bluuebunny/crossref_metadata_2025_split huggingface dataset:
EthSEQ: ethnicity annotation from whole exome sequencing data
Authors: Romanel Alessandro , Zhang Tuo , Elemento Olivier , Demichelis Francesca 
Published: March 2017

Abstract

Summary
Whole exome sequencing (WES) is widely utilized both in translational cancer genomics studies and in the setting of precision medicine. Stratification of individual’s ethnicity is fundamental for the correct interpretation of personal genomic variation impact. We implemented EthSEQ to provide reliable and rapid ethnicity annotation from whole exome sequencing individual’s data, validated it on 1000 Genome Project and TCGA data (2700 samples) demonstrating high precision, and finally assessed computational performances compared to other tools. EthSEQ can be integrated into any WES based processing pipeline and exploits multi-core capabilities.

Availability and Implementation
R package available at github.com/aromanel/EthSEQ and CRAN repository.

Supplementary information
Supplementary data are available at Bioinformatics online.
Local Group ultra-faint dwarf galaxies in the reionization era
Authors: Weisz Daniel R. , Boylan-Kolchin Michael 
Published: March 2017

Abstract
Motivated by the stellar fossil record of Local Group (LG) dwarf galaxies, we show that the star-forming ancestors of the faintest ultra-faint dwarf galaxies (UFDs; MV ∼ −2 or M⋆ ∼ 102 at z = 0) had ultraviolet (UV) luminosities of MUV ∼ −3 to −6 during reionization (z ∼ 6–10). The existence of such faint galaxies has substantial implications for early epochs of galaxy formation and reionization. If the faint-end slopes of the UV luminosity functions (UVLFs) during reionization are steep (α ≲ −2) to MUV ∼ −3, then (i) the ancestors of UFDs produced &gt;50 per cent of UV flux from galaxies; (ii) galaxies can maintain reionization with escape fractions that are more than two times lower than currently adopted values; (iii) direct Hubble Space Telescope and James Webb Space Telescope observations may detect only ∼10–50 per cent of the UV light from galaxies; and (iv) the cosmic star formation history increases by ≳ 4–6 at z ≳ 6. Significant flux from UFDs, and resultant tensions with LG dwarf galaxy counts, is reduced if the high-redshift UVLF turns over. Independent of the UVLF shape, the existence of a large population of UFDs requires a non-zero luminosity function to MUV ∼ −3 during reionization.
Convex-Rod Derotation Maneuver on Lenke Type I Adolescent Idiopathic Scoliosis
Authors: Zifang Huang , Hengwei Fan , Yaolong Deng , Wenyuan Sui , Qifei Wang , Lei Cao , Li Fobao , Junlin Yang 
Published: March 2017

Abstract

BACKGROUND
Convex-rod derotation may have potential advantages for adolescent idiopathic scoliosis (AIS) correction; however, study of this technique has been limited.

OBJECTIVE
To compare the radiographic outcomes of Lenke type I AIS patients treated by the convex- or concave-rod derotation maneuvers.

METHODS
A retrospective study was designed to compare 2 cohorts, including 81 Lenke type I AIS patients treated with convex-rod derotation (n = 38) or concave-rod derotation (n = 43), between July 2008 and September 2012. All patients had complete clinical records and radiographic data, which were collected and compared between groups.

RESULTS
In comparing 9 radiographic parameters, significant differences were found in the incidence of screw misplacement, the postoperative main-curve angle, and the corrective rate between groups. The major-curve angles in both the convex- and the concave-rod derotation groups were corrected from 54.0° ± 10.6° and 53.0° ± 11.1° preoperatively, to 8.5° ± 6.9° and 12.9° ± 6.8° postoperatively, with corrective rates of 85.3% and 76.0%, respectively (P = .001). Final T5-T12 kyphosis and appropriate coronal-to-sagittal balance were achieved in both groups. The incidence of screw misplacement in the convex and concave sides of all patients was 1.8% and 3.7%, respectively (P = .047), and 1.8% and 3.6%, respectively, in the convex- and the concave-rod derotation groups (P = .044).

CONCLUSION
Compared with concave-rod derotation, convex-rod derotation can potentially improve the major-curve corrective rate and tends to reduce the risk of pedicle breach in Lenke type I AIS patients.
Self-assembled semiconductor quantum dots decorating the facets of GaAs nanowire for single-photon emission
Authors: Yu Ying , Zha Guo-Wei , Shang Xiang-Jun , Yang Shuang , Sun Ban-Quan , Ni Hai-Qiao , Niu Zhi-Chuan 
Published: March 2017

Abstract
In this chapter, we discuss the epitaxial growth of self-assembled quantum dots (QDs) in GaAs nanowires (NWs) and the characteristics of their single-photon emissions. We demonstrate Ga droplet-induced gold-free vapor-liquid-solid growth of hexagonal GaAs/AlGaAs core–shell NWs, branched GaAs NWs and tailored nanostructured morphologies on the NW facets. Particularly, we show two new types of QD-in-NW systems: one is a single InAs QD formed at the corner of a branched GaAs NW, and the other is a single GaAs QD formed on the NW facet. Sharp excitonic emission spectral lines are observed with vanishing two-photon emission probability. Furthermore, a single GaAs QD is achieved at the site of a single AlGaAs quantum ring (QR) on the NW facet. In addition, these NW-based single QDs are in-situ probed and integrated with single-mode optical fibers to achieve all-fiber-output single-photon sources for potential application in quantum integrated networks.
Human Coronavirus-HKU1 Infection Among Adults in Cleveland, Ohio
Authors: Kanwar Anubhav , Selvaraju Suresh , Esper Frank 
Published: March 2017

Abstract

Background
Human coronaviruses (CoV) have been long recognized as a common cause of respiratory tract disease including severe respiratory tract illness. Coronavirus-HKU1 has been described predominantly among children less than 5 years of age in the United States with few studies characterizing the disease spectrum among adults.

Methods
Nasopharyngeal specimens of patients with respiratory symptoms were analyzed for CoV-HKU1 by NxTAG Respiratory Pathogen Panel multiplex assay from February 7, 2016 to April 30, 2016. Epidemiologic, clinical, and laboratory data were collected on adults (patients &gt;18 years) whose samples screened positive.

Results
Of 832 adult respiratory specimens screened, 13 (1.6%) cases of CoV-HKU1 were identified. Adults age ranged between 23 and 75 years and 6 (46%) were males. All of whom had 1 or more respiratory symptoms, and 5 (38%) also reported 1 or more gastrointestinal symptoms. Eleven (85%) reported history of smoking and 5 (38%) used inhaled steroids. Seven (54%) required hospitalization, 5 (71%) of these needed supplemental oxygen, and 2 (29%) were admitted to intensive care. Median length of hospitalization was 5 days. Eight (62%) received antibiotics despite identification of CoV-HKU1. Infectious work-up in 1 patient who died did not reveal any other pathogen. In 2 (15%) CoV-HKU1-positive adults, the only viral coinfection detected was influenza A.

Conclusions
Coronavirus-HKU1 accounted for 1.6% of adult respiratory infections and should be considered in differential diagnosis of severe respiratory illnesses among adults.
A Report of Adult Human Adenovirus Infections in a Tertiary Hospital
Authors: Kalimuddin Shirin , Chan Yvonne F. Z. , Wu Ian Q. , Tan Qiao Li , Murthee Kavitha G. , Tan Ban Hock , Oon Lynette L. E. , Yang Yong , Lin Raymond T. P. , Joseph Udayan , Sessions October M. , Smith Gavin J. D. , Ooi Eng Eong , Low Jenny G. H. 
Published: March 2017

AbstractWe describe a review of human adenovirus (HAdV) infections occurring among adults in a tertiary hospital in Singapore from February to May 2013. A similar increase in cases was observed among children and military personnel during the same time period. The majority of isolates were identified as HAdV-7, likely an emerging pathogen in Asia.
Evaluation of a Novel Alcohol-Based Surface Disinfectant for Disinfection of Hard and Soft Surfaces in Healthcare Facilities
Authors: Alhmidi Heba , Koganti Sreelatha , Cadnum Jennifer L. , Rai Herleen , Jencson Annette L. , Donskey Curtis J. 
Published: March 2017

Abstract
We examined the efficacy of a new 1-step cleaner and disinfectant containing 30% ethanol that is applied as a spray. The product rapidly reduced vegetative bacterial pathogens on carriers and on hard and soft surfaces in healthcare settings, but it did not stain clothing.
Curative Effects for B-Cell Lymphoma Accomplished by Direct-Acting Antiviral Agents of Hepatitis C
Authors: Hattori Nobuhiro , Ikeda Hiroki , Nakano Hiroyasu , Matsumoto Nobuyuki , Watanabe Tsunamasa , Shigefuku Ryuta , Noguchi Yohei , Matsunaga Kotaro , Sakai Hirotaka , Okuse Chiaki , Yamamoto Hiroyuki , Miura Ikuo , Suzuki Michihiro , Itoh Fumio 
Published: March 2017

Abstract
Hepatitis C virus (HCV) is a hepatotropic and lymphotropic virus with the capabilities of tumorigenesis. We present an HCV-infected patient affected with B-cell lymphomas after suffering from hepatocellular carcinoma. The patient exhibited curative effects for lymphomas after treatment with sofosbuvir and ledipasvir, which is shown clearly with a positron emission tomography scanner.
Pyogenic Arthritis of the Fingers and the Wrist: Can We Shorten Antimicrobial Treatment Duration?
Authors: Meier Rahel , Wirth Thomas , Hahn Frederik , Vögelin Esther , Sendi Parham 
Published: March 2017

Abstract

Background
Pyogenic arthritis of the small joints of the hand and wrist is a known but poorly described entity. The objective of this work was to characterize the clinical presentation, antimicrobial treatment, and surgical interventions of native small joint arthritis (SJA) treated in our tertiary center.

Methods
According to predefined variables, medical records of adult patients with SJA treated in a Swiss university hospital between 2005 and 2013 were retrospectively analyzed.

Results
The median age of 97 patients (101 joints) was 52 years (interquartile range [IQR], 38–68 years); 52% had no comorbidity. Small joint arthritis of the second and third fingers accounted for 53% of infections, with metacarpal-phalangeal and proximal interphalangeal joints most commonly involved. Of 86 (89%) episodes with an exogenous source, 63 (65%) followed a trauma. The most commonly isolated microorganism was Staphylococcus aureus (38%), followed by β-hemolytic streptococci (13%) and Pasteurella spp (11%). Eighty-seven episodes (89 joints) in patients with follow-up examinations were included in treatment and outcome analyses. Up to 2 surgical interventions were required to cure infection in 74 (83%) joints. Median antimicrobial treatment duration was 14 days (IQR, 12–28 days), with amoxicillin/clavulanate administered in 74 (85%) episodes. At follow up, cure of infection was noted in all episodes and good functional outcome in 79% of episodes.

Conclusions
Small joint arthritis shows considerable differences from clinical patterns reported for larger joints. In our series, the outcome was good with no more than 2 surgical interventions and median treatment duration of 14 days in 79% of episodes.
Patient Comprehension and Compliance Survey to Assess Postoperative Pain Regimens in the Orthopaedic Trauma Population
Authors: Gangavalli Anup K. , Malige Ajith , Rehman Saqib , Nwachuku Chinenye O. 
Published: March 2017

Objective:
This study aims to determine the groups of patients who are at risk for noncompliance and misunderstanding of their pain regimen.

Design:
Survey-based cohort study.

Setting:
Suburban Level-I trauma center.

Patients/Participants:
A total of 171 patients between the ages of 18–89 years who underwent surgical fixation of fractures involving the pelvis, long bones, or periarticular regions of the knee, ankle, elbow, and wrist.

Main Outcome Measurements:
Patients who cannot accurately reproduce their prescribed pain medication list and patients who modify this pain medication regimen were analyzed by age, employment status, income level, education level, time between surgery and follow-up, and whether pain interfered with activities of daily living.

Results:
Overall, 147 patients completed the survey. Seventy percent (n = 114) of patients could not accurately reproduce their pain medication regimen, regardless of age, employment status, income level, education level, time between surgery and follow-up, and whether pain interfered with activities of daily living. Patients (61.2%; n = 90), regardless of the 6 aforementioned demographic factors, also admitted to modifying their pain medication regimen with non-prescribed medications, with 55.8% (n = 82) of patients adding over-the-counter medications to surgeon-prescribed narcotic medications.

Conclusions:
Misunderstanding and noncompliance of surgeon-prescribed pain regimens are prevalent across all patient demographics. Knowledge of the potential effects these augmentative medications can have on fracture healing and any drug-drug interactions that may arise is an important aspect of patient postoperative care. Surgeons must be wary of these trends and screen for any unintended side effects a patient's pain regimen may have.

Level of Evidence:
Prognostic Level IV. See Instructions for Authors for a complete description of levels of evidence.
Social to Moderate Alcohol Consumption Provides a Protective Effect for Functional Outcomes After Fixation of Orthopaedic Fractures
Authors: Saleh Hesham , Driesman Adam , Fisher Nina , Leucht Philipp , Konda Sanjit , Egol Kenneth 
Published: March 2017

Objectives:
To identify the association between social and moderate alcohol consumption and functional outcomes after surgical management of orthopaedic fractures.

Design:
Prospective cohort study.

Setting:
Level 1 trauma center.

Patients/Participants:
Seven hundred eighty-four patients who were operatively treated for an isolated orthopaedic fracture were prospectively followed. Patients were categorized into groups according to self-reported drinking frequencies based on NIAAA guidelines.

Main Outcome Measurements:
SMFA scores at baseline, 3, 6, and 12 months postoperatively; postoperative complications; and subsequent operations.

Results:
There were 367 (46.8%) abstinent, 327 (41.7%) social, 52 (6.6%) moderate, and 38 (4.8%) heavy drinkers. Mean SMFA scores of social and moderate drinkers were significantly lower than those of abstinent patients at 3-, 6-, and 12-month follow-ups, denoting better functional outcomes (social: 24.3 vs. 30.5, P = 0.001; 14.8 vs. 21.5, P < 0.005; and 10.1 vs. 18.8, P < 0.005); (moderate: 18.3 vs. 30.5, P = 0.001; 9.7 vs. 21.5, P = 0.001; and 5.4 vs. 18.8, P < 0.005). Multiple linear regression revealed that social drinking and baseline SMFA scores were the only statistically significant independent predictors of lower SMFA scores at 12 months after surgery.

Conclusions:
Social to moderate drinking may have a protective effect on functional outcomes at 3, 6, and 12 months after surgery. Social drinking may also have a protective effect on postoperative complications and reoperation rates. Further studies should be performed to fully appreciate the clinical effect of social and moderate drinking after operative treatment of orthopaedic fractures.

Level of Evidence:
Prognostic Level III. See Instructions for Authors for a complete description of levels of evidence.
Does Concurrent Tibial Intramedullary Nailing and Fibular Fixation Increase Rates of Tibial Nonunion? A Matched Cohort Study
Authors: Githens Michael , Haller Justin , Agel Julie , Firoozabadi Reza 
Published: March 2017

Objectives:
To determine if there is a difference in rates of tibial nonunion in patients undergoing tibial intramedullary (IM) nailing and fibular fixation as compared to a matched cohort undergoing tibial IM nailing alone.

Design:
Retrospective matched cohort study.

Setting:
Single Level 1 academic trauma center.

Patients:
Consecutive patients 18 years and older with a tibia and fibula fracture treated with tibial IM nailing and fibular fixation who were determined radiographically and clinically healed or had a minimum 1-year follow-up were included. A matched cohort who underwent tibial IM nailing without fibular fixation was used for comparison.

Intervention:
Fibular fixation at the time of tibial IM nailing.

Main Outcome Measurement:
Tibial nonunion, defined as a persistently symptomatic fracture with no radiographic progression toward healing at 9 months on consecutive radiographs over a 2-month period.

Results:
One hundred sixty six patients met inclusion criteria for the intervention group. Mean follow-up was 21 months. There was a 12% rate of tibial nonunion. In a matched cohort of 174 patients without fibular fixation there was no significant difference in patient demographics, injury characteristics, infection rates, time to union, postoperative complications, or rates of tibial nonunion. The rate of nonunion in both groups was significantly higher in patients with high energy mechanisms, open fractures, and postoperative infections.

Conclusion:
Fibular fixation did not impact rates of tibial nonunion. The rate of tibial nonunion in both cohorts is comparable with published rates of tibial nonunion after IM nailing without fibular fixation. Open fractures, high energy mechanism, and postoperative infection are significantly associated with tibial nonunion.

Level of Evidence:
Therapeutic Level III. See Instructions for Authors for a complete description of levels of evidence.
Tibial Eminence Involvement With Tibial Plateau Fracture Predicts Slower Recovery and Worse Postoperative Range of Knee Motion
Authors: Konda Sanjit R. , Driesman Adam , Manoli Arthur , Davidovitch Roy I. , Egol Kenneth A. 
Published: March 2017

Objectives:
To examine 1-year functional and clinical outcomes in patients with tibial plateau fractures with tibial eminence involvement.

Design:
Retrospective analysis of prospectively collected data.

Setting:
Academic Medical Center.

Patients/Participants:
All patients who presented with a tibial plateau fracture (Orthopaedic Trauma Association (OTA) 41-B and 41-C).

Intervention:
Patients were divided into fractures with a tibial eminence component (+TE) and those without (−TE) cohorts. All patients underwent similar surgical approaches and fixation techniques for fractures. No tibial eminence fractures received fixation specifically.

Main Outcome Measurements:
Short musculoskeletal functional assessment (SMFA), pain (Visual Analogue Scale), and knee range-of-motion (ROM) were evaluated at 3, 6, and 12 months postoperatively and compared between cohorts.

Results:
Two hundred ninety-three patients were included for review. Patients with OTA 41-C fractures were more likely to have an associated TE compared with 41-B fractures (63% vs. 28%, P < 0.01). At 3 months postoperatively, the +TE cohort was noted to have worse knee ROM (75.16 ± 51 vs. 86.82 ± 53 degree, P = 0.06). At 6 months, total SMFA and knee ROM was significantly worse in the +TE cohort (29 ± 17 vs. 21 ± 18, P ≤ 0.01; 115.6 ± 20 vs. 124.1 ± 15, P = 0.01). By 12 months postoperatively, only knee ROM remained significantly worse in the +TE cohort (118.7 ± 15 vs. 126.9 ± 13, P < 0.01). Multivariate analysis revealed that tibial eminence involvement was a significant predictor of ROM at 6 and 12 months and SFMA at 6 months. Body mass index was found to be a significant predictor of ROM and age was a significant predictor of total SMFA at all time points.

Conclusion:
Knee ROM remains worse throughout the postoperative period in the +TE cohort. Functional outcome improves less rapidly in the +TE cohort but achieves similar results by 1 year.

Level of Evidence:
Prognostic Level III. See Instructions for Authors for a complete description of levels of evidence.
Patterns of Opioid Prescribing for an Orthopaedic Trauma Population
Authors: Ruder John , Wally Meghan K. , Oliverio McKell , Seymour Rachel B. , Hsu Joseph R. ,   the PRIMUM Group
Published: March 2017

Objectives:
To determine opioid-prescribing practices to the orthopaedic trauma (OT) population at one Level I trauma center.

Design:
A retrospective study of discharge prescriptions for adult patients with OT. Prescription details, injury burden, and patient demographics were abstracted for patients from initial injury through a 2-month follow-up.

Setting:
Level I trauma center.

Patients/Participants:
Adult patients with OT admitted over a 30-day period (n = 110).

Intervention:
All discharge and follow-up opioid prescriptions were recorded.

Main Outcome Measurements:
Morphine milligram equivalents (MMEs) per day, number of opioid prescriptions, type/dose of medication prescribed.

Results:
One hundred thirty-five discharge prescriptions were written for 110 patients with orthopaedic injuries during the review period. All patients received opioids at the time of discharge. The MMEs prescribed at the time of discharge was 114 mg (54–300 mg) for a mean of 7.21 days (2–36.7 days). Although patients with preinjury risk factors were prescribed discharge opioids for a similar duration (7.00 days vs. 7.30 days, P = 0.81) than those without risk factors, they were prescribed significantly more MMEs than those without (130 vs. 108, P < 0.05) and were more likely to receive extended-release and long-acting opioids than those without (42.11% vs. 21.98%).

Conclusions:
Pain management after OT continues to be opioid-centric despite involving a population at risk. Further focus on prescriber and patient education, risk evaluation with mitigation, guideline development, and comprehensive pain management strategies are warranted in the OT population.

Level of Evidence:
Prognostic Level IV. See Instructions for Authors for a complete description of levels of evidence.
Tranexamic Acid Safely Reduced Blood Loss in Hemi- and Total Hip Arthroplasty for Acute Femoral Neck Fracture: A Randomized Clinical Trial
Authors: Watts Chad D. , Houdek Matthew T. , Sems S. Andrew , Cross William W. , Pagnano Mark W. 
Published: March 2017

Objectives:
We aimed to determine whether (1) tranexamic acid (TXA) reduces the incidence of transfusion (2) TXA reduces the calculated blood loss, and (3) there are any observable differences in 30- and 90-day complications with TXA administration during arthroplasty for femoral neck fracture (FNF).

Design:
Prospective, double-blinded, randomized controlled trial.

Setting:
Level 1 Academic Trauma Center.

Patients/Participants:
One hundred thirty-eight patients who presented with a low-energy, isolated, FNF (AO 31B) treated with either hemi- or total hip arthroplasty within 72 hours of injury were randomized to either the TXA group (69 patients) or placebo group (69 patients).

Intervention:
In the TXA group, patients received 2 doses of 15 mg/kg intravenous TXA dissolved in 100 mL of saline, each administered over 10 minutes; 1 dose just before incision, and the second at wound closure. In the placebo group, 100 mL of saline solution was administered in a similar fashion. Perioperative care was otherwise standardized including conservative transfusion criteria.

Main Outcome Measurements:
Our primary outcome was to determine the proportion of patients who underwent blood transfusion during hospitalization. Secondary outcomes were calculated blood loss, number of units transfused during hospitalization, and incidence of adverse events at 30 and 90 days including thromboembolic event, wound complications, reoperation, hospital readmission, and all-cause mortality.

Results:
TXA reduced mean incidence of transfusion by 305 mL (P = 0.0005). There was a trend toward decreased transfusion rate in the TXA group (17% vs. 26%, P = 0.22). TXA was safe with no differences in adverse events at 30 and 90 days.

Conclusions:
This randomized clinical trial found that TXA administration safely reduced blood loss with a tendency for decreased transfusion rate and total blood product consumption for patients undergoing hip arthroplasty for acute FNF. More studies are needed to further ascertain the role of TXA in the management of patients with FNF.

Level of Evidence:
Therapeutic Level I. See Instructions for Authors for a complete description of levels of evidence.