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Cell lineage tracing using nuclease barcoding [article]

Stephanie Tzouanas Schmidt, Stephanie M. Zimmerman, Jianbin Wang, Stuart K. Kim, Stephen R. Quake
2016 arXiv   pre-print
Lineage tracing, the determination and mapping of progeny arising from single cells, is an important approach enabling the elucidation of mechanisms underlying diverse biological processes ranging from development to disease. We developed a dynamic sequence-based barcode for lineage tracing and have demonstrated its performance in C. elegans, a model organism whose lineage tree is well established. The strategy we use creates lineage trees based upon the introduction of specific mutations into
more » ... ells and the propagation of these mutations to daughter cells at each cell division. We present an experimental proof of concept along with a corresponding simulation and analytical model for deeper understanding of the coding capacity of the system. By introducing mutations in a predictable manner using CRISPR/Cas9, our technology will enable more complete investigations of cellular processes.
arXiv:1606.00786v1 fatcat:hijohfxlrne75lcrv46gn6m3ai

Holographic Principle and the Second Law in Stephani Cosmology Revisited [article]

Daniele Gregoris, Yen Chin Ong, Bin Wang
2019 arXiv   pre-print
We show in a model-independent way that the inhomogeneous cosmological class II Stephani model fulfills both the the cosmological holographic principle, and that the entropy is increasing with time.  ...  Recently a specific Stephani model was investigated along this line [48] .  ...  DUST MODELING IN A STEPHANI MODEL Consider the Stephani cosmological model given by the metric tensor ds 2 = − c 2 V 2 (t , r ) dt 2 + R 2 (t ) V 2 (t , r ) [dr 2 + r 2 (dθ 2 + sin 2 θ dφ 2 )], (1) with  ... 
arXiv:1906.02879v1 fatcat:lvsbwfqrgbh4jhdkfga6alq4z4

P-partition power sums [article]

Farid Aliniaeifard, Victor Wang, Stephanie van Willigenburg
2021 arXiv   pre-print
Motivated by the theory of P-partitions, we introduce the basis of combinatorial power sums for the Hopf algebra of quasisymmetric functions, refining the power sum symmetric functions. These share many properties with the type 1 and type 2 quasisymmetric power sums introduced by Ballantine, Daugherty, Hicks, Mason and Niese, and moreover expand into the monomial basis of quasisymmetric functions with nonnegative integer coefficients. We prove formulas for products, coproducts and classical
more » ... isymmetric involutions via the combinatorics of P-partitions, and give combinatorial interpretations for the coefficients when expanded into the monomial and fundamental bases.
arXiv:2112.06457v1 fatcat:ziayua4razeyxndhum6ozm5mt4

Stephani cosmology: entropically viable but observationally challenged

Yen Chin Ong, S. Sedigheh Hashemi, Rui An, Bin Wang
2018 European Physical Journal C: Particles and Fields  
Working with a concrete, popular model of the Stephani cosmology -- the Stephani-Dabrowski model, we found that it is entropically viable.  ...  Inhomogeneous cosmological models such as the Stephani universes could, in principle, provide an explanation for the observed accelerated expansion of the Universe.  ...  In the work of Wang et al. [70] , it was shown that in contrast to flat homogeneous models, the holographic principle may break down in some LTB models.  ... 
doi:10.1140/epjc/s10052-018-5866-1 fatcat:z7hf25galvfproouurfisdsx4q

Weighing Dirac fermions by nonlinear Hall effect [article]

Yang Wang, Sivakumar V. Mambakkam, Yong Wang, Stephanie A. Law, John. Q. Xiao
2022 arXiv   pre-print
Breaking the time-reversal symmetry on the surface of a topological insulator can open a gap for the linear dispersion and make the Dirac fermions massive. This can be achieved by either doping a topological insulator with magnetic elements or proximity-coupling it to magnetic insulators. While the exchange gap can be directly imaged in the former case, measuring it at the buried magnetic insulator/topological insulator interface remains to be challenging. Here, we report the observation of a
more » ... rge nonlinear Hall effect in iron garnet/Bi2Se3 heterostructures. Besides illuminating its magnetic origin, we also show that this nonlinear Hall effect can be utilized to measure the size of the exchange gap and the magnetic-proximity onset temperature. Our results demonstrate the nonlinear Hall effect as a spectroscopic tool to probe the modified band structure at magnetic insulator/topological insulator interfaces.
arXiv:2203.06293v1 fatcat:2myeqvbfcbh4jevk7hqtsq2vhy

Approaches Mediating Oxytocin Regulation of the Immune System

Tong Li, Ping Wang, Stephani C. Wang, Yu-Feng Wang
2017 Frontiers in Immunology  
The hypothalamic neuroendocrine system is mainly composed of the neural structures regulating hormone secretion from the pituitary gland and has been considered as the higher regulatory center of the immune system. Recently, the hypothalamo-neurohypophysial system (HNS) emerged as an important component of neuroendocrine-immune network, wherein the oxytocin (OT)-secreting system (OSS) plays an essential role. The OSS, consisting of OT neurons in the supraoptic nucleus, paraventricular nucleus,
more » ... heir several accessory nuclei and associated structures, can integrate neural, endocrine, metabolic, and immune information and plays a pivotal role in the development and functions of the immune system. The OSS can promote the development of thymus and bone marrow, perform immune surveillance, strengthen immune defense, and maintain immune homeostasis. Correspondingly, OT can inhibit inflammation, exert antibiotic-like effect, promote wound healing and regeneration, and suppress stress-associated immune disorders. In this process, the OSS can release OT to act on immune system directly by activating OT receptors or through modulating activities of other hypothalamic-pituitary-immune axes and autonomic nervous system indirectly. However, our understandings of the role of the OSS in neuroendocrine regulation of immune system are largely incomplete, particularly its relationship with other hypothalamic-pituitary-immune axes and the vasopressin-secreting system that coexists with the OSS in the HNS. In addition, it remains unclear about the relationship between the OSS and peripherally produced OT in immune regulation, particularly intrathymic OT that is known to elicit central immunological self-tolerance of T-cells to hypophysial hormones. In this work, we provide a brief review of current knowledge of the features of OSS regulation of the immune system and of potential approaches that mediate OSS coordination of the activities of entire neuroendocrine-immune network.
doi:10.3389/fimmu.2016.00693 pmid:28119696 pmcid:PMC5223438 fatcat:thejmv3rkbbstog6sscad77cs4

Nonsocial Functions of Hypothalamic Oxytocin

Hai-Peng Yang, Liwei Wang, Liqun Han, Stephani C. Wang
2013 ISRN Neuroscience  
Yu-Feng Wang for advice.  ... 
doi:10.1155/2013/179272 pmid:24967304 pmcid:PMC4045544 fatcat:vvir5dsjrrdstcxl4nrbvhaw7e

Receptor binding may directly activate the fusion machinery in coronavirus spike glycoproteins [article]

Yuzhang Wang, Lucy Fallon, Lauren Raguette, Stephanie Budhan, Kellon Belfon, Darya Stepanenko, Stephanie Helbock, Sarah Varghese, Carlos Simmerling
2021 bioRxiv   pre-print
SARS-CoV-2, the causative agent of the COVID-19 pandemic, is an enveloped RNA virus. Trimeric spike glycoproteins extend outward from the virion; these class I viral membrane fusion proteins mediate entry of the virus into a host cell and are the dominant antigen for immune response. Cryo-EM studies have generated a large number of structures for the spike either alone, or bound to the cognate receptor ACE2 or antibodies, with the three receptor binding domains (RBDs) seen closed, open, or in
more » ... rious combinations. Binding to ACE2 requires an open RBD, and is believed to trigger the series of dramatic conformational changes in the spike that lead to the shedding of the S1 subunit and transition of the spring-loaded S2 subunit to the experimentally observed post-fusion structure. The steps following ACE2 binding are poorly understood despite extensive characterization of the spike through X-ray, cryo-EM, and computation. Here, we use all-atom simulations, guided by analysis of 81 existing experimental structures, to develop a model for the structural and energetic coupling that connects receptor binding to activation of the membrane fusion machinery.
doi:10.1101/2021.05.10.443496 fatcat:xfukapucfbhwnctatugy4ctwky

Censorship 2.0

Robert Faris, Stephanie Wang, John Palfrey
2008 Innovations Technology Governance Globalization  
Robert Faris, Stephanie Wang, and John Palfrey Censorship 2.0 mary search service, Google.com.  ...  This is Robert Faris, Stephanie Wang, and John Palfrey Censorship 2.0 undoubtedly an attractive notion for many other countries around the world.  ... 
doi:10.1162/itgg.2008.3.2.165 fatcat:vgc4ltjbivflnaka6flafg3dje

Migration regulates cellular mechanical states

Stephanie S. Chang, Andrew D. Rape, Stephanie A. Wong, Wei-hui Guo, Yu-li Wang, Valerie Marie Weaver
2019 Molecular Biology of the Cell  
., 2000; Wang et al., 2002; Trichet et al., 2012) .  ...  Glass substrates micropatterned with linear polyacrylamide to generate nonadhesive areas were prepared as described previously (Guo and Wang, 2011) .  ... 
doi:10.1091/mbc.e19-02-0099 pmid:31693433 pmcid:PMC6938245 fatcat:nzeio3p75fdcbh2ga6c4qxsnjq

Pathological basis of cardiac arrhythmias: vicious cycle of immune-metabolic dysregulation

Stephani C. Wang, Dexin Meng, Haipeng Yang, Xiaoran Wang, Shuwei Jia, Yu-Feng Wang, Ping Wang
2017 Cardiovascular Disorders and Medicine  
Cardiac arrhythmias are a major type of cardiovascular diseases and account for high morbidity and mortality. The occurrence of cardiac arrhythmias is closely associated with abnormal neurohumoral regulation of heart rhythmicity and the pathogenesis of many cardiovascular diseases, particularly coronary artery disease (CAD). Normal immunometabolic coupling between endoplasmic reticulum (ER) and mitochondria is an essential condition for normal heart rhythm. ER stress -and mitochondrial
more » ... stress-evoked immunometabolic challenges can cause inflammation, lipotoxicity and cell apoptosis, leading to CAD and the ensuing arrhythmias. These disorders are associated with activation of inducible nitric oxide synthase, excessive protein nitrosylation, malfunctioned chaperone, abnormal calcium signaling through mitochondria-associated ER membrane, disruption of oxidative phosphorylation, and activation of inflammatory and apoptotic pathways. In this review, we highlight the mechanisms underlying arrhythmias, specifically involving disorders in immuno-metabolic network and the underlying signaling process.
doi:10.15761/cdm.1000158 fatcat:4xkangkcnjg7dmbuwf5f5munpu

Quantitative Analysis of Synthetic Cell Lineage Tracing Using Nuclease Barcoding

Stephanie Tzouanas Schmidt, Stephanie M. Zimmerman, Jianbin Wang, Stuart K. Kim, Stephen R. Quake
2017 ACS Synthetic Biology  
Lineage tracing by the determination and mapping of progeny arising from single cells is an important approach enabling the elucidation of mechanisms underlying diverse biological processes ranging from development to disease. We developed a dynamic sequence-based barcode system for synthetic lineage tracing and have demonstrated its performance in C. elegans, a model organism whose lineage tree is well established. The strategy we use creates lineage trees based upon the introduction of
more » ... ically controlled mutations into cells and the propagation of these mutations to daughter cells at each cell division. We analyzed this experimental proof of concept along with a corresponding simulation and analytical model to gain a deeper understanding of the coding capacity of the system. Our results provide specific bounds on the fidelity of lineage tracing using such approaches.
doi:10.1021/acssynbio.6b00309 pmid:28264564 pmcid:PMC5724935 fatcat:wwtl6apnvngdvm3g7slqbz3l2e

Practical Volume-Based Attacks on Encrypted Databases [article]

Rishabh Poddar, Stephanie Wang, Jianan Lu, Raluca Ada Popa
2020 arXiv   pre-print
Recent years have seen an increased interest towards strong security primitives for encrypted databases (such as oblivious protocols), that hide the access patterns of query execution, and reveal only the volume of results. However, recent work has shown that even volume leakage can enable the reconstruction of entire columns in the database. Yet, existing attacks rely on a set of assumptions that are unrealistic in practice: for example, they (i) require a large number of queries to be issued
more » ... y the user, or (ii) assume certain distributions on the queries or underlying data (e.g., that the queries are distributed uniformly at random, or that the database does not contain missing values). In this work, we present new attacks for recovering the content of individual user queries, assuming no leakage from the system except the number of results and avoiding the limiting assumptions above. Unlike prior attacks, our attacks require only a single query to be issued by the user for recovering the keyword. Furthermore, our attacks make no assumptions about the distribution of issued queries or the underlying data. Instead, our key insight is to exploit the behavior of real-world applications. We start by surveying 11 applications to identify two key characteristics that can be exploited by attackers: (i) file injection, and (ii) automatic query replay. We present attacks that leverage these two properties in concert with volume leakage, independent of the details of any encrypted database system. Subsequently, we perform an attack on the real Gmail web client by simulating a server-side adversary. Our attack on Gmail completes within a matter of minutes, demonstrating the feasibility of our techniques. We also present three ancillary attacks for situations when certain mitigation strategies are employed.
arXiv:2008.06627v1 fatcat:3pgvb6w3pbe4pcrtuchfl273xe

Role of Connexin 36 in Autoregulation of Oxytocin Neuronal Activity in Rat Supraoptic Nucleus

Ping Wang, Stephani C. Wang, Dongyang Li, Tong Li, Hai-Peng Yang, Liwei Wang, Yu-Feng Wang, Vladimir Parpura
2019 ASN Neuro  
The author(s) disclosed receipt of the following financial support for the research, authorship, and/or publication of this article: This work was supported by the National Natural ORCID iD Yu-Feng Wang  ...  et al., 1995 (Wang et al., , 1996a (Wang et al., , 1996b .  ...  Functionally, this is consistent with the appearance of synchronized activation of OT neurons in burst firing during suckling (Wang et al., 1995 (Wang et al., , 1996b .  ... 
doi:10.1177/1759091419843762 pmid:31091986 pmcid:PMC6535915 fatcat:byxdevqodrc6poioox2lshurpm

Telomere and Its Role in Diseases

Stephanie Wang, Chikezie O. Madu, Yi Lu
2019 Oncomedicine  
Telomeres are highly conservative repeated nucleotide sequences at the ends of linear chromosomes. Allowing effective DNA replication to keep the integrity of gene structure and the stability of chromosomes, telomeres protect the ends of the chromosome from deterioration or from fusion with neighboring chromosomes. Reduction in the telomere length leads to the cessation of cell division and thus cellular senescence. On the other hand, telomerase is a ribonucleoprotein complex with reverse
more » ... riptase activity, protecting the telomere from being shortened. Thus, it is inactivated by synthesis and adds the repeated sequences onto the telomeres. Telomerase plays an important role in cell senescence and tumor formation. Telomere length and telomerase activity may be mediated by immune, endocrine, and metabolic pathways and accelerate cellular dysfunction, ageing, and even induce cancer over one's lifespan. Significant attainment of telomerase to maintain telomere length could stop the cell senescence and aging related disease and also is required for the evolution of malignancy. This review discusses the role of telomeres and telomerase in humans during senescence and cancer. The evidence indicates that telomerase-induced telomere length manipulations could be targeted for anti-aging and anti-cancer therapy in the future.
doi:10.7150/oncm.28210 fatcat:yhvalkxvg5ecdh2y6u2gjw3vta
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