bluuebunny/crossref_metadata_2025_split huggingface dataset:
Neuropsychological Correlates of Anosognosia for Objective Functional Difficulties in Older Adults on the Mild Cognitive Impairment Spectrum
Authors: Steward Kayla A , Bull Tyler P , Kennedy Richard , Crowe Michael , Wadley Virginia G 
Published: October 2019

AbstractObjectiveTo examine the neuropsychological correlates of anosognosia for instrumental activities of daily living (IADLs) in older adults with mild cognitive impairment (MCI) and mild dementia.MethodParticipants (n = 103; age range = 54–88, 52% female) with MCI and mild dementia were recruited from neurology and geriatrics clinics for cross-sectional analysis. They completed neuropsychological tests along with subjective and performance-based assessments of six IADLs: financial management, driving, grocery shopping, nutrition evaluation, telephone use, and medication management. For each IADL, participants were classified as having anosognosia when there was objective difficulty but no subjective complaints.ResultsDepending on functional domain, 13–39% of the sample had objective IADL difficulty, and of those, 65–93% lacked insight into these deficits. Binomial logistic regression models controlling for demographic variables revealed that measures of global cognition, executive function, visual attention, and verbal memory predicted classification of anosognosia, and these relationships varied across IADLs. In contrast, basic auditory attention, working memory, depressive symptoms, nor cognitive reserve were significantly related to anosognosia for any IADL.ConclusionResults support the Conscious Awareness Model, which theorizes that accurate metacognitive output is reliant on attentional, memory, and executive functioning systems. Findings from this study suggest that anosognosia for different IADLs may arise from breakdowns at varying points in this model, explaining both inter- and intra-patient variability in self-awareness of functional deficits.
LARMD: integration of bioinformatic resources to profile ligand-driven protein dynamics with a case on the activation of estrogen receptor
Authors: Yang Jing-Fang , Wang Fan , Chen Yu-Zong , Hao Ge-Fei , Yang Guang-Fu 
Published: October 2019

Abstract
Protein dynamics is central to all biological processes, including signal transduction, cellular regulation and biological catalysis. Among them, in-depth exploration of ligand-driven protein dynamics contributes to an optimal understanding of protein function, which is particularly relevant to drug discovery. Hence, a wide range of computational tools have been designed to investigate the important dynamic information in proteins. However, performing and analyzing protein dynamics is still challenging due to the complicated operation steps, giving rise to great difficulty, especially for nonexperts. Moreover, there is a lack of web protocol to provide online facility to investigate and visualize ligand-driven protein dynamics. To this end, in this study, we integrated several bioinformatic tools to develop a protocol, named Ligand and Receptor Molecular Dynamics (LARMD, http://chemyang.ccnu.edu.cn/ccb/server/LARMD/ and http://agroda.gzu.edu.cn:9999/ccb/server/LARMD/), for profiling ligand-driven protein dynamics. To be specific, estrogen receptor (ER) was used as a case to reveal ERβ-selective mechanism, which plays a vital role in the treatment of inflammatory diseases and many types of cancers in clinical practice. Two different residues (Ile373/Met421 and Met336/Leu384) in the pocket of ERβ/ERα were the significant determinants for selectivity, especially Met336 of ERβ. The helix H8, helix H11 and H7-H8 loop influenced the migration of selective agonist (WAY-244). These computational results were consistent with the experimental results. Therefore, LARMD provides a user-friendly online protocol to study the dynamic property of protein and to design new ligand or site-directed mutagenesis.
CSMD: a computational subtraction-based microbiome discovery pipeline for species-level characterization of clinical metagenomic samples
Authors: Liu Yu , Bible Paul W , Zou Bin , Liang Qiaoxing , Dong Cong , Wen Xiaofeng , Li Yan , Ge Xiaofei , Li Xifang , Deng Xiuli , Ma Rong , Guo Shixin , Liang Juanran , Chen Tingting , Pan Wenliang , Liu Lixin , Chen Wei , Wang Xueqin , Wei Lai 
Published: October 2019

AbstractMotivationMicrobiome analyses of clinical samples with low microbial biomass are challenging because of the very small quantities of microbial DNA relative to the human host, ubiquitous contaminating DNA in sequencing experiments and the large and rapidly growing microbial reference databases.ResultsWe present computational subtraction-based microbiome discovery (CSMD), a bioinformatics pipeline specifically developed to generate accurate species-level microbiome profiles for clinical samples with low microbial loads. CSMD applies strategies for the maximal elimination of host sequences with minimal loss of microbial signal and effectively detects microorganisms present in the sample with minimal false positives using a stepwise convergent solution. CSMD was benchmarked in a comparative evaluation with other classic tools on previously published well-characterized datasets. It showed higher sensitivity and specificity in host sequence removal and higher specificity in microbial identification, which led to more accurate abundance estimation. All these features are integrated into a free and easy-to-use tool. Additionally, CSMD applied to cell-free plasma DNA showed that microbial diversity within these samples is substantially broader than previously believed.Availability and implementationCSMD is freely available at https://github.com/liuyu8721/csmd.Supplementary informationSupplementary data are available at Bioinformatics online.
Fertility as a constraint on group size in African great Apes
Authors: Dunbar R I M 
Published: October 2019

AbstractGorillas and chimpanzees live in social groups of very different size and structure. Here I test the hypothesis that this difference might reflect the way fertility maps onto group demography as it does in other Catarrhines. For both genera, birth rates and the number of surviving offspring per female are quadratic (or ∩-shaped) functions of the number of adult females in the group, and this is independent of environmental effects. The rate at which fertility declines ultimately imposes a constraint on the size of social groups that can be maintained in both taxa. The differences in group size between the two genera seem to reflect a contrast in the way females buffer themselves against this cost. Gorillas do this by using males as bodyguards, whereas chimpanzees exploit fission–fusion sociality to do so. The latter allows chimpanzees to live in much larger groups without paying a fertility cost (albeit at a cognitive cost).
Clinical and neuroimaging phenotypes of genetic parkinsonism from infancy to adolescence
Authors: Morales-Briceño Hugo , Mohammad Shekeeb S , Post Bart , Fois Alessandro F , Dale Russell C , Tchan Michel , Fung Victor S C 
Published: October 2019

AbstractGenetic early-onset parkinsonism presenting from infancy to adolescence (≤21 years old) is a clinically diverse syndrome often combined with other hyperkinetic movement disorders, neurological and imaging abnormalities. The syndrome is genetically heterogeneous, with many causative genes already known. With the increased use of next-generation sequencing in clinical practice, there have been novel and unexpected insights into phenotype-genotype correlations and the discovery of new disease-causing genes. It is now recognized that mutations in a single gene can give rise to a broad phenotypic spectrum and that, conversely different genetic disorders can manifest with a similar phenotype. Accurate phenotypic characterization remains an essential step in interpreting genetic findings in undiagnosed patients. However, in the past decade, there has been a marked expansion in knowledge about the number of both disease-causing genes and phenotypic spectrum of early-onset cases. Detailed knowledge of genetic disorders and their clinical expression is required for rational planning of genetic and molecular testing, as well as correct interpretation of next-generation sequencing results. In this review we examine the relevant literature of genetic parkinsonism with ≤21 years onset, extracting data on associated movement disorders as well as other neurological and imaging features, to delineate syndromic patterns associated with early-onset parkinsonism. Excluding PRKN (parkin) mutations, &gt;90% of the presenting phenotypes have a complex or atypical presentation, with dystonia, abnormal cognition, pyramidal signs, neuropsychiatric disorders, abnormal imaging and abnormal eye movements being the most common features. Furthermore, several imaging features and extraneurological manifestations are relatively specific for certain disorders and are important diagnostic clues. From the currently available literature, the most commonly implicated causes of early-onset parkinsonism have been elucidated but diagnosis is still challenging in many cases. Mutations in ∼70 different genes have been associated with early-onset parkinsonism or may feature parkinsonism as part of their phenotypic spectrum. Most of the cases are caused by recessively inherited mutations, followed by dominant and X-linked mutations, and rarely by mitochondrially inherited mutations. In infantile-onset parkinsonism, the phenotype of hypokinetic-rigid syndrome is most commonly caused by disorders of monoamine synthesis. In childhood and juvenile-onset cases, common genotypes include PRKN, HTT, ATP13A2, ATP1A3, FBX07, PINK1 and PLA2G6 mutations. Moreover, Wilson’s disease and mutations in the manganese transporter are potentially treatable conditions and should always be considered in the differential diagnosis in any patient with early-onset parkinsonism.
Dependence, withdrawal and rebound of CNS drugs: an update and regulatory considerations for new drugs development
Authors: Lerner Alicja , Klein Michael 
Published: October 2019

AbstractThe purpose of this article is to describe dependence and withdrawal phenomena related to CNS drugs discontinuation and to clarify issues related to the evaluation of clinical drug withdrawal and rebound as they relate to safety in new drug development. The article presents current understanding and definitions of drug dependence and withdrawal which are also relevant and important features of addiction, though not the same. Addiction, called substance use disorder in DSM-5, affects an individual’s brain and behaviour, represents uncontrollable drug abuse and inability to stop taking a drug regardless of the harm it causes. Characteristic withdrawal syndromes following abrupt discontinuation of CNS-active drugs from numerous drug classes are described. These include drugs both scheduled and non-scheduled in the Controlled Substances Act, which categorizes drugs in five schedules based on their relative abuse potentials and dependence liabilities and for regulatory purposes. Schedules 1 and 2 contain drugs identified as those with the highest abuse potential and strictest regulations. Less recognized aspects of drug withdrawal, such as rebound and protracted withdrawal syndromes for several drug classes are also addressed. Part I presents relevant definitions and describes clinical withdrawal and dependence phenomena. Part II reviews known withdrawal syndromes for the different drug classes, Part III describes rebound and Part IV describes protracted withdrawal syndromes. To our knowledge, this is the first compilation of withdrawal syndromes for CNS drugs. Part V provides details of evaluation of dependence and withdrawal in the clinical trials for CNS drugs, which includes general design recommendations, and several tools, such as withdrawal questionnaires and multiple scales that are helpful in the systematic evaluation of withdrawal. The limitations of different aspects of this method of dependence and withdrawal evaluation are also discussed.
Functional annotation of melanoma risk loci identifies novel susceptibility genes
Authors: Fang Shenying , Lu Jiachun , Zhou Xinke , Wang Yuling , Ross Merrick I , Gershenwald Jeffrey E , Cormier Janice N , Wargo Jennifer , Sui Dawen , Amos Christopher I , Lee Jeffrey E 
Published: October 2019

Abstract
Genome-wide association study (GWAS)-identified single-nucleotide polymorphisms (SNPs) are tag SNPs located in both transcribed and non-coding regulatory DNA regions, rather than representing causal or functional variants for disease. To identify functional variants or genes for melanoma susceptibility, we used functional mapping and annotation (FUMA) to perform functional annotation of the summary statistics of 2541 significant melanoma risk SNPs (P &lt; 5 × 10−8) identified by GWAS. The original GWAS melanoma study included 15 990 cases and 26 409 controls, representing the largest international meta-analysis of melanoma susceptibility. We prioritized 330 unique genes, including those in immune cytokine signaling pathways, from 19 loci through positional, expression quantitative trait locus, and chromatin interaction mapping. In comparison, only 38 melanoma-related genes were identified in the original meta-analysis. In addition to the well-known melanoma susceptibility genes confirmed in the meta-analysis (MC1R, CDKN2A, TERT, OCA2 and ARNT/SETDB1), we also identified additional novel genes using FUMA to map SNPs to genes. Through chromatin interaction mapping, we prioritized IFNA7, IFNA10, IFNA16, IFNA17, IFNA14, IFNA6, IFNA21, IFNA4, IFNE and IFNA5; these 10 most significant genes are all involved in immune system and cytokine signaling pathways. In the gene analysis, we identified 72 genes with a P &lt; 2.5 × 10−6. The genes associated with melanoma risk were DEF8 (P = 1.09 × 10−57), DBNDD1 (P = 2.19 × 10−42), SPATA33 (P = 3.54 × 10−38) and MC1R (P = 1.04 × 10−36). In summary, this study identifies novel putative melanoma susceptibility genes and provides a guide for further experimental validation of functional variants and disease-related genes.
The Spirit, Giver of Life: Pneumatology and the Re-Enchantment of Medicine
Authors: De La Fuente David 
Published: October 2019

AbstractIn “Science as a Vocation,” Max Weber identifies a trajectory within modernity of increased rationalization, which results in a dangerous loss of meaning, a marginalization of religion, and a disenchanted view of the world. Weber’s misunderstanding of religion as premodern and “magical” results in his underestimating how religion can contribute to “re-enchanting” a field of knowledge, specifically medicine. This article proposes to turn to a theology of the Holy Spirit as “giver of life” for resources to “re-enchant” medicine. Re-enchantment does not require returning to a magical view of the world but retrieving a real sense of God at work in the world, thereby enabling the health care worker and scientist to arrive at a deeper understanding of vocation.
Infant Respiratory Syncytial Virus Bronchiolitis and Subsequent Risk of Pneumonia, Otitis Media, and Antibiotic Utilization
Authors: Abreo Andrew , Wu Pingsheng , Donovan Brittney M , Ding Tan , Gebretsadik Tebeb , Huang Xiang , Stone Cosby A , Turi Kedir N , Hartert Tina V 
Published: October 2019

Abstract
Infant respiratory syncytial virus (RSV) bronchiolitis in the first 6 months of life was associated with increased odds of pneumonia, otitis media, and antibiotic prescription fills in the second 6 months of life. These data suggest a potential value of future RSV vaccination programs on subsequent respiratory health.
The Effectiveness of Contact Precautions on Methicillin-Resistant Staphylococcus aureus in Long-term Care Across the United States
Authors: Morgan Daniel J , Zhan Min , Goto Michihiko , Franciscus Carrie , Alexander Bruce , Vaughan-Sarrazin Mary , Roghmann Mary-Claire , Pineles Lisa 
Published: October 2019

Abstract

Background
Methicillin-resistant Staphylococcus aureus (MRSA) is a common cause of health care–associated infections in long-term care facilities (LTCFs). The Centers for Disease Control and Prevention recommends contact precautions for the prevention of MRSA within acute care facilities, which are being used within the United States Department of Veterans Affairs (VA) for LTCFs in a modified fashion. The impact of contact precautions in long-term care is unknown.

Methods
To evaluate whether contact precautions decreased MRSA acquisition in LTCFs, compared to standard precautions, we performed a retrospective effectiveness study (pre-post, with concurrent controls) using data from the VA health-care system from 1 January 2011 until 31 December 2015, 2 years before and after a 2013 policy recommending a more aggressive form of contact precautions.

Results
Across 75 414 patient admissions from 74 long-term care facilities in the United States, the overall unadjusted rate of MRSA acquisition was 2.6/1000 patient days. Patients were no more likely to acquire MRSA if they were cared for using standard precautions versus contact precautions in a multivariable, discrete time survival analysis, controlling for patient demographics, risk factors, and year of admission (odds ratio, 0.97; 95% confidence interval, .85–1.12; P = .71).

Conclusions
MRSA acquisition and infections were not impacted by the use of active surveillance and contact precautions in LTCFs in the VA.
Cefiderocol: A Novel Siderophore Cephalosporin Defeating Carbapenem-resistant Pathogens
Authors: Bonomo Robert A 
Published: October 2019

AbstractCefiderocol, a novel siderophore cephalosporin in late-stage clinical development, utilizes a “Trojan horse” active transport mechanism to enter bacteria and has proven in vitro activity against carbapenem-resistant gram-negative pathogens, including those with major carbapenem-resistance mechanisms, and stability against all carbapenemases.
Student teachers’ perceptions of critical thinking and its teaching
Authors: Yuan Rui , Stapleton Paul 
Published: October 2019

Abstract
Although the importance of critical thinking (CT) has been stressed in English language education, little attention has been paid to language teachers’ perceptions and experiences regarding CT during the pre-service stage of their careers. Drawing on data from a focus group and follow-up email interviews with pre-service language teachers, this study shows that the participants had a limited understanding of CT, and lacked preparation and support in their programmes regarding how to implement CT-oriented teaching practices. The findings also revealed a range of individual and contextual challenges faced by the participants when they tried to integrate CT into their language teaching. The study concludes with recommendations on how to cultivate a critical mindset among language teachers while developing CT-oriented pedagogies.
Illustrating formative assessment in task-based language teaching
Authors: Gan Zhengdong , Leung Constant 
Published: October 2019

Abstract
There has been an increasing professional and policy interest in using formative assessment as part of the learning process in the classroom, with increasing numbers of educators regarding it as an effective means of closing the gap between students’ current and desired performance. However, there is a range of different views on what actually constitutes formative assessment and how it may be incorporated into regular classroom teaching. Furthermore, formative assessment is often misconstrued in reality, and teachers face considerable challenges in implementing formative assessment in their daily classes, particularly in the ESL teaching context. The purpose of this article is, therefore, to review how formative assessment has recently been discussed in both general education and L2 assessment fields, and to illustrate how formative assessment can be implemented in task-based language teaching in the daily ESL classroom.
Training planning in second language narrative writing
Authors: Khezrlou Sima 
Published: October 2019

Abstract
This study attempted to explore whether learners could be trained to use effective planning behaviours and whether this could affect their writing performance. A complete class of Iranian learners (n = 42) of English as a foreign language received training in effective pre-task planning based on a number of operating principles. Writing performance, prior to and after the training, was measured through written narrative tasks. Retrospective interviews were also used to examine what learners did during planning. Results revealed that the effective planning behaviours are learnable, with many learners reporting positive ideas about the training programme. The findings also indicated significant improvements in learners’ writing quality in terms of complexity, accuracy and fluency. Based on these collective findings, it is suggested that L2 learners need to be guided towards using more helpful planning behaviours, particularly those that are not forgotten with time.
Soil hydrology drives ecological niche differentiation in a native prairie microbiome
Authors: Griffin James S , Haug Loren A , Rivera Vivien A , Gonzalez Liliana M Hernandez , Kelly John J , Miller William M , Wells George F , Packman Aaron I 
Published: October 2019

ABSTRACT
While the impacts of soil moisture on soil microbiome diversity and composition are well characterized, the influence of hydrological regime has been overlooked. As precipitation patterns are altered by climate change, understanding the impact of soil hydrology on community structure and function is critical. In this work, water level was continuously monitored for over a year in a Midwestern prairie-wetland at 10 cm depth increments up to a depth of 120 cm in 10 locations. We analyzed microbiome composition and edaphic factors in soil cores collected from this unique spatially distributed, longitudinal data set. We demonstrate that the fraction of time that each sample was inundated explains more variability in diversity and composition across this site than other commonly assessed edaphic factors, such as soil pH or depth. Finally, we show that these compositional changes influence abundance of ammonia oxidizers. The observed patterns in community composition and diversity are fundamentally regulated by the interaction of water with a structured landscape, particularly an elevated sand ridge characterized by drier conditions and a lower-lying wetland with more clayey soils. Similar processes are generally expected to influence the biogeography of many terrestrial environments, as morphology, hydrology and soil properties generally co-vary.
Peer pressure: evolutionary responses to biotic pressures in wine yeasts
Authors: Conacher C G , Rossouw D , Bauer F F B 
Published: October 2019

ABSTRACT
In the macroscopic world, ecological interactions between multiple species of fauna and flora are recognised as major role-players in the evolution of any particular species. By comparison, research on ecological interactions as a driver of evolutionary adaptation in microbial ecosystems has been neglected. The evolutionary history of the budding yeast Saccharomyces cerevisiae has been extensively researched, providing an unmatched foundation for exploring adaptive evolution of microorganisms. However, in most studies, the habitat is only defined by physical and chemical parameters, and little attention is paid to the impact of cohabiting species. Such ecological interactions arguably provide a more relevant evolutionary framework. Within the genomic phylogenetic tree of S. cerevisiae strains, wine associated isolates form a distinct clade, also matched by phenotypic evidence. This domestication signature in genomes and phenomes suggests that the wine fermentation environment is of significant evolutionary relevance. Data also show that the microbiological composition of wine fermentation ecosystems is dominated by the same species globally, suggesting that these species have co-evolved within this ecosystem. This system therefore presents an excellent model for investigating the origins and mechanisms of interspecific yeast interactions. This review explores the role of biotic stress in the adaptive evolution of wine yeast.