bluuebunny/crossref_metadata_2025_split huggingface dataset:
Optimization of Data Collection during Public Health Emergencies—Experience with APACHE II Score
Authors: White Elizabeth , Collins Rossetti Sarah , Karipineni Neelima , Maviglia Saverio , Bartz Raquel , Bhagwanjee Satish , Cobb J. Perren , Rocha Roberto , Rocha Beatriz 
Published: April 2019

Background Capturing accurate clinical data in real time is a challenge during public health emergencies. The United States Critical Illness and Injury Trials Group-Program for Emergency Preparedness is committed to improving these preparedness efforts.
Objectives We aimed to create an electronic Acute Physiology and Chronic Health Evaluation (APACHE) II data collection instrument that (1) leverages Research Electronic Data Capture (REDCap) automated calculations and logic, (2) may be shared across sites, (3) overcomes limitations in existing APACHE II instruments in the REDCap library, and (4) suggests changes to be made to data collection instruments during emergencies.
Methods The APACHE II instrument was implemented using REDCap. Data fields were divided into four sections: age, Acute Physiology, Glasgow Coma Scale, and chronic health status. Usability testing was followed by two preliminary evaluations: a comparison to existing APACHE II instruments and a simulated emergency exercise.
Results The final instrument consisted of 34 data fields. It produced an accurate APACHE II score and was faster to complete than two previous implementations (average of 97.5 seconds vs. 323.5 and 183.5 seconds). During the simulated emergency exercise, the instrument was used at 10 sites to create 34 patient records; median time to complete the instrument was 150.5 seconds.
Conclusion This project demonstrated feasibility of improving the accuracy and efficiency of a data collection instrument. Future efforts should focus on expanding these methods to develop other scoring tools for use during emergencies and additional testing to ensure it is ready for use during a real emergency.
Dorsal Roof Technique for Dorsum Preservation in Rhinoplasty
Authors: Taş Süleyman 
Published: April 2019

Abstract

Background
Management of the nasal dorsum is an important part of rhinoplasty. Hump removal results in the destruction of the internal valve and keystone area, which are reconstructed with either spreader flaps or grafts for aesthetic and functional reasons.

Objectives
The goal of this work was to present the dorsal roof technique for both dorsum reduction and narrowing during rhinoplasty.

Methods
Fifty-two patients (35 females, 17 males) underwent septorhinoplasty surgery with the dorsal roof technique. During the follow-up period, all patients were photographed in the standard views. Photos were examined by two independent plastic surgeons. The pyramidal angles of the patients were measured with a protractor preoperatively and 1 year postoperatively. A rhinoplasty outcomes evaluation questionnaire was administered to all patients at the 1-year follow-up visit. Functional improvement was assessed utilizing self-evaluated nasal patency. The chi-square test was employed for statistical analyses. Data were evaluated retrospectively.

Results
Of the 52 patients, 44 completed the 1-year follow-up period and rhinoplasty outcomes evaluation questionnaire. During the follow-up period, no irregularity or residual hump was detected. Significant narrowing was achieved (P &lt; 0.001). High patient satisfaction was achieved, and no functional or aesthetic complications were encountered.

Conclusions
Whenever possible, the dorsal roof technique is preferred to resection or camouflage the dorsum. This technique allows treatment of the wide dorsum, wide nasal base, and dorsal hump without resection, thus maintaining the integrity of the dorsal bone-cartilage complex.

Level of Evidence: 4
ORCA: a comprehensive bioinformatics container environment for education and research
Authors: Jackman Shaun D , Mozgacheva Tatyana , Chen Susie , O’Huiginn Brendan , Bailey Lance , Birol Inanc , Jones Steven J M 
Published: April 2019

Abstract

Summary
The ORCA bioinformatics environment is a Docker image that contains hundreds of bioinformatics tools and their dependencies. The ORCA image and accompanying server infrastructure provide a comprehensive bioinformatics environment for education and research. The ORCA environment on a server is implemented using Docker containers, but without requiring users to interact directly with Docker, suitable for novices who may not yet have familiarity with managing containers. ORCA has been used successfully to provide a private bioinformatics environment to external collaborators at a large genome institute, for teaching an undergraduate class on bioinformatics targeted at biologists, and to provide a ready-to-go bioinformatics suite for a hackathon. Using ORCA eliminates time that would be spent debugging software installation issues, so that time may be better spent on education and research.

Availability and implementation
The ORCA Docker image is available at https://hub.docker.com/r/bcgsc/orca/. The source code of ORCA is available at https://github.com/bcgsc/orca under the MIT license.
BHap: a novel approach for bacterial haplotype reconstruction
Authors: Li Xin , Saadat Samaneh , Hu Haiyan , Li Xiaoman 
Published: April 2019

Abstract

Motivation
The bacterial haplotype reconstruction is critical for selecting proper treatments for diseases caused by unknown haplotypes. Existing methods and tools do not work well on this task, because they are usually developed for viral instead of bacterial populations.

Results
In this study, we developed BHap, a novel algorithm based on fuzzy flow networks, for reconstructing bacterial haplotypes from next generation sequencing data. Tested on simulated and experimental datasets, we showed that BHap was capable of reconstructing haplotypes of bacterial populations with an average F1 score of 0.87, an average precision of 0.87 and an average recall of 0.88. We also demonstrated that BHap had a low susceptibility to sequencing errors, was capable of reconstructing haplotypes with low coverage and could handle a wide range of mutation rates. Compared with existing approaches, BHap outperformed them in terms of higher F1 scores, better precision, better recall and more accurate estimation of the number of haplotypes.

Availability and implementation
The BHap tool is available at http://www.cs.ucf.edu/∼xiaoman/BHap/.

Supplementary information
Supplementary data are available at Bioinformatics online.
Active peristaltic movements and fluid production of the mouse oviduct: their roles in fluid and sperm transport and fertilization†
Authors: Hino Toshiaki , Yanagimachi Ryuzo 
Published: April 2019

AbstractTo study how the oviduct behaves in relation to fluid secretion and sperm transport, ovary–oviduct–uterus complexes of the mouse were installed in a fluid-circulating chamber without disturbing the blood circulation or parasympathetic innervation. Injection of a bolus of Indian ink into the lower isthmus revealed very active adovarian peristalsis of the isthmus, which was most prominent during the periovulatory period. Oviduct fluid, secreted by the entire length of the isthmus, was rapidly transported to the ampulla and ovarian bursa before draining into the peritoneal cavity. The upper isthmus, in particular the isthmic–ampullary junction, was responsible for this adovarian fluid flow. Peristalsis of the oviduct, undisturbed flow of oviduct fluid from the isthmus to the peritoneal cavity, and the spermatozoon's own motility all contribute to efficient sperm ascent and to fertilization within the oviduct. Therefore, chemotaxis, rheotaxis, and thermotaxis of spermatozoa toward oocyte–cumulus complexes in the ampulla are all unlikely mechanisms for explaining sperm–oocyte contact and successful fertilization, given the rapid adovarian flow of oviduct fluid in this species.
Conservation of chicken male germline by orthotopic transplantation of primordial germ cells from genetically distant donors†
Authors: Mucksová Jitka , Reinišová Markéta , Kalina Jiří , Lejčková Barbora , Hejnar Jiří , Trefil Pavel 
Published: April 2019

Abstract
Successful derivation and cultivation of primordial germ cells (PGCs) opened the way to efficient transgenesis and genome editing in the chicken. Furthermore, implantation of male PGCs from non-chicken galliform species into the chicken embryos resulted in cross-species germline chimeras and viable offspring. We have recently improved the PGC technology by demonstrating that chicken male PGCs transplanted into the testes of adult cockerel recipients mature into functional sperms. However, the availability of this orthotopic transplantation for cross-species transfer remains to be explored. Here we tested the capacity of genetically distant male PGCs to mature in the microenvironment of adult testes. We derived PGCs from the Chinese black-bone Silkie and transplanted them into infertile White Leghorn cockerels. Within 15–18 weeks after transplantation, we observed restoration of spermatogenesis in recipient cockerels and production of healthy progeny derived from the transplanted PGCs. Our findings also indicate the possibility of cross-species orthotopic transplantation of PGCs. Thus, our results might contribute to the preservation of endangered avian species and maintaining the genetic variability of the domestic chicken.
How to Make a Weed: The Saga of the Slender False Brome Invasion in the North American West and Lessons for the Future
Authors: Cruzan Mitchell B 
Published: April 2019

Abstract
Historical herbarium collections and genetic analyses indicate that slender false brome (Brachypodium sylvaticum) was first introduced in test gardens in Oregon in the early 1900 s as part of the USDA’s plant introduction program. A small number of naturalized populations were established, but it was not until several decades later that this alien species became an aggressive invader. The Oregon invasive strains of false brome were generated as a consequence of mating among genetically divergent lineages. The resulting hybrid populations contained high levels of genetic variation that fueled the evolution of specific adaptations to the Pacific Northwest climate and ultimately generated genetically superior lineages. Although the false brome invasion has caused significant ecological and economic harm and is expected to continue spreading across western North America, understanding the circumstances that have promoted its success may provide valuable lessons for the management of native plants under pressure from global climate change.
Effective treatment improves the body composition of patients with esophageal motility disorders
Authors: Abe Hirofumi , Tanaka Shinwa , Kawara Fumiaki , Toyonaga Takashi , Ariyoshi Ryusuke , Nakano Yoshiko , Sakaguchi Hiroya , Morita Yoshinori , Umegaki Eiji , Kodama Yuzo 
Published: April 2019

SUMMARY
Although treatment for esophageal motility disorder improves dysphagia and increases body weight, the effect of the treatment on body composition is unclear. This study aimed to assess the change in body composition between before and after treatment, the preoperative predictors of muscle increase, and the association between muscle increase and quality of life. Sixty-one patients (achalasia, n = 55; spastic esophageal disorder n = 6) who underwent per-oral endoscopic myotomy were analyzed in a single-arm prospective observational study. Appendicular skeletal muscle mass was measured with dual X-ray absorptiometry before and 3 months after per-oral endoscopic myotomy. For subgroup analysis, patients with postoperative appendicular skeletal muscle mass increase were defined as the muscle-increase group and the rest as the non-muscle-increase group. Preoperative factors related to the muscle-increase group were clarified via multivariate analysis. Further, the improvement after per-oral endoscopic myotomy in health-related quality-of-life score (Short Form-36) was compared between the muscle-increase and non-muscle-increase groups. Appendicular skeletal muscle mass increased significantly 3 months after per-oral endoscopic myotomy (P = 0.0002). The patients who underwent effective treatment (postoperative Eckardt score < 3) showed a significant improvement in appendicular skeletal muscle mass compared to those who did not (P = 0.04). In the stepwise logistic regression analysis, the preoperative Eckardt score (odds ratio: 1.95, 95% confidence interval 1.30–3.26, P = 0.0005) and preoperative serum prealbumin (odds ratio: 0.83, 95% confidence interval 0.70–0.97, P = 0.02) were identified as independent factors related to postoperative muscle increase. The improvements in the Short Form-36 domains of General Health (P = 0.0007) and Vitality (P = 0.003) were significantly higher in the muscle-increase group. The findings show that effective treatment improved the body composition of patients with esophageal motility disorder and that the Eckardt score and serum prealbumin may aid the prediction of increased appendicular skeletal muscle mass after treatment, resulting in a better quality of life.
Development and validation of a prediction model for long-term unsuccess of early treatment of Class III malocclusion
Authors: Souki Bernardo Quiroga , Nieri Michele , Pavoni Chiara , Pavan Barros Helena Maria , Junqueira Pereira Tarcisio , Giuntini Veronica , Cozza Paola , Franchi Lorenzo 
Published: April 2019

Summary

Aim
To develop and validate a prediction model to forecast long-term stability of early treatment with rapid maxillary expansion (RME) and facemask (FM) in a large sample of Class III growing patients.

Methods
The Brazilian Group (BG) consisted of 73 consecutively treated Caucasian Class III patients (41 females and 32 males). Mean age at T0 (before treatment) was 7.1 ± 1.6 years, while mean age at T1 (long-term follow-up) was 21.8 ± 3.2 years. The Italian Group (IG, validation cohort) comprised 28 consecutively treated Caucasian Class III patients (14 females and 14 males, mean age at T0 9.0 ± 1.3 years and mean age at T1 18.2 ± 1.4 years). Cephalometric analysis was performed on lateral cephalograms at T0. Gender and cephalometric variables, chronologic age, and dentition phase at T0 were used as predictors for long-term unsuccessful treatment at T1. All predictors for unsuccessful treatment in the BG were subjected to bivariate logistic regression. Only those statistically significant predictors in the bivariate logistic regression entered mixed stepwise logistic regression with P = 0.05 to enter and to leave. The validity of the prediction model derived from the BG was then tested on the IG.

Results
The prediction model consisted of only one cephalometric variable: the angle between the Condylar Axis and the Mandibular Plane (CondAx–MP) (odds ratio: 1.52, 95% confidence interval: 1.25–1.85, P &lt; 0.0001). Unsuccessful treatment at T1 was predicted for values of CondAx–MP at T0 greater than the cut-off value of 147.8 degrees. BG patients predicted incorrectly were 3 out of 22 for the unsuccessful cases and 1 out of 51 for the successful cases. Therefore, accuracy was 0.95, sensitivity 0.86, specificity 0.98, and positive and negative predictive values were 0.95 and 0.94. When the predictive model was applied on IG, all five unsuccessful cases were predicted correctly, while only 1 out of 23 successful patients was predicted incorrectly.

Conclusion
CondAx-ML was identified as a reliable predictor for long-term stability of early Class III treatment with RME and FM.
Greater Periaortic Fat Volume at Midlife Is Associated with Slower Gait Speed Later in Life in Women: The SWAN Cardiovascular Fat Ancillary Study
Authors: El Khoudary Samar R , Chen Xirun , Nasr Alexis , Shields Kelly , Barinas-Mitchell Emma , Janssen Imke , Everson-Rose Susan A , Powell Lynda , Matthews Karen 
Published: April 2019

AbstractBackgroundHigher perivascular adipose tissue (PVAT) contributes to adverse physiologic alterations in the vascular wall, and thus could potentially limit normal physical function later in life. We hypothesize that higher PVAT volume at midlife is prospectively associated with slower gait speed later in life, independent of overall adiposity and other risk factors.MethodsParticipants from the Study of Women’s Health Across the Nation (SWAN) cardiovascular fat ancillary study were included. PVAT volume around the descending aorta was quantified using existing computed tomography scans at midlife, while gait speed was measured after an average of 10.4 ± 0.7 years.ResultsTwo hundred and seventy-six women (aged 51.3 ± 2.8 years at PVAT assessment) were included. Mean gait speed was 0.96 ± 0.21 m/s. Adjusting for study site, race, education level, menopausal status, and length of descending aorta at PVAT assessment, and age, body mass index, difficulty paying for basics, overall health and smoking status at gait speed assessment, a higher midlife PVAT volume was associated with a slower gait speed later in life (p = .03). With further adjustment for presence of any comorbid conditions by the time of gait speed assessment, the association persisted; every 1SD increase in log-PVAT was associated with 3.3% slower gait speed (95% confidence interval: 0.3–6.3%; p = .03).ConclusionGreater PVAT in midlife women may contribute to poorer physical function in older age supporting a potential role of midlife PVAT in multiple domains of healthy aging. Additional research is needed to fully elucidate the physiologic changes associated with PVAT that may underlie the observed associations.
What Is Meaningful Participation for Older People? An Analysis of Aging Policies
Authors: Dizon Lovely , Wiles Janine , Peiris-John Roshini 
Published: April 2019

AbstractBackground and ObjectivesThe language used to construct policy problems influences the solutions created. Recent aging policies emphasize participation as essential to aging well, encouraging independence and active involvement in all aspects of life. However, it is less clear whether participation in the creation of policies or in policy goals and aspirations is meaningful. This article addresses the question: “How is meaningful participation reflected and enabled in policy?”Research Design and MethodsEleven global, national, and local policies were purposively selected and analyzed using thematic and discourse analysis.ResultsPolicies framed population aging as a challenge and active aging as a value as or part of the policy-making process, participation is enabled (or not) through the types of participation encouraged by policy makers and the kinds of participation used to engage with older people.Discussion and ImplicationsOur analysis identifies a strong pattern of discourses regarding individual responsibility to age well; underlying tensions between productive and passive participation; and tensions inherent to the concept of consultation. Implications include the need for those in the consultative phase of policy making to engage with diverse older people and to use participatory methods to explore what meaningful participation means for older people themselves.
An efficient and robust laboratory workflow and tetrapod database for larger scale environmental DNA studies
Authors: Axtner Jan , Crampton-Platt Alex , Hörig Lisa A , Mohamed Azlan , Xu Charles C Y , Yu Douglas W , Wilting Andreas 
Published: April 2019

Abstract

Background
The use of environmental DNA for species detection via metabarcoding is growing rapidly. We present a co-designed lab workflow and bioinformatic pipeline to mitigate the 2 most important risks of environmental DNA use: sample contamination and taxonomic misassignment. These risks arise from the need for polymerase chain reaction (PCR) amplification to detect the trace amounts of DNA combined with the necessity of using short target regions due to DNA degradation.

Findings
Our high-throughput workflow minimizes these risks via a 4-step strategy: (i) technical replication with 2 PCR replicates and 2 extraction replicates; (ii) using multi-markers (12S,16S,CytB); (iii) a “twin-tagging,” 2-step PCR protocol; and (iv) use of the probabilistic taxonomic assignment method PROTAX, which can account for incomplete reference databases. Because annotation errors in the reference sequences can result in taxonomic misassignment, we supply a protocol for curating sequence datasets. For some taxonomic groups and some markers, curation resulted in &gt;50% of sequences being deleted from public reference databases, owing to (i) limited overlap between our target amplicon and reference sequences, (ii) mislabelling of reference sequences, and (iii) redundancy. Finally, we provide a bioinformatic pipeline to process amplicons and conduct PROTAX assignment and tested it on an invertebrate-derived DNA dataset from 1,532 leeches from Sabah, Malaysia. Twin-tagging allowed us to detect and exclude sequences with non-matching tags. The smallest DNA fragment (16S) amplified most frequently for all samples but was less powerful for discriminating at species rank. Using a stringent and lax acceptance criterion we found 162 (stringent) and 190 (lax) vertebrate detections of 95 (stringent) and 109 (lax) leech samples.

Conclusions
Our metabarcoding workflow should help research groups increase the robustness of their results and therefore facilitate wider use of environmental and invertebrate-derived DNA, which is turning into a valuable source of ecological and conservation information on tetrapods.
Trade, Inclusive Development, and the Global Order
Authors: Draper Peter , Freytag Andreas , Dörffel Christoph , Schuhmann Sebastian 
Published: April 2019

AbstractEconomic globalization has increasingly affected countries across the world, through participation in global value chains (GVCs) and helping to lift over one billion human beings out of extreme poverty since 1990. However, there are still too many people living in poverty, even in rich countries, and so concerns over exclusion of certain groups from the gains of economic globalization are rising internationally. Using the concept of inclusiveness based on Amartya Sen’s capability approach, we find that G20 countries perform better than non-G20 countries. We then review how economic theory contributes to understanding the causes of (missing) inclusiveness by reviewing the literature pertaining to five drivers: growth, technology, structural change, trade, and political economy. Overall, domestic policies tailored to specific national circumstances are the main instruments for promoting inclusiveness. The danger is that in pursuing these domestic policies, states may undermine international arrangements constituting the liberal economic order. We argue that the liberal economic order generates insufficient global governance because there is always a fraction of countries opposing global policy coordination as they believe it harms them, and that this group of countries is increasing propelled by the surge of populism. This dynamic implies that global governance focus will increasingly shift to “coalitions of the willing”, rendering multilateralism an increasingly challenging, and a la carte, proposition.