Miracle-dz/UniFAR-FTUs huggingface dataset:
Co‐ordinated regulation of the extracytoplasmic stress factor, sigmaE, with other Escherichia coli sigma factors by (p)ppGpp and DksA may be achieved by specific regulation of individual holoenzymes

The E. coli alternative sigma factor, σE, transcribes genes required to maintain the cell envelope and is activated by conditions that destabilize the envelope. σE is also activated during entry into stationary phase in the absence of envelope stress by the alarmone (p)ppGpp. (p)ppGpp controls a large regulatory network, reducing expression of σ70‐dependent genes required for rapid growth and activating σ70‐dependent and alternative sigma factor‐dependent genes required for stress survival. The DksA protein often potentiates the effects of (p)ppGpp. Here we examine regulation of σE by (p)ppGpp and DksA following starvation for nutrients. We find that (p)ppGpp is required for increased σE activity under all conditions tested, but the requirement for DksA varies. DksA is required during amino acid starvation, but is dispensable during phosphate starvation. In contrast, regulation of σS is (p)ppGpp‐ and DksA‐dependent under all conditions tested, while negative regulation of σ70 is DksA‐ but not (p)ppGpp‐dependent during phosphate starvation, yet requires both factors during amino acid starvation. These findings suggest that the mechanism of transcriptional regulation by (p)ppGpp and/or DksA cannot yet be explained by a unifying model and is specific to individual promoters, individual holoenzymes, and specific starvation conditions.
The month of birth effect in multiple sclerosis: systematic review, meta-analysis and effect of latitude

Background Month of birth has previously been described as a risk factor for multiple sclerosis (MS). This has been hypothesised to be related to maternal vitamin D levels during pregnancy, although conclusive evidence to support this is lacking. To date, no large studies of latitudinal variation in the month of birth effect have been performed to advance this hypothesis. Methods Previously published data on month of birth from 151 978 MS patients were compared to expected birth rates. A linear regression model was used to assess the relationship between latitude and observed:expected birth ratio of MS patients for each month. Results Analysis of all reported data demonstrated a significant excess of MS risk in those born in April (observed:expected 1.05, p=0.05) and reduction in risk in those born in October (0.95, p=0.04) and November (0.92 p=0.01). A conservative analysis of 78 488 patients revealed an excess MS risk in those born in April (1.07, p=0.002) and May (1.11, p=0.0006), and a reduced risk in those born in October (ratio 0.94, p=0.004) and November (0.88, p=0.0002). A significant relationship between latitude and observed:expected ratio was demonstrated in December, and borderline significant relationships in May and August. Conclusions Month of birth has a significant effect on subsequent MS risk. This is likely to be due to ultraviolet light exposure and maternal vitamin D levels, as demonstrated by the relationship between risk and latitude.
Potential for Smoke-Free Policies in Social Venues to Prevent Smoking Uptake and Reduce Relapse: A Qualitative Study

The purpose of this article is to better understand the utility of smoking in pubs/bars and nightclubs and explore perceptions of how smoke-free policies might influence smoking behavior. Qualitative focus group methodology was used involving young social smokers and older regular smokers. Pubs/bars and nightclubs were valued as the few remaining indoor public places where people could relax and smoke. These venues were perceived to provide encouragement for smoking more cigarettes by increasing smoking rate and facilitating smoking relapse. For young social smokers, smoking provided an opportunity to be part of a “cool” in-group. Older regular smokers felt pubs/bars provided strong cues for smoking relapse. Smokers felt they would adapt to smoke-free policies and expected these policies to reduce their smoking or assist quitting. Smoke-free policies in pubs/bars and nightclubs may assist smokers to quit and make it less likely that young social smokers will progress to regular smoking.
GATA1 Function, a Paradigm for Transcription Factors in Hematopoiesis

TRANSCRIPTIONAL CONTROL OF HEMATOPOIESIS The development of mature blood cells of distinct lineages, from the hematopoietic stem cells (HSCs), involves a progressive restriction of differentiation potential and the establishment of lineage-specific gene expression profiles (Fig. 1). The establishment of these expression profiles relies on lineagespecific transcription factors to modulate the expression of their target genes. Therefore, hematopoiesis is an excellent model system to investigate how particular transcription factors influence the establishment of lineage-specific expression profiles and how their activity is regulated. In this review we focus on the present knowledge of the biological functions of the hematopoietic transcription factor GATA1. Many aspects of its function have been revealed since its first description in 1988. Yet many new questions have surfaced, and many old questions remain to be answered. Thus, GATA1 has been in the floodlight of modern biology as a paradigm for hematopoietic transcription factors in general and GATA factors in particular.
Photocurrent and Surface Photovoltage Spectroscopy Investigations of CdTe-Based Compounds

The potentiality of photocurrent (PC) and surface photovoltage spectroscopy (SPS) analyses in the determination of the band gap of CdTe-based ternary alloys was investigated. Both methods can detect band-to-band and defect state-to-band transitions. The role played by the surface states in both experimental methods has been studied since it may significantly alter the results. The below-band gap energy levels have also been detected by PC and SPS and the different information that can be obtained in the two cases has been discussed. The results obtained by PC and SPS have been compared in order to extract the contribution of the surface and bulk states.
Recursive estimation and time-series analysis

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Immunohistochemical detection of p53 in differentiated, poorly differentiated and undifferentiated carcinomas of the thyroid

In an attempt to find whether or not p53 immunoreactivity in the thyroid gland is restricted to undifferentiated carcinomas and to evaluate the putative prognostic usefulness of its detection, we investigated p53 immunoreactivity in a series of 14 benign thyroid lesions and 65 thyroid carcinomas (12 papillary; six minimally invasive follicular; four widely invasive follicular; 31 poorly differentiated and 12 undifferentiated tumours). Unequivocal nuclear immunostaining for p53 was observed in two widely invasive follicular carcinoma (20.0%), five poorly differentiated carcinomas (16.1%) and in 10 undifferentiated carcinomas (83.3%). The percentage of immunoreactive cells was much smaller in the former groups than in undifferentiated carcinomas. Despite a trend to a more aggressive behaviour of the p53 immunoreactive cases no significant differences in the outcome of patients with positive and negative tumours was found when the comparison was made within each category of carcinomas. We conclude that p53 immunoreactivity can be detected both in undifferentiated carcinomas and in some differentiated and poorly differentiated thyroid carcinomas. Larger series of cases are necessary to evaluate the prognostic usefulness of this finding.
Knowledge derivation and data mining strategies for probabilistic functional integrated networks

One of the fundamental goals of systems biology is the experimental verification of the interactome: the entire complement of molecular interactions occurring in the cell. Vast amounts of high-throughput data have been produced to aid this effort. However these data are incomplete and contain high levels of both false positives and false negatives. In order to combat these limitations in data quality, computational techniques have been developed to evaluate the datasets and integrate them in a systematic fashion using graph theory. The result is an integrated network which can be analysed using a variety of network analysis techniques to draw new inferences about biological questions and to guide laboratory experiments. Individual research groups are interested in specific biological problems and, consequently, network analyses are normally performed with regard to a specific question. However, the majority of existing data integration techniques are global and do not focus on specific areas of biology. Currently this issue is addressed by using known annotation data (such as that from the Gene Ontology) to produce process-specific subnetworks. However, this approach discards useful information and is of limited use in poorly annotated areas of the interactome. Therefore, there is a need for network integration techniques that produce process-specific networks without loss of data. The work described here addresses this requirement by extending one of the most powerful integration techniques, probabilistic functional integrated networks (PFINs), to incorporate a concept of biological relevance. Initially, the available functional data for the baker’s yeast Saccharomyces cerevisiae was evaluated to identify areas of bias and specificity which could be exploited during network integration. This information was used to develop an integration technique which emphasises interactions relevant to specific biological questions, using yeast ageing as an exemplar. The integration method improves performance during network-based protein functional prediction in relation to this process. Further, the process-relevant networks complement classical network integration techniques and significantly improve network analysis in a wide range of biological processes. The method developed has been used to produce novel predictions for 505 Gene Ontology biological processes. Of these predictions 41,610 are consistent with existing computational annotations, and 906 are consistent with known expert-curated annotations. The approach significantly reduces the hypothesis space for experimental validation of genes hypothesised to be involved in the oxidative stress response. Therefore, incorporation of biological relevance into network integration can significantly improve network analysis with regard to individual biological questions.
Cognitive Rest and School-Based Recommendations Following Pediatric Concussion

Objectives. (1) Assess pediatric primary care providers’ understanding of cognitive rest for concussion and (2) describe their concussion management practices. Methods. This study included (1) a survey of general pediatric providers and (2) an electronic medical record (EMR) review of children 5 to 18 years old treated for concussion from September 1, 2010, to May 31, 2011. The survey asked about treatment recommendations for concussion, and results were coded to identify cognitive rest recommendations. The EMR review included the following: injury details, medical evaluation, and recommendations for resuming school and sports/recreation. Results. In all, 89 of 201 providers responded to the survey, and 52 of the 84 clinicians who included comments about concussion management mentioned cognitive rest (62%, 95% confidence interval [CI] = 51%-72%). Of the 91 EMRs reviewed for patients’ first visits following the concussion, only 10 (11%, 95% CI = 6%-19%) included written cognitive rest recommendations. Conclusions. Although the majority of pediatric providers identified cognitive rest as important in pediatric concussion management, few provided written recommendations in the EMR.
Water-physical characteristics of a latosol under different management systems.

A expansao da agricultura no cerrado vem afetando prejudicialmente as propriedades fisicas do solo. Sendo agravado pelo manejo inapropriado e uso inadequado do solo, onde nao sao levadas em consideracao suas caracteristicas fisicas para implantacao do sistema de cultivo. Objetivou-se nesse trabalho observar o impacto da agricultura nos solos do sudoeste goiano, demonstrando os estagios de degradacao de solos sob diferentes condicoes de uso antropico. As areas estudadas localizam-se no Instituto Federal Goiano – Câmpus Rio Verde, GO. O solo da regiao foi classificado como Latossolo Vermelho distroferrico (LVdf). Foram avaliados o manejo de quatro areas distintas: cultivo de cana-de-acucar primeiro ano; plantio convencional de culturas anuais (soja/milho); ILPF (3 anos) e area de Cerrado permanente. Foram determinadas as curvas de velocidade de infiltracao (VI), velocidade de infiltracao basica (VIB), condutividade hidraulica (Kfs), densidade do solo (Ds), macroporosidade (Macro), microporosidade (Micro), porosidade total (PT), densidade de particulas (Dp). O sistema manejado com cana obteve as condicoes de solo favoraveis principalmente em relacao a Ds, Dp, PT e Macro de 0 a 20 cm e PT de 20 a 40 cm. O cerrado por manter as suas caracterizas do solo, apresentou o maior valor de VIB (56,89 cm h -1 ). Em medio prazo, o intenso sistema de preparo do solo mostrou-se mais correlacionado com a capacidade do solo de infiltracao do que o proprio processo de compactacao em si.
2 Implicit-Explicit Peer Methods Based on Extrapolation 2 . 1 Implicit Peer methods

In this paper we investigate a new class of implicit-explicit (IMEX) twostep methods of Peer type for systems of ordinary differential equations with both non-stiff and stiff parts included in the source term. An extrapolation approach based on already computed stage values is applied to construct IMEX methods with favourable stability properties. Optimised IMEX-Peer methods of order p = 2, 3, 4, are given as result of a search algorithm carefully designed to balance the size of the stability regions and the extrapolation errors. Numerical experiments and a comparison to other implicit-explicit methods are included.
The Mediating Role of Emotional State toward Pervasive Information System Acceptance

The present study proposes a new approach for the examination of the individual user’s acceptance of technology and Information Systems. In particular, it examines the mediating role of Emotional State toward the individual acceptance of Pervasive Information Systems. The proposed research model was tested with data collected through an exploratory experiment (n=33) using a mobile Augmented Reality application. The results confirm the appropriateness of the developed instrument, the research model and that Performance Expectancy is the strongest predictor of user adoption, mediated through the user’s Emotional State as formed while interacting with the system.
What employers look for when recruiting the unemployed and inactive: skills, characteristics and qualifications

This study examines the evidence relating to what employers are looking for when recruiting, and the extent to which government provision meets their needs, focusing on unemployed and inactive adults between 16 and state pension age (SPA). The study also explores whether there are differences in employers’ requirements by age. The review covers: What sort of characteristics, skills and qualifications do employers look for when recruiting employees? How important are qualifications to employers? Are employers more interested in soft skills/employability skills and if so, how do employers recognise soft skills in the interview process and afterwards? In addition to a summary, the report contains three chapters. The introductory chapter outlines the methodology and discusses definitions of age, learning and training, skills and qualifications, skills shortages and skills gaps, and occupational groups. Chapter two reviews the findings from the academic, policy and evaluation literature to identify the issues as they apply to younger or older people in the unemployed or inactive communities, and to other groups within this community where appropriate. Chapter three provides expert views of employers’ needs on recruitment, specifically the characteristics, skills and qualifications employers look for when recruiting and employers’ views of training. Findings indicate that: employers continue to face recruitment difficulties - one-fifth of reported vacancies could not be filled due to a lack of applicants with the necessary skills; overall, employers are less demanding of technical skills, considering them trainable, if candidates exhibit employability and soft skills, and positive attributes; amongst core characteristics employers look for are motivation and flexibility; qualifications do not appear to be important for a large number of employers and jobs, consistently ranking beneath characteristics and soft skills in recruitment frameworks; and age stereotypes persist about older and younger workers (and other inactive groups) and while they benefit some groups, they disadvantage others.
Dural Tears in Spine Surgery

&NA; Dural tears are among the most commonly seen complications in spine surgery. Most studies in the literature indicate that long‐term outcomes are not negatively affected, provided that the tears are diagnosed early and managed appropriately. Direct suture repair remains the preferred method for the management of durotomy caused by or found during surgery. However, recent literature reports encouraging results with sutureless repair. Understanding dural anatomy, dural healing, and cerebrospinal fluid dynamics is helpful in choosing among the available management options for dural tear.
Oxygen Sensing : Life and Death of a Cell Acute intermittent hypoxia activates myocardial cell survival signaling

Park A-M, Nagase H, Vinod Kumar S, Suzuki YJ. Acute intermittent hypoxia activates myocardial cell survival signaling. Am J Physiol Heart Circ Physiol 292: H751–H757, 2007. First published November 10, 2006; doi:10.1152/ajpheart.01016. 2006. —Intermittent hypoxia (IH) with repeated episodes of hypoxia-normoxia cycle has been shown to exert preconditioning-like cardioprotective effects. To understand the mechanism of these events, we investigated the changes in cardiac gene expression in response to acute IH. Mice were subjected to five cycles of 2 min of 10% O2 plus 2 min of 21% O2. RNA was isolated, and gene array analysis was performed. Results show that the expression of antiapoptotic genes, such as Bcl-2 and Bcl-xL, were increased after acute IH. GATA-4 regulates transcription of these genes, and, consistently, GATA-4 activity was increased by acute IH. Although the phosphorylation of GATA-4 has been shown to regulate its activity, no changes in GATA-4 phosphorylation status by acute IH were noted. Gene transcription of gata4 was increased by acute IH, and this might be responsible for the enhanced GATA activity. To understand the mechanism of acute IH activation of gata4 gene transcription, we identified a promoter region of the mouse gata4 gene that is 1,000 bp immediately upstream from the transcriptional start site. In cardiac muscle cells, truncation of 1,000 to 250 bp did not alter the transcriptional activity, suggesting that the proximal 250-bp region contains important transcriptional regulatory sites. We further found that acute IH activates factors which bind to the proximal 100-bp region. Thus acute IH activates not yet identified factors that bind to the proximal 100-bp region of the gata4 promoter and, in turn, increases gata4 gene transcription, leading to enhanced expression of Bcl-2 and Bcl-xL.
Vasoactive mediators (VEGF and TNF‐α) in patients with malignant and tuberculous pleural effusions

Objective: Vascular endothelial growth factor (VEGF) is a potent endothelial cell‐specific mitogen that promotes angiogenesis, vascular hyperpermeability, and vasodilatation by autocrine mechanisms involving nitric oxide (NO). This study was undertaken to determine the potential role of VEGF in the pathogenesis of pleural effusions, and its relationship with tumour necrosis factor (TNF)‐α and NO in the pleural fluid and serum of patients with tuberculous and malignant pleural effusions.
Thermal stability of β-lactoglobulins A and B: effect of SDS, urea, cysteine and N-ethylmaleimide

Fourier transform infrared spectroscopy (FTIR) and differential scanning calorimetry (DSC) were used to monitor changes in the secondary structure and thermal stability of β-lactoglobulin A and B in the presence of sodium dodecyl sulphate (SDS), N-ethylmaleimide (NEM), urea and cysteine. An increase in the thermal stabilities of both proteins was noted in the presence of 10 mM-SDS. In the presence of 50 mM-SDS, there was extensive denaturation of both variants. In general, the β-strand/β-sheet regions in the secondary structure of both variants were very susceptible to denaturation by SDS and cysteine, suggesting that these regions may be held by hydrophobic and disulphide bonds. At ambient temperature and physiological pH, a notable difference was observed in the 1636 and 1627 cm−1 regions of the FTIR spectra of the two β-lg variants. The results suggest possible differences in the nature of the β-sheet/β-strand distribution/content of the two proteins. Urea and NEM at a concentration of 50 mM, had little effect on the secondary structure and denaturation of both variants. New findings are presented which further indicate that although the β-lg B variant showed greater thermal stability than the A variant in all the cases studied, its denaturation temperature and secondary structure were affected to a greater extent by the protein perturbants than β-lg A.
Novel Macula-Like Virus Identified in Bombyx mori Cultured Cells

ABSTRACT We identified a novel, 6,513-bp-long RNA, termed Bombyx mori macula-like latent virus (BmMLV) RNA, which abundantly expressed in B. mori cultured BmN cells. BmMLV RNA potentially encodes two proteins, putative RNA replicase and coat protein, which share structural features and sequence similarities with those of a plant RNA virus, the genus Maculavirus. Northern blot analysis showed that two transcripts were expressed in BmN cells: a 6.5-kb-long RNA, which contains both putative RNA replicase and coat protein genes, and a 1.2-kb-long RNA, which contains only a coat protein gene. Southern blot analysis showed that BmMLV RNA is not carried by the B. mori genome. RT-PCR analysis also revealed the presence of BmMLV RNA in several B. mori cell lines other than BmN cells, suggesting that BmMLV RNA latently exists in B. mori cultured cells. Infection studies showed that BmMLV virions were able to infect BmMLV-negative Spodoptera frugiperda Sf-9 cells and B. mori larvae. Electron microscopy and Northern blot analysis of a purified BmMLV revealed that isometric virions appear to be 28 to 30 nm in diameter and contain a 6.5-kb genomic RNA. These results showed that BmMLV is a novel macula-like virus infectious to and replicable in B. mori-derived cells.