bluuebunny/crossref_metadata_2025_split huggingface dataset:
Citizen science to further precision medicine: from vision to implementation
Authors: Petersen Carolyn , Austin Robin R , Backonja Uba , Campos Hugo , Chung Arlene E , Hekler Eric B , Hsueh Pei-Yun S , Kim Katherine K , Pho Anthony , Salmi Liz , Solomonides Anthony , Valdez Rupa S 
Published: December 2019

AbstractThe active involvement of citizen scientists in setting research agendas, partnering with academic investigators to conduct research, analyzing and disseminating results, and implementing learnings from research can improve both processes and outcomes. Adopting a citizen science approach to the practice of precision medicine in clinical care and research will require healthcare providers, researchers, and institutions to address a number of technical, organizational, and citizen scientist collaboration issues. Some changes can be made with relative ease, while others will necessitate cultural shifts, redistribution of power, recommitment to shared goals, and improved communication. This perspective, based on a workshop held at the 2018 AMIA Annual Symposium, identifies current barriers and needed changes to facilitate broad adoption of a citizen science-based approach in healthcare.
Political cycles, spatial interactions and yardstick competition: evidence from Italian cities
Authors: Ferraresi Massimiliano 
Published: December 2019

AbstractI aim to identify the presence of spatial interactions among local governments by exploiting a novel strategy. Specifically, I take advantage of the political cycle of Italian municipalities over the period of 2001–2011 to isolate the effect of the spending decisions of one municipality on neighboring municipalities. The results of this analysis point to the presence of strategic interactions between neighboring municipalities and indicate that such fiscal behavior is more pronounced during electoral years compared to non-electoral ones, when municipalities are governed by coalitions backed by a small majority, and in cities guided by a mayor who can run for re-election. Taken together, these results suggest that the observed spatial dependence in spending decisions seems to be consistent with the yardstick competition hypothesis.
Availability and Nature of Commercial Tick Control Services in Three Lyme Disease Endemic States
Authors: Jordan Robert A , Schulze Terry L 
Published: December 2019

AbstractIn an update of earlier surveys conducted in Connecticut and New Jersey in the mid-1990s, an online survey of private commercial pest control firms engaged in residential tick control showed that the application of synthetic acaricides continues to be the primary method of control used. The carbamate and organophospate acaricides, previously the most commonly used against ticks, have given way to synthetic pyrethroids and, to a lesser extent, the use of natural product/organic acaricides. Typical costs for a single acaricide application today ($100–$200 for a 1 acre [0.4 ha] property) remain similar to those reported from the earlier surveys, although the frequency of applications and, therefore, also the overall annual cost has increased. The application habitats within residential properties, life stages targeted, and application equipment used have not changed appreciably since the mid-1990s. While most survey respondents expressed knowledge of natural product acaricides and Damminix Tick Tubes, many reported that they either did not employ or knew very little about other alternative tick control methods (including entomopathogenic fungus and topical application of acaricides to tick hosts via 4-Poster deer treatment stations or Select TCS rodent bait boxes). This suggests either a failure to adequately inform the pest management industry and their potential client base of the availability of alternate methods, and/or industry concerns about cost and effectiveness of the alternatives.
Cholera in travellers: a systematic review
Authors: Connor Bradley A , Dawood Richard , Riddle Mark S , Hamer Davidson H 
Published: December 2019

Abstract
Exposure to cholera is a risk for individuals and groups travelling to endemic areas, and the bacteria can be imported to cholera-free countries by returning travellers. This systematic review of the literature describes the circumstances in which cholera infection can occur in travellers and considers the possible value of the cholera vaccine for prevention in travellers. PubMed and EMBASE were searched for case reports of cholera or diarrhoea among travellers, with date limits of 1 January 1990–30 April 2018. Search results were screened to exclude the following articles: diarrhoea not caused by cholera, cholera in animals, intentional cholera infection in humans, non-English articles and publications on epidemics that did not report clinical details of individual cases and publications of cases pre-dating 1990. Articles were reviewed through descriptive analytic methods and information summarized. We identified 156 cases of cholera imported as a consequence of travel, and these were reviewed for type of traveller, source country, serogroup of cholera, treatment and outcomes. The case reports retrieved in the search did not report consistent levels of detail, making it difficult to synthesize data across reports and draw firm conclusions from the data. This clinical review sheds light on the paucity of actionable published data regarding the risk of cholera in travellers and identifies a number of gaps that should drive additional effort. Further information is needed to better inform evidence-based disease prevention strategies, including vaccination for travellers visiting areas of cholera risk. Modifications to current vaccination recommendations to include or exclude current or additional traveller populations may be considered as additional risk data become available. The protocol for this systematic review is registered with PROSPERO (registration number: 122797).
Estimating Pangenomes with Roary
Authors: Sitto Farrah , Battistuzzi Fabia U 
Published: December 2019

Abstract
A description of the genetic makeup of a species based on a single genome is often insufficient because it ignores the variability in gene repertoire among multiple strains. The estimation of the pangenome of a species is a solution to this issue as it provides an overview of genes that are shared by all strains and genes that are present in only some of the genomes. These different sets of genes can then be analyzed functionally to explore correlations with unique phenotypes and adaptations. This protocol presents the usage of Roary, a Linux-native pangenome application. Roary is a straightforward software that provides 1) an overview about core and accessory genes for those interested in general trends and, also, 2) detailed information on gene presence/absence in each genome for in-depth analyses. Results are provided both in text and graphic format.
Homologous recombination repair intermediates promote efficient de novo telomere addition at DNA double-strand breaks
Authors: Davé Anoushka , Pai Chen-Chun , Durley Samuel C , Hulme Lydia , Sarkar Sovan , Wee Boon-Yu , Prudden John , Tinline-Purvis Helen , Cullen Jason K , Walker Carol , Watson Adam , Carr Antony M , Murray Johanne M , Humphrey Timothy C 
Published: December 2019

AbstractThe healing of broken chromosomes by de novo telomere addition, while a normal developmental process in some organisms, has the potential to cause extensive loss of heterozygosity, genetic disease, or cell death. However, it is unclear how de novo telomere addition (dnTA) is regulated at DNA double-strand breaks (DSBs). Here, using a non-essential minichromosome in fission yeast, we identify roles for the HR factors Rqh1 helicase, in concert with Rad55, in suppressing dnTA at or near a DSB. We find the frequency of dnTA in rqh1Δ rad55Δ cells is reduced following loss of Exo1, Swi5 or Rad51. Strikingly, in the absence of the distal homologous chromosome arm dnTA is further increased, with nearly half of the breaks being healed in rqh1Δ rad55Δ or rqh1Δ exo1Δ cells. These findings provide new insights into the genetic context of highly efficient dnTA within HR intermediates, and how such events are normally suppressed to maintain genome stability.
A Novel, Minimally Invasive Hybrid Technique to Approach Intracanal Herniated Thoracic Discs
Authors: Quillo-Olvera Javier , Kim Jin-Sung 
Published: December 2019

Abstract

BACKGROUND
Multiple options exist for thoracic disc herniation (TDH). However, when a specific technique is chosen, the goal is to avoid the manipulation of the spinal cord, which is already compressed.

OBJECTIVE
To describe a hybrid endoscopic technique for intracanal TDH by combining an oblique paraspinal approach (OPA) and transforaminal full-endoscopic discectomy.

METHODS
We describe the step-by-step operative technique and present the clinical and radiological outcomes of a case series of hybrid endoscopic thoracic discectomy.

RESULTS
A total of 3 patients were treated. We observed the usefulness of an OPA to enlarge the intervertebral foramen through the rigid tubular retractor and the feasibility of a full-endoscopic transforaminal approach to reach intracanal TDHs.

CONCLUSION
Early experience with the hybrid endoscopic technique for TDHs demonstrated acceptable clinical and radiological outcomes in the 3 patients treated; however, a larger sample size and a methodologically advantageous study to compare this procedure with conventional options are necessary to probe the full benefits of the hybrid technique.
Risk factors for re-hospitalization following neonatal discharge of extremely preterm infants in Canada
Authors: Puthattayil Zakariya Bambala , Luu Thuy Mai , Beltempo Marc , Cross Shannon , Pillay Thevanisha , Ballantyne Marilyn , Synnes Anne , Shah Prakesh , Daboval Thierry ,   Canadian Neonatal Follow-Up Network, Pillay Thevanisha , Synnes Anne , Hendson Leonora , Reichert Amber , Bodani Jaya , Daspal Sibasis , Moddemann Diane , Nwaesei Chukwuma , Daboval Thierry , McKnight Sarah , Coughlin Kevin , Ly Linh , Kelly Edmond , Saigal Saroj , Thomas Karen , Church Paige , Pelausa Ermelinda , Khairy M , Luu Thuy Mai , Demers Charlotte , Morin Alyssa , Bélanger Sylvie , Canning Roderick , Monterrosa Luis , Makary Hala , Afifi Jehier , Murphy Phil , Janeway Charles 
Published: December 2019

Abstract

Objective
Survivors of extremely preterm birth are at risk of re-hospitalization but risk factors in the Canadian population are unknown. Our objective is to identify neonatal, sociodemographic, and geographic characteristics that predict re-hospitalization in Canadian extremely preterm neonates.

Methods
This is a retrospective analysis of a prospective observational cohort study that included preterm infants born 22 to 28 weeks’ gestational age from April 1, 2009 to September 30, 2011 and seen at 18 to 24 months corrected gestational age in a Canadian Neonatal Follow-Up Network clinic. Characteristics of infants re-hospitalized versus not re-hospitalized are compared. The potential neonatal, sociodemographic, and geographic factors with significant association in the univariate analysis are included in a multivariate model.

Results
From a total of 2,275 preterm infants born at 22 to 28 weeks gestation included, 838 (36.8%) were re-hospitalized at least once. There were significant disparities between Canadian provincial regions, ranging from 25.9% to 49.4%. In the multivariate logistic regression analysis, factors associated with an increased risk for re-hospitalization were region of residence, male sex, bronchopulmonary dysplasia, necrotizing enterocolitis, prolonged neonatal intensive care unit (NICU) stay, ethnicity, Indigenous ethnicity, and sibling(s) in the home.

Conclusion
Various neonatal, sociodemographic, and geographic factors predict re-hospitalization of extremely preterm infants born in Canada. The risk factors of re-hospitalization provide insights to help health care leaders explore potential preventative approaches to improve child health and reduce health care system costs.
Estimating Diversification Rates on Incompletely Sampled Phylogenies: Theoretical Concerns and Practical Solutions
Authors: Chang Jonathan , Rabosky Daniel L , Alfaro Michael E 
Published: December 2019

Abstract
Molecular phylogenies are a key source of information about the tempo and mode of species diversification. However, most empirical phylogenies do not contain representatives of all species, such that diversification rates are typically estimated from incompletely sampled data. Most researchers recognize that incomplete sampling can lead to biased rate estimates, but the statistical properties of methods for accommodating incomplete sampling remain poorly known. In this point of view, we demonstrate theoretical concerns with the widespread use of analytical sampling corrections for sparsely sampled phylogenies of higher taxonomic groups. In particular, corrections based on “sampling fractions” can lead to low statistical power to infer rate variation when it is present, depending on the likelihood function used for inference. In the extreme, the sampling fraction correction can lead to spurious patterns of diversification that are driven solely by unbalanced sampling across the tree in concert with low overall power to infer shifts. Stochastic polytomy resolution provides an alternative to sampling fraction approaches that avoids some of these biases. We show that stochastic polytomy resolvers can greatly improve the power of common analyses to estimate shifts in diversification rates. We introduce a new stochastic polytomy resolution method (Taxonomic Addition for Complete Trees [TACT]) that uses birth–death-sampling estimators across an ultrametric phylogeny to estimate branching times for unsampled taxa, with taxonomic information to compatibly place new taxa onto a backbone phylogeny. We close with practical recommendations for diversification inference under several common scenarios of incomplete sampling. [Birth–death process; diversification; incomplete sampling; phylogenetic uncertainty; rate heterogeneity; rate shifts; stochastic polytomy resolution.]
Influence of St. John’s Wort on Intravenous Fentanyl Pharmacokinetics, Pharmacodynamics, and Clinical Effects
Authors: Loughren Michael J. , Kharasch Evan D. , Kelton-Rehkopf Megan C. , Syrjala Karen L. , Shen Danny D. 
Published: December 2019

Abstract

Background
Patients often use complementary and alternative herbal medicines, hence, potential exists for adverse herb–drug interactions. Fentanyl is metabolized by hepatic CYP3A4 and considered transported by blood–brain barrier P-glycoprotein. Both disposition processes could be upregulated by the herbal St. John’s wort. This investigation evaluated effects of St. John’s wort on fixed-dose and apparent steady-state IV fentanyl pharmacokinetics, pharmacodynamics, and clinical effects.

Methods
Healthy volunteers received a fentanyl fixed-dose infusion and an individually tailored target controlled infusion on separate days, before and after 30-day St. John’s wort (300 mg thrice daily; n = 8) or placebo control (n = 8) in a randomized parallel-group design. Fentanyl plasma concentrations, pupil diameter, analgesic response to experimental pain (cold pressor), subjective side effects, and cognitive effects were measured. Plasma fentanyl concentrations and changes in pupil diameter were subjected to pharmacokinetic–pharmacodynamic modeling.

Results
St. John’s wort did not alter fentanyl pharmacokinetics. Clearance (l/min) before and after St. John’s wort (1.13 ± 0.29 and 1.24 ± 0.26, respectively) or placebo (0.96 ± 0.28 and 1.12 ± 0.27, respectively) were not different. St. John’s wort also did not affect fentanyl pharmacodynamics as measured by pupil constriction after fixed-dose and tailored fentanyl infusions. EC50 (ng/ml) was 1.1 ± 0.7 and 1.4 ± 0.9 before and after St. John’s wort versus 1.2 ± 0.8 and 1.4 ± 1.7 before and after placebo. Effect site equilibration time, T½,ke0 (min), was 12.8 ± 5.3 and 11.3 ± 6.4 before and after St. John’s wort versus 11.4 ± 6.4 and 11.1 ± 5.6 before and after placebo. St. John’s wort had no influence on analgesia, cognitive performance, or somatic cognitive–affective effects of fentanyl.

Conclusions
St. John’s wort did not alter fentanyl pharmacokinetics, pharmacodynamics or clinical effects, suggesting no effect on hepatic clearance or blood-brain barrier efflux. Patients taking St. John’s wort will likely not respond differently to IV fentanyl for anesthesia or analgesia.

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What We Already Know about This Topic

What This Article Tells Us That Is New
Radiostereometric Analysis of Stability and Inducible Micromotion After Locked Lateral Plating of Distal Femur Fractures
Authors: Galea Vincent P. , Botros Mina A. , McTague Michael F. , Weaver Michael J. , Vrahas Mark S. , Malchau Henrik , Heng Marilyn , Bragdon Charles 
Published: December 2019

Objectives:
To evaluate interfragmentary motion over 1 year after distal femoral fracture fixation using radiostereometric analysis (RSA). The secondary aim was to assess whether RSA data are consistent with diagnoses of nonunion.

Design:
Prospective cohort study.

Setting:
Level I urban trauma center.

Patients:
Sixteen patients between 22 and 89 years of age with distal femoral fracture (OTA/AO type 33).

Intervention:
All fractures were treated with a lateral locking plate, and tantalum markers were inserted into the main proximal and distal fracture fragments. RSA was performed at 2, 6, 12, 18, and 52 weeks postoperatively. Both unloaded and loaded RSA measurements were performed.

Main Outcome Measurements:
Unloaded fracture migration over time and inducible micromotion at the fracture site in the coronal plane were determined at each follow-up interval.

Results:
RSA precision in the coronal plane of interfragmentary motion over time and inducible micromotion were 1.2 and 0.9 mm in the coronal plane, respectively. Two cases required revision surgery for nonunion 1 year postoperatively. For cases of union, unloaded fracture migration stopped being detectable between 12 and 18 weeks, and inducible micromotion was no longer detectable by the 12-week visit. For cases of nonunion, both unloaded migration and inducible micromotion were detected throughout the study period.

Conclusions:
RSA may be used to reliably assess distal femoral fracture healing. RSA revealed differences in cases of union and nonunion by 3 months and more consistently than traditional x-rays.

Level of Evidence:
Diagnostic Level II. See Instructions for Authors for a complete description of levels of evidence.
Understanding Relationships Between Chlamydial Infection, Symptoms, and Testing Behavior
Authors: Lewis Joanna , White Peter J. 
Published: December 2019

Background:
Genital chlamydia is the most commonly diagnosed sexually transmitted infection worldwide and can have serious long-term sequelae. Numerous countries invest substantially in testing but evidence for programs’ effectiveness is inconclusive. It is important to understand the effects of testing programs in different groups of people.

Methods:
We analyzed data on sexual behavior and chlamydia tests from 16-to 24-year olds in Britain’s third National Survey of Sexual Attitudes and Lifestyles, considering test setting, reason, and result. We conducted descriptive analysis accounting for survey design and nonresponse, and Bayesian analysis using a mathematical model.

Results:
Most men testing due to symptoms tested in sexual health settings (63%; 95% confidence interval 43%–84%) but most women testing due to symptoms were tested by general practitioners (59%; 43%–76%). Within behavioral groups, positivity of chlamydia screens (tests not prompted by symptoms or partner notification) was similar to population prevalence. Screening rates were higher in women and in those reporting more partners: median (95% credible interval) rates per year in men were 0.30 (0.25–0.36) (0 new partners), 0.45 (0.37–0.54) (1 new partner), and 0.60 (0.50–0.73) (≥2 new partners). In women, they were 0.61 (0.53–0.69) (0 new partners), 0.89 (0.75–1.04) (1 new partner), and 1.2 (1.0–1.4) (≥2 new partners).

Conclusions:
Proportion of testing occurring in sexual health is not a proxy for proportion prompted by symptoms. Test positivity depends on a combination of force of infection and screening rate and does not simply reflect prevalence or behavioral risk. The analysis highlights the value of recording testing reason and behavioral characteristics to inform cost-effective control.
Daily luteal serum and urinary hormone profiles in the menopause transition: Study of Women's Health Across the Nation
Authors: Santoro Nanette , El Khoudary Samar R. , Nasr Alexis , Gold Ellen B. , Greendale Gail , McConnell Dan , Neal-Perry Genevieve , Pavlovic Jelena , Derby Carol , Crawford Sybil 
Published: December 2019

Abstract

Objective:
To further characterize the endocrinology of the menopause transition, we sought to determine: whether relationships between urine and serum hormones are maintained as women enter their sixth decade; whether a single luteal phase serum progesterone (P) is reflective of integrated-luteal urinary pregnanediol glucuronide (uPdg); and whether serum P, like luteal uPdg, declines as women approach their final menses (FMP).

Methods:
The Study of Women's Health Across the Nation (SWAN) Daily Hormone Study's (DHS) is a community-based observational study. A subset of participants underwent a timed, luteal blood draw planned for cycle days 16 to 24 during the same month of DHS collection. Serum-luteinizing hormone (LH), follicle-stimulating hormone (FSH), estradiol and P, and urine LH, FSH, estrone conjugates (E1c), and daily and integrated luteal uPdg were measured in 268 samples from 170 women. Serum/urine hormone associations were determined using Pearson's correlation and linear regression, adjusted for concurrent age, body mass index, smoking status, and race/ethnicity.

Results:
Pearson's r ranged from 0.573 (for LH) to 0.843 (for FSH) for serum/urine correlations. Integrated luteal uPdg weakly correlated with serum P (Pearson's r = 0.26, P = 0.004) and explained 7% of the variability in serum P in adjusted linear regression (total R
2 0.09, P = 0.002). Serum P demonstrated a marginally significant decline with approaching FMP in adjusted analysis (P = 0.04).

Conclusions:
Urine and serum hormones maintain a close relationship in women into their sixth decade of life. Serum luteal P was weakly reflective of luteal Pdg excretion.