bluuebunny/crossref_metadata_2025_split huggingface dataset:
Long-term Sustained Cognitive Benefits of Vagus Nerve Stimulation in Refractory Depression
Authors: Desbeaumes Jodoin Véronique , Richer François , Miron Jean-Philippe , Fournier-Gosselin Marie-Pierre , Lespérance Paul 
Published: June 2018

Background
Treatment-resistant depression (TRD) is a serious chronic condition disabling patients functionally and cognitively. Chronic vagus nerve stimulation (VNS) is recognized for the management of TRD, but few studies have examined its long-term effects on cognitive dysfunction in unipolar and bipolar resistant depression.

Objective
The purpose of this study was to assess the course of cognitive functions and clinical symptoms in a cohort of patients treated with VNS for TRD.

Methods
In 14 TRD patients with VNS, standardized clinical and neuropsychological measures covering memory, attention/executive functions, and psychomotor speed were analyzed prestimulation and up to 2 years poststimulation.

Results
Vagus nerve stimulation patients significantly improved on cognitive and clinical measures. Learning and memory improved rapidly after 1 month of stimulation, and other cognitive functions improved gradually over time. Cognitive improvements were sustained up to 2 years of treatment. At 1 month, improvement in Montgomery-Åsberg Depression Rating Scale scores was not correlated with changes in any of the cognitive scores, whereas at 12 months, the change in Montgomery-Åsberg Depression Rating Scale score was significantly correlated with several measures (Stroop interference, verbal fluency, and Rey-Osterrieth Complex Figure delayed recall).

Conclusions
In recent years, a growing interest in cognitive dysfunction in depression has emerged. Our results suggest that chronic VNS produces sustained clinical and cognitive improvements in TRD patients, with some mental functions improving as soon as 1 month after the initiation of the VNS therapy. Vagus nerve stimulation seems a very promising adjunctive therapy for TRD patients with cognitive impairment.
Factors Associated with Scientific Misconduct and Questionable Research Practices in Health Professions Education
Authors: Maggio Lauren A. , Dong Ting , Driessen Erik W. , Artino Anthony R. 
Published: June 2018

AbstractIntroductionEngaging in scientific misconduct and questionable research practices (QRPs) is a noted problem across fields, including health professions education (HPE). To mitigate these practices, other disciplines have enacted strategies based on researcher characteristics and practice factors. Thus, to inform HPE, this article seeks to determine which researcher characteristics and practice factors, if any, might explain the frequency of irresponsible research practices.MethodIn 2017, a cross-sectional survey of HPE researchers was conducted. The survey included 66 items derived from two published QRP surveys and a publication pressure scale adapted from the literature. The study outcome was the self-reported misconduct frequency score, which is a weighted mean score for each respondent on all misconduct and QRP items. Statistical analysis included descriptive statistics, correlation analysis, and multiple linear regression analysis.Results and DiscussionIn total, 590 researchers took the survey. Results from the regression analysis indicated that researcher age had a negative association with the misconduct frequency score (b = −.01, t = −2.91, p<.05) suggesting that older researchers tended to have lower misconduct frequency scores. Publication pressure (b = .20, t = 7.82, p<.001) and number of publications (b = .001, t = 3.27, p<.01) had positive associations with the misconduct frequency score. The greater the publication pressure or the more publications a researcher reported, the higher the misconduct frequency score. Overall, the explanatory variables accounted for 21% of the variance in the misconduct frequency score, and publication pressure was the strongest predictor. These findings provide an evidence base from which HPE might tailor strategies to address scientific misconduct and QRPs.
High-resolution sweep metagenomics using fast probabilistic inference
Authors: Mäklin Tommi , Kallonen Teemu , David Sophia , Boinett Christine J. , Pascoe Ben , Méric Guillaume , Aanensen David M. , Feil Edward J. , Baker Stephen , Parkhill Julian , Sheppard Samuel K. , Corander Jukka , Honkela Antti 
Published: June 2018

AbstractDetermining the composition of bacterial communities beyond the level of a genus or species is challenging because of the considerable overlap between genomes representing close relatives. Here, we present the mSWEEP method for identifying and estimating the relative abundances of bacterial lineages from plate sweeps of enrichment cultures. mSWEEP leverages biologically grouped sequence assembly databases, applying probabilistic modelling, and provides controls for false positive results. Using sequencing data from major pathogens, we demonstrate significant improvements in lineage quantification and detection accuracy. Our method facilitates investigating cultures comprising mixtures of bacteria, and opens up a new field of plate sweep metagenomics.
Optogenetic silencing of immature and mature neurons in dentate gyrus to assess their roles in memory discriminations
Authors: van Dijk Milenna T. , Yu Zejia Angel , Lim Younghun , Hen René , Fenton André A. 
Published: June 2018

ABSTRACTDiscriminating similar memories and events depends on the dentate gyrus region of the hippocampus. This region is also distinctive because neurogenesis continues in adulthood. Whether both mature and immature granule cells play a role in memory discrimination, and whether the roles are distinct is actively investigated. Here we demonstrate that manipulating either mature or immature granule cells can impair discrimination of similar active place avoidance memories, but the manipulations have different effects. We also observe that prior experience modulates which memories are compromised by inactivation of immature neurons. These data demonstrate the importance of the dentate gyrus network of cells for memory discrimination.
A non-canonical metal center drives activity of the Sediminispirochaeta smaragdinae metallo-β- lactamase SPS-1
Authors: Cheng Zishuo , VanPelt Jamie , Bergstrom Alexander , Bethel Christopher , Katko Andrew , Miller Callie , Mason Kelly , Cumming Erin , Zhang Huan , Kimble Robert , Fullington Sarah , Bretz Stacey Lowery , Nix Jay C. , Bonomo Robert A. , Tierney David L. , Page Richard C. , Crowder Michael W 
Published: June 2018

ABSTRACTIn an effort to evaluate whether a recently reported putative metallo-β-lactamase (MβL) contains a novel MβL active site, SPS-1 from Sediminispirochaeta smaragdinae was over-expressed, purified, and characterized using spectroscopic and crystallographic studies. Metal analyses demonstrate that recombinant SPS-1 binds nearly 2 equivalents of Zn (II), and steady-state kinetic studies show that the enzyme hydrolyzes carbapenems and certain cephalosporins but not β-lactam substrates with bulky substituents in the 6-7 position. Spectroscopic studies on Co (II)-substituted SPS-1 suggest a novel metal center in SPS-1, with reduced spin coupling between the metal ions and a novel Zn1 metal binding site. This site was confirmed with a crystal structure of the enzyme. The structure shows a Zn2 site that is similar that that in NDM-1 and other subclass B1 MβLs; however, the Zn1 metal ion is coordinated by 2 histidine residues and a water molecule, which is held in position by a hydrogen bond network. The Zn1 metal is displaced nearly 1 Å from the position reported in other MβLs. The structure also shows extended helices above the active site, which create a binding pocket that precludes the binding of substrates with large, bulky substituents in the 6/7 position of β-lactam antibiotics. This study reveals a novel metal binding site in MβLs, and suggests that the targeting of metal binding sites in MβLs with inhibitors is now more challenging with the identification of this new MβL.
Anti-V2 Antibody Deficiency in Individuals Infected With HIV-1
Authors: Liu Lily , Li Liuzhe , Nanfack Aubin , Mayr Luzia M. , Soni Sonal , Kohutnicki Adam , Agyingi Lucy , Wang Xiao-Hong , Tuen Michael , Shao Yongzhao , Totrov Maxim , Zolla-Pazner Susan , Kong Xian-Peng , Duerr Ralf , Gorny Miroslaw K. 
Published: June 2018

ABSTRACTThe positive correlation of high levels of plasma anti-V2 antibodies (Abs) with protective immunity in the Phase III anti-HIV RV144 vaccine trial generated interest in the induction of these Abs for HIV vaccine development. We analyzed plasma samples from 79 chronically infected Cameroonian individuals for Ab reactivity against three V1V2 fusion proteins and five cyclic V2 peptides and found that HIV-1 infection induces different levels of anti-V2 Abs. While the majority of plasma samples reacted strongly with one or more V2 antigens, 10% (8) of the samples were nonreactive. Deficiency of anti-V2 Abs was consistently found in longitudinal plasma samples tested over 8 to 54 months of HIV infection. There was a strong correlation between binding activities of plasma anti-V2 Abs and anti-gp120 and anti-gp41 Abs, suggesting that deficiency of V2 Abs could be related, in part, to a limited ability to elicit strong Ab responses. Analysis of gp120 sequences revealed that the V2 region of viruses from donors with V2-deficient versus V2-reactive Abs displayed a tendency toward longer length, more glycans, and lower isoelectric point and charge. No differences between these two patient groups were noted in the same parameters measured in the V1 region. These data suggest that immunogens containing a shorter V2 region with fewer glycosylation sites and higher electrostatic charges would be beneficial for induction of anti-V2 Abs, but the ability to mount a strong general Ab response to HIV-1 appears to be a dominant factor.IMPORTANCEThe results of the RV144 vaccine clinical trial showed a correlation between plasma Abs against a V1V2 fusion protein and a decreased risk of acquiring HIV-1 infection. This turned the focus of some HIV vaccine design to the induction of elevated levels of anti-V2 Abs to increase vaccine efficacy. In plasma samples from Cameroonian individuals infected with HIV-1, we observed broad variations in levels of anti-V2 Abs, and 8 of the 79 plasma samples tested displayed substantial deficiency of V2 Abs. Sequence analysis of the V2 region from plasma viruses and multivariate analyses of V2 characteristics showed a significant difference in several features between V2-deficient and V2-reactive plasma Abs. These results suggest that HIV vaccine immunogens containing a V2 region with shorter length, fewer glycosylation sites, and higher electrostatic charges may be beneficial for induction of a higher level of anti-V2 Abs and thus contribute to HIV vaccine efficacy.
The identification of critical lethal action in antimicrobial mechanism of glycerol monomyristate against foodborne pathogens
Authors: Zhang Song , Xiong Jian , Lou Wenyong , Ning Zhengxiang , Zhang Denghui , Yang Jiguo 
Published: June 2018

AbstractGlycerol monomyristate (GMM) is a promising antimicrobial substance due to its broad antibacterial spectrum: however, the critical lethal action in its antimicrobial mechanism for foodborne pathogens remains unclear. In the present study, the inhibitory activities of GMM onEscherichia coli(E. coli),Staphylococcus aureus(S. aureus) andCandida albicans(C. albicans) were compared, and its membrane and intracellular action mechanism was investigated. The results showed that the susceptibility ofE. colito GMM was the highest, followed byS. aureus, andC. albicansbeing the poorest. Using flow cytometry, the GMM dose causing above 50% permeability ratio onE. coliwas lower than that onS. aureus. The images from scanning electron microscope revealed no doses difference existed between the two strains when the obvious cell damage occurred. Furthermore, cell cycle and multiple fluorescent staining assays showed only the cell division ofE. coliandS. aureus, excluding that ofC. albicans, was obviously affected at 1/4 MIC and 1/2 MIC, indicating that the DNA interfere and subsequent cell division inhibition was likely to be the critical lethal action with doses near MIC, which can also explain the poor sensitivity ofC. albicans.ImportanceFoodbornepathogens, as a common source of biological pollution in the food industry, can cause millions of food poisoning incidents each year, which poses great risks to consumers’ health and safety. The use of monoglyceride as an edible surfactant to inhibit the growth of food-borne microorganisms has been a long time, but the relevant antibacterial mechanism is too broad to accurately grasp its key lethal effect and its action doses, which not only affects the antibacterial efficiency, but also may result in the abnormalities of food flavor when adding at overdoses. The significance of the study is to identify the key lethal effect and its action doses, which will greatly enhance the understanding of the response mechanism of different types of foodborne pathogens to monoglycerides, and provide a more reasonable reference for differential control and treatment of different gastrointestinal infections when combined with antibiotics in clinical.
Biofilm formation by Mycobacterium avium ssp. paratuberculosis in aqueous extract of schmutzdecke for clarifying untreated water in water treatment operations
Authors: Aboagye G. , Rowe M.T. 
Published: June 2018

ABSTRACTAIMSTo determine the effect of aqueous extract of schmutzdecke on adhesion and biofilm formation by three isolates of Mycobacterium avium ssp. paratuberculosis (Map) under laboratory conditions.METHODS AND RESULTSStrains of Mycobacterium avium ssp. paratuberculosis in aqueous extract of schmutzdecke were subjected to adhesion tests on two topologically different substrata i.e. aluminium and stainless steel coupons. Biofilm formation was then monitored in polyvinyl chloride (PVC) plates. All the three strains adhered onto both coupons, howbeit greatly on aluminium than stainless steel. In the PVC plates, however, all strains developed biofilms which were observed by spectrophotometric analysis.CONCLUSIONSThe environmental isolates of Map attained higher cell proliferation in both filtered and unfiltered aqueous extracts of schmutzdecke (FAES and UAES respectively) compared with the human isolate. Furthermore, the results showed that irrespective of the media used, Map might have developed biofilm by its genetic competence to do so under favourable conditions that the immediate environment might have provided.Significance and impact of the studyComposites of the schmutzdecke which is the dirty layer formed within 10 to 20 days of operation of a slow sand filter bed had a proliferative effect on Map. Therefore when entrapped, Map could form a biofilm and access human populations through potable water. Therefore, schmutzdecke should be monitored and scraped periodically to curtail its support for environmentally persistent pathogens that can pose health risks to humans.HighlightsSchmutzdecke; a reservoir of nutrient composites atop slow sand filter bedAdhesion by Map on aluminium and stainless steel coupons was achievedMap strains from water sources developed biofilms better than the human strainIn distilled water, biofilm formation by all strains was evidentProtracted build-up of schmutzdecke may proliferate waterborne pathogens
Identification of pathogens in culture-negative infective endocarditis cases by metagenomic analysis
Authors: Cheng Jun , Hu Huan , Kang Yue , Chen Weizhi , Fang Wei , Wang Kaijuan , Zhang Qian , Fu Aisi , Zhou Shuilian , Cheng Chen , Cao Qingqing , Wang FeiYan , Lee Shela , Zhou Zhou 
Published: June 2018

AbstractPathogens identification is critical for the proper diagnosis and precise treatment of infective endocarditis. Although blood and valve cultures are the gold standard for IE pathogens detection, many cases are culture-negative, especially in patients who had received long-term antibiotic treatment, and precise diagnosis has therefore become a major challenge in the clinic. Metagenomic sequencing can provide both information on the pathogenic strain and the antibiotic susceptibility profile of patient samples without culturing, offering a powerful method to deal with culture-negative cases. In this work, we assessed the feasibility of a metagenomic approach to detect the causative pathogens in resected valves from IE patients.Using our in-house developed bioinformatics pipeline, we analyzed the sequencing results generated from both next-generation sequencing and Oxford Nanopore Technologies MinION nanopore sequencing for the direct identification of pathogens from the resected valves of seven clinically culture-negative IE patients according to the modified Duke criteria. Moreover, we were able to simultaneously characterize respective antimicrobial resistance features. This provides clinicians with valuable information to diagnose and treat IE patients after valve replacement surgery.
Novel Staphylococcal Cassette Chromosome composite island (SCC-CI) with a new subtype ofSCCmecVI cassette found in ST5 MRSA in France
Authors: Barraud Olivier , Laurent Frédéric , Dyon-Tafani Virginie , Dupieux-Chabert Céline , Bes Michèle , Ploy Marie-Cécile , Garnier Fabien , Simões Patricia Martins 
Published: June 2018

ABSTRACTAn emergent kanamycin-susceptible ST5-MRSA lineage has been identified in France. Whole genome sequencing revealed a 40 kb SCC composite island with a mosaic structure including 3 SCC elements: a ΨSCCcop/ars, a SCCLim88Awith accrC recombinase, and a novel subtype of SCCmectype VI (VIb). This mosaic structure suggests a high recombination rate of SCC elements from distinct staphylococci species.
Species tree-aware simultaneous reconstruction of gene and domain evolution
Authors: Muhammad Sayyed Auwn , Sennblad Bengt , Lagergren Jens 
Published: June 2018

AbstractMost genes are composed of multiple domains, with a common evolutionary history, that typically perform a specific function in the resulting protein. As witnessed by many studies of key gene families, it is important to understand how domains have been duplicated, lost, transferred between genes, and rearranged. Analogously to the case of evolutionary events affecting entire genes, these domain events have large consequences for phylogenetic reconstruction and, in addition, they create considerable obstacles for gene sequence alignment algorithms, a prerequisite for phylogenetic reconstruction.We introduce the DomainDLRS model, a hierarchical, generative probabilistic model containing three levels corresponding to species, genes, and domains, respectively. From a dated species tree, a gene tree is generated according to the DL model, which is a birth-death model generalized to occur in a dated tree. Then, from the dated gene tree, a pre-specified number of dated domain trees are generated using the DL model and the molecular clock is relaxed, effectively converting edge times to edge lengths. Finally, for each domain tree and its lengths, domain sequences are generated for the leaves based on a selected model of sequence evolution.For this model, we present a MCMC-based inference framework called DomainDLRS that takes a dated species tree together with a multiple sequence alignment for each domain family as input and outputs an estimated posterior distribution over reconciled gene and domain trees. By requiring aligned domains rather than genes, our framework evades the problem of aligning full-length genes that have been exposed to domain duplications, in particular non-tandem domain duplications. We show that DomainDLRS performs better than MrBayes on synthetic data and that it outperforms MrBayes on biological data. We analyse several zincfinger genes and show that most domain duplications have been tandem duplications, some involving two or more domains, but non-tandem duplications have also been common.
Membrane-mediated interactions induce spontaneous filament bundling
Authors: Vahid Afshin , Dadunashvili George , Idema Timon 
Published: June 2018

AbstractThe plasma membrane and cytoskeleton of living cells are closely coupled dynamical systems. Internal cytoskeletal elements such as actin filaments and microtubules continually exert forces on the membrane, resulting in the formation of membrane protrusions. In this paper we investigate the interplay between the shape of a cell distorted by pushing and pulling forces generated by microtubules and the resulting rearrangement of the microtubule network. From analytical calculations, we find that two microtubules that deform the vesicle can both attract or repel each other, depending on their angular separations and the direction of the imposed forces. We also show how the existence of attractive interactions between multiple microtubules can be deduced analytically, and further explore general interactions through Monte Carlo simulations. Our results suggest that the commonly reported parallel structures of microtubules in both biological and artificial systems can be a natural consequence of membrane mediated interactions.
Comparative transcriptomics of albino and warningly coloured caterpillars
Authors: Galarza Juan A. 
Published: June 2018

AbstractColouration is perhaps one of the most prominent adaptations for survival and reproduction of most taxa. Colouration is of particular importance for aposematic species, which rely on their colouring and patterning to act as a warning signal against predators. Most research has focused on the evolution of warning colouration by natural selection. However, little information is available for colour mutants of aposematic species, particularly at the genomic level. Here I compare the transcriptomes of albino mutant caterpillars of the wood tiger moth (Arctia plantaginis) to those of their full-sibs having their distinctive orange-black warning colouration. The results showed >300 differentially expressed genes transcriptome-wide. Genes involved in the immune system, structural constituents of cuticle, and peptidase activity were mostly down-regulated in the albino larvae. Surprisingly, higher expression was observed in core melanin genes from albino larvae, suggesting that melanin synthesis may be disrupted in terminal ends of the pathway during its final conversion. I further identified 25 novel genes uniquely expressed in the albino larvae. Functional annotation showed that these genes are involved in nucleotide biosynthesis, copper ion transmembrane transport, and nucleic acid binding. Taken together, these results suggest that caterpillar albinism may not be due to a depletion of melanin precursor genes. In contrast, the albino condition may result from the combination of faulty melanin conversion late in its synthesis and structural deficiencies in the cuticle preventing its deposition.