bluuebunny/crossref_metadata_2025_split huggingface dataset:
Carotid Flow Velocities and Blood Pressures Are Independently Associated With Cognitive Function
Authors: Chuang Shao-Yuan , Cheng Hao-Min , Mitchell Gary F , Sung Shih-Hsien , Chen Chen-Huan , Pan Wen-Harn , Hwang An-Chun , Chen Liang-Kung , Wang Pei-Ning 
Published: November 2018

Abstract

BACKGROUND
Few studies simultaneously addressed associations between carotid flow velocities, blood pressure (BP), and cognitive function.

MATERIALS AND METHODS
Subject without dementia (N = 1,684) underwent measurements of BP and biochemical markers. Mini-Mental State Examination (MMSE) and comprehensive neuropsychological tests were used to evaluate cognitive function. Peak systolic velocity (PSV) and end-diastolic velocity (EDV) were measured in common and internal carotid artery. Subjects with MMSE score of ≤24 (25th percentile) was defined as low MMSE. Multivariable linear and logistic regression were used to evaluate the relationship of cognitive function with carotid flow velocities and BP.

RESULTS
Carotid flow velocities (PSV: standardized β = 0.067, P = 0.0009; and EDV: standardized β = 0.067, P = 0.0021) and systolic blood pressure (standardized β = −0.061, P = 0.005) were positively and negatively associated with MMSE, respectively, in the model with adjustments for age, sex, educational attainment, nutritional status, and smoking. Similar trends were noted for the associations between flow velocities and different neuropsychological tests.
By multivariable logistic regression, the group with the lowest quartile (&lt;25th percentile) of flow velocities had increased probability of low MMSE (odds ratio: 1.538; 95% confidence intervals: 1.142 to 2.071, P = 0.0046 for PSV; and odds ratio: 1.699; 95% confidence intervals: 1.233 to 2.341; P = 0.0012 for EDV), compared to those with the highest quartile (≥75th) flow velocities.

CONCLUSION
Both low carotid flow velocity and high BP were independently and comparably associated with cognitive dysfunction.
FAVITES: simultaneous simulation of transmission networks, phylogenetic trees and sequences
Authors: Moshiri Niema , Ragonnet-Cronin Manon , Wertheim Joel O , Mirarab Siavash 
Published: November 2018

Abstract

Motivation
The ability to simulate epidemics as a function of model parameters allows insights that are unobtainable from real datasets. Further, reconstructing transmission networks for fast-evolving viruses like Human Immunodeficiency Virus (HIV) may have the potential to greatly enhance epidemic intervention, but transmission network reconstruction methods have been inadequately studied, largely because it is difficult to obtain ‘truth’ sets on which to test them and properly measure their performance.

Results
We introduce FrAmework for VIral Transmission and Evolution Simulation (FAVITES), a robust framework for simulating realistic datasets for epidemics that are caused by fast-evolving pathogens like HIV. FAVITES creates a generative model to produce contact networks, transmission networks, phylogenetic trees and sequence datasets, and to add error to the data. FAVITES is designed to be extensible by dividing the generative model into modules, each of which is expressed as a fixed API that can be implemented using various models. We use FAVITES to simulate HIV datasets and study the realism of the simulated datasets. We then use the simulated data to study the impact of the increased treatment efforts on epidemiological outcomes. We also study two transmission network reconstruction methods and their effectiveness in detecting fast-growing clusters.

Availability and implementation
FAVITES is available at https://github.com/niemasd/FAVITES, and a Docker image can be found on DockerHub (https://hub.docker.com/r/niemasd/favites).

Supplementary information
Supplementary data are available at Bioinformatics online.
Biomarkers in abnormal uterine bleeding†
Authors: Chodankar Rohan , Critchley Hilary O D 
Published: November 2018

Abstract
Abnormal uterine bleeding (AUB) is an extremely common problem and represents a clinical area of unmet need. It has clinical implications and a high cost for the healthcare system. The PALM-COEIN acronym proposed by FIGO may be used as a foundation of care; it improves the understanding of the causes of AUB, and in doing so facilitates effective history taking, examination, investigations, and management.
Heavy menstrual bleeding, a subset of AUB, is a subjective diagnosis and should be managed in the context of improving the woman's quality of life. Available evidence suggests that there is poor satisfaction with standard treatment options often resulting in women opting for major surgery such as hysterectomy. Such women would benefit from a tailored approach, both for diagnosis and treatment, highlighting the deficiency of biomarkers in this area.
This article focuses on the causes of AUB as per the PALM-COEIN acronym, the researched biomarkers in this area, and the potential pathogenetic mechanisms. In the future, these approaches may improve our understanding of AUB, thereby enabling us to direct women to most suitable current treatments and tailor investigative and treatment strategies to ensure best outcomes, in keeping with the principles of personalized or precision medicine.
Blood Schizonticidal Activity and Safety of Tafenoquine When Administered as Chemoprophylaxis to Healthy, Nonimmune Participants Followed by Blood Stage Plasmodium falciparum Challenge: A Randomized, Double-blind, Placebo-controlled Phase 1b Study
Authors: McCarthy James S , Smith Bryan , Reid Mark , Berman Jonathan , Marquart Louise , Dobbin Caroline , West Leanne , Read Lisa T , Dow Geoff S 
Published: November 2018

Abstract

Background
Tafenoquine was recently approved for chemoprophylaxis of malaria. Its specific activity against liver and blood stages of Plasmodium species has been separately characterized in animals but not in humans.

Methods
In this randomized, double-blind, placebo-controlled study, 16 malaria-naive, glucose-6-phosphate dehydrogenase–normal participants aged 20–42 years received tafenoquine chemoprophylaxis prior to challenge with blood stage Plasmodium falciparum. Participants were randomly assigned to either tafenoquine (n = 12) or placebo (n = 4) and took blinded study medication (single 200-mg dose) on days 1, 2, 3, and 10, followed by intravenous inoculation with approximately 2800 P. falciparum parasitized erythrocytes on day 13. The primary endpoint was the number of participants requiring rescue treatment with artemether/lumefantrine due to the onset of parasitemia as determined by quantitative polymerase chain reaction.

Results
None of the 12 participants who received tafenoquine developed parasitemia, whereas all placebo participants developed parasitemia (P = .0005). Two cases of mild hemoglobin decrease and a single case of mild hyperbilirubinemia occurred in the tafenoquine group.

Conclusions
Tafenoquine chemoprophylaxis is safe and effective in preventing malaria in healthy nonimmune participants challenged with blood stage P. falciparum.

Clinical Trials Registration
Australian and New Zealand Clinical Trials Registry (ANZCTR): ACTRN12617000102370.
Simplifying the World Health Organization Protocol: 3 Steps Versus 6 Steps for Performance of Hand Hygiene in a Cluster-randomized Trial
Authors: Tschudin-Sutter Sarah , Sepulcri Daniel , Dangel Marc , Ulrich Anja , Frei Reno , Widmer Andreas F 
Published: November 2018

Abstract

Background
In an experimental setting, a simplified, 3-step hand hygiene technique for applying alcohol-based hand rub was non inferior in terms of reduction of bacterial counts, as compared to the conventional World Health Organization 6-step technique. We therefore compared compliance and microbiological efficacy between both hand hygiene techniques in routine clinical practice.

Methods
We performed a cluster-randomized trial from October–November 2015 at the University Hospital Basel, Switzerland: a tertiary, academic care center (ISRCTN45923734). We randomly assigned 12 wards to either the 3-step technique or the conventional 6-step technique of hand rubbing. The primary endpoints were compliance with the assigned technique and reduction of bacterial counts on the hands of health-care workers.

Results
Overall, 2923 hand hygiene indications were observed, and compliance was 70.7% (2066/2923). Compliance with technique and indications was 51.7% (595/1151) and 75.9% (1151/1516) on wards assigned to the 3-step technique, respectively, as compared to 12.7% (116/915) and 65.0% (915/1407) on wards assigned to the 6-step technique (P < .001). The reduction factor (RF) of bacterial colony counts did not differ between techniques (median RF 0.97 log10 colony-forming units [CFU] [interquartile range 0.39–1.59] for the 3-step technique vs median RF 1.04 log10 CFU [interquartile range 0.49–1.52] for the 6-step technique; P = .629).

Conclusions
In a clinical setting, the simpler hand hygiene technique, consisting of 3 steps, resulted in higher compliance with both hand hygiene indications and technique, as compared to the 6 steps. As the results of the microbiological analyses exclude inferiority, the conventional 6 steps could be safely replaced by a simpler hand hygiene technique.

Clinical Trials Registration
ISRCTN45923734.
Cardiac remodelling following thoracic endovascular aortic repair for descending aortic aneurysms
Authors: van Bakel Theodorus M J , Arthurs Christopher J , Nauta Foeke J H , Eagle Kim A , van Herwaarden Joost A , Moll Frans L , Trimarchi Santi , Patel Himanshu J , Figueroa C Alberto 
Published: November 2018

Abstract

OBJECTIVES
Current endografts for thoracic endovascular aortic repair (TEVAR) are much stiffer than the aorta and have been shown to induce acute stiffening. In this study, we aimed to estimate the impact of TEVAR on left ventricular (LV) stroke work (SW) and mass using a non-invasive image-based workflow.

METHODS
The University of Michigan database was searched for patients treated with TEVAR for descending aortic pathologies (2013–2016). Patients with available pre-TEVAR and post-TEVAR computed tomography angiography and echocardiography data were selected. LV SW was estimated via patient-specific fluid–structure interaction analyses. LV remodelling was quantified through morphological measurements using echocardiography and electrocardiographic-gated computed tomography angiography data.

RESULTS
Eight subjects were included in this study, the mean age of the patients was 68 (73, 25) years, and 6 patients were women. All patients were prescribed antihypertensive drugs following TEVAR. The fluid–structure interaction simulations computed a 26% increase in LV SW post-TEVAR [0.94 (0.89, 0.34) J to 1.18 (1.11, 0.65) J, P = 0.012]. Morphological measurements revealed an increase in the LV mass index post-TEVAR of +26% in echocardiography [72 (73, 17)  g/m2 to 91 (87, 26)  g/m2, P = 0.017] and +15% in computed tomography angiography [52 (46, 29)  g/m2 to 60 (57, 22)  g/m2, P = 0.043]. The post- to pre-TEVAR LV mass index ratio was positively correlated with the post- to pre-TEVAR ratios of SW and the mean blood pressure (ρ = 0.690, P = 0.058 and ρ = 0.786, P = 0.021, respectively).

CONCLUSIONS
TEVAR was associated with increased LV SW and mass during follow-up. Medical device manufacturers should develop more compliant devices to reduce the stiffness mismatch with the aorta. Additionally, intensive antihypertensive management is needed to control blood pressure post-TEVAR.
The Lec5 glycosylation mutant links homeobox genes with cholesterol and lipid-linked oligosaccharides
Authors: Lu Hua , Sathe Adwait Amod , Xing Chao , Lehrman Mark A 
Published: November 2018

AbstractDiscovered 40 years ago, the Lec5 glycosylation mutant cell line has a complex recessive genotype and is characterized by accumulation of lipid-linked oligosaccharide assembly intermediates, reduced conversion of polyprenols to dolichols, and an unusual phenotypic dependence upon cell culture conditions such as temperature, plating density and medium quality. The heritable defect in Lec5 is unknown. Here we demonstrate an unexpected epigenetic basis for Lec5, with a surprising linkage to increased expression of homeobox genes, which in turn is associated with increased transcription of cholesterol biosynthesis genes. These results suggest testable hypotheses for the biochemical abnormalities of the Lec5 mutant.
Partial female migration and cool-water migration pathways in an overfished shark
Authors: McMillan M N , Huveneers C , Semmens J M , Gillanders B M 
Published: November 2018

AbstractKnowledge about reproductive movements can be of important conservation value for over-exploited species that are vulnerable when moving between and within key reproductive habitats. Lack of knowledge persists around such movements in the overfished school shark Galeorhinus galeus in Australia. Management assumes all pregnant females migrate between adult aggregations in the Great Australian Bight, South Australia, and nursery areas around Bass Strait and Tasmania. We tracked 14 late-term pregnant females tagged in South Australia using satellite-linked pop-up archival tags to investigate extent, timing, and routes of migrations. We found partial migration, with some females (n = 7) remaining near aggregating areas throughout the pupping season, some migrating to known nursery areas (n = 3), and one migrating ∼3 000 km to New Zealand. We conclude female movements and pupping habitats are less spatially constrained than assumed and propose females use cool-water routes along the shelf break to reduce energy costs of migration. Migrating females using these routes faced greater fishing pressure than sharks in inshore areas and were not protected by inshore shark fishing closures designed to protect them. This study demonstrates the complexity of reproductive movements that can occur in wide-ranging species and highlights the value of explicit movement data.
On the Geometry of Some Equivariantly Related Manifolds
Authors: Cavenaghi Leonardo F , Sperança Llohann D 
Published: November 2018

Abstract
We provide geometric realizations of both classical and “exotic” $G$-manifolds such as spheres, Kervaire manifolds, bundles over spheres, homogeneous spaces, and connected sums among them. As an application, we apply the process known as Cheeger deformation to produce new metrics of both positive Ricci and almost non-negative curvature on such objects.
Ulcerative Colitis Patients Continue to Improve Over the First Six Months of Vedolizumab Treatment: 12-Month Clinical and Mucosal Healing Effectiveness
Authors: Zezos Petros , Kabakchiev Boyko , Weizman Adam V , Nguyen Geoffrey C , Narula Neeraj , Croitoru Kenneth , Steinhart A Hillary , Silverberg Mark S 
Published: November 2018

Abstract

Background
Vedolizumab (VDZ) is a humanized monoclonal IgG1 antibody which inhibits leukocyte vascular adhesion and migration into the gastrointestinal tract through α4β7 integrin blockade.

Aims
We retrospectively assessed the 12-month, real-world efficacy and safety of VDZ as induction and maintenance therapy in adult patients with ulcerative colitis (UC).

Methods
The rates of clinical remission (CR, partial Mayo score &lt; 2), steroid-free clinical remission (SFCR), and mucosal healing were assessed with nonresponder imputation analysis. Baseline independent predictors of clinical remission were investigated, and adverse events were recorded.

Results
We analyzed outcomes in 74 patients; 32% were anti-TNF naïve, 68% had pancolitis, and 46% were on systemic steroids at baseline. At week six, week 14, six months and one year, the CR rates were 26%, 34%, 39% and 39% respectively, and the SFCR rates were 24%, 31%, 38% and 39%, respectively. Among patients not in CR after induction, the probability of remission at six months was 20%. Sustained SFCR between weeks 14 and 52 and between weeks 22 and 52 was found in 69% and 86% of the patients, respectively. Steroid-free clinical remission at 12 months was significantly associated with remission after the induction phase (OR = 30.4; 95% CI, 6 to 150; P &lt; 0.001). Mucosal healing rate at one year was 39%. The most common side effect was headache (7%).

Conclusions
Increasing remission rates were observed over the first six months of VDZ treatment. One-fifth of patients not in remission post-induction achieved remission by six months of continued therapy. Mucosal healing was associated with higher rates of one-year steroid-free remission and VDZ treatment continuation.
ERASE: a novel surface reconditioning strategy for single-molecule experiments
Authors: Broadwater D W Bo , Altman Roger B , Blanchard Scott C , Kim Harold D 
Published: November 2018

Abstract
While surface-based single-molecule experiments have revolutionized our understanding of biology and biomolecules, the workflow in preparing for such experiments, especially surface cleaning and functionalization, remains labor-intensive and time-consuming. Even worse, meticulously assembled flow channels can be used only once for most experiments. A reusable surface would thus dramatically increase productivity and efficiency of single-molecule experiments. In this paper, we report a novel surface reconditioning strategy termed ERASE (Epitaxial Removal Aided by Strand Exchange) that allows a single flow cell to be used for vast repetition of single-molecule experiments. In this method, biomolecules immobilized to the surface through a nucleic acid duplex are liberated when a competing DNA strand disrupts the duplex via toehold-mediated strand displacement. We demonstrate the wide-range applicability of this method with various common surface preparation techniques, fluorescent dyes, and biomolecules including the bacterial ribosome. Beyond time and cost savings, we also show ERASE can assort molecules based on a nucleic acid barcode sequence, thus allowing experiments on different molecules in parallel. Our method increases the utility of prepared surfaces and is a significant improvement to the current single-use paradigm.
Comparison of high glomerular filtration rate thresholds for identifying hyperfiltration
Authors: Chakkera Harini A , Denic Aleksandar , Kremers Walter K , Stegall Mark D , Larson Joseph J , Ravipati Harish , Taler Sandra J , Lieske John C , Lerman Lilach O , Augustine Joshua J , Rule Andrew D 
Published: November 2018

Abstract

Background
High glomerular filtration rate (GFR) is often used as a surrogate for single-nephron hyperfiltration. Our objective was to determine the definition for high GFR that best reflects clinical and structural characteristics of hyperfiltration.

Methods
We studied living kidney donors at the Mayo Clinic and Cleveland Clinic. Potential donors underwent evaluations that included measured GFR (mGFR) by iothalamate clearance and estimated GFR (eGFR) by the serum creatinine–based Chronic Kidney Disease-Epidemiology collaboration (CKD-EPI) equation. High GFR was defined by the 95th percentile for each method (mGFR or eGFR) using either overall or age-specific thresholds. High mGFR was defined as both corrected and uncorrected for body surface area. The association of high GFR by each definition with clinical characteristics and radiologic findings (kidney volume) was assessed. In the subset that donated, the association of high GFR with kidney biopsy findings (nephron number and glomerular volume) and single-nephron GFR was assessed.

Results
We studied 3317 potential donors, including 2125 actual donors. The overall 95th percentile for corrected mGFR was 134 mL/min/1.73 m2 and for eGFR was 118 mL/min/1.73 m2. The age-based threshold for uncorrected mGFR was 198 mL/min − 0.943×Age, for corrected mGFR it was 164 mL/min/1.73 m2 − 0.730×Age and for eGFR it was 146 mL/min/1.73 m2 − 0.813×Age. High age-based uncorrected mGFR had the strongest associations with higher single-nephron GFR, larger glomerular volume, larger kidney volume, male gender, higher body mass index and higher 24-h urine albumin, but also had the strongest association with high nephron number. A high age-height-gender–based uncorrected mGFR definition performed almost as well but had a weaker association with nephron number and did not associate with male gender.

Conclusions
High age-based uncorrected mGFR showed the most consistent associations reflective of hyperfiltration. However, high age-based uncorrected mGFR has limited clinical utility because it does not distinguish between hyperfiltration and high nephron number.
Brauer equivalent number fields and the geometry of quaternionic Shimura varieties
Authors: Linowitz Benjamin 
Published: November 2018

Abstract
Two number fields are said to be Brauer equivalent if there is an isomorphism between their Brauer groups that commutes with restriction. In this paper, we prove a variety of number theoretic results about Brauer equivalent number fields (for example, they must have the same signature). These results are then applied to the geometry of certain arithmetic locally symmetric spaces. As an example, we construct incommensurable arithmetic locally symmetric spaces containing exactly the same set of proper immersed totally geodesic surfaces.
Association of author’s financial conflict of interest with characteristics and outcome of rheumatoid arthritis randomized controlled trials
Authors: Khan Nasim Ahmed , Nguyen Chau L , Khawar Talha , Spencer Horace , Torralba Karina D 
Published: November 2018

Abstract

Objective
To examine the prevalence, types and temporal trends of reported financial conflicts of interest (FCOIs) among authors of drug therapy randomized controlled trials (RCTs) for RA and their association with study outcomes.

Methods
We identified original, non–phase 1, parallel-group, drug therapy RA RCTs published in the years 2002–03, 2006–07, and 2010–11. Two investigators independently obtained trial characteristics data. Authors’ FCOIs were classified as honoraria/consultation fees receipt, employee status, research grant, and stock ownership. Multivariable logistic regression was performed to identify whether FCOIs were independently associated with study outcome.

Results
A total of 146 eligible RCTs were identified. Of these, 83 (58.4%) RCTs had at least one author with an FCOI [employee status: 63 (43.2%), honoraria/consultation fees receipt: 49 (33.6%), research grant: 30 (20.5%), and stock ownership: 28 (19.2%)]. A remarkable temporal increase in reporting of honoraria/consultation fees receipt, research grant, and stock ownership was seen. The reporting of any FCOI itself was not associated with positive outcome [50/73 (68.5%) with author FCOI vs 36/52 (69.2%) without author FCOI, P = 0.93]. However, honoraria/consulting fees receipt was independently associated with increased likelihood of a positive outcome [adjusted odds ratio (95% CI) of 3.24 (1.06–9.88)]. In general, trials with FCOIs were significantly more likely to be multicentre, have larger enrolment, use biologic or a small molecule as the experimental intervention, and have better reporting of some methodological quality measures.

Conclusion
FCOI reporting in RA drug RCT authors is common and temporally increasing. Receipt of honoraria/consulting fees was independently associated with a positive study outcome.