bluuebunny/crossref_metadata_2025_split huggingface dataset:
Barriers and facilitators to the implementation of individual placement and support (IPS) for patients with offending histories in the community: The United Kingdom experience
Authors: Khalifa Najat , Hadfield Sarah , Thomson Louise , Talbot Emily , Bird Yvonne , Schneider Justine , Attfield Julie , Völlm Birgit , Bates Peter , Walker Dawn-Marie 
Published: November 2019

Introduction We aimed to identify the barriers and facilitators to the implementation of a high fidelity individual placement and support service in a community forensic mental health setting. Method In-depth interviews were conducted with clinical staff ( n = 11), patients ( n = 3), and employers ( n = 5) to examine barriers and facilitators to implementation of a high fidelity individual placement and support service. Data was analysed using thematic analysis, and themes were mapped onto individual placement and support fidelity criteria. Results Barriers cited included competing interests between employment support and psychological therapies, perceptions of patients’ readiness for work, and concerns about the impact of returning to work on welfare benefits. Facilitators of implementation included clear communication of the benefits of individual placement and support, inter-disciplinary collaboration, and positive attitudes towards the support offered by the individual placement and support programme among stakeholders. Offences, rather than mental health history, were seen as a key issue from employers’ perspectives. Employers regarded disclosure of offending or mental health history as important to developing trust and to gauging their own capacity to offer support. Conclusions Implementation of individual placement and support in a community mental health forensic setting is complex and requires robust planning. Future studies should address the barriers identified, and adaptations to the individual placement and support model are needed to address difficulties encountered in forensic settings.
Open to competition? Competitive density and the growth of young New Zealand ventures
Authors: Whittaker D Hugh , Fath Benjamin , Fiedler Antje 
Published: November 2019

Drawing on 180 survey responses from young, New Zealand-based ventures, we investigate effects of the number of perceived serious competitors on venture growth. We find empirical evidence for an inverse U-shaped relationship between competitive density and young venture growth. We further find that persistent innovation – requiring both initial innovative intent and a recent record of innovation – not only promotes young growth but also moderates the relationship between competitive density and young venture growth. Overall, the study shows that the growth of young ventures committed to persistent innovation is less affected by competitive dynamics compared to non-innovators. JEL Classification: L10, L22, L26, O30
Perspectives on non-clinical health care workers’ moral obligation to report for work during virulent epidemics: an exploration in Guinea
Authors: Kpanake Lonzozou , Adjiwanou Vissého , Sorum Paul Clay , Mullet Etienne 
Published: November 2019

Objectives To examine the views of non-clinical health care workers (NCHW) and lay people in Guinea on NCHWs’ moral obligation to work during epidemics. Methods NCHWs ( N = 227) and lay people ( N = 253) were presented with theoretical vignettes of NCHWs who refused to work during a virulent epidemic and invited to rate the extent to which such decision was acceptable. Vignettes varied in four factors: level of risk of getting infected; the nature of the infection (Ebola, influenza, tuberculosis); working conditions and the NCHW’s family status. Results Three general qualitatively different positions were identified: (a) NCHWs have an unlimited moral obligation to work, irrespective of circumstances (10% of study participants); (b) NCHWs do not have a moral obligation to work (12%), and (c) the moral obligation to work depends entirely on circumstances (58%), while 19% of participants did not express any position. Conclusions Only a small proportion of NCHWs and lay people in Guinea considered that NCHWs’ refusal to work during an epidemic is always unacceptable. Policy makers planning for future epidemics need to take account of NCHWs’ moral dilemmas in deciding whether to report to work during epidemics and provide appropriate working conditions.
Horticultural Therapy in Patients With Dementia: A Systematic Review and Meta-Analysis
Authors: Lu Li-Chin , Lan Shao-Huan , Hsieh Yen-Ping , Yen Yea-Yin , Chen Jong-Chen , Lan Shou-Jen 
Published: November 2019

Background: World Health Organization has communicated that dementia as a public health priority in 2012. Behavioral and psychological symptoms of dementia are the main reason results in hospitalization of dementia patients. Horticulture is one of the favorite activity for many peoples to relax their minds. Objectives: To investigate psychological health benefits of horticulture intervention in dementia patients. Methods: The databases including Cochrane Library, ProQuest, PubMed, EMBASE, EBSCO, Web of Science, and Ovid Medline were searched up to August 2017. Results: Twenty-three articles for systematic review, whereas 8 articles were included in meta-analysis. Meta-analysis verified the beneficial effect of horticultural therapy (HT) on agitation level (standard mean difference: −0.59; P < .00001); increase time spent on activity engagement (mean differences [MD]: 45.10%, P < .00001); decrease time for doing nothing (MD: −29.36%, P = .02). Conclusions: Patients with dementia benefit from horticultural by alleviating their degrees of agitate behaviors, increasing time of engaging in activities and decrease time of doing nothing.
Intraoperative Fragmentation and Retention of Endovascular Devices: Clinical Consequences and Preventative Strategies
Authors: Endicott Kendal M. , Drucker Charles B. , Orbay Hakan , DuBose Joseph J. , Nagarsheth Khanjan , Toursavadkohi Shahab , Sarkar Rajabrata 
Published: November 2019

Background: Expanded applications and increasing volumes of complex endovascular procedures have increased the risk of unintended intraoperative fragmentation and retention of catheters and sheaths. We describe a series of retained or fragmented endovascular devices, a quality improvement program to address this unmet need for improved detection of catheter fragmentation, and the results of this program. Methods: Cases utilizing endovascular devices that resulted in a retained catheter fragment were identified and analyzed during divisional quality improvement review. One consistent area of concern was operating room (OR) staff unfamiliarity with verifying the integrity of an endovascular device. In response, a slide-based training protocol of focused, endovascular nursing education was implemented. Following perceived lack of improvement after this approach, we developed a handheld visual reference display of the tips of common catheters and sheaths. Staff was surveyed before and after intervention to assess the educational value of the display and the impact on staff device familiarity. Results: All 4 described cases resulted in an unplanned return to the OR for retrieval of the fragmented catheter or sheath. No thromboembolic complications were observed, although associated intra-arterial thrombus was noted in 2 cases. Thirty-four OR nurses were polled to trial the visual reference display initiative, with 70% of those reporting primary surgical assignments outside of cardiovascular ORs. Introduction of the new visual reference display improved staff confidence in their ability to identify a broken device (2.4-3.7, P < .001). This improvement was most significant in OR staff with primary assignments in noncardiovascular services. Conclusion: Current OR standard operating procedures fail to address the potential for unintentionally retained catheters and wires during endovascular procedures. Our novel visual reference display of common endovascular items rather than conventional in-service training improved the ability of staff to identify device fragmentation at the time of the index procedure.
Impact of body temperature at admission on inhospital outcomes in patients with takotsubo syndrome: insights from the Tokyo Cardiovascular Care Unit Network Registry
Authors: Kimura Akihisa , Yoshikawa Tsutomu , Isogai Toshiaki , Tanaka Hiroyuki , Ueda Tetsuro , Yamaguchi Tetsuo , Imori Yoichi , Maekawa Yuichiro , Sakata Konomi , Murakami Tsutomu , Arao Kenshiro , Nagao Ken , Yamamoto Takeshi , Takayama Morimasa 
Published: November 2019

Background:Takotsubo syndrome occasionally occurs in patients with fever due to underlying diseases. However, the impact of body temperature on inhospital prognosis of patients with takotsubo syndrome remains unknown.Methods:Using the patient cohort in the Tokyo Cardiovascular Care Unit Network Registry from 2013 to 2015, we identified 421 eligible patients whose data on body temperature at admission were available and classified them into three groups: high body temperature group (≥37.5°C; n=27), normal body temperature group (36.0–37.4°C; n=319), and low body temperature group (≤35.9°C; n=75). We compared the patient characteristics and inhospital outcomes among the three groups.Results:On admission, the high body temperature group showed a higher proportion of men and preceding physical triggers, higher heart and respiratory rates, and higher C-reactive protein level than the other groups. Inhospital all-cause mortality was significantly higher in the high body temperature group than in the normal or low body temperature group (18.5% vs. 2.2% vs. 4.0%, respectively, P&lt;0.001). Both cardiac mortality (11.1% vs. 1.3% vs. 1.3%, P=0.001) and non-cardiac mortality (7.4% vs. 0.9% vs. 2.7%, P=0.031) were also significantly higher in the high body temperature group. Multivariable logistic regression analysis showed that high body temperature (reference: normal body temperature) was significantly associated with higher inhospital mortality (adjusted odds ratio 4.22; 95% confidence interval 1.15–15.51; P=0.030).Conclusions:Our findings suggest that high body temperature at admission is a strong predictor of inhospital mortality in patients with takotsubo syndrome. Febrile takotsubo syndrome patients may need to be managed with recognition of life-threatening conditions from the time of diagnosis, no matter what the causes of fever are.
Don’t Interrupt! A Case Report of Continuing Peritoneal Dialysis After Endoscopic Gastric Tumor Resection
Authors: Silverstein William K. , Teshima Christopher , Jolly Simran , Perl Jeffrey 
Published: November 2019

Rationale: The evidence supporting the safety of restarting peritoneal dialysis (PD) immediately after abdominal surgery and interventions is scant. In particular, there are no reported cases characterizing periprocedural management of PD for patients undergoing endoscopic submucosal dissection for gastric intramucosal tumor removal. Presenting concerns of the patient: A 66-year-old female with end-stage kidney disease secondary to diabetic nephropathy, currently on nocturnal automatic PD, presented with new iron-deficiency anemia. Workup revealed an intramucosal gastric lesion proximal to the pylorus, without surrounding lymph node involvement. Endoscopic submucosal dissection was performed with en bloc endoscopic resection of a 5-cm, partially flat, partially sessile mass along the posterior wall and lesser curvature of the gastric antrum. Pathology revealed low-grade dysplasia without features of malignancy. There was no evidence of hemorrhage or leak post-dissection. Diagnoses: The clinical presentation was consistent with an uncomplicated endoscopic submucosal dissection. Interventions: Peritoneal dialysis was held for 48 hours and restarted thereafter with no complications. The patient did not require bridging with hemodialysis. Outcomes: The patient had an uncomplicated post-endoscopic course, with no subsequent episodes of PD-associated peritonitis after at least 6-month follow-up. Novel finding: This is the first reported case of PD reinitiation after endoscopic submucosal dissection of a gastric tumor.
Characteristics of Central Retinal Vein Occlusion in African Americans
Authors: Kiew Sieh Yean , Thomas George N. , Thomas Akshay S. , Fekrat Sharon 
Published: November 2019

Purpose: This article studies whether the characteristics and clinical course of African American patients with central retinal vein occlusion (CRVO) differ from other racial groups. Methods: This retrospective cohort study included consecutive patients diagnosed with CRVO at Duke Eye Center, Durham, North Carolina. Presenting characteristics, examination findings, treatment course, and functional and structural outcomes were compared based on patient-reported race. Results: A total of 479 patients with CRVO were included (64.7% white, 22.2% African American, 1.7% mixed race, and 11.4% other races). African American patients were older (68.1 vs 64.3 years, P = .049), more likely to be hypertensive ( P = .001) and diabetic ( P = .000), and had higher rates of open-angle glaucoma ( P < .000). Presenting visual acuity (VA) was worse in African Americans (logarithm of the minimum angle of resolution 1.25 vs 0.96, P = .010). There were no significant differences in the proportion of patients requiring panretinal photocoagulation, intravitreal antivascular endothelial growth factor (anti-VEGF), or intravitreal corticosteroid; however, analysis of treatment-naive individuals showed a higher number of anti-VEGF injections in the first year in African Americans. Final VA was not significantly different between groups, but African Americans had higher rates of neovascular sequelae (25.0% vs 11.8%, P = .019; odds ratio, 2.295, P = .088). Conclusions: African Americans with CRVO presented with more severe visual impairment and more systemic and ocular risk factors for CRVO. Treatment-naive African Americans had a greater treatment burden during the first year of follow-up.
Prevalence and burden of headache in children and adolescents in Austria – a nationwide study in a representative sample of pupils aged 10–18 years
Authors: Philipp Julia , Zeiler Michael , Wöber Christian , Wagner Gudrun , Karwautz Andreas F. K. , Steiner Timothy J. , Wöber-Bingöl Çiçek 
Published: November 2019

Abstract

Background
Headache disorders are highly prevalent worldwide, but not so well investigated in children and adolescents as in adults: few studies have included representative nationwide samples. No data exist for Austria until now. In a representative sample of children and adolescents in Austria, we estimated the prevalence and attributable burden of headache disorders, including the new diagnostic category of “undifferentiated headache” (UdH) defined as mild headache lasting less than 1 hour.

Methods
Within the context of a broader national mental health survey, children and adolescents aged 10–18 years were recruited from purposively selected schools. Mediated self-completed questionnaires included sociodemographic enquiry (gender, age, socioeconomic status, family constellation, residence [urban or rural] and migration background). Prevalence and attributable burden of all headache, UdH, migraine (definite plus probable), tension-type headache (TTH: definite plus probable) and headache on ≥15 days/month (H15+) were assessed using the Headache-Attributed Restriction, Disability, Social Handicap and Impaired Participation (HARDSHIP) questionnaire for children and adolescents. Health-related quality of life (HrQoL) was assessed using the KIDSCREEN questionnaire.

Results
Of 7643 selected pupils, 3386 (44.3%) completed the questionnaires. The 1-year prevalence of headache was 75.7%, increasing with age and higher in girls (82.1%) than in boys (67.7%; p < 0.001). UdH, migraine, TTH and H15+ were reported by 26.1%, 24.2%, 21.6% and 3.0% of participants. Attributable burden was high, with 42% of those with headache experiencing restrictions in daily activities. Medication use (50% overall) was highest in H15+ (67%) and still considerable in UdH (29%). HrQoL was reduced for all headache types except UdH. Participants in single parent or patchwork families had a higher probability of migraine (respectively, OR 1.5, p < 0.001; OR 1.5, p < 0.01). Participants with a migration background had a lower probability of TTH (OR 0.7, p < 0.01).

Conclusions
Headache disorders are both very common and highly burdensome in children and adolescents in Austria. This study contributes to the global atlas of headache disorders in these age groups, and corroborates and adds knowledge of the new yet common and important diagnostic category of UdH. The findings call for action in national and international health policies, and for further epidemiological research.
De novo Nanopore read quality improvement using deep learning
Authors: LaPierre Nathan , Egan Rob , Wang Wei , Wang Zhong 
Published: November 2019

Abstract

Background
Long read sequencing technologies such as Oxford Nanopore can greatly decrease the complexity of de novo genome assembly and large structural variation identification. Currently Nanopore reads have high error rates, and the errors often cluster into low-quality segments within the reads. The limited sensitivity of existing read-based error correction methods can cause large-scale mis-assemblies in the assembled genomes, motivating further innovation in this area.

Results
Here we developed a Convolutional Neural Network (CNN) based method, called MiniScrub, for identification and subsequent “scrubbing” (removal) of low-quality Nanopore read segments to minimize their interference in downstream assembly process. MiniScrub first generates read-to-read overlaps via MiniMap2, then encodes the overlaps into images, and finally builds CNN models to predict low-quality segments. Applying MiniScrub to real world control datasets under several different parameters, we show that it robustly improves read quality, and improves read error correction in the metagenome setting. Compared to raw reads, de novo genome assembly with scrubbed reads produces many fewer mis-assemblies and large indel errors.

Conclusions
MiniScrub is able to robustly improve read quality of Oxford Nanopore reads, especially in the metagenome setting, making it useful for downstream applications such as de novo assembly. We propose MiniScrub as a tool for preprocessing Nanopore reads for downstream analyses. MiniScrub is open-source software and is available at https://bitbucket.org/berkeleylab/jgi-miniscrub.
Optimized sequencing depth and de novo assembler for deeply reconstructing the transcriptome of the tea plant, an economically important plant species
Authors: Li Fang-Dong , Tong Wei , Xia En-Hua , Wei Chao-Ling 
Published: November 2019

Abstract

Background
Tea is the oldest and among the world’s most popular non-alcoholic beverages, which has important economic, health and cultural values. Tea is commonly produced from the leaves of tea plants (Camellia sinensis), which belong to the genus Camellia of family Theaceae. In the last decade, many studies have generated the transcriptomes of tea plants at different developmental stages or under abiotic and/or biotic stresses to investigate the genetic basis of secondary metabolites that determine tea quality. However, these results exhibited large differences, particularly in the total number of reconstructed transcripts and the quality of the assembled transcriptomes. These differences largely result from limited knowledge regarding the optimized sequencing depth and assembler for transcriptome assembly of structurally complex plant species genomes.

Results
We employed different amounts of RNA-sequencing data, ranging from 4 to 84 Gb, to assemble the tea plant transcriptome using five well-known and representative transcript assemblers. Although the total number of assembled transcripts increased with increasing sequencing data, the proportion of unassembled transcripts became saturated as revealed by plant BUSCO datasets. Among the five representative assemblers, the Bridger package shows the best performance in both assembly completeness and accuracy as evaluated by the BUSCO datasets and genome alignment. In addition, we showed that Bridger and BinPacker harbored the shortest runtimes followed by SOAPdenovo and Trans-ABySS.

Conclusions
The present study compares the performance of five representative transcript assemblers and investigates the key factors that affect the assembly quality of the transcriptome of the tea plants. This study will be of significance in helping the tea research community obtain better sequencing and assembly of tea plant transcriptomes under conditions of interest and may thus help to answer major biological questions currently facing the tea industry.
Quality control of imbalanced mass spectra from isotopic labeling experiments
Authors: Li Tianjun , Chen Long , Gan Min 
Published: November 2019

Abstract

Background
Mass spectra are usually acquired from the Liquid Chromatography-Mass Spectrometry (LC-MS) analysis for isotope labeled proteomics experiments. In such experiments, the mass profiles of labeled (heavy) and unlabeled (light) peptide pairs are represented by isotope clusters (2D or 3D) that provide valuable information about the studied biological samples in different conditions. The core task of quality control in quantitative LC-MS experiment is to filter out low-quality peptides with questionable profiles. The commonly used methods for this problem are the classification approaches. However, the data imbalance problems in previous control methods are often ignored or mishandled. In this study, we introduced a quality control framework based on the extreme gradient boosting machine (XGBoost), and carefully addressed the imbalanced data problem in this framework.

Results
In the XGBoost based framework, we suggest the application of the Synthetic minority over-sampling technique (SMOTE) to re-balance data and use the balanced data to train the boosted trees as the classifier. Then the classifier is applied to other data for the peptide quality assessment. Experimental results show that our proposed framework increases the reliability of peptide heavy-light ratio estimation significantly.

Conclusions
Our results indicate that this framework is a powerful method for the peptide quality assessment. For the feature extraction part, the extracted ion chromatogram (XIC) based features contribute to the peptide quality assessment. To solve the imbalanced data problem, SMOTE brings a much better classification performance. Finally, the XGBoost is capable for the peptide quality control. Overall, our proposed framework provides reliable results for the further proteomics studies.