniel J and Ojeda-Lopez, Miguel A and Raviv, Uri and Miller, Herbert P and Wilson, Leslie and Safinya, Cyrus R}
}
@article {needleman2004synchrotron,
	title = {Synchrotron X-ray diffraction study of microtubules buckling and bundling under osmotic stress: a probe of interprotofilament interactions},
	journal = {Physical review letters},
	volume = {93},
	year = {2004},
	pages = {198104},
	publisher = {APS},
	author = {Needleman, Daniel J and Ojeda-Lopez, Miguel A and Raviv, Uri and Ewert, Kai and Jones, Jayna B and Miller, Herbert P and Wilson, Leslie and Safinya, Cyrus R}
}
@article {fygenson2004variability,
	title = {Variability-based sequence alignment identifies residues responsible for functional differences in $\alpha$ and $\beta$ tubulin},
	journal = {Protein science},
	volume = {13},
	year = {2004},
	pages = {25{\textendash}31},
	publisher = {Wiley Online Library},
	author = {Fygenson, D Kuchnir and Needleman, Daniel J and Sneppen, Kim}
}
@article {needleman2001collective,
	title = {Collective enhancement of precision in networks of coupled oscillators},
	journal = {Physica D: Nonlinear Phenomena},
	volume = {155},
	year = {2001},
	pages = {324{\textendash}336},
	publisher = {Elsevier},
	author = {Needleman, Daniel J and Tiesinga, Paul HE and Sejnowski, Terrence J}
}
