Miracle-dz/UniFAR-FTUs huggingface dataset:
Title : Prevalence and characterization of Staphylococcus aureus in pigs in the USA – NPB # 13-056 Revised

Over the last 10 years, concerns have grown about the possible importance of livestock reservoirs as a source of methicillin resistant Staphylococcus aureus (MRSA). S. aureus is a normal bacterial inhabitant of healthy people as well as many animal species including pigs. However, S. aureus is also an important cause of human infections, and among the most significant problems related to antibiotic resistance in human medicine. A small number of studies have confirmed the presence of several variants of MRSA in pigs (types ST398; ST5; ST9) in the USA, but the epidemiology of S. aureus in pigs in the US has not been well documented. We conducted a study of 36 farms located in 11 states of the US to describe the prevalence and types of S. aureus (including MRSA) in the swine reservoir. One additional farm, previously known to harbor MRSA, was included as a positive control farm. We also determined patterns of antimicrobial resistance and the presence of genes producing toxins that can cause food poisoning in people. Because zinc resistance has been implicated in the emergence of ‘livestock associated” MRSA in Europe, we also tested isolates for resistance to zinc and for the presence of a specific gene (czrC) linked to ST398 MRSA in Europe.
On the complexity of universal fault diagnosis for look-up table FPGAs

In this paper, we introduce universal fault diagnosis such that when applied to an unprogrammed FPGA, it locates a fault in any faulty programmed FPGA corresponding to the unprogrammed FPGA. If a faulty part in an FPGA can be identified prior to programming it, we can implement a required logic function on the fault-free part by isolating the faulty part. Then, we propose a universal fault diagnosis procedure that locates a faulty CLB in a look-up table FPGA. The complexity of the universal diagnosis procedure for FPGAs with block-sliced loading is independent of its array size, i.e., C-diagnosable.
The unsteady motion of a sphere in a viscoelastic fluid

The motion of a sphere accelerating from rest along the center line of a cylindrical tube filled with a polyisobutylene (PIB) Boger fluid is examined both experimentally, using a digital imaging system, and numerically via a Lagrangian finite element method for single and multimode Oldroyd models including inertia. Spheres of diameter 2.54 cm and varying densities are released in a tube of radius 5.23 cm. Deborah numbers in the range 0.4≤De≤11.7 are obtained, and the experimental results show transient velocity overshoots of up to 50% before the spheres approach their final constant settling velocity. Independent measurements of this settling velocity indicate significant drag increases at high De. The numerical calculations are compared with the experimental data, and markedly improved agreement is obtained for multimode simulations.
Lower Pectoralis Muscle Area Is Associated with a Worse Overall Survival in Non–Small Cell Lung Cancer

Background: Muscle wasting is a component of the diagnosis of cancer cachexia and has been associated with poor prognosis. However, recommended tools to measure sarcopenia are limited by poor sensitivity or the need to perform additional scans. We hypothesized that pectoralis muscle area (PMA) measured objectively on chest CT scan may be associated with overall survival (OS) in non–small cell lung cancer (NSCLC). Methods: We evaluated 252 cases from a prospectively enrolling lung cancer cohort. Eligible cases had CT scans performed prior to the initiation of surgery, radiation, or chemotherapy. PMA was measured in a semi-automated fashion while blinded to characteristics of the tumor, lung, and patient outcomes. Results: Men had a significantly greater PMA than women (37.59 vs. 26.19 cm2, P < 0.0001). In univariate analysis, PMA was associated with age and body mass index (BMI). A Cox proportional hazards model was constructed to account for confounders associated with survival. Lower pectoralis area (per cm2) at diagnosis was associated with an increased hazard of death of 2% (HRadj, 0.98; confidence interval, 0.96–0.99; P = 0.044) while adjusting for age, sex, smoking, chronic bronchitis, emphysema, histology, stage, chemotherapy, radiation, surgery, BMI, and ECOG performance status. Conclusions: Lower PMA measured from chest CT scans obtained at the time of diagnosis of NSCLC is associated with a worse OS. Impact: PMA may be a valuable CT biomarker for sarcopenia-associated lung cancer survival. Cancer Epidemiol Biomarkers Prev; 26(1); 38–43. ©2016 AACR. See all the articles in this CEBP Focus section, “The Obesity Paradox in Cancer: Evidence and New Directions. ”
Therapeutic Potential of α7 Nicotinic Acetylcholine Receptors

Progress in the fields of neuroscience and molecular biology has identified the forebrain cholinergic system as being important in many higher order brain functions. Further analysis of the genes encoding the nicotinic acetylcholine receptors (nAChRs) has highlighted, in particular, the role of α7 nAChRs in these higher order brain functions as evidenced by their peculiar physiologic and pharmacological properties. As this receptor has gained the attention of scientists from academia and industry, our knowledge of its roles in various brain and bodily functions has increased immensely. We have also seen the development of small molecules that have further refined our understanding of the roles of α7 nAChRs, and these molecules have begun to be tested in clinical trials for several indications. Although a large body of data has confirmed a role of α7 nAChRs in cognition, the translation of small molecules affecting α7 nAChRs into therapeutics has to date only progressed to the stage of testing in clinical trials. Notably, however, most recent human genetic and biochemical studies are further underscoring the crucial role of α7 nAChRs and associated genes in multiple organ systems and disease states. The aim of this review is to discuss our current knowledge of α7 nAChRs and their relevance as a target in specific functional systems and disease states.
PROKR2 and PROK2 mutations cause isolated congenital anosmia without gonadotropic deficiency.

OBJECTIVE Isolated congenital anosmia (ICA) is a rare phenotype defined as absent recall of any olfactory sensations since birth and the absence of any disease known to cause anosmia. Although most cases of ICA are sporadic, reports of familial cases suggest a genetic cause. ICA due to olfactory bulb agenesis and associated to hypogonadotropic hypogonadism defines Kallmann syndrome (KS), in which several gene defects have been described. In KS families, the phenotype may be restricted to ICA. We therefore hypothesized that mutations in KS genes cause ICA in patients, even in the absence of family history of reproduction disorders. DESIGN AND METHODS In 25 patients with ICA and olfactory bulb agenesis, a detailed phenotype analysis was conducted and the coding sequences of KAL1, FGFR1, FGF8, PROKR2, and PROK2 were sequenced. RESULTS Three PROKR2 mutations previously described in KS and one new PROK2 mutation were found. Investigation of the families showed incomplete penetrance of these mutations. CONCLUSIONS This study is the first to report genetic causes of ICA and indicates that KS genes must be screened in patients with ICA. It also confirms the considerable complexity of GNRH neuron development in humans.
Un réseau de neurones pour des associations multimodales

Les recherches en neuromimetisme (reseaux de neurones) s'inspirent des neurosciences pour proposer des modeles cerebraux de comportements cognitifs typiquement humains, visant a s'approcher de certains phenomenes corticaux, pour developper de nouveaux paradigmes de calculs. L'interet du present travail est de s'approcher du phenomene de l'integration multisensorielle. Nous avons mene une etude sur un modele de BAM [7] adapte propose par E. Reynaud [9] pour modeliser l'integration multisensorielle. Nous ameliorons les performances et la robustesse du modele de la BAM en modifiant les algorithmes d'apprentissage et de rappel. Nous avons propose un nouvel algorithme d'apprentissage en ligne pour la BAM, ainsi qu'une nouvelle approche pour la modelisation d'une memoire multiassociative, en se basant sur la synchronisation de la convergence et de la propagation des flux d'informations. Cet article resume ces travaux et presente l'experimentation et l'evaluation des performances de la BAM en terme d'association multimodale.
Inline detection of defects on free formed metal pressings using a single shot inverse fringe projection approach

With unavoidable vibrations, the position and orientation of the measuring components and the object itself will differ during the measurement (see Fig. 2a). Thus, an analysis based on a sequence of images is not possible. Furthermore, short cycle times often don’t allow solutions which require a sequence of several measurements. Fig. 2 Challenges of conventional fringe projection with press forming. a) Variation of position and orientation during the measurement. b) High dynamic range of the spatial frequency of projected fringes
Reliable gamma aminobutyric acid measurement using optimized PRESS at 3 T

Gamma aminobutyric acid (GABA) is the most important inhibitory neurotransmitter in the central nervous system and there is strong interest in noninvasive measurement of GABA levels to assess GABAergic dysfunction in a number of psychiatric and neurological diseases. GABA detection by proton MR spectroscopy is challenging due to its low concentration as well as its strong overlap with more highly concentrated metabolites; therefore, editing techniques are typically required. In this study, the parameters of a standard point resolved spectroscopy (PRESS) sequence were optimized through repeated simulations to reliably and simultaneously detect GABA and glutamate at 3 T. Experimental validation of the optimized sequence parameters of echo time (TE1) = 15 ms and TE = 105 ms and careful postprocessing with realignment yielded reliable GABA estimates in the anterior cingulate cortex and precuneus region with test‐retest coefficient of variation of 10.4%. The achieved reproducibitilty was thus similar to published MEGA‐PRESS data despite smaller voxels and shorter scan time in this study. In conclusion, the optimized sequence parameters reported here allow reliable GABA estimation without additional hardware or software adaptation on clinical scanners. Magn Reson Med, 2013. © 2012 Wiley Periodicals, Inc.
Overview of Gene Targeting by Homologous Recombination

The analysis of mutant organisms and cell lines is important in determining the function of specific proteins. Recent technological advances in gene targeting by homologous recombination in mammalian systems enable the production of mutants in any desired gene, and can be used to produce mutant mouse strains and mutant cell lines. The yeast Flp/FRT recombinase system and bacteriophage recombinases such as Cre and its recognition sequence, loxP, allow spatial and temporal control of knockouts. This unit discusses crucial issues for homologous recombination experiments, including requirements for the source of DNA, criteria for the targeting constructs, methods of enrichment for homologous recombinants, (positive and negative selection, and the use of endogenous promoters), and the types of mutations that can be created. Curr. Protoc. Neurosci. 40:4.29. 1‐4.29. 13. © by John Wiley & Sons, Inc.
Interactions among CotB, CotG, and CotH during Assembly of the Bacillus subtilis Spore Coat

ABSTRACT Spores formed by wild-type Bacillus subtilis are encased in a multilayered protein structure (called the coat) formed by the ordered assembly of over 30 polypeptides. One polypeptide (CotB) is a surface-exposed coat component that has been used as a vehicle for the display of heterologous antigens at the spore surface. The cotB gene was initially identified by reverse genetics as encoding an abundant coat component. cotB is predicted to code for a 43-kDa polypeptide, but the form that prevails in the spore coat has a molecular mass of about 66 kDa (herein designated CotB-66). Here we show that in good agreement with its predicted size, expression of cotB in Escherichia coli results in the accumulation of a 46-kDa protein (CotB-46). Expression of cotB in sporulating cells of B. subtilis also results in a 46-kDa polypeptide which appears to be rapidly converted into CotB-66. These results suggest that soon after synthesis, CotB undergoes a posttranslational modification. Assembly of CotB-66 has been shown to depend on expression of both the cotH and cotG loci. We found that CotB-46 is the predominant form found in extracts prepared from sporulating cells or in spore coat preparations of cotH or cotG mutants. Therefore, both cotH and cotG are required for the efficient conversion of CotB-46 into CotB-66 but are dispensable for the association of CotB-46 with the spore coat. We also show that CotG does not accumulate in sporulating cells of a cotH mutant, suggesting that CotH (or a CotH-controlled factor) stabilizes the otherwise unstable CotG. Thus, the need for CotH for formation of CotB-66 results in part from its role in the stabilization of CotG. We also found that CotB-46 is present in complexes with CotG at the time when formation of CotB-66 is detected. Moreover, using a yeast two-hybrid system, we found evidence that CotB directly interacts with CotG and that both CotB and CotG self-interact. We suggest that an interaction between CotG and CotB is required for the formation of CotB-66, which may represent a multimeric form of CotB.
Toward Automated, At-Home Assessment of Mobility Among Patients With Parkinson Disease, Using a Body-Worn Accelerometer

Objective. To develop an automated and objective method to assess mobility in Parkinson disease (PD) patients in daily-life settings and to investigate whether accelerometer-derived measures discriminate between PD and healthy controls as they walk and simulate activities of daily living (ADL). Methods. Healthy older adults (17) and patients with PD (22) wore a triaxial accelerometer on their lower back during short walks (validation study) and during a walk around the medical center to simulate daily activities (ADL simulation). The variability (consistency and rhythmicity) of stepping was assessed. The patients completed the walks before and after taking their anti-Parkinsonian medications. Frequency-based acceleration measures included dominant frequency, amplitude (strength of signal frequency), width (frequency dispersion), and slope (a combination reflecting amplitude and width) of the main frequency of the power spectral density in the 0.5- to 3.0-Hz band. A subset of the Unified Parkinson-Disease Rating Scale provided a clinical measure of gait impairment (UPDRS-Gait5). A PD patient and control wore the sensors for 3 days at home. Results. The width was larger, and the amplitude and slope were smaller in the PD patients compared to the controls in the validation study and ADL simulation (P < .02). The width decreased, and the amplitude and slope increased when patients took anti-Parkinsonian medications (P < .007). Significant correlations were observed between acceleration-derived measures and UPDRS-Gait5. The data obtained at home was similar to the clinic data. Conclusions. Frequency-derived measures are valid and sensitive estimates of stride-to-stride variability that can be used to assess the quality and consistency of walking in patients with PD in real-life settings.
Phosphorylation Events Modulate the Ability of Interferon Consensus Sequence Binding Protein to Interact with Interferon Regulatory Factors and to Bind DNA*

Two families of transcription factors mediate interferon (IFN) signaling. The first family, signal transducers and activators of transcription (STATs), is activated within minutes of IFN treatment. Specific phosphorylation events lead to their translocation to the nucleus, formation of transcriptional complexes, and the induction of the second family of transcription factors termed interferon regulatory factors (IRFs). Interferon consensus sequence binding protein (ICSBP) is a member of IRF family that is expressed only in cells of the immune system and acts as a transcriptional repressor. ICSBP binds DNA through the association with other transcription factors such as IRF-1 or IRF-2. In this communication, the domain that is involved in protein-protein interactions was mapped to the carboxyl terminus of ICSBP. This domain is also important for mediating ICSBP-repressing activity. In vitro studies demonstrated that direct binding of ICSBP to DNA is prevented by tyrosine (Tyr) phosphorylation. Yet, Tyr-phosphorylated ICSBP can bind target DNA only through the association with IRF-2 and IRF-1. This type of phosphorylation is essential for the formation of heterocomplexes. Tyr-phosphorylated ICSBP and IRF-2 are detected in expressing cells constitutively, and Tyr-phosphorylated IRF-1 is induced by IFN-γ. These results strongly suggest that like the STATs, the IRFs are also modulated by Tyr phosphorylation that affects their biological activities.
A Prenylated p67 phox -Rac1 Chimera Elicits NADPH-dependent Superoxide Production by Phagocyte Membranes in the Absence of an Activator and of p47 phox

Activation of the superoxide-generating NADPH oxidase of phagocytes is the result of the assembly of a membrane-localized flavocytochrome (cytochromeb 559) with the cytosolic components p47 phox , p67 phox , and the small GTPase Rac. Activation can be reproduced in an in vitro system in which cytochrome b 559-containing membranes are mixed with cytosolic components in the presence of an anionic amphiphile. We proposed that the essential event in activation is the interaction between p67 phox and cytochrome b 559 and that Rac and p47 phox serve as carriers for p67 phox to the membrane. When prenylated, Rac can fulfill the carrier function by itself, supporting oxidase activation by p67 phox in the absence of p47 phox and amphiphile. We now show that a single chimeric protein, consisting of residues 1–212 of p67 phox and full-length Rac1 (residues 1–192), prenylated in vitro and exchanged to GTP, becomes a potent oxidase activator in the absence of any other component or stimulus. Oxidase activation by prenylated chimera p67 phox (1–212)-Rac1 (1–192) is accompanied by its spontaneous association with membranes. Prenylated chimeras p67 phox (1–212)-Rac1 (178–192) and p67 phox (1–212)-Rac1 (189–192), containing specific C-terminal regions of Rac1, are inactive; the activity of the first but not of the second chimera can be rescued by supplementation with exogenous nonprenylated Rac1-GTP. An analysis of prenylated p67 phox -Rac1 chimeras suggests that the basic requirements for oxidase activation are: (i) a “two signals” membrane-localizing motif present in Rac, comprising the prenyl group and a C-terminal polybasic sequence and (ii) an intrachimeric or extrachimeric protein-protein interaction between p67 phox and Rac1, causing a conformational change in the “activation domain” in p67 phox .
Relative Income, Temporary Life Shocks and Subjective Wellbeing in the Long-run

We show how the concepts of remembered utility and experienced utility correspond to cognitive appraisals of life satisfaction and emotion/affect respectively, as these concepts are used in psychology. Cognitive life satisfaction, or remembered utility, is relatively stable over time and can be considered as reflecting subjective wellbeing in the long-run. Emotion/affect, or experienced utility, is a transitory phenomenon and can be considered as reflecting subjective wellbeing in the short-run. Using the personal wellbeing index (PWI) to measure cognitive life satisfaction, or remembered utility, and the Positive and Negative Affect Schedule (PANAS) to measure emotion/affect, or experienced utility, we examine how income relative to oneâ€™s comparator group and variations in short-run subjective wellbeing, effect subjective wellbeing in the long-run. We do so for the Korean minority in China, a population that is undergoing rapid change in a fast moving transitional economy.
Studies of the presence of membrane receptors for complement, IgG and the sheep erythrocyte rosetting capacity on the same human lymphocytes

Normal peripheral blood lymphocytes were tested by a mixed rosette method, employing different sized erythrocytes as indicators to identify lymphocytes simultaneously possessing membrane markers found commonly on B and T cells. Only small populations of these lymphocytes were detected regulary in normal lymphocyte preparations. One type of lymphocyte (ranged from 0.5%‐8%) was shown to possess the following markers: receptors for human and rabbit IgG, receptors for the third complement component C3b and C3b inactivator‐cleaved C3b (C3d), and the capacity to rosette spontaneously with uncoated sheep erythrocytes (SRBC). Another lymphocyte cell type was shown to possess both SRBC and IgG receptors but lack membrane immunoglobulins and complement receptors. This population was detected in lymphocyte preparations depleted of complement receptor cells, and an increased number of these cells was found in rosette preparations incubated with human serum. The possible presence of some lymphocytes possessing both complement and SRBC receptors and lacking other markers was considered.
Spontaneous mutagenesis associated with nucleotide excision repair in Escherichia coli

The vast majority of spontaneous mutations occurring in Escherichia coli are thought to be derived from spontaneous DNA lesions, which include oxidative base damage. Systems for removing intrinsic mutagens and repairing DNA lesions contribute to the suppression of spontaneous mutations. Nucleotide excision repair (NER) is a general DNA repair system that eliminates various kinds of lesions from DNA. We therefore predicted that NER might be involved in suppression of spontaneous mutations, and analyzed base substitutions occurring spontaneously within the rpoB gene in NER‐proficient (wild‐type), ‐deficient and ‐overproducing E. coli strains. Surprisingly, the mutation frequency was lower in NER‐deficient strains, and higher in NER‐overproducing strains, than in the NER‐proficient strain. These results suggest, paradoxically, that NER contributes to the generation of spontaneous mutation rather than to its suppression under normal growth conditions, and that transcription‐coupled repair also participates in this process. Using E. coli strains that carried an editing exonuclease‐deficient polA mutation, we further obtained data suggesting that unnecessary NER might account for these findings, so that errors introduced during repair DNA synthesis by DNA polymerase I would result in unwanted base substitutions. The repair system itself may thus be an important generator of spontaneous mutation.