Miracle-dz/UniFAR-FTUs huggingface dataset:
A Salmonella typhimurium genetic locus which confers copper tolerance on copper-sensitive mutants of Escherichia coli

Three distinct clones from a Salmonella typhimurium genomic library were identified which suppressed the copper-sensitive (Cu(s)) phenotype of cutF mutants of Escherichia coli. One of these clones, pCUTFS2, also increased the copper tolerance of cutA, -C, and -E mutants, as well as that of a lipoprotein diacylglyceryl transferase (lgt) mutant of E. coli. Characterization of pCUTFS2 revealed that the genes responsible for suppression of copper sensitivity (scs) reside on a 4.36-kb DNA fragment located near 25.4 min on the S. typhimurium genome. Sequence analysis of this fragment revealed four open reading frames (ORF120, ORF627, ORF207, and ORF168) that were organized into two operons. One operon consisted of a single gene, scsA (ORF120), whereas the other operon contained the genes scsB (ORF627), scsC (ORF207), and scsD (ORF168). Comparison of the deduced amino acid sequences of the predicted gene products showed that ScsB, ScsC, and ScsD have significant homology to thiol-disulfide interchange proteins (CutA2, DipZ, CycZ, and DsbD) from E. coli and Haemophilus influenzae, to an outer membrane protein (Com1) from Coxiella burnetii, and to thioredoxin and thioredoxin-like proteins, respectively. The two operons were subcloned on compatible plasmids, and complementation analyses indicated that all four proteins are required for the increased copper tolerance of E. coli mutants. In addition, the scs locus also restored lipoprotein modification in lgt mutants of E. coli. Sequence analyses of the S. typhimurium scs genes and adjacent DNAs revealed that the scs locus is flanked by genes with high homology to the cbpA (predicted curved DNA-binding protein) and agp (acid glucose phosphatase) genes of E. coli located at 22.90 min (1,062.07 kb) and 22.95 min (1,064.8 kb) of the E. coli chromosome, respectively. However, examination of the E. coli chromosome revealed that these genes are absent at this locus and no evidence has thus been obtained for the occurrence of the scs locus elsewhere on the genome.
Indirect lead exposure among children of radiator repair workers.

BACKGROUND Secondary exposure to lead has been identified as a public health problem since the late 1940s; we investigate the risk of lead exposure among families of radiator repair workers. METHODS A sample of the wives and children, aged 6 months to 6 years (exposed children) (n = 19), of radiator repair workers and a sample of children whose parents were not occupationally exposed to lead (non-exposed children) (n = 29) were matched for age and residence; their geometric mean blood lead levels are compared. Blood samples were obtained by the finger stick method and environmental dust samples by the wipe method; both were analyzed using a portable anodic stripping voltameter. RESULTS Dust lead levels were significantly higher in the houses of exposed children (143.8 vs. 3.9 microg/g; P < 0.01). In crude analyses, the highest lead levels were observed among children whose fathers worked in home-based workshops (22.4 microg/dl)(n = 6). Children whose fathers worked in an external workshop (n = 13) also had high levels (14.2 microg/dl) (P < 0.01), while blood lead levels in non-exposed children were significantly lower (5.6 microg/dl)(P < 0.01). The observed differences remained significant after adjustment for age and gender. CONCLUSIONS This study confirms that children of radiator repair workers are at increased risk of lead exposure and public health interventions are needed to protect them.
The Rhizobium leguminosarum tonB gene is required for the uptake of siderophore and haem as sources of iron

In the N2‐fixing bacterium Rhizobium leguminosarum, mutations in a homologue of tonB (tonBRl) block the import of vicibactin and haem as iron sources in free‐living bacteria. TonBRl mutants were normal for growth with ferric dicitrate and slightly reduced for growth with haemoglobin as sole iron sources. The deduced TonBRl product is larger than that of (for example) Escherichia coli, on account of an extended N‐terminal domain. Transcription of tonBRl was enhanced in low‐Fe growth conditions; this was not controlled by Fur, nor RpoI, an Fe‐regulated extracytoplasmic σ factor. Upstream of tonBRl and transcribed divergently is an operon, hmuPSTUV, whose products are homologous to ABC transporters involved in haem uptake in pathogenic bacteria. Expression of hmuPSTUV was enhanced in low‐Fe conditions, and hmu mutants show slightly diminished growth on haem as sole Fe source, suggesting that there is more than one system for the uptake of this molecule. hmuPSTUV expression appears to be from three closely linked promoters. Downstream of hmuPSTUV, a gene that may encode an extracytoplasmic σ factor was identified, but this gene, rpoZ, did not affect the transcription of tonBRl or hmuPSTUV. Mutations in tonBRl, hmu genes and rpoZ did not affect symbiotic N2 fixation in peas.
Detecting communities from tripartite networks

Online social media such as delicious and digg are represented as tripartite networks whose vertices are users, tags, and resources. Detecting communities from such tripartite networks is practically important. Modularity is often used as the criteria for evaluating the goodness of network divisions into communities. For tripartite networks, Neubauer defines a tripartite modularity which extends Murata's bipartite modularity. However, Neubauer's tripartite modularity still uses projections and it will lose information that original tripartite networks have. This paper proposes new tripartite modularity for tripartite networks that do not use projections. Experimental results show that better community structures can be detected by optimizing our tripartite modularity.
Survey mode effects on income inequality measurement Supplementary Appendix

This appendix includes material supplementing the manuscript “Survey mode effects on income inequality measurement. ” It includes background information in Section 1, an extended description of the methods used in Section 2 as well as robustness checks and additional results in Section 3. JEL Classification: C14, C21, C81, C83, D31
The role of comprehensive cancer centers in survivorship care

establishing theneeds of cancer survivors and survivor groups, including desi gning appropriate and effective programs and organizing themin an efficient and cost-effective way, is a vital goal. In this supplement, several aspects of survivorship care have been dis-cussed by European and American experts, paying specific attention to medical and social problems such as the long-termtoxic effects of cancer treatments, the education of stakeholder s, rehabilitation programs, and employment challenges. Theseexperts have shown the emergence of a complex scenario with mult ifaceted aspects, which will require an integrated and mul-tidisciplinary approach to care and research.
Performance analysis of graphene based transistors: Modelling and simulation

Graphene Nanoribbon FETs and Graphene Nanoribbon Tunnel FETs channel current models are simulated in MATLAB followed by implementation in PSpice as equivalent circuit models. Several characteristics of these transistors are compared to those of MOSFETs, keeping identical gate length of 20 nm for performance analysis. Based on the simulation results, it is found that graphene based transistors exhibit superior performance compared to MOSFETs.
Scanning electron microscopic observations of the vascular structure of vertebral end‐plates in rabbits

We used scanning electron microscopy to examine the microcirculation in the vertebral end‐plates of rabbits. The arteriola arborizes and swells at the end‐plate and then coils to make a microvessel loop. This loop is the structure we refer to as a vascular bud. We suggest that these loop structures of the capillaries play a major role in the nutrition of the intervertebral discs.
Emergence de la maladie de Chagas en Suisse: contexte et défis de santé publique

La maladie de Chagas est l'une des maladies tropicales les plus negligees. Cette infection parasitaire chronique, endemique en Amerique latine, affecte 8-10 millions de personnes. La fin du XXeme siecle a vu la migration de plus de 15 millions de personnes a risque vers l'Europe, l'Amerique du Nord et l'Australie, transformant la maladie de Chagas en un probleme de sante global. La Suisse, et Geneve en particulier, abrite une importante communaute de migrants latinoamericains. Cette these presente les investigations conduites a Geneve qui illustrent les dimensions epidemiologiques et sociales de cette emergence et identifie le double fardeau de sante lie au phenomene de transition epidemiologique en cours dans les pays d'origine. Les donnees locales sont discutees en regard du contexte europeen et illustrent les nouveaux defis de sante publique lies a l'hypermobilite des migrants.
The septal complex of the telencephalon of the lizard Podarcis hispanica. I. chemoarchitectonical organization

In this paper we study the septal complex architecture in the lizard Podarcis hispanica (Lacertidae). Histochemical and immunohistochemical techniques were used to define the distribution of zinc (Timm stain), acetyl cholinesterase (AChase), gamma‐aminobutyric acid (GABA), tyrosine hydroxylase (TH), dopamine (DA), serotonin (5‐HT), and two neuropeptides: leu‐enkephalin (L‐ENK) and substance P (SP). These reactions delineate a coherent map of nine septal nuclei that are named with a topographical nomenclature: anterior, lateral, ventromedial, medial, dorsolateral, ventrolateral, and dorsal septal nuclei, nucleus septalis impar, and nucleus of the posterior pallial commissure.
Lack of common NOD2 variants in Japanese patients with Crohn's disease.

BACKGROUND & AIMS Previous studies have linked Crohn's disease (CD) to the pericentromeric region of chromosome 16 (IBD1). Three independent studies of Western populations have recently shown that 3 variants of NOD2, a gene located at 16q12, are associated with susceptibility to CD. Here, we have evaluated the 3 NOD2 variants in Japanese patients to determine whether the gene is also associated with susceptibility to CD in a non-Western population. METHODS Blood samples were obtained from 350 patients with CD, 272 patients with ulcerative colitis, and 292 healthy controls at 3 hospitals in Japan. DNA was sequenced in the region of the 3 NOD2 variants (C2104T in exon 4, G2722C in exon 8, and 3020insC in exon 11) by genomic polymerase chain reaction followed by direct sequencing. RESULTS Among the subjects in our 3 study groups, including patients with CD, patients with ulcerative colitis, and healthy controls, none had common NOD2 variants that have been associated with CD in white patients. CONCLUSIONS These results indicate that genetic variation, which may predispose some human populations to CD, may not be present in other populations and specifically that common variants in NOD2 found in white patients with CD are not associated with CD in the Japanese population.
Mechanisms of Spatial Attention: The Relation of Macrostructure to Microstructure in Parietal Neglect

Parietal-damaged patients respond abnormally slowly to targets presented in the affected hemifield when preceded by cues in the intact hemifield. This inability to disengage attention from the ipsilesional field to reengage it in the contralesional field has been interpreted as evidence for a distinct disengage mechanism, localized in parietal cortex. We present a computational model that accounts for normal attentional effects by interactivity and competition among representations of different locations in space, without a dedicated disengage mechanism. We show that when the model is lesioned, it produces the disengage deficit shown by parietal-damaged patients. This suggests that the deficit observed in such patients can be understood as an emergent property of interactions among the remaining parts of the system, and need not imply the existence of a dedicated disengage mechanism in the normal brain.
neurobiology of cognitive control in successful cocaine abstinence olm

Introduction: Extensive evidence demonstrates that current cocaine abusers show hypoactivity in anterior cingulate and dorsolateral prefrontal cortex and respond poorly relative to drug-naïve controls on tests of executive function. Relatively little is known about the cognitive sequelae of long-term abstinence in cocaine addicts. Methods: Here, we use a GO–NOGO task in which successful performance necessitated withholding a prepotent response to assay cognitive control in shortand long-term abstinent cocaine users (1–5 weeks and 40–102 weeks, respectively). Results: We report significantly greater activity in prefrontal, cingulate, cerebellar and inferior frontal gyrii in abstinent cocaine users for both successful response inhibitions and errors of commission. Moreover, this relative hyperactivity was present in both abstinent groups, which, in the presence of comparable behavioral performance, suggests a functional compensation. Conclusions: Differences between the shortand long-abstinence groups in the patterns of functional recruitment suggest different cognitive control demands at different stages in abstinence. Short-term abstinence showed increased inhibition-related dorsolateral and inferior frontal activity indicative of the need for increased inhibitory control while long-term abstinence showed increased error-related ACC activity indicative of heightened behavioral monitoring. The results suggest that the integrity of prefrontal systems that underlie cognitive control functions may be an important characteristic of successful longterm abstinence. © 2011 Elsevier Ireland Ltd. All rights reserved.
Contingent Capital Structure

This paper studies the optimal financing contract of a bank with risk-shifting incentives and private information, in an environment with macroeconomic uncertainty. Leverage mitigates adverse selection problems owing to debt information-insensitivity, but leads to excessive risk-taking. I show that the optimal leverage is procyclical in the laissez-faire equilibrium, and contingent convertible (CoCo) bonds emerge as part of the implementation of the optimal contingent capital structure. However, the equilibrium entails excessive leverage and risk-taking, due to a bank’s private incentives to minimise market mispricing of its securities. It is socially optimal to impose countercyclical capital requirements, implemented by CoCo bonds in addition to straight debt and equity.
Quo Vadis: Polarized Membrane Recycling in Motility and Phagocytosis

The colloquial expression “let's go out to eat” implies a relationship between movement and ingestion that can also be found at the cellular level. Phagocytic cells, such as neutrophils and Dictyostelium discoideum amoebae, have a marked capacity to move towards their intended meals by detecting
Utility of ampicillin-sulbactam for empiric treatment of ventilator-associated pneumonia in a trauma population.

BACKGROUND Ampicillin-sulbactam is guideline-recommended treatment for early-onset ventilator-associated pneumonia (VAP). However, intensive care unit clinicians are encountering increasing resistance to ampicillin-sulbactam. We sought to analyze the time period for early-onset VAP in our trauma population by using daily evaluation of resistance to ampicillin-sulbactam. METHODS A retrospective cohort study was completed on all mechanically ventilated trauma patients admitted to a rural level-1 trauma center from January 2003 to December 2008 who were diagnosed with VAP. Daily bacterial resistance to ampicillin-sulbactam > 15% was defined as the threshold for early empiric antibiotic failure for the first episode of VAP. A univariate analysis of risk factors for multi-drug resistant pathogens (MDRPs) and comorbidities was completed to assess for predisposing factors for ampicillin-sulbactam resistance. RESULTS One hundred sixty-three pathogens were identified in 121 trauma patients diagnosed with VAP. Of these isolates, 71% were gram-negative, 28% were gram-positive, and 1% was fungal. Methicillin-susceptible Staphylococcus aureus (23.9%), H aemophilus influenzae (20.9%), and Pseudomonas aeruginosa (11.7%) were the most common infecting organisms. Daily ampicillin-sulbactam resistance was 40%, 26%, 32%, 43%, 50%, and 60% on days 3 to 7 and ≥ 8 days, respectively. Only the presence of MDRP risk factors (89% vs. 65%, p < 0.01) and hospital LOS (36.8 [22.8-49.0] vs. 25.7 days [19.0-32.5], p < 0.01) was different between ampicillin- sulbactam resistant and ampicillin-sulbactam susceptible VAP groups. On univariate analysis, hospital length of stay >4 days and antibiotic use within 90 days were associated with ampicillin-sulbactam resistant VAP (p < 0.01). CONCLUSIONS Ampicillin-sulbactam is not an effective empiric therapy for early-onset VAP in our rural trauma population. The utility of ampicillin-sulbactam should be reviewed at other institutions to assess for appropriate empiricism.
On the Use of Age-Adjusted Mortality Rates in Studies of Income Inequality and Population Health

In our recent article published in the June 2001 issue of this journal (Mellor and Milyo 2001b), we demonstrate that the statistical association between either country-level or state-level inequality and population health is not robust to minor and reasonable changes in the model specification or the time period examined.1 Two excellent commentaries appear along with our article. James S. House (2001) accepts our evidence and concludes that the income inequality hypothesis has proven a dry well; he urges public health researchers to move on to more promising areas of inquiry within the field of social determinants of health. In
Characterization of exponential divergence of the Kalman filter for time-varying systems

This paper studies semistability of the recursive Kalman filter in the context of linear time-varying (LTV), possibly nondetectable systems with incorrect noise information. Semistability is a key property, as it ensures that the actual estimation error does not diverge exponentially. We explore structural properties of the filter to obtain a necessary and sufficient condition for semistability. The condition does not involve limiting gains nor the solution of Riccati equations, as they can be difficult to obtain numerically and may not exist. In the linear time invariant scenario we obtain algebraic, easy to test conditions for semistability and stability, which complement results available in the context of detectable systems. Illustrative examples are included.
The effects of different levels of sodium caseinate on rumen fermentation pattern, digestibility and microbial protein synthesis of Holstein dairy cows

This study was conducted to investigate the effects of different levels of peptide supplementation on rumen fermentation pattern, digestibility and microbial protein synthesis. Three rumen-cannulated Holstein dairy cows were used in a 3 × 3 Latin square experiment within 21 days period. The ruminal infusion of sodium caseinate (CN) was 0 (control), 50 and 100 g/d. Dry matter intake, milk yield and composition , total tract apparent digestibility of nutrient, rumen parameters and purine derivatives in urine of cows were measured. Results showed that dairy cows received sodium caseinate, had significantly increased microbial protein synthesis, milk fat yield, acetate and branched chain fatty acids concentrations in rumen fluid and fiber digestibility compared with the control treatment (P < 0.05). CN significantly affected the concentrations of rumen ammonia nitrogen (NH3-N), rumen peptide nitrogen (Pep-N) and the ratio of rumen ammonia nitrogen/ rumen peptide nitrogen (P < 0.05) and consequently blood urea nitrogen, milk urea nitrogen and urinary urea nitrogen concentrations. However digestibility of dry matter and crude protein did not differ among treatments. In conclusion, if the optimum level of NH3-N/Pep-N was the best compromise among the need for rumen fermentation, microbial protein synthesis and nitrogen excretion through urine in animal, the recommended level from this study would be 0.86 in rumen fluid.
Perinatal Environment and Endometriosis

Background/Aims: Perinatal environmental exposure may affect fetal development and reprogram the developing organism for adult-onset disease. In this case-control study, we aimed at assessing this pathogenetic model in endometriosis. Methods: Consecutive patients with a first laparoscopic diagnosis of endometriosis were selected as cases. Controls were women who underwent laparoscopy during the same study period, but who were found to be free of the disease. Selected women and their mothers were interviewed. Results: Ninety-one women with endometriosis and 82 controls were selected. Handedness, a variable believed to be determined prenatally by hormonal environment in utero significantly differed between the study groups. Women with the disease were less likely to be left- or mixed-handed (adjusted OR: 0.24, 95% CI: 0.08–0.71). In contrast, we failed to detect any association with birth order, maternal age, smoking, nausea, weight gain, prematurity, birth weight and breast-feeding. Conclusions: Our results generally do not support the view that in utero exposure may play a major role in the pathogenesis of endometriosis. The association with handedness, however, is intriguing in this regard and deserves further investigation.
REOVIRUS INDUCTION OF MHC CLASS II ANTIGEN IN RAT THYROID CELLS

We have previously demonstrated that cultured rat thyroid cells do not exhibit constitutive expression of major histocompatability (MHC) class II antigens. Using reovirus types 1 and 3, we infected 1B-6 cells (a cloned derivative of the Fisher rat cell line FRTL-5), and found a dose-dependent induction of thyroid cell MHC class II antigen expression as determined by laser flow cytometry and FITC-labelled OX-6 anti-RTl.B. As the number of viral particles/cell used for the infections increased from 5 to 100, the number of antigen positive cells increased, in reovirus type 3 infections to 50%, and in reovirus type 1 infections to 15%. Kinetic studies indicated that MHC class II antigen expression continues to increase three days after infection. Viral infection and the resulting MHC class II antigen expression may allow presentation of thyroid antigen to the immune system and participate in the initiation of autoimmune thyroid disease.
An OXA-48-producing Escherichia coli isolated from a Danish patient with no hospitalization abroad

Abstract Carbapenemase-producing organisms are disseminating globally and are now emerging as a worrying threat in Scandinavia. Before August 2013, OXA-48-producing organisms had not been detected in Danish patients. Here we report the isolation of an ST746 OXA-48-producing Escherichia coli with the plasmid pOXA-48a carrying the blaOXA-48 gene isolated from a Danish patient without history of hospitalization abroad. The patient reported tourist travel to Egypt and Turkey. The potential acquisition of carbapenemase-producing organisms by ingestion of contaminated food is discussed.