Miracle-dz/UniFAR-FTUs huggingface dataset:
Autoregressive models for estimating phylogenetic and environmental effects: accounting for within-species variations.

Comparative methods are used to investigate the attributes of present species or higher taxa. Difficulties arise from the phylogenetic heritage: taxa are not independent and neglecting phylogenetic inertia can lead to inaccurate results. Within-species variations in life-history traits are also not negligible, but most comparative methods are not designed to take them into account. Taxa are generally described by a single value for each trait. We have developed a new model which permits the incorporation of both the phylogenetic relationships among populations and within-species variations. This is an extension of classical autoregressive models. This family of models was used to study the effect of fishing on six demographic traits measured on 77 populations of teleost fishes.
Algorithm for Mapping Multilayer BP Networks onto the SpiNNaker Neuromorphic Hardware

This paper demonstrates the feasibility and evaluates the performance of using the SpiNNaker neuromorphic hardware to simulate traditional non-spiking multi-layer perceptron networks with the back propagation learning rule. In addition to investigating the mapping of checker-boarding partitioning scheme onto SpiNNaker, we propose a new algorithm called pipelined checker-boarding partitioning which introduces a pipelined mode and captures the parallelism within each partition of the weight matrix, allowing the overlapping of communication and computation. Not only does the proposed algorithm localize communication, but it can also hide a part of or even all the communication. The performance is evaluated with SpiNNaker configurations up to 1000 nodes (20000 cores).
Intimate partner violence screening barriers as perceived by Jordanian nurses: A qualitative descriptive study

Intimate partner violence screening is an important component of patient assessment; however, not all nurses routinely conduct this screening with their patients. The purpose of this qualitative descriptive study was to describe the barriers to intimate partner violence screening and strategies to overcome these barriers. A purposive sample of 12 male and female Jordanian nurses working at a university hospital in the city of Irbid, Jordan participated in this study. Participants were interviewed using a semi-structured interview guide. Interviews were audio-recorded and transcribed verbatim. Steps of Colaizzi’s steps for procedural analysis were used to analyze the transcript data. Four themes were derived from the data: Jordanian culture, system-based IPV screening barriers, IPV victims as barriers to IPV screening, and nurses’ attitudes and beliefs for IPV screening. Jordanian nurses encounter many barriers that affect their ability to screen for IPV. Screening for IPV remains an important nursing function even in Jordanian healthcare settings.
A home education program for older adults with hearing impairment and their significant others: A randomized trial evaluating short- and long-term effects

This paper addresses the development and effectiveness of a home education program. The program, designed for hearing-impaired elders and their significant others (SO), deals with communication strategies and speech reading. Participants were randomly assigned to a training group (hearing aid fitting + home education program) or a control group (hearing aid fitting). The training group included 24 hearing-impaired subjects and 24 SO's. Controls were 24 affected individuals and 22 SO's. Questionnaires addressing emotional response, communication strategies and the IOI-HA, IOI-AI and IOI-SO were used. A repeated measures analysis of variance was applied to test group differences between pre, post, and 6-months follow-up measures. Increased awareness of benefits of speech reading and improved interaction with the SO were observed in the training group only (p < 0.05). No group difference on ‘emotional response’ was found. IOI-AI and IOI-SO demonstrated favorable attitudes towards the program. Follow-up measures showed improved quality of life and satisfaction in the training group, while a decrease was observed among the controls (p < 0.05). Some effects differed between first-time and experienced hearing aid users. Addition of services to amplification and involvement of the SO are relevant in aural rehabilitation.
HLA Class I-Mediated Control of HIV-1 in the Japanese Population, in Which the Protective HLA-B*57 and HLA-B*27 Alleles Are Absent

ABSTRACT We investigated the effect of HLA class I alleles on clinical parameters for HIV-1 disease progression in the Japanese population, where two strongly protective alleles, HLA-B*57 and HLA-B*27, are virtually nonexistent. HLA-B alleles showed a dominant role, primarily through HLA-B*67:01 and the HLA-B*52:01-C*12:02 haplotype. Neither a rare-allele nor a heterozygote advantage was found, suggesting that the effect of HLA alleles in the Japanese population is either different from those observed in Africans and Caucasians or undetectable due to limited power.
Systematic Review: Association of Shift Length, Protected Sleep Time, and Night Float With Patient Care, Residents' Health, and Education

BACKGROUND The Accreditation Council for Graduate Medical Education's new duty-hour standards limit interns' shifts to 16 hours and night float to 6 consecutive nights. Protected sleep time (that is, "nap") is strongly encouraged. As duty-hour reforms are implemented, examination of the quality and outcomes of the relevant literature is important. PURPOSE To systematically review the literature examining shift length, protected sleep time, and night float. DATA SOURCES MEDLINE, PREMEDLINE, and EMBASE from January 1989 through May 2010. STUDY SELECTION Studies examined the associations of shift length, protected sleep time, or night float with patient care, resident health, and education outcomes among residents in practice settings. DATA EXTRACTION Study quality was measured by using the validated Medical Education Research Study Quality Instrument and the U.S. Preventive Services Task Force criteria. Two investigators independently rated study quality, and interrater agreement was calculated. DATA SYNTHESIS Sixty-four studies met inclusion criteria. Most studies used single-group cross-sectional (19 studies [29.7%]) or pre-post (41 studies [64.1%]) designs, and 4 (6.3%) were randomized, controlled trials. Five studies (7.8%) were multi-institutional. Twenty-four of 33 (72.7%) studies examining shift length reported that shorter shifts were associated with decreased medical errors, motor vehicle crashes, and percutaneous injuries. Only 2 studies assessed protected sleep time and reported that residents' adherence to naps was poor. Night floats described in 33 studies involved 5 to 7 consecutive nights. LIMITATIONS Most studies used single-institution, observational designs. Publication bias is likely but difficult to assess in this methodologically weak and heterogeneous body of evidence. CONCLUSION For the limited outcomes measured, most studies supported reducing shift length but did not adequately address the optimal shift duration. Studies had numerous methodological limitations and unclear generalizability for most outcomes. Specific recommendations about shift length, protected sleep time, and night float should acknowledge the limitations of this evidence. PRIMARY FUNDING SOURCE Accreditation Council for Graduate Medical Education.
Functional connectivity estimation in fMRI data: Influence of preprocessing and time course selection

A number of techniques have been used to provide functional connectivity estimates for a given fMRI data set. In this study we compared two methods: a ‘rest‐like’ method where the functional connectivity was estimated for the whitened residuals after regressing out the task‐induced effects, and a within‐condition method where the functional connectivity was estimated separately for each experimental condition. In both cases four pre‐processing strategies were used: 1) time courses extracted from standard pre‐processed data (standard); 2) adjusted time courses extracted using the volume of interest routines in SPM2 from standard pre‐processed data (spm); 3) time courses extracted from ICA denoised data (standard denoised); and 4) adjusted time courses extracted from ICA denoised data (spm denoised). The temporal correlation between time series extracted from two cortical regions were statistically compared with the temporal correlation between a time series extracted from a cortical region and a time series extracted form a region placed in CSF. Since the later correlation is due to physiological noise and other artifacts, we used this comparison to investigate whether rest‐like and task modulated connectivity could be estimated from the same data set. The pre‐processing strategy had a significant effect on the connectivity estimates with the standard time courses providing larger connectivity values than the spm time courses for both estimation methods. The CSF comparison indicated that for our data set only rest‐like connectivity could be estimated. The rest‐like connectivity values were similar with connectivity estimated from resting state data. Hum Brain Mapp 2008. © 2007 Wiley‐Liss, Inc.
Discovering Subsumption Hierarchies of Ontology Concepts from Text Corpora

This paper proposes a method for learning ontologies given a corpus of text documents. The method identifies concepts in documents and organizes them into a subsumption hierarchy, without presupposing the existence of a seed ontology. The method uncovers latent topics in terms of which document text is being generated. These topics form the concepts of the new ontology. This is done in a language neutral way, using probabilistic space reduction techniques over the original term space of the corpus. Given multiple sets of concepts (latent topics) being discovered, the proposed method constructs a subsumption hierarchy by performing conditional independence tests among pairs of latent topics, given a third one. The paper provides experimental results over the GENIA corpus from the domain of biomedicine.
3D Multistroke Mapping (3DMM): Transfer of Hand-Drawn Pattern Representation for Skeleton-Based Gesture Recognition

Exergames involve using the fullbody to interact with an immersive world, which raises the challenge of capturing, processing and recognizing the action of the user even for cheap mocap systems such as the Microsoft Kinect. In fact, these recent technological advances have renewed interest in skeleton-based action recognition. Our review of related literature reveals that the issues encountered are not the result of random processes, which could simply be studied by using statistical tools, but are instead due to the fact that the pattern to be recognized, i.e. an action, was produced by a human being. 2D hand-drawn symbols are further examples of patterns resulting from a human motion. Therefore, the main contribution of this paper is to examine the validity of transferring the expertise of hand-drawn symbol representation to better recognize actions based on skeleton data. Principally, we propose a new action representation, namely the 3DMM, as an initial case-study illustrating how such transfer could be conducted. The experimental results, obtained over two benchmarks, confirm the soundness of our approach and encourage more thorough examination of the transfer.
Assessing symptoms of terminally-ill patients by different raters: A prospective study

Objective: For patients who are terminally ill, the efficiency of symptom management is dependent, among other factors, on an accurate assessment by proxy raters. The aim of this prospective study is to describe differences in symptom severity ratings between patients and their nurses, physicians, and family members during their stay in different departments with acute care, and to identify variables associated with the accuracy of the ratings by others. Methods: Physical, psychological, social, and functional disorders were assessed for 41 in-patients with a standardized 13-item Symptom List for Quality Assurance in Palliative Care drafted by the Working Group on the Core Documentation for Palliative Care Units in Germany. Symptom assessment was completed by different raters (patient, nurse, physician, family member) within the first four days after admission. Socio-demographic, disease-related, and hospitalization data were taken from patient charts. Results: Reliability of the symptom list was computed with Cronbach's alpha measures for the present sample. Between-group-comparisons on the individual items and on the sum-score level were analyzed separately for the different rater-pairs: patients-nurses (n = 41), patients-physicians (n = 39), patients-family members (n = 12). Multiple regression analyses calculated predictive variables of the staff's deviation scores. Significance of results: Significant differences for nurses and physicians were found on the sum-score level for psychological and social symptoms, but not for physical and functional symptoms. Family members rated the intensities of the symptoms generally higher than the patients. Suggestions for further analyses are presented and discussed.
MicroRNA-146a Downregulates NFκB Activity via Targeting TRAF6 and Functions as a Tumor Suppressor Having Strong Prognostic Implications in NK/T Cell Lymphoma

Purpose: We investigated prognostic implications of microRNAs in extranodal NK/T cell lymphoma (NKTL). Experimental Design: We measured miRNA expression in NKTL tissues and cell lines, using real-time PCR, and analyzed its role in NKTL, using cell lines. Results: Multivariate analysis showed low miR-146a expression (P < 0.001; HR = 13.110), primary non–upper aerodigestive tract lesion (non-UAT; P = 0.008; HR = 5.376) and high International Prognostic Index (IPI; ≥3; P = 0.013; HR = 3.584) to be independent poor prognostic factors. miR-146a expression could subdivide UAT-NKTL into 2 prognostic groups, resulting in the following prognostic groups: (i) UATLow-146a, (ii) UATHigh-146a, and (iii) non-UAT. Compared with UATHigh-146a, UATLow-146a showed distinctively poor prognosis (P < 0.001; HR = 15.620), similar to the non-UAT group. In vitro, miR-146a overexpression in NKTL cell lines, SNK6 and YT, inhibited nuclear factor κB (NFκB) activity, suppressed cell proliferation, induced apoptosis, and enhanced chemosensitivity. TNF receptor–associated factor 6, a target of miR-146a and a known NFκB activator, was downregulated by miR-146a in SNK6 and YT cells. Promoter methylation of miR-146a gene was observed in SNK6 and YT cells, as well as in NKTL tissues with low miR-146a expression, and miR-146a expression was induced by the conversion of methylation status with a demethylating agent in SNK6 and YT cells. Conclusions: These results suggest that miR-146a might function as a potent tumor suppressor in NKTL and be useful for patient assessment and therapeutic targeting. Clin Cancer Res; 17(14); 4761–71. ©2011 AACR.
Tracing metals: an archaeo-metallurgical investigation of metal working remains and artefacts from Thaba Nkulu in the Waterberg, South Africa

ii ACKNOWLEDGEMENTS . iii CONTENTS . v LIST OF FIGURES . xvi LIST OF TABLES . xxii CHAPTER 1: INTRODUCTION . 1 1.1: Research aims . 2 1.2: Thaba Nkulu . 3 1.3: Organisation of the dissertation . 5 CHAPTER 2: BACKGROUND . 6 Introduction: . 6 2.1: Archaeology of the Waterberg . 6 2.1.1: Introduction . 6 2.1.2: Hunter-gatherers of the Waterberg . 6 2.1.3: Farming communities of the Waterberg . 10 2.2: Smelting vs. Smithing sites. 16 2.2.1: Introduction . 16 2.2.2: Smelting and smithing . 17 2.2.3: Archaeo-metallurgy in the spatial belief debate . 22 2.3: Archaeo-metallurgy: Various metals and their trace elements . 24 2.3. 1: History of archaeo-metallurgical research in the Waterberg . 24 2.3. 2: Various archaeo-metallurgy instruments, uses and discoveries . 24 2.3. 3: Early theories on sourcing artefacts . 26
Classification via Minimum Incremental Coding Length

We present a simple new criterion for classification, based on principles from lossy data compression. The criterion assigns a test sample to the class that uses the minimum number of additional bits to code the test sample, subject to an allowable distortion. We demonstrate the asymptotic optimality of this criterion for Gaussian distributions and analyze its relationships to classical classifiers. The theoretical results clarify the connections between our approach and popular classifiers such as maximum a posteriori (MAP), regularized discriminant analysis (RDA), $k$-nearest neighbor ($k$-NN), and support vector machine (SVM), as well as unsupervised methods based on lossy coding. Our formulation induces several good effects on the resulting classifier. First, minimizing the lossy coding length induces a regularization effect which stabilizes the (implicit) density estimate in a small sample setting. Second, compression provides a uniform means of handling classes of varying dimension. The new criterion and its kernel and local versions perform competitively on synthetic examples, as well as on real imagery data such as handwritten digits and face images. On these problems, the performance of our simple classifier approaches the best reported results, without using domain-specific information. All MATLAB code and classification results are publicly available for peer evaluation at http://perception.csl. uiuc.edu/coding/home.htm.
Moorland vegetation burning debates should avoid contextomy and anachronism: a comment on Davies et al. (2016)

Davies et al . [[1][1]] called for informed and unbiased debate into the role of fire in UK peatland and moorland management. This general message is something we wholeheartedly agree with, having seen our research presented in various outlets in both a sensationalist and/or a partisan manner (see
Pharmacological Correction of Trafficking Defects in ATP-sensitive Potassium Channels Caused by Sulfonylurea Receptor 1 Mutations*

ATP-sensitive potassium (KATP) channels play a key role in mediating glucose-stimulated insulin secretion by coupling metabolic signals to β-cell membrane potential. Loss of KATP channel function due to mutations in ABCC8 or KCNJ11, genes encoding the sulfonylurea receptor 1 (SUR1) or the inwardly rectifying potassium channel Kir6.2, respectively, results in congenital hyperinsulinism. Many SUR1 mutations prevent trafficking of channel proteins from the endoplasmic reticulum to the cell surface. Channel inhibitors, including sulfonylureas and carbamazepine, have been shown to correct channel trafficking defects. In the present study, we identified 13 novel SUR1 mutations that cause channel trafficking defects, the majority of which are amenable to pharmacological rescue by glibenclamide and carbamazepine. By contrast, none of the mutant channels were rescued by KATP channel openers. Cross-linking experiments showed that KATP channel inhibitors promoted interactions between the N terminus of Kir6.2 and SUR1, whereas channel openers did not, suggesting the inhibitors enhance intersubunit interactions to overcome channel biogenesis and trafficking defects. Functional studies of rescued mutant channels indicate that most mutants rescued to the cell surface exhibited WT-like sensitivity to ATP, MgADP, and diazoxide. In intact cells, recovery of channel function upon trafficking rescue by reversible sulfonylureas or carbamazepine was facilitated by the KATP channel opener diazoxide. Our study expands the list of KATP channel trafficking mutations whose function can be recovered by pharmacological ligands and provides further insight into the structural mechanism by which channel inhibitors correct channel biogenesis and trafficking defects.
Neural correlates of high-risk behavior tendencies and impulsivity in an emotional Go/NoGo fMRI task

Improved neuroscientific understanding of high-risk behaviors such as alcohol binging, drug use, and unsafe sex will lead to therapeutic advances for high-risk groups. High-risk behavior often occurs in an emotionally-charged context, and behavioral inhibition and emotion regulation play important roles in risk-related decision making. High impulsivity is an important potential contributor to high-risk behavior tendencies. We explored the relationships between high-risk behavior tendencies, impulsivity, and fMRI brain activations in an emotional Go/NoGo task. This task presented emotional distractor pictures (aversive vs. neutral) simultaneously with Go/NoGo stimuli (square vs. circle) that required a button press or withholding of the press, respectively. Participants' risk behavior tendencies were assessed with the Cognitive Appraisal of Risky Events (CARE) scale. The Barratt Impulsivity Scale 11 (BIS) was used to assess participant impulsivity. Individuals with higher CARE risk scores exhibited reduced activation related to response inhibition (NoGo−Go) in right orbital frontal cortex (OFC) and ventromedial prefrontal cortex. These regions did not show a significant relationship with impulsivity scores. Conversely, more impulsive individuals showed reduced emotion-related activity (aversive−neutral distractors) in dorsomedial prefrontal cortex, perigenual anterior cingulate cortex, and right posterior OFC. There were distinct neural correlates of high-risk behavior tendency and impulsivity in terms of brain activity in the emotional Go/NoGo task. This dissociation supports the conception of high-risk behavior tendency as a distinct construct from that of impulsivity. Our results suggest that treatment for high-risk behavior may be more effective with a nuanced approach that does not conflate high impulsivity necessarily with high-risk behavior tendencies.
Clenbuterol diminishes aerobic performance in horses.

PURPOSE The purpose of this 8-wk study was to examine the effect of therapeutic levels of clenbuterol on aerobic performance and hemodynamics associated with exercise. METHODS Twenty-three unfit Standardbred mares were divided into four experimental groups, clenbuterol (2.4 microg x kg(-1) body weight twice daily) plus exercise (20 min at 50% O2max; CLENEX; N = 6), clenbuterol only (CLEN; N = 6), exercise only (EX; N = 5), and control (CON; N = 6). All horses performed an incremental exercise test (GXT) to measure maximal oxygen consumption (O2max), blood lactate concentration, total plasma protein concentration, and hematocrit. Plasma volume, heart rate, right ventricular pressure (RVP), and pulmonary artery pressure (PAP) were measured before and after the treatment/training. Each horse also performed an exercise capacity test (ECT) in which they ran at their pretreatment O2max speed until exhausted. RESULTS There were no significant changes in blood lactate, total protein, or hematocrit for any group during either the GXT or ECT. CLENEX decreased (P < 0.05) O2max (-6.2%) and velocity to O2max (-10.0%), whereas both CLENEX and CLEN decreased (P < 0.05) in time to exhaustion (-20.5+/-4.7 and -20.9 +/- 5.6%). EX alone increased (P < 0.05) O2max (+6.5%), velocity to O2max (+10.0%), velocity to produces lactate concentration of 4 mmol (+13.5%), and time to exhaustion (+32.3 +/- 15.0%). Plasma volume was altered (P < 0.05) in CLENEX (-10%) and EX (+27%) but not in CLEN. Posttest recovery HR was higher (P < 0.05) at 2 min post-GXT in the CLENEX, CLEN, and CON compared with their pretest values; RVP remained elevated at 2 min of recovery in the CLEN and CON groups; however, in the EX, recovery HR and RVP had returned to pre-GXT levels by 2 min of recovery. CONCLUSIONS These data suggest that the combined effect of therapeutic levels of clenbuterol and training decrease aerobic performance and that the resultant reduction in plasma volume may affect improvements in cardiovascular function during recovery normally seen with exercise training.