Miracle-dz/UniFAR-FTUs huggingface dataset:
Human Immunodeficiency Virus Type 1 (HIV-1) Subtype B Epidemic in Panama Is Mainly Driven by Dissemination of Country-Specific Clades

The Human immunodeficiency virus type-1 (HIV-1) subtype B is the most predominant clade in Central America; but information about the evolutionary history of this virus in this geographic region is scarce. In this study, we reconstructed the spatiotemporal and population dynamics of the HIV-1 subtype B epidemic in Panama. A total of 761 HIV-1 subtype B pol sequences obtained in Panama between 2004 and 2013 were combined with subtype B pol sequences from the Americas and Europe. Maximum Likelihood phylogenetic analyses revealed that HIV-1 subtype B infections in Panama derived from the dissemination of multiple founder viruses. Most Panamanian subtype B viruses (94.5%) belong to the pandemic viral strain proposed as originated in the US, whereas others (5.5%) were intermixed among non-pandemic Caribbean strains. The bulk (76.6%) of subtype B sequences from Panama grouped within 12 country-specific clades that were not detected in other Central American countries. Bayesian coalescent-based analyses suggest that most Panamanian clades probably originated between the early 1970s and the early 1980s. The root location of major Panamanian clades was traced to the most densely populated districts of Panama province. Major Panamanian clades appear to have experienced one or two periods of exponential growth of variable duration between the 1970s and the 2000s, with median growth rates from 0.2 to 0.4 year− 1. Thus, the HIV-1 subtype B epidemic in Panama is driven by the expansion of local viral strains that were introduced from the Caribbean and other American countries at an early stage of the AIDS pandemic.
Three‐dimensional maximum probability atlas of the human brain, with particular reference to the temporal lobe

Probabilistic atlases of neuroanatomy are more representative of population anatomy than single brain atlases. They allow anatomical labeling of the results of group studies in stereotaxic space, automated anatomical labeling of individual brain imaging datasets, and the statistical assessment of normal ranges for structure volumes and extents. No such manually constructed atlas is currently available for the frequently studied group of young adults. We studied 20 normal subjects (10 women, median age 31 years) with high‐resolution magnetic resonance imaging (MRI) scanning. Images were nonuniformity corrected and reoriented along both the anterior‐posterior commissure (AC–PC) line horizontally and the midsagittal plane sagittally. Building on our previous work, we have expanded and refined existing algorithms for the subdivision of MRI datasets into anatomical structures. The resulting algorithm is presented in the Appendix . Forty‐nine structures were interactively defined as three‐dimensional volumes‐of‐interest (VOIs). The resulting 20 individual atlases were spatially transformed (normalized) into standard stereotaxic space, using SPM99 software and the MNI/ICBM 152 template. We evaluated volume data for all structures both in native space and after spatial normalization, and used the normalized superimposed atlases to create a maximum probability map in stereotaxic space, which retains quantitative information regarding inter‐subject variability. Its potential applications range from the automatic labeling of new scans to the detection of anatomical abnormalities in patients. Further data can be extracted from the atlas for the detailed analysis of individual structures. Hum. Brain Mapping 19:224–247,2003. ©2003 Wiley‐Liss,Inc.
CSR Practices in Polish and Spanish Stock Listed Companies: A Comparative Analysis

In recent years, many studies have been carried out on corporate social responsibility (CSR) reporting by enterprises. However, none of the previous surveys have covered CSR reporting in countries in Western Europe (Spain) and Central Europe (Poland). In our research, we looked for answers to two research questions. The first was aimed at answering whether the industry represented by a given company influenced the number of disclosures in CSR reporting. The second question was to answer whether there were differences between Poland and Spain in the amount of disclosure in CSR reporting. We carried out a statistical analysis of the collected research material, under which we performed non-parametric tests as all of the variables for the distribution were not normal (Shapiro–Wilk test). We performed both the U Mann–Whitney and Kruskal–Wallis tests, which allowed us to answer our questions. The obtained results indicated that enterprises from the fuel and energy sectors as well as the financial industry provided more CSR disclosure than the other industries. There was a significant difference in the number of CSR disclosures between Poland and Spain, where more disclosures in CSR reporting were recorded in Spain.
The Role of Komite Persiapan Penegakan Syariat Islam (KPPSI) Organization for Development of Islamic Civil Society in the Bugis Community of South Sulawesi, Indonesia

This writing describes the role Komite Persiapan Penegakan Syariah Islam (KPPSI) organization for development of civil society in Bugis community of South Sulawesi. The study used interviews as the data collection. Secondary data are collected from books, journals, and documents. This study used Antony Gidden’s theory of structure to understand the role of KPPSI organization in developing of Islamic civil society in South Sulawesi. There are some civil society agendas of KPPSI, such as the implementation of Islamic law, Islamic economy, dakwah, and democracy. The basic concept of Islamic law is through state formal legislation. In terms of economic aspect, the intention of the KPPSI is the establishment of Perda (Peraturan Daerah) Act No. 2/2003 in Bulukumba, about compulsory payment for professional zakat, infaq and sadaqah. In regard to dakwah aspect, KPPSI focuses on Islamic structural dakwah that is oriented to get legitimation from local government. Another important aspect is democracy. KPPSI shows that democratization in South Sulawesi is part of Islamic ideology that is always considered as contradict with the concept of democracy. Since the Reformation Era, KPPSI exploits to demand special autonomy for the implementation of Islamic law in South Sulawesi. Keywords—civil society; Bugis community; South Sulawesi; islamic law; Komite Persiapan Penegakan Syariat Islam
Fast set‐up of doxycycline‐inducible protein expression in human cell lines with a single plasmid based on Epstein–Barr virus replication and the simple tetracycline repressor

We have developed a novel plasmid vector, pEBTetD, for full establishment of doxycycline‐inducible protein expression by just a single transfection. pEBTetD contains an Epstein–Barr virus origin of replication for stable and efficient episomal propagation in human cell lines, a cassette for continuous expression of the simple tetracycline repressor, and a cytomegalovirus‐type 2 tetracycline operator (tetO2)‐tetO2 promoter. As there is no integration of vector into the genome, clonal isolation of transfected cells is not necessary. Cells are thus ready for use 1 week after transfection; this contrasts with 3–12 weeks for other systems. Adequate regulation of protein expression was accomplished by abrogation of mRNA polyadenylation. In northern analysis of seven cDNAs coding for transport proteins, pools of transfected human embryonic kidney 293 cells showed on/off mRNA ratios in the order of 100 : 1. Cell pools were also analyzed for regulation of protein function. With two transport proteins of the plasma membrane, the on/off activity ratios were 24 : 1 and 34 : 1, respectively. With enhanced green fluorescent protein, a 23 : 1 ratio was observed based on fluorescence intensity data from flow cytometry. The unique advantage of our system rests on the unmodified tetracycline repressor, which is less likely, by relocation upon binding of doxycycline, to cause cellular disturbances than chimera of tetracycline repressor and eukaryotic transactivation domains. Thus, in a comprehensive comparison of on‐ and off‐states, a steady cellular background is provided. Finally, in contrast to a system based on Flp recombinase, the set‐up of our system is inherently reliable.
An enhanced high-rate WPAN MAC for mesh networks with dynamic bandwidth management

A mesh-enabled WPAN (mesh-WPAN) built on the standard IEEE 802.15. 3 MAC allocates channel time node by node along a route. This allocation causes unnecessary packet delays, which is not desirable for multimedia-dominating scenarios. Also, the variability of wireless link may result in relaying nodes' starvation or buffer overflow. In this work an enhanced MAC protocol for high-rate mesh-WPAN named group relay and token solicitation (GRATS) is proposed. Group relay enables dynamic channel time sharing among the nodes along a route. Token solicitation allows for temporarily adjusting the number of packets in a group. Both mathematical analysis and simulation results show that the GRATS not only solves the relaying nodes' starvation and buffer overflow problems, but also reduces average packet delay noticeably. Simulation results also show that the GRATS outperforms the IEEE 802.15. 3 MAC significantly for delay bounded VBR video traffic in terms of job failure rate
Multiple, Conserved Iron-responsive Elements in the 3′-Untranslated Region of Transferrin Receptor mRNA Enhance Binding of Iron Regulatory Protein 2*

Synthesis of proteins for iron homeostasis is regulated by specific, combinatorial mRNA/protein interactions between RNA stem-loop structures (iron-responsive elements, IREs) and iron-regulatory proteins (IRP1 and IRP2), controlling either mRNA translation or stability. The transferrin receptor 3′-untranslated region (TfR-3′-UTR) mRNA is unique in having five IREs, linked by AU-rich elements. A C-bulge in the stem of each TfR-IRE folds into an IRE that has low IRP2 binding, whereas a loop/bulge in the stem of the ferritin-IRE allows equivalent IRP1 and IRP2 binding. Effects of multiple IRE interactions with IRP1 and IRP2 were compared between the native TfR-3′-UTR sequence (5xIRE) and RNA with only 3 or 2 IREs. We show 1) equivalent IRP1 and IRP2 binding to multiple TfR-IRE RNAs; 2) increased IRP-dependent nuclease resistance of 5xIRE compared with lower IRE copy-number RNAs; 3) distorted TfR-IRE helix structure within the context of 5xIRE, detected by Cu-(phen)2 binding/cleavage, that coincides with ferritin-IRE conformation and enhanced IRP2 binding; and 4) variable IRP1 and IRP2 expression in human cells and during development (IRP2-mRNA predominated). Changes in TfR-IRE structure conferred by the full length TfR-3′-UTR mRNA explain in part evolutionary conservation of multiple IRE-RNA, which allows TfR mRNA stabilization and receptor synthesis when IRP activity varies, and ensures iron uptake for cell growth.
Reliability and validity of the Performance Recorder 1 for measuring isometric knee flexor and extensor strength

Background Muscular strength is a key parameter of rehabilitation programs and a strong predictor of functional capacity. Traditional methods to measure strength, such as manual muscle testing (MMT) and hand-held dynamometry (HHD), are limited by the strength and experience of the tester. The Performance Recorder 1 (PR1) is a strength assessment tool attached to resistance training equipment and may be a time- and cost-effective tool to measure strength in clinical practice that overcomes some limitations of MMT and HHD. However, reliability and validity of the PR1 have not been reported. Methods: Test-retest and inter-rater reliability was assessed using the PR1 in healthy adults (n = 15) during isometric knee flexion and extension. Criterion-related validity was assessed through comparison of values obtained from the PR1 and Biodex® isokinetic dynamometer. Results: Test-retest reliability was excellent for peak knee flexion (intra-class correlation coefficient [ICC] of 0.96, 95% CI: 0.85, 0.99) and knee extension (ICC = 0.96, 95% CI: 0.87, 0.99). Inter-rater reliability was also excellent for peak knee flexion (ICC = 0.95, 95% CI: 0.85, 0.99) and peak knee extension (ICC = 0.97, 95% CI: 0.91, 0.99). Validity was moderate for peak knee flexion (ICC = 0.75, 95% CI: 0.38, 0.92) but poor for peak knee extension (ICC = 0.37, 95% CI: 0, 0.73). Conclusions: The PR1 provides a reliable measure of isometric knee flexor and extensor strength in healthy adults that could be used in the clinical setting, but absolute values may not be comparable to strength assessment by gold-standard measures.
Geographical Economics and Income Disparities Across Ecuadorian Regions: Analysis for the period 2007-2014

This paper focuses on the analysis of the role played by market potential in the spatial income structure observed in Ecuador over the period 2007-2014. Based on the geographical economics theory we derive the so called nominal wage equation which establishes a relationship between nominal wages and a distance weighted sum of the volume of economic activities in surrounding locations which is usually known as market potential. The estimation of this equation using Ecuadorian provincial data over the period 2007-2014 reveals that market potential plays a crucial role in explanation of the spatial distribution of per capita income. The results of our estimations are robust to the potential endogeneity problems of market potential which have been dealt with by using historical values of market potential and instrumental variables. Finally, we have also discovered a potential channel that could be affecting the spatial structure of per capita income in Ecuador, which is human capital.
An efficient non-linear cascade filtering algorithm for removal of high density salt and pepper noise in image and video sequence

In this paper, an efficient non-linear cascade filter for the removal of high density salt and pepper noise in image and video is proposed. The proposed method consists of two stages to enhance the filtering. The first stage is the Decision based Median Filter (DMF) which is used to identify pixels likely to be contaminated by salt and pepper noise and replaces them by the median value. The second stage is the Unsymmetric Trimmed Filter, either Mean Filter (UTMF) or Midpoint Filter (UTMP) which is used to trim the noisy pixels in an unsymmetric manner and processes with the remaining pixels The basic idea is that, though the level of denoising in the first stage is lesser at high noise densities, the second stage helps to increase the noise suppression. Hence, the proposed cascaded filter, as a whole is very suitable for low, medium as well as high noise densities even above 90%. The existing non-linear filters such as Standard Median Filter (SMF), Adaptive Median Filter (AMF), Weighted Median Filter (WMF), Recursive Weighted Median Filter (RWM) performs well only for low and medium noise densities. The recently proposed Decision Based Algorithm (DBA) shows better results upto 70% noise density and at high noise densities, the restored image quality is poor. The proposed algorithm shows better image and video quality in terms of visual appearance and quantitative measures.
A Semiparametric Joint Model for Longitudinal and Survival Data with Application to Hemodialysis Study

Summary In many longitudinal clinical studies, the level and progression rate of repeatedly measured biomarkers on each subject quantify the severity of the disease and that subject's susceptibility to progression of the disease. It is of scientific and clinical interest to relate such quantities to a later time‐to‐event clinical endpoint such as patient survival. This is usually done with a shared parameter model. In such models, the longitudinal biomarker data and the survival outcome of each subject are assumed to be conditionally independent given subject‐level severity or susceptibility (also called frailty in statistical terms). In this article, we study the case where the conditional distribution of longitudinal data is modeled by a linear mixed‐effect model, and the conditional distribution of the survival data is given by a Cox proportional hazard model. We allow unknown regression coefficients and time‐dependent covariates in both models. The proposed estimators are maximizers of an exact correction to the joint log likelihood with the frailties eliminated as nuisance parameters, an idea that originated from correction of covariate measurement error in measurement error models. The corrected joint log likelihood is shown to be asymptotically concave and leads to consistent and asymptotically normal estimators. Unlike most published methods for joint modeling, the proposed estimation procedure does not rely on distributional assumptions of the frailties. The proposed method was studied in simulations and applied to a data set from the Hemodialysis Study.
Operative Strategies for Diverticular Peritonitis: A Decision Analysis Between Primary Resection and Anastomosis Versus Hartmann's Procedures

Objective:To compare primary resection and anastomosis (PRA) with and without defunctioning stoma to Hartmann's procedure (HP) as the optimal operative strategy for patients presenting with Hinchey stage III-IV, perforated diverticulitis. Summary Background Data:The choice of operation for perforated diverticulitis lies between HP and PRA. Postoperative mortality and morbidity can be high, and the long-term consequences life-altering, with no established criteria guiding clinicians towards selecting a particular procedure. Methods:Probability estimates for 6879 patients with Hinchey III-IV perforated diverticulitis were obtained from two databases (n = 204), supplemented by expert opinion and summary data from 12 studies (n = 6675) published between 1980 and 2005. The primary outcome was quality-adjusted life-years (QALYs) gained from each strategy. Factors considered were the risk of permanent stoma, morbidity, and mortality from the primary or reversal operations. Decision analysis from the patient's perspective was used to calculate the optimal operative strategy and sensitivity analysis performed. Results:A total of 135 PRA, 126 primary anastomoses with defunctioning stoma (PADS), and 6619 Hartmann's procedures (HP) were considered. The probability of morbidity and mortality was 55% and 30% for PRA, 40% and 25% for PADS, and 35% and 20% for HP, respectively. Stomas remained permanent in 27% of HP and in 8% of PADS. Analysis revealed the optimal strategy to be PADS with 9.98 QALYs, compared with 9.44 QALYs after HP and 9.02 QALYs after PRA. Complications after PRA reduced patients QALYs to a baseline of 2.713. Patients with postoperative complications during both primary and reversal operations for PADS and HP had QALYs of 0.366 and 0.325, respectively. HP became the optimal strategy only when risk of complications after PRA and PADS reached 50% and 44%, respectively. Conclusion:Primary anastomosis with defunctioning stoma may be the optimal strategy for selected patients with diverticular peritonitis as may represent a good compromise between postoperative adverse events, long-term quality of life and risk of permanent stoma. HP may be reserved for patients with risk of complications >40% to 50% after consideration of long-term implications.
pophelper: an R package and web app to analyse and visualize population structure

The pophelper r package and web app are software tools to aid in population structure analyses. They can be used for the analyses and visualization of output generated from population assignment programs such as admixture, structure and tess. Some of the functions include parsing output run files to tabulate data, estimating K using the Evanno method, generating files for clumpp and functionality to create barplots. These functions can be streamlined into standard r analysis workflows. The latest version of the package is available on github (https://github.com/royfrancis/pophelper). An interactive web version of the pophelper package is available which covers the same functionalities as the r package version with features such as interactive plots, cluster alignment during plotting, sorting individuals and ordering of population groups. The interactive version is available at http://pophelper.com/.
Androgen receptor expressing neurons that project to the paraventricular nucleus of the hypothalamus in the male rat

Androgen receptors are distributed throughout the central nervous system and are contained by a variety of nuclei that are known to project to or regulate the paraventricular nucleus (PVN) of the hypothalamus, the final common pathway by which the brain regulates the hypothalamic–pituitary–adrenal (HPA) response to homeostatic threat. Here we characterized androgen receptor staining within cells identified as projecting to the PVN in male rats bearing iontophoretic or crystalline injections of the retrograde tracer FluoroGold aimed at the caudal two‐thirds of the nucleus, where corticotropin‐releasing hormone‐expressing neurons are amassed. Androgen receptor (AR) and FluoroGold (FG) double labeling was revealed throughout the limbic forebrain, including scattered numbers of cells within the anterior and posterior subdivisions of the bed nuclei of the stria terminalis; the medial zone of the hypothalamus, including large numbers of AR‐FG‐positive cells within the anteroventral periventricular and medial preoptic cell groups. Strong and consistent colabeling was also revealed throughout the hindbrain, predominantly within the periaqueductal gray and the lateral parabrachial nucleus, and within various medullary cell groups identified as catecholaminergic, predominantly C1 and A1 neurons of the ventral medulla. These connectional data predict that androgens can act on a large assortment of multimodal inputs to the PVN, including those involved with the processing of various types of sensory and limbic information, and provide an anatomical framework for understanding how gonadal status could contribute to individual differences in HPA function. J. Comp. Neurol. 503:717–740, 2007. © 2007 Wiley‐Liss, Inc.