bluuebunny/crossref_metadata_2025_split huggingface dataset:
Human Immunodeficiency Virus-associated Neurocognitive Impairment in Diverse Resource-limited Settings
Authors: Robertson Kevin R , Jiang Hongyu , Kumwenda Johnstone , Supparatpinyo Khuanchai , Marra Christina M , Berzins Baiba , Hakim James , Sacktor Ned , Campbell Thomas B , Schouten Jeffrey , Mollan Katie , Tripathy Srikanth , Kumarasamy Nagalingeswaran , La Rosa Alberto , Santos Breno , Silva Marcus T , Kanyama Cecilia , Firhnhaber Cindy , Murphy Robert , Hall Colin , Marcus Cheryl , Naini Linda , Masih Reena , Hosseinipour Mina C , Mngqibisa Rosie , Badal-Faesen Sharlaa , Yosief Sarah , Vecchio Alyssa , Nair Apsara ,   AIDS Clinical Trials Group
Published: September 2018

Abstract

Background
Neurocognitive impairment remains a common complication of human immunodeficiency virus (HIV) despite effective antiretroviral therapy (ART). We previously reported improved neurocognitive functioning with ART initiation in 7 resource-limited countries for HIV+ participants from the AIDS Clinical Trials Group (ACTG) 5199 International Neurological Study (INS). Here, we apply normative data from the International Neurocognitive Normative Study (INNS) to INS to provide previously unknown rates of neurocognitive impairment.

Methods
The A5199 INS assessed neurocognitive and neurological performance within a randomized clinical trial with 3 arms containing World Health Organization first-line recommended ART regimens (ACTG 5175; PEARLS). The ACTG 5271 INNS collected normative comparison data on 2400 high-risk HIV-negative participants from 10 voluntary counseling and testing sites aligned with INS. Normative comparison data were used to create impairment ratings for HIV+ participants in INS; associations were estimated using generalized estimating equations.

Results
Among 860 HIV+ adults enrolled in ACTG 5199, 55% had no neurocognitive impairment at baseline. Mild neurocognitive impairment was found in 25%, moderate in 17%, and severe in 3% of participants. With the initiation of ART, the estimated odds of impairment were reduced 12% (95% confidence interval, 9%, 14%) for every 24 weeks (P &lt; .0001) on ART. Mild impairment dropped slightly and then remained at about 18% out to week 168.

Conclusions
Almost half of HIV+ participants had neurocognitive impairment at baseline before ART, based on local norms. With ART initiation, there were significant overall reductions in neurocognitive impairment over time, especially in those with moderate and severe impairments.

Clinical Trials Registration
NCT00096824.
Pattern of antibiotic prescriptions for outpatients with acute respiratory tract infections in Japan, 2013–15: a retrospective observational study
Authors: Teratani Yusuke , Hagiya Hideharu , Koyama Toshihiro , Adachi Mayu , Ohshima Ayako , Zamami Yoshito , Tanaka Hiroyoshi Y , Tatebe Yasuhisa , Tasaka Ken , Mikami Naoko , Shinomiya Kazuaki , Kitamura Yoshihisa , Kano Mitsunobu R , Hinotsu Shiro , Sendo Toshiaki 
Published: September 2018

Abstract

Background
In this age of antimicrobial resistance, unnecessary use of antibiotics to treat non-bacterial acute respiratory tract infections (ARTIs) and inappropriate use of antibiotics in treating bacterial ARTIs are public health concerns.

Purpose
Our aim is to identify the pattern of oral antibiotic prescriptions for outpatients with ARTIs in Japan.

Methods
We analysed health insurance claims data of patients (aged ≤74 years) from 2013 to 2015, to determine the pattern of antibiotic prescriptions for outpatient ARTIs and calculated the proportion of each antibiotic.

Results
Data on 4.6 million antibiotic prescriptions among 1559394 outpatients with ARTIs were analysed. The most commonly prescribed classes of antibiotics included cephalosporins (41.9%), macrolides (32.8%) and fluoroquinolones (14.7%). The proportion of first-, second- and third-generation cephalosporins was 1.0%, 1.7% and 97.3%, respectively. Fluoroquinolones accounted for a quarter of the prescriptions for ARTIs in patients aged >20 years. In contrast, penicillins accounted for just 8.0% of the total number of antibiotic prescriptions for ARTIs.

Conclusions
According to clinical guidelines, penicillins are first-line antibiotics against ARTIs. However, third-generation cephalosporins, macrolides and fluoroquinolones are more frequently prescribed in Japan. Although we could not assess the extent to which appropriate antibiotics are selected, our results support the necessity of improving antibiotic choices in the treatment of ARTIs.
Cordycepin activates autophagy through AMPK phosphorylation to reduce abnormalities in Machado–Joseph disease models
Authors: Marcelo Adriana , Brito Filipa , Carmo-Silva Sara , Matos Carlos A , Alves-Cruzeiro João , Vasconcelos-Ferreira Ana , Koppenol Rebekah , Mendonça Liliana , de Almeida Luís Pereira , Nóbrega Clévio 
Published: September 2018

Abstract
Machado–Joseph disease (MJD) is a neurodegenerative disorder caused by an abnormal expansion of citosine-adenine-guanine trinucleotide repeats in the disease-causing gene. This mutation leads to an abnormal polyglutamine tract in the protein ataxin-3 (Atx3), resulting in formation of mutant Atx3 aggregates. Despite several attempts to develop a therapeutic option for MJD, currently there are no available therapies capable of delaying or stopping disease progression. Recently, our group reported that reducing the expression levels of mutant Atx3 lead to a mitigation of several MJD-related behavior and neuropathological abnormalities. Aiming a more rapid translation to the human clinics, in this study we investigate a pharmacological inhibitor of translation—cordycepin—in several preclinical models. We found that cordycepin treatment significantly reduced (i) the levels of mutant Atx3, (ii) the neuropathological abnormalities in a lentiviral mouse model, (iii) the motor and neuropathological deficits in a transgenic mouse model and (iv) the number of ubiquitin aggregates in a human neural model. We hypothesize that the effect of cordycepin is mediated by the increase of phosphorylated adenosine monophosphate-activated protein kinase (AMPK) levels, which is accompanied by a reduction in the global translation levels and by a significant activation of the autophagy pathway. Overall, this study suggests that cordycepin might constitute an effective and safe therapeutic approach for MJD, and probably for the other polyglutamine diseases.
A century of change in North Sea plankton communities explored through integrating historical datasets
Authors: Bedford Jacob , Johns David , McQuatters-Gollop Abigail 
Published: September 2018

Abstract
Plankton communities make useful ecosystem indicators, and taking a historical perspective on plankton community composition provides insights into large-scale environmental change. Much of our understanding of long temporal-scale change in plankton communities in the North Sea has been provided by the Continuous Plankton Recorder (CPR) survey, operating since 1931, with consistent time-series data available since 1958. This article further increases the temporal scale of our understanding of community change in the North Sea by combining the CPR dataset with a digitized collection of plankton surveys undertaken by ICES from 1902 to 1912. After steps taken to integrate the two disparate datasets, differences in overall community composition between time periods suggest that the multidecadal changes observed through the CPR survey time period may have occurred from a non-stable baseline that was already on a trajectory of change. Therefore, a stable historical time period in which plankton communities are assessed against for any impact of human pressures may be hard to define for the North Sea and instead underlying variation needs to be encompassed within any baseline chosen. Further evidence for the influence of large-scale changes in sea surface temperature driving change in plankton community composition was found using the extended dataset.
Using voice to create inpatient progress notes: effects on note timeliness, quality, and physician satisfaction
Authors: Payne Thomas H , Alonso W David , Markiel J Andrew , Lybarger Kevin , Lordon Ross , Yetisgen Meliha , Zech Jennifer M , White Andrew A 
Published: September 2018

Abstract

Objectives
We describe the evaluation of a system to create hospital progress notes using voice and electronic health record integration to determine if note timeliness, quality, and physician satisfaction are improved.

Materials and methods
We conducted a randomized controlled trial to measure effects of this new method of writing inpatient progress notes, which evolved over time, on important outcomes.

Results
Intervention subjects created 709 notes and control subjects created 1143 notes. When adjusting for clustering by provider and secular trends, there was no significant difference between the intervention and control groups in the time between when patients were seen on rounds and when progress notes were viewable by others (95% confidence interval −106.9 to 12.2 min). There were no significant differences in physician satisfaction or note quality between intervention and control.

Discussion
Though we did not find support for the superiority of this system (Voice-Generated Enhanced Electronic Note System [VGEENS]) for our 3 primary outcomes, if notes are created using voice during or soon after rounds they are available within 10 min. Shortcomings that likely influenced subject satisfaction include the early state of our VGEENS and the short interval for system development before the randomized trial began.

Conclusion
VGEENS permits voice dictation on rounds to create progress notes and can reduce delay in note availability and may reduce dependence on copy/paste within notes. Timing of dictation determines when notes are available. Capturing notes in near-real-time has potential to apply NLP and decision support sooner than when notes are typed later in the day, and to improve note accuracy.
Diet Macronutrient Composition, Physical Activity, and Body Composition in Soldiers During 6 Months Deployment
Authors: Nykänen Tarja , Pihlainen Kai , Santtila Matti , Vasankari Tommi , Fogelholm Mikael , Kyröläinen Heikki 
Published: September 2018

Abstract

Introduction
Optimal diet together with good physical fitness maintains readiness and military performance during longer deployments. The purpose of this study was to describe changes in dietary macronutrient and energy intake, total physical activity and body composition during a 6-month deployment in South Lebanon. Furthermore, associations of diet macronutrient intake and physical activity on body composition were also studied.

Materials and Methods
Forty male soldiers kept a 3-day food diary and their body composition was measured via bioimpedance and ultrasonography. Total physical activity was evaluated by accelerometers in a subgroup of participants. Measurements were conducted in the PRE-, MID-, and POST-deployment.

Results
Mean carbohydrate intakes were 39.5–42.6 E%, protein intakes 18.7–22.3 E%, and fat intakes 34.9–35.7 E%. Daily energy intake remained stable (10.1–10.3 MJ/D). Total physical activity was decreased during deployment (e.g., step count from 9,835 ± 2,743 to 8,388 ± 2,875 steps/day, p = 0.007). Skeletal muscle mass and subcutaneous fat increased by 1.3% (p = 0.019) and 1.9% (p = 0.006), respectively. Energy and fat intake associated positively with body mass and skeletal muscle mass (r = 0.31–0.48, p &lt; 0.05–0.001).

Conclusions
Carbohydrate intakes and physical activity were low, compared with the general recommendations. Protein intakes were relatively high. Skeletal muscle mass and subcutaneous fat increased. Suboptimal diet together with low level of physical activity may have a negative impact on body composition, physical performance, and cardiometabolic health. Consequently, soldiers should be encouraged to consume more fiber-rich carbohydrates and less saturated fatty acids as well as maintain a high level of physical fitness to sustain military readiness during long-term deployments.
Epidemiological survey of onychomycosis pathogens in Japan by real-time PCR
Authors: Shimoyama Harunari , Satoh Kazuo , Makimura Koichi , Sei Yoshihiro 
Published: September 2018

AbstractIn Japan, an epidemiological survey of onychomycosis pathogens was performed using culture methods; however, the positive culture rate was 40% or less. As part of an epidemiological survey of dermatomycoses in Japan, we overcame this low positive rate by employing a real-time polymerase chain reaction (PCR) assay that allowed rapid and accurate detection and identification. In 2011, nail specimens were collected from patients at nine institutes in various prefectures in Japan and diagnosed as onychomycosis. For the detection and identification of the main pathogens causing onychomycosis, we performed real-time PCR using specific TaqMan® MGB probes and primer sets. Of the 496 onychomycosis samples, real-time PCR detected 382 cases (77.0%) caused by Trichophyton rubrum; 74 cases (15.0%) caused by Trichophyton interdigitale; and eight cases (1.6%) caused by Candida albicans. The real-time PCR positive rate was 96.2%. The most frequent pathogen was T. rubrum throughout life, with the number of patients affected peaking in the range of 60 to 69 years of age and no significant differences in the composition of causative pathogens by sex. We were able to detect and identify pathogens from almost all specimens and succeeded in analyzing the pathogens involved in onychomycosis cases in Japan. These data confirmed that our real-time PCR method was effective for detecting and identifying the main fungal pathogens from onychomycosis specimens.
Effect of ferric citrate on serum phosphate and fibroblast growth factor 23 among patients with nondialysis-dependent chronic kidney disease: path analyses
Authors: Block Geoffrey A , Pergola Pablo E , Fishbane Steven , Martins Julian G , LeWinter Robin D , Uhlig Katrin , Neylan John F , Chertow Glenn M 
Published: September 2018

Abstract

Background
Among patients with nondialysis-dependent chronic kidney disease (NDD-CKD) and iron-deficiency anemia (IDA), ferric citrate increases hemoglobin and iron parameters and reduces serum phosphate and fibroblast growth factor 23 (FGF23), a key phosphate-regulating hormone. We conducted post hoc analyses of a phase 3 trial to explore associations between iron replacement, serum phosphate changes and FGF23 regulation.

Methods
We employed multivariable regression and longitudinal mixed-effects models to identify and confirm, respectively, whether baseline demographic and laboratory variables were associated with ferric citrate-induced changes in serum phosphate or FGF23 concentrations. We employed path analyses to determine whether changes in FGF23 concentrations were mediated via changes in serum phosphate and/or transferrin saturation (TSAT).

Results
We analyzed a total of 117 and 115 ferric citrate-treated and placebo-treated patients, respectively. At 16 weeks, ferric citrate significantly reduced serum phosphate versus placebo (P = 0.006) only among patients with elevated baseline serum phosphate (≥4.5 mg/dL) and did not reduce serum phosphate among patients with baseline serum phosphate within the population reference range. Ferric citrate reduced intact FGF23 and C-terminal FGF23 partially via changes in TSAT (for C-terminal FGF23) and serum phosphate (for intact FGF23) and partially via unknown/unmeasured mechanisms.

Conclusions
Ferric citrate reduced serum FGF23 concentrations (partially via effects on serum phosphate and iron balance) and did not reduce serum phosphate among patients with baseline serum phosphate concentrations within the population reference range.
Accelerating Soybean Breeding in a CO2-Supplemented Growth Chamber
Authors: Nagatoshi Yukari , Fujita Yasunari 
Published: September 2018

Abstract
Soybean (Glycine max) is the most important dicot crop worldwide, and is increasingly used as a model legume due to the wide availability of genomic soybean resources; however, the slow generation times of soybean plants are currently a major hindrance to research. Here, we demonstrate a method for accelerating soybean breeding in compact growth chambers, which greatly shortens the generation time of the plants and accelerates breeding and research projects. Our breeding method utilizes commonly used fluorescent lamps (220 ï¿½mol m–2 s–1 at the canopy level), a 14 h light (30ï¿½C)/10 h dark (25ï¿½C) cycle and carbon dioxide (CO2) supplementation at >400 p.p.m. Using this approach, the generation time of the best-characterized elite Japanese soybean cultivar, Enrei, was shortened from 102–132 d reported in the field to just 70 d, thereby allowing up to 5 generations per year instead of the 1–2 generations currently possible in the field and/or greenhouse. The method also facilitates the highly efficient and controlled crossing of soybean plants. Our method uses CO2 supplementation to promote the growth and yield of plants, appropriate light and temperature conditions to reduce the days to flowering, and the reaping and sowing of immature seeds to shorten the reproductive period greatly. Thus, the appropriate parameters enable acceleration of soybean breeding in the compact growth chambers commonly used for laboratory research. The parameters used in our method could therefore be optimized for other species, cultivars, accessions and experimental designs to facilitate rapid breeding in a wide range of crops.
Randomised study demonstrates sustained benefits of a pre-school intervention designed to improve nutrition and physical activity practices
Authors: de Zwarte Diewerke , Kearney John , Corish Clare A , Glennon Corina , Maher Lorraine , Johnston Molloy Charlotte 
Published: September 2018

Abstract

Background
Health-promoting programmes must demonstrate sustained efficacy in order to make a true impact on public health. This study aimed to determine the effect of the Healthy Incentive for Pre-schools project on health-promoting practices in full-day-care pre-schools 18 months after a training intervention.

Methods
Thirty-seven pre-schools completed the initial study and were included in this follow-up study. The intervention consisted of one training session with either the pre-school ‘manager-only’ or ‘manager and staff’ using a specifically developed needs-based training resource pack comprised of written educational material and a validated health-promoting practice evaluation tool. Direct observation data of health-promoting practices were collected and allocated a score using the evaluation tool by a research dietitian at three time points; pre-intervention, between 6 and 9 months post-intervention and at 18-month follow-up. An award system was used to incentivise pre-schools to improve their scores.

Results
Health-promoting practice scores improved significantly (P &lt; 0.001) from the 6–9 month post-intervention to the 18-month follow-up evaluation. No significant differences were observed between ‘manager-only’ and ‘manager and staff’ trained pre-schools.

Conclusions
The introduction of a pre-school evaluation tool supported by a training resource was successfully used to incentivise pre-schools to sustain and improve health-promoting practices 18 months after intervention training.
A SCREENING SURVEY EXERCISE FOR THYROID INTERNAL EXPOSURE FROM RADIOIODINE AFTER A NUCLEAR ACCIDENT
Authors: Yajima Kazuaki , Kim Eunjoo , Tani Kotaro , Tatsuzaki Hideo , Li Chunsheng , Kurihara Osamu 
Published: September 2018

Abstract
In the aftermath of the 2011 Fukushima nuclear disaster, a screening survey for thyroid internal exposure from intake of radioiodine was performed on 1080 children using handheld NaI(Tl) survey meters. This article presents the design and results of a practical exercise conducted to develop the skills of personnel who would be potentially engaged in such a survey. Participants of this exercise were asked to measure manikin heads in which point sources were installed under normal (~0.05 μSv h−1) and elevated (~0.5 μSv h−1) background conditions. The results demonstrated that the measurements were less dependent on the background radiation level, and the deviation of net signals obtained by the participants were within 10–20% for dose rates above 0.2 μSv h−1. This result suggests that dose rates can be reliably obtained above a provisional operational intervention level for the device, 0.5 μSv h−1 under a real nuclear accident situation.
Link between the numbers of particles and variants founding new HIV-1 infections depends on the timing of transmission
Authors: Thompson Robin N. , Wymant Chris , Spriggs Rebecca A. , Raghwani Jayna , Fraser Christophe , Lythgoe Katrina A. 
Published: September 2018

ABSTRACTUnderstanding which HIV-1 variants are most likely to be transmitted is important for vaccine design and predicting virus evolution. Since most infections are founded by single variants, it has been suggested that selection at transmission has a key role in governing which variants are transmitted. We show that the composition of the viral population within the donor at the time of transmission is also important. To support this argument, we developed a probabilistic model describing HIV-1 transmission in an untreated population, and parameterised the model using both within-host next generation sequencing data and population-level epidemiological data on heterosexual transmission. The most basic HIV-1 transmission models cannot explain simultaneously the low probability of transmission and the non-negligible proportion of infections founded by multiple variants. In our model, transmission can only occur when environmental conditions are appropriate (e.g. abrasions are present in the genital tract of the potential recipient), allowing these observations to be reconciled. As well as reproducing features of transmission in real populations, our model demonstrates that, contrary to expectation, there is not a simple link between the number of viral variants and the number of viral particles founding each new infection. These quantities depend on the timing of transmission, and infections can be founded with small numbers of variants yet large numbers of particles. Including selection, or a bias towards early transmission (e.g. due to treatment) acts to enhance this conclusion. In addition, we find that infections initiated by multiple variants are most likely to have derived from donors with intermediate set-point viral loads, and not from individuals with high set-point viral loads as might be expected. We therefore emphasise the importance of considering viral diversity in donors, and the timings of transmissions, when trying to discern the complex factors governing single or multiple variant transmission.
Using genetics to examine a general liability to childhood psychopathology
Authors: Riglin Lucy , Thapar Ajay K , Leppert Beate , Martin Joanna , Richards Alexander , Anney Richard , Smith George Davey , Tilling Kate , Stergiakouli Evie , Lahey Benjamin B. , O’Donovan Michael C , Collishaw Stephan , Thapar Anita 
Published: September 2018

AbstractPsychiatric disorders show phenotypic as well as genetic overlaps. There are however also marked developmental changes throughout childhood. We investigated the extent to which, for a full range of early childhood psychopathology, a general “p” factor was explained by genetic liability, as indexed by multiple different psychiatric polygenic risk scores (PRS) and whether these relationships altered with age. The sample was a UK, prospective, population-based cohort with psychopathology data at age 7 (N=8161) and age 13 (N=7017). PRS were generated from large published genome-wide association studies. At both ages, we found evidence for a childhood “p” factor as well as for specific factors. Schizophrenia and attention-deficit/hyperactivity disorder (ADHD) PRS were associated with this general “p” factor at both ages but depression and autism spectrum disorder (ASD) PRS were not. Schizophrenia, ADHD and depression PRS were also associated with specific factors but there was evidence for developmental changes.FundingThis work was supported by the Wellcome Trust (204895/Z/16/Z).