bluuebunny/crossref_metadata_2025_split huggingface dataset:
Predicting Adaptive Genetic Variation of Loblolly Pine (Pinus taeda L.) Populations Under Projected Future Climates Based on Multivariate Models
Authors: Lu Mengmeng , Krutovsky Konstantin V , Loopstra Carol A 
Published: October 2019

Abstract
Greenhouse gas emission and global warming are likely to cause rapid climate change within the natural range of loblolly pine over the next few decades, thus bringing uncertainty to their adaptation to the environment. Here, we studied adaptive genetic variation of loblolly pine and correlated genetic variation with bioclimatic variables using multivariate modeling methods—Redundancy Analysis, Generalized Dissimilarity Modeling, and Gradient Forests. Studied trees (N = 299) were originally sampled from their native range across eight states on the east side of the Mississippi River. Genetic variation was calculated using a total of 44,317 single-nucleotide polymorphisms acquired by exome target sequencing. The fitted models were used to predict the adaptive genetic variation on a large spatial and temporal scale. We observed east-to-west spatial genetic variation across the range, which presented evidence of isolation by distance. Different key factors drive adaptation of loblolly pine from different geographical regions. Trees residing near the northeastern edge of the range, spanning across Delaware and Maryland and mountainous areas of  Virginia, North Carolina, South Carolina, and northern Georgia, were identified to be most likely impacted by climate change based on the large difference in genetic composition under current and future climate conditions. This study provides new perspectives on adaptive genetic variation of loblolly pine in response to different climate scenarios, and the results can be used to target particular populations while developing adaptive forest management guidelines.
Virginia opossum distributions are influenced by human-modified landscapes and water availability in tallgrass prairies
Authors: Wait Kyle R , Ahlers Adam A 
Published: October 2019

AbstractThe Flint Hills represent the largest tract of tallgrass prairie in North America and is located near the western edge of the native range of the Virginia opossum (Didelphis virginiana). This region is undergoing rapid landscape changes (e.g., urbanization, agriculture, woody encroachment) that are negatively affecting mammal communities. Although previous research has revealed northward distributional expansions of Virginia opossums facilitated by urban development, no studies have assessed how landscape change affects distribution patterns along the western edge of their geographic range. During 2016–2018, we monitored site (n = 74) occupancy along urban–rural transects in the Flint Hills to assess the influence of landscape change (i.e., urban, grassland, agriculture, woody encroachment) and water availability on the distribution of Virginia opossums. Sites surrounded by urban land cover had greater initial occupancy probabilities and lower extinction rates. Sites closer to permanent water sources experienced greater colonization rates and lower extinction rates. In addition, site extinction rates were lower in areas surrounded by woody encroachment. Our results concur with other studies suggesting that growing urban areas may expand opossum distributions along the edges of their geographic range. Our study also suggests that woody encroachment into tallgrass prairies may provide an alternative pathway for future distributional expansions. Future research must consider the potential for landscape change, along with dynamic water availability, in models predicting the distribution of Virginia opossums.
CancerTracer: a curated database for intrapatient tumor heterogeneity
Authors: Wang Chen , Yang Jian , Luo Hong , Wang Kun , Wang Yu , Xiao Zhi-Xiong , Tao Xiang , Jiang Hao , Cai Haoyang 
Published: October 2019

Abstract
Comprehensive genomic analyses of cancers have revealed substantial intrapatient molecular heterogeneities that may explain some instances of drug resistance and treatment failures. Examination of the clonal composition of an individual tumor and its evolution through disease progression and treatment may enable identification of precise therapeutic targets for drug design. Multi-region and single-cell sequencing are powerful tools that can be used to capture intratumor heterogeneity. Here, we present a database we’ve named CancerTracer (http://cailab.labshare.cn/cancertracer): a manually curated database designed to track and characterize the evolutionary trajectories of tumor growth in individual patients. We collected over 6000 tumor samples from 1548 patients corresponding to 45 different types of cancer. Patient-specific tumor phylogenetic trees were constructed based on somatic mutations or copy number alterations identified in multiple biopsies. Using the structured heterogeneity data, researchers can identify common driver events shared by all tumor regions, and the heterogeneous somatic events present in different regions of a tumor of interest. The database can also be used to investigate the phylogenetic relationships between primary and metastatic tumors. It is our hope that CancerTracer will significantly improve our understanding of the evolutionary histories of tumors, and may facilitate the identification of predictive biomarkers for personalized cancer therapies.
PDBe: improved findability of macromolecular structure data in the PDB
Authors: Armstrong David R , Berrisford John M , Conroy Matthew J , Gutmanas Aleksandras , Anyango Stephen , Choudhary Preeti , Clark Alice R , Dana Jose M , Deshpande Mandar , Dunlop Roisin , Gane Paul , Gáborová Romana , Gupta Deepti , Haslam Pauline , Koča Jaroslav , Mak Lora , Mir Saqib , Mukhopadhyay Abhik , Nadzirin Nurul , Nair Sreenath , Paysan-Lafosse Typhaine , Pravda Lukas , Sehnal David , Salih Osman , Smart Oliver , Tolchard James , Varadi Mihaly , Svobodova-Vařeková Radka , Zaki Hossam , Kleywegt Gerard J , Velankar Sameer 
Published: October 2019

AbstractThe Protein Data Bank in Europe (PDBe), a founding member of the Worldwide Protein Data Bank (wwPDB), actively participates in the deposition, curation, validation, archiving and dissemination of macromolecular structure data. PDBe supports diverse research communities in their use of macromolecular structures by enriching the PDB data and by providing advanced tools and services for effective data access, visualization and analysis. This paper details the enrichment of data at PDBe, including mapping of RNA structures to Rfam, and identification of molecules that act as cofactors. PDBe has developed an advanced search facility with ∼100 data categories and sequence searches. New features have been included in the LiteMol viewer at PDBe, with updated visualization of carbohydrates and nucleic acids. Small molecules are now mapped more extensively to external databases and their visual representation has been enhanced. These advances help users to more easily find and interpret macromolecular structure data in order to solve scientific problems.
Optimizing Coverage vs Frequency for Sexually Transmitted Infection Screening of Men Who Have Sex With Men
Authors: Weiss Kevin M , Jones Jeb S , Anderson Emeli J , Gift Thomas , Chesson Harrell , Bernstein Kyle , Workowski Kimberly , Tuite Ashleigh , Rosenberg Eli S , Sullivan Patrick S , Jenness Samuel M 
Published: October 2019

AbstractBackgroundThe incidence of bacterial sexually transmitted infections (STIs) in men who have sex with men (MSM) has increased substantially despite availability of effective antibiotics. The US Centers for Disease Control and Prevention (CDC) recommends annual screening for all sexually active (SA) MSM and more frequent screening for high-risk (HR) MSM. The population-level benefits of improved coverage vs increased frequency of STI screening among SA vs HR MSM are unknown.MethodsWe used a network transmission model of gonorrhea (NG) and chlamydia (CT) among MSM to simulate the implementation of STI screening across different scenarios, starting with the CDC guidelines at current coverage levels. Counterfactual model scenarios varied screening coverage and frequency for SA MSM and HR MSM (MSM with multiple recent partners). We estimated infections averted and the number needed to screen to prevent 1 new infection.ResultsCompared with current recommendations, increasing the frequency of screening to biannually for all SA MSM and adding some HR screening could avert 72% of NG and 78% of CT infections over 10 years. Biannual screening of 30% of HR MSM at empirical coverage levels for annual SA screening could avert 76% of NG and 84% of CT infections. Other scenarios, including higher coverage among SA MSM and increasing frequency for HR MSM, averted fewer infections but did so at a lower number needed to screen.ConclusionsThe optimal screening scenarios in this model to reduce STI incidence among MSM included more frequent screening for all sexually active MSM and higher coverage of screening for HR men with multiple partners.
Asymptotic Approximant for the Falkner–Skan Boundary Layer Equation
Authors: Belden E R , Dickman Z A , Weinstein S J , Archibee A D , Burroughs E , Barlow N S 
Published: October 2019

Summary
We demonstrate that the asymptotic approximant applied to the Blasius boundary layer flow over a flat plat (Barlow et al., Q. J. Mech. Appl. Math. 70 (2017) 21–48.) yields accurate analytic closed-form solutions to the Falkner–Skan boundary layer equation for flow over a wedge having angle $\beta\pi/2$ to the horizontal. A wide range of wedge angles satisfying $\beta\in[-0.198837735, 1]$ are considered, and the previously established non-unique solutions for $\beta&lt;0$ having positive and negative shear rates along the wedge are accurately represented. The approximant is used to determine the singularities in the complex plane that prescribe the radius of convergence of the power series solution to the Falkner–Skan equation. An attractive feature of the approximant is that it may be constructed quickly by recursion compared with traditional Padé approximants that require a matrix inversion. The accuracy of the approximant is verified by numerical solutions, and benchmark numerical values are obtained that characterize the asymptotic behavior of the Falkner–Skan solution at large distances from the wedge.
High water vs. ad libitum water intake for autosomal dominant polycystic kidney disease: a randomized controlled feasibility trial
Authors: El-Damanawi R , Lee M , Harris T , Cowley L B , Bond S , Pavey H , Sandford R N , Wilkinson I B , Karet Frankl F E , Hiemstra T F 
Published: October 2019

AbstractBackgroundVasopressin stimulates cyst growth in autosomal dominant polycystic kidney disease (ADPKD) and is a key therapeutic target. Evaluation of high water intake as an alternative to pharmacological vasopressin blockade is supported by patients. However feasibility, safety and adherence-promoting strategies required to deliver this remain unknown.AimsAssess the feasibility of a definitive randomized high water intake trial in ADPKD.MethodsIn this prospective open-label randomized trial, adult ADPKD patients with eGFR ≥ 20 ml/min/1.73 m2 were randomized to prescribed high water (HW) intake targeting urine osmolality (UOsm) ≤270 mOsm/kg, or ad libitum (AW) intake (UOsm &gt;300 mOsm/kg). Self-management strategies including home-monitoring of urine-specific gravity (USG) were employed to promote adherence.ResultsWe enrolled 42 participants, baseline median eGFR (HW 68.4 [interquartile range (IQR) 35.9–107.2] vs. AW 75.8 [IQR 59.0–111.0 ml/min/1.73 m2, P = 0.22) and UOsm (HW 353 [IQR 190–438] vs. AW 350 [IQR 240–452] mOsm/kg, P = 0.71) were similar between groups. After 8 weeks, 67% in the HW vs. 24% in AW group achieved UOsm ≤270 mOsm/kg, P = 0.001. HW group achieved lower UOsm (194 [IQR 190–438] vs. 379 [IQR 235–503] mOsm/kg, P = 0.01) and higher urine volumes (3155 [IQR 2270–4295] vs. 1920 [IQR 1670–2960] ml/day, P = 0.02). Two cases of hyponatraemia occurred in HW group. No acute GFR effects were detected. In total 79% (519/672) of USG were submitted and 90% (468/519) were within target. Overall, 17% withdrew during the study.ConclusionDRINK demonstrated successful recruitment and adherence leading to separation between treatment arms in primary outcomes. These findings suggest a definitive trial assessing the impact of high water on kidney disease progression in ADPKD is feasible.
Increased rates of hypernatraemia during modest heatwaves in temperate climates
Authors: Brennan M , Murray O , O’Shea P M , Mulkerrin E C 
Published: October 2019

Abstract

Background
Hypernatraemia is associated with morbidity and mortality, particularly in the older person. Last summer, Ireland experienced prolonged periods of excessive heat. The Irish meteorological service defines a heatwave as temperatures exceeding 25°C for five consecutive days.

Aim
This study sought to compare the frequency of hypernatraemia (sodium (Na+) &gt;145 mmol/l) observed during a modest heatwave with that during average ambient temperature in the temperate Irish climate.

Design
Retrospective cross-sectional analysis with nested case–control study.

Methods
The 10-day period from 24 June to 3 July in 2017 and 2018 were chosen as the control and heatwave periods, respectively. Patients aged &gt;65 with at least one Na+ value recorded on the laboratory information system were included. Local meteorological data, age, gender and Na+ levels were evaluated.

Results
Maximum air temperatures were significantly higher during the heatwave period (mean 27°C vs. 16.8°C, P &lt; 0.0001). Hypernatraemia was present in 3.6% (66/1840) of samples collected during the heatwave compared to 1.4% (23/1593) in the control period. The mean age of affected patients was similar in both groups, 75 years ±7 (P = 1.000). Almost half of participants (49.5%) were male. The frequency of hypernatraemia observed was not influenced by gender, P = 0.33. The median sodium concentrations were similar in both groups, P = 1.00.

Conclusion
Hypernatraemia was 2.5 times more frequent in samples drawn during the heatwave compared to the control period. In this study, neither age nor gender impacted the profile of patients diagnosed with hypernatraemia. A modest rise in temperatures increases hypernatraemia rates in temperate climates.
The Microfoundations of Bureaucratic Outcomes: Causes and Consequences of Interpretive Disjuncture in Eviction Cases
Authors: Nelson Kyle 
Published: October 2019

AbstractEviction transforms landlords into plaintiffs and tenants into defendants, reframing expansive histories of housing trouble into legal problems. Researchers note high rates of default judgments against tenants, a majority of tenants without attorneys, and a disconnect between the ways that landlords and tenants understand cases. This study reveals the micro-foundations of case outcomes by explaining causes and consequences of “interpretive disjuncture.” How does interpretive disjuncture shape case trajectories and outcomes as housing trouble transforms into an eviction lawsuit? Drawing on one year of ethnographic fieldwork in tenants’ rights clinics in Los Angeles County, I follow tenants’ cases back to their roots and explain how both everyday and institutional challenges shape tenants’ interpretive processes as they navigate eviction.
A Bayesian Approach for Inferring the Impact of a Discrete Character on Rates of Continuous-Character Evolution in the Presence of Background-Rate Variation
Authors: May Michael R , Moore Brian R 
Published: October 2019

AbstractUnderstanding how and why rates of character evolution vary across the Tree of Life is central to many evolutionary questions; for example, does the trophic apparatus (a set of continuous characters) evolve at a higher rate in fish lineages that dwell in reef versus nonreef habitats (a discrete character)? Existing approaches for inferring the relationship between a discrete character and rates of continuous-character evolution rely on comparing a null model (in which rates of continuous-character evolution are constant across lineages) to an alternative model (in which rates of continuous-character evolution depend on the state of the discrete character under consideration). However, these approaches are susceptible to a “straw-man” effect: the influence of the discrete character is inflated because the null model is extremely unrealistic. Here, we describe MuSSCRat, a Bayesian approach for inferring the impact of a discrete trait on rates of continuous-character evolution in the presence of alternative sources of rate variation (“background-rate variation”). We demonstrate by simulation that our method is able to reliably infer the degree of state-dependent rate variation, and show that ignoring background-rate variation leads to biased inferences regarding the degree of state-dependent rate variation in grunts (the fish group Haemulidae). [Bayesian phylogenetic comparative methods; continuous-character evolution; data augmentation; discrete-character evolution.]
Whose privilege is it anyway?
Authors: Morrison Matthew 
Published: October 2019

Abstract
The £10 subject access request served by Ashley Dawson-Damer on Taylor Wessing LLP (TW) in August 2014 has already resulted in two substantial hearings in the Chancery Division1, and a two-day trip to the Court of Appeal. It is understood that the case is headed back to the Court of Appeal and that the appeal will be heard at some point in the new year.
New Drug for Prostate Cancer
Authors: Aschenbrenner Diane S. 
Published: October 2019

The Food and Drug Administration has approved darolutamide (Nubeqa), an androgen receptor inhibitor, for the treatment of nonmetastatic castration-resistant prostate cancer.The most common adverse effects of darolutamide are fatigue, pain in the extremity, and rash. The drug can also cause fetal harm and male infertility.
Cutaneous Elastic Tissue Anomalies
Authors: Andrés-Ramos Irene , Alegría-Landa Victoria , Gimeno Ignacio , Pérez-Plaza Alejandra , Rütten Arno , Kutzner Heinz , Requena Luis 
Published: October 2019

Abstract:After a review of the physiology in the formation and degradation of cutaneous elastic tissue, we describe the clinicopathologic disorders characterized by increased and decreased cutaneous elastic tissue. Cutaneous disorders characterized by increased and/or abnormal elastic tissue in the dermis include elastoma, also named nevus elasticus, dermatosis lenticularis disseminata, pseudoxanthoma elasticum, late-onset focal dermal elastosis, linear focal elastosis, elastoderma, elastofibroma dorsi, and elastosis perforans serpiginosa. In some of these conditions, the specific histopathologic diagnosis may be rendered with hematoxylin-eosin stain, whereas in other ones special elastic tissue stains are necessary to demonstrate the anomalies. Cutaneous disorders characterized by decreased dermal elastic tissue include nevus anelasticus, papular elastorrhexis, perifollicular elastolysis, anetoderma cutis laxa, postinflammatory elastolysis and cutis laxa, white fibrous papulosis of the neck, pseudoxanthoma elasticum–like papillary dermal elastolysis, and mid dermal elastolysis. In most of these conditions, the histopathologic anomalies are only seen with elastic tissue stains, and cutaneous biopsies of these processes stained with hematoxylin-eosin show appearance of normal skin. The diagnosis of some of these disorders characterized by increased or decreased elastic dermal tissue should be followed by general exploration of the patient to rule out associated severe systemic anomalies, and in some cases, a genetic counseling should be offered to the family.
Hyfrecation and Interference With Implantable Cardiac Devices
Authors: Amin Sima D. , Homan Katie B. , Assar Manish , Lee Mary , Housewright Chad D. 
Published: October 2019

BACKGROUND
Mohs micrographic surgery, excisional surgery, and electrodessication and curettage (ED&C) are common dermatologic procedures that often use electrodessication through hyfrecators to achieve hemostasis. According to in vitro studies, electrodessication is considered safe in patients with implanted cardiac devices. To the authors' knowledge, there are no in vivo data to support this claim.

OBJECTIVE
In this study, the authors aim to describe the outcomes of hyfrecation during dermatologic procedures in patients with pacemakers and implantable cardiac devices.

METHODS
Retrospective chart review was completed from March 2014 to April 2018 at a single center. Forty-five patients met criteria of having a cardiac device and having undergone an electrosurgery procedure using the Conmed 2000 Hyfrecator (Utica, NY). Adverse perioperative and postoperative outcomes, as well as device malfunction, were evaluated.

RESULTS
No adverse perioperative effects were reported. Device reports were examined for inappropriate firing of the defibrillator, loss of capture, temporary inhibition of pacing, battery drainage, pacing at an elevated or erratic rate, failure to deliver antitachycardia, reversion to asynchronous pacing, induction of arrhythmias, or tissue damage at lead tissue, but no such issues were found.

CONCLUSION
The lack of complications associated with cardiac devices with hyfrecation is reassuring. However, prospective and larger retrospective studies are warranted.
Efficacy of Intralesional Cryosurgery in the Treatment of Multiple Extragenital Cutaneous Warts: A Randomized Controlled Study
Authors: Awad Sara M. , El-Badawy Omnia , Abou-Taleb Doaa A.E. 
Published: October 2019

BACKGROUND
The efficacy of intralesional (IL) cryosurgery in the treatment of cutaneous warts has not been previously studied.

OBJECTIVE
To compare the efficacy and safety of IL cryosurgery versus electrosurgery in multiple extragenital warts and investigate their effect on serum interleukin (IL)-12 and interferon-gamma (IFN-γ).

MATERIALS AND METHODS
Thirty-one patients were included; 18 received IL cryosurgery, and 13 had electrosurgery. Treatment was performed for the largest or few (2–3) small warts (target) until cleared, leaving the remaining (distant) warts untreated. Clinical response of the target and distant warts and adverse effects were evaluated. Serum IL-12 and IFN-γ levels were assessed before and after treatment.

RESULTS
All patients had complete clearing of the treated wart in both groups. IL cryosurgery was well tolerated; infection, ulceration, and recurrence occurred only with electrosurgery. Complete/near-complete resolution of the distant untreated warts was seen in 33.3% versus none of patients in the IL cryosurgery and electrosurgery groups, respectively (p = .003). Furthermore, IL-12 and IFN-γ levels showed a tendency to increase after IL cryosurgery, and their increase correlated with distant wart response.

CONCLUSION
Intralesional cryosurgery is effective not only in clearing treated warts but also resolving untreated warts and possibly enhances human papillomavirus–directed immune response.
Family planning in adolescents
Authors: Ganti Amitha K. , Hillard Paula J.A. 
Published: October 2019

Purpose of review
As politics continue to shape contraception and abortion care, providers have a responsibility to address the specific needs of the adolescent patient. Here we review the current literature on contraception and abortion in adolescents.

Recent findings
Shared decision-making among patients, parents, and providers is the cornerstone of successful adolescent family planning. Providers should be aware of local state regulations related to consent in minors. When provided directive and noncoercive contraception counseling at no cost, adolescents are motivated and effective decision-makers in their care. Long-acting reversible contraceptives should be offered as the first-line method of contraception in adolescents.

Summary
Family planning in adolescents presents unique challenges to obstetrician-gynecologists. Improved access to contraception and abortion services is significantly lowering unintended pregnancies rates in adolescents, but more data assessing the effectiveness of interventions in marginalized communities are needed.