bluuebunny/crossref_metadata_2025_split huggingface dataset:
CoreTracker: accurate codon reassignment prediction, applied to mitochondrial genomes
Authors: Noutahi Emmanuel , Calderon Virginie , Blanchette Mathieu , Lang Franz B , El-Mabrouk Nadia 
Published: June 2017

AbstractMotivationCodon reassignments have been reported across all domains of life. With the increasing number of sequenced genomes, the development of systematic approaches for genetic code detection is essential for accurate downstream analyses. Three automated prediction tools exist so far: FACIL, GenDecoder and Bagheera; the last two respectively restricted to metazoan mitochondrial genomes and CUG reassignments in yeast nuclear genomes. These tools can only analyze a single genome at a time and are often not followed by a validation procedure, resulting in a high rate of false positives.ResultsWe present CoreTracker, a new algorithm for the inference of sense-to-sense codon reassignments. CoreTracker identifies potential codon reassignments in a set of related genomes, then uses statistical evaluations and a random forest classifier to predict those that are the most likely to be correct. Predicted reassignments are then validated through a phylogeny-aware step that evaluates the impact of the new genetic code on the protein alignment. Handling simultaneously a set of genomes in a phylogenetic framework, allows tracing back the evolution of each reassignment, which provides information on its underlying mechanism. Applied to metazoan and yeast genomes, CoreTracker significantly outperforms existing methods on both precision and sensitivity.Availability and implementationCoreTracker is written in Python and available at https://github.com/UdeM-LBIT/CoreTracker.Supplementary informationSupplementary data are available at Bioinformatics online.
Uterine responses to early pre-attachment embryos in the domestic dog and comparisons with other domestic animal species†
Authors: Graubner Felix R , Gram Aykut , Kautz Ewa , Bauersachs Stefan , Aslan Selim , Agaoglu Ali R , Boos Alois , Kowalewski Mariusz P 
Published: June 2017

AbstractIn the dog, there is no luteolysis in the absence of pregnancy. Thus, this species lacks any anti-luteolytic endocrine signal as found in other species that modulate uterine function during the critical period of pregnancy establishment. Nevertheless, in the dog an embryo-maternal communication must occur in order to prevent rejection of embryos. Based on this hypothesis, we performed microarray analysis of canine uterine samples collected during pre-attachment phase (days 10-12) and in corresponding non-pregnant controls, in order to elucidate the embryo attachment signal. An additional goal was to identify differences in uterine responses to pre-attachment embryos between dogs and other mammalian species exhibiting different reproductive patterns with regard to luteolysis, implantation, and preparation for placentation. Therefore, the canine microarray data were compared with gene sets from pigs, cattle, horses, and humans. We found 412 genes differentially regulated between the two experimental groups. The functional terms most strongly enriched in response to pre-attachment embryos related to extracellular matrix function and remodeling, and to immune and inflammatory responses. Several candidate genes were validated by semi-quantitative PCR. When compared with other species, best matches were found with human and equine counterparts. Especially for the pig, the majority of overlapping genes showed opposite expression patterns. Interestingly, 1926 genes did not pair with any of the other gene sets. Using a microarray approach, we report the uterine changes in the dog driven by the presence of embryos and compare these results with datasets from other mammalian species, finding common-, contrary-, and exclusively canine-regulated genes.
An update on type 2 diabetes management in primary care
Authors: Waddell Jeffrey 
Published: June 2017

Abstract:
Diabetes mellitus is a chronic disease impacting glucose metabolism. Type 2 diabetes mellitus (T2DM) stems from the inability of the body to utilize endogenous insulin properly. Approximately 90% to 95% of newly diagnosed cases of diabetes are T2DM. This article focuses on the initial treatment of T2DM based on the 2017 American Association of Clinical Endocrinologists and the American College of Endocrinology clinical practice guidelines. The 2017 update includes changes and additions regarding psychosocial management, physical activity, surgery, and hypoglycemia.
Videolaryngoscopy versus Fiber-optic Intubation through a Supraglottic Airway in Children with a Difficult Airway
Authors: Burjek Nicholas E. , Nishisaki Akira , Fiadjoe John E. , Adams H. Daniel , Peeples Kenneth N. , Raman Vidya T. , Olomu Patrick N. , Kovatsis Pete G. , Jagannathan Narasimhan ,   for the PeDI Collaborative Investigators
Published: June 2017

Abstract

Background
The success rates and related complications of various techniques for intubation in children with difficult airways remain unknown. The primary aim of this study is to compare the success rates of fiber-optic intubation via supraglottic airway to videolaryngoscopy in children with difficult airways. Our secondary aim is to compare the complication rates of these techniques.

Methods
Observational data were collected from 14 sites after management of difficult pediatric airways. Patient age, intubation technique, success per attempt, use of continuous ventilation, and complications were recorded for each case. First-attempt success and complications were compared in subjects managed with fiber-optic intubation via supraglottic airway and videolaryngoscopy.

Results
Fiber-optic intubation via supraglottic airway and videolaryngoscopy had similar first-attempt success rates (67 of 114, 59% vs. 404 of 786, 51%; odds ratio 1.35; 95% CI, 0.91 to 2.00; P = 0.16). In subjects less than 1 yr old, fiber-optic intubation via supraglottic airway was more successful on the first attempt than videolaryngoscopy (19 of 35, 54% vs. 79 of 220, 36%; odds ratio, 2.12; 95% CI, 1.04 to 4.31; P = 0.042). Complication rates were similar in the two groups (20 vs. 13%; P = 0.096). The incidence of hypoxemia was lower when continuous ventilation through the supraglottic airway was used throughout the fiber-optic intubation attempt.

Conclusions
In this nonrandomized study, first-attempt success rates were similar for fiber-optic intubation via supraglottic airway and videolaryngoscopy. Fiber-optic intubation via supraglottic airway is associated with higher first-attempt success than videolaryngoscopy in infants with difficult airways. Continuous ventilation through the supraglottic airway during fiber-optic intubation attempts may lower the incidence of hypoxemia.
Combined Thoracic Ultrasound Assessment during a Successful Weaning Trial Predicts Postextubation Distress
Authors: Silva Stein , Ait Aissa Dalinda , Cocquet Pierre , Hoarau Lucille , Ruiz Jean , Ferre Fabrice , Rousset David , Mora Michel , Mari Arnaud , Fourcade Olivier , Riu Béatrice , Jaber Samir , Bataille Bénoît 
Published: June 2017

Abstract

Background
Recent studies suggest that isolated sonographic assessment of the respiratory, cardiac, or neuromuscular functions in mechanically ventilated patients may assist in identifying patients at risk of postextubation distress. The aim of the present study was to prospectively investigate the value of an integrated thoracic ultrasound evaluation, encompassing bedside respiratory, cardiac, and diaphragm sonographic data in predicting postextubation distress.

Methods
Longitudinal ultrasound data from 136 patients who were extubated after passing a trial of pressure support ventilation were measured immediately after the start and at the end of this trial. In case of postextubation distress (31 of 136 patients), an additional combined ultrasound assessment was performed while the patient was still in acute respiratory failure. We applied machine-learning methods to improve the accuracy of the related predictive assessments.

Results
Overall, integrated thoracic ultrasound models accurately predict postextubation distress when applied to thoracic ultrasound data immediately recorded before the start and at the end of the trial of pressure support ventilation (learning sample area under the curve: start, 0.921; end, 0.951; test sample area under the curve: start, 0.972; end, 0.920). Among integrated thoracic ultrasound data, the recognition of lung interstitial edema and the increased telediastolic left ventricular pressure were the most relevant predictive factors. In addition, the use of thoracic ultrasound appeared to be highly accurate in identifying the causes of postextubation distress.

Conclusions
The decision to attempt extubation could be significantly assisted by an integrative, dynamic, and fully bedside ultrasonographic assessment of cardiac, lung, and diaphragm functions.
Direct anterior approach total hip arthroplasty requires less supplemental acetabular screw fixation and fewer blood transfusions than posterior approach
Authors: Colacchio Nicholas D. , Cleary Mark X. , Reid Daniel , Trofa David , Pevear Mary E. , Smith Eric L. 
Published: June 2017

Background:
This study evaluates the use of supplemental acetabular cup screw fixation during direct anterior approach (DAA) versus posterior approach total hip arthroplasty (THA).

Methods:
A retrospective review of all THAs performed by a single fellowship-trained total joint surgeon at a tertiary academic medical center between January 2010 and January 2013 identified 136 primary THAs (124 patients). The following variables were analyzed: age, body mass index (BMI), American Society of Anesthesiologists (ASA) score, operative side, surgical approach, operative time, estimated blood loss, blood transfusion, implant design, number of acetabular screws used, offset (high, standard, or coxa vara), cup anteversion, and cup abduction.

Results:
There were 31 DAA and 105 posterior-approach primary THAs performed. Significantly fewer acetabular screws were used in DAA compared to posterior approach (1.0 vs. 1.9 screws, P<0.001). Patients who received acetabular screws had a significantly increased likelihood of requiring a blood transfusion (OR=4.4). Patients who received blood transfusions had significantly more acetabular screws placed than patients who did not receive transfusions (2 vs. 1.2 screws, P<0.001). DAA patients had a significantly lower mean BMI than posterior approach patients (26.2 vs. 30.6). There were no significant differences in age, gender, operative time, cup abduction, cup anteversion, estimated blood loss, or blood transfusions between the two cohorts.

Conclusions:
The number of supplemental acetabular screws used in THA performed by DAA was significantly less than during a posterior surgical approach, and supplemental screw fixation was associated with a significantly increased likelihood of requiring a blood transfusion. Surgeons should consider these factors when deciding which THA approach may be best for an individual patient.
Application of Quality by Design Approach to Bioanalysis: Development of a Method for Elvitegravir Quantification in Human Plasma
Authors: Baldelli Sara , Marrubini Giorgio , Cattaneo Dario , Clementi Emilio , Cerea Matteo 
Published: June 2017

Background:
The application of Quality by Design (QbD) principles in clinical laboratories can help to develop an analytical method through a systematic approach, providing a significant advance over the traditional heuristic and empirical methodology. In this work, we applied for the first time the QbD concept in the development of a method for drug quantification in human plasma using elvitegravir as the test molecule.

Methods:
The goal of the study was to develop a fast and inexpensive quantification method, with precision and accuracy as requested by the European Medicines Agency guidelines on bioanalytical method validation. The method was divided into operative units, and for each unit critical variables affecting the results were identified. A risk analysis was performed to select critical process parameters that should be introduced in the design of experiments (DoEs). Different DoEs were used depending on the phase of advancement of the study.

Results:
Protein precipitation and high-performance liquid chromatography–tandem mass spectrometry were selected as the techniques to be investigated. For every operative unit (sample preparation, chromatographic conditions, and detector settings), a model based on factors affecting the responses was developed and optimized. The obtained method was validated and clinically applied with success.

Conclusions:
To the best of our knowledge, this is the first investigation thoroughly addressing the application of QbD to the analysis of a drug in a biological matrix applied in a clinical laboratory. The extensive optimization process generated a robust method compliant with its intended use. The performance of the method is continuously monitored using control charts.
Tissue Expanders and Proton Beam Radiotherapy: What You Need to Know
Authors: Howarth Ashley L. , Niska Joshua R. , Brooks Kenneth , Anand Aman , Bues Martin , Vargas Carlos E. , Mahabir Raman C. 
Published: June 2017

Summary:
Proton beam radiotherapy (PBR) has gained acceptance for the treatment of breast cancer because of unique beam characteristics that allow superior dose distributions with optimal dose to the target and limited collateral damage to adjacent normal tissue, especially to the heart and lungs. To determine the compatibility of breast tissue expanders (TEs) with PBR, we evaluated the structural and dosimetric properties of 2 ex vivo models: 1 model with internal struts and another model without an internal structure. Although the struts appeared to have minimal impact, we found that the metal TE port alters PBR dynamics, which may increase proton beam range uncertainty. Therefore, submuscular TE placement may be preferable to subcutaneous TE placement to reduce the interaction of the TE and proton beam. This will reduce range uncertainty and allow for more ideal radiation dose distribution.
A Unique Lymphaticovenous Supermicrosurgery Training Curriculum: Reflections on Validation and Competency Thresholds
Authors: Pafitanis Georgios , Narushima Mitsunaga , Harima Mitsunobu , Ghanem Ali , Myers Simon , Koshima Isao 
Published: June 2017

Summary:
Supermicrosurgery is becoming a commonly used technique in various subspecialties of reconstructive surgery. However, there is a lack of standardization and validation in novel supermicrosurgical training. Current simulation training programs are not adequately focused on the challenges encountered during clinical supermicrosurgery practice. This article describes the authors’ experience utilizing a supermicrosurgery competency-based training curriculum, in a simulation-based environment, toward safe clinical practice for lymphatic submillimeter supermicrovascular surgery. This article demonstrates the senior authors’ (I.K.) Halstedian competency-based curriculum for lymphaticovenous anastomosis training. Further, a step-by-step training utilizing the chicken thigh and the living rat high fidelity simulation models, which subsequently allows supervised one-to-one clinical training with verified clinical competency outcomes, are demonstrated.
A systems analysis of ward rounds in plastic surgery at a single center
Authors: Agha Riaz 
Published: June 2017

Introduction:
Ward rounds permeate health care delivery worldwide and form an important daily activity within all hospitals. In this study, the daily morning ward round in plastic surgery was examined from a teleological and systems point of view.

Methods:
Data were gathered from the following sources to inform the systems analysis: patient interviews, staff interviews, direct observations of the ward round on multiple occasions, and through process mapping.

Results:
To better understand the ward and its layout, a schematic of it was developed. Following observations of the ward round and the way in which decisions are made on it, an IDEF0 map was developed. Three patients were invited to take part in the study. Three members of staff were interviewed. The overarching themes from the interviews related to aspects of communication which this paper details.

Conclusions:
This small-scale study demonstrates how the ward round as a process can be assessed, including product quality, process quality, the measurement and management of capacity, the role of standardization, the role and significance of bottlenecks, the key information flows, including the role of feedback, and the motivation and incentives of system participants and ideas for improvement generated.
Randomized Trial of Reducing Ambulatory Malpractice and Safety Risk
Authors: Schiff Gordon D. , Reyes Nieva Harry , Griswold Paula , Leydon Nicholas , Ling Judy , Federico Frank , Keohane Carol , Ellis Bonnie R. , Foskett Cathy , Orav E. John , Yoon Catherine , Goldmann Don , Weissman Joel S. , Bates David W. , Biondolillo Madeleine , Singer Sara J. 
Published: June 2017

Objective:
Evaluate application of quality improvement approaches to key ambulatory malpractice risk and safety areas.

Study Setting:
In total, 25 small-to-medium-sized primary care practices (16 intervention; 9 control) in Massachusetts.

Study Design:
Controlled trial of a 15-month intervention including exposure to a learning network, webinars, face-to-face meetings, and coaching by improvement advisors targeting “3+1” high-risk domains: test result, referral, and medication management plus culture/communication issues evaluated by survey and chart review tools.

Data Collection Methods:
Chart reviews conducted at baseline and postintervention for intervention sites. Staff and patient survey data collected at baseline and postintervention for intervention and control sites.

Principal Findings:
Chart reviews demonstrated significant improvements in documentation of abnormal results, patient notification, documentation of an action or treatment plan, and evidence of a completed plan (all P<0.001). Mean days between laboratory test date and evidence of completed action/treatment plan decreased by 19.4 days (P<0.001). Staff surveys showed modest but nonsignificant improvement for intervention practices relative to controls overall and for the 3 high-risk domains that were the focus of PROMISES.

Conclusions:
A consortium of stakeholders, quality improvement tools, coaches, and learning network decreased selected ambulatory safety risks often seen in malpractice claims.
Pediatric Procedural Sedation Using the Combination of Ketamine and Propofol Outside of the Emergency Department: A Report From the Pediatric Sedation Research Consortium
Authors: Grunwell Jocelyn R. , Travers Curtis , Stormorken Anne G. , Scherrer Patricia D. , Chumpitazi Corrie E. , Stockwell Jana A. , Roback Mark G. , Cravero Joseph , Kamat Pradip P. 
Published: June 2017

Objectives:
Outcomes associated with a sedative regimen comprised ketamine + propofol for pediatric procedural sedation outside of both the pediatric emergency department and operating room are underreported. We used the Pediatric Sedation Research Consortium database to describe a multicenter experience with ketamine + propofol by pediatric sedation providers.

Design:
Prospective observational study of children receiving IV ketamine + propofol for procedural sedation outside of the operating room and emergency department using data abstracted from the Pediatric Sedation Research Consortium during 2007–2015.

Setting:
Procedural sedation services from academic, community, free-standing children’s hospitals, and pediatric wards within general hospitals.

Patients:
Children from birth to less than or equal to 21 years old.

Interventions:
None.

Measurements and Main Results:
A total of 7,313 pediatric procedural sedations were performed using IV ketamine + propofol as the primary sedative regimen. Median age was 84 months (range, < 1 mo to ≤ 21 yr; interquartile range, 36–144); 80.6% were American Society of Anesthesiologists-Physical Status less than III. The majority of sedation was performed in dedicated sedation or radiology units (76.1%). Procedures were successfully completed in 99.8% of patients. Anticholinergics (glycopyrrolate and atropine) or benzodiazepines (midazolam and lorazepam) were used in 14.2% and 41.3%, respectively. The overall adverse event and serious adverse event rates were 9.79% (95% CI, 9.12–10.49%) and 3.47% (95% CI, 3.07–3.92%), respectively. No deaths occurred. Risk factors associated with an increase in odds of adverse event included ASA status greater than or equal to III, dental suite, cardiac catheterization laboratory or radiology/sedation suite location, a primary diagnosis of having a gastrointestinal illness, and the coadministration of an anticholinergic.

Conclusions:
Using Pediatric Sedation Research Consortium data, we describe the diverse use of IV ketamine + propofol for procedural sedation in the largest reported cohort of children to date. Data from this study may be used to design sufficiently powered prospective randomized, double-blind studies comparing outcomes of sedation between commonly administered sedative and analgesic medication regimens.
Population Pharmacokinetics and Pharmacodynamic Target Attainment of Vancomycin in Neonates on Extracorporeal Life Support
Authors: Cies Jeffrey J. , Moore Wayne S. , Nichols Kristen , Knoderer Chad A. , Carella Dominick M. , Chopra Arun 
Published: June 2017

Objectives:To evaluate the population pharmacokinetics and pharmacodynamic target attainment of vancomycin in neonates with a contemporary ¼-inch extracorporeal life support circuit with a Quadrox-iD Pediatric oxygenator (Maquet Cardiovascular, LLC, Wayne, NJ).Design:Retrospective medical record review.Setting:Two free-standing tertiary/quaternary pediatric children’s hospitals.Patients:Neonates receiving either veno-arterial or veno-venous extracorporeal life support and vancomycin for empiric or definitive therapy with resulting serum concentrations.Interventions:None.Measurements and Main Results:Twelve patients with a median gestations age of 39 weeks (range 36–41 wk) and a median postnatal age of 9.5 days (range 0–28 d) accounted for 14 courses of vancomycin therapy while on extracorporeal life support and were included in the analysis. The median weight was 3.1 kg (range 2.2–4.41 kg) with five of 12 patients (41.7%) being female. Vancomycin concentrations were best described by an one-compartment model incorporating allometric scaling of estimated glomerular filtration rate on clearance. The mean total body clearance (mL/min/kg) for the population was 3.48 ± 1.31 mL/min/kg, and the mean total volume of distribution (L/kg) for the population was 1.2 ± 0.4 L/kg. The intermittent and continuous infusion dosing regimens that provided for the highest percentage of trough concentrations in the range of 10–20 mg/L were the 10 mg/kg/dose IV q8h, 12.5 mg/kg/dose IV q8–12h, 15 mg/kg/dose IV q12h, and 20 mg/kg/dose IV q12h, and the 20, 25, and 30 mg/kg/d continuous infusion regimens, respectively. All regimens allowed for an area under the concentration:minimum inhibitory concentration ratio of 400:1 for minimum inhibitory concentrations of less than or equal to 0.5 mg/L for a 90% PTA. None of the simulated regimens had a greater than 90% probability of achieving an area under the concentration:minimum inhibitory concentration ratio of 400:1 for vancomycin minimum inhibitory concentrations greater than or equal to 1 mg/L while maintaining trough concentrations in the range of 10–20 mg/L.Conclusions:To our knowledge, this is the first pharmacokinetic and pharmacodynamic study of neonates receiving vancomycin with a contemporary ¼-inch extracorporeal life support circuit including the Quadrox-iD Pediatric oxygenator (Maquet Cardiovascular, LLC). The data suggest differences in vancomycin pharmacokinetics compared with previous extracorporeal life support data, notably a more rapid clearance, which could result in lower vancomycin concentrations. Considering this, a more aggressive initial dosing regimen may need to be employed in infants on extracorporeal life support.