bluuebunny/crossref_metadata_2025_split huggingface dataset:
The neXtProt knowledgebase in 2020: data, tools and usability improvements
Authors: Zahn-Zabal Monique , Michel Pierre-André , Gateau Alain , Nikitin Frédéric , Schaeffer Mathieu , Audot Estelle , Gaudet Pascale , Duek Paula D , Teixeira Daniel , Rech de Laval Valentine , Samarasinghe Kasun , Bairoch Amos , Lane Lydie 
Published: October 2019

Abstract
The neXtProt knowledgebase (https://www.nextprot.org) is an integrative resource providing both data on human protein and the tools to explore these. In order to provide comprehensive and up-to-date data, we evaluate and add new data sets. We describe the incorporation of three new data sets that provide expression, function, protein-protein binary interaction, post-translational modifications (PTM) and variant information. New SPARQL query examples illustrating uses of the new data were added. neXtProt has continued to develop tools for proteomics. We have improved the peptide uniqueness checker and have implemented a new protein digestion tool. Together, these tools make it possible to determine which proteases can be used to identify trypsin-resistant proteins by mass spectrometry. In terms of usability, we have finished revamping our web interface and completely rewritten our API. Our SPARQL endpoint now supports federated queries. All the neXtProt data are available via our user interface, API, SPARQL endpoint and FTP site, including the new PEFF 1.0 format files. Finally, the data on our FTP site is now CC BY 4.0 to promote its reuse.
Generation of diffuse intrinsic pontine glioma mouse models by brainstem targeted in utero electroporation
Authors: Patel Smruti K , Hartley Rachel M , Wei Xin , Furnish Robin , Escobar-Riquelme Fernanda , Bear Heather , Choi Kwangmin , Fuller Christine , Phoenix Timothy N 
Published: October 2019

Abstract

Background
Diffuse intrinsic pontine gliomas (DIPGs) are highly lethal childhood brain tumors. Their unique genetic makeup, pathological heterogeneity, and brainstem location all present challenges to treatment. Developing mouse models that accurately reflect each of these distinct features will be critical to advance our understanding of DIPG development, progression, and therapeutic resistance. The aim of this study was to generate new mouse models of DIPG, and characterize the role of specific oncogenic combinations in DIPG pathogenesis.

Methods
We used in utero electroporation (IUE) to transfect neural stem cells in the developing brainstem with PiggyBac DNA transposon plasmids. Combinations of PDGFB, PdgfraD842V, or PdgfraWT, combined with dominant negative Trp53 (DNp53) and H3.3K27M expression induced fully penetrant brainstem gliomas.

Results
IUE enabled the targeted transfection of brainstem neural stem cells. PDGFB + DNp53 + H3.3K27M induced the rapid development of grade-IV gliomas. PdgfraD842V + DNp53 + H3.3K27M produced slower forming grade-III gliomas. PdgfraWT + DNp53 + H3.3K27M produced high and low-grade gliomas with extended latencies. PDGFB, PdgfraD842V, and PdgfraWT DIPG models display unique histopathological and molecular features found in human DIPGs.

Conclusion
Brainstem targeted in utero electroporation provides a rapid and flexible system to generate diverse DIPG mouse models. Using IUE to investigate mutation and pathohistological heterogeneity of DIPG will provide a valuable tool for future genetic and preclinical studies.
Back Pain in a 23-Year-Old Male With X-Linked Chronic Granulomatous Disease
Authors: Sabo Michelle C , Blain Michela , McCulloch Denise , Glasgow Heather L , Sengupta Dhruba J , Le Thang , Cookson Brad T , Pottinger Paul S , Liles W Conrad , Graham Susan M 
Published: October 2019

Abstract
Patients with chronic granulomatous disease are at increased risk for invasive aspergillosis. Cryptic Aspergillus species are being increasingly recognized as distinct causes of infection in this population. In this study, we describe the first case of Aspergillus udagawae vertebral osteomyelitis in a patient with X-linked chronic granulomatous disease.
5G and intelligence medicine—how the next generation of wireless technology will reconstruct healthcare?
Authors: Li Dong 
Published: October 2019

Abstract
Despite intensive efforts, there are still enormous challenges in provision of healthcare services to the increasing aging population. Recent observations have raised concerns regarding the soaring costs of healthcare, the imbalance of medical resources, inefficient healthcare system administration, and inconvenient medical experiences. However, cutting-edge technologies are being developed to meet these challenges, including, but not limited to, Internet of Things (IoT), big data, artificial intelligence, and 5G wireless transmission technology to improve the patient experience and healthcare service quality, while cutting the total cost attributable to healthcare. This is not an unrealistic fantasy, as these emerging technologies are beginning to impact and reconstruct healthcare in subtle ways. Although the technologies mentioned above are integrated, in this review we take a brief look at cases focusing on the application of 5G wireless transmission technology in healthcare. We also highlight the potential pitfalls to availability of 5G technologies.
Do Decision Aids Benefit Patients with Chronic Musculoskeletal Pain? A Systematic Review
Authors: Bowen Emily , Nayfe Rabih , Milburn Nathaniel , Mayo Helen , Reid M C , Fraenkel Liana , Weiner Debra , Halm Ethan A , Makris Una E 
Published: October 2019

Abstract

Objective
To review the effect of patient decision aids for adults making treatment decisions regarding the management of chronic musculoskeletal pain.

Methods
We performed a systematic review of randomized controlled trials of adults using patient decision aids to make treatment decisions for chronic musculoskeletal pain in the outpatient setting.

Results
Of 477 records screened, 17 met the inclusion criteria. Chronic musculoskeletal pain conditions included osteoarthritis of the hip, knee, or trapeziometacarpal joint and back pain. Thirteen studies evaluated the use of a decision aid for deciding between surgical and nonsurgical management. The remaining four studies evaluated decision aids for nonsurgical treatment options. Outcomes included decision quality, pain, function, and surgery utilization. The effects of decision aids on decision-making outcomes were mixed. Comparing decision aids with usual care, all five studies that examined knowledge scores found improvement in patient knowledge. None of the four studies that evaluated satisfaction with the decision-making process found a difference with use of a decision aid. There was limited and inconsistent data on other decision-related outcomes. Of the eight studies that evaluated surgery utilization, seven found no difference in surgery rates with use of a decision aid. Five studies made comparisons between different types of decision aids, and there was no clearly superior format.

Conclusions
Decision aids may improve patients’ knowledge about treatment options for chronic musculoskeletal pain but largely did not impact other outcomes. Future efforts should focus on improving the effectiveness of decision aids and incorporating nonpharmacologic and nonsurgical management options.
Changes in tobacco use patterns and motivation to quit related to the new smoke-free legislation in the Czech Republic
Authors: Kulhánek Adam , Lukavská Kateřina , Švancarová Iveta , Fidesová Hana , Gabrhelík Roman 
Published: October 2019

ABSTRACT

Background
Smoke-free policy belongs to key public health instruments to promote health in populations. In 2017, new comprehensive smoke-free law prohibiting smoking in indoor public places was implemented. We aimed to measure changes in tobacco smoking patterns and changes in motivation to quit in adult smokers prior to and after the new smoke-free legislation came into force.

Methods
We conducted a prospective cohort study prior to and post the implementation of Act No. 65/2017 Coll. Self-reported questionnaires were administered to 131 adult smokers by trained nurses in general practitioner offices in Prague. We analysed changes in cigarette consumption per day; ratio of cigarettes smoked in pub, street, work and home; and motivation to quit using regression modelling.

Results
We found a statistically significant decrease in the daily consumption of cigarettes (an average of 1.7 cigarettes per day, P &lt; 0.001, d = 0.34). Smoking in indoor public spaces decreased to almost zero, while tobacco consumption in outdoor public spaces (such as streets and squares) increased by nearly 20%. We observed statistically significant increase of motivation to quit smoking (P = 0.021, d = 0.21).

Conclusion
The study brings valuable indication of the desired public health impact related to key legislative change in the Czech Republic.
Epidemiological and clinical characteristics of patients with malaria admitted to a hospital in Mérida, Venezuela
Authors: Gabaldón-Figueira Juan C , Salmen Siham , Silva Nubia , Mancilla Betania , Vielma Silvana 
Published: October 2019

Abstract

Background
Malaria is expanding rapidly across Venezuela, spreading outwards from traditional high transmission regions in the southeast of the country, but the lack of official data make it impossible to understand the reasons for this expansion and to estimate its real magnitude. This study aims to evaluate the epidemiological characteristics driving the re-emergence of malaria in Mérida, a state in the west of Venezuela, where no cases have been reported since 2003, and also to study the clinical presentation of the disease in patients presenting with malaria.

Methods
Thirty-three patients who presented with anemia and fever and with a microscopic diagnosis of malaria were examined and interviewed. Data were collected in standardized forms and analyzed. One-way analysis of variance was used to study differences among patients infected with different parasites.

Results
Twenty-two patients were from the Zulia state and eleven were from the Mérida state, mainly from the lowlands south of Lake Maracaibo. Six of these patients traveled to the Bolívar state between 2017 and 2019. Thirteen patients presented with the WHO criteria for severe malaria.
Conclusions:
Domestic migration to the southeast of Venezuela may have played an important role in the expansion of malaria in previously existing endemic areas of transmission and also in the increase in the number of cases of severe malaria.
Introgression obscures lineage boundaries and phylogeographic history in the western banded gecko, Coleonyx variegatus (Squamata: Eublepharidae)
Authors: Leavitt Dean H , Hollingsworth Bradford D , Fisher Robert N , Reeder Tod W 
Published: October 2019

AbstractThe geomorphological formation of the Baja California peninsula and the Gulf of California is a principal driver of diversification for the reptiles of North America’s warm deserts. The western banded gecko, Coleonyx variegatus, is distributed throughout the Mojave, Sonoran and Peninsular deserts. In this study we use multilocus sequence data to address deep phylogeographic structure within C. variegatus. Analyses of mtDNA data recover six divergent clades throughout the range of C. variegatus. Topology of the mtDNA gene tree suggests separate origins of peninsular populations with an older lineage in the south and a younger one in the north. In contrast, analyses of multilocus nuclear data provide support for four lineages, corresponding to the subspecies C. v. abbotti, C. v. peninsularis, C. v. sonoriensis and C. v. variegatus. Phylogenetic analyses of the nuclear data recover C. v. abbotti and C. v. peninsularis as a clade, indicating a single origin of the peninsular populations. Discordance between the nuclear and mtDNA data is largely the result of repeated episodes of mtDNA introgression that have obscured both lineage boundaries and biogeographic history. Dating analyses of the combined nuclear and mtDNA data suggest that the peninsular clade diverged from the continental group in the Late Miocene.
Pulmonary rehabilitation: promising nonpharmacological approach for treating asthma?
Authors: Zampogna Elisabetta , Spanevello Antonio , Visca Dina 
Published: October 2019

Purpose of review
Asthma is a heterogeneous disease, usually characterized by chronic airway inflammation with a history of respiratory symptoms that vary over time and in intensity, together with variable expiratory airflow limitation. The goal of asthma treatment is to reach symptoms control, reduction in future risk and improvement in quality of life (QoL). Guideline-based pharmacologic therapies and the effect of inhaled steroids and bronchodilators have been widely studied over the past decades. We provide an overview of the available evidence on pulmonary rehabilitation as a nonpharmacologic therapy in asthmatic patients.

Recent findings
Recently, some studies have highlighted the promising role of nonpharmacologic therapies in asthma, such as pulmonary rehabilitation demonstrating that a pulmonary rehabilitation programme consisting of exercise training, breathing retraining, educational and psychological support, improve exercise capacity, asthma control and QoL and reduce dyspnea, anxiety, depression and bronchial inflammation at any step of the disease.

Summary
Pulmonary rehabilitation shows positive results on exercise tolerance, respiratory symptoms and QoL in asthmatic patients at any steps of the diseases. However, additional information is required to better characterize rehabilitation programmes in order to improve clinical care in asthma.
Does Intramedullary Nail Fixation of the Tibia Pose the Same Risk of Pulmonary Complications as Intramedullary Nail Fixation of the Femur? A Propensity Score–Matched Analysis
Authors: Wheatley Benjamin M. , O'Hara Nathan N. , Coale Max , O'Toole Robert V. 
Published: October 2019

Objectives:
To compare duration of mechanical ventilation and pulmonary outcomes in patients treated with intramedullary nail (IMN) fixation of the tibia versus the femur.

Design:
Retrospective cohort study.

Setting:
Level I trauma center.

Patients:
One thousand thirty patients were categorized based on treatment: those treated with IMN of the tibia (n = 515) and those treated with IMN of the femur (n = 515).

Intervention:
IMN fixation of tibial and femoral fractures.

Outcome Measurements:
The primary outcome was duration of mechanical ventilation. Secondary outcomes included length of intensive care unit (ICU) stay and risk of tracheostomy, pulmonary embolism (PE), acute respiratory distress syndrome (ARDS), and mortality.

Results:
In an unadjusted analysis, femoral fractures were associated with increase in ventilator days (mean difference, 1.4; P < 0.001), ICU days (mean difference, 1.8; P < 0.001), and odds of tracheostomy (odds ratio, 1.7; P < 0.01). No difference was shown in likelihood of PE, ARDS, or mortality (P > 0.2). Propensity score–matched estimates showed no differences in any measured outcomes (P > 0.40). In patients with Injury Severity Scores >17, we found no difference in length of ventilator or ICU days or likelihood of tracheostomy, PE, ARDS, or mortality in the unadjusted (P > 0.2) or propensity score–matched estimates (P > 0.3).

Conclusions:
These findings suggest that IMN fixation of the tibia is associated with duration of mechanical ventilation and risk of poor pulmonary outcomes similar to those of femoral nailing, after adjustment for baseline characteristics.

Level of Evidence:
Therapeutic Level III. See Instructions for Authors for a complete description of levels of evidence.
Comparison of Automated Sepsis Identification Methods and Electronic Health Record–based Sepsis Phenotyping: Improving Case Identification Accuracy by Accounting for Confounding Comorbid Conditions
Authors: Henry Katharine E. , Hager David N. , Osborn Tiffany M. , Wu Albert W. , Saria Suchi 
Published: October 2019

Objective:
To develop and evaluate a novel strategy that automates the retrospective identification of sepsis using electronic health record data.

Design:
Retrospective cohort study of emergency department and in-hospital patient encounters from 2014 to 2018.

Setting:
One community and two academic hospitals in Maryland.

Patients:
All patients 18 years old or older presenting to the emergency department or admitted to any acute inpatient medical or surgical unit including patients discharged from the emergency department.

Interventions:
None.

Measurements and Main Results:
From the electronic health record, 233,252 emergency department and inpatient encounters were identified. Patient data were used to develop and validate electronic health record–based sepsis phenotyping, an adaptation of “the Centers for Disease Control Adult Sepsis Event toolkit” that accounts for comorbid conditions when identifying sepsis patients. The performance of this novel system was then compared with 1) physician case review and 2) three other commonly used strategies using metrics of sensitivity and precision relative to sepsis billing codes, termed “billing code sensitivity” and “billing code predictive value.” Physician review of electronic health record–based sepsis phenotyping identified cases confirmed 79% as having sepsis; 88% were confirmed or had a billing code for sepsis; and 99% were confirmed, had a billing code, or received at least 4 days of antibiotics. At comparable billing code sensitivity (0.91; 95% CI, 0.88–0.93), electronic health record–based sepsis phenotyping had a higher billing code predictive value (0.32; 95% CI, 0.30–0.34) than either the Centers for Medicare and Medicaid Services Sepsis Core Measure (SEP-1) definition or the Sepsis-3 consensus definition (0.12; 95% CI, 0.11–0.13; and 0.07; 95% CI, 0.07–0.08, respectively). When compared with electronic health record–based sepsis phenotyping, Adult Sepsis Event had a lower billing code sensitivity (0.75; 95% CI, 0.72–0.78) and similar billing code predictive value (0.29; 95% CI, 0.26–0.31). Electronic health record–based sepsis phenotyping identified patients with higher in-hospital mortality and nearly one-half as many false-positive cases when compared with SEP-1 and Sepsis-3.

Conclusions:
By accounting for comorbid conditions, electronic health record–based sepsis phenotyping exhibited better performance when compared with other automated definitions of sepsis.
Incidence and Outcomes of Acute Laryngeal Injury After Prolonged Mechanical Ventilation*
Authors: Shinn Justin R. , Kimura Kyle S. , Campbell Benjamin R. , Sun Lowery Anne , Wootten Christopher T. , Garrett C. Gaelyn , Francis David O. , Hillel Alexander T. , Du Liping , Casey Jonathan D. , Ely E. Wesley , Gelbard Alexander 
Published: October 2019

Objectives:
Upper airway injury is a recognized complication of prolonged endotracheal intubation, yet little attention has been paid to the consequences of laryngeal injury and functional impact. The purpose of our study was to prospectively define the incidence of acute laryngeal injury and investigate the impact of injury on breathing and voice outcomes.

Design:
Prospective cohort study.

Setting:
Tertiary referral critical care center.

Patients:
Consecutive adult patients intubated greater than 12 hours in the medical ICU from August 2017 to May 2018 who underwent laryngoscopy within 36 hours of extubation.

Interventions:
Laryngoscopy following endotracheal intubation.

Measurements and Main Results:
One hundred consecutive patients (62% male; median age, 58.5 yr) underwent endoscopic examination after extubation. Acute laryngeal injury (i.e., mucosal ulceration or granulation tissue in the larynx) was present in 57 patients (57%). Patients with laryngeal injury had significantly worse patient-reported breathing (Clinical Chronic Obstructive Pulmonary Disease Questionnaire: median, 1.05; interquartile range, 0.48–2.10) and vocal symptoms (Voice Handicap Index-10: median, 2; interquartile range, 0–6) compared with patients without injury (Clinical Chronic Obstructive Pulmonary Disease Questionnaire: median, 0.20; interquartile range, 0–0.80; p < 0.001; and Voice Handicap Index-10: median, 0; interquartile range, 0–1; p = 0.005). Multivariable logistic regression independently associated diabetes, body habitus, and endotracheal tube size greater than 7.0 with the development of laryngeal injury.

Conclusions:
Acute laryngeal injury occurs in more than half of patients who receive mechanical ventilation and is associated with significantly worse breathing and voicing 10 weeks after extubation. An endotracheal tube greater than size 7.0, diabetes, and larger body habitus may predispose to injury. Our results suggest that acute laryngeal injury impacts functional recovery from critical illness.
Leadership Gender Disparity Within Research-Intensive Medical Schools: A Transcontinental Thematic Analysis
Authors: Abdellatif Waleed , Ding Jeffrey , Jalal Sabeena , Chopra Sanjiv , Butler Javed , Ali Ismail Tawakol , Shah Samad , Khosa Faisal 
Published: October 2019

Background:The underrepresentation of women in senior leadership positions of academic medicine continues to prevail despite the ongoing efforts to advance gender parity. Our aim was to compare the extent of gender imbalance in the leadership of the top 100 medical schools and to critically analyze the contributing factors through a comprehensive theoretical framework.Methods:We adopted the theoretical framework of the Systems and Career Influences Model. The leadership was classified into four tiers of leadership hierarchy. Variables of interest included gender,h-index, number of documents published, total number of citations, and number of years in active research. A total of 2448 (77.59%) men and 707 (22.41%) women met the inclusion criteria.Results:Male majority was found in all regions with a significant difference in all levels of leadership (chi square = 91.66;Pvalue = .001). Women had a lower meanh-index across all positions in all regions, and when we adjusted for number of years invested, M Index for women was still significantly lower than men (T test = 6.52;Pvalue = .02).Discussion:Organizational and individual influences are transcontinental within the top 100 medical school leadership hierarchy. Those factors were critically assessed through in-depth analysis of the Systems and Career Influences Model. Evidence-driven actionable recommendations to remedy those influences were outlined.
Neurotized Diagonal Profunda Artery Perforator Flaps for Breast Reconstruction
Authors: Dayan Joseph H. , Allen Robert J. 
Published: October 2019

Summary:
Although the deep inferior epigastric artery perforator flap remains the gold standard for autologous breast reconstruction, many patients are not candidates for this surgery. A variety of thigh-based flaps have been used including the diagonal upper gracilis (DUG) flap, vertical upper gracilis flap, profunda artery perforator (PAP) flap, and lateral thigh perforator flap. However, each of these techniques has a unique set of benefits and drawbacks in terms of wound healing, donor site morbidity, and potential for lymphedema. We describe the first report of a sensate diagonal PAP flap for breast reconstruction: combining the benefits of the DUG (wider skin paddle and reliable wound healing) with the benefits of the PAP (muscle-sparing technique and greater distance from the lymphatic collectors). This was the authors' sentinel case in a woman with paraplegia and chronic leg swelling. Preoperative imaging, markings, and technical details are presented along with postoperative results. In the appropriately selected patient, this flap offers several advantages: a 2-team approach to reconstruction, ample tissue for breast reconstruction, potential neurotization for breast sensibility, wound closure in resting skin tension lines, and avoidance of the lymphatic drainage to the lower extremity. The diagonal PAP flap provides a muscle-sparing alternative to the DUG flap while minimizing the risk of lymphedema. Future studies are needed to assess the donor site morbidity of this flap; however, this case proves the safety and reliability of the diagonal PAP flap in our breast reconstruction population.