Miracle-dz/UniFAR-FTUs huggingface dataset:
Genome sequence of Phaeobacter daeponensis type strain (DSM 23529T), a facultatively anaerobic bacterium isolated from marine sediment, and emendation of Phaeobacter daeponensis

TF-218T is the type strain of the species Phaeobacter daeponensis Yoon et al. 2007, a facultatively anaerobic Phaeobacter species isolated from tidal flats. Here we describe the draft genome sequence and annotation of this bacterium together with previously unreported aspects of its phenotype. We analyzed the genome for genes involved in secondary metabolite production and its anaerobic lifestyle, which have also been described for its closest relative Phaeobacter caeruleus. The 4,642,596 bp long genome of strain TF-218T contains 4,310 protein-coding genes and 78 RNA genes including four rRNA operons and consists of five replicons: one chromosome and four extrachromosomal elements with sizes of 276 kb, 174 kb, 117 kb and 90 kb. Genome analysis showed that TF-218T possesses all of the genes for indigoidine biosynthesis, and on specific media the strain showed a blue pigmentation. We also found genes for dissimilatory nitrate reduction, gene-transfer agents, NRPS/PKS genes and signaling systems homologous to the LuxR/I system.
Forkhead Box Protein A1 Regulates UDP-Glucuronosyltransferase 2B15 Gene Transcription in LNCaP Prostate Cancer Cells

The UDP-glucuronosyltransferases (UGTs) 2B15 and 2B17 are the major UGTs involved in the inactivation and elimination of the active androgens, dihydrotestosterone and testosterone. Although regulation of these UGT genes by various endogenous and exogenous ligands, including steroid hormones and bile acids, is well documented, the mechanisms controlling their basal gene expression are poorly understood. We recently reported that Forkhead box protein A1 (FOXA1) regulates the basal expression of the UGT2B17 gene in prostate cancer cells. In this study, we show that FOXA1 also regulates basal expression of the UGT2B15 gene in the prostate cell line LNCaP (lymph node carcinoma of the prostate). FOXA1 binds to a site −208 to −217 base pairs relative to the UGT2B15 translation start site, as shown by electromobility shift and chromatin immunoprecipitation assays. Mutation of this site prevents binding and substantially decreases basal UGT2B15 promoter activity. Silencing of FOXA1 expression by small interfering RNA significantly reduced UGT2B15 transcript levels, further confirming a crucial role of FOXA1 in controlling UGT2B15 gene expression. Because local inactivation of active androgens by UGT2B15 and UGT2B17 has been shown to be a major determinant of androgen response and signaling activity, regulation of the UGT2B15 and UGT2B17 genes by FOXA1 may have an important role in the maintenance of androgen homeostasis within prostate cancer cells.
Improving the performance of speech recognition systems using fault-tolerant techniques

In this paper, using of fault tolerant techniques are studied and experimented in speech recognition systems to make these systems robust to noise. Recognizer redundancy is implemented to utilize the strengths of several recognition methods that each one has acceptable performance in a specific condition. Duplication-with-comparison and NMR methods are experimented with majority and plurality voting on a telephony Persian speech-enabled IVR system. Results of evaluations present two promising outcomes, first, it improves the performance considerably; second, it enables us to detect the outputs with low confidence.
Physiological Control of Molluscan Gill Cilia by 5-Hydroxytryptamine

An examination is made of the hypothesis that endogenous 5-hydroxytryptamine (5-HT) serves as a local hormone regulating ciliary activity in the lamellibranch gill. These cilia are sensitive to exogenous 5-HT and respond to it by a prompt, sustained, and reversible rise in beat frequency; at the same time the carbohydrate metabolism is stimulated, as described elsewhere. Control gill contains small but definite amounts of endogenous 5-HT according to bioassay, fluorometry, and chromatography. The amount can be increased markedly by exposing the isolated gill to the precursor substance 5-hydroxytryptophan but not l-tryptophan. As the tissue level of 5-HT rises, the spontaneous beat frequency also rises. Both remain elevated for hours and perhaps for days. The gill of Mytilus edulis is richer than the gill of Modiolus demissus in both endogenous 5-HT and effective 5-hydroxytryptophan decarboxylase activity. Modiolus gill lacks the 5-hydroxyindole oxidase by which Mytilus gill destroys 5-HT. What if any mechanism exists in Modiolus for degrading 5-HT is not known, but monoamine oxidase is not present. The 5-HT content of Mytilus and Modiolus gill cannot be modified by treatment with reserpine or α-methyl-dopa. Which cells of the gill synthesize and destroy 5-HT has not been established, but these observations support the concept that the physiological activity of lamellibranch gill cilia is controlled by a serotonergic mechanism.
Burden of Cardiovascular Morbidity and Mortality Following Humanitarian Emergencies: A Systematic Literature Review

Abstract Background The global burden of cardiovascular mortality is increasing, as is the number of large-scale humanitarian emergencies. The interaction between these phenomena is not well understood. This review aims to clarify the relationship between humanitarian emergencies and cardiovascular morbidity and mortality. Methods With assistance from a research librarian, electronic databases (PubMed, Scopus, CINAHL, and Global Health) were searched in January 2014. Findings were supplemented by reviewing citations of included trials. Observational studies reporting the effect of natural disasters and conflict events on cardiovascular morbidity and mortality in adults since 1997 were included. Studies without a comparison group were not included. Double-data extraction was utilized to abstract information on acute coronary syndrome (ACS), acute decompensated heart failure (ADHF), and sudden cardiac death (SCD). Review Manager 5.0 (Version 5.2, The Nordic Cochrane Centre; Copenhagen Denmark,) was used to create figures for qualitative synthesis. Results The search retrieved 1,697 unique records; 24 studies were included (17 studies of natural disasters and seven studies of conflict). These studies involved 14,583 cardiac events. All studies utilized retrospective designs: four were population-based, 15 were single-center, and five were multicenter studies. Twenty-three studies utilized historical controls in the primary analysis, and one utilized primarily geographical controls. Discussion Conflicts are associated with an increase in long-term morbidity from ACS; the short-term effects of conflict vary by study. Natural disasters exhibit heterogeneous effects, including increased occurrence of ACS, ADHF, and SCD. Conclusions In certain settings, humanitarian emergencies are associated with increased cardiac morbidity and mortality that may persist for years following the event. Humanitarian aid organizations should consider morbidity from noncommunicable disease when planning relief and recuperation projects. HaymanKG, SharmaD, WardlowRDII, SinghS. Burden of cardiovascular morbidity and mortality following humanitarian emergencies: a systematic literature review. Prehosp Disaster Med. 2015;30(1):1-9 .
Cloud microphysics, radiation and vertical velocities in two‐ and three‐dimensional simulations of deep convection

This study investigates the importance of dimensionality for the characteristics of simulations performed with cloud‐system resolving models (CSRMs). In addition to intrinsic questions related to dimensionality in CSRMs, the issue has gained added interest since CSRMs can be utilized instead of conventional cloud parametrizations to represent deep convection within global climate models. Such CSRMs may be either two‐ or three‐dimensional.
Contemporary issues of enterprise content management: the case of statoil

The concept of Enterprise Content Management (ECM) represents integrated enterprise-wide management of the life cycles of all forms of recorded information content and their metadata, organized according to corporate taxonomies, and supported by appropriate technological and administrative infrastructures. Based on a case study of a Norwegian oil company (Statoil), we identify a wide range of issues related to management of content, infrastructure, and change. The ECM perspective is found to integrate and extend the existing research areas of information resource management and document management, as well as the repository model of knowledge management. ECM thus deserves further attention beyond its current market hype, as a potential area of IS research crossing several previously separate areas of information management from the viewpoint of the enterprise.
Lipoxygenase-Quercetin Interaction: A Kinetic Study Through Biochemical and Spectroscopy Approaches

Lipoxygenases (EC 1.13.11.12, linoleate:oxygen, oxidoreductases, LOXs) which are widely found in plants, fungi, and animals, are a large monomeric protein family with non-heme, non-sulphur, iron cofactor containing dioxygenases that catalyze the oxidation of polyunsaturated fatty acids (PUFA) as substrate with at least one 1Z, 4Z-pentadiene moiety such as linoleic, linolenic and arachidonic acid to yield hydroperoxides (Gardner, 1991).
Now Dasher! Dash away!: longitudinal study of fast text entry by Eye Gaze

Dasher is one of the best known inventions in the area of text entry in recent years. It can be used with many input devices, but studies on user performance with it are still scarce. We ran a longitudinal study where 12 participants transcribed Finnish text with Dasher in ten 15-minute sessions using a Tobii 1750 eye tracker as a pointing device. The mean text entry rate was 2.5 wpm during the first session and 17.3 wpm during the tenth session. Our results show that very high text entry rates can be achieved with eye-operated Dasher, but only after several hours of training.
To Be or Not To Be Pseudocapacitive

There are an increasing number of studies regarding active electrode materials that undergo faradaic reactions but are used for electrochemical capacitor applications. Unfortunately, some of these materials are described as “pseudocapacitive” materials despite the fact that their electrochemical signature (e.g., cyclic voltammogram and charge/discharge curve) is analogous to that of a “battery” material, as commonly observed for Ni(OH)2 and cobalt oxides in KOH electrolyte. Conversely, true pseudocapacitive electrode materials such as MnO2 display electrochemical behavior typical of that observed for a capacitive carbon electrode. The difference between these two classes of materials will be explained, and we demonstrate why it is inappropriate to describe nickel oxide or hydroxide and cobalt oxide/hydroxide as pseudocapacitive electrode materials. © The Author(s) 2015. Published by ECS. This is an open access article distributed under the terms of the Creative Commons Attribution Non-Commercial No Derivatives 4.0 License (CC BY-NC-ND, http://creativecommons.org/licenses/by-nc-nd/4.0/), which permits non-commercial reuse, distribution, and reproduction in any medium, provided the original work is not changed in any way and is properly cited. For permission for commercial reuse, please email: oa@electrochem.org. [DOI: 10.1149/2.0201505jes] All rights reserved.
Neuroeconomics of Suicide

Suicidal behavior is a leading cause of injury and death worldwide. Suicide has been associated with psychiatric illnesses such as depression and schizophrenia, as well as economic uncertainty, and social/cultural factors. This study proposes a neuroeconomic framework of suicide. Neuroeconomic parameters (e.g., risk-attitude, probability weighting, time discounting in intertemporal choice, and loss aversion) are predicted to be related to suicidal behavior. Neurobiological and neuroendocrinological substrates such as serotonin, dopamine, cortisol (HPA axis), nitric oxide, serum cholesterol, epinephrine, norepinephrine, gonadal hormones (e.g., estradiol and progesterone), dehydroepiandrosterone (DHEA) in brain regiouns such as the orbitofrontal/dorsolateral prefrontal cortex and limbic regions (e.g., the amygdala) may supposedly be related to the neuroeconomic parameters modulating the risk of suicide. The present framework puts foundations for "molecular neuroeconomics" of decision-making processes underlying suicidal behavior.
Exposure to Medical Test Irradiation and Acute Leukemia Among Children With Down Syndrome: A Report From the Children's Oncology Group

OBJECTIVE. The etiology of acute childhood leukemia is not well understood, particularly among children with Down syndrome, in whom a 10- to 20-fold increased risk of leukemogenesis has been reported compared with children without Down syndrome. We explored the association between medical test irradiation, a postulated leukemogenic agent, and acute leukemia among children with Down syndrome. PATIENTS AND METHODS. Children with Down syndrome (controls) were frequency matched on age to children with Down syndrome and leukemia (cases) diagnosed at ages 0 to 19 years during the period 1997–2002 at participating Children's Oncology Group institutions in North America. Telephone interviews were completed with mothers of 158 cases (n = 97 acute lymphoblastic leukemia and n = 61 acute myeloid leukemia) and 173 controls. Paternal interviews were completed with 275 fathers and 40 mothers serving as surrogates. Three irradiation exposure periods were examined: preconception, in utero, and postnatal. Multivariate unconditional logistic regression models were constructed to evaluate the associations of interest, resulting in odds ratios and 95% confidence intervals. RESULTS. There was little evidence that maternal or paternal preconception irradiation exposure, intrauterine exposure, or postnatal exposure contributes to leukemogenesis in children with Down syndrome. Overall, no evidence for an effect of any periconceptional exposure was observed. Similar results were observed among acute lymphoblastic leukemia and acute myeloid leukemia cases analyzed separately. CONCLUSIONS. This was the first study, to our knowledge, to examine such an association among this unique patient population. The results do not provide evidence of a positive association between ionizing radiation exposure and acute leukemia among children with Down syndrome. The absence of an association should be encouraging for concerned parents of children with Down syndrome who undergo a series of diagnostic radiographs in the course of their standard care.
Atrial Myocyte Function and Ca2+ Handling Is Associated with Inborn Aerobic Capacity

Background Although high aerobic capacity is associated with effective cardiac function, the effect of aerobic capacity on atrial function, especially in terms of cellular mechanisms, is not known. We aimed to investigate whether rats with low inborn maximal oxygen uptake (VO2 max) had impaired atrial myocyte contractile function when compared to rats with high inborn VO2 max. Methods and Results Atrial myocyte function was depressed in Low Capacity Runners (LCR) relative to High Capacity Runners (HCR) which was associated with impaired Ca2+ handling. Fractional shortening was 52% lower at 2 Hz and 60% lower at 5 Hz stimulation while time to 50% relengthening was 43% prolonged and 55% prolonged, respectively. Differences in Ca2+ amplitude and diastolic Ca2+ level were observed at 5 Hz stimulation where Ca2+ amplitude was 70% lower and diastolic Ca2+ level was 11% higher in LCR rats. Prolonged time to 50% Ca2+ decay was associated with reduced sarcoplasmic reticulum (SR) Ca2+ ATPase function in LCR (39%). Na+/Ca2+ exchanger activity was comparable between the groups. Diastolic SR Ca2+ leak was increased by 109%. This could be partly explained by increased ryanodine receptors phosphorylation at the Ca2+-calmodulin-dependent protein kinase-II specific Ser-2814 site in LCR rats. T-tubules were present in 68% of HCR cells whereas only 33% LCR cells had these structures. In HCR, the significantly higher numbers of cells with T-tubules were combined with greater numbers of myocytes where Ca2+ release in the cell occurred simultaneously in central and peripheral regions, giving rise to faster and more spatial homogenous Ca2+-signal onset. Conclusion This data demonstrates that contrasting for low or high aerobic capacity leads to diverse functional and structural remodelling of atrial myocytes, with impaired contractile function in LCR compared to HCR rats.
Discovering Regulatory Network Topologies Using Ensemble Methods on GPGPUs With Special Reference to the Biological Clock of Neurospora crassa

Most genetic networks, such as that for the biological clock, are part of much larger modules controlling fundamental processes in the cell, such as metabolism, development, and response to environmental signals. For example, the biological clock is part of a much larger network controlling the circadian rhythms of about 2418 distinct genes in the genome (with 11 000 genes) of the model system, Neurospora crassa. Predicting and understanding the dynamics of all of these genes and their products in a genetic network describing how the clock functions is a challenge and beyond the current capability of the fastest serial computers. We have implemented a novel variable-topology supernet ensemble method using Markov chain Monte Carlo simulations to fit and discover a regulatory network of unknown topology composed of 2418 genes describing the entire clock circadian network, a network that is found in organisms ranging from bacteria to humans, by harnessing the power of the general-purpose graphics processing unit and exploiting the hierarchical structure of that genetic network. The result is the construction of a genetic network that explains mechanistically how the biological clock functions in the filamentous fungus N. crassa and is validated against over 31 000 data points from microarray experiments. Two transcription factors are identified targeting ribosome biogenesis in the clock network.
Gender and Religiousness: Deconstructing Universality, Constructing Complexity

The universality of higher female religiousness and insufficiency of any social explanation have led to proposals that it is a product of psychological or physiological differences. However, the female advantage in religiousness is not universal. Distinguishing Affective (personal piety) from Active (organizational participation) religiousness, in a third of nations (World Values Survey) women are no higher than men in active religiousness. Among Jews and Muslims worldwide, men are more religious than women. Combined, social factors actually explain much of the gender disparity in U.S. religiousness (General Social Survey); with personality, all of it in active religiousness. The author discusses implications for understanding gender.
Stem- and Progenitor Cell Proliferation in the Dentate Gyrus of the Reeler Mouse

Adult hippocampal neurogenesis has been implicated in hippocampus-dependent learning and memory. Furthermore, the decline of neurogenesis accompanying aging could be involved in age-related cognitive deficits. It is believed that the neural stem cell niche comprises a specialized microenvironment regulating stem cell activation and maintenance. However, little is known about the significance of the extracellular matrix in controlling adult stem cells. Reelin is a large glycoprotein of the extracelluar matrix known to be of crucial importance for neuronal migration. Here, we examined the local interrelation between Reelin expressing interneurons and putative hippocampal stem cells and investigated the effects of Reelin deficiency on stem cell and progenitor cell proliferation. Reelin-positive cells are found in close vicinity to putative stem cell processes, which would allow for stem cell regulation by Reelin. We investigated the proliferation of stem cells in the Reelin-deficient reeler hippocampus by Ki67 labeling and found a strong reduction of mitotic cells. A detailed analysis of dividing Type 1, type 2 and type 3 cells indicated that once a stem cell is recruited for proliferation, the progression to the next progenitor stage as well as the number of mitotic cycles is not altered in reeler. Our data point to a role for Reelin in either regulating stem cell quiescence or maintenance.
Signaling through erbB receptors is a critical functional regulator in the mature cochlea

Noise, ototoxic substances and various genetic factors are common causes of profound hearing loss. Cochlear implants can often restore hearing in these cases, but only if a sufficient number of responsive auditory nerve fibers remain. Over time, these nerve fibers degenerate in the damaged ear, and it is therefore important to establish factors that control neuronal survival and maintain neural excitability. Recent studies show that neuregulins and their receptors are important for survival and proper targeting of neurons in the developing inner ear. A role for neuregulins as maintainers of the neuronal population in the mature inner ear was therefore hypothesized. Here, this hypothesis was directly tested by chronic local application of substances that block neuregulin receptors. Using auditory brainstem response measurements, we demonstrate that such receptor block leads to a progressive hearing impairment that develops over the course of weeks. This impairment occurs despite a normal number of auditory neurons and preserved outer hair cell function. Real‐time quantitative reverse transcriptase‐polymerase chain reaction shows alterations in neurotrophin‐3 expression, suggesting that this growth factor participates in regulating cochlear sensitivity. The present work demonstrates the critical importance of neuregulin/erbB signaling in long‐term functional regulation in the mature guinea pig hearing organ.
Recovery of Burkholderia cenocepacia strain PHDC from cystic fibrosis patients in Europe

Background:Burkholderia cenocepacia can cause life threatening respiratory tract infections in patients with cystic fibrosis (CF) and has a significant impact on survival. There is extensive evidence for patient to patient spread and nosocomial transmission of this organism, and several widespread B cenocepacia strains have been described including the transatlantic ET12 clone. A study was performed to compare B cenocepacia isolates recovered from CF patients receiving care in several European countries and strains isolated from other clinical samples and the environment, with reference isolates from the epidemic B cenocepacia strain PHDC which has so far only been recovered from CF patients and soil in the USA. Methods: A large collection of B cenocepacia isolates, including a large number recovered from CF patients receiving care in several European countries, Canada and the USA, were genotyped by means of randomly amplified polymorphic DNA typing (RAPD) and rep-PCR using the BOX-A1R primer (BOX-PCR). Results: Nineteen Burkholderia cenocepacia isolates cultured from clinical samples in Europe (18 recently recovered from CF patients in France and Italy and one recovered in 1964 from urine in the UK) showed RAPD fingerprinting patterns that were similar to patterns obtained from isolates of B cenocepacia strain PHDC. Subsequent analysis of these isolates using BOX-PCR confirmed that the European isolates and strain PHDC represent the same clone. Conclusion: Strain PHDC represents a second transatlantic B cenocepacia clone capable of colonising patients with CF.