Miracle-dz/UniFAR-FTUs huggingface dataset:
pETM: a penalized Exponential Tilt Model for analysis of correlated high‐dimensional DNA methylation data

Motivation: DNA methylation plays an important role in many biological processes and cancer progression. Recent studies have found that there are also differences in methylation variations in different groups other than differences in methylation means. Several methods have been developed that consider both mean and variance signals in order to improve statistical power of detecting differentially methylated loci. Moreover, as methylation levels of neighboring CpG sites are known to be strongly correlated, methods that incorporate correlations have also been developed. We previously developed a network‐based penalized logistic regression for correlated methylation data, but only focusing on mean signals. We have also developed a generalized exponential tilt model that captures both mean and variance signals but only examining one CpG site at a time. Results: In this article, we proposed a penalized Exponential Tilt Model (pETM) using network‐based regularization that captures both mean and variance signals in DNA methylation data and takes into account the correlations among nearby CpG sites. By combining the strength of the two models we previously developed, we demonstrated the superior power and better performance of the pETM method through simulations and the applications to the 450K DNA methylation array data of the four breast invasive carcinoma cancer subtypes from The Cancer Genome Atlas (TCGA) project. The developed pETM method identifies many cancer‐related methylation loci that were missed by our previously developed method that considers correlations among nearby methylation loci but not variance signals. Availability and Implementation: The R package ‘pETM’ is publicly available through CRAN: http://cran.r‐project.org. Contact : sw2206@columbia.edu Supplementary information: Supplementary data are available at Bioinformatics online.
FastTree 2 – Approximately Maximum-Likelihood Trees for Large Alignments

Background We recently described FastTree, a tool for inferring phylogenies for alignments with up to hundreds of thousands of sequences. Here, we describe improvements to FastTree that improve its accuracy without sacrificing scalability. Methodology/Principal Findings Where FastTree 1 used nearest-neighbor interchanges (NNIs) and the minimum-evolution criterion to improve the tree, FastTree 2 adds minimum-evolution subtree-pruning-regrafting (SPRs) and maximum-likelihood NNIs. FastTree 2 uses heuristics to restrict the search for better trees and estimates a rate of evolution for each site (the “CAT” approximation). Nevertheless, for both simulated and genuine alignments, FastTree 2 is slightly more accurate than a standard implementation of maximum-likelihood NNIs (PhyML 3 with default settings). Although FastTree 2 is not quite as accurate as methods that use maximum-likelihood SPRs, most of the splits that disagree are poorly supported, and for large alignments, FastTree 2 is 100–1,000 times faster. FastTree 2 inferred a topology and likelihood-based local support values for 237,882 distinct 16S ribosomal RNAs on a desktop computer in 22 hours and 5.8 gigabytes of memory. Conclusions/Significance FastTree 2 allows the inference of maximum-likelihood phylogenies for huge alignments. FastTree 2 is freely available at http://www.microbesonline. org/fasttree.
Bayesian Nonparametric Poisson-Process Allocation for Time-Sequence Modeling

Analyzing the underlying structure of multiple time-sequences provides insights into the understanding of social networks and human activities. In this work, we present the \emph{Bayesian nonparametric Poisson process allocation} (BaNPPA), a latent-function model for time-sequences, which automatically infers the number of latent functions. We model the intensity of each sequence as an infinite mixture of latent functions, each of which is obtained using a function drawn from a Gaussian process. We show that a technical challenge for the inference of such mixture models is the unidentifiability of the weights of the latent functions. We propose to cope with the issue by regulating the volume of each latent function within a variational inference algorithm. Our algorithm is computationally efficient and scales well to large data sets. We demonstrate the usefulness of our proposed model through experiments on both synthetic and real-world data sets.
V2X Routing in a VANET Based on the Hidden Markov Model

It is very difficult to establish and maintain end-to-end connections in a vehicle ad hoc network (VANET) as a result of high vehicle speed, long inter-vehicle distance, and varying vehicle density. Instead, a store-and-forward strategy has been considered for vehicle communications. The success of this strategy, however, depends heavily on the cooperation among nodes. Different from exiting store-and-forward solutions, we propose predictive routing based on the hidden Markov model (PRHMM) for VANETS, which exploits the regularity of vehicle moving behaviors to increase the transmission performance. As vehicle movements often exhibit a high degree of repetition, including regular visits to certain places and regular contacts during daily activities, we can predict a vehicle’s future locations based on the knowledge of past traces and the hidden Markov model. Consequently, the short-term route of a vehicle and its packet delivery probability for a specific mobile destination can be predicted. Moreover, PRHMM enables seamless handoff between vehicle-to-vehicle and vehicle-to-infrastructure communications so that the transmission performance will not be constrained by the vehicle density and moving speed. Simulation evaluation demonstrates that PRHMM performs much better in terms of delivery ratio, end-to-end delay, traffic overhead, and buffer occupancy.
Effects of conformational isomerism on the desorption kinetics of n-alkanes from graphite

The dynamics of oligomer desorption from surfaces have been studied by measuring the desorption kinetics of a set of n-alkanes from the surface of single crystalline graphite. Desorption rates were measured using a set of 21 monodispersed n-alkanes (CNH2N+2,5⩽N⩽60) each adsorbed at coverages in the range 1 monolayers. Desorption is observed to be a first-order process with a desorption barrier (ΔEdes‡) that is independent of coverage. The pre-exponential of the desorption rate constant is independent of the oligomer chain length and has a value of ν=1019.6±0.5 s−1. We also find that ΔEdes‡ has a nonlinear dependence on chain length and takes the empirical form ΔEdes‡=a+bNγ, with the exponent having a value of γ=0.50±0.01. More interestingly, we have proposed a mechanism for the desorption process and a model for the energetics and the entropy of the oligomers on the surface that provide an extremely good quantitative fit to the observed chain length dependence of ΔEdes‡. ΔEdes‡ is given by the di.
Genotype-Temperature Interaction in the Regulation of Development, Growth, and Morphometrics in Wild-Type, and Growth-Hormone Transgenic Coho Salmon

Background The neuroendocrine system is an important modulator of phenotype, directing cellular genetic responses to external cues such as temperature. Behavioural and physiological processes in poikilothermic organisms (e.g. most fishes), are particularly influenced by surrounding temperatures. Methodology/Principal Findings By comparing the development and growth of two genotypes of coho salmon (wild-type and transgenic with greatly enhanced growth hormone production) at six different temperatures, ranging between 8° and 18°C, we observed a genotype-temperature interaction and possible trend in directed neuroendocrine selection. Differences in growth patterns of the two genotypes were compared by using mathematical models, and morphometric analyses of juvenile salmon were performed to detect differences in body shape. The maximum hatching and alevin survival rates of both genotypes occurred at 12°C. At lower temperatures, eggs containing embryos with enhanced GH production hatched after a shorter incubation period than wild-type eggs, but this difference was not apparent at and above 16°C. GH transgenesis led to lower body weights at the time when the yolk sack was completely absorbed compared to the wild genotype. The growth of juvenile GH-enhanced salmon was to a greater extent stimulated by higher temperatures than the growth of the wild-type. Increased GH production significantly influenced the shape of the salmon growth curves. Conclusions Growth hormone overexpression by transgenesis is able to stimulate the growth of coho salmon over a wide range of temperatures. Temperature was found to affect growth rate, survival, and body morphology between GH transgenic and wild genotype coho salmon, and differential responses to temperature observed between the genotypes suggests they would experience different selective forces should they ever enter natural ecosystems. Thus, GH transgenic fish would be expected to differentially respond and adapt to shifts in environmental conditions compared with wild type, influencing their ability to survive and interact in ecosystems. Understanding these relationships would assist environmental risk assessments evaluating potential ecological effects.
Detection of voltage variation events using variational mode decomposition

This paper presents a method of detecting voltage sag, swell and interruption events based on a signal processing tool viz. variational mode decomposition (VMD). The proposed method is able to keep track of variations in amplitude, phase, frequency and undelivered energy due to such events. Voltage signal is half-wave rectified and then decomposed by VMD to get DC part representing instantaneous amplitude envelope, thereby obtaining start/end times and depth of sag/swell. The phase jump and frequency deviations are observed from instantaneous phase, obtained from analytic signal of VMD mode having center frequency nearer to fundamental. Algorithm is tested for various cases of synthetic and simulated signals in MATLAB/Simulink. Comparative performance with recursive discrete Fourier transform and Hilbert transform based method is demonstrated.
Rapid activation of tumor-associated macrophages boosts preexisting tumor immunity

Depletion of immunosuppressive tumor-associated macrophages (TAMs) or reprogramming toward a proinflammatory activation state represent different strategies to therapeutically target this abundant myeloid population. In this study, we report that inhibition of colony-stimulating factor-1 receptor (CSF-1R) signaling sensitizes TAMs to profound and rapid reprogramming in the presence of a CD40 agonist before their depletion. Despite the short-lived nature of macrophage hyperactivation, combined CSF-1R+CD40 stimulation of macrophages is sufficient to create a proinflammatory tumor milieu that reinvigorates an effective T cell response in transplanted tumors that are either responsive or insensitive to immune checkpoint blockade. The central role of macrophages in regulating preexisting immunity is substantiated by depletion experiments, transcriptome analysis of ex vivo sorted TAMs, and gene expression profiling of whole tumor lysates at an early treatment time point. This approach enabled the identification of specific combination-induced changes among the pleiotropic activation spectrum of the CD40 agonist. In patients, CD40 expression on human TAMs was detected in mesothelioma and colorectal adenocarcinoma.
Tubulins, rhythms and cell walls in poplar leaves: it’s all in the timing

Plant cell walls exhibit architectural and compositional changes throughout their development and in response to external cues. While tubulins are involved in cell wall biogenesis, much remains unknown about the scope of their involvement during the orchestration of this resource-demanding process. A transgenic approach coupled with cell wall compositional analysis, RNA-seq and mining of publicly available diurnal gene expression data was used to assess the involvement of tubulins in poplar leaf cell wall biogenesis. Leaf cell walls of transgenic poplar lines with constitutive overexpression of α-tubulin (TUA) exhibited an increased abundance of homogalacturonan, along with a reduction in xylose. These changes were traced to altered expression of UDP-glucuronic acid decarboxylase (GADC) in the transgenic leaves. A model is postulated by which altered diurnal control of TUA through its constitutive overexpression led to a metabolic tradeoff affecting cellular utilization of GADC substrate UDP-glucuronic acid. While there were no effects on cellulose, hemicellulose or lignin abundance, subtle effects on hemicellulose composition and associated gene expression were noted. In addition, expression and enzymatic activity of pectin methylesterase (PME) decreased in the transgenic leaves. The change is discussed in a context of increased levels of PME substrate homogalacturonan, slow stomatal kinetics and the fate of PME product methanol. Since stomatal opening and closing depend on fundamentally contrasting microtubule dynamics, the slowing of both processes in the transgenic lines as previously reported appears to be directly related to underlying cell wall compositional changes that were caused by tubulin manipulation.
A Randomized Controlled Trial to Evaluate Approaches to Auditory Rehabilitation for Blast-Exposed Veterans with Normal or Near-Normal Hearing Who Report Hearing Problems in Difficult Listening Situations

Abstract Background: Blast exposure is a major source of injury among Service members in the Iraq and Afghanistan conflicts. Many of these blast-exposed veterans report hearing-related problems such as difficulties understanding speech in noise and rapid speech, and following instructions and long conversations that are disproportionate to their measured peripheral hearing sensitivity. Evidence is mounting that these complaints result from damage to the central auditory processing system. Purpose: To evaluate the effectiveness of audiological rehabilitative interventions for blast-exposed veterans with normal or near-normal peripheral hearing and functional hearing difficulties. Research Design: A randomized controlled trial with four intervention arms. Study Sample: Ninety-nine blast-exposed veterans with normal or near-normal peripheral hearing who reported functional hearing difficulties. Intervention: Four interventions were compared: compensatory communication strategies (CCS) education, CCS and use of a personal frequency modulation system (FM + CCS), CCS and use of an auditory training program (AT + CCS), and use of all three interventions combined (FM + AT + CCS). Data Collection and Analysis: All participants tested before, and immediately following an 8-week intervention period. The primary outcome measures upon which the study was powered assessed speech understanding in noise and self-reported psychosocial impacts of the intervention. In addition, auditory temporal processing, auditory working memory, allocation of attention, and hearing and cognitive self-report outcomes were assessed. Results: Use of FM + CCS resulted in significant benefit for speech understanding in noise and self-reported hearing benefits, and FM + AT + CCS provided more self-reported cognitive benefits than FM + CCS, AT + CCS, or CCS. Further, individuals liked and reported using the FM system, but there was poor adherence to and high attrition among individuals assigned to receive AT. Conclusions: It is concluded that a FM system (or remote microphone via Bluetooth system) is an effective intervention for blast-exposed veterans with normal or near-normal hearing and functional hearing difficulties and should be routinely considered as an intervention approach for this population when possible.
Responsive Content-Centric Delivery in Large Urban Communication Networks: A LinkNYC Use-Case

Large urban communication networks such as smart cities are an ecosystem of devices and services cooperating to address multiple issues that greatly benefit end users, cities, and the environment. LinkNYC is a first-of-its-kind urban communications network aiming to replace all payphones in the five boroughs of New York City (NYC) with kiosk-like structures providing free public Wi-Fi. We consolidate these networks with standalone edge cloud devices known as cloudlets and introduce geographically distributed content delivery cloudlets (CDCs) to store popular Internet content closer to end users; essential in environments with diverse and dynamic content interests. A content-centric and delivery framework is proposed leveraging NYC’s population densities and CDCs for interest-based in-network caching. Analysis shows that although the adoption of multiple CDCs dramatically improves overall network performance, advanced caching policies are needed when considering increased content heterogeneity. Thus, we propose popularity-driven and cooperation-based caching policies at individual CDCs to account for user and content dynamics over time. The amalgamation of urban population densities, multiple CDC placements and smarter caching techniques helps exploit the ultimate benefits of a content-centric urban communications network and dramatically improves overall network performance and responsiveness. Our proposed solutions are validated using LinkNYC as a use-case.
Study on rheological properties and statistical damage rheological model for Q_2 loess

By means of indoor uniaxial and triaxial creep tests under different pressure of Q2 loess with different water contents in Xi'an areas,the uniaxial and triaxial creep curves and stress -strain isochronous curves are got. The results show that Q2 loess has nonlinearity rheological properties. On the basis of these,viscoelastic creep phase is simulated by the generalized Kelvin model,linear viscoplastic creep phase is simulated by the Maxwell model which is parallel connected by a slider,and nonlinear viscoplastic creep phase is reflected by couple of damage and plastic strain. Based on the statistical damage evolution equation,considering stress damage threshold and linear mutiple rheological model of loess,the statistical damage rheological constitutional model is estabished from hypothesis of strain equivalence. This indicates that the damage rheological constitutional model can effectively describe the nonlinear rheological property of loess,for the parameters are less,and the model can be applied to practice.
Intuitive Cognition and Models of Human–Automation Interaction

Objective: The aim of this study was to provide an analysis of the implications of the dominance of intuitive cognition in human reasoning and decision making for conceptualizing models and taxonomies of human–automation interaction, focusing on the Parasuraman et al. model and taxonomy. Background: Knowledge about how humans reason and make decisions, which has been shown to be largely intuitive, has implications for the design of future human–machine systems. Method: One hundred twenty articles and books cited in other works as well as those obtained from an Internet search were reviewed. Works were deemed eligible if they were published within the past 50 years and common to a given literature. Results: Analysis shows that intuitive cognition dominates human reasoning and decision making in all situations examined. The implications of the dominance of intuitive cognition for the Parasuraman et al. model and taxonomy are discussed. A taxonomy of human–automation interaction that incorporates intuitive cognition is suggested. Application: Understanding the ways in which human reasoning and decision making is intuitive can provide insight for future models and taxonomies of human–automation interaction.
Comparative Probabilistic Assessment of Occupational Pesticide Exposures Based on Regulatory Assessments

Implementation of probabilistic analyses in exposure assessment can provide valuable insight into the risks of those at the extremes of population distributions, including more vulnerable or sensitive subgroups. Incorporation of these analyses into current regulatory methods for occupational pesticide exposure is enabled by the exposure data sets and associated data currently used in the risk assessment approach of the Environmental Protection Agency (EPA). Monte Carlo simulations were performed on exposure measurements from the Agricultural Handler Exposure Database and the Pesticide Handler Exposure Database along with data from the Exposure Factors Handbook and other sources to calculate exposure rates for three different neurotoxic compounds (azinphos methyl, acetamiprid, emamectin benzoate) across four pesticide‐handling scenarios. Probabilistic estimates of doses were compared with the no observable effect levels used in the EPA occupational risk assessments. Some percentage of workers were predicted to exceed the level of concern for all three compounds: 54% for azinphos methyl, 5% for acetamiprid, and 20% for emamectin benzoate. This finding has implications for pesticide risk assessment and offers an alternative procedure that may be more protective of those at the extremes of exposure than the current approach.
Sex differences in risk for coronary heart disease mortality associated with diabetes and established coronary heart disease.

BACKGROUND The sex-specific independent effect of diabetes mellitus and established coronary heart disease (CHD) on subsequent CHD mortality is not known. METHODS This is an analysis of pooled data (n = 5243) from the Framingham Heart Study and the Framingham Offspring Study with follow-up of 20 years. At baseline (1971-1975), 134 men and 95 women had diabetes, while 222 men and 129 women had CHD. Risk for CHD death was analyzed by proportional hazards models, adjusting for age, hypertension, serum cholesterol levels, smoking, and body mass index. The comparative effect of established CHD vs diabetes on the risk of CHD mortality was tested by testing the difference in log hazards. RESULTS The adjusted hazard ratios (HRs) with 95% confidence intervals (CIs) for death from CHD were 2.1 (95% CI, 1.3-3.3) in men with diabetes only, and 4.2 (95% CI, 3.2-5.6) in men with CHD only compared with men without diabetes or CHD. The HR for CHD death was 3.8 (95% CI, 2.2-6.6) in women with diabetes, and 1.9 (95% CI, 1.1-3.4) in women with CHD. The difference between the CHD and the diabetes log hazards was +0.73 (95% CI, 0.72-0.75) in men and -0.65 (95% CI, -0.68 to -0.63) in women. CONCLUSIONS In men, established CHD signifies a higher risk for CHD mortality than diabetes. This is reversed in women, with diabetes being associated with greater risk for CHD mortality. Current treatment recommendations for women with diabetes may need to be more aggressive to match CHD mortality risk.