Miracle-dz/UniFAR-FTUs huggingface dataset:
Expression of Rhizobium leguminosarum CFN42 genes for lipopolysaccharide in strains derived from different R. leguminosarum soil isolates

Two mutant derivatives of Rhizobium leguminosarum ANU843 defective in lipopolysaccharide (LPS) were isolated. The LPS of both mutants lacked O antigen and some sugar residues of the LPS core oligosaccharides. Genetic regions previously cloned from another Rhizobium leguminosarum wild-type isolate, strain CFN42, were used to complement these mutants. One mutant was complemented to give LPS that was apparently identical to the LPS of strain ANU843 in antigenicity, electrophoretic mobility, and sugar composition. The other mutant was complemented by a second CFN42 lps genetic region. In this case the resulting LPS contained O-antigen sugars characteristic of donor strain CFN42 and reacted weakly with antiserum against CFN42 cells, but did not react detectably with antiserum against ANU843 cells. Therefore, one of the CFN42 lps genetic regions specifies a function that is conserved between the two R. leguminosarum wild-type isolates, whereas the other region, at least in part, specifies a strain-specific LPS structure. Transfer of these two genetic regions into wild-type strains derived from R. leguminosarum ANU843 and 128C53 gave results consistent with this conclusion. The mutants derived from strain ANU843 elicited incompletely developed clover nodules that exhibited low bacterial populations and very low nitrogenase activity. Both mutants elicited normally developed, nitrogen-fixing clover nodules when they carried CFN42 lps DNA that permitted synthesis of O-antigen-containing LPS, regardless of whether the O antigen was the one originally made by strain ANU843.
Relative validity of a semi-quantitative food-frequency questionnaire in an elderly Mediterranean population of Spain

The aim of the present study was to assess reproducibility and relative validity of a self-administered FFQ used in the PREDIMED Study, a clinical trial for primary prevention of CVD by Mediterranean diet in a population at high cardiovascular risk. The FFQ was administered twice (FFQ1 and FFQ2) to explore reproducibility at 1 year. Four 3 d dietary records (DR) were used as reference to explore validity; participants therefore recorded their food intake over 12 d in the course of 1 year. The degree of misclassification in the FFQ was also evaluated by a contingency table of quintiles comparing the information from the FFQ2 and the DR. A total of 158 men and women (aged 55–80 years) were asked not to modify their dietary habits during the study period. Reproducibility for food groups, energy and nutrient intake, explored by the Pearson correlation coefficient (r) ranged 0·50–0·82, and the intraclass correlation coefficient (ICC) ranged from 0·63 to 0·90. The FFQ2 tended to report higher energy and nutrient intake than the DR. The validity indices of the FFQ in relation to the DR for food groups and energy and nutrient intake ranged (r) from 0·24 to 0·72, while the range of the ICC was between 0·40 and 0·84. With regard to food groups, 68–83 % of individuals were in the same or adjacent quintile in both methods, a figure which decreased to 55–75 % for energy and nutrient intake. We concluded that FFQ measurements had good reproducibility and a relative validity similar to those of FFQ used in other prospective studies.
High-dimension Tensor Completion via Gradient-based Optimization Under Tensor-train Format

Tensor train (TT) decomposition has drawn people's attention due to its powerful representation ability and performance stability in high-order tensors. In this paper, we propose a novel approach to recover the missing entries of incomplete data represented by higher-order tensors. We attempt to find the low-rank TT decomposition of the incomplete data which captures the latent features of the whole data and then reconstruct the missing entries. By applying gradient descent algorithms, tensor completion problem is efficiently solved by optimization models. We propose two TT-based algorithms: Tensor Train Weighted Optimization (TT-WOPT) and Tensor Train Stochastic Gradient Descent (TT-SGD) to optimize TT decomposition factors. In addition, a method named Visual Data Tensorization (VDT) is proposed to transform visual data into higher-order tensors, resulting in the performance improvement of our algorithms. The experiments in synthetic data and visual data show high efficiency and performance of our algorithms compared to the state-of-the-art completion algorithms, especially in high-order, high missing rate, and large-scale tensor completion situations.
USING CRITICAL SUCCESS FACTORS FOR ASSESSING CRITICAL ACTIVITIES IN ERP IMPLEMENTATION WITHIN SMES

Aim of this research is the investigation and analysis of the critical success factors (CSF) in the implementation of ERP systems within SMEs. Papers in the ERP research field have focused on successes and failures of implementing systems into large organizations. Within the highly differentiated set of computer based systems available, the ERP systems represent the most common solution adopted by large companies to pursue their strategies. On the contrary, until now small and medium enterprises (SMEs) have shown little interest in ERP systems due to the lack of internal competence and resources that characterize those companies. Nevertheless, now that ERP vendors’ offer shows a noteworthy adjustment to SMEs organizational and business characteristics it seems of a certain interest to study and deeply analyze the reasons that can inhibit or foster ERP adoption within SMEs. This approach cannot leave out of consideration the analysis of the CSFs in ERP implementation: despite their wide outline in the most qualified literature, very seldom these research efforts have been addressed to SMEs. This paper aims at proposing a methodology to support the small medium entrepreneur in identifying the critical factors to be monitored along the whole ERP adoption process.
Competition and Cooperation among Relational Memory Representations

Mnemonic processing engages multiple systems that cooperate and compete to support task performance. Exploring these systems’ interaction requires memory tasks that produce rich data with multiple patterns of performance sensitive to different processing sub-components. Here we present a novel context-dependent relational memory paradigm designed to engage multiple learning and memory systems. In this task, participants learned unique face-room associations in two distinct contexts (i.e., different colored buildings). Faces occupied rooms as determined by an implicit gender-by-side rule structure (e.g., male faces on the left and female faces on the right) and all faces were seen in both contexts. In two experiments, we use behavioral and eye-tracking measures to investigate interactions among different memory representations in both younger and older adult populations; furthermore we link these representations to volumetric variations in hippocampus and ventromedial PFC among older adults. Overall, performance was very accurate. Successful face placement into a studied room systematically varied with hippocampal volume. Selecting the studied room in the wrong context was the most typical error. The proportion of these errors to correct responses positively correlated with ventromedial prefrontal volume. This novel task provides a powerful tool for investigating both the unique and interacting contributions of these systems in support of relational memory.
Analysing the Woo-Lam Protocol Using CSP and Rank Functions

Designing security protocols is a challenging and deceptive exercise. Even small protocols providing straightforward security goals, such as authentication, have been hard to design correctly, leading to the presence of many subtle attacks. Over the years various formal approaches have emerged to analyse security protocols making use of different formalisms. Schneider has developed a formal approach to modelling security protocols using the process algebra CSP (Communicating Sequential Processes). He introduces the notion of rank functions to analyse the protocols. We demonstrate an application of this approach to the Woo-Lam protocol. We describe the protocol in detail along with an established attack on its goals. We then describe Schneider’s rank function theorem and use it to analyse the protocol. ACM Classification: C.2. 2 (Communication/Networking and Information Technology – Network Protocols – Protocol Verification), D.2. 4 (Software Engineering – Software/Program Verification – Formal Methods), D.4. 6 (Operating Systems – Security and Privacy Protection – Authentication)
Microbiological aspects of the biofilm on wooden utensils used to make a Brazilian artisanal cheese

The artisanal Minas cheese is produced from raw cow’s milk and wooden utensils were employed in its manufacture, which were replaced by other materials at the request of local laws. This substitution caused changes in the traditional characteristics of cheese. Due to the absence of scientific studies indicating the microbial composition of biofilms formed on wooden forms, tables and shelves used in these cheese production, the present work evaluated the counts of Staphylococcus aureus, Escherichia coli, coliforms at 32 °C, yeasts, presumptive mesophilic Lactobacillus spp. and Lactococcus spp. in these biofilms, milk, whey endogenous culture and ripened cheese in two traditional regions: Serro and Serra da Canastra. Also, we checked for the presence of Salmonella sp. and Listeria monocytogenes in the ripened cheeses. The ultra structure of the biofilms was also assessed. Counts above legislation (> 2 log cfu/mL) for the pathogens evaluated were found in milk samples from both regions. Only one shelf and one form from Serro were above limits proposed (5 cfu/cm2 for S. aureus and E. coli and 25 cfu/cm2 for coliforms) in this study for contaminants evaluated. In Canastra, few utensils presented safe counting of pathogens. There was no Salmonella sp. and Listeria monocytogenes in the cheeses after ripening. Thus, the quality of the cheese is related to improving the microbiological quality of milk, implementation and maintenance of good manufacturing practices, correct cleaning of wooden utensils, and not its replacement.
Efficacy of Self-guided Internet-Based Cognitive Behavioral Therapy in the Treatment of Depressive Symptoms: A Meta-analysis of Individual Participant Data

Importance Self-guided internet-based cognitive behavioral therapy (iCBT) has the potential to increase access and availability of evidence-based therapy and reduce the cost of depression treatment. Objectives To estimate the effect of self-guided iCBT in treating adults with depressive symptoms compared with controls and evaluate the moderating effects of treatment outcome and response. Data Sources A total of 13 384 abstracts were retrieved through a systematic literature search in PubMed, Embase, PsycINFO, and Cochrane Library from database inception to January 1, 2016. Study Selection Randomized clinical trials in which self-guided iCBT was compared with a control (usual care, waiting list, or attention control) in individuals with symptoms of depression. Data Extraction and Synthesis Primary authors provided individual participant data from 3876 participants from 13 of 16 eligible studies. Missing data were handled using multiple imputations. Mixed-effects models with participants nested within studies were used to examine treatment outcomes and moderators. Main Outcomes and Measures Outcomes included the Beck Depression Inventory, Center for Epidemiological Studies–Depression Scale, and 9-item Patient Health Questionnaire scores. Scales were standardized across the pool of the included studies. Results Of the 3876 study participants, the mean (SD) age was 42.0 (11.7) years, 2531 (66.0%) of 3832 were female, 1368 (53.1%) of 2574 completed secondary education, and 2262 (71.9%) of 3146 were employed. Self-guided iCBT was significantly more effective than controls on depressive symptoms severity (&bgr; = −0.21; Hedges g = 0.27) and treatment response (&bgr; = 0.53; odds ratio, 1.95; 95% CI, 1.52-2.50; number needed to treat, 8). Adherence to treatment was associated with lower depressive symptoms (&bgr; = −0.19; P = .001) and greater response to treatment (&bgr; = 0.90; P < .001). None of the examined participant and study-level variables moderated treatment outcomes. Conclusions and Relevance Self-guided iCBT is effective in treating depressive symptoms. The use of meta-analyses of individual participant data provides substantial evidence for clinical and policy decision making because self-guided iCBT can be considered as an evidence-based first-step approach in treating symptoms of depression. Several limitations of the iCBT should be addressed before it can be disseminated into routine care.
Imbalanced nutrients as triggers for black shale formation in a shallow shelf setting during the OAE 2 (Wunstorf, Germany)

Abstract. During the oceanic anoxic event 2 (OAE 2) in the Mid-Cretaceous Period, widespread black shale (BS) formation occurred, reflecting perturbations in major biogeochemical cycles. Here we present geochemical and biomarker data of the OAE 2 from a shelf setting situated at about 100–150 m water depth (Wunstorf, Germany). Our data support that processes inducing BS deposition were related to orbital cyclicity in Wunstorf and that they were not restricted to the time of the OAE 2 carbon isotope excursion. Correlations of total organic carbon (TOC) and δ15N and high relative abundances of functionalized hopanoids (including 2-methylated structures) suggest that BS were formed during times of imbalanced nutrients with high phosphorus inputs and increased cyanobacterial nitrogen fixation. Periods of BS formation were also characterized by enhanced growth of dinoflagellates and bacteriovorous ciliates, the latter supporting the presence of a stratified water body. The lack of biomarkers specific for green sulfur bacteria excludes photic zone euxinia during OAE 2 in Wunstorf. Conflicting maturities and biomarker distributions in kerogen and extractable organic matter and, interestingly, a negative correlation of the diagenetically resistant 2-methyl hopane hydrocarbons with TOC indicate a complex depositional setting at Wunstorf. This might have been induced by high continental runoff during BS formation and the accompanying mobilisation of refractory OM from the shelves and near shore areas.
Formal Verification of Transactional Systems

Today, the trend in software is toward bigger, more complex systems. This is due in part to the fact that computers become more powerful every year leading users to expect more from them. People want software that is better adapted to their need which, in turn, merely makes software more complex. This trend has also been influenced by the expanding use of the internet for exchanging all kinds of information. As a new computational infra-structure has become available, new distributed applications which were previously too expensive or too complex have become common. In this context, web based systems has become a popular topic for business and academic research. However, web applications tend to generate complex systems. As new services are created, the frequency with which errors appear has increased significantly. This paper presents the UML-CAFE, an environment which can be used to help the designer in the development of transactional systems, such as web based ones. It is divided into the UML-CAFE Methodology, a set of transformation patterns, and the UML-CAFE translator to describe and map UML specifications into a formal model to be verified.
MaxiK channel mediates beta2-adrenoceptor-activated relaxation to isoprenaline through cAMP-dependent and -independent mechanisms in guinea-pig tracheal smooth muscle.

We examined the contribution of large-conductance, Ca(2+)-sensitive K+ (MaxiK) channel to beta2-adrenoceptor-activated relaxation to isoprenaline in guinea-pig tracheal smooth muscle focusing on the role for cAMP in the coupling between beta2-adrenoceptor and MaxiK channel. Isoprenaline-elicited relaxation was confirmed to be mediated through beta2-type of adrenoceptor since the response was antagonized in a competitive fashion by a beta2-selective adrenoceptor antagonist butoxamine with a pA2 value of 6.56. Isoprenaline-induced relaxation was significantly potentiated by a selective inhibitor of cyclic AMP-specific phosphodiesterase, Ro-20-1724 (0.1-1 microM). cAMP-dependent mediation of MaxiK channel in the relaxant response to isoprenaline was evidenced since the potentiated response to isoprenaline by the presence of Ro-20-1724 (1 microM) was inhibited by the channel selective blocker, iberiotoxin (IbTx, 100 nM). This concept was supported by the finding that the relaxation to a membrane permeable cAMP analogue, 8-bromo-cAMP (1 mM), was susceptible to the inhibition by IbTx. On the other hand, isoprenaline-induced relaxation was not practically diminished by an adenylyl cyclase inhibitor SQ 22,536 (100 microM). However, isoprenaline-induced relaxation in the presence of SQ 22,536 was suppressed by IbTx. Characteristics of isoprenaline-induced relaxant response, i.e., impervious to SQ 22,536 but susceptible to IbTx, were practically mimicked by cholera toxin (CTX, 5 microg/ml), an activator of adenylyl cyclase coupled-heterotrimeric guanine nucleotide-binding regulatory protein Gs. These findings indicate that in guinea-pig tracheal smooth muscle: 1) MaxiK channel substantially mediates beta2-adrenoceptor-activated relaxation; 2) both cAMP-dependent and -independent mechanisms underlie the functional coupling between beta2-adrenoceptor and MaxiK channel to induce muscle relaxation; and 3) direct regulation of MaxiK channel by Gs operates in cAMP-independent coupling between beta2-adrenoceptor and this ion channel.
Infectious Diseases Society of America/American Thoracic Society Consensus Guidelines on the Management of Community-Acquired Pneumonia in Adults

Lionel A. Mandell, Richard G. Wunderink, Antonio Anzueto, John G. Bartlett, G. Douglas Campbell, Nathan C. Dean, Scott F. Dowell, Thomas M. File, Jr. Daniel M. Musher, Michael S. Niederman, Antonio Torres, and Cynthia G. Whitney McMaster University Medical School, Hamilton, Ontario, Canada; Northwestern University Feinberg School of Medicine, Chicago, Illinois; University of Texas Health Science Center and South Texas Veterans Health Care System, San Antonio, and Michael E. DeBakey Veterans Affairs Medical Center and Baylor College of Medicine, Houston, Texas; Johns Hopkins University School of Medicine, Baltimore, Maryland; Division of Pulmonary, Critical Care, and Sleep Medicine, University of Mississippi School of Medicine, Jackson; Division of Pulmonary and Critical Care Medicine, LDS Hospital, and University of Utah, Salt Lake City, Utah; Centers for Disease Control and Prevention, Atlanta, Georgia; Northeastern Ohio Universities College of Medicine, Rootstown, and Summa Health System, Akron, Ohio; State University of New York at Stony Brook, Stony Brook, and Department of Medicine, Winthrop University Hospital, Mineola, New York; and Cap de Servei de Pneumologia i Allergia Respiratoria, Institut Clinic del Torax, Hospital Clinic de Barcelona, Facultat de Medicina, Universitat de Barcelona, Institut d’Investigacions Biomediques August Pi i Sunyer, CIBER CB06/06/0028, Barcelona, Spain.
Scienti fi c evidence for health effects attributed to the consumption of probiotics and prebiotics : an update for current perspectives and future challenges

Probiotics and prebiotics, mainly commercialised as food ingredients and also as supplements, are considered highly profitable niche markets. However, in recent years, the food industry has suffered from a series of health claim restrictions on probiotics and prebiotics in many parts of the world, including those made by the European Food Safety Authority. Therefore, we reviewed the core benefits of probiotic and prebiotic consumption on health. A number of studies have examined the prevention and/or management of intestinal infections, respiratory tract infections, CVD, osteoporosis, urogenital infections, cavities, periodontal disease and halitosis, allergic reactions, inflammatory bowel disease and irritable bowel syndrome and Helicobacter pylori gastric infections. In fact, a deeper understanding of the mechanisms involved in human microbiota and immune system modulation by probiotics and prebiotics relies on continuous efforts to establish suitable biomarkers of health and diseases risk factors for the design of clinical trials required for health claim approval. In spite of the promising results, the performance of large, long-term, well-planned, well-aligned clinical studies is crucial to provide more reliability and a more solid basis for the outcomes achieved and to support the potential use of probiotics and prebiotics in clinical practice.
Gene expression profile identifies potential biomarkers for human intervertebral disc degeneration

The present study aimed to reveal the potential genes associated with the pathogenesis of intervertebral disc degeneration (IDD) by analyzing microarray data using bioinformatics. Gene expression profiles of two regions of the intervertebral disc were compared between patients with IDD and controls. GSE70362 containing two groups of gene expression profiles, 16 nucleus pulposus (NP) samples from patients with IDD and 8 from controls, and 16 annulus fibrosus (AF) samples from patients with IDD and 8 from controls, was downloaded from the Gene Expression Omnibus database. A total of 93 and 114 differentially expressed genes (DEGs) were identified in NP and AF samples, respectively, using a limma software package for the R programming environment. Gene Ontology (GO) function enrichment analysis was performed to identify the associated biological functions of DEGs in IDD, which indicated that the DEGs may be involved in various processes, including cell adhesion, biological adhesion and extracellular matrix organization. Pathway enrichment analysis using the Kyoto Encyclopedia of Genes and Genomes (KEGG) demonstrated that the identified DEGs were potentially involved in focal adhesion and the p53 signaling pathway. Further analysis revealed that there were 35 common DEGs observed between the two regions (NP and AF), which may be further regulated by 6 clusters of microRNAs (miRNAs) retrieved with WebGestalt. The genes in the DEG-miRNA regulatory network were annotated using GO function and KEGG pathway enrichment analysis, among which extracellular matrix organization was the most significant disrupted biological process and focal adhesion was the most significant dysregulated pathway. In addition, the result of protein-protein interaction network modules demonstrated the involvement of inflammatory cytokine interferon signaling in IDD. These findings may not only advance the understanding of the pathogenesis of IDD, but also identify novel potential biomarkers for this disease.
Comparison of Human Immunodeficiency Virus Type 1 Viral Loads in Kenyan Women, Men, and Infants during Primary and Early Infection

ABSTRACT Steady-state levels of human immunodeficiency virus type 1 (HIV-1) RNA in plasma reached at approximately 4 months postinfection are highly predictive of disease progression. Several studies have investigated viral levels in adults or infants during primary and early infection. However, no studies have directly compared these groups. We compared differences in peak and set point plasma HIV-1 RNA viral loads among antiretrovirus-naive Kenyan infants and adults for whom the timing of infection was well defined. Peak and set point viral loads were significantly higher in infants than in adults. We did not observe any gender-specific differences in viral set point in either adults or infants. However, infants who acquired HIV-1 in the first 2 months of life, either in utero, intrapartum, or through early breast milk transmission, had significantly higher set point HIV-1 RNA levels than infants who were infected after 2 months of age through late breast milk transmission or adults who were infected through heterosexual transmission.