bluuebunny/crossref_metadata_2025_split huggingface dataset:
Discourses of technology, ageing and participation
Authors: Fleming Aysha , Mason Claire , Paxton Gillian 
Published: May 2018

AbstractThe proliferation of digital technology has brought about rapid social and economic change, the consequences of which have not been evenly distributed. Older people, in particular, tend to be less engaged with digital technology and as a result, are said to be at risk of 'digital exclusion'. In this paper, we explore how digital technology is discursively linked to ageing and social and economic participation. The analysis is based on 38 interviews with representatives of industry, government and civil society asked to share their views of the opportunities and risks associated with age and participation in the context of rapid developments in digital technology. Using discourse analysis we identify two competing ways interview participants made connections between digital technology and its perceived effects on the economic and social participation of an ageing population. In the first, digital technology drives human progress as a ‘fix’ to some of the social and economic challenges associated with ageing but also demands a cautious approach to minimise unforeseen negative consequences. In the second, digital technology is a tool, whose development can be driven by humans in order to solve a range of problems, including economic and social participation in later life. We consider the implications of these two discourses, discussing the potential of each for achieving a sense of empowerment in the ageing community and addressing the challenge of lifelong participation.
Rewiring of auxin signaling under persistent shade
Authors: Pucciariello Ornella , Legris Martina , Costigliolo Rojas Cecilia , Iglesias María José , Hernando Carlos Esteban , Dezar Carlos , Vazquez Martín , Yanovsky Marcelo J. , Finlayson Scott A. , Prat Salomé , Casal Jorge J. 
Published: May 2018

Significance
In agricultural crops, plants are cultivated in close proximity, exposed to mutual shading. Photosensory receptors perceive this light environment and initiate growth responses that adjust the position of plant organs within the canopy to maximize light capture. During the early hours under shade, these responses are mediated by elevated levels of the hormone auxin. Here we show that under prolonged shade, the PHYTOCHROME INTERACTING FACTOR 4 light-signaling transcription factor, selected auxin receptors, their upstream regulatory miRNA, and downstream transcriptional regulators change their abundance to enhance growth responses, while auxin levels return to those observed before shade. Thus, in the presence of persistent shade, plants elicit a system-level rearrangement of auxin signaling, which sustains growth without increased auxin.
Microbial genomic island discovery, visualization and analysis
Authors: Bertelli Claire , Tilley Keith E , Brinkman Fiona S L 
Published: May 2018

Abstract
Horizontal gene transfer (also called lateral gene transfer) is a major mechanism for microbial genome evolution, enabling rapid adaptation and survival in specific niches. Genomic islands (GIs), commonly defined as clusters of bacterial or archaeal genes of probable horizontal origin, are of particular medical, environmental and/or industrial interest, as they disproportionately encode virulence factors and some antimicrobial resistance genes and may harbor entire metabolic pathways that confer a specific adaptation (solvent resistance, symbiosis properties, etc). As large-scale analyses of microbial genomes increases, such as for genomic epidemiology investigations of infectious disease outbreaks in public health, there is increased appreciation of the need to accurately predict and track GIs. Over the past decade, numerous computational tools have been developed to tackle the challenges inherent in accurate GI prediction. We review here the main types of GI prediction methods and discuss their advantages and limitations for a routine analysis of microbial genomes in this era of rapid whole-genome sequencing. An assessment is provided of 20 GI prediction software methods that use sequence-composition bias to identify the GIs, using a reference GI data set from 104 genomes obtained using an independent comparative genomics approach. Finally, we present guidelines to assist researchers in effectively identifying these key genomic regions.
REGGAE: a novel approach for the identification of key transcriptional regulators
Authors: Kehl Tim , Schneider Lara , Kattler Kathrin , Stöckel Daniel , Wegert Jenny , Gerstner Nico , Ludwig Nicole , Distler Ute , Schick Markus , Keller Ulrich , Tenzer Stefan , Gessler Manfred , Walter Jörn , Keller Andreas , Graf Norbert , Meese Eckart , Lenhof Hans-Peter 
Published: May 2018

Abstract

Motivation
Transcriptional regulators play a major role in most biological processes. Alterations in their activities are associated with a variety of diseases and in particular with tumor development and progression. Hence, it is important to assess the effects of deregulated regulators on pathological processes.

Results
Here, we present REGulator-Gene Association Enrichment (REGGAE), a novel method for the identification of key transcriptional regulators that have a significant effect on the expression of a given set of genes, e.g. genes that are differentially expressed between two sample groups. REGGAE uses a Kolmogorov–Smirnov-like test statistic that implicitly combines associations between regulators and their target genes with an enrichment approach to prioritize the influence of transcriptional regulators. We evaluated our method in two different application scenarios, which demonstrate that REGGAE is well suited for uncovering the influence of transcriptional regulators and is a valuable tool for the elucidation of complex regulatory mechanisms.

Availability and implementation
REGGAE is freely available at https://regulatortrail.bioinf.uni-sb.de.

Supplementary information
Supplementary data are available at Bioinformatics online.
Grouper: graph-based clustering and annotation for improved de novo transcriptome analysis
Authors: Malik Laraib , Almodaresi Fatemeh , Patro Rob 
Published: May 2018

Abstract

Motivation
De novo transcriptome analysis using RNA-seq offers a promising means to study gene expression in non-model organisms. Yet, the difficulty of transcriptome assembly means that the contigs provided by the assembler often represent a fractured and incomplete view of the transcriptome, complicating downstream analysis. We introduce Grouper, a new method for clustering contigs from de novo assemblies that are likely to belong to the same transcripts and genes; these groups can subsequently be analyzed more robustly. When provided with access to the genome of a related organism, Grouper can transfer annotations to the de novo assembly, further improving the clustering.

Results
On de novo assemblies from four different species, we show that Grouper is able to accurately cluster a larger number of contigs than the existing state-of-the-art method. The Grouper pipeline is able to map greater than 10% more reads against the contigs, leading to accurate downstream differential expression analyses. The labeling module, in the presence of a closely related annotated genome, can efficiently transfer annotations to the contigs and use this information to further improve clustering. Overall, Grouper provides a complete and efficient pipeline for processing de novo transcriptomic assemblies.

Availability and implementation
The Grouper software is freely available at https://github.com/COMBINE-lab/grouper under the 2-clause BSD license.

Supplementary information
Supplementary data are available at Bioinformatics online.
Optimal sampling rates for approximating analytic functions from pointwise samples
Authors: Adcock Ben , Platte Rodrigo B , Shadrin Alexei 
Published: May 2018

AbstractWe consider the problem of approximating an analytic function on a compact interval from its values at $M+1$ distinct points. When the points are equispaced, a recent result (the so-called impossibility theorem) has shown that the best possible convergence rate of a stable method is root-exponential in M, and that any method with faster exponential convergence must also be exponentially ill conditioned at a certain rate. This result hinges on a classical theorem of Coppersmith & Rivlin concerning the maximal behavior of polynomials bounded on an equispaced grid. In this paper, we first generalize this theorem to arbitrary point distributions. We then present an extension of the impossibility theorem valid for general nonequispaced points and apply it to the case of points that are equidistributed with respect to (modified) Jacobi weight functions. This leads to a necessary sampling rate for stable approximation from such points. We prove that this rate is also sufficient, and therefore exactly quantify (up to constants) the precise sampling rate for approximating analytic functions from such node distributions with stable methods. Numerical results—based on computing the maximal polynomial via a variant of the classical Remez algorithm—confirm our main theorems. Finally, we discuss the implications of our results for polynomial least-squares approximations. In particular, we theoretically confirm the well-known heuristic that stable least-squares approximation using polynomials of degree N &lt; M is possible only once M is sufficiently large for there to be a subset of N of the nodes that mimic the behavior of the $N$th set of Chebyshev nodes.
Good intentions are not enough: how informatics interventions can worsen inequality
Authors: Veinot Tiffany C , Mitchell Hannah , Ancker Jessica S 
Published: May 2018

AbstractHealth informatics interventions are designed to help people avoid, recover from, or cope with disease and disability, or to improve the quality and safety of healthcare. Unfortunately, they pose a risk of producing intervention-generated inequalities (IGI) by disproportionately benefiting more advantaged people. In this perspective paper, we discuss characteristics of health-related interventions known to produce IGI, explain why health informatics interventions are particularly vulnerable to this phenomenon, and describe safeguards that can be implemented to improve health equity. We provide examples in which health informatics interventions produced inequality because they were more accessible to, heavily used by, adhered to, or effective for those from socioeconomically advantaged groups. We provide a brief outline of precautions that intervention developers and implementers can take to guard against creating or worsening inequality through health informatics. We conclude by discussing evaluation approaches that will ensure that IGIs are recognized and studied.
Military-Tailored Yoga for Veterans with Post-traumatic Stress Disorder†
Authors: Cushing Robin E , Braun Kathryn L , Alden, C-IAYT Susan W , Katz Alan R 
Published: May 2018

Abstract

Introduction
Among veterans of post-9/11 conflicts, estimates of post-traumatic stress disorder (PTSD) range from 9% shortly after returning from deployment to 31% a year after deployment. Clinical and pharmaceutically based treatments are underutilized. This could be due to concerns related to lost duty days, as well as PTSD patients’ fears of stigma of having a mental health condition. Yoga has been shown to reduce PTSD symptoms in the civilian population, but few studies have tested the impact of yoga on veterans of post-9/11 conflicts. The purpose of this study is to test the impact of yoga on post-9/11 veterans diagnosed with PTSD.

Materials and Methods
Participants were 18 yr of age or older and veterans of post-9/11 conflicts. They had subthreshold or diagnostic-level PTSD related to their combat military service, as determined by a score of 30 or higher on the PTSD Checklist-Military version (PCL-M). Veterans participated in 60-min weekly yoga sessions for 6 wk taught by a Warriors at Ease-trained yoga instructor who is a, post-9/11 veteran. The yoga sessions incorporated Vinyasa-style yoga and a trauma-sensitive, military-culture informed approach advocated by two separate organizations: Warriors at Ease and Meghan's Foundation. Data were collected at baseline and again after 7 wk. The primary outcome was PCL-M score. Participants also completed the Patient Health Questionnaire, the Beck Anxiety Inventory, the Pittsburgh Sleep Quality Index, and the Mindful Attention Awareness Scale at both time points.

Results
Eighteen Operation Enduring Freedom, Operation Iraqi Freedom, and Operation New Dawn veterans completed the pre- and post-intervention self-report questionnaires. Age ranged from 26 to 62 yr (median = 43 yr), length of service ranged from 2 to 34 yr (median = 18.8 yr), and 13 (72.2%) had completed college. Decreased PTSD symptomatology was demonstrated in the three-symptom clusters represented in the PCL-M (i.e., hyperarousal, re-experiencing, and avoidance). In addition, the total score on the PCL-M decreased significantly, by both statistical and clinical measures. The participants also demonstrated improved mindfulness scores and reported decreased insomnia, depression, and anxiety symptoms.

Conclusion
This study demonstrates that a trauma-sensitive yoga intervention may be effective for veterans with PTSD symptoms, whether as stand-alone or adjunctive therapy. The impressive decrease in PTSD symptomatology may be due to the tailored military-specific nature of this intervention and the fact that it was led by a veteran of post-9/11 conflicts. More research is needed with a larger sample and a more diverse veteran population.
Outcome After Clipping and Coiling for Aneurysmal Subarachnoid Hemorrhage in Clinical Practice in Europe, USA, and Australia
Authors: Lindgren Antti , Turner Ellie Bragan , Sillekens Tomas , Meretoja Atte , Lee Jin-Moo , Hemmen Thomas M , Koivisto Timo , Alberts Mark , Lemmens Robin , Jääskeläinen Juha E , Vergouwen Mervyn D I , Rinkel Gabriel J E ,   Stroke GOAL Group, Dr Foster Global Comparators Project, Dr Foster Ltd, Lemmens Robin , Rinkel Gabriel , Shaw Louise , Vaux Emma , Randall Marc , Spencer Mary , Lee Jin-Moo , Matzkiw Gudridur (“Peggy”) H , Rost Natalia , Hemmen Thomas , Alberts Mark , Tveiten Arnstein , Meretoja Atte ,   Dr Foster Unit at Imperial College London
Published: May 2018

Abstract

BACKGROUND
Within randomized clinical trials (RCTs), coiling of the ruptured aneurysm to prevent rebleeding results in better outcomes than clipping in patients with aneurysmal subarachnoid hemorrhage (aSAH).

OBJECTIVE
To study the association of coiling and clipping with outcome after aSAH in daily clinical practice.

METHODS
In this controlled, nonrandomized study, we compared outcomes after endovascular coiling and neurosurgical clipping of ruptured intracranial aneurysms in an administrative dataset of 7658 aSAH patients (22 tertiary care hospitals from Europe, USA, Australia; 2007-2013). Because the results contradicted those of the randomized trials, findings were further explored in a large clinical dataset from 2 European centers (2006-2016) of 1501 patients.

RESULTS
In the administrative dataset, the crude 14-d case-fatality rate was 6.4% (95% confidence interval [CI] 5.6%-7.2%) after clipping and 8.2% (95% CI 7.4%-9.1%) after coiling. After adjustment for age, sex, and comorbidity/severity, the odds ratio (OR) for 14-d case-fatality after coiling compared to clipping was 1.32 (95% CI 1.10-1.58). In the clinical dataset crude 14-d case fatality rate was 5.7% (95% CI 4.2%-7.8%) for clipping and 9.0% (95% CI 7.3%-11.2%) for coiling. In multivariable logistic regression analysis, the OR for 14-d case-fatality after coiling compared to clipping was 1.7 (95% CI 1.1–2.7), for 90-d case-fatality 1.28 (95% CI 0.91–1.82) and for 90-d poor functional outcome 0.78 (95% CI 0.6–1.01).

CONCLUSION
In clinical practice, coiling after aSAH is associated with higher 14-d case-fatality than clipping and nonsuperior outcomes at 90 d. Both options need to be considered in aSAH patients. Further studies should address the reasons for the discrepancy between current data and those from the RCTs.
Two-Year Clinical, Cerebral Hemodynamic, and Cognitive Outcomes of Adult Patients Undergoing Medication Alone for Symptomatically Ischemic Moyamoya Disease Without Cerebral Misery Perfusion: A Prospective Cohort Study
Authors: Miyoshi Kenya , Chida Kohei , Kobayashi Masakazu , Kubo Yoshitaka , Yoshida Kenji , Terasaki Kazunori , Ogasawara Kuniaki 
Published: May 2018

Abstract

BACKGROUND
In nonsurgical adult moyamoya disease (MMD) patients with ischemic onset and stable hemodynamics, the cerebral hemodynamic and cognitive course remains unclear.

OBJECTIVE
To clarify, through a prospective cohort study, 2-yr clinical, cerebral hemodynamic, and cognitive outcomes of adult patients receiving medication alone for symptomatically ischemic MMD without cerebral misery perfusion.

METHODS
Seventy patients without cerebral misery perfusion on the first 15O gas positron emission tomography (PET) were clinically followed up for 2 yr. The second PET was performed at the end of the 2-yr follow-up. Neuropsychological tests were also performed at the study entry and the end of the 2-yr follow-up.

RESULTS
During the 2-yr follow-up period, 2 patients (3%) developed further cerebral ischemic symptoms and showed new cerebral misery perfusion on PET performed at recurrence. None of the 68 patients without further ischemic symptoms showed cerebral misery perfusion on second PET. All 66 patients who underwent the first and second neuropsychological tests displayed unchanged interval cognition at the 2-yr follow-up.

CONCLUSION
Among adult patients receiving medication alone for symptomatically ischemic MMD without cerebral misery perfusion, the incidence of recurrent ischemic events was 3% per 2 yr. In patients without recurrent ischemic events, cerebral hemodynamics and cognitive function had not deteriorated by 2 yr after the last event.
Virtual Reality Exploration and Planning for Precision Colorectal Surgery
Authors: Guerriero Ludovica , Quero Giuseppe , Diana Michele , Soler Luc , Agnus Vincent , Marescaux Jacques , Corcione Francesco 
Published: May 2018

BACKGROUND:
Medical software can build a digital clone of the patient with 3-dimensional reconstruction of Digital Imaging and Communication in Medicine images. The virtual clone can be manipulated (rotations, zooms, etc), and the various organs can be selectively displayed or hidden to facilitate a virtual reality preoperative surgical exploration and planning.

OBJECTIVE:
We present preliminary cases showing the potential interest of virtual reality in colorectal surgery for both cases of diverticular disease and colonic neoplasms.

DESIGN:
This was a single-center feasibility study.

SETTINGS:
The study was conducted at a tertiary care institution.

PATIENTS:
Two patients underwent a laparoscopic left hemicolectomy for diverticular disease, and 1 patient underwent a laparoscopic right hemicolectomy for cancer. The 3-dimensional virtual models were obtained from preoperative CT scans. The virtual model was used to perform preoperative exploration and planning. Intraoperatively, one of the surgeons was manipulating the virtual reality model, using the touch screen of a tablet, which was interactively displayed to the surgical team.

MAIN OUTCOME MEASURES:
The main outcome was evaluation of the precision of virtual reality in colorectal surgery planning and exploration.

RESULTS:
In 1 patient undergoing laparoscopic left hemicolectomy, an abnormal origin of the left colic artery beginning as an extremely short common trunk from the inferior mesenteric artery was clearly seen in the virtual reality model. This finding was missed by the radiologist on CT scan. The precise identification of this vascular variant granted a safe and adequate surgery. In the remaining cases, the virtual reality model helped to precisely estimate the vascular anatomy, providing key landmarks for a safer dissection.

LIMITATIONS:
A larger sample size would be necessary to definitively assess the efficacy of virtual reality in colorectal surgery.

CONCLUSIONS:
Virtual reality can provide an enhanced understanding of crucial anatomical details, both preoperatively and intraoperatively, which could contribute to improve safety in colorectal surgery.
Antegrade Enema After Total Mesorectal Excision for Rectal Cancer: The Last Chance to Avoid Definitive Colostomy for Refractory Low Anterior Resection Syndrome and Fecal Incontinence
Authors: Didailler Romain , Denost Quentin , Loughlin Paula , Chabrun Edouard , Ricard Julie , Picard Flor , Zerbib Frank , Rullier Eric 
Published: May 2018

BACKGROUND:
Total mesorectal excision and preoperative radiotherapy in mid and low rectal cancer allow us to achieve very good oncological results. However, major and refractory low anterior resection syndrome and fecal incontinence alter the quality of life of patients with a long expected life span.

OBJECTIVE:
We assessed the functional results of patients treated by antegrade enema for refractory low anterior resection syndrome and fecal incontinence after total mesorectal excision.

DESIGN:
This is a prospective monocentric study from 2012 to 2016.

PATIENTS:
Patients who underwent percutaneous endoscopic cecostomy for refractory low anterior resection syndrome and fecal incontinence after total mesorectal excision were prospectively analyzed.

MAIN OUTCOME MEASURES:
We assessed the morbidity of the procedure and compared low anterior resection syndrome score, Wexner score, and Gastrointestinal Quality of Life Index before and after the use of antegrade enema.

RESULTS:
Of 25 patients treated by antegrade enema over the study period, 6 (24%) had a low anterior resection, 18 (72%) had a coloanal anastomosis, and 1 (4%) had a perineal colostomy. Postoperatively, the rate of local abscess was 8%, all treated by antibiotics. Low anterior resection syndrome score (33 vs 4, p < 0.001), Wexner score (16 vs 4, p <0.001), and Gastrointestinal Quality of Life Index (73 vs 104, p < 0.001) were all significantly improved after antegrade enema. The 2 main symptoms reported by patients were sweating (28%) and local pain (36%). At the end of the follow-up, 16% (n = 4) catheters were removed, and the rate of definitive colostomy was 12% (n = 3).

LIMITATIONS:
The main limitations of this study are the monocentric features and the sample size.

CONCLUSION:
Antegrade enema for major and refractory low anterior resection syndrome and fecal incontinence after total mesorectal excision appears to be a promising treatment to avoid definitive colostomy. See Video Abstract at http://links.lww.com/DCR/A608.
Alternatives to Biologics in Management of Knee Osteoarthritis: A Systematic Review
Authors: Hassan Fadi , Murrell William D. , Refalo Andrew , Maffulli Nicola 
Published: May 2018

Background:
Knee osteoarthritis (KOA) is a common condition encountered by physicians. KOA is addressed by a wide array of modalities including a number of nonbiological treatments.

Methods:
PubMed, ISI Web of Science, and SPORTDiscus were searched for level 1 to 4 studies published from inception to August 2017.

Results:
A total of 18 studies were evaluated and results demonstrated moderate supporting evidence for prolotherapy and limited evidence for botulinum toxin type A, sodium bicarbonate and calcium gluconate, and low–molecular weight fraction of 5% human serum albumin. Evidence for local anesthetic agents was conflicting.

Conclusion:
There is moderate supportive evidence for the effectiveness of prolotherapy in improving pain and function in both, short-term and long-term. Limited supporting evidence found for botulinum toxin type A, sodium bicarbonate and calcium gluconate, and low–molecular weight fraction of 5% human serum albumin in improving pain and function. There is conflicting evidence for the use of local anesthetic agents in patients with KOA.