bluuebunny/crossref_metadata_2025_split huggingface dataset:
BulkVis: a graphical viewer for Oxford nanopore bulk FAST5 files
Authors: Payne Alexander , Holmes Nadine , Rakyan Vardhman , Loose Matthew 
Published: October 2018

Abstract

Motivation
The Oxford Nanopore Technologies (ONT) MinION is used for sequencing a wide variety of sample types with diverse methods of sample extraction. Nanopore sequencers output FAST5 files containing signal data subsequently base called to FASTQ format. Optionally, ONT devices can collect data from all sequencing channels simultaneously in a bulk FAST5 file enabling inspection of signal in any channel at any point. We sought to visualize this signal to inspect challenging or difficult to sequence samples.

Results
The BulkVis tool can load a bulk FAST5 file and overlays MinKNOW (the software that controls ONT sequencers) classifications on the signal trace and can show mappings to a reference. Users can navigate to a channel and time or, given a FASTQ header from a read, jump to its specific position. BulkVis can export regions as Nanopore base caller compatible reads. Using BulkVis, we find long reads can be incorrectly divided by MinKNOW resulting in single DNA molecules being split into two or more reads. The longest seen to date is 2 272 580 bases in length and reported in eleven consecutive reads. We provide helper scripts that identify and reconstruct split reads given a sequencing summary file and alignment to a reference. We note that incorrect read splitting appears to vary according to input sample type and is more common in ’ultra-long’ read preparations.

Availability and implementation
The software is available freely under an MIT license at https://github.com/LooseLab/bulkvis.

Supplementary information
Supplementary data are available at Bioinformatics online.
Diagnostic methods for uncovering outcome dependent visit processes
Authors: McCulloch Charles E , Neuhaus John M 
Published: October 2018

Summary
With the advent of electronic health records, information collected in the course of regular health care is increasingly being used for clinical research. The hope is that the wealth of clinical data and the realistic setting (compared with information derived from highly controlled experiments like randomized trials) will aid in the investigation of determinants of disease and understanding of which treatments are effective in regular practice and for which patients. The availability of information in such databases is often driven by how a patient feels and may therefore be associated with the health outcomes being considered. We call this an outcome dependent visit process and recent work has shown that ignoring the outcome dependence can produce significant bias in the regression coefficients when fitting longitudinal data models. It is therefore important to have tools to recognize datasets exhibiting outcome dependence. We develop a score statistic to motivate the form of diagnostic test statistics, suggest a variety of approaches for diagnosing such situations, and evaluate their performance. Simple diagnostic tests achieve high power for diagnosing outcome dependent visit processes. This occurs when generalized estimating equations methods begin to be exhibit bias in estimating regression coefficients and before likelihood based methods are substantially biased.
Youngsters’ Perspectives on Continuity in Their Contacts with Youth-Care Services
Authors: Naert Jan , Roets Griet , Roose Rudi , Vanderplasschen Wouter 
Published: October 2018

AbstractContinuity is seen as an important aim for the quality of youth-care services. However, views on continuity are predominantly guided by experts, without much attention to user perspectives. This paper focuses on youngsters’ experienced continuity in relation to youth-care services. Twenty-five youngsters, who were in residential care or reached by low-threshold youth services, were interviewed about their experiences in and out of care. In thematically exploring the biographical narratives for important experiences of continuity, three major themes emerged: (i) the need for footholds in moments of existential chaos, (ii) the importance of timing of interventions to match the youngsters’ perspectives and (iii) the importance of the youngsters’ impact on their own care pathways. This study shows the need for support that is imbedded in a relational network within the context of youngsters in vulnerable situations. Rethinking youth services towards a better connection with these contexts is essential. Furthermore, the amount of control youngsters experience in their care interventions seems to be beneficial to the experience of continuity. It is argued that continuity should be seen as a process, in order to leave more space for negotiation and flexibility throughout the youngsters’ experiences in youth-care services.
The Role of Elders in the Wellbeing of a Contemporary Australian Indigenous Community
Authors: Busija Lucy , Cinelli Renata , Toombs Maree R , Easton Caitlin , Hampton Ron , Holdsworth Kristen , Macleod, BPsySc(Hons) Ashley , Nicholson Geoffrey C , Nasir Bushra F , Sanders Kerrie M , McCabe Marita P 
Published: October 2018

Abstract

Background and Objectives
Traditional Elders are integral to the social structure of Australian Indigenous communities. Due to progressive loss of traditional way of life, however, the role of Elders has been eroding. This study aims to develop a conceptual model of the role of Elders in an Australian Indigenous community, with the goal of attaining strategies to strengthen the role of Elders.

Research Design and Methods
The study, conducted in a regional Indigenous community in Australia, adopted a community-based participatory approach. Design and focus of the project were informed by a community forum (Yarning Circle). One-on-one semistructured interviews and focus groups with community members were conducted by Indigenous researchers. Group concept mapping (GCM) was applied to elicit major themes in qualitative data, from the point of view of community members, and to derive a conceptual model of the role of Elders.

Results
Fifty members of the Indigenous community took part in interviews and focus groups. The participants’ median age was 45 years (range 18–76 years); 31 (62%) were female. An additional 24 Indigenous community members took part in the data sorting task of GCM. GCM identified seven major aspects of the role of Elders, including Community relations, Passing down the knowledge, Dealing with racism and oppression, Building a better resourced community, Intergenerational connectedness, Safeguarding our identity, and Caring for our youth.

Discussion and Implications
Elders fulfill many important roles in contemporary Indigenous communities. Our results can be used to assist the community to codesign a program to increase community wellbeing.
Directional bilateral asymmetry in otolith morphology may affect fish stock discrimination based on otolith shape analysis
Authors: Mahé Kélig , Ider Djamila , Massaro Andrea , Hamed Oussama , Jurado-Ruzafa Alba , Gonçalves Patrícia , Anastasopoulou Aikaterini , Jadaud Angelique , Mytilineou Chryssi , Elleboode Romain , Ramdane Zohir , Bacha Mahmoud , Amara Rachid , de Pontual Hélène , Ernande Bruno 
Published: October 2018

AbstractOtolith shape analysis is an efficient fish stock identification tool. However, most applications used left and right otoliths or only one of them arbitrarily chosen without testing for biases resulting from potential directional bilateral asymmetry (DA) in otolith shape, i.e. a unimodal population-level deviation form bilateral symmetry between right and left otolith shapes. In this study, 560 bogues (Boops boops) were sampled from 11 geographical locations from the Canary Islands to the Aegean Sea and elliptical Fourier descriptors were used to describe their otoliths’ shape. First, a significant otolith DA was observed at the global scale with an average amplitude of 2.77%. However, at the scale of sampling locations, DA was not always significant and varied in amplitude and direction. Second, population structure was investigated using the shape of either right otoliths or left otoliths or both together. Analyses based on right otoliths or both otoliths together, suggested three stock units: a North-Western Mediterranean Sea stock, an Eastern Mediterranean Sea stock, and a Central-Eastern Atlantic Ocean and South-Western Mediterranean Sea stock. In contrast, no coherent geographical pattern was found based on left otoliths. Our results highlight the importance of accounting for potential otolith DA in otolith shape-based stock identification.
Improving inpatient mental health medication safety through the process of obtaining HIMSS Stage 7: a case report
Authors: Sulkers Heather , Tajirian Tania , Paterson Jane , Mucuceanu Daniela , MacArthur Tracey , Strauss John , Kalia Kamini , Strudwick Gillian , Jankowicz Damian 
Published: October 2018

Abstract
Although electronic health record systems have been implemented in many health settings globally, how organizations can best implement these systems to improve medication safety in mental health contexts is not well documented in the literature. The purpose of this case report is to describe how a mental health hospital in Toronto, Canada, leveraged the process of obtaining Healthcare Information Management Systems Society (HIMSS) Stage 7 on the Electronic Medical Record Adoption Model to improve clinical care specific to medication safety in its inpatient settings. Examples of how the organization met several of these HIMSS criteria are described as they relate to utilizing data from the system to support clinician practice and/or decision-making for medication safety.
Drugs linked to plasma homoarginine in chronic kidney disease patients—a cross-sectional analysis of the German Chronic Kidney Disease cohort
Authors: Maas Renke , Mieth Maren , Titze Stephanie I , Hübner Silvia , Fromm Martin F , Kielstein Jan T , Schmid Matthias , Köttgen Anna , Kronenberg Florian , Krane Vera , Hausknecht Birgit , Eckardt Kai-Uwe , Schneider Markus P 
Published: October 2018

Abstract

Background
Elevated plasma concentrations of symmetric and asymmetric dimethylarginine (SDMA and ADMA, respectively) and a lower plasma concentration of the structurally related homoarginine are commonly observed in patients with chronic kidney disease (CKD) and independently predict total mortality as well as progression of renal disease. We aimed to identify drugs that may alter this adverse metabolite pattern in a favourable fashion.

Methods
Plasma ADMA, SDMA, homoarginine and l-arginine were determined by liquid chromatography–tandem mass spectrometry in 4756 CKD patients ages 18–74 years with an estimated glomerular filtration rate (eGFR) of 30–60 mL/min/1.73 m2 or an eGFR &gt;60 mL/min/1.73 m2 and overt proteinuria who were enrolled in the German Chronic Kidney Disease (GCKD) study. Associations between laboratory, clinical and medication data were assessed.

Results
Intake of several commonly used drugs was independently associated with plasma concentrations of homoarginine and/or related metabolites. Among these, the peroxisome proliferator-activated receptor alpha (PPAR-α) agonist fenofibrate was associated with the most profound differences in ADMA, SDMA and homoarginine plasma concentrations: 66 patients taking fenofibrate had a multivariable adjusted odds ratio (OR) of 5.83 [95% confidence interval (CI) 2.82–12.03, P &lt; 0.001] to have a plasma homoarginine concentration above the median. The median homoarginine plasma concentration in patients taking fenofibrate was 2.30 µmol/L versus 1.55 in patients not taking the drug (P &lt; 0.001). In addition, fibrates were significantly associated with lower plasma SDMA and higher l-arginine concentrations. In contrast, glucocorticoids were associated with lower plasma homoarginine, with adjusted ORs of 0.52 (95% CI 0.40–0.67, P &lt; 0.001) and 0.53 (95% CI 0.31–0.90, P = 0.018) for prednisolone and methylprednisolone, respectively.

Conclusions
In a large cohort of CKD patients, intake of fenofibrate and glucocorticoids were independently associated with higher and lower plasma homoarginine concentrations, respectively. Effects on plasma homoarginine and methylarginines warrant further investigation as potential mechanisms mediating beneficial or adverse drug effects.
Variability of Zika Virus Incubation Period in Humans
Authors: Fourié Toscane , Grard Gilda , Leparc-Goffart Isabelle , Briolant Sébastien , Fontaine Albin 
Published: October 2018

Abstract
Zika virus (ZIKV) has recently emerged in numerous tropical countries worldwide. In this study, we estimated ZIKV incubation period distribution using time-to-event models adapted to interval-censored data based on declared date of travels from 123 symptomatic travelers returning from areas with active ZIKV transmission. The median time and 95th percentile of ZIKV incubation period was estimated to 6.8 days (95% confidence interval [CI], 5.8–7.7 days) and 15.4 days (95% CI, 12.7–19.7 days), respectively. Determining the incubation period for ZIKV is beneficial to improve protection guidelines.
When Do Professionals Envision and Trust Fathers as Caregivers over the Course of Giving Birth? A Comparison of Pre- and Postnatal Healthcare Professionals’ Assessments of Fathers in the Netherlands, Germany, and Poland
Authors: Veltkamp Gerlieke 
Published: October 2018

AbstractWhen fathers are involved in caregiving from the beginning of their child’s life, they are more likely to stay involved, resulting in more gender equality between spouses and in positive cognitive and psychosocial health outcomes for children. It has been shown, however, that professional experts often focus predominantly on and build trust relationships with mothers rather than fathers. In this paper, drawing on interviews with and observations of pre- and postnatal healthcare professionals in the Netherlands, Germany, and Poland, I examine in which institutional contexts these professionals did activate and build trust relationships with fathers, while envisioning them as caregivers.
Increased lysine: metabolizable energy ratio improves grower pig performance during a porcine reproductive and respiratory syndrome virus challenge
Authors: Schweer Wesley P , Mendoza Omarh F , Shull Caleb M , Lehman James , Gaines Aaron M , Schwartz Kent J , Gabler Nicholas K 
Published: October 2018

Abstract
Porcine reproductive and respiratory syndrome virus (PRRSV) reduces grower pig performance. The amino acid (AA) requirements and lysine:metabolizable energy ratio (Lys:ME) of health-challenged pigs for optimum performance are poorly understood. Two experiments were conducted to evaluate the effect of increasing standardized ileal digestible (SID) Lys:ME (g SID Lys per Mcal ME) on growth performance during a PRRSV challenge. In Exp. 1, a total of 379 barrows (51.3 ± 0.3 kg body weight [BW]) were allotted to one of six diets (1.87 to 3.41 Lys:ME) for a 35-d growth study. In Exp. 2, a total of 389 barrows (29.2 ± 0.23 kg BW) were allotted to one of six diets (2.39 to 3.91 Lys:ME) for a 49-d growth study. These isocaloric diets represented 80% to 130% of National Research Council (NRC) SID Lys requirement. For each experiment, pigs were randomly allotted across two barns of 24 pens each with seven to nine pigs per pen (four pens per diet per health status). On day 0, one barn was inoculated with live PRRSV, one barn sham inoculated (control), and all pigs were started on experimental diets. Pen growth performance and feed intake were recorded weekly and gain-to-feed ratio (G:F) was calculated. Breakpoint analysis was used to determine the Lys:ME that maximized average daily gain (ADG) and G:F over the 35 or 49-d test periods for Exp. 1 and 2, respectively. In Exp. 1, increasing Lys:ME increased ADG (quadratic P = 0.01) and G:F (linear and quadratic P = 0.04) in control pigs over 35 d. In PRRSV-infected pigs, ADG and G:F increased linearly with increasing Lys:ME (P &lt; 0.01). The Lys:ME for optimum ADG and G:F during PRRSV challenge was 2.83 and 3.17, respectively, compared to 2.24 and 2.83, respectively, in control pigs using a one-slope broken-line model. In Exp. 2, pigs in the control barn became naturally infected after 21 days post inoculation. Before infection, ADG and G:F increased with increasing Lys:ME in control and PRRSV-infected pigs (linear and quadratic P &lt; 0.05), and optimum ADG and G:F were achieved at 3.02 and 2.92 Lys:ME, respectively, in PRRSV-infected pigs compared to 2.82 and 3.22 Lys:ME, respectively, in control pigs. Over the 49-d period, increasing Lys:ME improved ADG (P &lt; 0.01, linear and quadratic) and G:F (linear P &lt; 0.01) in naturally infected pigs. The response was similar in experimental infection for ADG (P &lt; 0.01, linear and quadratic) and G:F (linear P = 0.01). The optimum ratio for ADG (2.86 vs. 3.12 Lys:ME) and G:F (3.18 vs. 3.08 Lys:ME) were similar between natural and experimental infection. In summary, increasing Lys:ME by 10% to 20% above NRC requirements improved performance and feed efficiency during an experimental and natural PRRSV challenge.
Coronal Imbalance in Adult Spinal Deformity Following Posterior Spinal Fusion With Instrument
Authors: Zhang Zifang , Song Kai , Wu Bing , Chi Pengfei , Wang Zhaohan , Wang Zheng 
Published: October 2018

Study Design.
A retrospective radiographic study.

Objective.
To explore the radiological parameters which correlated to postoperative immediately coronal imbalance in adult spinal deformity (ASD) and to determine whether preoperative coronal imbalance affects postoperative coronal imbalance following posterior multi-level fusion with instruments and osteotomy operation.

Summary of Background Data.
There was paucity of literature paying attention to the postoperative immediately coronal imbalance after operation.

Methods.
The study included 67 consecutive patients with ASD who underwent posterior multi-level fusion with instruments and osteotomy operation. The radiological parameters, measured on the pre- and postoperative anteroposterior and lateral radiographs, were compared and analyzed. Patients were divided into three groups (group A, B, and C) according to preoperative coronal balance distance (pre-CBD) and the relation of cervical 7 plumb line (C7PL), and the convex of curvature. To analyze the radiological parameters of the three groups.

Result.
Differences of the radiological parameters between pre- and postoperation concerning Cobb angles, degree of apical vertebra rotation, thoracic kyphosis (TK), thoracic lumber kyphosis (TLK), lumber lordosis (LL), sacral slope (SS), pelvic tilt (PT), and sagittal vertical axis (SVA), were significant (P < 0.05). Pelvic incidence (PI), pre-CBD, and postoperative coronal balance distance (post-CBD) had no change (P > 0.05). The ratio of coronal imbalance in pre- and postoperation was 31.34% (21/67) and 40.30% (27/67), respectively, which had significant difference (P = 0.02). Significant correlations were observed among post-CBD, pre-CBD (P < 0.001), and d-Cobb (pre-Cobb – post-Cobb) (P = 0.002), post-CBD = –2.737 – 0.924∗d-Cobb + 0.356∗pre-CBD. The ratio of postoperative immediately coronal imbalance of the group C was much higher than other two groups (P = 0.01).

Conclusion.
The sagittal alignments in ASD patients would be improved effectively after posterior multi-level fusion with instruments and osteotomy operation. There were significant correlations among post-CBD, pre-CBD, and d-Cobb. Patients in group C may be at greater risk for immediate postoperative coronal imbalance after operation.

Level of Evidence: 3
Additional Sacroplasty Does Not Improve Clinical Outcome in Minimally Invasive Navigation-Assisted Screw Fixation Procedures for Nondisplaced Insufficiency Fractures of the Sacrum
Authors: Balling Horst 
Published: October 2018

Study Design.
Prospective single-center cohort study (noninferiority study).

Objective.
To compare clinical results of navigation-assisted screw fixation (NSF) to those of NSF with additional sacroplasty (NSF + SP) for immobilizing nondisplaced insufficiency fractures of the sacrum.

Summary of Background Data.
NSF for sacral insufficiency fractures is a new, technically demanding procedure requiring surgical skills and experience. Up to date, controversies exist about the benefit of additional sacroplasty in surgically stabilized insufficiency fractures of the sacrum.

Methods.
From February 2011 to May 2017, all individuals with immobilizing nondisplaced sacral insufficiency fractures surgically treated using 3D-fluoroscopy for 3D-real-time navigation and postinstrumentation screw control in the form of NSF (I) or NSF + SP (II) were enrolled. SP was performed only in absence of transforaminal or central fractures. Outcome parameters were postsurgical pain relief determined by visual analog scale, postsurgical improvement of disability evaluated using the Oswestry Disability Index, and length of postsurgical hospital stay.

Results.
In 2 groups of 26 individuals, each, a total of 124 insufficiency fractures of sacral vertebrae were surgically treated. Postoperative pain-level decrease was comparable in both groups (5.3 vs. 5.4 visual analog scale points). Extent of postoperative disability score improvement (53.4 vs. 57.7 Oswestry Disability Index points) led to successful remobilization after similar durations of postsurgical hospital stay (9.3 vs. 9.6 days). Minimum clinically important differences of outcome parameters were not reached in the comparison of study group results. In procedures with SP, no major complications occurred, in those without SP, no specific complications were observed.

Conclusion.
This comparative study indicates noninferiority of NSF compared to NSF + SP for sacral insufficiency fractures, and could not confirm clinical advantages of additional SP concerning pain relief, improvement of fracture-related disability, or time from surgery to discharge. Therefore, additional sacroplasty is not recommended to enhance the clinical benefit for patients receiving image-guided sacral screw fixation.

Level of Evidence: 2