bluuebunny/crossref_metadata_2025_split huggingface dataset:
Reference Values for Shear Wave Elastography of Neck and Shoulder Muscles in Healthy Individuals
Authors: Ewertsen Caroline , Carlsen Jonathan , Perveez Mohammed , Schytz Henrik 
Published: April 2018

Abstract
Purpose to establish reference values for ultrasound shear-wave elastography for pericranial muscles in healthy individuals (m. trapezius, m. splenius capitis, m. semispinalis capitis, m. sternocleidomastoideus and m. masseter). Also to evaluate day-to-day variations in the shear-wave speeds and evaluate the effect of the pennation of the muscle fibers, ie scanning parallel or perpendicularly to the fibers.
Materials and Methods 10 healthy individuals (5 males and 5 females) had their pericranial muscles examined with shear-wave elastography in two orthogonal planes on two different days for their dominant and non-dominant side. Mean shear wave speeds from 5 ROI’s in each muscle, for each scan plane for the dominant and non-dominant side for the two days were calculated. The effect of the different parameters – muscle pennation, gender, dominant vs non-dominant side and day was evaluated.
Results The effect of scan plane in relation to muscle pennation was statistically significant (p<0.0001). The mean shear-wave speed when scanning parallel to the muscle fibers was significantly higher than the mean shear-wave speed when scanning perpendicularly to the fibers. The day-to-day variation was statistically significant (p=0.0258), but not clinically relevant. Shear-wave speeds differed significantly between muscles. Mean shear wave speeds (m/s) for the muscles in the parallel plane were: for masseter 2.45 (SD:+/−0.25), semispinal 3.36 (SD:+/−0.75), splenius 3.04 (SD:+/−0.65), sternocleidomastoid 2.75 (SD:+/−0.23), trapezius 3.20 (SD:+/−0.27) and trapezius lateral 3.87 (SD:+/−3.87).
Conclusion The shear wave speed variation depended on the direction of scanning. Shear wave elastography may be a method to evaluate muscle stiffness in patients suffering from chronic neck pain.
Objectively measured physical activity, body composition and physical fitness: Cross‐sectional associations in 9‐ to 15‐year‐old children
Authors: Joensuu Laura , Syväoja Heidi , Kallio Jouni , Kulmala Janne , Kujala Urho M. , Tammelin Tuija H. 
Published: April 2018

AbstractThe aim of this study was to examine and quantify the cross‐sectional associations of body composition (BC), physical activity (PA) and sedentary time (ST) with physical fitness (PF) in children and adolescents. A sample of 594 Finnish students (56% girls), aged 9–15 (12.4 ± 1.3 years) were selected for a study performed in 2013. The measurements of the Move! monitoring system for physical functional capacity were used to measure cardiorespiratory and musculoskeletal fitness and fundamental movement skills. Moderate‐to‐vigorous PA (MVPA) and ST were measured objectively with an accelerometer and BC by a bioelectrical impedance analysis. Fat mass index (FMI) and fat‐free mass index (FFMI) were calculated to represent height‐adjusted BC. Associations were explored with a linear regression model. In general, FMI had statistically significant negative associations, while FFMI and MVPA had positive associations with PF. No statistically significant associations were observed between ST and PF. In general, FMI had the strongest association with PF, although some variation occurred with sex and PF component. However, associations were practically relevant only in 20‐m shuttle run, push‐up, curl‐up and 5‐leaps test. For example, approximately 5 kg increase in fat mass in 155 cm tall children was estimated to correspond to  8 laps in 20‐m shuttle run. Similar increase in fat‐free mass corresponded to +4 and +6 laps, and 10 min increase in daily MVPA +3 and +2 laps in 20‐m shuttle run, in boys and girls, respectively. Understanding these associations is necessary when interpreting children's PF and designing interventions.
The Influence Analysis of the Rainfall Meteorological Conditions on the Operation of the Balloon Borne Radar in Plateau
Authors: Li Qiong , Geng Fangzhi 
Published: April 2018

Abstract
Based on the characteristics of complex terrain and different seasons’ weather in Qinghai Tibet Plateau, through statistic the daily rainfall that from 2002 to 2012, nearly 11 years, by Bomi meteorological station, Bomi area rainfall forecast model is established, and which can provide the basis forecasting for dangerous weather warning system on the balloon borne radar in the next step, to protect the balloon borne radar equipment’s safety work and combat effectiveness.
B-cell receptor reconstruction from single-cell RNA-seq with VDJPuzzle
Authors: Rizzetto Simone , Koppstein David N P , Samir Jerome , Singh Mandeep , Reed Joanne H , Cai Curtis H , Lloyd Andrew R , Eltahla Auda A , Goodnow Christopher C , Luciani Fabio 
Published: April 2018

Abstract

Motivation
The B-cell receptor (BCR) performs essential functions for the adaptive immune system including recognition of pathogen-derived antigens. The vast repertoire and adaptive variation of BCR sequences due to V(D)J recombination and somatic hypermutation necessitates single-cell characterization of BCR sequences. Single-cell RNA sequencing presents the opportunity for simultaneous capture of paired BCR heavy and light chains and the transcriptomic signature.

Results
We developed VDJPuzzle, a novel bioinformatic tool that reconstructs productive, full-length B-cell receptor sequences of both heavy and light chains and extract somatic mutations on the VDJ region. VDJPuzzle successfully reconstructed BCRs from 100% (n=117) human and 96.5% (n=200) murine B cells. The reconstructed BCRs were successfully validated with single-cell Sanger sequencing.

Availability and implementation
VDJPuzzle is available at https://bitbucket.org/kirbyvisp/vdjpuzzle2.

Supplementary information
Supplementary data are available at Bioinformatics online.
Sox17 is essential for proper formation of the marginal zone of extraembryonic endoderm adjacent to a developing mouse placental disk†
Authors: Igarashi Hitomi , Uemura Mami , Hiramatsu Ryuji , Hiramatsu Ryuto , Segami Saki , Pattarapanawan Montri , Hirate Yoshikazu , Yoshimura Yuki , Hashimoto Haruo , Higashiyama Hiroki , Sumitomo Hiroyuki , Kurohmaru Masamichi , Saijoh Yukio , Suemizu Hiroshi , Kanai-Azuma Masami , Kanai Yoshiakira 
Published: April 2018

AbstractIn mouse conceptus, two yolk-sac membranes, the parietal endoderm (PE) and visceral endoderm (VE), are involved in protecting and nourishing early-somite-stage embryos prior to the establishment of placental circulation. Both PE and VE membranes are tightly anchored to the marginal edge of the developing placental disk, in which the extraembryonic endoderm (marginal zone endoderm: ME) shows the typical flat epithelial morphology intermediate between those of PE and VE in vivo. However, the molecular characteristics and functions of the ME in mouse placentation remain unclear. Here, we show that SOX17, not SOX7, is continuously expressed in the ME cells, whereas both SOX17 and SOX7 are coexpressed in PE cells, by at least 10.5 days postconception. The Sox17-null conceptus, but not the Sox7-null one, showed the ectopic appearance of squamous VE-like epithelial cells in the presumptive ME region, together with reduced cell density and aberrant morphology of PE cells. Such aberrant ME formation in the Sox17-null extraembryonic endoderm was not rescued by the chimeric embryo replaced with the wild-type gut endoderm by the injection of wild-type ES cells into the Sox17-null blastocyst, suggesting the cell autonomous defects in the extraembryonic endoderm of Sox17-null concepti. These findings provide direct evidence of the crucial roles of SOX17 in proper formation and maintenance of the ME region, highlighting a novel entry point to understand the in vivo VE-to-PE transition in the marginal edge of developing placenta.
Training to Teach Science: Experimental Evidence from Argentina
Authors: Albornoz Facundo , Anauati María Victoria , Furman Melina , Luzuriaga Mariana , Podestá María Eugenia , Taylor Inés 
Published: April 2018

AbstractThis paper evaluates the learning impact of different teacher training methods using a randomized controlled trial implemented in 70 state schools in Buenos Aires, Argentina. A control group receiving standard teacher training was compared with two alternative treatment arms: providing a structured curriculum unit or receiving both the unit and weekly coaching. Following a 12-week intervention, there are substantial learning gains for students whose teachers were trained using structured curriculum units, as well as for those whose teachers received coaching (between 55 percent and 64 percent of a standard deviation more than those students in the control group). Coaching teachers does not appear to be cost-effective, as the unit cost per 0.1 standard deviation is more than twice the cost of using only the structured curriculum unit. However, additional coaching is particularly beneficial for inexperienced teachers with less than two years of teaching science. Coaching teachers also showed specific gains for girls, who both learned and declared to enjoy science lessons more. High-performing students especially benefited from both interventions, with students from coached teachers performing particularly well in harder questions. Using structured curriculum units and providing coaching also affected teacher perceptions: teachers expressed that they enjoyed teaching science more and taught more hours of science, and that their students developed more skills. Results from a follow-up survey suggest persistent change in teacher practice, with the vast majority reporting using the structured curriculum unit one year after the intervention.
Moulages: Art and History of Medicine
Authors: Nocito Ana L. , Berra Hector H. 
Published: April 2018

Abstract:
The aim of this article is to introduce the museum we have at the Pathology Department, School of Medicine of the National University of Rosario, Argentina. The origin dates from to 1922 when Dermatology Professor Dr. Enrique P. Fidanza bought moulages at L'Hôpital Saint-Louis in Paris for the purpose of teaching. The collection included around 100 moulages and was worth approximately 1000 dollars. These pieces were exhibited at the Dermatology Department for many years and later moved to the Pathology Department where some pieces started being repaired, whereas others have deteriorated. The collection is composed of 100 moulages done by a French craftsman by the name of Niclet and 258 made by Argentine craftsmen including Alba Ramirez and G. Rouzaut, among others. The pieces are classified according to different dermatological diseases such as: the different stages of syphilis, lupus, benign and malignant neoplasm, infectious diseases, etc.
The Importance of Heart Rate in Heart Failure and Reduced Ejection Fraction
Authors: Prasun Marilyn A. , Albert Nancy M. 
Published: April 2018

Background:
Heart failure with reduced ejection fraction (HFrEF) is a progressive, chronic, and burdensome cardiovascular condition. It is associated with limiting symptoms, such as dyspnea and fatigue; a decline in functional capacity; and premature mortality and hospitalization. In heart failure (HF) management, heart rate is commonly assessed yet frequently overlooked as a modifiable risk factor and a predictor of mortality. An elevated heart rate increases myocardial demand and decreases diastolic filling time. Hospitalized patients with HFrEF who have a heart rate greater than 70 beats per minute at discharge were found to have lower survival rates.

Purpose:
The aims of this study were to review the association between heart rate and clinical outcome in patients with HF and discuss the contribution of heart rate to HFrEF pathophysiology. Medications currently used to modulate heart rate in patients with HF are also reviewed.

Conclusions:
In patients with HFrEF, an elevated heart rate contributes to HF progression, and it is both a prognostic and modifiable risk factor. Medications such as an evidence-based β-blockers, digoxin, and ivabradine are recommended for modulation of heart rate in patients with HFrEF.

Clinical Implications:
Nurses play a pivotal role in managing HFrEF and must understand current evidence of the pathophysiology of elevated heart rate, risks, and management strategies. Early recognition of elevated heart rate and application of guideline-directed pharmacologic treatment for patients with HFrEF and an elevated heart rate remains key to improving patient outcomes.
Genetic Polymorphisms Associated With Constipation and Anticholinergic Symptoms in Patients Receiving Clozapine
Authors: Solismaa Anssi , Kampman Olli , Lyytikäinen Leo-Pekka , Seppälä Niko , Viikki Merja , Mononen Nina , Lehtimäki Terho , Leinonen Esa 
Published: April 2018

Abstract

Background
Clozapine impairs gastrointestinal motility owing to its anticholinergic and antiserotonergic properties. This commonly leads to constipation and potentially to more severe complications such as bowel obstruction and ischemia. The aim of this study was to determine whether genetic variations in the genes encoding muscarinic and serotonergic receptors (CHRM2, CHRM3, HTR2, HTR3, HTR4, and HTR7) explain the variations in incidence of constipation and anticholinergic symptoms during clozapine treatment. Genes associated with opiate-induced constipation were also included in this analysis (TPH1, OPRM1, ABCB1, and COMT).

Procedures
Blood samples from 176 clozapine-treated, Finnish, white patients with schizophrenia were genotyped. Constipation and anticholinergic symptoms were rated using the Liverpool University Neuroleptic Side Effect Rating Scale self-report questionnaire. In total, 192 single-nucleotide polymorphisms (SNPs) were detected and grouped to formulate a weighted genetic-risk score (GRS).

Results
No significant associations between individual SNPs or GRSs and constipation or laxative use were observed. A GRS of 19 SNPs in CHRM2, CHRM3, HTR3C, HTR7, ABCB1, OPRM1, and TPH1 was associated with anticholinergic symptoms in a generalized linear univariate model, with body mass index, clozapine monotherapy, and GRS as explaining variables (permuted P = 0.014). Generalized linear univariate model analysis performed on the opiate-induced constipation–associated SNPs and a single CHRM3 SNP revealed an association between anticholinergic symptoms and a score of 8 SNPs (adjusted P = 0.038, permuted P = 0.002).

Conclusions
Two GRSs are able to predict the risk of anticholinergic symptoms in patients receiving clozapine and possibly an increased risk of gastrointestinal hypomotility.
A Comprehensive Onboarding and Orientation Plan for Neurocritical Care Advanced Practice Providers
Authors: Langley Tamra M. , Dority Jeremy , Fraser Justin F. , Hatton Kevin W. 
Published: April 2018

ABSTRACT

Background: As the role of advanced practice providers (APPs) expands to include increasingly complex patient care within the intensive care unit, the educational needs of these providers must also be expanded. An onboarding process was designed for APPs in the neurocritical care service line. Methods: Onboarding for new APPs revolved around 5 specific areas: candidate selection, proctor assignment, 3-phased orientation process, remediation, and mentorship. To ensure effective training for APPs, using the most time-conscious approach, the backbone of the process is a structured curriculum. This was developed and integrated within the standard orientation and onboarding process. The curriculum design incorporated measurable learning goals, objective assessments of phased goal achievements, and opportunities for remediation. Results: The neurocritical care service implemented an onboarding process in 2014. Four APPs (3 nurse practitioners and 1 physician assistant) were employed by the department before the implementation of the orientation program. The length of employment ranged from 1 to 4 years. Lack of clinical knowledge and/or sufficient training was cited as reasons for departure from the position in 2 of the 4 APPs, as either self-expression or peer evaluation. Since implementation of this program, 12 APPs have completed the program, of which 10 remain within the division, creating an 83% retention rate. Discussion: The onboarding process, including a 3-phased, structured orientation plan for neurocritical care, has increased APP retention since its implementation. The educational model, along with proctoring and mentorship, has improved clinical knowledge and increased nurse practitioner retention. A larger-scale study would help to support the validity of this onboarding process.
Electronic Health Records in Simulation Education
Authors: Wilbanks Bryan A. , Watts Penni I. , Epps Chad A. 
Published: April 2018

Summary Statement
During the last decade, the use of electronic health records (EHRs) in clinical settings has risen sharply. Many clinical education programs have not incorporated the use of electronic documentation into their curriculum. It is important to incorporate technologies that will be used in real-world settings into educational clinical simulations to better prepare students for clinical practice and promote patient safety. Electronic documentation can be harder to teach to students because it requires a more in-depth orientation on how to use the electronic documentation system and because health care organizations often give students limited or no access to the documentation system. This review will include a discussion on the benefits and disadvantages of using educational EHRs, barriers and facilitators to implementing educational EHRs, and best practices for incorporating educational EHRs into current educational curriculums.
Distinguishing cells from empty droplets in droplet-based single-cell RNA sequencing data
Authors: Lun Aaron T. L. , Riesenfeld Samantha , Andrews Tallulah ,   The Phuong Dao, Gomes Tomas ,   participants in the 1st Human Cell Atlas Jamboree, Marioni John C. 
Published: April 2018

AbstractDroplet-based single-cell RNA sequencing protocols have dramatically increased the throughput and efficiency of single-cell transcriptomics studies. A key computational challenge when processing these data is to distinguish libraries for real cells from empty droplets. Existing methods for cell calling set a minimum threshold on the total unique molecular identifier (UMI) count for each library, which indiscriminately discards cell libraries with low UMI counts. Here, we describe a new statistical method for calling cells from droplet-based data, based on detecting significant deviations from the expression profile of the ambient solution. Using simulations, we demonstrate that our method has greater power than existing approaches for detecting cell libraries with low UMI counts, while controlling the false discovery rate among detected cells. We also apply our method to real data, where we show that the use of our method results in the retention of distinct cell types that would otherwise have been discarded.
A systematic review of social contact surveys to inform transmission models of close contact infections
Authors: Hoang Thang Van , Coletti Pietro , Melegaro Alessia , Wallinga Jacco , Grijalva Carlos , Edmunds W. John , Beutels Philippe , Hens Niel 
Published: April 2018

AbstractSocial contact data are increasingly being used to inform models for infectious disease spread with the aim of guiding effective policies on disease prevention and control. In this paper, we undertake a systematic review of the study design, statistical analyses and outcomes of the many social contact surveys that have been published. Our primary focus is to identify the designs that have worked best and the most important determinants and to highlight the most robust ﬁndings.Two publicly accessible online databases were systematically searched for articles regarding social contact surveys. PRISMA guidelines were followed as closely as possible. In total, 64 social contact surveys were identiﬁed. These surveys were conducted in 24 countries, and more than 80% of the surveys were conducted in high-income countries. Study settings included general population (58%), schools/universities (37%) and health care/conference/research institutes (5%). The majority of studies did not focus on a speciﬁc age group (38%), whereas others focused on adults (32%) or children (19%). Retrospective and prospective designs were used mostly (45% and 41% of the surveys, respectively) with 6% using both for comparison purposes. The deﬁnition of a contact varied among surveys, e.g. a non-physical contact may require conversation, close proximity or both. Age, time schedule (e.g., weekday/weekend) and household size were identiﬁed as relevant determinants for contact pattern across a large number of studies. The surveys present a wide range of study designs. Throughout, we found that the overall contact patterns were remarkably robust for the study details. By considering the most common approach in each aspect of design (e.g., sampling schemes, data collection, deﬁnition of contact), we could identify a common practice approach that can be used to facilitate comparison between studies and for benchmarking future studies.
Natural selection on gene-specific codon usage bias is common across eukaryotes
Authors: Peng Zhen , Zaher Hani , Ben-Shahar Yehuda 
Published: April 2018

SUMMARYAlthough the actual molecular evolutionary forces that shape differences in codon usage across species remain poorly understood, majority of synonymous mutations are assumed to be functionally neutral because they do not affect protein sequences. However, empirical studies suggest that some synonymous mutations can have phenotypic consequences. Here we show that in contrast to the current dogma, natural selection on gene-specific codon usage bias is common across Eukaryota. Furthermore, by using bioinformatic and experimental approaches, we demonstrate that specific combinations of rare codons contribute to the spatial and sex-related regulation of some protein-coding genes inDrosophila melanogaster.Together, these data indicate that natural selection can shape gene-specific codon usage bias, which therefore, represents an overlooked genomic feature that is likely to play an important role in the spatial and temporal regulation of gene functions. Hence, the broadly accepted dogma that synonymous mutations are in general functionally neutral should be reconsidered.