Miracle-dz/UniFAR-FTUs huggingface dataset:
Identification of Regions Important for Resistance and Signalling within the Antimicrobial Peptide Transporter BceAB of Bacillus subtilis

ABSTRACT In the low-G+C-content Gram-positive bacteria, resistance to antimicrobial peptides is often mediated by so-called resistance modules. These consist of a two-component system and an ATP-binding cassette transporter and are characterized by an unusual mode of signal transduction where the transporter acts as a sensor of antimicrobial peptides, because the histidine kinase alone cannot detect the substrates directly. Thus, the transporters fulfill a dual function as sensors and detoxification systems to confer resistance, but the mechanistic details of these processes are unknown. The paradigm and best-understood example for this is the BceRS-BceAB module of Bacillus subtilis, which mediates resistance to bacitracin, mersacidin, and actagardine. Using a random mutagenesis approach, we here show that mutations that affect specific functions of the transporter BceAB are primarily found in the C-terminal region of the permease, BceB, particularly in the eighth transmembrane helix. Further, we show that while signaling and resistance are functionally interconnected, several mutations could be identified that strongly affected one activity of the transporter but had only minor effects on the other. Thus, a partial genetic separation of the two properties could be achieved by single amino acid replacements, providing first insights into the signaling mechanism of these unusual modules.
Zeroth-order resonator with tunable reflectors based on nonreciprocal CRLH metamaterials

In this paper, a pair of tunable reactive elements for reflectors with impedances having a relation of complex conjugate is proposed based on nonreciprocal composite right/left handed transmission lines using a ferrite rod embedded substrate. These reflectors are inserted at both ends of a zeroth-order resonator. Numerical simulation results clearly show that the field profile on the zeroth-order resonator is continuously tunable by changing the applied DC magnetic field to the ferrite rods.
Differences in glomerular filtration rate estimates by 2 cystatin C-based equations.

Glomerular filtration rate (GFR) represents the best overall index of kidney function (1), and the National Kidney Foundation has recommended that clinical laboratories routinely report an estimate of GFR(1)(2). Several cystatin C–based equations for calculation of GFR have been reported(3)(4). The most recent equations have been published by Larsson et al. (GFRLarsson = 99.43 × cystatin C−1.5837)(4) and Grubb et al. [GFRGrubb = 84.69 × cystatin C−1.680 (× 0.948 if female)](5). Both groups report on GFR estimates obtained from particle-enhanced turbidimetric immunoassay measurements of cystatin C (DakoCytomation). After correcting the Larsson estimate for …
Improved PSK classification using spectral correlation functions

This paper proposes an improved PSK classifier using the spectral correlation function(SCF). It shows why the SCF is unable to classify higher order PSK signals. A set of new features are extracted from SCF and used for classification as a solution to this problem. It also explains the differentiating capability of the newly extracted features.
A Software Defined Semi Distributed Mobility Management System Based on Layer 2 Backhaul Network

This paper presents a software defined networking (SDN) based semi-distributed mobility management system. By both using an SDN approach and leveraging layer 2 technology, i.e., carrier grade Ethernet and the 802.1ad standard, it is possible to simplify the network architecture by removing the need for the relatively complex GPRS tunneling protocol currently in use in the user plane. An analytical model is used to evaluate the control overhead of the proposed approach and a proof of concept testbed based on OpenFlow running the Floodlight controller is presented. Obtained results demonstrate that, as long as the SDN controller can quickly react to user mobility, frame loss can be mitigated and the proposed architecture is viable.
Structural and biochemical insights into 7β‐hydroxysteroid dehydrogenase stereoselectivity

Hydroxysteroid dehydrogenases are of great interest as biocatalysts for transformations involving steroid substrates. They feature a high degree of stereo‐ and regio‐selectivity, acting on a defined atom with a specific configuration of the steroid nucleus. The crystal structure of 7β‐hydroxysteroid dehydrogenase from Collinsella aerofaciens reveals a loop gating active‐site accessibility, the bases of the specificity for NADP+, and the general architecture of the steroid binding site. Comparison with 7α‐hydroxysteroid dehydrogenase provides a rationale for the opposite stereoselectivity. The presence of a C‐terminal extension reshapes the substrate site of the β‐selective enzyme, possibly leading to an inverted orientation of the bound substrate. Proteins 2016; 84:859–865. © 2016 Wiley Periodicals, Inc.
Non‐Hodgkin's lymphoma among asthmatics exposed to pesticides

We conducted a pooled analysis of population‐based case‐control studies in Iowa, Minnesota and Nebraska to investigate whether asthma modifies risk of non‐Hodgkin's lymphoma (NHL) associated with pesticide exposures. Cases (n = 872) diagnosed with NHL from 1980 to 1986 and frequency‐matched controls (n = 2,381) randomly selected from the same geographic areas as the cases were included. Information on use of pesticides and history of asthma was based on interviews. Unconditional logistic regression was used to calculate ORs, adjusted for age, state and vital status. Of all subjects, 177 (45 cases, 132 controls) reported having been told by their doctor that they had asthma. Subjects with an asthma history had a nonsignificantly lower risk of NHL than nonasthmatics (OR = 0.6, 95% CI 0.3–1.4), and there was no main effect of pesticide exposure (OR = 1.0, 95% CI 0.8–1.2). However, asthmatics tended to have larger ORs associated with exposure to pesticides than nonasthmatics. The OR among asthmatics was 1.8 (95% CI 1.1–3.2) for ever‐use of crop insecticides, 2.7 (95% CI 1.0–7.2) for chlordane, 2.4 (95% CI 1.0–5.7) for lindane and 3.7 (95% CI 1.3–10.9) for fonofos. Among nonasthmatics, ORs were 1.1 (0.9–1.3), 1.5 (1.1–2.2), 1.3 (0.97–1.8) and 1.6 (1.0–2.4), respectively. Although there is limited power for assessing interaction, our results suggest that the risk of NHL among asthmatics with pesticide exposure may be higher than among nonasthmatics with pesticide exposure. © 2004 Wiley‐Liss, Inc.
Can hepatitis B virus infection predict tuberculosis treatment liver toxicity? Development of a preliminary prediction rule.

BACKGROUND Liver toxicity due to tuberculosis (TB) treatment is a frequent cause of treatment interruption, and may sometimes lead to a change in therapy to a less potent regimen. OBJECTIVE To estimate the risk of hepatotoxicity in patients with or without hepatitis B virus (HBV) infection receiving TB treatment and to develop a clinical prediction rule. DESIGN A prospective observational follow-up was conducted. Data from 154 patients who underwent TB treatment were analysed. Crude risk ratios were estimated and a Cox proportional hazards model was fit. RESULTS The mean follow-up time was 187 days. Crude risk ratios showed that ethnicity, human immunodeficiency virus infection, multiple sexual partners, highly active antiretroviral treatment, and clinical forms of TB were possible predictors of liver toxicity. HBV infection and other sexually transmitted diseases showed considerable relative risk, although not statistically significant. The Cox proportional hazards model identified the following predictors of hepatotoxicity: White ethnicity, multiple sexual partners, high baseline alanine transferase and clinical forms of TB. Active HBV, indicated by the detection of surface antigen HBV, could predict hepatotoxicity, although with low precision. CONCLUSION Using this information, we were able to apply a score and draw a nomogram to estimate survival probabilities and median times to event for each patient.
Preparation of pseudotyped lentiviral vectors resistant to inactivation by serum complement.

INTRODUCTION A major obstacle to in vivo delivery of lentivirus or other retroviral vectors is their lability in the presence of serum. In vivo, these viral particles are rapidly destroyed by nonspecific complement-mediated degradation mechanisms. The eventual effective use of retroviral vectors for in vivo gene delivery would be greatly facilitated by the development of methods to protect the viral particles from such degradation. This protocol describes methods for the production of complement-stabilized lentiviral vectors either by pseudotyping the viral particles with a fusion envelope protein containing the complement-regulatory protein CD55 (decay accelerating factor, DAF) or by coassembly with the native DAF protein. An in vitro serum inactivation assay is also described.
Gene Names as Proper Names of Individuals: An Assessment

According to a recent suggestion, the names of gene taxa should be conceived of as referring to individuals with concrete genes as their parts, just as the names of biological species are often understood as denoting individuals with organisms as their parts. Although prima facie this suggestion might advance the debate on gene concepts in a similar way as the species-are-individuals thesis advanced the debate on species concepts, I argue that the principal arguments in support of the gene-individuality thesis are much less compelling than the parallel arguments in the species case. In addition, I argue that the notion of biological function invoked in the gene-individuality thesis (selected effect) is not the one that biologists actually use when individuating genes. Contra the gene-individuality thesis, I argue that gene names refer to kinds, defined primarily (though not exclusively) by causal-role functions. 1. Introduction2. Species as Individuals: The Two Main Arguments3. Gene-Lineages as Individuals: Rosenberg's Argumentation4. Assessing the GAI-Thesis 4.1. Metaphysics: What biology tells us about lineages4.2. Epistemology: How biologists individuate the parts of genomes5. What Do Gene Names Refer To? 6. Why the GAI-thesis Won't Solve the Gene Problem Introduction Species as Individuals: The Two Main Arguments Gene-Lineages as Individuals: Rosenberg's Argumentation Assessing the GAI-Thesis 4.1. Metaphysics: What biology tells us about lineages4.2. Epistemology: How biologists individuate the parts of genomes Metaphysics: What biology tells us about lineages Epistemology: How biologists individuate the parts of genomes What Do Gene Names Refer To? Why the GAI-thesis Won't Solve the Gene Problem
Molecular inference, multivariate morphometrics and ecological assessment are applied in concert to delimit species in the Russula clavipes complex

Species of Russula subsect. Xerampelinae are notoriously difficult to identify and name and have not been subject to molecular study. A group of species, referred to here as the R. clavipes complex, growing in association with Salix, Betula and Populus as well as coniferous tree species from temperate to arctic and alpine habitats, were examined. Analyses of the nuc rDNA internal transcribed spacer (ITS) region and a numerical analysis of morphological characters were used. The R. clavipes complex is a monophyletic group within Russula subsect. Xerampelinae, according to molecular results. The complex includes three species: R. nuoljae is a phylogenetically and morphologically well-supported species while the other two, R. clavipes and R. pascua, are similar based on ITS data and morphology but separate based on their ecology. Russula pseudoolivascens is conspecific with R. clavipes. Several combinations of characters traditionally used in the taxonomy of R. subsect. Xerampelinae are inappropriate for species delimitation in this group and the adequacy of the ITS for species identification in this group is discussed. Detailed microscopic observations on the type collection of R. nuoljae are presented and illustrated, along with a key to the European members of R. subsect. Xerampelinae.
TGFβ superfamily signals are required for morphogenesis of the kidney mesenchyme progenitor population

The TGFβ superfamily plays diverse and essential roles in kidney development. Gdf11 and Bmp4 are essential for outgrowth and positioning of the ureteric bud, the inducer of metanephric mesenchyme. During nephrogenesis, Bmp7 is required for renewal of the mesenchyme progenitor population. Additionally, in vitro studies demonstrate inhibitory effects of BMPs and TGFβs on collecting duct branching and growth. Here, we explore the predicted models of TGFβ superfamily function by cell-specific inactivation of Smad4, a key mediator of TGFβ signaling. Using a HoxB7cre transgene expressed in ureteric bud and collecting duct, we find that development of the collecting duct is Smad4 independent. By contrast, removal of Smad4 in nephrogenic mesenchyme using the Bmp7cre/+ allele leads to disorganization of the nephrogenic mesenchyme and impairment of mesenchyme induction. Smad4-deficient metanephric mesenchyme does not display defects in inducibility in LiCl or spinal cord induction assays. However, in situ hybridization and lineage analysis of Smad4 null mesenchyme cells at E11.5 show that the nephrogenic mesenchyme does not aggregate tightly around the ureteric bud tips, but remains loosely associated, embedded within a population of cells expressing markers of both nephrogenic mesenchyme and peripheral stroma. We conclude that the failure of recruitment of nephrogenic mesenchyme leaves a primitive population of mesenchyme at the periphery of the kidney. This population is gradually depleted, and by E16.5 the periphery is composed of cells of stromal phenotype. This study uncovers a novel role for TGFβ superfamily signaling in the recruitment and/or organization of the nephrogenic mesenchyme at early time-points of kidney development. Additionally, we present conclusive genetic lineage mapping of the collecting duct and nephrogenic mesenchyme.
Source code transformations for efficient SIMD code generation

Despite the effort inverted the last years in commercial compilers to generate efficient SIMD instructions based code sequences from conventional sequential programs, the small numbers of compilers that can automatically use these instructions achieve in most cases unsatisfactory results. This work shows how exposing register level reuse in source codes helps vectorizing compilers as ICC to generate efficient SIMD code that exploits vectorial register reuse. To this end we use reverse-engineering to know the limitations of ICC compiler. We compare performance of compiler generated code to performance of hand-optimized assembly-written numerical libraries achieving around the 72% performance of MKL for example.
Alkylamino derivatives of N-benzylpyrazine-2-carboxamide: synthesis and antimycobacterial evaluation

A series of alkylamino derivatives of N-benzylpyrazine-2-carboxamide was designed, synthesized and assayed in vitro for their antimycobacterial, antibacterial, antifungal as well as antiviral activities. Final structures were prepared from 6-chloro (1), 5-chloro (2) or 3-chloro (3) derivatives of N-benzylpyrazine-2-carboxamide by nucleophilic substitution of chlorine with n-alkylamines in the range from butylamine to octylamine (labelled a–e). Series 1a–e and 2a–e exerted higher activity against Mycobacterium tuberculosis H37Rv compared to the corresponding pattern compounds and the reference compound pyrazinamide. The most active derivatives reached an activity MIC = 4.6–10 μM (M. tbc H37Rv). More importantly, activity was also observed against other tested mycobacterial strains (including drug-resistant strains). Substitution of 3-chlorine was disadvantageous and led to completely inactive compounds 3a–e. Some compounds showed activity against Gram-positive bacterial strains (including MRSA) or influenza virus, but no antifungal activity was observed.
Relationships Among Caregiver Factors and Quality of Life in Care Recipients with Irreversible Dementia

Using Lawton's (1983) model of quality of life (QoL) in older adults as a guiding framework, the central purpose of this ongoing longitudinal, prospective study is to examine predictors of QoL outcomes in persons with irreversible dementia as they move through the disease stages. From an initial sample of 96 caregiver/care recipient pairs, 73 (N = 146) pairs remain at the 18-month data collection point. Changes in care recipient outcomes from baseline to the 18-month assessment include significant declines in mental status, productive behaviors, and functional ability, with a statistically significant improvement in depression. Controlling for 12-month mental ability, caregiver factors at 12 months predicting care recipient QoL outcomes at 18 months include psychologic well being predicted by the quality of the relationship with the caregiver and activity participation. Depression was predicted by activity participation as well. Care recipient functional ability was predicted by activity participation and caregiver role stress (disruption to routines and social functioning). Two of the three aspects of care recipient productive behaviors were predicted by caregiver factors, with quality of the relationship predicting problem solving and caregiver role stress (negative attitudes toward care recipient) and total social contacts predicting care recipient social behaviors in the expected direction. Lawton's QoL model was supported by this analysis, with a total explained variance of 32% for three (psychologic well being, productive behaviors, functional ability) of the five (physical impairment and perceived personal control not included) components of care recipient QoL outcomes.
What determines self-employment? A comparative study

This article consists of a comparative study of the incidence of self-employment (SE) between Greece, which has the highest rate of SE in the European Union and the United Kingdom, which has amongst the lowest. Data from the Greek and the UK Labour Force Surveys are used in order to assess how personal attributes of an individual have an impact on the incidence of SE. It is found that common patterns exist between these two countries. In particular, it is found that for both countries, males have greater odds of being self-employed than females, older people have greater odds than younger, individuals employed in the primary and tertiary sectors have greater odds than the ones employed in the secondary, and that individuals with primary or secondary education have greater odds of being self-employed than individuals holding higher degrees. The incidence of SE is also found to differ according to the occupation of the individual. On the other hand, the findings indicate that individuals, residing in London, have greater odds of being self-employed than individuals working outside UK's capital, whereas in Greece the pattern is reversed.
Male and female involvement in the birth and child-rearing process.

AIMS AND OBJECTIVES To know the male involvement during pregnancy and childbirth, with special attention to their participation in public services of perinatal health and the impact that this participation has on their subsequent involvement in child-rearing, to compare the male and female involvement in child-rearing and to identify the factors associated with a greater male involvement. BACKGROUND Most of the research on male involvement in birth and child-rearing comes from Anglo-Saxon and Scandinavian countries. These studies show a lower involvement of men in relation to women, even in countries with instruments to promote gender shared responsibility. The Spanish Ministry of Health has developed strategies to improve the male involvement in the public services of perinatal health to advance in gender equality. This is a suitable context to contribute to the lack of information about fatherhood and the gender inequalities in the Spanish context. DESIGN Transversal design. METHODS A questionnaire was administered to 150 fathers and 157 mothers residing in Granada, with at least one biological child aged 2 months to 3 years. RESULTS A minority of the men attended the childbirth education whereas most of them attended pregnancy check-ups and were present at birth. Women spent more time with their children and took charge of tasks of child-rearing to a larger extent. The profile of an involved father is a man with a higher level of education, not married, his partner has a full-time employment, born in Spain and attended to the childbirth education classes. CONCLUSION This study shows gender inequalities in the reproductive field beyond the biological conditions. RELEVANCE TO CLINICAL PRACTICE The challenge of the health services is to promote social change and identify areas for improvement to include the father figure in public services of perinatal health.
Human performance estimating with analogy and regression models: an empirical validation

Most cost estimation models seem to be validated without testing human performance and using data sets from custom software projects where the software typically is sized in lines of code (SLOC) or function points. From a practitioner's point of view this research seems not to address some important aspects of IT projects that we observe: estimating in an industrial environment is performed by people, not models; COTS projects are increasing their market share replacing traditional custom software projects; and industrial projects use a large variety of metrics to size the project deliverables and estimate the costs. Estimation by analogy tools like ANGEL and multiple regression analysis provide the necessary flexibility in terms of choice of input parameters. We describe an experiment to evaluate human performance where the subjects were aided by analogy and regression tools respectively. 68 partners and managers in Andersen Consulting estimated 48 different COTS projects. The results in terms of MMRE indicate that users benefit from both tools, however more from regression models than from analogy models as ANGEL. Furthermore, the performance of the ANGEL tool itself is not superior to the performance of the regression model. This result is contradictory to previous studies that claim that ANGEL outperforms multiple regression.
Mouse muscle denervation increases expression of an α7 nicotinic receptor with unusual pharmacology

Neuronal nicotinic α7 subunits have been found in chick and rat skeletal muscle during development and denervation. In the present study, reverse transcriptase‐polymerase chain reaction was used to detect α7 subunit mRNA in denervated mouse muscle. To determine whether the α7 subunit forms functional nicotinic acetylcholine receptors (nAChRs) in muscle, choline was used to induce a membrane depolarization because choline has been considered a specific agonist of α7‐containing (α7*) nAChRs. We found, however, that choline (3–10 mm) also weakly activates muscle nAChRs. After inhibiting muscle nAChRs with a specific muscle nAChR inhibitor, α‐conotoxin GI (αCTxGI), choline was used to activate the α7* nAChRs on muscle selectively. Four weeks after denervation, rapid application of choline (10 mm) elicited a substantial depolarization in the presence of αCTxGI (0.1 µm). This component of the depolarization was never present in denervated muscles obtained from mutant mice lacking the α7 subunit (i.e. α7‐null mice). The depolarization component that is resistant to αCTxGI was antagonized by pancuronium (3–10 µm) and by a 4‐oxystilbene derivative (F3, 0.1–0.5 µm) at concentrations considered highly specific for α7* nAChRs. Another selective α7 antagonist, methyllycaconitine (0.05–5 µm), did not strongly inhibit this choline‐induced depolarization. Furthermore, the choline‐sensitive nAChRs showed little desensitization over 10 s of application with choline (10–30 mm). These results indicate that functional α7* nAChRs are significantly present on denervated muscle, and that these receptors display unusual functional and pharmacological characteristics.