Miracle-dz/UniFAR-FTUs huggingface dataset:
Type IV Pili and the CcpA Protein Are Needed for Maximal Biofilm Formation by the Gram-Positive Anaerobic Pathogen Clostridium perfringens

ABSTRACT The predominant organizational state of bacteria in nature is biofilms. Biofilms have been shown to increase bacterial resistance to a variety of stresses. We demonstrate for the first time that the anaerobic gram-positive pathogen Clostridium perfringens forms biofilms. At the same concentration of glucose in the medium, optimal biofilm formation depended on a functional CcpA protein. While the ratio of biofilm to planktonic growth was higher in the wild type than in a ccpA mutant strain in middle to late stages of biofilm development, the bacteria shifted from a predominantly biofilm state to planktonic growth as the concentration of glucose in the medium increased in a CcpA-independent manner. As is the case in some gram-negative bacteria, type IV pilus (TFP)-dependent gliding motility was necessary for efficient biofilm formation, as demonstrated by laser confocal and electron microscopy. However, TFP were not associated with the bacteria in the biofilm but with the extracellular matrix. Biofilms afforded C. perfringens protection from environmental stress, including exposure to atmospheric oxygen for 6 h and 24 h and to 10 mM H2O2 for 5 min. Biofilm cells also showed 5- to 15-fold-increased survival over planktonic cells after exposure to 20 μg/ml (27 times the MIC) of penicillin G for 6 h and 24 h, respectively. These results indicate C. perfringens biofilms play an important role in the persistence of the bacteria in response to environmental stress and that they may be a factor in diseases, such as antibiotic-associated diarrhea and gas gangrene, that are caused by C. perfringens.
Characterization of Mutants of the Vitamin‐D‐Binding Protein/Group Specific Component: GC Aborigine (1A1) from Australian Aborigines and South African Blacks, and 2A9 from South Germany

The structure and organization of the human vitamin‐D‐binding protein gene (DBP, group‐specific component, GC) have recently been determined. Each ex‐on may now be amplified by the PCR method using oligonucleotide primers deduced from the intron sequences near their 5′ ends and 3′ ends. In this study we examined the anodal GC variants 1A1 and 2A9. Genomic DNA of the variant 1A1 was obtained from Australian Aborigines and from South African Bantu‐speaking Blacks. Amplification and sequencing of exon 11 of 1A1 revealed a point mutation in codon 429 at the second position. It is remarkable that this mutation was found in the Australian 1A1 variant and in the African 1A1 variant, and raises the question whether the mutation in these two ethnic groups has a common origin. Genomic DNA of the 2A variant called 2A9 was obtained from South Germany and a point mutation also concerning position 429 in exon 11 was found. The nucleotide exchange in this case, however, was at the first position of the codon. The widely distributed genetic polymorphism of DBP/GC is located in exon 11 and is characterized by substitution at amino acid positions 416 and 420. Variant 1A1 is due to a second site mutation of the allele GC*1F; variant 2A9 is due to a mutation in the GC*2 allele.
INVESTIGATION ON THE EFFECTS OF INHERENT FACTOR AND TIME- INTERVAL DECISION IN ARTIFICIAL NEURAL NETWORKS FOR DETERMINING THE OPTIMAL COAGULANT DOSAGE IN DRINKING WATER TREATMENT

Artificial neutral network (ANN) approach has been used in the drinking water treatment process for determining optimal coagulant dosage in the process. In such approach, a significant amount of input variables is typically required. To remedy the constraint, this study investigates the effects of input variables on the output performance of ANN models, using the real time coagulant dosage data collected in a drinking water treatment plant in Taipei, Taiwan. In this paper, ANN models are developed and applied to predict the optimal coagulant dosage, considering the effects of different model input parameters. Past coagulant dosages, defined as the inherent factor, along with the time interval between two dosages, were considered in investigating the effects and evaluated by the Pearson correlation coefficient. The root mean square error criterion was used in evaluating the performance of ANN models, and the Levenberg-Marquardt method in combination with weight decay regularization was applied to avoid over-fitting. From the results of this study, it is found that the ANN models with the inherent factor provide the optimal coagulant dosage prediction, while the increasing use of the inherent factor does not significantly improve the predictability of ANN models. The use of the inherent factor is also found useful when influent water does not provide sufficient information on water quality.
Detection and differentiation of avian adenoviruses: A review

Avian adenoviruses are a very diverse group of pathogens causing a variety of problems for poultry production. For a long time, the diagnosis of an adenovirus infection was restricted to the isolation of the respective virus followed by various serological typing methods, such as immunofluorescence assay, neutralization test or haemagglutination-inhibition test. In addition, restriction enzyme analysis has been reported for differentiation of avian adenoviruses. Besides summarizing the classical diagnostic methods, this review is mainly focused on the challenges that occurred recently in the field of avian adenovirus diagnosis at the molecular level. Several polymerase chain reactions (PCRs) have been published to diagnose all three groups of avian adenoviruses. Most PCRs were established to detect fowl adenovirus (FAV) DNA. Some of them were combined with restriction enzyme analysis to investigate whether FAV reference strains and field isolates could be typed according to the restriction profiles of the PCR products. The great advantage of direct detection of the viral DNA in tissue samples was demonstrated for the haemorrhagic enteritis virus and egg drop syndrome virus. Other PCRs were developed with the aim of detecting viral DNA from all three groups of avian adenoviruses partially in target cells. Whereas the value of these PCRs for avian adenovirus diagnostics is not disputable, the problems and open questions that are still present are also discussed.
TNF-α Polymorphisms in Juvenile Idiopathic Arthritis: Which Potential Clinical Implications?

Whether tumor necrosis factor alpha (TNF-α) gene polymorphisms (SNPs) influence disease susceptibility and treatment of patients with juvenile idiopathic arthritis (JIA) is presently uncertain. TNF-α is one of the most important cytokine involved in JIA pathogenesis. Several single nucleotide polymorphisms (SNPs) have been identified within the region of the TNF-α gene but only a very small minority have proven functional consequences and have been associated with susceptibility to JIA. An association between some TNF-α SNPs and adult rheumatoid arthritis (RA) susceptibility, severity and clinical response to anti-TNF-α treatment has been reported. The most frenquetly studied TNF-α SNP is located at −308 position, where a substitution of the G allele with the rare A allele has been found. The presence of the allele −308A is associated to JIA and to a poor prognosis. Besides, the −308G genotype has been associated with a better response to anti-TNF-α therapy in JIA patients, confirming adult data. Psoriatic and oligoarticular arthritis are significantly associated to the −238 SNP only in some works. Studies considering other SNPs are conflicting and inconclusive. Large scale studies are required to define the contribution of TNF-α gene products to disease pathogenesis and anti-TNF-α therapeutic efficacy in JIA.
A Treebank of Visual and Linguistic Data

The treebank is a new resource for researchers working at the intersection between vision and language. It will be a freely-available corpus of images and corresponding text for the development and evaluation of models for natural language generation, image annotation, and structure induction. The treebank differs from existing datasets because it contains syntactic representations of the data, which makes it applicable to a wider range of tasks. The images are provided in their original form, a set of gold-standard object annotations, and as gold-standard visual dependency graphs derived from the annotations and corresponding text. The annotations are made with respect to the corresponding text so they cover a wide range of object classes and are directly related to the image description. The visual dependency graphs are generated using a geometric dependency grammar, which defines how relations between pairs of objects can be generated. The text is provided in its original form and as a syntactic dependency tree, which is produced by a state-of-the-art parser. The treebank currently contains several hundred completely annotated pairs of data and is being scaled up to several thousand pairs.
GUITAR AS CONTROLLER

In this project we present a series of algorithms developed to detect the following guitar playing techniques : bend, hammer-on, pull-off, slide, palm muting, harmonic, plucking point. Via the detection of these information, the instrument can be extended as a natural way to control external content (i.e. loops, audio effects, videos, light changes, etc.). The guitar used is a Godin Multiac with an under-saddle RMC hexaphonic piezo pickup (one pickup per string, i.e six mono signals, one per string). Two exhaustive databases have been recorded by two different guitarists with different playing technics (finger style picking and plectrum style picking) to test the different algorithms. Off-line implementation of the algorithms are showing good results. A global implementation on a dedicated software seems to be the solution to provide a more robust solution to real-time hexaphonic use. Implementation on FPGA have been investigated as well, in order to asses the problem of the big amount of processing power needed for hexaphonic detection.
Further empirical evidence for the non‐linearity of the period–luminosity relations as seen in the Large Magellanic Cloud Cepheids

Recent studies, using OGLE data for LMC Cepheids in the optical, strongly suggest that the period-luminosity (PL) relation for the Large Magellanic Cloud (LMC) Cepheids shows a break or non-linearity at a period of 10 days. In this paper we apply statistical tests, the chi-square test and the F-test, to the Cepheid data from the MACHO project to test for a non-linearity of the V- and R-band PL relations at 10 days, and extend these tests to the near infrared (JHK-band) PL relations with 2MASS data. We correct the extinction for these data by applying an extinction map towards the LMC. The statistical test we use, the F-test, is able to take account of small numbers of data points and the nature of that data on either side of the period cut at 10 days. With our data, the results we obtained imply that the VRJH-band PL relations are non-linear around a period of 10 days, while the K-band PL relation is (marginally) consistent with a single-line regression. The choice of a period of 10 days, around which this non-linearity occurs, is consistent with the results obtained when this ”break” period is estimated from the data. We show that robust parametric (including least squares, least absolute deviation, robust regression) and non-parametric regression methods, which restrict the influence of outliers, produce similar results. Long period Cepheids are supplemented from the literature to increase our sample size. The photometry of these long period Cepheids is compared with our data and no trend with period is found. Our main results remain unchanged when we supplement our dataset with these long period Cepheids. By examining our data at maximum light, we also suggest arguments why errors in reddening are unlikely to be responsible for our results. The non-linearity of the mean V-band PL relation as seen in both of the OGLE and MACHO data, using different extinction maps, suggests that this non-linearity is real.
Organizational adoption of e‐HRM in Europe

Purpose – The purpose of this paper is to examine which factors influence the cross‐national organizational adoption of electronic human resource management (e‐HRM) in Europe.Design/methodology/approach – Major general and contextual influence factors are derived and tested based on a large‐scale survey with a sample of 2,336 organizations in 23 European countries using logistic regression.Findings – The findings first reveal that e‐HRM is a common practice throughout Europe since two‐thirds of all organizations have already adopted e‐HRM. Major general determinants of e‐HRM adoption are size, work organization, and configuration of HRM. In addition, there are major cross‐national differences in e‐HRM adoption, unexpectedly revealing Eastern post‐communist countries to lead e‐HRM adoption.Research limitations/implications – Abundance of general and scarcity of contextual factors imply that there should be further important factors of adoption not considered in this paper. Owing to its cross‐sectional char.
Solution to the "ARF" (Agriculture, Rural Land, Farmers) Problems in China: An Intellectual Capital Framework

The intellectual capital (IC) theory is a whole new one booming in present academic society , and it provides a new view for organization development and region development. The "ARF" (agriculture, rural land, farmers) problems has been the hotspot and crux in Chinese socialist construction. We innovate in bringing the IC theory into the study of the "ARF " problems, and draw practical and dominant conclusions thereby. We hold that different strategies may be brought out when analysing the "ARF" problems from different angels. From the prospect of human capital, we should implement rural human capital engineering(RHCE) to improve the farmer' diathesis. From the prospect of structure capital, we should start systematic reformation, mechanism construction, and institution construction in rural lands. From the prospect of relational dimension of intellectual capital, we need to induce some new growth variables for economy development and promote investment. Based on above considerations, we bring forward an IC-framework model for the "ARF" problems, and further optimize and re-formulate our 4D model of rural human capital engineering (hereafter referred to as RHCE) which was brought forth two years ago, and also give birth to a new 3D systematic model of RHCE based on the IC theory. In this way, we provide a new view and practical guidance for implementing RHCE.
Correlations between anaerobic threshold determination protocols and aerobic performance in adolescent swimmers

The purpose of this study was to correlate the anaerobic threshold speeds (ATS) obtained from fixed lactate blood concentration (ATS 4 e ATS 3.5 mM), lactate minimum speed (LacminS) and the critical speed (CS) determined from different distances and number of coordinates: CS1 (50/100/200 m), CS2 (100/200/400 m), CS3 (50/100/200/400 m) and CS4 (200/400 m) with the performance in 400 meters (s) in adolescent swimmers. The sample was constituted by 15 swimmers (10 boys and five girls = 14.7 ± 0.7 years; 61.9 ± 8.5 kg; 171.1 ± 8.8 cm) of national level, with five to seven years of experience in competitive swimming. The correlation between the indexes and the performance in 400 m (s) was made using Pearson correlation coefficients. Significance was set at p < 0.01. The correlations between ATS 4 mM, ATS 3.5 mM, LacminS and the performance in 400 m (s) were: r = -0.63, r = -0.90 e r = -0.91, respectively (p < 0.01). The correlations between CS1 (50/ 100/200 m), CS2 (100/200/400 m), CS3 (50/100/200/400 m), CS4 (200/400 m) and the performance in 400 m (s) were: r = -0.62, r = -0.97, r = -0.98 e r = -0.94, respectively (p < 0.01). We suggest that ATS obtained from fixed lactate blood concentration of 3.5 mM, as well as LacminS and the CS obtained through larger distances seem to be the most fitted indexes of prediction of the aerobic performance in the studied adolescent swimmers. Additionally, the number of coordinates seems no influencing the relation between CS and aerobic performance.
Ca2+-activation kinetics modulate successive puff/spark amplitude, duration and inter-event-interval correlations in a Langevin model of stochastic Ca2+ release

Through theoretical analysis of the statistics of stochastic calcium (Ca2+) release (i.e., the amplitude, duration and inter-event interval of simulated Ca2+ puffs and sparks), we show that a Langevin description of the collective gating of Ca2+ channels may be a good approximation to the corresponding Markov chain model when the number of Ca2+ channels per Ca2+ release unit (CaRU) is in the physiological range. The Langevin description of stochastic Ca2+ release facilitates our investigation of correlations between successive puff/spark amplitudes, durations and inter-spark intervals, and how such puff/spark statistics depend on the number of channels per release site and the kinetics of Ca2+-mediated inactivation of open channels. When Ca2+ inactivation/de-inactivation rates are intermediate—i.e., the termination of Ca2+ puff/sparks is caused by the recruitment of inactivated channels—the correlation between successive puff/spark amplitudes is negative, while the correlations between puff/spark amplitudes and the duration of the preceding or subsequent inter-spark interval are positive. These correlations are significantly reduced when inactivation/deinactivation rates are extreme (slow or fast) and puff/sparks terminate via stochastic attrition.
DASH Diet Lowers Blood Pressure and Lipid-Induced Oxidative Stress in Obesity

Abstract—Evidence suggests that obesity may raise blood pressure (BP) through oxidative stress–sensitive mechanisms and that the Dietary Approaches to Stop Hypertension combination diet (DASH-CD) may decrease BP by enhancing antioxidant capacity. To address this question, 12 obese patients with high-normal–to–stage 1 hypertension (hypertensives) and 12 lean normotensives were studied on their usual diets and after following the DASH-CD and a low-antioxidant diet in random sequence for 4 weeks each. Acute oxidative stress was induced by a 4-hour infusion of intralipid and heparin. Ferric-reducing activity of plasma (FRAP) and plasma F2-isoprostanes were measured as biomarkers of antioxidant capacity and oxidative stress, respectively. BP was lower in obese hypertensives on the DASH-CD than on the usual and low-antioxidant diets (−8.1±1.5/−7.4±1.6 mm Hg, P <0.05). BP did not change significantly in lean normotensives after 4 weeks on the DASH-CD but tended to rise on the low-antioxidant diet. FRAP on usual diets was higher in lean subjects than in obese subjects. FRAP increased in obese but not lean volunteers on the DASH-CD compared with usual diet, and the group difference disappeared. F2-isoprostanes increased from baseline during intralipid and heparin in both groups on the low-antioxidant diet but not in obese hypertensives on the DASH-CD. Among free-living obese hypertensives, the DASH-CD raises antioxidant capacity, lowers BP, and reduces oxidative stress induced by acute hyperlipidemia. The findings are consistent with evidence that elevated BP in obese subjects may reflect an imbalance between antioxidant capacity and oxidative stress that is improved by the DASH-CD.
Editorial: Controversies and Perspectives in the Use of Postoperative Radiotherapy for Prostate Cancer

HAL is a multi-disciplinary open access archive for the deposit and dissemination of scientific research documents, whether they are published or not. The documents may come from teaching and research institutions in France or abroad, or from public or private research centers. L’archive ouverte pluridisciplinaire HAL, est destinée au dépôt et à la diffusion de documents scientifiques de niveau recherche, publiés ou non, émanant des établissements d’enseignement et de recherche français ou étrangers, des laboratoires publics ou privés. Editorial: Controversies and Perspectives in the Use of Postoperative radiotherapy for Prostate Cancer Alan Dal Pra, Thomas Zilli, Stéphane Supiot
Anatomies of Kinship: Diversity in the Formal Structures of American Families

Anatomies of Kinship: Diversity in the Formal Structures of American Families by Gertrude Robin Gauthier Department of Sociology Duke University Date:_______________________ Approved: ___________________________ James Moody, Supervisor ___________________________ Lynn Smith-Lovin ___________________________ Giovanna Merli ___________________________ S. Philip Morgan An abstract of a dissertation submitted in partial fulfillment of the requirements for the degree of Doctor of Philosophy in the Department of Sociology in the Graduate School of Duke University 2014 Copyright by Gertrude Robin Gauthier 2014
Evaluation of Real-Time PCR, Galactomannan Enzyme-Linked Immunosorbent Assay (ELISA), and a Novel Lateral-Flow Device for Diagnosis of Invasive Aspergillosis

ABSTRACT Diagnosis of invasive aspergillosis (IA) remains challenging. With a relatively low incidence of disease, the use of expensive empirical antifungal therapy exposes many patients to unnecessary toxicity. Diagnosis places emphasis on specific but temporal radiological evidence. Circulating biomarker diagnosis has shown potential, but assays show variable performance, take several hours to perform, and require a degree of technical ability. A novel and simple lateral-flow device (LFD) using monoclonal antibody JF5, which targets an extracellular glycoprotein, has been developed and potentially removes any technical requirements, reducing processing time considerably. In this study, we evaluate the performance of this LFD compared to real-time PCR (targeting the 28S rRNA gene) and galactomannan (GM) detection when testing serum from a European Organization for Research and Treatment of Cancer/Invasive Fungal Infections Cooperative Group, National Institute of Allergy and Infectious Diseases Mycoses Study Group (EORTC/MSG)-defined hematological population. In a proven/probable-IA population versus a no-IA population, the LFD performance was comparable to that of both PCR and galactomannan enzyme immunoassay. Specificity (98.0%) was similar to that of PCR (96.6%) and slightly superior to that of GM (91.5%). Sensitivity (81.8%) was inferior to that of PCR (95.5%) but better than that of GM (77.3%). In combination with PCR, it provided both 100% sensitivity and 100% specificity. The LFD permits rapid testing of easily obtainable specimens, to be used as an adjunct test, before confirmation by other investigations. Its simplicity provides centers without specialist diagnostics with a test with clinical performance superior to that of classical microbiological approaches and results that can be used to direct antifungal management. In summary, microbiological diagnosis of IA is difficult and options are limited, with variable performance. An LFD assay targeting a novel specific biomarker has been developed, one which is methodologically simple and provides good clinical performance, particularly if combined with PCR.