bluuebunny/crossref_metadata_2025_split huggingface dataset:
Vitamin D deficiency in a European inflammatory bowel disease inception cohort: an Epi-IBD study
Authors: Chetcuti Zammit Stefania , Ellul Pierre , Girardin Giulia , Valpiani Daniela , Nielsen Kári R. , Olsen Jóngerð , Goldis Adrian , Lazar Daniela , Shonová Olga , Nováková Marie , Sebastian Shaji , Whitehead Emma , Carmona Amalia , Martinez-Cadilla Jesus , Dahlerup Jens F. , Kievit Adriana L.H. , Thorsgaard Niels , Katsanos Konstantinos H. , Christodoulou Dimitrios K. , Magro Fernando , Salupere Riina , Pedersen Natalia , Kjeldsen Jens , Carlsen Katrine , Ioannis Kaimaklioti , Bergemalm Daniel , Halfvarson Jonas , Duricova Dana , Bortlik Martin , Collin Pekka , Oksanen Pia , Kiudelis Gediminas , Kupcinskas Limas , Kudsk Karen , Andersen Vibeke , O’Morain Colm , Bailey Yvonne , Doron Schwartz , Shmuel Odes , Almer Sven , Arebi Naila , Misra Ravi , Čuković-Čavka Silvija , Brinar Marko , Munkholm Pia , Vegh Zsuzsanna , Burisch Johan 
Published: August 2018

BackgroundSerum vitamin D level is commonly low in patients with inflammatory bowel disease (IBD). Although there is a growing body of evidence that links low vitamin D level to certain aspects of IBD such as disease activity and quality of life, data on its prevalence and how it varies across disease phenotype, smoking status and treatment groups are still missing.Materials and methodsPatients diagnosed with IBD between 2010 and 2011 were recruited. Demographic data and serum vitamin D levels were collected. Variance of vitamin D level was then assessed across different treatment groups, disease phenotype, disease activity and quality of life scores.ResultsA total of 238 (55.9% male) patients were included. Overall, 79% of the patients had either insufficient or deficient levels of vitamin D at diagnosis. Patients needing corticosteroid treatment at 1 year had significantly lower vitamin D levels at diagnosis (median 36.0 nmol/l) (P=0.035). Harvey–Bradshaw Index (P=0.0001) and Simple Clinical Colitis Activity Index scores (P=0.0001) were significantly lower in patients with higher vitamin D level. Serum vitamin D level correlated significantly with SIBQ score (P=0.0001) and with multiple components of SF12. Smokers at diagnosis had the lowest vitamin D levels (vitamin D: 34 nmol/l;P=0.053).ConclusionThis study demonstrates the high prevalence of low vitamin D levels in treatment-naive European IBD populations. Furthermore, it demonstrates the presence of low vitamin D levels in patients with IBD who smoke.
Effect of an Evidence-based Inpatient Tobacco Dependence Treatment Service on 1-Year Postdischarge Health Care Costs
Authors: Cartmell Kathleen B. , Dismuke Clara E. , Dooley Mary , Mueller Martina , Nahhas Georges J. , Warren Graham W. , Fallis Peter , Cummings K. Michael 
Published: August 2018

Background:
In 2014, the Medical University of South Carolina (MUSC) implemented a Tobacco Dependence Treatment Service (TDTS) consistent with the Joint Commission (JC) standards recommending that hospitals screen patients for smoking, provide cessation support, and follow-up contact for relapse prevention within 1 month of discharge. We previously demonstrated that patients exposed to the MUSC TDTS were approximately half as likely to be smoking one month after discharge and 23% less likely to have a 30-day hospital readmission. This paper examines whether exposure to the TDTS influenced downstream health care charges 12 months after patients were discharged from the hospital.

Methods:
Data from MUSC’s electronic health records, the TDTS, and statewide health care utilization datasets (eg, hospitalization, emergency department, and ambulatory surgery visits) were linked to assess how exposure to the MUSC TDTS impacted health care charges. Total health care charges were compared for patients with and without TDTS exposure. To reduce potential TDTS exposure selection bias, propensity score weighting was used to balance baseline characteristics between groups. The cost of delivering the MUSC TDTS intervention was calculated, along with cost per smoker.

Results:
The overall adjusted mean health care charges for smokers exposed to the TDTS were $7299 lower than for those who did not receive TDTS services (P=0.047). The TDTS cost per smoker was modest by comparison at $34.21 per smoker eligible for the service.

Discussion:
Results suggest that implementation of a TDTS consistent with JC standards for smoking cessation can be affordably implemented and yield substantial health care savings that would benefit patients, hospitals, and insurers.
Top Citations of Pediatric Emergency Medicine Publications in the Emergency Medicine Literature
Authors: Waseem Muhammad , Rodriguez Javier , Josephson Elaine 
Published: August 2018

ObjectivesThe goal of this study was to identify and analyze the 100 most frequently cited journal articles pertaining to the field of pediatric emergency medicine (PEM) and published in emergency medicine (EM) peer-reviewed literature.MethodsThe 3 databases, Scopus Library, Google Scholar, and Web of Science, were subjected to a search by topic, keyword, and publication journal to identify the 100 most frequently cited articles addressing PEM issues in the EM literature. Our search included articles published beginning in 1983 and ending in 2016. Median citation frequency, study topics within the specialty of PEM, years of publication, and countries of origin were each compiled and analyzed. Mean citation frequencies were used to rank the articles, which accounted for differences in the results among the 3 databases. Once organized into a list of the 100 most often cited articles in PEM, those with an outcome of the same mean citation frequency were ranked in alphabetical order, according to the initial letter of last name of the first author of the publication.ResultsA ranking was created of the 100 most frequently cited articles in pediatric emergency medicine by the mean number of citations. Citation counts ranged from a high of 249 to a low of 71, with a median frequency of 101. The United States had 92 articles on the list, whereas the remainder was comprised of the following countries: Australia (3), Canada (3), Germany (1), and Spain (1). The most common topic areas (and their numbers) noted were related to resuscitation (23) and anesthesia (22). The most frequently cited 100 articles were all published between the years 1983 and 2010. Top publication years (and number of articles) included 2000 (11), 2002 (8), and 2003 (8). The years ranging from 1993 to 2005 covered 69% of published articles. Journals of publications (and article counts) wereAnnals of Emergency Medicine(69),Pediatric Emergency Care(15),Academic Emergency Medicine(12), andResuscitation(4).ConclusionsThis analysis provides a review of citation frequency of top-cited PEM articles published in EM journals. This determines the influence of these PEM publications on the EM specialty. The importance of education on resuscitation and anesthesia topics in PEM was evident. Most of the articles were published more than 10 to 15 years ago, indicating that they could be considered landmarks in the subspecialty of PEM. This signifies their importance to other authors in this field, who chose to cite them as having created a significant impact on their own publications.
Invasive Bacterial Infections in Infants Younger Than 60 Days With Skin and Soft Tissue Infections
Authors: Foradori Dana M. , Lopez Michelle A. , Hall Matt , Cruz Andrea T. , Markham Jessica L. , Colvin Jeffrey D. , Nead Jennifer A. , Queen Mary Ann , Raphael Jean L. , Wallace Sowdhamini S. 
Published: August 2018

Objective
The objective of this study was to describe the frequency of invasive bacterial infections (IBIs) in young infants with skin and soft tissue infections (SSTIs) and the impact of IBI evaluation on disposition, length of stay (LOS), and cost.

Methods
This retrospective (2009–2014) cohort study used data from 35 children's hospitals in the Pediatric Health Information System. We included infants younger than 60 days who presented to an emergency department (ED) with SSTI. Invasive bacterial infection was defined as bacteremia/sepsis, bone/joint infection, or bacterial meningitis. Readmission and return ED visits within 30 days were evaluated to identify missed IBIs for infants.

Results
A total of 2734 infants were included (median age, 33 days; interquartile range [IQR], 21–44); 62% were hospitalized. Invasive bacterial infection was identified in 2%: bacteremia (1.8%), osteomyelitis (0.1%), and bacterial meningitis (0.1%). Hospitalization occurred in 78% of infants with blood cultures, 95% with cerebrospinal fluid cultures, and 23% without cultures. Median hospitalization LOS was 2 days (IQR, 1–3). Median cost was US $4943 for infants with cerebrospinal fluid cultures (IQR, US $3475–6780) compared with US $419 (IQR, US $215–1149) for infants without IBI evaluations (P < 0.001). Five infants (0.2%) returned to the ED within 30 days with new IBI diagnoses (4 bacteremia, 1 meningitis).

Conclusions
Invasive bacterial infection occurs infrequently in infants younger than 60 days who present to children's hospital EDs with SSTI. Bacteremia is the most common IBI. More extensive evaluation for IBI is associated with increased rate of admission, LOS, and cost. Further studies are needed to evaluate the safety of a limited IBI evaluation in young infants with SSTI.
Epidemiology of and Risk Factors for BK Polyomavirus Replication and Nephropathy in Pediatric Renal Transplant Recipients: An International CERTAIN Registry Study
Authors: Höcker Britta , Schneble Lukas , Murer Luisa , Carraro Andrea , Pape Lars , Kranz Birgitta , Oh Jun , Zirngibl Matthias , Dello Strologo Luca , Büscher Anja , Weber Lutz T. , Awan Atif , Pohl Martin , Bald Martin , Printza Nikoleta , Rusai Krisztina , Peruzzi Licia , Topaloglu Rezan , Fichtner Alexander , Krupka Kai , Köster Lennart , Bruckner Thomas , Schnitzler Paul , Hirsch Hans H. , Tönshoff Burkhard 
Published: August 2018

Background.
BK polyomavirus-associated nephropathy (BKPyVAN) constitutes a serious cause of kidney allograft failure, but large-scale data in pediatric renal transplant recipients and a comprehensive analysis of specific risk factors are lacking.

Methods.
We analyzed the data of 313 patients in the Cooperative European Pediatric Renal Transplant Initiative Registry, with an observation period of 3.3 years (range, 1–5). The net state of immunosuppressive therapy was assessed by the modified Vasudev score.

Results.
Presumptive BKPyVAN (defined as sustained [>3 wk] high-level BK viremia >104 copies/mL) within 5 years posttransplant occurred in 49 (15.8%) of 311 patients, and biopsy-proven BKPyVAN in 14 (4.5%) of 313. BKPyV viremia was observed in 115 (36.7%) of 311 patients, of whom 11 (9.6%) of 115 developed viremia late, that is, after the second year posttransplant. In 6 (12.5%) of 48 patients with high-level viremia and in 3 (21.4%) of 14 with BKPyVAN, this respective event occurred late. According to multivariable analysis, BKPyV viremia and/or BKPyVAN were associated not only with a higher net state of immunosuppression (odds ratio [OR], 1.3; P < 0.01) and with tacrolimus-based versus ciclosporin-based immunosuppression (OR, 3.6; P < 0.01) but also with younger recipient age (OR, 1.1 per y younger; P < 0.001) and obstructive uropathy (OR, 12.4; P < 0.01) as primary renal disease.

Conclusions.
Uncontrolled BKPyV replication affects a significant proportion of pediatric renal transplant recipients and is associated with unique features of epidemiology and risk factors, such as young recipient age, obstructive uropathy, and overall intensity of immunosuppressive therapy. BKPyV surveillance should be considered beyond 2 years posttransplant in pediatric patients at higher risk.
A Gene Regulatory Model of Cortical Neurogenesis
Authors: Pfister Sabina S. , Hauri Andreas , Zubler Frederic , Michel Gabriela , Kennedy Henry , Dehay Colette , Douglas Rodney J. 
Published: August 2018

AbstractSparse data describing mouse cortical neurogenesis were used to derive a model gene regulatory network (GRN) that is then able to control the quantitative cellular dynamics of the observed neurogenesis. Derivation of the network begins by estimating from the biological data a set of cell states and transition probabilities necessary to explain neurogenesis. We show that the stochastic transition between states can be implemented by the dynamics of a GRN comprising only 36 abstract genes. Finally, we demonstrate using detailed physical simulations of cell mitosis, and differentiation that this GRN is able to steer a population of neuroepithelial precursors through mitotic expansion and differentiation to form the quantitatively correct complex multicellular architectures of mouse cortical areas 3 and 6. We find that the same GRN is able to generate both areas though modulation of only one gene, suggesting that arealization of the cortical sheet may require only simple improvisations on a fundamental gene network. We conclude that even sparse phenotypic and cell lineage data can be used to infer fundamental properties of neurogenesis and its organization.1.HighlightsEstimation of the cell states and transition probabilities of neurogenesis from experimental data.Design of an abstract gene regulatory network (GRN) whose dynamics implement cell states and their stochastic transitions.Detailed simulation of GRN-guided neurogenesis for mouse cortical areas 3 and 6.Different dynamics of neurogenesis of distinct cortical areas arise through modulation of only a single gene.2.In briefPfister et al. show how sparse phenotypic and cell lineage data can be used to infer a small abstract gene regulatory network (GRN), which, when inserted into model precursor cells, is able to control in a distributed manner the quantitative cellular dynamics of neocortical neurogenesis.
Response Inhibition in Adolescents is Moderated by Brain Connectivity and Social Network Structure
Authors: Tompson Steven H. , Falk Emily B. , O’Donnell Matthew Brook , Cascio Christopher N. , Bayer Joseph B. , Vettel Jean M. , Bassett Danielle S. 
Published: August 2018

AbstractSelf-control is vital for a wide range of outcomes across our lifespan, yet the developmental trajectory of its core components during adolescence remains elusive. Many adolescents can successfully regulate their behavior even when they do not show strong activation in brain regions typically recruited during self-control in adults. Thus, adolescents may rely on other neural and cognitive resources to compensate, including daily experiences navigating and managing complex social relationships that likely bolster self-control processes. Here, we tested whether activity and connectivity in brain systems associated with social cognition (i.e., self-processing and mentalizing) facilitated successful self-control. We measured brain activity using fMRI as 62 adolescents completed a Go/No-Go response inhibition task. Recruitment of social brain systems, especially the self-processing system, was associated with better response inhibition in adolescents. Interestingly, the reliance on the self-processing system was stronger in adolescents with weaker activation in the canonical response inhibition system, suggesting a compensatory role for social brain systems during adolescent development. Furthermore, we examined the importance of social context by computing the size, number of communities, and modularity of our participants’ real-life social network. We found that adolescents with more friends and more communities in their social networks demonstrated a stronger relationship between response inhibition and recruitment of social brain systems. Collectively, our results identify the importance of social context and its moderating role on the relationship between brain activity and behavior. Furthermore, our results indicate a critical role for social brain systems during the developmental trajectory of self-control throughout adolescence.Significance StatementWe employed a network neuroscience approach to investigate the role of social context and social brain systems in facilitating self-control in adolescents. We found that recruitment of social brain systems was associated with better response inhibition in adolescents, especially for adolescents with weaker activation in the response inhibition system. Moreover, adolescents with more friends and communities in their social networks showed stronger relationships between response inhibition and recruitment of social brain systems. Our results advance understanding of how brain systems facilitate self-control in adolescents, and how these brain responses are associated with features of an adolescent’s real-life social network. Bringing together findings related to brain networks and social networks provides key insights into how biology and environment mutually influence development.
Glenohumeral Injection Using Anatomic Landmark Versus Sonographic Needle Guidance
Authors: Moore Timothy S. , Paffett Cole L. , Sibbitt Wilmer L. , Hayward William A. , Gibb James I. , Kettwich Selma D. , Fields Roderick A. , Emil N. Suzanne , Fangtham Monthida , Bankhurst Arthur D 
Published: August 2018

ABSTRACTObjectiveWe hypothesized ultrasound (US) guidance improves outcomes of corticosteroid injection of the painful shoulder.Methods30 patients with symptomatic shoulders due to osteoarthritis were randomized to glenohumeral injection with 3 milliliters of 1% lidocaine and 60 mg of triamcinolone acetonide using the anterior approach with 1) conventional anatomic landmark palpation-guidance or 2) US-guidance. Injection pain (visual analogue pain scale (VAS)), pain at outcome (2 weeks and 6 months), therapeutic duration, time-to-next-injection, and costs were determined.ResultsInjection pain was less with US (VAS: 0.3±0.6 cm) vs. landmark-guidance (VAS: 1.4±2.4 cm, 95% CI of difference: 0.5<1.1<1.7, p=0.05). Pain scores were similar at 2 weeks: US: 2.2±2.4 cm; Landmark: 1.8±2.7 cm, 95% CI of difference: −2.2<−0.4<1.4, p=0.66 and 6 months: US: 5.8±2.8 cm; Landmark: 6.4±2.9 cm, 95% CI of difference: −0.4<0.6< 1.1, p =0.71. Therapeutic duration (US: 3.9±1.5 months; Landmark: 3.0±1.2 months, 95% CI of difference: − 1.4 <−0.9<−0.4, p=0.045) and time-to-next-injection (US: 8.1±3.5 months; Landmark: 5.7±2.9 months, 95% CI of difference: −3.6<−2.4<−1.3, p=0.025) were longer, and fewer injections per year (29% less) were required: US: 1.5±0.2 injections/year; Landmark: 2.1±0.2 injections/year (p<0.037; 95% CI of difference −0.9<−0.6<−0.3). However, cost/patient/year was modestly greater with US (US: $318±89, Landmark: $301±67; p=0.28).ConclusionAnatomic landmark guidance in the short-term is equally effective as US for injection of the osteoarthritic shoulder and modestly less costly, however, US may reduce the need for repetitive injections by prolonging the therapeutic effect and thus time to next injection.IRB StatementThis project was in compliance with the Helsinki Declaration, was approved by the Institutional Review Board (IRB) as ultrasound subset of a syringe safety trial (Human Research Review Committee approval 04-347), and was registered at ClinicalTrials.gov (Clinical Trial Identifier NCT00651625). The subjects gave informed consent to participate prior to all studies and interventions. Patient confidentiality was protected according to the U.S. Health Insurance Portability and Accountability Act (HIPAA) and all data was de-identified.
Probabilistic modeling of personalized drug combinations from integrated chemical screen and molecular data in sarcoma
Authors: Berlow Noah E. , Rikhi Rikhi , Geltzeiler Mathew N. , Abraham Jinu , Svalina Matthew N. , Davis Lara E. , Wise Erin , Mancini Maria , Noujaim Jonathan , Mansoor Atiya , Quist Michael J. , Matlock Kevin L. , Goros Martin W. , Hernandez Brian S. , Doung Yee C. , Thway Khin , Tsukahara Tomohide , Nishio Jun , Huang Elaine C. Huang , Airhart Susan , Bult Carol J. , Gandour-Edwards Regina , Maki Robert G. , Jones Robin L. , Michalek Joel E. , Milovancev Milan , Ghosh Souparno , Pal Ranadip , Keller Charles 
Published: August 2018

ABSTRACTCancer patients with advanced disease exhaust available clinical regimens and lack actionable genomic medicine results, leaving a large patient population without effective treatments options when their disease inevitably progresses. To address the unmet clinical need for evidence-based therapy assignment when standard clinical approaches have failed, we have developed a probabilistic computational modeling approach which integrates sequencing data with functional assay data to develop patient-specific combination cancer treatments. This computational modeling approach addresses three major challenges in personalized cancer therapy, which we validate across multiple species via computationally-designed personalized synergistic drug combination predictions, identification of unifying therapeutic targets to overcome intra-tumor heterogeneity, and mitigation of cancer cell resistance and rewiring mechanisms. These proof-of-concept studies support the use of an integrative functional approach to personalized combination therapy prediction for the population of high-risk cancer patients lacking viable clinical options and without actionable DNA sequencing-based therapy.
Systems therapeutics analyses identify genomic signatures defining responsiveness to allopurinol and combination therapy for lung cancer
Authors: Tavassoly Iman , Hu Yuan , Zhao Shan , Mariottini Chiara , Boran Aislyn , Chen Yibang , Li Lisa , Tolentino Rosa E. , Jayaraman Gomathi , Goldfarb Joseph , Gallo James , Iyengar Ravi 
Published: August 2018

AbstractThe ability to predict responsiveness to drugs in individual patients is limited. We hypothesized that integrating molecular information from databases would yield predictions that could be experimentally tested to develop genomic signatures for sensitivity or resistance to specific drugs. We analyzed TCGA data for lung adenocarcinoma (LUAD) patients and identified a subset where xanthine dehydrogenase expression correlated with decreased survival. We tested allopurinol, a FDA approved drug that inhibits xanthine dehydrogenase on a library of human Non Small Cell Lung Cancer (NSCLC) cell lines from CCLE and identified sensitive and resistant cell lines. We utilized the gene expression profiles of these cell lines to identify six-gene signatures for allopurinol sensitive and resistant cell lines. Network building and analyses identified JAK2 as an additional target in allopurinol-resistant lines. Treatment of resistant cell lines with allopurinol and CEP-33779 (a JAK2 inhibitor) resulted in cell death. The effectiveness of allopurinol alone or allopurinol and CEP-33779 were verified in vivo using tumor formation in NCR-nude mice. We utilized the six-gene signatures to predict five additional allopurinolsensitive NSCLC lines, and four allopurinol-resistant lines susceptible to combination therapy. We found that drug treatment of all cell lines yielded responses as predicted by the genomic signatures. We searched the library of patient derived NSCLC tumors from Jackson Laboratory to identify tumors that would be predicted to be sensitive or resistant to allopurinol treatment. Both patient derived tumors predicted to be allopurinol sensitive showed the predicted sensitivity, and the predicted resistant tumors were sensitive to combination therapy. These data indicate that we can use integrated molecular information from cancer databases to predict drug responsiveness in individual patients and thus enable precision medicine.