bluuebunny/crossref_metadata_2025_split huggingface dataset:
Genomic analysis of respiratory syncytial virus infections in households and utility in inferring who infects the infant
Authors: Agoti Charles N. , Phan My V. T. , Munywoki Patrick K. , Githinji George , Medley Graham F. , Cane Patricia A. , Kellam Paul , Cotten Matthew , Nokes D. James 
Published: July 2019

AbstractInfants (under 1-year-old) are at most risk of life threatening respiratory syncytial virus (RSV) disease. RSV epidemiological data alone has been insufficient in defining who acquires infection from whom (WAIFW) within households. We investigated RSV genomic variation within and between infected individuals and assessed its potential utility in tracking transmission in households. Over an entire single RSV season in coastal Kenya, nasal swabs were collected from members of 20 households every 3–4 days regardless of symptom status and screened for RSV nucleic acid. Next generation sequencing was used to generate >90% RSV full-length genomes for 51.1% of positive samples (191/374). Single nucleotide polymorphisms (SNPs) observed during household infection outbreaks ranged from 0–21 (median: 3) while SNPs observed during single-host infection episodes ranged from 0–17 (median: 1). Using the viral genomic data alone there was insufficient resolution to fully reconstruct within-household transmission chains. For households with clear index cases, the most likely source of infant infection was via a toddler (aged 1 to <3 years-old) or school-aged (aged 6 to <12 years-old) co-occupant. However, for best resolution of WAIFW within households, we suggest an integrated analysis of RSV genomic and epidemiological data.
Caffeine intake modulates the functioning of the attentional networks depending on consumption habits and acute exercise demands
Authors: Huertas Florentino , Blasco Esther , Moratal Consuelo , Lupiañez Juan 
Published: July 2019

AbstractConsume of stimulants (as caffeine) is very usual in different contexts where the performers have to take quick and accurate decisions during physical effort. Decision-making processes are mediated by the attentional networks. An experiment was carried out to examine the effect of caffeine intake on attention (alerting, orienting, and executive control) as a function of consumption habit under two physical exertion conditions (rest vs. aerobic exercise). Two groups of participants with different caffeine consumption profiles (moderate consumers vs. low consumers) performed the Attention Network Test–Interactions under four different conditions regarding activity (rest vs. exercise) and intake (caffeine vs. placebo). Results showed that whereas exercise led to faster reaction times (RT) in all cases, caffeine intake accelerated RT but only at rest and in moderate caffeine consumers. More importantly, caffeine intake reduced the alertness effect in moderate consumers only at the rest condition. No interactions between Intake and Activity were observed in the other attentional networks, with exercise reducing orienting independently of caffeine intake, which suggests that physical exercise and caffeine are different modulators of attention but can interact. Caffeine intake had differential effects on reaction speed at rest and during physical exercise depending on the individual consumption habit. On the basis of these finding it seems that mainly alertness is modulated differently by internal and external “arousing” conditions.
HCV Phylogeography of the General Population and High-Risk Groups in Cyprus Identifies the Island as a Global Sink for and Source of Infection
Authors: Paraskevis Dimitrios , Stylianou Dora C. , Hezka Johana , Stern Zachariah , Oikonomopoulou Martha , Mamais Ioannis ,   Cyprus PWID Network, Georgiou Chrysanthos , Savvopoulou Natasa , Veresies Kyriakos L. , Pavlou Tina , Argyriou Argyris , Zarouna Elena , Kostrikis Leondios G. 
Published: July 2019

AbstractHepatitis C virus (HCV) genotype and subtype distribution differs according to geographic origin and transmission risk category. Previous molecular epidemiology studies suggest the presence of multiple subtypes among Cypriot subjects. To investigate HCV genotype- and subtype-specific dissemination patterns, origins, and transmission in Cyprus, we analyzed HCV sequences encoding partial Core-E1 and NS5B regions. Analyzed populations comprised the general population and high-risk cohorts in Cyprus and a globally sampled dataset. Maximum-likelihood phylogeny reconstruction with bootstrap evaluation, character reconstruction using parsimony, and bootstrap trees estimated by ML were performed to identify the geographic origin of HCV subtypes and statistically significant dispersal pathways among geographic regions. Phylogeographic analyses traced the origin of subtypes in the general population and among PWID in Cyprus to unique and overlapping globally distributed regions. Phylogenetic analysis in Core-E1 revealed that most sequences from incarcerated populations in Cyprus clustered with the general population and PWID. We estimate that HCV infections in Cyprus originate from multiple global sources while most HCV transmissions among incarcerated individuals occur locally. This analysis is one of a few studies tracing HCV dispersal patterns using global datasets, and these practices and findings should inform how HCV epidemics are targeted by future prevention policies.
Aerosol mixing state revealed by transmission electron microscopy pertaining to cloud formation and human airway deposition
Authors: Ching Joseph , Adachi Kouji , Zaizen Yuji , Igarashi Yasuhito , Kajino Mizuo 
Published: July 2019

AbstractAerosol mixing state is one of the most important factors determining the impacts of aerosol particles on aerosol-cloud-climate interactions and human health. The size, composition, and morphology of about 32,000 single particles are analyzed using transmission electron microscopy (TEM) to evaluate per-particle mixing state. Based on the TEM analysis, we quantify aerosol mixing state and examine the impacts of per-particle mixing state on cloud condensation nuclei (CCN) properties and particle deposition efficiency along the human respiratory tract. Assuming homogeneous chemical composition across the aerosol population, a common practice in many global and regional models to various extents, we show that such simplification of mixing state representation could potentially lead to remarkable errors, a maximum of about 90% and 35%, in CCN concentrations and deposition efficiency calculations respectively. Our results from ambient per-particle observations highlight the importance of considering aerosol mixing state in both air quality models and climate models.
Deformation of the moving magnetic skyrmion lattice in MnSi under electric current flow
Authors: Okuyama D. , Bleuel M. , White J. S. , Ye Q. , Krzywon J. , Nagy G. , Im Z. Q. , Živković I. , Bartkowiak M. , Rønnow H. M. , Hoshino S. , Iwasaki J. , Nagaosa N. , Kikkawa A. , Taguchi Y. , Tokura Y. , Higashi D. , Reim J. D. , Nambu Y. , Sato T. J. 
Published: July 2019

AbstractTopological defects are found ubiquitously in various kinds of matter, such as vortices in type-II superconductors, and magnetic skyrmions in chiral ferromagnets. While knowledge on the static behavior of magnetic skyrmions is accumulating steadily, their dynamics under forced flow is still a widely open issue. Here, we report the deformation of the moving magnetic skyrmion lattice in MnSi under electric current flow observed using small-angle neutron scattering. A spatially inhomogeneous rotation of the skyrmion lattice, with an inverse rotation sense for opposite sample edges, is observed for current densities greater than a threshold value jt ~ 1 MA m−2 (106 A m−2). Our result show that skyrmion lattices under current flow experience significant friction near the sample edges due to pinning, this being a critical effect that must be considered for anticipated skyrmion-based applications at the nanoscale.
Fine-needle biopsy is superior to fine-needle aspiration of suspected gastrointestinal stromal tumors: a large multicenter study
Authors: Trindade Arvind J. , Benias Petros C. , Alshelleh Mohammed , Bazarbashi Ahmad N. , Tharian Benjamin , Inamdar Sumant , Sharma Neil , Zelt Christina , Korrapati Praneet , Barakat Mohamed , Sejpal Divyesh V. , Ryou Marvin 
Published: July 2019

Abstract
Background and study aims There are numerous studies published on the diagnostic yield of the new fine-needle biopsy (FNB) needles in pancreas masses. However, there are limited studies in suspected gastrointestinal stromal tumors (GIST lesions). The aim of this study was to evaluate the diagnostic yield of a new fork-tip FNB needle.
Patients and methods This was a multicenter retrospective study of consecutive patients from prospectively maintained databases comparing endoscopic ultrasound-guided fine-needle aspiration (EUS-FNA) versus endoscopic ultrasound-guided FNB (EUS-FNB) using the fork-tip needle. Outcomes measured were cytopathology yield (ability to obtain tissue for analysis of cytology), ability to analyze the tissue for immunohistochemistry (IHC yield), and diagnostic yield (ability to provide a definitive diagnosis).
Results A total of 147 patients were included in the study of which 101 underwent EUS-FNB and 46 patients underwent EUS-FNA. Median lesion size in each group was similar (21 mm vs 25 mm, P = 0.25). Cytopathology yield, IHC yield, and diagnostic yield were 92 % vs 46 % (P = 0.001), 89 % vs 41 % (P = 0.001), and 89 % vs 37 % (P = 0.001) between the FNB and FNA groups, respectively. Median number of passes was the same between the two groups at 3.5.
Conclusion EUS-FNB is superior to EUS-FNA for diagnostic yield of suspected GIST lesions. This should be confirmed with a prospective study.
Association of Bacterial Vaginosis with Vitamin D in Pregnancy: Secondary Analysis from the Kellogg Pregnancy Study
Authors: Powell Anna Maya , Shary Judy R. , Louden Christopher , Ramakrishnan Vishwanathan , Eckard Allison Ross , Wagner Carol L. 
Published: July 2019

Objective Bacterial vaginosis (BV) is associated with vitamin D deficiency and poor pregnancy outcomes. We studied a nested cohort from a randomized controlled trial to investigate the association between BV and vitamin D concentration in pregnancy.
Study Design Subjects with randomly assigned 400 versus 4,400 IU of daily cholecalciferol (vitamin D3) had vaginal swabs collected for Gram staining and Nugent score calculation, as well as plasma 25-hydroxyvitamin D (25(OH)D) measurement at three pregnancy time points.
Results Fifty-two (21.2%) of the 245 women included in the analysis were diagnosed with BV at study entry. Women with BV were also more likely to be African American (p < 0.0001) and have lower 25(OH)D concentrations at 22 to 24 weeks' gestation (p = 0.03). There were no differences in pregnancy outcomes of interest within this group compared with the remaining study subjects. In mixed regression modeling, while race (p = 0.001) and age (p = 0.03) were significant predictors of BV prevalence independently, 25(OH)D concentration (p = 0.81), gestational age (p = 0.06), and body mass index (p = 0.87) were not.
Conclusion Neither vitamin D deficiency in early pregnancy nor supplementation decreased BV incidence during pregnancy. Pregnancy outcomes (preterm birth and hypertensive disorders of pregnancy) were similar among women with and without BV.
The plastidial pentose phosphate pathway is essential for postglobular embryo development in
Arabidopsis
Authors: Andriotis Vasilios M. E. , Smith Alison M. 
Published: July 2019

Significance
Many mutations that affect plastidial metabolism are embryo-lethal, as expected if the disrupted genes encode enzymes with essential housekeeping functions. However, some mutations that disrupt the plastidial oxidative pentose phosphate pathway (OPPP) cause developmental defects, as well as embryo arrest at the globular stage of development. We show that the OPPP provides the substrate for the pathway of purine synthesis, ribose-5-phosphate, and is thus essential for the generation of nucleic acids during the very early stages of embryo development. Inadequate purine synthesis leads to abnormal patterns of cell division in the embryo and blocks development beyond the globular stage. Therefore, defects in primary metabolic pathways can have profound consequences for development as well as simply reducing growth.
Hydrogen molecule-antihydrogen atom potential energy surface and scattering calculations
Authors: Mant B P , Law M M , Strasburger K 
Published: July 2019

Abstract
We have calculated ground state interaction energies for an antihydrogen atom and a hydrogen molecule within the Born–Oppenheimer approximation. Leptonic energies were calculated using a large basis set of explicitly correlated Gaussian functions. Energies were calculated at over 2800 geometries including different proton–proton distances. The energies have been fit to functional forms using a neural network for the short-range interaction which is combined with asymptotic formulas at long range. A two-dimensional rigid rotor and a three-dimensional atom–molecule potential energy surface (PES) have been determined. Rigid-rotor scattering calculations on these surfaces have been carried out using the S-matrix Kohn variational method with a two-dimensional Gaussian basis set. We have calculated cross sections for elastic, rotationally inelastic and annihilation collisions on the two-dimensional PES. This includes the first calculation of leptonic annihilation for this system.
Apolipoprotein ε4 allele is associated with frailty syndrome: results from the hellenic longitudinal investigation of ageing and diet study
Authors: Mourtzi Niki , Ntanasi Eva , Yannakoulia Mary , Kosmidis Mary , Anastasiou Costas , Dardiotis Efthimios , Hadjigeorgiou Giorgos , Sakka Paraskevi , Scarmeas Nikolaos 
Published: July 2019

Abstract
Apolipoprotein (APOE) ε4 allele has been associated with a number of age-related diseases but previous studies failed to identify any link with Frailty syndrome. The aim of the present study is to investigate the association between APOE ε4 allele and frailty syndrome. We operationalised Frailty according to the Fried definition, and we determined the APOE genotype in 1234 participants of the hellenic longitudinal investigation of ageing and diet study. Logistic regression analyses were performed to examine the association between APOE ε4 allele and frailty. Models were adjusted for age, education, sex, presence (or absence) of hypertension, diabetes, myocardial infraction, coronary disease, congestive heart failure, arrhythmia or other heart disease, family history of dementia and current smoking. The same models were performed after exclusion of patients with dementia and participants with APOE ε2/ε4 genotype. In the fully adjusted model, carriers of APOE ε4 allele had 2.753 higher odds of frailty relative to non-carriers. After trichotomization of APOE genotype, APOE ε4 heterozygotes had 2.675 higher risk of frailty compared to non-carriers while exclusion of patients with dementia or/and APOE ε2/ε4 genotype did not alter the association. The APOE ε4 allele may be a significant biomarker of frailty with diagnostic and prognostic capacity.
Optimization of the Order Menu in the Electronic Health Record Facilitates Test Patterns Consistent With Recommendations in the Choosing Wisely Initiative
Authors: Barry Courtney , Kaufman Steven , Feinstein David , Kim Nami , Gandhi Snehal , Nikolic Dejan , Edmonston Tina Bocker , Bierl Charlene 
Published: July 2019

AbstractObjectivesThyroid and rheumatologic autoimmune testing are areas where evidence-based guidance from specialty organizations and Choosing Wisely support utilizing screening tests for autoimmune and thyroid disorders prior to more specialized testing. Adjustment of the orderable options in the electronic health record (EHR) can influence ordering patterns without requiring manual review or additional effort by the clinician.MethodsThe menu was adjusted to reflect recommendations from Choosing Wisely to favor screening tests that automatically reflex to specialized testing on primary care providers’ preference lists. Effectiveness was evaluated by reviewing total orders for individual tests.ResultsShifts in ordering from individual screening tests (antinuclear antibody and thyrotropin) to ones that reflexed to specialized testing were observed in parallel with significant reductions in the corresponding specialized testing.ConclusionsOptimization of the EHR laboratory ordering menu can be used to shift ordering patterns toward Choosing Wisely recommendations.
From Pleasure to Pain, and Back Again: The Intricate Relationship Between Alcohol and Nociception
Authors: Robins Meridith T , Heinricher Mary M , Ryabinin Andrey E 
Published: July 2019

AbstractAimsA close and bidirectional relationship between alcohol consumption and pain has been previously reported and discussed in influential reviews. The goal of the present narrative review is to provide an update on the developments in this field in order to guide future research objectives.MethodsWe evaluated both epidemiological and neurobiological literature interrogating the relationship between alcohol use and pain for the presence of significant effects. We outlined studies on interactions between alcohol use and pain using both self-reports and objective experimental measures and discussed potential underlying mechanisms of these interactions.ResultsEpidemiological, preclinical and clinical literature point to three major interactions between alcohol use and pain: (a) alcohol use leading to hyperalgesia, (b) alcohol use moderating pain and hyperalgesia and (c) chronic pain as a risk factor predisposing to alcohol relapse. Neurobiological studies using animal models to assess these interactions have transitioned from mostly involuntary modes of experimenter-controlled alcohol administration to self-administration procedures, and increasingly indicate that neuronal circuits implicated in both withdrawal and anticipation stages of alcohol use disorder also have a role in chronic pain. Mechanistically, alterations in GABA, glutamate, the corticotropin-releasing factor system, endogenous opioids and protein kinase C appear to play crucial roles in this maladaptive overlap.ConclusionsMany of the principles explaining the interactions between alcohol and pain remain on a strong foundation, but continuing progress in modeling these interactions and underlying systems will provide a clearer basis for understanding, and ultimately treating, the damaging aspects of this interaction.
Critical assessment of bioinformatics methods for the characterization of pathological repeat expansions with single-molecule sequencing data
Authors: Chiara Matteo , Zambelli Federico , Picardi Ernesto , Horner David S , Pesole Graziano 
Published: July 2019

Abstract
A number of studies have reported the successful application of single-molecule sequencing technologies to the determination of the size and sequence of pathological expanded microsatellite repeats over the last 5 years. However, different custom bioinformatics pipelines were employed in each study, preventing meaningful comparisons and somewhat limiting the reproducibility of the results. In this review, we provide a brief summary of state-of-the-art methods for the characterization of expanded repeats alleles, along with a detailed comparison of bioinformatics tools for the determination of repeat length and sequence, using both real and simulated data. Our reanalysis of publicly available human genome sequencing data suggests a modest, but statistically significant, increase of the error rate of single-molecule sequencing technologies at genomic regions containing short tandem repeats. However, we observe that all the methods herein tested, irrespective of the strategy used for the analysis of the data (either based on the alignment or assembly of the reads), show high levels of sensitivity in both the detection of expanded tandem repeats and the estimation of the expansion size, suggesting that approaches based on single-molecule sequencing technologies are highly effective for the detection and quantification of tandem repeat expansions and contractions.
Prevention of Criminal Offending: The Intervening and Protective Effects of Education for Aggressive Youth
Authors: Kennedy-Turner Kathleen , Serbin Lisa A , Stack Dale M , Dickson Daniel J , Ledingham Jane E , Schwartzman Alex E 
Published: July 2019

AbstractChildren from poor neighbourhoods showing early aggressive behaviour are at risk for criminal offending. The role of education as a mediator, neighbourhood disadvantage and aggression as moderators for criminal offending were examined in a lower-income, community sample (n = 3,521; 48% males), across a 40-year period from childhood to mid-adulthood. Educational attainment accounted for 15–59% of the effect from childhood risk factors. Aggression was found to be a moderator such that aggressive children with low education had the highest odds of criminal offending. A protective effect was found where aggressive children who managed to obtain more education had reduced odds of offending. Research conceptualizing education as a ‘control’ variable does not address its role in the processes leading to criminal offending.
Association of non-invasive measures of subclinical atherosclerosis and arterial stiffness with mortality and major cardiovascular events in chronic kidney disease: systematic review and meta-analysis of cohort studies
Authors: Kouis Panayiotis , Kousios Andreas , Kanari Athina , Kleopa Daphne , Papatheodorou Stephania I , Panayiotou Andrie G 
Published: July 2019

AbstractBackgroundNon-invasive cardiovascular disease (CVD) risk prediction, in subclinical stages, aiming to stratify patients and tailor interventions remains an unmet need in chronic kidney disease (CKD). In this meta-analysis, we summarize the association of carotid intima–media thickness (cIMT), coronary artery calcium score (CACS) and pulse wave velocity (PWV) with all-cause mortality, cardiovascular (CV) mortality and CV events in non-dialysis CKD and patients on haemodialysis.MethodsSystematic review and meta-analysis of prospective cohort studies.ResultsOut of 27 984 records, a total of 45 studies were eligible for quantitative synthesis; 11 for cIMT, 18 for CACS and 16 for PWV involving 2235, 4904 and 5717 patients, respectively. Meta-analysis was possible from pooled data of five cIMT studies (708 subjects), eight CACS studies (862 subjects) and nine PWV studies (1508 subjects). In dialysis patients, cIMT was associated with all-cause mortality [relative risk (RR) per unit increase: 1.08, 95% confidence interval (CI) 1.00–1.17, I2: 68%] and CV mortality (RR: 1.29, 95% CI 1.14–1.47, I2: 0%). High versus low CACS was associated with all-cause mortality (RR: 2.51, 95% CI 1.66–3.79, I2: 5.7%) and CV events (RR: 3.77 95% CI 2.16–6.58, I2: 20.2%). High versus low PWV was associated with all-cause (RR: 5.34, 95% CI 3.01–9.47, I2: 0%) and CV mortality (RR: 8.55, 95% CI 4.37–16.73, I2: 0%). The combined estimated for all-cause mortality per 1 m/s increment unit in PWV was 1.25 (95% CI 1.17–1.34, I2: 0%) and for CV mortality was 1.24 (95% CI 1.16–1.34, I2: 15.5%). In non-dialysis patients, CACS was associated with CV events (RR: 4.02, 95% CI 1.57–10.29, I2: 63.4%). High versus low PWV was associated with all-cause mortality (RR: 2.52, 95% CI 1.40–4.55, I2: 62.6%).ConclusionsNon-invasive measures of atherosclerosis and arterial stiffening are associated with all-cause and CV mortality as well as CV events among patients with all stages of CKD. These markers could be considered for the evaluation of CV morbidity and mortality risks. Moreover, the results of this meta-analysis support the study of interventions, with effect on these markers of vascular disease, on long-term CVD outcomes.