Miracle-dz/UniFAR-FTUs huggingface dataset:
Characterization of the Lactobacillus casei Group and the Lactobacillus acidophilus Group by Automated Ribotyping

A total of 91 type and reference strains of the Lactobacillus casei group and the L. acidophilus group were characterized by the automated ribotyping device Riboprinter® microbial characterization system. The L. casei group was divided into five (C1–C5) genotypes by ribotyping. Among them, the strain of L. casei ATCC 334 was clustered to the same genotype group as most of L. paracasei strains and L. casei JCM 1134T generated a riboprint pattern that was different from the type strain of L. zeae. These results supported the designation of L. casei ATCC 334 as the neotype strain, but were not consistent with the reclassification of L. casei JCM 1134T as L. zeae. The L. acidophilus group was also divided into 14 (A1–A11, B1–B3) genotypes by ribotyping. L. acidophilus, L. amylovorus, L. crispatus and L. gallinarum generated ribotype patterns that were distinct from the patterns produced by L. gasseri and L. johnsonii. This result confirmed previous data that the L. acidophilus group divided to two major clusters. Five strains of L. acidophilus and two strains of L. gasseri were correctly reidentified by ribotyping. Most strains belonging to the L. casei group and the L. acidophilus group were discriminated at the species level by automated ribotyping. Thus this RiboPrinter® system yields rapid, accurate and reproducible genetic information for the identification of many strains.
Level-weighted averaging in elevation to synchronous amplitude-modulated sounds

To program a goal-directed response in the presence of multiple sounds, the audiomotor system should separate the sound sources. The authors examined whether the brain can segregate synchronous broadband sounds in the midsagittal plane, using amplitude modulations as an acoustic discrimination cue. To succeed in this task, the brain has to use pinna-induced spectral-shape cues and temporal envelope information. The authors tested spatial segregation performance in the midsagittal plane in two paradigms in which human listeners were required to localize, or distinguish, a target amplitude-modulated broadband sound when a non-modulated broadband distractor was played simultaneously at another location. The level difference between the amplitude-modulated and distractor stimuli was systematically varied, as well as the modulation frequency of the target sound. The authors found that participants were unable to segregate, or localize, the synchronous sounds. Instead, they invariably responded toward a level-weighted average of both sound locations, irrespective of the modulation frequency. An increased variance in the response distributions for double sounds of equal level was also observed, which cannot be accounted for by a segregation model, or by a probabilistic averaging model.
Torpor in Dark Times: Patterns of Heterothermy Are Associated with the Lunar Cycle in a Nocturnal Bird

Many studies have shown that endotherms become more heterothermic when the costs of thermoregulation are high and/or when limited energy availability constrains thermoregulatory capacity. However, the roles of many ecological variables, including constraints on foraging opportunities and/or success, remain largely unknown. To test the prediction that thermoregulatory patterns should be related to foraging opportunities in a heterothermic endotherm, we examined the relationship between the lunar cycle and heterothermy in Freckled Nightjars (Caprimulgus tristigma), which are visually orienting, nocturnal insectivores that are dependent on ambient light to forage. This model system provides an opportunity to assess whether variation in foraging opportunities influences the expression of heterothermy. The nightjars were active and foraged for insects when moonlight was available but became inactive and heterothermic in the absence of moonlight. Lunar illumination was a much stronger predictor of the magnitude of heterothermic responses than was air temperature (Ta). Our data suggest that heterothermy was strongly related to variation in foraging opportunities associated with the lunar cycle, even though food abundance appeared to remain relatively high throughout the study period. Patterns of thermoregulation in this population of Freckled Nightjars provide novel insights into the environmental and ecological determinants of heterothermy, with the lunar cycle, and not Ta, being the strongest predictor of torpor use.
Adaptive Density Level Set Clustering

Clusters are often dened to be the connected components of a density level set. Unfortunately, this denition depends on a level that needs to be user specied by some means. In this paper we present a simple algorithm that is able to asymptotically determine the optimal level, that is, the level at which there is the rst split in the cluster tree of the data generating distribution. We further show that this algorithm asymptotically recovers the corresponding connected components. Unlike previous work, our analysis does not require strong assumptions on the density such as continuity or even smoothness.
Metabolic adaptation to a high-fat diet is associated with a change in the gut microbiota

Objective The gut microbiota, which is considered a causal factor in metabolic diseases as shown best in animals, is under the dual influence of the host genome and nutritional environment. This study investigated whether the gut microbiota per se, aside from changes in genetic background and diet, could sign different metabolic phenotypes in mice. Methods The unique animal model of metabolic adaptation was used, whereby C57Bl/6 male mice fed a high-fat carbohydrate-free diet (HFD) became either diabetic (HFD diabetic, HFD-D) or resisted diabetes (HFD diabetes-resistant, HFD-DR). Pyrosequencing of the gut microbiota was carried out to profile the gut microbial community of different metabolic phenotypes. Inflammation, gut permeability, features of white adipose tissue, liver and skeletal muscle were studied. Furthermore, to modify the gut microbiota directly, an additional group of mice was given a gluco-oligosaccharide (GOS)-supplemented HFD (HFD+GOS). Results Despite the mice having the same genetic background and nutritional status, a gut microbial profile specific to each metabolic phenotype was identified. The HFD-D gut microbial profile was associated with increased gut permeability linked to increased endotoxaemia and to a dramatic increase in cell number in the stroma vascular fraction from visceral white adipose tissue. Most of the physiological characteristics of the HFD-fed mice were modulated when gut microbiota was intentionally modified by GOS dietary fibres. Conclusions The gut microbiota is a signature of the metabolic phenotypes independent of differences in host genetic background and diet.
Impacts of Bromide and Nitrogen Wastewater Discharges on Downstream Drinking Water Treatment Plant Disinfection Byproducts

Bromide and nitrogen are wastewater effluent constituents that have raised concern for their potential to affect disinfection byproduct (DBP) formation at drinking water treatment plants (DWTPs) downstream of wastewater discharges. Despite the toxicity of brominated and nitrogenous DBPs, wastewater treatment does not usually remove bromide and nitrogen prior to discharge. Bromide is a conservative chemical and thus is not removed from surface waters via natural transformations after being released, although it may be diluted. Nitrogen is biologically reactive; it can be transformed and removed by bacteria in the environment and in wastewater treatment plants (WWTPs). While this nitrogen cycling may reduce impacts on downstream DWTPs, it also produces nitrous oxide (N2O), a greenhouse gas, as a byproduct. Thus, interaction with the environment alters the potential impact of bromide and nitrogen on drinking water systems. The objective of this work was to examine the impacts of nitrogen and bromide present in wastewater effluent on DBP formation at downstream DWTPs, within the context of current and possible future DBP regulations. Three major conclusions were reached. First, within Southwestern Pennsylvania, an area where surface water bromide concentrations have increased due to fossil fuel extraction-based wastewater discharge, no statistically significant improvement in species-specific risk was observed over the past 20 years, despite decreasing TTHM levels. Second, nitrogen treatment decisions at WWTPs influence the formation of N-nitrosodimethylamine (NDMA), an unregulated but toxic DBP, at downstream DWTPs in areas of high de facto reuse (DFR). More plants using nitrifying wastewater treatment resulted in significantly lower NDMA detection rates and concentrations observed at chloraminating DWTPs located downstream. Third, the current approach to estimating national emissions of N2O related to wastewater treatment may underestimate emissions by an order of magnitude. Further, nitrogen removal at wastewater treatment plants reduces total N2O emissions attributable to wastewater treatment by reducing the N2O that would be generated in receiving surface waters. Thus, in both cases, impacts of WWTPs on downstream DWTP DBPs were observable. While natural cycling may remove nitrogen from surface water, in-plant removal of nitrogen prevents large amounts of N2O emissions.
Ecological Dynamics Model and Ecopedagogy-Based Outdoor Experiential Education.

Environmental awareness is evaluated related to cognitive and affective areas so it might be considered one of the important points in order to predict environmental behavioural change. One of the behavioural change models is ecological dynamics model (EDM) and this model’s characteristics overlap with ecopedagogy-based outdoor experiential education (EOEE) and the titles of Agenda 21. The aim of this study is to examine the efficiency of an EOEE program intended for in-service teachers on environmental awareness and to evaluate EDM within EOEE. Mixed methodology was used and the data were collected by an environmental awareness scale, participants’ diaries, non-participant observation, and meeting documents. The study found that the participants developed environmental awareness and tended to have holistic perspective at the end of the education. It is come up with that holistic perspective may be added to the EDM and this model can be checked out by mathematical models such as structural equation modelling.
A Draft Genome of the Honey Bee Trypanosomatid Parasite Crithidia mellificae

Since 2006, honey bee colonies in North America and Europe have experienced increased annual mortality. These losses correlate with increased pathogen incidence and abundance, though no single etiologic agent has been identified. Crithidia mellificae is a unicellular eukaryotic honey bee parasite that has been associated with colony losses in the USA and Belgium. C. mellificae is a member of the family Trypanosomatidae, which primarily includes other insect-infecting species (e.g., the bumble bee pathogen Crithidia bombi), as well as species that infect both invertebrate and vertebrate hosts including human pathogens (e.g.,Trypanosoma cruzi, T. brucei, and Leishmania spp.). To better characterize C. mellificae, we sequenced the genome and transcriptome of strain SF, which was isolated and cultured in 2010. The 32 megabase draft genome, presented herein, shares a high degree of conservation with the related species Leishmania major. We estimate that C. mellificae encodes over 8,300 genes, the majority of which are orthologs of genes encoded by L. major and other Leishmania or Trypanosoma species. Genes unique to C. mellificae, including those of possible bacterial origin, were annotated based on function and include genes putatively involved in carbohydrate metabolism. This draft genome will facilitate additional investigations of the impact of C. mellificae infection on honey bee health and provide insight into the evolution of this unique family.
Genome-wide association studies in asthma: progress and pitfalls

: Genetic studies of asthma have revealed that there is considerable heritability to the phenotype. An extensive history of candidate-gene studies has identified a long list of genes associated with immune function that are potentially involved in asthma pathogenesis. However, many of the results of candidate-gene studies have failed to be replicated, leaving in question the true impact of the implicated biological pathways on asthma. With the advent of genome-wide association studies, geneticists are able to examine the association of hundreds of thousands of genetic markers with a phenotype, allowing the hypothesis-free identification of variants associated with disease. Many such studies examining asthma or related phenotypes have been published, and several themes have begun to emerge regarding the biological pathways under-pinning asthma. The results of many genome-wide association studies have currently not been replicated, and the large sample sizes required for this experimental strategy invoke difficulties with sample stratification and phenotypic heterogeneity. Recently, large collaborative groups of researchers have formed consortia focused on asthma, with the goals of sharing material and data and standardizing diagnosis and experimental methods. Additionally, research has begun to focus on genetic variants that affect the response to asthma medications and on the biology that generates the heterogeneity in the asthma phenotype. As this work progresses, it will move asthma patients closer to more specific
Facets of Subjective Health From Early Adulthood to Old Age

Objective: Subjective health is a complex indicator predicting longevity independent of objective health. Few studies examine genetic and environmental mechanisms underlying different facets of subjective health across the life course. Method: Three subjective health measures were examined in 12,900 twins (Mage = 63.38, range = 25-102) from nine studies in the Interplay of Genes and Environment across Multiple Studies Consortium: self-rated health (SRH), health compared with others (COMP), and health interfering with activities (ACT). Results: Analyses indicated age and sex differences in mean scores depending on the measure. SRH and ACT showed significant linear and non-linear moderation by age for individual differences in both genetic and environmental variance. Significant sex differences in components of variance were found for SRH and ACT, but not COMP. Discussion: Subjective health appears to be dependent on frame of reference and reflect different aspects of health. Results suggest different genetic and environmental mechanisms underlie each facet.
Pharmacokinetics of Tacrolimus and Cyclosporine in Liver Transplant Recipients Receiving 3 Direct-Acting Antivirals as Treatment for Hepatitis C Infection

Background: Interactions between tacrolimus and cyclosporine (CSA) and the 3 direct-acting antiviral regimen (3D) of ombitasvir, paritaprevir/ritonavir, and dasabuvir necessitate a priori dose adjustments for the immunosuppressants to achieve desired levels. Modeling and simulations based on data in healthy subjects predicted that tacrolimus 0.5 mg every 7 days or 0.2 mg every 3 days, and CSA at one-fifth the total daily dose administered once daily, would achieve desired trough concentrations (Ctrough) during 3D treatment. The success of these dosing recommendations was evaluated by analyzing pharmacokinetic data from liver transplant recipients in the CORAL-I study. Methods: A population pharmacokinetic model was developed using tacrolimus dosing and Ctrough data before and during 3D treatment (n = 29). The model was used to simulate various tacrolimus dosing regimens and predict tacrolimus concentration–time profiles during 3D treatment. CSA Ctrough data before and during 3D treatment (n = 5) were also summarized. Results: A one-compartment model with first-order absorption adequately described tacrolimus pharmacokinetic profiles during the first 4 weeks of 3D treatment. Estimated tacrolimus Ctrough values (median; interquartile range) before and during 3D treatment were comparable (5.7 ng/mL; 4.9–6.5 ng/mL versus 5.2 ng/mL; 4.2–6.3 ng/mL, respectively). Based on simulations, in a patient with a starting Ctrough of 6 ng/mL, 0.5 mg tacrolimus every 7 or 14 days or 0.2 mg tacrolimus every 3 days will result in Ctrough levels of 6–9 ng/mL, 4–6 ng/mL, and 6–10 ng/mL, respectively, during 3D treatment. For CSA, Ctrough values (median; interquartile range) before and during 3D treatment were comparable (126 ng/mL; 94–140 ng/mL versus 104 ng/mL; 82–140 ng/mL). Conclusions: Observed data for tacrolimus and CSA in liver transplant recipients confirm that the recommended dosing strategies are valid and therapeutic levels of immunosuppression can be maintained during 3D treatment.
Genetic variations in cancer-related significantly mutated genes and lung cancer susceptibility

Background Cancer initiation and development are driven by key mutations in driver genes. Applying high-throughput sequencing technologies and bioinformatic analyses, The Cancer Genome Atlas (TCGA) project has identified panels of somatic mutations that contributed to the etiology of various cancers. However, there are few studies investigating the germline genetic variations in these significantly mutated genes (SMGs) and lung cancer susceptibility. Patients and methods We comprehensively evaluated 1655 tagged single nucleotide polymorphisms (SNPs) located in 127 SMGs identified by TCGA, and test their association with lung cancer risk in large-scale case-control study. Functional effect of the validated SNPs, gene mutation frequency and pathways were analyzed. Results We found 11 SNPs in 8 genes showed consistent association (P < 0.1) and 8 SNPs significantly associated with lung cancer risk (P < 0.05) in both discovery and validation phases. The most significant association was rs10412613 in PPP2R1A, with the minor G allele associated with a decreased risk of lung cancer [odds ratio = 0.91, 95% confidence interval (CI): 0.87-0.96, P = 2.3 × 10-4]. Cumulative analysis of risk score built as a weight sum of the 11 SNPs showed consistently elevated risk with increasing risk score (P for trend = 9.5 × 10-9). In stratified analyses, the association of PPP2R1A:rs10412613 and lung cancer risk appeared stronger among population of younger age at diagnosis and never smokers. The expression quantitative trait loci analysis indicated that rs10412613, rs10804682, rs635469 and rs6742399 genotypes significantly correlated with the expression of PPP2R1A, ATR, SETBP1 and ERBB4, respectively. From TCGA data, expression of the identified genes was significantly different in lung tumors compared with normal tissues, and the genes' highest mutation frequency was found in lung cancers. Integrative pathway analysis indicated the identified genes were mainly involved in AKT/NF-κB regulatory pathway suggesting the underlying biological processes. Conclusion This study revealed novel genetic variants in SMGs associated with lung cancer risk, which might contribute to elucidating the biological network involved in lung cancer development.
Effects of a Single Lyric Analysis Intervention on Withdrawal and Craving With Inpatients on a Detoxification Unit: A Cluster-Randomized Effectiveness Study

ABSTRACT Background: For patients hospitalized on inpatient detoxification units, reducing negative symptoms such as withdrawal and craving is a key treatment area. Although lyric analysis is a commonly utilized music therapy intervention for clients in substance abuse rehabilitation, there is a lack of randomized controlled music therapy studies systematically investigating how lyric analysis interventions can affect patients on a detoxification unit. Objective: The purpose of this cluster-randomized effectiveness study was to measure the effects of single-session group lyric analysis interventions on withdrawal and craving with patients on a detoxification unit. A secondary purpose of this study was to determine if relationships existed between treatment effects and participants’ familiarity with the song. Methods: Participants (N = 144) were cluster-randomized to experimental (posttest only) or wait-list control (pretest only) conditions to provide treatment to all participants in an inclusive single-session design. Results: Although participants in the experimental condition had lower withdrawal and craving means than participants in the control condition, these differences were not significant. Familiarity of the song in the lyric analysis was not related to withdrawal or craving. Conclusion: Group-based lyric analysis interventions may be effective for temporarily relieving withdrawal and craving in patients on a detoxification unit. Familiarity of the song did not affect results. Implications for clinical practice, suggestions for future research, and limitations are provided.
The Xenopus TRPV6 homolog encodes a Mg2+‐permeant channel that is inhibited by interaction with TRPC1

The TRP gene family encodes primarily cation non‐selective, Ca2+ permeant channels that are involved in a dizzying array of sensory mechanisms. Two channels in this large family TRPV5 and TRPV6 are highly Ca2+ selective and are expressed in epithelia where they are important in Ca2+ uptake. TRPV5/6 are constitutively active, yet the mechanisms regulating their activation in native tissue remains elusive. Here we functionally characterize the Xenopus TRPV6 homolog. xTRPV6 is expressed in the oocyte and encodes a channel that is permeant to divalents including Ca2+, and displays a high permeability to Mg2+. The oocyte does not exhibit functional TRPV6‐like current at rest, showing that the endogenous channel is somehow maintained in an inactive state. We show that endogenous as well as overexpressed xTRPV6 interacts with xTRPC1 and that this interaction inhibits xTRPV6 currents. As such TRPC1 is likely to regulate the activity of TRPV6 under physiological conditions. J. Cell. Physiol. 228: 2386–2398, 2013. © 2013 The Authors. Journal of Cellular Physiology Published by Wiley Periodicals, Inc.
Gene expression profiling of human adrenocortical tumors using cDNA microarrays identifies several candidate genes as markers of malignancy

INSERM EMI 01-05, Department of Cell Regulation and Dynamics, Commissariat à l’Energie Atomique (CEA), Grenoble, France Department of Integrative Biology, University Hospital of Grenoble, France COMETE : The French Network for Studies on human adrenal cortical and medullary tumors Transcriptome Analysis Platform, Genopole Rhône-Alpes, University Hospital of Grenoble, France INSERM ERIT-M 02-06, University of Méditerranée, Marseille, France Department of Endocrinology, Cochin Hospital, Paris, France Department of Hypertension, European Hospital Georges Pompidou, Paris, France Department of Endocrine Cancerology, Gustave-Roussy Institute, Villejuif, France Laboratory of Functional Endocrine Explorations, Trousseau Hospital, Paris, France Department of Endocrinology, University Hospital of Grenoble, France