bluuebunny/crossref_metadata_2025_split huggingface dataset:
QuantumClone: clonal assessment of functional mutations in cancer based on a genotype-aware method for clonal reconstruction
Authors: Deveau Paul , Colmet Daage Leo , Oldridge Derek , Bernard Virginie , Bellini Angela , Chicard Mathieu , Clement Nathalie , Lapouble Eve , Combaret Valerie , Boland Anne , Meyer Vincent , Deleuze Jean-Francois , Janoueix-Lerosey Isabelle , Barillot Emmanuel , Delattre Olivier , Maris John M , Schleiermacher Gudrun , Boeva Valentina 
Published: January 2018

Abstract

Motivation
In cancer, clonal evolution is assessed based on information coming from single nucleotide variants and copy number alterations. Nonetheless, existing methods often fail to accurately combine information from both sources to truthfully reconstruct clonal populations in a given tumor sample or in a set of tumor samples coming from the same patient. Moreover, previously published methods detect clones from a single set of variants. As a result, compromises have to be done between stringent variant filtering [reducing dispersion in variant allele frequency estimates (VAFs)] and using all biologically relevant variants.

Results
We present a framework for defining cancer clones using most reliable variants of high depth of coverage and assigning functional mutations to the detected clones. The key element of our framework is QuantumClone, a method for variant clustering into clones based on VAFs, genotypes of corresponding regions and information about tumor purity. We validated QuantumClone and our framework on simulated data. We then applied our framework to whole genome sequencing data for 19 neuroblastoma trios each including constitutional, diagnosis and relapse samples. We confirmed an enrichment of damaging variants within such pathways as MAPK (mitogen-activated protein kinases), neuritogenesis, epithelial-mesenchymal transition, cell survival and DNA repair. Most pathways had more damaging variants in the expanding clones compared to shrinking ones, which can be explained by the increased total number of variants between these two populations. Functional mutational rate varied for ancestral clones and clones shrinking or expanding upon treatment, suggesting changes in clone selection mechanisms at different time points of tumor evolution.

Availability and implementation
Source code and binaries of the QuantumClone R package are freely available for download at https://CRAN.R-project.org/package=QuantumClone.

Supplementary information
Supplementary data are available at Bioinformatics online.
Changes in Socioeconomic Differences in Hospital Days With Age: Cumulative Disadvantage, Age-as-Leveler, or Both?
Authors: Hu Yaoyue , Leinonen Taina , Myrskylä Mikko , Martikainen Pekka 
Published: January 2018

Abstract

Objectives
Length of hospital stay is inversely associated with socioeconomic status (SES). It is less clear whether socioeconomic disparities in numbers of hospital days diverge or converge with age.

Method
Longitudinal linked Finnish registry data (1988–2007) from 137,653 men and women aged 50–79 years at the end of 1987 were used. Trajectories of annual total hospital days by education, household income, and occupational class were estimated using negative binomial models.

Results
Men and women with higher education, household income, and occupational class had fewer hospital days in 1988 than those with lower SES. Hospital days increased between 1988 and 2007. For some age groups, higher SES was associated with a faster annual rate of increase, resulting in narrowing rate ratios of hospital days between SES groups (relative differences); the rate ratios remained stable for other groups. Absolute SES differences in numbers of hospital days appeared to diverge with age among those aged 50–69 years at baseline, but converge among those aged 70–79 years at baseline.

Discussion
The hypotheses that socioeconomic disparities in health diverge or converge with age may not be mutually exclusive; we demonstrated convergence/maintenance in relative differences for all age groups, but divergence or convergence in absolute differences depending on age.
Pregnancy-Associated Hypertension and Offspring Cardiometabolic Health
Authors: Rice Madeline Murguia , Landon Mark B. , Varner Michael W. , Casey Brian M. , Reddy Uma M. , Wapner Ronald J. , Rouse Dwight J. , Tita Alan T. N. , Thorp John M. , Chien Edward K. , Saade George , Peaceman Alan M. , Blackwell Sean C. ,   for the Eunice Kennedy Shriver National Institute of Child Health and Human Development (NICHD) Maternal-Fetal Medicine Units (MFMU) Network
Published: January 2018

OBJECTIVE:
To evaluate whether pregnancy-associated hypertension (gestational hypertension and preeclampsia) was associated with the cardiometabolic health of young offspring.

METHODS:
This was a prospective observational follow-up study from 2012 to 2013 of children born to women previously enrolled in a mild gestational diabetes mellitus treatment trial or nongestational diabetes mellitus observational study. At 5–10 years after birth, children were examined and fasting blood samples obtained to determine the following cardiometabolic risk factors: blood pressure (BP), high-density lipoprotein cholesterol, triglycerides, glucose, homeostatic model assessment of insulin resistance, waist circumference, and body mass index (BMI).

RESULTS:
This analysis included 979 children evaluated at a median 7 years of age. Twenty-three (2%) were born preterm from a hypertensive pregnancy, 73 (7%) were born at term from a hypertensive pregnancy, 58 (6%) were born preterm from a normotensive pregnancy, and 825 (84%) were born at term from a normotensive pregnancy (reference group). After adjusting for confounding factors, mean adjusted systolic BP was significantly higher in the children who were born at term to mothers who experienced pregnancy-associated hypertension compared with those born at term to normotensive mothers (systolic BP of 104 mm Hg, 95% CI 101–106 vs systolic BP of 99 mm Hg, 95% CI 99–100, P=.001). No other significant differences were observed.

CONCLUSION:
Pregnancy-associated hypertension in women who deliver at term was associated with higher systolic BP in the offspring, but not with their measures of diastolic BP, BMI, waist circumference, homeostatic model assessment of insulin resistance, glucose, or lipids.

CLINICAL TRIAL REGISTRATION:
ClinicalTrials.gov, NCT00069576.
Risk Factors for the Development of Obstetric Anal Sphincter Injuries in Modern Obstetric Practice
Authors: Ramm Olga , Woo Victoria G. , Hung Yun-Yi , Chen Hsuan-Chih , Ritterman Weintraub Miranda L. 
Published: January 2018

OBJECTIVE:
To characterize the rate of obstetric anal sphincter injuries and identify key risk factors of obstetric anal sphincter injuries, including duration of the second stage of labor.

METHODS:
This retrospective cohort study included all singleton, term, cephalic vaginal deliveries within Kaiser Permanente Northern California between January 2013 and December 2014 (N=22,741). Incidence of obstetric anal sphincter injuries, defined as third- or fourth-degree perineal lacerations, was the primary outcome. Multiple logistic regression models were conducted to identify obstetric anal sphincter injury risk factors and high-risk subpopulations.

RESULTS:
The overall incidence rate of obstetric anal sphincter injuries was 4.9% (3.6% of women who delivered spontaneously vs 24.0% of women who had a vacuum-assisted vaginal delivery, P<.001, CI 18.1–22.6%). In bivariate and multivariate analyses, obstetric anal sphincter injury incidence was higher among women with second stage of labor longer than 2 hours, Asian race, nulliparity, vaginal birth after cesarean delivery, episiotomy, and vacuum delivery. Women with a vacuum-assisted vaginal delivery had four times the odds of obstetric anal sphincter injury (adjusted odds ratio [OR] 4.23, 95% CI 3.59–4.98) and those whose second stage of labor lasted at least 180 minutes vs less than 60 minutes had three times the odds of incurring obstetric anal sphincter injury (adjusted OR 3.20, 95% CI 2.62–3.89).

CONCLUSION:
Vacuum-assisted vaginal delivery conferred the highest odds of obstetric anal sphincter injury followed by prolonged duration of the second stage of labor, particularly among certain subpopulations. Understanding these risk factors and their complex interactions can inform antepartum and intrapartum decision-making with the goal of reducing obstetric anal sphincter injury incidence.
INTRAOPERATIVE AND POSTOPERATIVE COMPLICATIONS IN PHACOVITRECTOMY FOR EPIRETINAL MEMBRANE AND MACULAR HOLE
Authors: Fajgenbaum Mark A. P. , Neffendorf James E. , Wong Roger S. , Laidlaw David A. H. , Williamson Tom H. 
Published: January 2018

Purpose:
The aim of this study was to report the intraoperative and postoperative complications of phacovitrectomy for epiretinal membrane (ERM) and macular hole (MH).

Methods:
This was a retrospective audit of 1,052 phacovitrectomy operations (410 for ERM and 642 for MH) by the same surgical team between 1998 and 2017. Outcome measures included rates of intraoperative anterior segment and posterior segment complications such as posterior capsule rupture and retinal breaks. A subgroup analysis of 189 procedures in which postoperative complications were rigorously recorded was also undertaken.

Results:
The rate of posterior capsule rupture was 2.2%, with no difference between ERM and MH (1.7 vs. 2.5%; P = 0.40). Iatrogenic retinal tears were more common in MH than in ERM surgery (15.6 vs. 6.8%; P < 0.001). The chance of one or more anterior segment or posterior segment intraoperative complications occurring (excluding iatrogenic retinal breaks) was not associated with: indication for surgery, grade of surgeon, gauge of surgery, surgical machine, diabetic status, patient sex, or patient age. Subgroup analysis showed postoperative events as follows: posterior capsular opacification 10.6% (20/189), posterior synechiae 4.2% (8/189), uveitis 2.1% (4/189), angle closure glaucoma 1.6% (3/189), and rhegmatogenous retinal detachment 1.1% (2/189).

Conclusion:
Phacovitrectomy seems to be safe in phakic patients with ERM or MH, performed either by fellows or consultants. It avoids the requirement for repeat surgery and is more cost and resource efficient.
Assuring Quality for Non‐hospital–based Biologic Infusions in Pediatric Inflammatory Bowel Disease
Authors: Barfield Elaine , Sockolow Robbyn , Hoffenberg Edward , Saeed Shehzad , Kim Sandra , Siebold Leah , Picoraro Joseph , Moses Jonathan , Dykes Dana , Grossman Andrew , Wahbeh Ghassan , Park K.T. 
Published: January 2018

ABSTRACTThe primary aim of this Clinical Report by the North American Society for Pediatric Gastroenterology, Hepatology and Nutrition is to provide formal guidance to pediatric gastroenterologists and clinicians, health systems, and insurance payers regarding home‐ and office‐based infusions for biologic therapies in pediatric inflammatory bowel disease. Patients in North America are increasingly denied coverage by payers based on “place of service” codes at hospital‐based infusion units where the treating clinicians primarily provide care. A task force with topic expertise generated 8 best practice recommendations to ensure quality of care for pediatric patients with inflammatory bowel disease receiving non‐hospital–based biologic infusions. Pragmatic considerations discussed in this report include patient safety, pediatric‐trained nurse availability, care coordination, patient‐centeredness, shared liability, administrative support, clinical governance, and costs of care.
Pharmacy Students' Preparedness to Communicate With Mental Health Disorders Patients
Authors: Chow Claudia , Morrissey Hana , Ball Patrick 
Published: January 2018

Abstract
The aim of this project was to explore whether fourth-year pharmacy students in England are prepared to communicate with mental health patients. Mental health problems are rising in the United Kingdom, affecting around one in four people. A questionnaire-based study measured the knowledge about and attitude toward mental health problems. Participants were fourth-year pharmacy students from two west midlands universities. More males than females correctly answered the “attitude towards mental health” questions. However, overall, only 45.5% of students answered the “attitude towards mental health problems” questions correctly. Males demonstrated a better level of knowledge than females, with 33% overall answering 6 or more questions of the 13 knowledge questions correctly. Sixty-five percent of participants scored under 50%. The highest total score was 81%, and the lowest was 19%, three people did not answer any questions. In conclusion, a gap in knowledge was identified within the fourth-year pharmacy student cohort, and more intervention will be required to improve knowledge and attitudes such as the Mental Health First Aid courses.
Pediatric Electric Bicycle Injuries
Authors: Hermon Karin , Capua Tali , Glatstein Miguel , Scolnik Dennis , Tavor Oren , Rimon Ayelet 
Published: January 2018

Background
Electric bicycles (E-bikes) are one of a wide range of light electric vehicles that provide convenient local transportation and attractive recreational opportunities. The aim of this study was to report E-bike–related injuries in children presenting to a trauma center.

Methods
Retrospective observational study, from December 2014 to November 2015, which included all pediatrics patients admitted to the emergency department with an injury related to E-bike use, was performed.

Results
A total of 97 E-bike injuries presented to the emergency department during this period. Mean age of E-bikers was 13.7 years (range, 7.5–16 years). Injuries to the head and the upper and the lower extremities were the most common. Thirteen patients (15%) were admitted, and 4 underwent surgery.

Conclusions
Children are mainly injured as riders when using E-bikes. There is a need for regulation regarding the use of E-bikes to enhance the safety of both bikers and other road and pavement users.
Chair Lift Falls and Injuries in Children
Authors: Glissmeyer Eric W. , Metzger Ryan R. , Bolte Robert 
Published: January 2018

Objective
The objective of this study was to compare demographic injury and treatment characteristics of hospitalized pediatric cases of falls from chair lifts to cases of other ski and snowboarding injuries and identify potential interventions for preventing falls from chair lifts.

Methods
Retrospective query of the trauma registry of Utah's only pediatric trauma center for children younger than 18 years requiring hospitalization for a ski or snowboarding injury from November 2004 to February 2014.

Results
There were 443 cases of hospitalized ski and snowboarding injuries during the study period. Twenty-nine cases (7%) fell from height while riding a chair lift. Children falling from chair lifts were more likely to be younger (6.9 years vs 12.1, P < 0.0001), female (41% vs 20%, P < 0.01), and elicit trauma team activation (72% vs 34%, P = <0.0001) but were less frequently treated in the operating room (14 vs 24%, P = 0.02) than children with other ski and snowboarding injuries. There were no differences in mortality, injury severity score, length of hospital stay, or airway intubation outside the operating room. When stated (11/29 cases), mean estimated height of fall from lift was 26 feet. The most common body region in chair lift falls with a significant injury (abbreviated injury scale, ≥3) was lower extremity (4/29, all femur fractures). Patient age discriminated chair lift falls well (area under the receiver operating characteristic curve, 0.87) with age of 7 years and below predicting chair lift fall with a sensitivity of 76% and a specificity of 91%.

Conclusions
Injuries requiring hospitalization after falls from chair lifts occur at regulated facilities and are more common in younger female children when compared with other ski and snowboarding injuries. Interventions for reducing falls from chair lifts may be most effective applied to children 7 years and younger.
Diagnostic Value of Serum Urokinase-Type Plasminogen Activator Receptor in Children With Acute Appendicitis
Authors: Oztan Mustafa Onur , Aksoy Gokmen Aysegul , Arslan Fatma Demet , Cakir Ebru , Sayan Ali , Abay Elif , Kaya Selçuk , Koyluoglu Gokhan 
Published: January 2018

Objectives
Acute appendicitis (AA) is the most common surgical emergency in children. The accurate and timely diagnosis of AA in children can be challenging, and delayed diagnosis rates have been reported to range from 5.9% to 27.6%. Although combining clinical history and repeated physical examination with laboratory tests and radiographic imaging modalities help reach the diagnosis, novel biomarkers can support the surgeons' decision as well. The aims of this study were to evaluate a new plasma marker, urokinase-type plasminogen activator receptor (uPAR), to improve diagnostic accuracy in AA patients, and to determine a cutoff value of uPAR, which can safely include/exclude the diagnosis of AA.

Methods
We conducted a prospective study of children who underwent surgery for AA. Patients were categorized into the following 3 groups: group 1, controls consisted of 32 healthy volunteers; group 2, patients underwent surgery for nonperforated AA (n = 35); and group 3, patients underwent surgery for perforated AA (n = 21). Blood was sampled from group 1 at the admission and from group 2 and 3 before appendectomy. Serum uPAR, white blood cell count, absolute neutrophil count (ANC), and C-reactive protein concentrations were measured.

Results
Urokinase-type plasminogen activator receptor, ANC, and white blood cell count values were significantly higher in group 2 and 3 than group 1, but there was no significant difference between group 2 and 3. C-reactive protein values were significantly higher only in group 3 than other groups. The cutoff value for uPAR is 2.2 ng/mL with sensitivity of 85.7% and specificity of 84.3% and ANC is 5900 cells/mm3 with sensitivity of 91.1% and specificity of 96.9% to diagnose appendicitis. The specificity was 81.3% and sensitivity was raised to 98.2% when evaluated together.

Conclusions
The incorporation of uPAR count and ANC could be a strong predictor of AA in children.
Successful First Gait of a Child With Hip-Disarticulation Prosthesis
Authors: Hara Hitomi , Kawamoto Teruya , Fukase Naomasa , Katayama Etsuko , Takemori Toshiyuki , Fujiwara Shuichi , Sakai Yoshitada , Nishida Kotaro , Kuroda Ryosuke , Akisue Toshihiro 
Published: January 2018

Abstract
An infant boy underwent hip disarticulation for infantile fibrosarcoma immediately after birth. His rehabilitation began when he was 4 mos old and involved training with his left (residual) leg. He could stand with support at 12 mos. His initial prosthesis fitting was performed at the age of 13 mos. He could stand and walk with support at 15 mos of age and could walk with no additional support and go up and down stairs at 2 yrs. A single-axis prosthetic knee joint was introduced at the age of 2 yrs 3 mos. His first gait using a hip prosthesis was successful, and his prosthesis was replaced at appropriate intervals with no major problems. The authors believe that the key to achieving a successful prosthetic gait in children is good communication among the medical team, which should comprise an orthopedic doctor, rehabilitation doctor, nurse, physical therapist, prosthetist/orthotist, and the patient's parents.
When to switch to an oral treatment and/or to discharge a patient with skin and soft tissue infections
Authors: Bassetti Matteo , Eckmann Christian , Peghin Maddalena , Carnelutti Alessia , Righi Elda 
Published: January 2018

Purpose of review
Skin and soft tissue infections prevalence is increasing and represent a frequent cause of hospital admission. New guidelines have become available in order to better define these infections and their response to antimicrobial treatment. Gram-positive bacteria, in particular Staphylococcus aureus, remain the most frequently isolated pathogens in skin and soft tissue infections. To treat complicated forms and infections caused by drug-resistant bacteria, hospital admission and administration of intravenous antibiotics are often required, impacting on healthcare costs and patients’ morbidity.

Recent findings
New therapeutic options offer efficacy against drug-resistant Gram-positive bacteria as well as potential to favor early patients’ discharge, including the possibility for intravenous to oral switch and infrequent drug administration because of prolonged drug half-life. Although data from real-world studies on new antimicrobials is awaited, clinicians need clear direction on how to optimize the treatment of skin and soft tissue infections in order to avoid prolonged hospitalizations and extra costs. Early assessment of patient's clinical conditions and response to treatment appear useful in order to facilitate patients’ discharge.

Summary
We have reported the evidence for early intravenous to oral switch and early hospital discharge for patients with skin and soft tissue infections. New therapeutic options that represent promising tools in promoting an optimized management of these infections have also been reviewed.
Long-Term Outcomes After Overlapping Sphincteroplasty for Cloacal-Like Deformities
Authors: Maldonado Pedro A. , Mcintire Donald , Corton Marlene M. 
Published: January 2018

Objective
The aim of this study was to report subjective, long-term outcomes and describe patient demographics, presenting symptoms, perioperative management, and complications after overlapping sphincteroplasty repair for chronic fourth-degree lacerations (cloacal-like deformities).

Methods
In this retrospective study, hospital records were reviewed for women who underwent overlapping anal sphincteroplasty for a cloacal-like deformity of the perineum at a single institution from 1996 to 2013. Details including patient demographics, presenting symptoms, perioperative management, and complications were abstracted from the medical record. As a follow-up, subjects were contacted by telephone and were administered the validated Modified Manchester Health Questionnaire to assess anal continence status and anal incontinence-related quality of life since the time of surgery.

Results
Of 57 women who underwent an anal sphincteroplasty within the study period, 29 met inclusion criteria. Median parity was 3 (range, 1–7) and 24.5% reported a history of forceps or vacuum-assisted vaginal delivery. Presenting symptoms included fecal incontinence (58.6%), flatal incontinence (41%), sexual dysfunction (20.7%), and poor body self-image (3.4%). Thirteen (45%) women could be contacted by telephone and all agreed to participate. Overall, 46.2% of the 13 women who completed the Modified Manchester Health Questionnaire reported some form anal of incontinence, whereas 53.8% reported complete continence at a mean follow-up of 7.0 ± 3.6 years. Perioperative morbidity was uncommon, and postoperative antibiotics were used in 75.9% of cases for a median duration of 8.8 ± 3.3 days.

Conclusions
Perioperative morbidity after overlapping sphincteroplasty for cloacal-like deformities after obstetrical injury is rare. Although long-term complete anal continence may be difficult to achieve in all cases, good quality of life measures and low symptom severity were noted at a mean interval of 7 years after surgery.