bluuebunny/crossref_metadata_2025_split huggingface dataset:
Amplification of the V5 – V8 region of the 16S rRNA gene effectively speciates medically important genital tractLactobacillusspecies in the upper female genital tract
Authors: O’Callaghan Jessica L. , Willner Dana , Buttini Melissa , Huygens Flavia , Pelzer Elise S. 
Published: May 2019

ABSTRACTBackgroundThe endometrial cavity is an upper genital tract site largely heralded as sterile, however, advances in culture-independent, next generation sequencing technology have revealed that this site harbours a rich microbial community which includes multipleLactobacillusspecies. These bacteria are considered to be the most common non-pathogenic genital tract commensals. Next-generation sequencing of the female lower genital tract has revealed significant variation amongst microbial community composition with respect toLactobacillussp. in samples collected from healthy and diseased women. The aim of this study was to evaluate the ability of the 16S rRNA gene to characterize genital tract lactobacilli to species-level taxonomy.MethodsSamples were interrogated for the presence of microbial DNA using two-step next generation sequencing technology to exploit the V5–V8 regions of the 16S rRNA gene and compared to standard speciation using qPCR.ResultsThe V5-V8 region of the 16S rRNA gene has sufficient sequence variation within frequently encountered genital tract lactobacilli to allow accurate determination of relative abundance within the community, and speciation for several key community members without completing additional experimentation.ConclusionsNext-generation sequencing of clinical genital tract isolates is an effective method for high throughput identification to species-level of keyLactobacillussp.IMPORTANCEHuman microbiome experiments, including the low biomass organs such as the upper genital tract, require the development of consensus protocols to ensure accurate comparison between such studies and our data forms an important foundation for future protocols.This paper provides evidence to support the selection of the V5-V8 regions of the 16S rRNA gene improvedLactobacillusspeciation using next generation sequencing technology. The choice of variable region for broad-range amplification in microbiome studies is important due to preferential primer binding associated with some genera based on nucleotide sequence patterns. By utilising the V5-V8 region, multiple species ofLactobacilluscan be characterised with relative confidence.
Characterization of a β-lactamase that contributes to intrinsic β-lactam resistance inClostridioides difficile
Authors: Sandhu Brindar K. , Edwards Adrianne N. , Anderson Sarah E. , Woods Emily C. , McBride Shonna M. 
Published: May 2019

ABSTRACTClostrididioides difficilecauses severe antibiotic-associated diarrhea and colitis.C. difficileis an anaerobic, Gram-positive spore former that is highly resistant to β-lactams, the most commonly prescribed antibiotics. The resistance ofC. difficileto β-lactam antibiotics allows the pathogen to replicate and cause disease in antibiotic-treated patients. However, the mechanisms of β-lactam resistance inC. difficileare not fully understood. Our data reinforce prior evidence thatC. difficileproduces a β-lactamase, which is a common β-lactam resistance mechanism found in other bacterial species. We identified an operon encoding a lipoprotein of unknown function and a β-lactamase that was greatly induced in response to several classes of β-lactam antibiotics. An in-frame deletion of the operon abolished β-lactamase activity inC. difficilestrain 630Δermand resulted in decreased resistance to the β-lactam ampicillin. We found that the activity of this β-lactamase, herein named BlaD, is dependent upon the redox state of the enzyme. In addition, we observed that transport of BlaD out of the cytosol and to the cell surface is facilitated by an N-terminal signal sequence. Our data demonstrate that a co-transcribed lipoprotein, BlaX, aids in BlaD activity. Further, we identified a conserved BlaRI regulatory system and demonstrated via insertional disruption that BlaRI controls transcription of theblaXDoperon in response to β-lactams. These results provide support for the function of a β-lactamase inC. difficileantibiotic resistance, and reveal the unique roles of a co-regulated lipoprotein and reducing environment in β-lactamase activity.IMPORTANCEClostridioides difficileis an anaerobic, gastrointestinal human pathogen. One of the highest risk factors for contractingC. difficileinfection is antibiotic treatment, which causes microbiome dysbiosis.C. difficileis resistant to β-lactam antibiotics, the most commonly prescribed class of antibiotics.C. difficileproduces a recently discovered β-lactamase, which cleaves and inactivates numerous β-lactams. In this study, we report the contribution of this anaerobic β-lactamase to ampicillin resistance inC. difficile, as well as the transcriptional regulation of the gene,blaD, by a BlaRI system. In addition, our data demonstrate co-transcription ofblaDwithblaX, which encodes a membrane protein of previously unknown function. Furthermore, we provide evidence that BlaX enhances β-lactamase activity in a portion ofC. difficilestrains. This study demonstrates a novel interaction between a β-lactamase and a membrane protein in a Gram-positive pathogen, and due to the anaerobic nature of the β-lactamase activity, suggests that more β-lactamases are yet to be identified in other anaerobes.
Large Scale-Free Network Organization is Likely Key for Biofilm Phase Transition
Authors: Selvarajoo Kumar 
Published: May 2019

AbstractNon-linear Kuramoto model has been used to study synchronized or sync behavior in numerous fields, however, its application in biology is scare. Here, I introduce the basic model and provide examples where large scale small-world or scale-free networks are crucial for spontaneous sync even for low coupling strength. This information was next checked for relevance in living systems where it is now well-known that biological networks are scale-free. Our recent transcriptome-wide data analysis of Saccharomyces cerevisiae biofilm showed that low to middle expressed genes are key for scale invariance in biology. Together, the current data indicate that biological network connectivity structure with low coupling strength, or expression levels, is sufficient for sync behavior. For biofilm regulation, it may, therefore, be necessary to investigate large scale low expression genes rather than small scale high expression genes.
The photoactive site modulates current rectification and channel closing in the natural anion channelrhodopsin GtACR1
Authors: Sineshchekov Oleg A. , Govorunova Elena G. , Li Hai , Wang Xin , Spudich John L. 
Published: May 2019

ABSTRACTThe crystal structure of GtACR1 from Guillardia theta revealed an intramolecular tunnel predicted to expand to form the anion-conducting channel upon photoactivation (Li et al. 2019). The location of the retinylidene photoactive site within the tunnel raised the question of whether, in addition to triggering channel opening by photoisomerization, the site also participates in later channel processes. Here we demonstrate the involvement of the photoactive site in chloride conductance and channel closing. Electrostatic perturbation of the photoactive retinylidene Schiff base region by glutamate substitutions alters the rectification of the photocurrent as well as channel closing kinetics. Substitutions on opposite sides of the photoactive site causes opposite changes, with channel closing kinetically correlated with Schiff base deprotonation, and the extent of these effects closely correlate with distance of the introduced glutamyl residue from the photoactive site.
Comparison of silhouette-based reallocation methods for vegetation classification
Authors: Lengyel Attila , Roberts David W. , Botta-Dukát Zoltán 
Published: May 2019

AbstractAimsTo introduce REMOS, a new iterative reallocation method (with two variants) for vegetation classification, and to compare its performance with OPTSIL. We test (1) how effectively REMOS and OPTSIL maximize mean silhouette width and minimize the number of negative silhouette widths when run on classifications with different structure; (2) how these three methods differ in runtime with different sample sizes; and (3) if classifications by the three reallocation methods differ in the number of diagnostic species, a surrogate for interpretability.Study areaSimulation; example data sets from grasslands in Hungary and forests in Wyoming and Utah, USA.MethodsWe classified random subsets of simulated data with the flexible-beta algorithm for different values of beta. These classifications were subsequently optimized by REMOS and OPTSIL and compared for mean silhouette widths and proportion of negative silhouette widths. Then, we classified three vegetation data sets of different sizes from two to ten clusters, optimized them with the reallocation methods, and compared their runtimes, mean silhouette widths, numbers of negative silhouette widths, and the number of diagnostic species.ResultsIn terms of mean silhouette width, OPTSIL performed the best when the initial classifications already had high mean silhouette width. REMOS algorithms had slightly lower mean silhouette width than what was maximally achievable with OPTSIL but their efficiency was consistent across different initial classifications; thus REMOS was significantly superior to OPTSIL when the initial classification had low mean silhouette width. REMOS resulted in zero or a negligible number of negative silhouette widths across all classifications. OPTSIL performed similarly when the initial classification was effective but could not reach as low proportion of misclassified objects when the initial classification was inefficient. REMOS algorithms were typically more than an order of magnitude faster to calculate than OPTSIL. There was no clear difference between REMOS and OPTSIL in the number of diagnostic species.ConclusionsREMOS algorithms may be preferable to OPTSIL when (1) the primary objective is to reduce or eliminate negative silhouette widths in a classification, (2) the initial classification has low mean silhouette width, or (3) when the time efficiency of the algorithm is important because of the size of the data set or the high number of clusters.
Co-regulation and functional cooperativity of FOXM1 and RHNO1 bidirectional genes in ovarian cancer
Authors: Barger Carter J , Branick Connor , Chee Linda , Albahrani Mustafa , Klinkebiel David , Drapkin Ronny , Odunsi Kunle , Zou Lee , Karpf Adam R. 
Published: May 2019

SummaryWe report that the oncogenic transcription factorFOXM1is arranged in a head-to-head configuration withRHNO1, a gene involved in the ATR/CHK1-dependent DNA replication stress (DRS) response.FOXM1andRHNO1are both amplified and upregulated in high-grade serous ovarian cancer (HGSC).FOXM1andRHNO1expression are closely associated in normal and cancer tissues, including single cells, and a bidirectional promoter (F/R-BDP) mediates balanced expression. Targeting of FOXM1 and RHNO1 in HGSC cells using shRNA, CRISPR mutagenesis, or CRISPR interference directed to the F/R-BDP reduced DNA homologous recombination repair (HR) capacity, increased DNA damage, reduced clonogenic survival, and sensitized HGSC cells to the poly-ADP ribosylase inhibitor (PARPi) olaparib. Thus, there is functional cooperativity between FOXM1 and RHNO1 in cancer cells, and combinatorial targeting of this bidirectional gene pair may be a novel cancer therapeutic strategy. More broadly, our data provide evidence that bidirectional gene units function in human cancer.
“Health literacy assessment of primary care patients in Low and Middle Income Countries”
Authors: Pasha F. , Dreshaj D. , Ismaili A. , Sopjani I. , Brooke J. , Dreshaj Sh. 
Published: May 2019

ABSTRACTAimTo explore health literacy levels of primary care patients, and associations with demographic variables, frequency of visits, hospitalization rates, and self-perception of health.BackgroundHealth literacy is the ability to obtain, read, understand and apply healthcare information to inform decision-making to commence or adhere to treatment. The benefits of a population proficient in health literacy include enhanced communication, adherence to treatment, engagement in self-care, and ultimately improved health with financial savings for healthcare providers.DesignCross-sectional epidemiological study, reported using STROBE guidelines.Materials and MethodsData were collected from patients attending a primary care center in Prishtina, Kosovo from August to September 2018. Data collection included the Short Test of Functional Health Literacy in Adults (S-TOFHLA), gender, age, socioeconomic status, education, self-perception of health, number of visits to the doctor and hospital. Data were analyzed with SPSS software (version 20).ResultsParticipants (n=557) ages ranged from 15 to >65 (mean 27.82) years, were female (57.85%), Albanian (97.13%), with a response rate of 92.83%, 79% were health literate, 9% had moderate health literacy, 12% were health illiterate. Four variables determined health literacy, level of education (p < .01), gender (p = .033), hospitalization rates (p < .05), socioeconomic status of unemployed compared to being a student (p<.01).ConclusionsThere remains a need to address health literacy levels in Kosovo, through the development or adaptation of health literacy tools appropriate for this population, which will support and positively impact on patient’s wellbeing. Nurses are the best-placed professionals to implement these tools and support patients with low health literacy.Relevance to clinical practiceNurses have a key role in implementing health literacy tools and supporting patients by adapting their communication styles in accordance with each patient’s level of health literacy, which will support adherence to advice, safety and treatment outcomes.What does this paper contribute to the wider global clinical community?Health literacy is associated with level of education, gender and socioeconomic status and hospitalization rates of primary care patients.A focus on health literacy is essential to address the inequalities of health for those with marginal or inadequate health literacy.Nurses are the best-placed health care professionals to support individuals with low levels of health literacy through interventions, and adapting their communication styles.
Commercial or educational orientations
Authors: Ho Amaly 
Published: May 2019

Purpose
Taught postgraduate (TPg) education is the resource for lifelong learning and continuing education in respond to the demands of a qualified workforce in the digital era. Good TPg governance is crucial for ensuring the quality of student learning outcomes. The purpose of this paper is to discuss the framework of the market-oriented governance model of TPg education in Hong Kong from the aspects of provision, finance and quality assurance. The framework is applied to analyse the pitfalls of TPg students’ learning in curriculum, assessment and management, of which data were collected from an empirical study.

Design/methodology/approach
Based on the grounded theory approach, semi-structured interviews were conducted with 23 TPg students from four universities in Hong Kong at individual or group level to understand their motivation towards further study. The interview protocols were analysed to develop a thematic framework, and a part of it is presented in this paper to discuss the programme factors that caused negative student learning outcomes in the light of the drawbacks of the TPg governance model in Hong Kong.

Findings
A balance between commercial purposes and educational orientations of TPg provision could be sought by adjust the power distribution of the central government and institutions in terms of quality assurance mechanism, and the setting and implementation of general and specific goals of TPg education.

Originality/value
TPg education is an under investigation area. It is an important education sector that provides opportunities for lifelong learning with the purpose of cultivating a skilful workforce. This paper contributes to the development of efficient TPg governance for ensuring the qualities of TPg programmes to benefit the advancement of society in the Hong Kong context.
Inpatient treatment of borderline personality disorder in adults with intellectual disability: reflections on practice
Authors: Iversen Trine Elisabeth , Horndalsveen Kristin , Matre Espen , Henriksen Tine Finstad , Fusche Sarah , Kildahl Arvid Nikolai , Bakken Trine Lise 
Published: May 2019

Purpose
There are few publications on personality disorder in adults with intellectual disability (ID), and on borderline personality disorder (BPD) specifically. Publications concerning treatment are sparse, despite the high symptom burden in these patients. This paper aims to discuss these issues.

Design/methodology/approach
Six patients with BPD and ID were recruited from the same inpatient unit. Behaviour problems and mental health symptoms were scored on admission and discharge. Information about treatment, length of stay, etc. was taken from case files.

Findings
Both mental health symptoms measured by the SCL-90-R, and behaviour problems measured by the Aberrant Behaviour Checklist were significantly reduced on discharge. In the active treatment period, the two main aspects of treatment were validation and practicing new solutions when emotional and behavioural problems occur, i.e. skills training.

Research limitations/implications
The limitations related to this study are that the study is conducted in one milieu only. Another limitation is that the patients were admitted over a five-year period, where, some changes were made in the treatment approach.

Practical implications
Inpatient treatment of this patient group seems to be effective if individually adjusted to the patient’s psychopathology, ID and communication style. Close co-operation between the individual therapist and milieu therapists is essential.

Originality/value
There is a need for intervention studies on BPD in ID. This study may be a valuable contribution.
What’s the penalty for using the Square Root Law of inventory centralisation?
Authors: Oeser Gerald 
Published: May 2019

PurposeThe square root law (SRL) is a popular model for assessing inventory levels when changing the number of warehouses. Previous empirical research, however, has shown that mostly its underlying assumptions do not hold in practice. This sparks the question how inaccurate the SRL’s results are. The paper aims to discuss this issue.Design/methodology/approachIn 26 company cases of reducing the number of warehouses, the estimation error of the SRL is analysed irrespective of its underlying assumptions.FindingsThe analysis reveals an average estimation error for total inventory of 27.85 per cent (median=27.84 per cent), but a high variability across the cases. The SRL seems to mostly overestimate inventory savings from centralisation and inventory increases from decentralisation. Managers should only use the SRL if inventory depends on the number of warehouses in their situation, i.e. if they use the economic order or production quantity policy and safety factor approach. Suggestions for coping with the SRL’s estimation error are given.Research limitations/implicationsThis paper is based on the 26 cases that could be found in a thorough literature review in the ten most widely spoken languages and that contained or allowed to deduce the necessary information. In order to enable wider generalisations, this sample could be extended.Originality/valueMost past research has been more theoretical in nature. This research is the first to investigate the SRL’s estimation error using a variety of company cases and how to cope with this error.
“It’s a bit of freedom away from home and cleaning all the time”
Authors: Cudworth Dave 
Published: May 2019

PurposeMuch has been written over the past 50 years about the concerns associated with the educational underachievement of Gypsy children in England. This work has usually focussed on ethnicity and mobility as key factors that affect school attendance. However, it is only relatively recently that a concern with gender relations has entered the debate. Therefore, the purpose of this paper is to provide an empirically driven contribution to this fledging area of enquiry.Design/methodology/approachThis paper draws on semi-structured interview material and a focus group discussion about the educational experiences and aspirations of three mothers and six young women from the community. Further, interview materials were collected from two head teachers with Gypsy children in their schools and two Traveller Education Support Staff.FindingsThis paper finds how educational “public” space is providing a place for girls and young women to think differently and even begin to challenge the gender regimes embedded within the “private” space of their communities.Originality/valueIn line with the idea that space and place are fundamental in formulating gender relations, this paper frames this phenomenon within a socio-spatial context.
Psoriasis is associated with increased risk of bullous pemphigoid: A nationwide population‐based cohort study in Taiwan
Authors: Ho Yi‐Hsin , Hu Hsiao‐Yun , Chang Yun‐Ting , Li Chung‐Pin , Wu Chen‐Yi 
Published: May 2019

AbstractPsoriasis may coexist with bullous pemphigoid (BP); however, no cohort studies have investigated the relationship between psoriasis and the risk of BP. This study aims to investigate the relationship between psoriasis and the risk of BP in Taiwan. This cohort study consists of 109 777 psoriatic patients and 109 777 matched non‐exposed controls. Psoriatic patients diagnosed between 2002 and 2012 were identified from the Taiwan National Health Insurance Research Database. The age‐, sex‐ and index date‐matched non‐exposed group was selected from the same database. The relationship between psoriasis and the risk of BP was investigated using Cox proportional hazards analyses. Psoriasis was significantly associated with an increased risk of BP (hazard ratio, 3.05; 95% confidence interval, 2.10–4.43; P < 0.001). The mean interval between the diagnoses of psoriasis and BP was 2.86 years, with the highest occurrence in the first year after psoriasis diagnosis, and gradually decreasing with each year of observation. Psoriatic patients with BP were significantly younger than BP patients in the non‐exposed group (71.6 ± 13.9 vs 76.6 ± 7.7 years, respectively; P = 0.030). A higher proportion of patients with coexisting psoriasis and BP received phototherapy (20%). In conclusion, psoriasis was independently associated with a 3.05‐fold increased risk of BP, and psoriatic patients with BP were younger, with over one‐third of BP cases diagnosed in the first year after incident psoriasis. Therefore, clinicians treating patients with psoriasis may be aware of the possibility of the development of BP.