Miracle-dz/UniFAR-FTUs huggingface dataset:
fastSTRUCTURE: Variational Inference of Population Structure in Large SNP Data Sets

Tools for estimating population structure from genetic data are now used in a wide variety of applications in population genetics. However, inferring population structure in large modern data sets imposes severe computational challenges. Here, we develop efficient algorithms for approximate inference of the model underlying the STRUCTURE program using a variational Bayesian framework. Variational methods pose the problem of computing relevant posterior distributions as an optimization problem, allowing us to build on recent advances in optimization theory to develop fast inference tools. In addition, we propose useful heuristic scores to identify the number of populations represented in a data set and a new hierarchical prior to detect weak population structure in the data. We test the variational algorithms on simulated data and illustrate using genotype data from the CEPH–Human Genome Diversity Panel. The variational algorithms are almost two orders of magnitude faster than STRUCTURE and achieve accuracies comparable to those of ADMIXTURE. Furthermore, our results show that the heuristic scores for choosing model complexity provide a reasonable range of values for the number of populations represented in the data, with minimal bias toward detecting structure when it is very weak. Our algorithm, fastSTRUCTURE, is freely available online at http://pritchardlab.stanford. edu/structure.html.
Human memory FOXP3+ Tregs secrete IL-17 ex vivo and constitutively express the TH17 lineage-specific transcription factor RORγt

Recent studies have suggested a close relationship between CD4+FOXP3+ regulatory T cells (Tregs) and proinflammatory IL-17-producing T helper cells (TH17) expressing the lineage-specific transcription factor RORγt. We report here the unexpected finding that human memory Tregs secrete IL-17 ex vivo and constitutively express RORγt. IL-17-secreting Tregs share some phenotypic and functional features with conventional TH17 cells, expressing high levels of CCR4 and CCR6 and low levels of CXCR3. However, unlike conventional TH17 cells, they express low levels of CD161 and mostly fail to cosecrete IL-22 and TNF-α ex vivo. Ex vivo secretion of IL-17 and constitutive expression of RORγt by human memory Tregs suggest that, in addition to their well-known suppressive functions, these cells likely play additional, as yet undescribed, proinflammatory functions.
Sex differences in the social behavior of wild spider monkeys (Ateles geoffroyi yucatanensis)

Competition for resources and the need for cooperation are reported to affect patterns of social interactions and thus the quality of social relationships in primates. Relationships may be described as high quality when both individuals behave in a way that benefits their partner. We investigated the distribution of a wide range of social behaviors across sex partner combinations of adult spider monkeys with specific reference to contested resources. Data were collected from two communities of wild spider monkeys (Ateles geoffroyi yucatanensis) in the Otoch Ma'ax Yetel Kooh reserve in Yucatan, Mexico. Affiliative behavior was exchanged most frequently between males, and as male–male aggression was rare, male–male social relationships were characterized as high quality. Female–female social relationships were best described as low quality as females showed no preference to be in proximity with other females and female–female affiliative behavior was rare. Relationships between the sexes generally were characterized by high rates of female‐directed male aggression, although additional investigation into the effects of kinship and female reproductive state on male–female relationships is required before further conclusions can be drawn. Dyadic and coalitionary female–female aggression was significantly higher than expected in a feeding context, confirming that female spider monkeys primarily compete for access to food. Male–male aggression did not increase significantly when in the presence of females, but males embraced at higher rates when in mixed‐sex subgroups. As embraces serve to reduce the likelihood of aggression during tense situations, high rates of male–male embraces in mixed‐sex subgroups may mitigate male conflicts over access to females. Am. J. Primatol. 71:21–29, 2009. © 2008 Wiley‐Liss, Inc.
Reinforcement sensitivity theory (RST): Introduction

The Reinforcement Sensitivity Theory (RST) of personality is a theoretical account of the neural and psychological processes underlying the major dimensions of personality. The first section of this introductory chapter traces the development of RST, from its official birth in 1970, through to Gray's highly influential 1982 The Neuropsychology of Anxiety , and on to its major revision in 2000 with the second edition of this book (co-authored with Neil McNaughton) – this section may be read as an overview tutorial of RST. The second section discusses some of the major issues facing future RST research. The third section turns attention to the question of the level of behavioural control exerted by ‘biological’ and ‘cognitive’ processes, and discusses the implications of findings from consciousness studies for conceptualizing the role of these processes in RST. Past and present At the time of writing (2006), most empirical studies continue to test the unrevised (pre-2000) version of RST. But, in many crucial respects, the revised (2000) theory is very different, leading to the formulation of new hypotheses, some of which stand in opposition to those generated from the unrevised theory. This reluctance, or slowness, to adopt the new model is, no doubt, motivated as much by unfamiliarity and research inertia as it is by a careful evaluation of the merits of both versions. But there may be a different reason for this state of affairs, and one that may continue to prevail in the RST research.
The simulation heuristic

Our original treatment of the availability heuristic (Tversky & Kahneman, 1973, 11) discussed two classes of mental operations that “bring things to mind”: the retrieval of instances and the construction of examples or scenarios. Recall and construction are quite different ways of bringing things to mind; they are used to answer different questions, and they follow different rules. Past research has dealt mainly with the retrieval of instances from memory, and the process of mental construction has been relatively neglected. To advance the study of availability for construction, we now sketch a mental operation that we label the simulation heuristic. Our starting point is a common introspection: There appear to be many situations in which questions about events are answered by an operation that resembles the running of a simulation model. The simulation can be constrained and controlled in several ways: The starting conditions for a “run” can be left at their realistic default values or modified to assume some special contingency; the outcomes can be left unspecified, or else a target state may be set, with the task of finding a path to that state from the initial conditions. A simulation does not necessarily produce a single story, which starts at the beginning and ends with a definite outcome. Rather, we construe the output of simulation as an assessment of the ease with which the model could produce different outcomes, given its initial conditions and operating parameters.
A Digitally Assisted, Signal Folding Neural Recording Amplifier

A novel signal folding and reconstruction scheme for neural recording applications that exploits the 1/fn characteristics of neural signals is described in this paper. The amplified output is `folded' into a predefined range of voltages by using comparison and reset circuits along with the core amplifier. After this output signal is digitized and transmitted, a reconstruction algorithm can be applied in the digital domain to recover the amplified signal from the folded waveform. This scheme enables the use of an analog-to-digital convertor with less number of bits for the same effective dynamic range. It also reduces the transmission data rate of the recording chip. Both of these features allow power and area savings at the system level. Other advantages of the proposed topology are increased reliability due to the removal of pseudo-resistors, lower harmonic distortion and low-voltage operation. An analysis of the reconstruction error introduced by this scheme is presented along with a behavioral model to provide a quick estimate of the post reconstruction dynamic range. Measurement results from two different core amplifier designs in 65 nm and 180 nm CMOS processes are presented to prove the generality of the proposed scheme in the neural recording applications. Operating from a 1 V power supply, the amplifier in 180 nm CMOS has a gain of 54.2 dB, bandwidth of 5.7 kHz, input referred noise of 3.8 μVrms and power dissipation of 2.52 μW leading to a NEF of 3.1 in spike band. It exhibits a dynamic range of 66 dB and maximum SNDR of 43 dB in LFP band. It also reduces system level power (by reducing the number of bits in the ADC by 2) as well as data rate to 80% of a conventional design. In vivo measurements validate the ability of this amplifier to simultaneously record spike and LFP signals.
Slip–Stick Mechanism in Training the Superconducting Magnets in the Large Hadron Collider

Superconducting magnets can exhibit training quenches during successive powering to reaching nominal performance. The slip-stick motion of the conductors is considered to be one of the mechanisms of training. In this paper, we present a simple quantitative model where the training is described as a discrete dynamical system matching the equilibrium between the energy margin of the superconducting cable and the frictional energy released during the conductor motion. The model can be explicitly solved in the linearized case, showing that the short sample limit is reached via a power law. Training phenomena have a large random component. A large set of data of the large hadron collider magnet tests is postprocessed according to previously defined methods to extract an average training curve for dipoles and quadrupoles. These curves show the asymptotic power law predicted by the model. The curves are then fit through the model, which has two free parameters. The model shows good agreement over a large range, but it fails to describe the very initial part of the training.
The Simultaneous Symbiotic Origin of Mitochondria, Chloroplasts, and Microbodies

The purpose of this paper is not to discuss the continually growing evidence for the symbiotic origin of both chloroplasts and mitochondria. ’ It is to argue that many uncritically accepted features of the conventional serial endosymbiosis theory’,’ are so seriously in error that they need to be replaced by a more realistic symbiotic theory. I shall first state and then justify the seven major changes needed:
Patterns Of Infidelity And Their Treatment

Introduction Section I: Patterns of Infidelity Chapter 1: An Affair is a Family Issue Chapter 2: Types of Affairs and their Messages Section II: Critical Issues in Treatment Chapter 3: Hiding, Telling, or Getting Caught: Issues in Revealing an Affair Chapter 4: Disclosing the Affair Chapter 5: Managing the Crisis Chapter 6: Rebuilding for Conflict and Intimacy Avoiders Chapter 7: Rebuilding for the Addictive Family Chapter 8: Rebuilding and the Split Self Affair Chapter 9: When the Marriage Ends with an Affair Chapter 10: The Unmarried Third Party Chapter 11: The Use of Group Treatment Chapter 12: Trust, Forgiveness, and Closure Chapter 13: Children and Affairs: Issues and Interventions Chapter 14: Affairs and Violence Section III: Legacies: Our Clients' and Our Own Chapter 15: Affairs, Divorce, and Remarriage Chapter 16: Family Therapists, Family Patterns, Family Secrets, and Affairs Appendix Bibliography Resources
Maternal–Fetal Transfer of Domoic Acid in Rats at Two Gestational Time Points

Background and objectives Prenatal exposure to asymptomatic doses of domoic acid (DA) causes learning and memory deficits later in life; therefore, we sought to measure distribution of DA in maternal plasma and brain, prenatal brain, and amniotic fluid 1 hr after exposure, a time frame that normally encompasses acute seizure behavior. Methods Pregnant rats were given a single intravenous dose of DA (0.6 or 1.6 mg/kg body weight) at either gestational day (GD) 13 or GD20, which correspond to the beginning of rat embryo neurogenesis and the last day of gestation, respectively. Using a direct ELISA, dose-dependent levels of DA were detected in each sample matrix tested. Results An average of 6.6 and 14 ng DA/g brain tissue was found in GD13 and GD20 prenatal rats, respectively. Brain concentrations of DA in the GD13 prenates were identical to amniotic fluid levels, consistent with no restriction for DA to enter the GD13 prenatal brain. At GD20 the prenatal brain contained half the concentration of DA in the amniotic fluid, and was approximately half that found in the brain of the dams. After 1 hr, fetal brain and amniotic fluid contained between 1 and 5% of DA found in the maternal circulation. The amniotic fluid levels of DA in this study were also within the same range measured in stranded California sea lions that showed reproductive failure. Conclusions DA crosses the placenta, enters brain tissue of prenates, and accumulates in the amniotic fluid. Amniotic fluid appears to be a useful fluid to monitor DA exposure.
Retrospective cohort study of the risk of impaired glucose tolerance among shift workers.

OBJECTIVES The aim of this study was to investigate the effect of shift working on the risk of developing impaired glucose tolerance (IGT). METHODS This study comprised 6413 male employees (5608 daytime workers, 512 3-shift workers and 293 2-shift workers) whose work schedules remained constant during the follow-up period (mean follow-up period 9.9 years). IGT was defined as Hemoglobin A1c ≥ 5.9%. The Cox proportional hazards model was used to estimate the risk of developing IGT, after making adjustments for age, smoking, alcohol consumption, leisure-time physical activity, body mass index (BMI) and Hemoglobin A1c (HbA1c) at baseline. Analysis was additionally performed for a sub-cohort of 1625 workers with BMI of 20.0-25.0 kg/m² that did not change by >2.0 kg/m² during the follow up period. RESULTS The risk of developing IGT was significantly elevated among both 3-shift workers [hazard ratio (HR) 1.78, 95% confidence interval (95% CI) 1.49- 2.14] and 2-shift workers (HR 2.62, 95% CI 2.17-3.17). Significant elevations of the risk were still observed at the additional analysis on the sub-cohort (3-shift work: HR 3.55, 95% CI 2.02-6.25; 2-shift work: HR 4.86, 95% CI 2.62-9.01). CONCLUSIONS Both 2- and 3-shift workers were associated with a high risk factor of developing IGT compared to day workers. Moreover, 2-shift workers had a higher risk than 3-shift workers. The risk was observed even among workers whose body mass remained within the normal range.
Implementation of a Statewide Surveillance System for Neonatal Abstinence Syndrome — Tennessee, 2013

Over the last decade, rates of opioid pain reliever prescribing grew substantially in the United States, affecting many segments of the population, including pregnant women. Nationally, Tennessee ranks second in the rate of prescriptions written for opioid pain relievers, with 1.4 per person in 2012. The rising prevalence of opioid pain reliever use and misuse in Tennessee led to an increase in adverse outcomes in the state, including neonatal abstinence syndrome (NAS). NAS is a withdrawal syndrome experienced by infants shortly after birth. The syndrome most commonly occurs after antenatal exposure to opioids, although other medications have also been implicated. From 2000 to 2009, the incidence rate of NAS in Tennessee increased from 0.7 to 5.1 per 1,000 births, exceeding the national average, which increased from 1.2 to 3.4 per 1,000 births. NAS is associated with numerous morbidities for the infant, including low birth weight, poor feeding, and respiratory problems. Previous population-based analyses of NAS relied on hospital discharge data, which typically become available for analysis only after substantial delay. In Tennessee, the rising incidence of NAS and its associated public health burden created an urgent need for timelier incidence figures to drive policy and prevention efforts. Beginning January 1, 2013, the Tennessee Department of Health (TDH) made NAS reporting mandatory. A total of 921 cases were reported in 2013 (among 79,954 births), with the most cases clustered in eastern Tennessee; 63% of cases occurred to mothers who were reported to be using at least one substance prescribed by a health care provider (e.g., opioid pain relievers or maintenance medications for opioid dependency), and 33% of cases occurred among women using illicit or diverted substances (e.g., heroin or medications prescribed for someone else). The first year's surveillance results highlight the need for primary prevention activities focused on reducing dependence/addiction among women of childbearing age and preventing unintended pregnancy among female opioid users.
New Strategy to Optimize the Performance of Epidemic Routing Protocol

delay tolerant networks (DTN, Delay Tolerant Networks) are networks where connectivity is intermittent because of the difficulties encountered in the environment such as climate, mobility, the breakdowns of energy, etc. To achieve a good delivery of data despite all these challenges, new network architecture was developed. This one consists on the addition of a supplementary layer in the OSI protocol stack, above the transport layer. This new policy is called: the bundle protocol. Its main role is to store data until an opportunity of transmission appears by using the Store and Forward technique and the concept of custody transfer. Routing protocols in this type of network do not try to find the shortest path as it is the case in the conventional protocols, but they focus on the increase in data delivery. The techniques used for this purpose can be divided into two large families. Some protocols adopt the approach of replication, which involves the duplication of messages in the network by providing multiple copies in order to increase the likelihood of transmission. Others, are based on knowledge, that is to gather information about the network status and manage shipments efficiently. In DTN routing protocol forwarding decision and buffer management strategy are important to improve the chance of message delivery. In this paper, the new strategy proposed optimizes Epidemic routing protocol; it consists on using the path of ACKs messages and the path of all messages that have reached their destination to resolve the disadvantages of Epidemic routing protocol with the FIFO method. According to the simulation, the proposed method shows better delivery rate, better delivery probability and lower communication overhead compared to FIFO strategy and it is suitable for Epidemic.
Multiscale Two-Dimensional Modeling of a Motile Simple-Shaped Cell

Cell crawling is an important biological phenomenon underlying coordinated cell movement in morphogenesis, cancer, and wound healing. In recent decades the process of cell crawling has been experimentally and theoretically dissected into further subprocesses: protrusion of the cell at its leading edge, retraction of the cell body, and graded adhesion. A number of one-dimensional (1-D) models explain successfully a proximal-distal organization and movement of the motile cell. However, more adequate two-dimensional (2-D) models are lacking. We propose a multiscale 2-D computational model of the lamellipodium (motile appendage) of a simply shaped, rapidly crawling fish keratocyte cell. We couple submodels of (i) protrusion and adhesion at the leading edge, (ii) the elastic 2-D lamellipodial actin network, (iii) the actin-myosin contractile bundle at the rear edge, and (iv) the convection-reaction-diffusion actin transport on the free boundary lamellipodial domain. We simulate the combined model numerically using a finite element approach. The simulations reproduce observed cell shapes, forces, and movements and explain some experimental results on perturbations of the actin machinery. This novel 2-D model of the crawling cell makes testable predictions and posits questions to be answered by future modeling.
A GO-driven semantic similarity measure for quantifying the biological relatedness of gene products

Advances in biological experiments, such as DNA microarrays, have produced large multidimensional data sets for examination and retrospective analysis. Scientists however, heavily rely on existing biomedical knowledge in order to fully analyze and comprehend such datasets. Our proposed framework relies on the Gene Ontology for integrating a priori biomedical knowledge into traditional data analysis approaches. We explore the impact of considering each aspect of the Gene Ontology individually for quantifying the biological relatedness between gene products. We discuss two figure of merit scores for quantifying the pair-wise biological relatedness between gene products and the intra-cluster biological coherency of groups of gene products. Finally, we perform cluster deterioration simulation experiments on a well scrutinized Saccharomyces cerevisiae data set consisting of hybridization measurements. The results presented illustrate a strong correlation between the devised cluster coherency figure of merit and the randomization of cluster membership.
Normalization of RNA-Sequencing Data from Samples with Varying mRNA Levels

Methods for normalization of RNA-sequencing gene expression data commonly assume equal total expression between compared samples. In contrast, scenarios of global gene expression shifts are many and increasing. Here we compare the performance of three normalization methods when polyA+ RNA content fluctuates significantly during zebrafish early developmental stages. As a benchmark we have used reverse transcription-quantitative PCR. The results show that reads per kilobase per million (RPKM) and trimmed mean of M-values (TMM) normalization systematically leads to biased gene expression estimates. Biological scaling normalization (BSN), designed to handle differences in total expression, showed improved accuracy compared to the two other methods in estimating transcript level dynamics. The results have implications for past and future studies using RNA-sequencing on samples with different levels of total or polyA+ RNA.
Random projections for non-negative matrix factorization

Non-negative matrix factorization (NMF) is a widely used tool for exploratory data analysis in many disciplines. In this paper, we describe an approach to NMF based on random projections and give a geometric analysis of a prototypical algorithm. Our main result shows the proto-algorithm requires $\bar{\kappa}k\log k$ optimizations to find all the extreme columns of the matrix, where $k$ is the number of extreme columns, and $\bar{\kappa}$ is a geometric condition number. We show empirically that the proto-algorithm is robust to noise and well-suited to modern distributed computing architectures.
The “Emotional Side” of Subjective Tinnitus

Roberto Teggi1, Daniela Caldirola2, Giampaolo Perna2,3 and Mario Bussi1 1Department of Otolaryngology, Vita-Salute University, San Raffaele Hospital, Milan, 2Department of Clinical Neuroscience, San Benedetto Hospital, Hermanas Hospitalarias, Albese con Cassano, 3Department of Psychiatry and Neuropsychology, Faculty of Health, Medicine and Life Sciences, University of Maastricht, Maastricht, 1,2Italy 3The Netherlands