Miracle-dz/UniFAR-FTUs huggingface dataset:
Transcriptomic analysis of different stages of pigeon ovaries by RNA‐sequencing

The pigeon ovary is an ideal model for deciphering the molecular mechanism of folliculogenesis. While most analysis has focused on the influence of hormones and factors on ovarian follicle development in this model, changes occurring in the ovarian stroma can also be extremely informative. Here, we profiled the transcriptome of pigeon ovaries at pre‐ovulation, post‐ovulation, and 5–6 days after ovulation using RNA‐sequencing to gain insights into the molecular and cellular events mediating ovary activity. We obtained 44,784,505 clean reads that aligned with 14,088 genes. Gene expression profile analysis identified 409 differentially expressed genes between pre‐ and post‐ovulation; 96 genes were up‐regulated genes while 313 genes were down‐regulated. Gene ontology analysis of the down‐regulated genes revealed significant enrichment in components of the immune response, immune system, antigen processing and presentation, receptor binding, and biological adhesion. Pathway analyses of the high‐expression genes of the post‐ovulation ovary identified enrichment in phagosomes, lysosomes, cytokine–cytokine receptor interactions, cell adhesion molecules, and the Toll‐like receptor signaling. These data together suggest that post‐ovulatory follicle regression and elimination occurs through an immune response. Mol. Reprod. Dev. 83: 640–648, 2016. © 2016 Wiley Periodicals, Inc.
Local Distributed Algorithms in Highly Dynamic Networks

We define a generalization of local distributed graph problems to (synchronous round-based) dynamic networks and present a framework for developing algorithms for these problems. The algorithms should satisfy non-trivial guarantees in every round. The guarantees should be stronger the more stable the graph has been during the last few rounds and coincide with the definition of the static graph problem if no topological change appeared recently. Moreover, if only a constant neighborhood around some part of the graph is stable during an interval, the algorithms should quickly converge to a solution for this part of the graph that remains unchanged throughout the interval. We demonstrate our generic framework with two classic distributed graph problems, namely (degree+1)-vertex coloring and maximal independent set (MIS). To illustrate the given guarantees consider the vertex coloring problem: Any conflict between two nodes caused by a newly inserted edge is resolved within T=O(log n) rounds. During this conflict resolving both nodes always output colors that are not in conflict with their respective 'old' neighbors. The largest color that a node is allowed to output is determined by the number of distinct neighbors that it has seen in the last T rounds.
Time‐varying coefficients models for recurrent event data when different varying coefficients admit different degrees of smoothness: application to heart disease modeling

We consider a class of semiparametric marginal rate models for analyzing recurrent event data. In these models, both time‐varying and time‐free effects are present, and the estimation of time‐varying effects may result in non‐smooth regression functions. A typical approach for avoiding this problem and producing smooth functions is based on kernel methods. The traditional kernel‐based approach, however, assumes a common degree of smoothness for all time‐varying regression functions, which may result in suboptimal estimators if the functions have different levels of smoothness. In this paper, we extend the traditional approach by introducing different bandwidths for different regression functions. First, we establish the asymptotic properties of the suggested estimators. Next, we demonstrate the superiority of our proposed method using two finite‐sample simulation studies. Finally, we illustrate our methodology by analyzing a real‐world heart disease dataset. Copyright © 2016 John Wiley & Sons, Ltd.
The Histone Variant MacroH2A Blocks Cellular Reprogramming by Inhibiting Mesenchymal-to-Epithelial Transition

ABSTRACT Transcription factor-induced reprogramming of somatic cells to pluripotency is mediated via profound alterations in the epigenetic landscape. The histone variant macroH2A1 (mH2A1) is a barrier to the cellular reprogramming process. We demonstrate here that mH2A1 blocks reprogramming and contributes to the preservation of cell identity by trapping cells at the very early stages of the process, namely, at the mesenchymal-to-epithelial transition (MET). We provide a comprehensive analysis of the genomic sites occupied by the mH2A1 nucleosomes in human fibroblasts and embryonic stem (ES) cells and how they affect the reprogramming of fibroblasts to pluripotency. We have integrated chromatin immunoprecipitation sequencing (ChIP-seq) data with transcriptome sequencing (RNA-seq) data using cells containing reduced levels of mH2A1 and have inferred mH2A1-centered gene-regulatory networks that support the fibroblast and ES cell fates. We found that the exact positions of mH2A1 nucleosomes in regulatory regions of specific network genes with key regulatory roles guarantee the functional robustness of the regulatory networks. Using the reconstructed networks, we can predict and validate several components and their interactions in the establishment of stable cell types by limiting progression to alternative cell fates.
Reduced low‐frequency power and phase locking reflect restoration in the auditory continuity illusion

Interruptions in auditory input can be perceptually restored if they coincide with a masking sound, resulting in a continuity illusion. Previous studies have shown that this continuity illusion is associated with reduced low‐frequency neural oscillations in the auditory cortex. However, the precise contribution of oscillatory amplitude changes and phase alignment to auditory restoration remains unclear. Using electroencephalography, we investigated induced power changes and phase locking in response to 3 Hz amplitude‐modulated tones during the interval of an interrupting noise. We experimentally manipulated both the physical continuity of the tone (continuous vs. interrupted) and the masking potential of the noise (notched vs. full). We observed an attenuation of 3 Hz power during continuity illusions in comparison with both continuous tones and veridically perceived interrupted tones. This illusion‐related suppression of low‐frequency oscillations likely reflects a blurring of auditory object boundaries that supports continuity perception. We further observed increased 3 Hz phase locking during fully masked continuous tones compared with the other conditions. This low‐frequency phase alignment may reflect the neural registration of the interrupting noise as a newly appearing object, whereas during continuity illusions, a spectral portion of this noise is delegated to filling the interruption. Taken together, our findings suggest that the suppression of slow cortical oscillations in both the power and phase domains supports perceptual restoration of interruptions in auditory input.
A High-Speed Accelerator for Homomorphic Encryption using the Karatsuba Algorithm

Somewhat Homomorphic Encryption (SHE) schemes can be used to carry out operations on ciphered data. In a cloud computing scenario, personal information can be processed secretly, inferring a high level of confidentiality. The principle limitation of SHE is the size of ciphertext compared to the size of the message. This issue can be addressed by using a batching technique that “packs” several messages into one ciphertext. However, this method leads to important drawbacks in standard implementations. This paper presents a fast hardware/software co-design implementation of an encryption procedure using the Karatsuba algorithm. Our hardware accelerator is 1.5 times faster than the state of the art for 1 encryption and 4 times faster for 4 encryptions.
Gender orientation and alcohol-related weight control behavior among male and female college students

ABSTRACT Objective: We examine weight control behavior used to (a) compensate for caloric content of heavy alcohol use; and (b) enhance the psychoactive effects of alcohol among college students. We evaluate the role of gender orientation and sex. Participants: Participants completed an online survey (N = 651; 59.9% women; 40.1% men). Method: Weight control behavior was assessed via the Compensatory-Eating-and-Behaviors-in Response-to-Alcohol-Consumption-Scale. Control variables included sex, race/ethnicity, age, and depressive symptoms. Gender orientation was measured by the Bem Sex Role Inventory. The prevalence and probability of alcohol-related weight control behavior using ordinal logistic regression are reported. Results: Men and women do not significantly differ in compensatory-weight-control-behavior. However, regression models suggest that recent binge drinking, other substance use, and masculine orientation are positively associated with alcohol-related weight control behavior. Conclusions: Sex was not a robust predictor of weight control behavior. Masculine orientation should be considered a possible risk factor for these behaviors and considered when designing prevention and intervention strategies.
Tissue specificity of in vitro drug sensitivity

Research in oncology traditionally focuses on specific tissue type from which the cancer develops. However, advances in high-throughput molecular profiling technologies have enabled the comprehensive characterization of molecular aberrations in multiple cancer types. It was hoped that these large-scale datasets would provide the foundation for a paradigm shift in oncology which would see tumors being classified by their molecular profiles rather than tissue types, but tumors with similar genomic aberrations may respond differently to targeted therapies depending on their tissue of origin. There is therefore a need to reassess the potential association between pharmacological response and tissue of origin for therapeutic drugs, and to test how these associations translate from preclinical to clinical settings. In this paper, we investigate the tissue specificity of drug sensitivities in large-scale pharmacological studies and compare these associations to those found in clinical trial descriptions. Our meta-analysis of the four largest in vitro drug screening datasets indicates that tissue of origin is strongly associated with drug response. We identify novel tissue-drug associations, which may present exciting new avenues for drug repurposing. One caveat is that the vast majority of the significant associations found in preclinical settings do not concur with clinical observations. Accordingly, our results call for more testing to find the root cause of the discrepancies between preclinical and clinical observations.
Highly Sensitive, Wearable, Durable Strain Sensors and Stretchable Conductors Using Graphene/Silicon Rubber Composites

Highly sensitive, wearable and durable strain sensors are vital to the development of health monitoring systems, smart robots and human machine interfaces. The recent sensor fabrication progress is respectable, but it is limited by complexity, low sensitivity and unideal service life. Herein a facile, cost‐effective and scalable method is presented for the development of high‐performance strain sensors and stretchable conductors based on a composite film consisting of graphene platelets (GnPs) and silicon rubber. Through calculation by the tunneling theory using experimental data, the composite film has demonstrated ideal linear and reproducible sensitivity to tensile strains, which is contributed by the superior piezoresistivity of GnPs having tunable gauge factors 27.7–164.5. The composite sensors fabricated in different days demonstrate pretty similar performance, enabling applications as a health‐monitoring device to detect various human motions from finger bending to pulse. They can be used as electronic skin, a vibration sensor and a human‐machine interface controller. Stretchable conductors are made by coating and encapsulating GnPs with polydimethyl siloxane to create another composite; this structure allows the conductor to be readily bent and stretched with sufficient mechanical robustness and cyclability.
Integration of high‐risk human papillomavirus into cellular cancer‐related genes in head and neck cancer cell lines

Human papillomavirus (HPV)‐positive oropharyngeal cancer is generally associated with excellent response to therapy, but some HPV‐positive tumors progress despite aggressive therapy. The purpose of this study was to evaluate viral oncogene expression and viral integration sites in HPV16‐ and HPV18‐positive squamous cell carcinoma lines.
Live Blog Corpus for Summarization

Live blogs are an increasingly popular news format to cover breaking news and live events in online journalism. Online news websites around the world are using this medium to give their readers a minute by minute update on an event. Good summaries enhance the value of the live blogs for a reader but are often not available. In this paper, we study a way of collecting corpora for automatic live blog summarization. In an empirical evaluation using well-known state-of-the-art summarization systems, we show that live blogs corpus poses new challenges in the field of summarization. We make our tools publicly available to reconstruct the corpus to encourage the research community and replicate our results.
Heavy Metal Contamination and Distribution in Soils around Pb - Zn Mines of Abakaliki District, South Eastern Nigeria

Forty-two {42} soil samples were collected from abandoned old Pb - Zn mines of Enyigba, Ameri and Ameka in the Abakaliki district of Ebonyi State south-eastern Nigeria and analysed for Fe, Mn, Cu, Zn, Pb, Cd, Ni, Cr, V, pH, organic carbon and Electrical Conductivity.The physico-chemical analyses show that pH is generally low (3.40) resulting from the dissolution of the sulphide ore waste dump. The Electrical Conductivity is high (305 µ s/cm) a value attributable to the numerous brine fields associated with the Pb - Zn mines. The organic carbon content in the soil is generally low. The heavy metal mean trend indicates that Pb(86) > Zn (64) > Cu (20) > Cd (15) > Ni (7) > Cr (6) > V(4). Fe and Mn are also high. The variations observed for the heavy metals suggest both geogenic and anthropogenic activities are responsible for their distribution. Soil contamination is assessed on the basis of contamination factor (CF) and enrichment factor (EF). The CF values for the soils indicate moderate contamination for Ni, Cr, V, Zn and Mn, while Pb and Cd show very high contamination. The results of enrichment factor (EF) show that using Fe concentration in the background value, Ni, Cr, V and Mn have moderate enrichment, Pb and Zn show significant enrichment while Cd indicates very high enrichment. The results of the principal component and cluster analyses show Zn, Cu, Cd, Pb metals originate from similar source but may have been significantly influenced by anthroprogenic activities, while Ni, Cr, V are attributable to geogenic sources.
Convex biclustering

In the biclustering problem, we seek to simultaneously group observations and features. While biclustering has applications in a wide array of domains, ranging from text mining to collaborative filtering, the problem of identifying structure in high‐dimensional genomic data motivates this work. In this context, biclustering enables us to identify subsets of genes that are co‐expressed only within a subset of experimental conditions. We present a convex formulation of the biclustering problem that possesses a unique global minimizer and an iterative algorithm, COBRA, that is guaranteed to identify it. Our approach generates an entire solution path of possible biclusters as a single tuning parameter is varied. We also show how to reduce the problem of selecting this tuning parameter to solving a trivial modification of the convex biclustering problem. The key contributions of our work are its simplicity, interpretability, and algorithmic guarantees—features that arguably are lacking in the current alternative algorithms. We demonstrate the advantages of our approach, which includes stably and reproducibly identifying biclusterings, on simulated and real microarray data.
Analyzing infant head flatness and asymmetry using kernel density estimation of directional surface data from a craniofacial 3D model

Infant skull deformation is analyzed using the distribution of head normal vector directions computed from a 3D image. Severity of flatness and asymmetry are quantified by functionals of the kernel estimate of the normal vector direction density. Using image data from 99 infants and clinical deformation ratings made by experts, our approach is compared with some recently suggested methods. The results show that the proposed method performs competitively. Copyright © 2016 John Wiley & Sons, Ltd.
Estimating varying coefficients for partial differential equation models

Partial differential equations (PDEs) are used to model complex dynamical systems in multiple dimensions, and their parameters often have important scientific interpretations. In some applications, PDE parameters are not constant but can change depending on the values of covariates, a feature that we call varying coefficients. We propose a parameter cascading method to estimate varying coefficients in PDE models from noisy data. Our estimates of the varying coefficients are shown to be consistent and asymptotically normally distributed. The performance of our method is evaluated by a simulation study and by an empirical study estimating three varying coefficients in a PDE model arising from LIDAR data.
Exercise-Mediated Neurogenesis in the Hippocampus via BDNF

Exercise is known to have numerous neuroprotective and cognitive benefits, especially pertaining to memory and learning related processes. One potential link connecting them is exercise-mediated hippocampal neurogenesis, in which new neurons are generated and incorporated into hippocampal circuits. The present review synthesizes the extant literature detailing the relationship between exercise and hippocampal neurogenesis, and identifies a key molecule mediating this process, brain-derived neurotrophic factor (BDNF). As a member of the neurotrophin family, BDNF regulates many of the processes within neurogenesis, such as differentiation and survival. Although much more is known about the direct role that exercise and BDNF have on hippocampal neurogenesis in rodents, their corresponding cognitive benefits in humans will also be discussed. Specifically, what is known about exercise-mediated hippocampal neurogenesis will be presented as it relates to BDNF to highlight the critical role that it plays. Due to the inaccessibility of the human brain, much less is known about the role BDNF plays in human hippocampal neurogenesis. Limitations and future areas of research with regards to human neurogenesis will thus be discussed, including indirect measures of neurogenesis and single nucleotide polymorphisms within the BDNF gene.
Medical Information Exchange

Objective Information technology has revolutionized health care. However, the development of dedicated mobile health software has been lagging, leading to the use of general mobile applications to fill in the void. The use of such applications has several legal, ethical, and regulatory implications. We examined the experience and practices governing the usage of a global mobile messenger application (WhatsApp) for mobile health purposes in a national cohort of practicing otolaryngologists in Israel, a known early adaptor information technology society. Methods Cross-sectional data were collected from practicing otolaryngologists and otolaryngology residents via self-administered questionnaire. The questionnaire was composed of a demographic section, a section surveying the practices of mobile application use, mobile health application use, and knowledge regarding institutional policies governing the transmission of medical data. Results The sample included 22 otolaryngology residents and 47 practicing otolaryngologists. Of the physicians, 83% worked in academic centers, and 88% and 40% of the physicians who worked in a hospital setting or a community clinic used WhatsApp for medical use, respectively. Working with residents increased the medical usage of WhatsApp from 50% to 91% (P = .006). Finally, 72% were unfamiliar with any institutional policy regarding the transfer of medical information by personal smartphones. Discussion Mobile health is becoming an integral part of modern medical systems, improving accessibility, efficiency, and possibly quality of medical care. Implications for Practice The need to incorporate personal mobile devices in the overall information technology standards, guidelines, and regulation is becoming more acute. Nonetheless, practices must be properly instituted to prevent unwanted consequences.
Landauer-Datta-Lundstrom Generalized Transport Model for Nanoelectronics

The Landauer-Datta-Lundstrom electron transport model is briefly summarized. If a band structure is given, the number of conduction modes can be evaluated and if a model for a mean-free-path for backscattering can be established, then the near-equilibrium thermoelectric transport coefficients can be calculated using the final expressions listed below for 1D, 2D, and 3D resistors in ballistic, quasiballistic, and diffusive linear response regimes when there are differences in both voltage and temperature across the device. The final expressions of thermoelectric transport coefficients through the Fermi-Dirac integrals are collected for 1D, 2D, and 3D semiconductors with parabolic band structure and for 2D graphene linear dispersion in ballistic and diffusive regimes with the power law scattering.
Personalized Multi-Scale Modeling of the Atria: Heterogeneities, Fiber Architecture, Hemodialysis and Ablation Therapy

This book targets three fields of computational multi-scale cardiac modeling. First, advanced models of the cellular atrial electrophysiology and fiber orientation are introduced. Second, novel methods to create patient-specific models of the atria are described. Third, applications of personalized models in basic research and clinical practice are presented. The results mark an important step towards the patient-specific model-based atrial fibrillation diagnosis, understanding and treatment.
Study of Grinding Hardening Force Based on the Influence of Grinding Arc Temperature and Workpiece Deformation

The grinding hardening workpiece deformation caused by high temperature leads to the variation of the grinding force. Grinding force of dynamic variation affects the grinding depth of hardened layer distribution. So it is necessary to study the variation rule of grinding hardening force. Through grinding arc temperature analysis and deformation analysis, the influence factor for grinding arc temperature and workpiece deformation on grinding force is analyzed. The analysis results are compared with the experimental results.