Miracle-dz/UniFAR-FTUs huggingface dataset:
Comparative Genomics and Transcriptional Analysis of Flavobacterium columnare Strain ATCC 49512

Flavobacterium columnare is a Gram-negative fish pathogen causing columnaris disease in wild and cultured fish species. Although the pathogen is widespread in aquatic environments and fish worldwide, little is known about biology of F. columnare and mechanisms of columnaris disease pathogenesis. Previously we presented the complete genome sequence of F. columnare strain ATCC 49512. Here we present a comparison of the strain ATCC 49512 genome to four other Flavobacterium genomes. In this analysis, we identified predicted proteins whose functions indicate F. columnare is capable of denitrification, which would enable anaerobic growth in aquatic pond sediments. Anaerobic growth of F. columnare ATCC 49512 with nitrate supplementation was detected experimentally. F. columnare ATCC 49512 had a relatively high number of insertion sequences and genomic islands compared to the other Flavobacterium species, suggesting a larger degree of horizontal gene exchange and genome plasticity. A type VI subtype III secretion system was encoded in F. columnare along with F. johnsoniae and F. branchiophilum. RNA sequencing proved to be a valuable technique to improve annotation quality; 41 novel protein coding regions were identified, 16 of which had a non-traditional start site (TTG, GTG, and CTT). Candidate small noncoding RNAs were also identified. Our results improve our understanding of F. columnare ATCC 49512 biology, and our results support the use of RNA sequencing to improve annotation of bacterial genomes, particularly for type strains.
Learning from Noisy Labels with Deep Neural Networks

The availability of large labeled datasets has allowed Convolutional Network models to achieve impressive recognition results. However, in many settings manual annotation of the data is impractical; instead our data has noisy labels, i.e. there is some freely available label for each image which may or may not be accurate. In this paper, we explore the performance of discriminatively-trained Convnets when trained on such noisy data. We introduce an extra noise layer into the network which adapts the network outputs to match the noisy label distribution. The parameters of this noise layer can be estimated as part of the training process and involve simple modifications to current training infrastructures for deep networks. We demonstrate the approaches on several datasets, including large scale experiments on the ImageNet classification benchmark.
CD40L‐expressing CD8 T cells prime CD8α+ DC for IL‐12p70 production

CD8α+ DC are implicated as the principle DC subset for cross‐presentation and cross‐priming of cytotoxic CD8 T cell responses. In this study, we demonstrate another unique facet of the CD8α+ DC and CD8 T cell relationship, by showing that CD8 T cells reciprocally activate CD8α+ DC, but not CD8α– DC, for IL‐12p70 production, the key Th1‐promoting cytokine. This effect was observed during an antigen‐specific interaction between DC and activated CD8 T cells, along with secondary TLR stimulation of DC by LPS. Activated CD8 T cells use a combination of IFN‐γ and CD40L, which is rapidly up‐regulated post‐stimulation, to prime DC for IL‐12p70 production during an antigen‐specific response. Our results suggest that the interaction between CD8α+ DC and antigen‐primed CD8 T cells may form an important component of Th1‐mediated immunity through the induction of IL‐12p70.
The Impact of Community Embeddedness on Turnover: An Investigation of the Moderating Effects of Career Plateauing, Occupational Portability, and Occupational Commutability

Abstract : This dissertation tested the effects of community embeddedness on predicting turnover decisions of members of an organization characterized by frequent relocation and limited discretionary organizational exit. The theoretical premise was that the organization's members would value the links and fit to their community such that thoughts of leaving or actually leaving the organization would be lessened by their desire to remain enmeshed in their communities. Community embeddedness was believed to account for significant incremental variance, beyond that of job satisfaction, organizational commitment, job search, and job alternatives, in predicting turnover of members of the U.S. Air Force using an archival data set. The moderating effects of perceptions of career plateauing, perceived occupational portability, and occupational commutability on intent to turnover and actual turnover also were tested, but no significant findings resulted. The author confirmed that community embeddedness did increase the prediction of actual turnover when considered in conjunction with turnover intentions, but community embeddedness did not increase the prediction of intent to turnover. Results suggested that reconsideration of process models of turnover that identify intent to turnover as the direct antecedent of actual turnover is necessary to evaluate the proper alignment of community embeddedness within the models. Theoretical refinement is necessary to refine the boundary conditions of community embeddedness.
Neural networks with dynamical thresholds.

On incorpore les fonctions de seuil locales dans la dynamique du modele d'Hopfield. Le diagramme resultant a des phases ferromagnetiques, paramagnetiques et periodiques. Ce modele est resolu par une equation maitresse et approximativement par des systemes d'equations simplifiees supportees par des simulations numeriques
IRIDIUM CATALYST SUPPORTED ON CONDUCTIVE TITANIUM OXIDES FOR POLYMER ELECTROLYTE MEMBRANE ELECTROLYSIS

1 National Research Center «Kurchatov Institute» 1, AkademikaKurchatovasq. , Moscow, 123182, Russia, e-mail: fateev_vn@nrcki.ru 2 National Research University «Moscow Power Engineering Institute» 14,Krasnokazarmennayastr. , Moscow, 111250, Russia 3 HySA Infrastructure Center of Competence, North-West University, Faculty of Engineering Private Bag X6001, Potchefstroom Campus, 2531, South Africa 4 Institute of Electrochemistry and Energy Systems, Bulgarian Academy of Sciences 10, Acad. GeorgiBonchevstr, Sofia, 1113, Bulgaria 5 Institute of Catalysis and Inorganic Chemistry of ANAS H.Javidave. , 113, Baku AZ 1143, Azerbaijan Republic
Comparison of the C4.5 and a Naive Bayes Classifier for the Prediction of Lung Cancer Survivability

Numerous data mining techniques have been developed to extract information and identify patterns and predict trends from large data sets. In this study, two classification techniques, the J48 implementation of the C4.5 algorithm and a Naive Bayes classifier are applied to predict lung cancer survivability from an extensive data set with fifteen years of patient records. The purpose of the project is to verify the predictive effectiveness of the two techniques on real, historical data. Besides the performance outcome that renders J48 marginally better than the Naive Bayes technique, there is a detailed description of the data and the required pre-processing activities. The performance results confirm expectations while some of the issues that appeared during experimentation, underscore the value of having domain-specific understanding to leverage any domain-specific characteristics inherent in the data.
A potential link among antioxidant enzymes, histopathology and trace elements in canine visceral leishmaniasis

Canine visceral leishmaniasis (CVL) is a severe and fatal systemic chronic inflammatory disease. We investigated the alterations in, and potential associations among, antioxidant enzymes, trace elements and histopathology in CVL. Blood and tissue levels of Cu‐Zn superoxide dismutase, catalase and glutathione peroxidase were measured in mixed‐breed dogs naturally infected with Leishmania infantum chagasi, symptomatic (n = 19) and asymptomatic (n = 11). Serum levels of copper, iron, zinc, selenium and nitric oxide, and plasma lipid peroxidation were measured. Histological and morphometric analyses were conducted of lesions in liver, spleen and lymph nodes. We found lower blood catalase and glutathione peroxidase activity to be correlated with lower iron and selenium respectively. However, higher activity of Cu‐Zn superoxide dismutase was not correlated with the increase in copper and decreased in zinc observed in infected animals compared to controls. Organ tissue was characterized by lower enzyme activity in infected dogs than in controls, but this was not correlated with trace elements. Lipid peroxidation was higher in symptomatic than in asymptomatic and control dogs and was associated with lesions such as chronic inflammatory reaction, congestion, haemosiderin and fibrosis. Systemic iron deposition was observed primarily in the symptomatic dogs showing a higher tissue parasite load. Dogs with symptomatic CVL displayed enhanced LPO and Fe tissue deposition associated with decreased levels of antioxidant enzymes. These results showed new points in the pathology of CVL and might open new treatment perspectives associated with antioxidants and the role of iron in the pathogenesis of CVL.
Anisotropy, Fiber Curvature, and Bath Loading Effects on Activation in Thin and Thick Cardiac Tissue Preparations:

Anisotropy Effects in a 3D Bidomain. Introduction: A modeling study is presented to explore the effects of tissue conductivity, fiber orientation, and presence of an adjoining extracellular volume conductor on electrical conduction in cardiac muscle. Simulated results are compared with those of classical in vitro experiments on superfused thin layer preparations and on whole hearts.
Soluble intercellular adhesion molecule 1-immunoglobulin G1 immunoadhesin mediates phagocytosis of malaria-infected erythrocytes

We describe an immunoadhesin molecule containing intercellular adhesion molecule 1 (ICAM-1) molecularly fused to hinge and CH2 and CH3 domains of the human immunoglobulin G1 H chain that binds Plasmodium falciparum- infected erythrocytes. This receptor-based immunoadhesin is an effective and specific inhibitor of P. falciparum-infected erythrocyte adhesion to ICAM-1-bearing surfaces, but does not inhibit leukocyte function antigen 1 (LFA-1) interaction with ICAM-1. Furthermore, the immunoadhesin promotes phagocytosis and destruction of parasitized erythrocytes by human monocytes. Each of these modes of action has potential for the therapy of malaria.
Evaluation of Colilert-18 for Detection of Coliforms and Eschericha coli in Subtropical Freshwater

ABSTRACT The accuracy of Colilert-18 as a test for coliforms and Escherichia coli in subtropical freshwater was evaluated by using API 20E strips and fatty acid methyl ester analysis. The false-positive and -negative rates of detection were 7.4 and 3.5%, respectively, for E. coli and 9.6 and 6.3%, respectively, for coliforms.
Support Consistency of Direct Sparse-Change Learning in Markov Networks

We study the problem of learning sparse structure changes between two Markov networks P and Q. Rather than fitting two Markov networks separately to two sets of data and figuring out their differences, a recent work proposed to learn changes directly via estimating the ratio between two Markov network models. Such a direct approach was demonstrated to perform excellently in experiments, although its theoretical properties remained unexplored. In this paper, we give sufficient conditions for successful change detection with respect to the sample size np, nq, the dimension of data m, and the number of changed edges d.
Susceptibility Effects of Bone Trabeculae Quantification In Vivo Using an Asymmetric Spin‐Echo Technique

RATIONALE AND OBJECTIVESThe authors assessed the capability of magnetic resonance imaging in measuring bone mineral density in vivo. METHODSUsing the in-phase asymmetric spin-echo technique, the susceptibility effect (T2*susceptibility) was measured in lumbar vertebrae in vivo. Calcium density was measured with single energy quantitative computed tomography scan. The values of the susceptibility effect were correlated with calcium density. RESULTSA statistically significant positive correlation was observed between signal loss due to susceptibility-induced in-homogeneity and the calcium density in the region of interest. The change in 1/T2*susceptibility per unit change in density was 0.114 seconds-1/mg/cm3. T2*susceptibility was 14.3 mseconds in volunteers and 17.4 mseconds in postoophorectomy patients. CONCLUSIONSTo some extent, quantification of bone density is possible using magnetic resonance imaging; however, the relatively wide dispersion of the susceptibility effect, plotted against the calcium density in the axial skeleton, indicates that other factors, such as the three-dimensional structure of bone trabeculae, may play important roles in determining magnetic resonance parameters.
Possible Ancestral Structure in Human Populations

Determining the evolutionary relationships between fossil hominid groups such as Neanderthals and modern humans has been a question of enduring interest in human evolutionary genetics. Here we present a new method for addressing whether archaic human groups contributed to the modern gene pool (called ancient admixture), using the patterns of variation in contemporary human populations. Our method improves on previous work by explicitly accounting for recent population history before performing the analyses. Using sequence data from the Environmental Genome Project, we find strong evidence for ancient admixture in both a European and a West African population (p ≈ 10−7), with contributions to the modern gene pool of at least 5%. While Neanderthals form an obvious archaic source population candidate in Europe, there is not yet a clear source population candidate in West Africa.
Angiotensin II Activates the Calcineurin/NFAT Signaling Pathway and Induces Cyclooxygenase-2 Expression in Rat Endometrial Stromal Cells

Cyclooxygenase (COX)-2, the inducible isoform of cyclooxygenase, plays a role in the process of uterine decidualization and blastocyst attachment. On the other hand, overexpression of COX-2 is involved in the proliferation of the endometrial tissue during endometriosis. Deregulation of the renin-angiotensin-system plays a role in the pathophysiology of endometriosis and pre-eclampsia. Angiotensin II increases intracellular Ca2+ concentration by targeting phospholypase C-gamma in endometrial stromal cells (ESC). A key element of the cellular response to Ca2+ signals is the activity of the Ca2+- and calmodulin-dependent phosphatase calcineurin. Our first aim was to study whether angiotensin II stimulated Cox-2 gene expression in rat ESC and to analyze whether calcineurin activity was involved. In cells isolated from non-pregnant uteri, COX-2 expression -both mRNA and protein- was induced by co-stimulation with phorbol ester and calcium ionophore (PIo), as well as by angiotensin II. Pretreatment with the calcineurin inhibitor cyclosporin A inhibited this induction. We further analyzed the role of the calcineurin/NFAT signaling pathway in the induction of Cox-2 gene expression in non-pregnant rat ESC. Cyclosporin A abolished NFATc1 dephosphorylation and translocation to the nucleus. Cyclosporin A also inhibited the transcriptional activity driven by the Cox-2 promoter. Exogenous expression of the peptide VIVIT -specific inhibitor of calcineurin/NFAT binding- blocked the activation of Cox-2 promoter and the up-regulation of COX-2 protein in these cells. Finally we analyzed Cox-2 gene expression in ESC of early-pregnant rats. COX-2 expression -both mRNA and protein- was induced by stimulation with PIo as well as by angiotensin II. This induction appears to be calcineurin independent, since it was not abrogated by cyclosporin A. In conclusion, angiotensin II induced Cox-2 gene expression by activating the calcineurin/NFAT signaling pathway in endometrial stromal cells of non-pregnant but not of early-pregnant rats. These results might be related to differential roles that COX-2 plays in the endometrium.
EEG Correlates of Self-Referential Processing

Self-referential processing has been principally investigated using functional magnetic resonance imaging (fMRI). However, understanding of the brain functioning is not possible without careful comparison of the evidence coming from different methodological domains. This paper aims to review electroencephalographic (EEG) studies of self-referential processing and to evaluate how they correspond, complement, or contradict the existing fMRI evidence. There are potentially two approaches to the study of EEG correlates of self-referential processing. Firstly, because simultaneous registration of EEG and fMRI has become possible, the degree of overlap between these two signals in brain regions related to self-referential processing could be determined. Second and more direct approach would be the study of EEG correlates of self-referential processing per se. In this review, I discuss studies, which employed both these approaches and show that in line with fMRI evidence, EEG correlates of self-referential processing are most frequently found in brain regions overlapping with the default network, particularly in the medial prefrontal cortex. In the time domain, the discrimination of self- and others-related information is mostly associated with the P300 ERP component, but sometimes is observed even earlier. In the frequency domain, different frequency oscillations have been shown to contribute to self-referential processing, with spontaneous self-referential mentation being mostly associated with the alpha frequency band.
A Regulatory Network for Coordinated Flower Maturation

For self-pollinating plants to reproduce, male and female organ development must be coordinated as flowers mature. The Arabidopsis transcription factors AUXIN RESPONSE FACTOR 6 (ARF6) and ARF8 regulate this complex process by promoting petal expansion, stamen filament elongation, anther dehiscence, and gynoecium maturation, thereby ensuring that pollen released from the anthers is deposited on the stigma of a receptive gynoecium. ARF6 and ARF8 induce jasmonate production, which in turn triggers expression of MYB21 and MYB24, encoding R2R3 MYB transcription factors that promote petal and stamen growth. To understand the dynamics of this flower maturation regulatory network, we have characterized morphological, chemical, and global gene expression phenotypes of arf, myb, and jasmonate pathway mutant flowers. We found that MYB21 and MYB24 promoted not only petal and stamen development but also gynoecium growth. As well as regulating reproductive competence, both the ARF and MYB factors promoted nectary development or function and volatile sesquiterpene production, which may attract insect pollinators and/or repel pathogens. Mutants lacking jasmonate synthesis or response had decreased MYB21 expression and stamen and petal growth at the stage when flowers normally open, but had increased MYB21 expression in petals of older flowers, resulting in renewed and persistent petal expansion at later stages. Both auxin response and jasmonate synthesis promoted positive feedbacks that may ensure rapid petal and stamen growth as flowers open. MYB21 also fed back negatively on expression of jasmonate biosynthesis pathway genes to decrease flower jasmonate level, which correlated with termination of growth after flowers have opened. These dynamic feedbacks may promote timely, coordinated, and transient growth of flower organs.
Clinical prediction of Alzheimer disease dementia across the spectrum of mild cognitive impairment.

OBJECTIVE To determine whether clinical assessment methods that grade the severity of impairments within the spectrum of mild cognitive impairment (MCI) can predict clinical course, particularly among very mildly impaired individuals who do not meet formal MCI criteria as implemented in clinical trials. DESIGN Cohort. SETTING Community volunteers. PARTICIPANTS From a longitudinal study of normal (Clinical Dementia Rating [CDR] = 0; n = 77) and mildly impaired (CDR = 0.5; n = 167) participants with 5 or more annual clinical assessments, baseline level of cognitive impairment in daily life was graded using CDR sum of boxes (CDR-SB) and level of cognitive performance impairment was graded using neuropsychological test scores. MAIN OUTCOME MEASURES Five-year outcome measures included (1) probable Alzheimer disease (AD) diagnosis and (2) clinical "decline" (CDR-SB increase > or = 1.0). Logistic regression models were used to assess the ability of baseline measures to predict outcomes in the full sample and separately in the subjects who did not meet formal MCI criteria as implemented in a multicenter clinical trial (n = 125; "very mild cognitive impairment" [vMCI]). RESULTS The presence of both higher CDR-SB and lower verbal memory and executive function at baseline predicted greater likelihood of probable AD and decline. Five-year rates of probable AD and decline in vMCI (20%, AD; 49%, decline) were intermediate between normal participants (0%, AD; 28%, decline) and participants with MCI (41%, AD; 62%, decline). Within vMCI, likelihood of probable AD was predicted by higher CDR-SB and lower executive function. CONCLUSIONS Even in very mildly impaired individuals who do not meet strict MCI criteria as implemented in clinical trials, the degree of cognitive impairment in daily life and performance on neuropsychological testing predict likelihood of an AD diagnosis within 5 years. The clinical determination of relative severity of impairment along the spectrum of MCI may be valuable for trials of putative disease-modifying compounds, particularly as target populations are broadened to include less impaired individuals.
APOE influences vasospasm and cognition of noncomatose patients with subarachnoid hemorrhage

Objective: To determine the influence of the APOE genotype on functional and cognitive outcome and on the incidence and prognosis of clinical vasospasm (delayed ischemic neurologic deficit [DIND]) in noncomatose patients with aneurysmal subarachnoid hemorrhage (SAH). Methods: The authors reviewed the data of patients admitted for SAH to the Neurosurgical Departments of the San Gerardo Hospital of Monza (January 1996 to December 2001) and the Ospedali Riuniti of Bergamo (January 2002 to September 2003). The authors considered only noncomatose patients and evaluated outcome by means of the Rankin Disability Index and the Mini-Mental State Examination at least 6 months after the SAH. Statistical analysis: Uni- and multivariate logistic regression. Results: The authors included 101 patients. They found the ε4 allele in 26 patients (25.7%). The presence of the ε4 allele negatively affected the overall outcome (functional morbidity or cognitive morbidity, or both) (p = 0.0087) and, particularly, cognitive morbidity (p = 0.0028). Those with an ε4 allele had delayed ischemic neurologic deficit DINDs more frequently (p = 0.024) and, in the presence of DIND, they were more likely to show permanent neurologic deficits (p = 0.0051). Conclusions: ApoE4 negatively affects cognitive morbidity and delayed ischemic neurologic deficit recovery. The presence of an ε4 allele increases the risk of delayed ischemic neurologic deficit.