Miracle-dz/UniFAR-FTUs huggingface dataset:
The Vascular Endothelium, a Benign Restrictive Barrier? NO! Role of Nitric Oxide in Regulating Insulin Action

Insulin resistance is the primary abnormality associated with obesity, type 2 diabetes, and hypertension (1,2). Interestingly, these disease processes also share a common underlying impairment of vascular endothelial function. For many years the endothelium was thought of as nothing more than a benign barrier between blood and extracellular space. But intensive investigations demonstrate a myriad of actions by the endothelium, including regulation of blood flow (3,4), vascular tone (5), vascular permeability (6), and the immune response (7). The capillary endothelium regulates blood flow via the release of several vasoactive agents, in particular nitric oxide (NO) (8). Baron (4) first demonstrated that insulin can stimulate the release of endothelial NO, thereby regulating blood flow and its own delivery. Insulin has multiple hemodynamic actions to enhance its ability to increase glucose uptake in skeletal muscle (4, 9–11). The three major methods include: 1 ) increasing blood flow to the tissue by modulation of endothelial factors; 2 ) increasing the number of capillaries that dilate within the tissue (increasing microvascular volume), which allows for an increase in total permeable surface area for insulin and glucose to enter the space that bathes the active myocytes (i.e., the interstitial space); and 3 ) increasing permeability of the capillaries, thus allowing more glucose and insulin to pass from the blood to the interstitial space. In insulin-resistant states, these hemodynamic actions of insulin are impaired, presumably due to reduced NO bioavailability (12). The seminal study by Bergman and colleagues …
Evolution of the Rab family of small GTP-binding proteins.

Rab proteins are small GTP-binding proteins that form the largest family within the Ras superfamily. Rab proteins regulate vesicular trafficking pathways, behaving as membrane-associated molecular switches. Here, we have identified the complete Rab families in the Caenorhabditis elegans (29 members), Drosophila melanogaster (29), Homo sapiens (60) and Arabidopsis thaliana (57), and we defined criteria for annotation of this protein family in each organism. We studied sequence conservation patterns and observed that the RabF motifs and the RabSF regions previously described in mammalian Rabs are conserved across species. This is consistent with conserved recognition mechanisms by general regulators and specific effectors. We used phylogenetic analysis and other approaches to reconstruct the multiplication of the Rab family and observed that this family shows a strict phylogeny of function as opposed to a phylogeny of species. Furthermore, we observed that Rabs co-segregating in phylogenetic trees show a pattern of similar cellular localisation and/or function. Therefore, animal and fungi Rab proteins can be grouped in "Rab functional groups" according to their segregating patterns in phylogenetic trees. These functional groups reflect similarity of sequence, localisation and/or function, and may also represent shared ancestry. Rab functional groups can help the understanding of the functional evolution of the Rab family in particular and vesicular transport in general, and may be used to predict general functions for novel Rab sequences.
The concept of health in One Health and some practical implications for research and education: what is One Health?

Abstract From a strict biological point of view, humans are just one species among other species, albeit one with very special capacities, characteristics, and skills. Among scientists, it is generally acknowledged that we share many features with other animal species, which are certainly relevant when the concepts of health and disease are discussed. The term ‘One Health’ is used in many different contexts and by people with varying backgrounds. However, there appears to be some confusion as to what the term really means, and it is used in a wide range of contexts, often including or bordering concepts such as infection biology, contagious diseases, zoonotic infections, evolutionary medicine, comparative medicine, and translational medicine. Without claiming to present the one and only true interpretation, we will argue for a wide approach using the ‘umbrella’ depiction developed by One Health Sweden. We argue that this one should, compared to other demarcations, be more useful to science. We will also analyze the concept of health on different levels: individual, population, and ecosystem health, and describe how these levels inherently influence each other for both humans and animals. Both these choices are normative and have practical consequences for research and education, a way of reasoning which we develop further in this paper. Finally, we conclude that the choice of term for the approach might be normative in deciding which disciplines or parts of disciplines that may be included.
4IPP Traffic Model for IEEE 802.16.3

The contribution defines a general traffic model which provides typical self-similar traffic for a point-to-multipoint fixed wireless WAN applications. The model accurate characterizes measured traffic for both Ethernet and Internet traffic. The contribution defines the traffic model for various proto-typical cases. It also provides a definition of what MAC/PHY performance metrics to calculate as a means of characterizing the performance of the MAC/PHY. Purpose The contribution describes a traffic model to be used for characterizing performance of MAC/PHY proposals for consideration as components of the common air interface standard for IEEE 802.16. 3. Notice This document has been prepared to assist IEEE 802.16. It is offered as a basis for discussion and is not binding on the contributing individual(s) or organization(s). The material in this document is subject to change in form and content after further study. The contributor(s) reserve(s) the right to add, amend or withdraw material contained herein. Release The contributor grants a free, irrevocable license to the IEEE to incorporate text contained in this contribution, and any modifications thereof, in the creation of an IEEE Standards publication; to copyright in the IEEE’s name any IEEE Standards publication even though it may include portions of this contribution; and at the IEEE’s sole discretion to permit others to reproduce in whole or in part the resulting IEEE Standards publication. The contributor also acknowledges and accepts that this contribution may be made public by IEEE 802.16. 2000-10-31 IEEE 802.16. 3c-00/51 1 Patent Policy and Procedures The contributor is familiar with the IEEE 802.16 Patent Policy and Procedures (Version 1.0) <http://ieee802.org/16/ipr/patents/policy.html>, including the statement “IEEE standards may include the known use of patent(s), including patent applications, if there is technical justification in the opinion of the standardsdeveloping committee and provided the IEEE receives assurance from the patent holder that it will license applicants under reasonable terms and conditions for the purpose of implementing the standard. ” Early disclosure to the Working Group of patent information that might be relevant to the standard is essential to reduce the possibility for delays in the development process and increase the likelihood that the draft publication will be approved for publication. Please notify the Chair <mailto:r.b. marks@ieee.org> as early as possible, in written or electronic form, of any patents (granted or under application) that may cover technology that is under consideration by or has been approved by IEEE 802.16. The Chair will disclose this notification via the IEEE 802.16 web site <http://ieee802.org/16/ipr/patents/notices>. 2000-10-31 IEEE 802.16. 3c-00/51 2 4IPP Traffic Model for IEEE 802.16. 3 C. R. Baugh, Ph.D.
Whole-Genome Sequence Variation among Multiple Isolates of Pseudomonas aeruginosa

ABSTRACT Whole-genome shotgun sequencing was used to study the sequence variation of three Pseudomonas aeruginosa isolates, two from clonal infections of cystic fibrosis patients and one from an aquatic environment, relative to the genomic sequence of reference strain PAO1. The majority of the PAO1 genome is represented in these strains; however, at least three prominent islands of PAO1-specific sequence are apparent. Conversely, ∼10% of the sequencing reads derived from each isolate fail to align with the PAO1 backbone. While average sequence variation among all strains is roughly 0.5%, regions of pronounced differences were evident in whole-genome scans of nucleotide diversity. We analyzed two such divergent loci, the pyoverdine and O-antigen biosynthesis regions, by complete resequencing. A thorough analysis of isolates collected over time from one of the cystic fibrosis patients revealed independent mutations resulting in the loss of O-antigen synthesis alternating with a mucoid phenotype. Overall, we conclude that most of the PAO1 genome represents a core P. aeruginosa backbone sequence while the strains addressed in this study possess additional genetic material that accounts for at least 10% of their genomes. Approximately half of these additional sequences are novel.
Evolution of 3GPP Core Network

A core network of UMTS has a very long development. The first version of core network corresponds to an improved GSM/GPRS core network. The interfaces are changed and later all conception. The main changes are in using Internet Protocol, adding IMS functionality and finally in complete new packet core of technology called long term evolution. From user point of view it means increasing bit rates from tens kbit/s to tens Mbit/s, offering multimedia services, access to Internet, etc. This paper gives an overview about evolution of UMTS core network.
Reducing susceptibility artifacts in fMRI using volume‐selective z‐shim compensation

Susceptibility‐induced magnetic field gradients (SFGs) can result in severe signal loss in the orbitofrontal cortex (OFC) in gradient‐echo‐based functional MRI (fMRI) studies. Although conventional z‐shim techniques can effectively recover the MRI signal in this region, the substantial penalty in imaging time hampers their use in routine fMRI studies. A modified z‐shim technique with high imaging efficiency is presented in this study. In this technique, z‐shim compensations are applied only to a selective volume where the susceptibility artifact is severe. The results of an fMRI study (N = 6) demonstrate the feasibility of detecting the OFC activation with z‐shim in whole‐brain fMRI studies at a temporal resolution of 2 s. Magn Reson Med 57:396–404, 2007. © 2007 Wiley‐Liss, Inc.
Fast face detection and localization from multi-views using statistical approach

Window-based face detection methods are fast. However their results are coarse, pose dependent and require fine face alignment for face analysis. Recently a statistical approach is introduced by Toews and Arbel [1], which is able to detect faces in multiple poses and does not require face alignment. However, their method is slow compared to the window-based method. In this paper, we proposed a method, which capable of detecting faces in multiple poses in near real time and also does not require face alignment. Experimental results show that our proposed method has comparable accuracy with the Toews and Arbel's method but has significantly lower processing time.
A nonlinear second-order digital oscillator for Virtual Acoustic Feedback

The guitar feedback effect, or howling, is well known to the general public and identified with many rock music genres and it is the only case of acoustic feedback employed for musical purposes. Virtual Acoustic Feedback (VAF), is regarded as the extension of this phenomenon to any instrument or sound source by means of virtual acoustics and is meant to enrich the sound palette of a musician. The study of the acoustic feedback as a musical tool and computational techniques for its emulation have been scarcely addressed in literature. In this paper a nonlinear feedback oscillator is proposed and its properties derived. The oscillator does not necessarily need to be connected to a virtual instrument, thus enables to process any kind of pitched real-time input.
Proteomics: Challenges, Techniques and Possibilities to Overcome Biological Sample Complexity

Proteomics is the large-scale study of the structure and function of proteins in complex biological sample. Such an approach has the potential value to understand the complex nature of the organism. Current proteomic tools allow large-scale, high-throughput analyses for the detection, identification, and functional investigation of proteome. Advances in protein fractionation and labeling techniques have improved protein identification to include the least abundant proteins. In addition, proteomics has been complemented by the analysis of posttranslational modifications and techniques for the quantitative comparison of different proteomes. However, the major limitation of proteomic investigations remains the complexity of biological structures and physiological processes, rendering the path of exploration paved with various difficulties and pitfalls. The quantity of data that is acquired with new techniques places new challenges on data processing and analysis. This article provides a brief overview of currently available proteomic techniques and their applications, followed by detailed description of advantages and technical challenges. Some solutions to circumvent technical difficulties are proposed.
Branch transition rate: a new metric for improved branch classification analysis

Recent studies have shown significantly improved branch prediction through the use of branch classification. By separating static branches into groups, or classes, with similar dynamic behavior predictors may be selected that are best suited for each class. Previous methods have classified branches according to taken rate (or bias). We propose a new metric for branch classification: branch transition rate, which is defined as the number of times a branch changes direction between taken and not taken during execution. We show that transition rate is a more appropriate indicator of branch behavior than taken rate for determining predictor performance. When both metrics are combined, an even clearer picture of dynamic branch behavior emerges, in which expected predictor performance for a branch is closely correlated with its combined taken and transition rate class. Using this classification, a small group of branches is identified for which two-level predictors are ineffective.
Swift: primary data analysis for the Illumina Solexa sequencing platform

Motivation: Primary data analysis methods are of critical importance in second generation DNA sequencing. Improved methods have the potential to increase yield and reduce the error rates. Openly documented analysis tools enable the user to understand the primary data, this is important for the optimization and validity of their scientific work. Results: In this article, we describe Swift, a new tool for performing primary data analysis on the Illumina Solexa Sequencing Platform. Swift is the first tool, outside of the vendors own software, which completes the full analysis process, from raw images through to base calls. As such it provides an alternative to, and independent validation of, the vendor supplied tool. Our results show that Swift is able to increase yield by 13.8%, at comparable error rate. Availability and Implementation: Swift is implemented in C++and supported under Linux. It is supplied under an open source license (LGPL3), allowing researchers to build upon the platform. Swift is available from http://swiftng.sourceforge. net. Contact: new@sgenomics.org; nava.whiteford@nanoporetech.com Supplementary information: Supplementary data are available at Bioinformatics online.
Modulation of the Disordered Conformational Ensembles of the p53 Transactivation Domain by Cancer-Associated Mutations

Intrinsically disordered proteins (IDPs) are frequently associated with human diseases such as cancers, and about one-fourth of disease-associated missense mutations have been mapped into predicted disordered regions. Understanding how these mutations affect the structure-function relationship of IDPs is a formidable task that requires detailed characterization of the disordered conformational ensembles. Implicit solvent coupled with enhanced sampling has been proposed to provide a balance between accuracy and efficiency necessary for systematic and comparative assessments of the effects of mutations as well as post-translational modifications on IDP structure and interaction. Here, we utilize a recently developed replica exchange with guided annealing enhanced sampling technique to calculate well-converged atomistic conformational ensembles of the intrinsically disordered transactivation domain (TAD) of tumor suppressor p53 and several cancer-associated mutants in implicit solvent. The simulations are critically assessed by quantitative comparisons with several types of experimental data that provide structural information on both secondary and tertiary levels. The results show that the calculated ensembles reproduce local structural features of wild-type p53-TAD and the effects of K24N mutation quantitatively. On the tertiary level, the simulated ensembles are overly compact, even though they appear to recapitulate the overall features of transient long-range contacts qualitatively. A key finding is that, while p53-TAD and its cancer mutants sample a similar set of conformational states, cancer mutants could introduce both local and long-range structural modulations to potentially perturb the balance of p53 binding to various regulatory proteins and further alter how this balance is regulated by multisite phosphorylation of p53-TAD. The current study clearly demonstrates the promise of atomistic simulations for detailed characterization of IDP conformations, and at the same time reveals important limitations in the current implicit solvent protein force field that must be sufficiently addressed for reliable description of long-range structural features of the disordered ensembles.
Genotyping Tools for Mycobacterium ulcerans-Drawbacks and Future Prospects

Mycobacterium ulcerans infection (Buruli ulcer) is a neglected but treatable skin disease endemic in over 30 countries. M. ulcerans is an environmental mycobacteria with an elusive mode of transmission to humans. Ecological and Molecular epidemiological studies to identify reservoirs and transmission vectors are important for source tracking infections especially during outbreaks and elucidating transmission routes. Research efforts have therefore focused on genotyping strains of the mycobacteria from clinical and environmental samples. This review discusses genotyping tools for differentiating M. ulcerans strains from other environmental and Mycolactone Producing Mycobacteria (MPMs). We highlight tools that have been adapted from related fields and propose ways these could be enhanced to resolve intra-species variation for epidemiological, transmission, evolutionary studies, and detection of emerging drug resistant strains. In the wake of increasing cases of Buruli ulcer, cumulative efforts including improvement in diagnostic methods and fine-tuning of genotyping tools are crucial to complement public health efforts in reducing infections.
A Partial-Current-Steering Biphasic Stimulation Driver for Vestibular Prostheses

This paper describes a novel partial-current-steering stimulation circuit for implantable vestibular prostheses. The drive hardware momentarily delivers a charge-balanced asymmetric stimulus to a dummy load before steering towards the stimulation electrodes. In this fashion, power is conserved while still gaining from the benefits of current steering. The circuit has been designed to be digitally programmable as part of an implantable vestibular prosthesis. The hardware has been implemented in AMS 0.35 mum 2P4M CMOS technology.
Causal relationships versus emergent patterns in the global controls of fire frequency

Global controls on month-by-month fractional burnt area (2000–2005) were investigated by fitting a generalised linear model (GLM) to Global Fire Emissions Database (GFED) data, with 11 predictor variables representing vegetation, climate, land use and potential ignition sources. Burnt area is shown to increase with annual net primary production (NPP), number of dry days, maximum temperature, grazing-land area, grass/shrub cover and diurnal temperature range, and to decrease with soil moisture, cropland area and population density. Lightning showed an apparent (weak) negative influence, but this disappeared when pure seasonal-cycle effects were taken into account. The model predicts observed geographic and seasonal patterns, as well as the emergent relationships seen when burnt area is plotted against each variable separately. Unimodal relationships with mean annual temperature and precipitation, population density and gross domestic product (GDP) are reproduced too, and are thus shown to be secondary consequences of correlations between different controls (e.g. high NPP with high precipitation; low NPP with low population density and GDP). These findings have major implications for the design of global fire models, as several assumptions in current models – most notably, the widely assumed dependence of fire frequency on ignition rates – are evidently incorrect.
Graph partition and identification of cluster number in data analysis

Modern computing with wide range of applications in different areas such as Internet, biology, and social science, involves large scale of data analysis. The relations of data can be modeled as graphs and graph partitioning problem can be effectively approximated by spectral approaches. A critically important problem in graph partition is determination of the cluster number k. Although eigengap heuristic is a principle for this problem and is supported by theory, it is difficult to be applied for the real-world data and complex graphs. In this paper, by considering the general data analysis scenario, we present an algorithm to determine the cluster number k and perform clustering task simultaneously. The experimental result shows that our algorithm works successfully even for the real world data, which is therefore a promising tool for future data analysis.