bluuebunny/crossref_metadata_2025_split huggingface dataset:
PatientExploreR: an extensible application for dynamic visualization of patient clinical history from electronic health records in the OMOP common data model
Authors: Glicksberg Benjamin S , Oskotsky Boris , Thangaraj Phyllis M , Giangreco Nicholas , Badgeley Marcus A , Johnson Kipp W , Datta Debajyoti , Rudrapatna Vivek A , Rappoport Nadav , Shervey Mark M , Miotto Riccardo , Goldstein Theodore C , Rutenberg Eugenia , Frazier Remi , Lee Nelson , Israni Sharat , Larsen Rick , Percha Bethany , Li Li , Dudley Joel T , Tatonetti Nicholas P , Butte Atul J 
Published: June 2019

Abstract

Motivation
Electronic health records (EHRs) are quickly becoming omnipresent in healthcare, but interoperability issues and technical demands limit their use for biomedical and clinical research. Interactive and flexible software that interfaces directly with EHR data structured around a common data model (CDM) could accelerate more EHR-based research by making the data more accessible to researchers who lack computational expertise and/or domain knowledge.

Results
We present PatientExploreR, an extensible application built on the R/Shiny framework that interfaces with a relational database of EHR data in the Observational Medical Outcomes Partnership CDM format. PatientExploreR produces patient-level interactive and dynamic reports and facilitates visualization of clinical data without any programming required. It allows researchers to easily construct and export patient cohorts from the EHR for analysis with other software. This application could enable easier exploration of patient-level data for physicians and researchers. PatientExploreR can incorporate EHR data from any institution that employs the CDM for users with approved access. The software code is free and open source under the MIT license, enabling institutions to install and users to expand and modify the application for their own purposes.

Availability and implementation
PatientExploreR can be freely obtained from GitHub: https://github.com/BenGlicksberg/PatientExploreR. We provide instructions for how researchers with approved access to their institutional EHR can use this package. We also release an open sandbox server of synthesized patient data for users without EHR access to explore: http://patientexplorer.ucsf.edu.

Supplementary information
Supplementary data are available at Bioinformatics online.
Asymmetries in reproductive anatomy: insights from promiscuous songbirds
Authors: Calhim Sara , Pruett-Jones Stephen , Webster Michael S , Rowe Melissah 
Published: June 2019

AbstractDirectional asymmetry in gonad size is commonly observed in vertebrates and is particularly pronounced in birds, where the left testis is frequently larger than the right. The adaptive significance of directional asymmetry in testis size is poorly understood, and whether it extends beyond the testes (i.e. side-correspondent asymmetry along the reproductive tract) has rarely been considered. Using the Maluridae, a songbird family exhibiting variation in levels of sperm competition and directional testis asymmetry, yet similar in ecology and life history, we investigated the relative roles of side-correspondence and sperm competition on male reproductive tract asymmetry at both inter- and intraspecific levels. We found some evidence for side-correspondent asymmetry. Additionally, sperm competition influenced directional asymmetry at each end of the reproductive tract: species experiencing higher levels of sperm competition had a relatively larger right testis and relatively more sperm in the right seminal glomerus. Within red-backed fairy-wrens (Malurus melanocephalus), auxiliary males had relatively more sperm in the left seminal glomerus, in contrast to a right-bias asymmetry throughout the reproductive tract in breeding males. Given that the number of sperm is important for competitive fertilization success, our results suggest that sperm competition shapes reproductive asymmetries beyond testis size, with likely functional consequences for male reproductive success.
The histone methyltransferase EZH2 is required for normal uterine development and function in mice†
Authors: Nanjappa Manjunatha K , Mesa Ana M , Medrano Theresa I , Jefferson Wendy N , DeMayo Francesco J , Williams Carmen J , Lydon John P , Levin Ellis R , Cooke Paul S 
Published: June 2019

Abstract
Enhancer of zeste homolog 2 (EZH2) is a rate-limiting catalytic subunit of a histone methyltransferase, polycomb repressive complex, which silences gene activity through the repressive histone mark H3K27me3. EZH2 is critical for epigenetic effects of early estrogen treatment, and may be involved in uterine development and pathologies. We investigated EZH2 expression, regulation, and its role in uterine development/function. Uterine epithelial EZH2 expression was associated with proliferation and was high neonatally then declined by weaning. Pre-weaning uterine EZH2 expression was comparable in wild-type and estrogen receptor 1 knockout mice, showing neonatal EZH2 expression is ESR1 independent. Epithelial EZH2 was upregulated by 17β-estradiol (E2) and inhibited by progesterone in adult uteri from ovariectomized mice. To investigate the uterine role of EZH2, we developed a EZH2 conditional knockout (Ezh2cKO) mouse using a cre recombinase driven by the progesterone receptor (Pgr) promoter that produced Ezh2cKO mice lacking EZH2 in Pgr-expressing tissues (e.g. uterus, mammary glands). In Ezh2cKO uteri, EZH2 was deleted neonatally. These uteri had reduced H3K27me3, were larger than WT, and showed adult cystic endometrial hyperplasia. Ovary-independent uterine epithelial proliferation and increased numbers of highly proliferative uterine glands were seen in adult Ezh2cKO mice. Female Ezh2cKO mice were initially subfertile, and then became infertile by 9 months. Mammary gland development in Ezh2cKO mice was inhibited. In summary, uterine EZH2 expression is developmentally and hormonally regulated, and its loss causes aberrant uterine epithelial proliferation, uterine hypertrophy, and cystic endometrial hyperplasia, indicating a critical role in uterine development and function.
Cortical Structure and Cognition in Infants and Toddlers
Authors: Girault Jessica B , Cornea Emil , Goldman Barbara D , Jha Shaili C , Murphy Veronica A , Li Gang , Wang Li , Shen Dinggang , Knickmeyer Rebecca C , Styner Martin , Gilmore John H 
Published: June 2019

ABSTRACTCortical structure has been consistently related to cognitive abilities in children and adults, yet we know little about how the cortex develops to support emergent cognition in infancy and toddlerhood when cortical thickness (CT) and surface area (SA) are maturing rapidly. In this report, we assessed how regional and global measures of CT and SA in a sample (N = 487) of healthy neonates, 1-year-olds, and 2-year-olds related to motor, language, visual reception, and general cognitive ability. We report novel findings that thicker cortices at ages 1 and 2 and larger SA at birth, age 1, and age 2 confer a cognitive advantage in infancy and toddlerhood. While several expected brain–cognition relationships were observed, overlapping cortical regions were also implicated across cognitive domains, suggesting that infancy marks a period of plasticity and refinement in cortical structure to support burgeoning motor, language, and cognitive abilities. CT may be a particularly important morphological indicator of ability, but its impact on cognition is relatively weak when compared with gestational age and maternal education. Findings suggest that prenatal and early postnatal cortical developments are important for cognition in infants and toddlers but should be considered in relation to other child and demographic factors.
Impact of preoperative atrial fibrillation on thromboembolic events and pump thrombosis in long-term left ventricular assist device therapy
Authors: Pedde David , Soltani Sajjad , Stein Julia , Tsyganenko Dmytro , Müller Markus , Schönrath Felix , Falk Volkmar , Potapov Evgenij V 
Published: June 2019

Abstract

OBJECTIVES
Pump thrombosis (PT) and thromboembolic events (TEs) remain major adverse events in left ventricular assist device (LVAD) therapy at an annual rate of 6–8% supported with the HeartWare HVAD and HeartMate II. PT and TEs are multifactorial events. Understanding the predisposing risk factors for PT and TE is paramount to define preventive strategies. Preoperative atrial fibrillation (AF) is considered a significant and potentially modifiable risk factor. This study investigates whether LVAD patients with AF exhibit a higher rate of PT and TE than those in sinus rhythm (SR).

METHODS
We evaluated medical records of consecutive patients who underwent implantation of the HeartMate II (n = 195; 25.4%) and HeartWare HVAD (n = 574; 74.6%) at our institution between 2006 and 2015. Only visually confirmed PT was included in the study. TE was defined as any peripheral embolism or cerebral embolism according to the INTERMACS definitions.

RESULTS
SR was documented preoperatively in 211 patients (SR group) and AF in 558 patients (AF group). The median duration of support was 0.78 years in the AF group and 1.03 years in the SR group. The mean age was 60.27 years in the AF group and 52.04 years in the SR group. In the AF group, 83.0% of the patients were male, compared to 77.3% in the SR group. The cumulative incidence of PT in the SR group was 2.5% [95% confidence interval (CI) 0.3–4.7%] after 1 year and 5.7% (95% CI 2.2–9.2%) after 2 years, and in the AF group 4.9% (95% CI 3.0–6.7%) and 7.8% (95% CI 5.4–10.2%), respectively (P = 0.129). TEs were recorded in the SR group in 4.4% (95% CI 1.6–7.2%) after 1 year and in 6.3% (95% CI 2.8–9.8%) after 2 years, and occurred after a median support time of 214 days (range 120–768). In the AF group, the cumulative incidence was 8.4% (95% CI 6.0–10.7%) and 10.7% (95% CI 8.0–13.4%), respectively, after a median support time of 116 days (range 37–375), P-value = 0.163. In the multivariate analysis, event-free survival was not influenced by the preoperative SR [hazard ratio (HR) 0.86, 95% CI 0.68–1.1; P = 0.19].

CONCLUSIONS
Our study showed that the preoperative rhythm has no impact on survival, PT and TEs despite different preoperative risk factor profiles in the AF and SR group. Thus, the effect of a maze procedure, catheter ablation or left atrial appendage closure on PT and TE’s for AF patients during LVAD implantation is questionable. However, to obtain a definitive answer, a prospective study would be of value.
Challenges with quality of race and ethnicity data in observational databases
Authors: Polubriaginof Fernanda C G , Ryan Patrick , Salmasian Hojjat , Shapiro Andrea Wells , Perotte Adler , Safford Monika M , Hripcsak George , Smith Shaun , Tatonetti Nicholas P , Vawdrey David K 
Published: June 2019

Abstract

Objective
We sought to assess the quality of race and ethnicity information in observational health databases, including electronic health records (EHRs), and to propose patient self-recording as an improvement strategy.

Materials and Methods
We assessed completeness of race and ethnicity information in large observational health databases in the United States (Healthcare Cost and Utilization Project and Optum Labs), and at a single healthcare system in New York City serving a racially and ethnically diverse population. We compared race and ethnicity data collected via administrative processes with data recorded directly by respondents via paper surveys (National Health and Nutrition Examination Survey and Hospital Consumer Assessment of Healthcare Providers and Systems). Respondent-recorded data were considered the gold standard for the collection of race and ethnicity information.

Results
Among the 160 million patients from the Healthcare Cost and Utilization Project and Optum Labs datasets, race or ethnicity was unknown for 25%. Among the 2.4 million patients in the single New York City healthcare system’s EHR, race or ethnicity was unknown for 57%. However, when patients directly recorded their race and ethnicity, 86% provided clinically meaningful information, and 66% of patients reported information that was discrepant with the EHR.

Discussion
Race and ethnicity data are critical to support precision medicine initiatives and to determine healthcare disparities; however, the quality of this information in observational databases is concerning. Patient self-recording through the use of patient-facing tools can substantially increase the quality of the information while engaging patients in their health.

Conclusions
Patient self-recording may improve the completeness of race and ethnicity information.
The Impact of Resource Scarcity on Price-Quality Judgments
Authors: Park Hanyong , Lalwani Ashok K , Silvera David H 
Published: June 2019

Abstract
Consumers routinely encounter situations in which they perceive that resources are scarce. However, little is known about how this perception influences consumers’ use of price in their purchase decisions. The present research seeks to fill this gap by examining the link between scarcity and the tendency to use price to judge product quality, and the mechanisms underlying that link. Six studies (and five more reported in the web appendix) using multiple product categories and a variety of operationalizations of both scarcity and price-quality judgments show that scarcity decreases consumers’ tendency to use price to judge product quality. This occurs because scarcity induces a desire to compensate for the shortage and seek abundance, and thereby reduces an individual’s general categorization tendency (because categorizing brings about a feeling of reduction); this, in turn, hinders consumers from viewing products as belonging to different price-tier groups, and thus lowers their tendency to use price as a basis for judging product quality. Boundary conditions for the proposed effect are also identified. The current research makes fundamental contributions to the literatures on scarcity, price-quality judgments, and categorization.
The absence of [C ii] 158 $\mu$m emission in spectroscopically confirmed galaxies at z &gt; 8
Authors: Laporte N , Katz H , Ellis R S , Lagache G , Bauer F E , Boone F , Inoue A K , Hashimoto T , Matsuo H , Mawatari K , Tamura Y 
Published: June 2019

ABSTRACT
The scatter in the relationship between the strength of [C ii] 158 $\mu$m emission and the star formation rate at high redshift has been the source of much recent interest. Although the relationship is well established locally, several intensely star-forming galaxies have been found whose [C ii] 158 $\mu$m emission is either weak, absent, or spatially offset from the young stars. Here we present new ALMA data for the two most distant gravitationally lensed and spectroscopically confirmed galaxies, A2744_YD4 at z = 8.38 and MACS1149_JD1 at z = 9.11, both of which reveal intense [O iii] 88 $\mu$m emission. In both cases we provide stringent upper limits on the presence of [C ii] 158 $\mu$m with respect to [O iii] 88 $\mu$m. We review possible explanations for this apparent redshift-dependent [C ii] deficit in the context of our recent hydrodynamical simulations. Our results highlight the importance of using several emission line diagnostics with ALMA to investigate the nature of the interstellar medium in early galaxies.
What is Foreign Relations Law?
Authors: Bradley Curtis A. 
Published: June 2019

Abstract
This chapter considers what is potentially encompassed by the term “foreign relations law,” and what it means to think about it as a distinct field of law that can be compared and contrasted across national jurisdictions. The term “foreign relations law” encompasses the domestic law of each nation that governs how that nation interacts with the rest of the world. Many issues of foreign relations law concern allocations of authority between political actors, such as the authority to represent the nation in diplomacy, to conclude and terminate international agreements, to recognize foreign governments and their territories, and to initiate or end the use of military force. But foreign relations law also encompasses issues relating to the role of the courts in transnational cases, such as whether certain issues are “nonjusticiable” and thus subject entirely to political branch determination, whether courts should take into account considerations of international comity when interpreting and applying domestic law, and whether and to what extent courts can apply international law directly to decide a particular case. The chapter describes the historical development of foreign relations law as a field of study within the United States and considers why it has not been treated as a field in many other countries. The chapter concludes by highlighting a central question for foreign relations law, which is the extent to which it should be treated differently than other types of domestic law—referred to in the United States as a debate over “foreign affairs exceptionalism.”
Rules of the Game: Exponential Random Graph Models of a Gang Homicide Network
Authors: Lewis Kevin , Papachristos Andrew V 
Published: June 2019

AbstractGang members frequently refer to street life as a “game” (or “The Game”): a social milieu in which status is lost or won by the way individuals and groups manage their reputations. Like other games, successfully participating in the street game may demand adherence to certain rules, such as the willingness to violently redress threats, the avoidance of “weak” behaviors, and the protection of one’s allies. This paper draws on detailed police records of violent exchanges among gangs in Chicago to ascertain which rules of the game in fact contribute to the relative social standing of groups. Specifically, we use exponential random graph models to identify the underlying micro-arrangements among gangs that collectively generate macro-level patterns of homicide. Findings illuminate a large and diverse array of generative mechanisms based on gangs’ attributes and structural positions. However, these mechanisms vary depending on which two gangs are at hand; provide evidence of a contested hierarchy with few intergroup alliances; and are surprisingly inconsistent over time. As all gangs engage in local and ongoing struggles for dominance—and as the rules constantly change—the street game is continually played but never truly won.
Characterization of the sleep disorder of anti-IgLON5 disease
Authors: Gaig Carles , Iranzo Alex , Cajochen Christian , Vilaseca Isabel , Embid Cristina , Dalmau Josep , Graus Francesc , Santamaria Joan 
Published: June 2019

AbstractStudy ObjectiveTo characterize the sleep disorder of anti-IgLON5 disease.MethodsWe reviewed 27 video-polysomnographies (V-PSG), 6 multiple sleep latency tests (MSLT), 2 videsomnoscopies with dexmedetomidine, and 10 actigraphies recorded during the disease course of five patients. Due to severe sleep architecture abnormalities, we used a novel modified sleep scoring system combining conventional stages with a descriptive approach in which two additional stages were identified: undifferentiated-NREM (UN-NREM) and poorly structured N2 (P-SN2) sleep that were characterized by abnormal motor activation and absence or sparse elements of conventional NREM sleep.ResultsSleep-related vocalizations, movements, behaviors, and respiratory abnormalities were reported by bed-partners. In all patients, NREM sleep onset and sleep reentering after an awakening occurred as UN-NREM (median: 29.8% of total sleep time [TST]) and P-SN2 sleep (14.5% TST) associated with vocalizations and simple and quasi-purposeful movements. Sleep initiation was normalized in one patient with a high dose of steroids, but NREM sleep abnormalities reappeared in subsequent V-PSG. In all patients, if sleep continued uninterrupted, there was a progressive normalization with normal N2 (11.7% TST) and N3 (22.3% TST) sleep but stridor and obstructive apnea emerged. REM sleep behavior disorder (RBD) occurred in four patients. Sleep initiation was also altered in MSLT and dexmedetomidine-induced sleep. Actigraphy showed a 10-fold increase of nocturnal activity compared with controls. Sleep abnormalities remained stable during the disease.ConclusionsThe sleep disorder of anti-IgLON5 disease presents as a complex sleep pattern characterized by abnormal sleep initiation with undifferentiated NREM sleep, RBD, periods of normal NREM sleep, stridor, and obstructive apnea.
Molecular phylogeny and systematics of cestodes with rudimentary rostellum (Cestoda: Hymenolepididae) from Holarctic Sorex shews (Eulipotyphla: Soricidae)
Authors: Kornienko Svetlana A , Binkienė Rasa , Dokuchaev Nikolai E , Tkach Vasyl V 
Published: June 2019

Abstract
We analyse the phylogenetic relationships and taxonomic status of hymenolepidid cestodes with rudimentary rostellum, parasitic in Holarctic shrews of the genus Sorex. These cestodes were previously termed as a ‘Ditestolepis clade’ and encompass eight genera: Diorchilepis, Ditestolepis, Ecrinolepis, Gulyaevilepis, Mathevolepis, Novobrachylepis, Spalania and Spasskylepis. Representatives of seven of these were available for molecular study, including type species of all seven genera. Phylogenetic analysis based on partial sequences of the 28S rRNA gene supports this group of genera as monophyletic. The ‘Ditestolepis clade’ consists of two subclades. One of these includes genera containing cestodes having suckers positioned inside bothrium-like depressions (Ditestolepis, Gulyaevilepis and Spasskylepis). The second subclade contains cestodes with suckers expanding far beyond the margins of the scolex (Mathevolepis, Ecrinolepis, Spalania and Novobrachylepis). The relative taxonomic value of several additional morphological characters is discussed. Genetic data convincingly demonstrate that Ditestolepis diaphana, Spasskylepis ovaluteri and Mathevolepis macyi represent complexes of morphologically similar species. Based on the phylogenetic analysis, we resurrect the genus Spalania. Amended generic diagnoses and keys to identification of the genera in the Ditestolepis clade, as well as keys to the known species, are provided.
Systemic and prophylactic intrathecal chemotherapy for primary adrenal lymphoma
Authors: Yuan Lei , Sun Lu , Bo Jian , Wang Quanshun , Zhao Yu 
Published: June 2019

Abstract
Primary adrenal lymphoma (PAL) is a rare entity of lymphoma with dismal prognosis using systemic chemotherapy. More clinical reports are needed to guide the treatment for PAL.
We performed a retrospective analysis of 20 patients diagnosed with PAL who presented to our center between January 2005 and January 2014.
Median age at presentation was 48 years (range: 27–73) with a male-to-female ratio of 7:3. Bilateral and right-sided adrenal involvement were seen in 11 of 20 and 7 of 20 patients, respectively. Adrenal insufficiency (AI) was seen in 6 of 10 evaluated patients. Diffuse large B cell lymphoma (DLBCL) was the most common immunophenotype (85.0%). Two patients died due to rapid disease progression before treatment. Two patients received autologous stem cell transplantation as consolidation therapy. All patients received prophylactic intrathecal chemotherapy. The estimated 5-year overall survival (OS) and progression-free survival (PFS) were 52.5% [95% confidence interval (95% CI: 28.2–72.0)] and 53.2% (95% CI: 29.0–72.5), respectively.
These findings suggest that PAL should always be considered in differential diagnosis of adrenal mass with AI. Despite the contrasting previous reports, long-term prognosis of PAL is not necessarily inferior to that of non-Hodgkin lymphoma in general.