bluuebunny/crossref_metadata_2025_split huggingface dataset:
A comprehensive overview of oncogenic pathways in human cancer
Authors: Li Feng , Wu Tan , Xu Yanjun , Dong Qun , Xiao Jing , Xu Yingqi , Li Qian , Zhang Chunlong , Gao Jianxia , Liu Liqiu , Hu Xiaoxu , Huang Jian , Li Xia , Zhang Yunpeng 
Published: April 2019

Abstract
Alterations of biological pathways can lead to oncogenesis. An overview of these oncogenic pathways would be highly valuable for researchers to reveal the pathogenic mechanism and develop novel therapeutic approaches for cancers. Here, we reviewed approximately 8500 literatures and documented experimentally validated cancer-pathway associations as benchmarking data set. This data resource includes 4709 manually curated relationships between 1557 paths and 49 cancers with 2427 upstream regulators in 7 species. Based on this resource, we first summarized the cancer-pathway associations and revealed some commonly deregulated pathways across tumor types. Then, we systematically analyzed these oncogenic pathways by integrating TCGA pan-cancer data sets. Multi-omics analysis showed oncogenic pathways may play different roles across tumor types under different omics contexts. We also charted the survival relevance landscape of oncogenic pathways in 26 tumor types, identified dominant omics features and found survival relevance for oncogenic pathways varied in tumor types and omics levels. Moreover, we predicted upstream regulators and constructed a hierarchical network model to understand the pathogenic mechanism of human cancers underlying oncogenic pathway context. Finally, we developed `CPAD’ (freely available at http://bio-bigdata.hrbmu.edu.cn/CPAD/), an online resource for exploring oncogenic pathways in human cancers, that integrated manually curated cancer-pathway associations, TCGA pan-cancer multi-omics data sets, drug–target data, drug sensitivity and multi-omics data for cancer cell lines. In summary, our study provides a comprehensive characterization of oncogenic pathways and also presents a valuable resource for investigating the pathogenesis of human cancer.
Modelling G×E with historical weather information improves genomic prediction in new environments
Authors: Gillberg Jussi , Marttinen Pekka , Mamitsuka Hiroshi , Kaski Samuel 
Published: April 2019

Abstract

Motivation
Interaction between the genotype and the environment (G×E) has a strong impact on the yield of major crop plants. Although influential, taking G×E explicitly into account in plant breeding has remained difficult. Recently G×E has been predicted from environmental and genomic covariates, but existing works have not shown that generalization to new environments and years without access to in-season data is possible and practical applicability remains unclear. Using data from a Barley breeding programme in Finland, we construct an in silico experiment to study the viability of G×E prediction under practical constraints.

Results
We show that the response to the environment of a new generation of untested Barley cultivars can be predicted in new locations and years using genomic data, machine learning and historical weather observations for the new locations. Our results highlight the need for models of G×E: non-linear effects clearly dominate linear ones, and the interaction between the soil type and daily rain is identified as the main driver for G×E for Barley in Finland. Our study implies that genomic selection can be used to capture the yield potential in G×E effects for future growth seasons, providing a possible means to achieve yield improvements, needed for feeding the growing population.

Availability and implementation
The data accompanied by the method code (http://research.cs.aalto.fi/pml/software/gxe/bioinformatics_codes.zip) is available in the form of kernels to allow reproducing the results.

Supplementary information
Supplementary data are available at Bioinformatics online.
The Potential of Equine-Assisted Psychotherapy for Treating Trauma in Australian Aboriginal Peoples
Authors: Bennett Bindi , Woodman Elise 
Published: April 2019

AbstractColonisation and subsequent policies targeting Aboriginal peoples in Australia have had devastating consequences, including trauma, disadvantage and marginalisation. These effects have passed from generation to generation and continue to manifest in poor health and well-being outcomes, particularly mental health disorders. Innovative and culturally relevant techniques are needed to remedy inequality and address intergenerational trauma. Equine-assisted psychotherapy (EAP)—an experiential therapy involving horses—is a new and increasingly evidence-based treatment approach, which offers potential for working with Aboriginal peoples. This article reviews the literature on outcomes of EAP to consider its potential as a culturally responsive therapy to treat trauma and increase well-being for Aboriginal people in Australia.
E6AP goes viral: the role of E6AP in viral- and non-viral-related cancers
Authors: Bandilovska Ivona , Keam Simon P , Gamell Cristina , Machicado Claudia , Haupt Sue , Haupt Ygal 
Published: April 2019

AbstractSince its discovery, the E3 ubiquitin ligase E6-associated protein (E6AP) has been studied extensively in two pathological contexts: infection by the human papillomavirus (HPV), and the neurodevelopmental disorder, Angelman syndrome. Vital biological links between E6AP and other viruses, namely hepatitis C virus and encephalomyocarditis virus, have been recently uncovered. Critically, oncogenic E6AP activities have been demonstrated to contribute to cancers of both viral and non-viral origins. HPV-associated cancers serve as the primary example of E6AP involvement in cancers driven by viruses. Studies over the past few years have exposed a role for E6AP in non-viral-related cancers. This has been demonstrated in B-cell lymphoma and prostate cancers, where oncogenic E6AP functions drive these cancers by acting on key tumour suppressors. In this review we discuss the role of E6AP in viral infection, viral propagation and viral-related cancer. We discuss processes affected by oncogenic E6AP, which promote cancers of viral and non-viral aetiology. Overall, recent findings support the role of oncogenic E6AP in disrupting key cellular processes, including tumour suppression and the immune response. E6AP is consequently emerging as an attractive therapeutic target for a number of specific cancers.
The Graded Change in Connectivity across the Ventromedial Prefrontal Cortex Reveals Distinct Subregions
Authors: Jackson Rebecca L , Bajada Claude J , Lambon Ralph Matthew A , Cloutman Lauren L 
Published: April 2019

Abstract
The functional heterogeneity of the ventromedial prefrontal cortex (vmPFC) suggests it may include distinct functional subregions. To date these have not been well elucidated. Regions with differentiable connectivity (and as a result likely dissociable functions) may be identified using emergent data-driven approaches. However, prior parcellations of the vmPFC have only considered hard splits between distinct regions, although both hard and graded connectivity changes may exist. Here we determine the full pattern of change in structural and functional connectivity across the vmPFC for the first time and extract core distinct regions. Both structural and functional connectivity varied along a dorsomedial to ventrolateral axis from relatively dorsal medial wall regions to relatively lateral basal orbitofrontal cortex. The pattern of connectivity shifted from default mode network to sensorimotor and multimodal semantic connections. This finding extends the classical distinction between primate medial and orbital regions by demonstrating a similar gradient in humans for the first time. Additionally, core distinct regions in the medial wall and orbitofrontal cortex were identified that may show greater correspondence to functional differences than prior hard parcellations. The possible functional roles of the orbitofrontal cortex and medial wall are discussed.
Arrhythmogenic propensity of the fibrotic substrate after atrial fibrillation ablation: a longitudinal study using magnetic resonance imaging-based atrial models
Authors: Ali Rheeda L , Hakim Joe B , Boyle Patrick M , Zahid Sohail , Sivasambu Bhradeev , Marine Joseph E , Calkins Hugh , Trayanova Natalia A , Spragg David D 
Published: April 2019

Abstract

Aims
Inadequate modification of the atrial fibrotic substrate necessary to sustain re-entrant drivers (RDs) may explain atrial fibrillation (AF) recurrence following failed pulmonary vein isolation (PVI). Personalized computational models of the fibrotic atrial substrate derived from late gadolinium enhanced (LGE)-magnetic resonance imaging (MRI) can be used to non-invasively determine the presence of RDs. The objective of this study is to assess the changes of the arrhythmogenic propensity of the fibrotic substrate after PVI.

Methods and results
Pre- and post-ablation individualized left atrial models were constructed from 12 AF patients who underwent pre- and post-PVI LGE-MRI, in six of whom PVI failed. Pre-ablation AF sustained by RDs was induced in 10 models. RDs in the post-ablation models were classified as either preserved or emergent. Pre-ablation models derived from patients for whom the procedure failed exhibited a higher number of RDs and larger areas defined as promoting RD formation when compared with atrial models from patients who had successful ablation, 2.6 ± 0.9 vs. 1.8 ± 0.2 and 18.9 ± 1.6% vs. 13.8 ± 1.5%, respectively. In cases of successful ablation, PVI eliminated completely the RDs sustaining AF. Preserved RDs unaffected by ablation were documented only in post-ablation models of patients who experienced recurrent AF (2/5 models); all of these models had also one or more emergent RDs at locations distinct from those of pre-ablation RDs. Emergent RDs occurred in regions that had the same characteristics of the fibrosis spatial distribution (entropy and density) as regions that harboured RDs in pre-ablation models.

Conclusion
Recurrent AF after PVI in the fibrotic atria may be attributable to both preserved RDs that sustain AF pre- and post-ablation, and the emergence of new RDs following ablation. The same levels of fibrosis entropy and density underlie the pro-RD propensity in both pre- and post-ablation substrates.
Rare complication of subacute renal artery intramural haematoma after renal artery stenting: a case report
Authors: Chen Yang , Dong Hui , Jiang Xiongjing , Che Wuqiang 
Published: April 2019

Abstract

Background
Renal artery intramural haematoma (IMH) is a rare cause of renal artery obstruction after stenting. Diagnosis and treatment are difficult as there are only a few cases reported.

Case summary
We present the case of sudden-onset abdominal pain and non-functional kidney 3 days after renal artery stent implantation. Subacute luminal narrowing of the renal artery was initially diagnosed using computed tomography angiography and renal artery angiography, and a final diagnosis of subacute renal artery IMH was made using intravascular ultrasound (IVUS). Subsequently, the patient was treated with percutaneous transluminal angioplasty from far to near and another stent implantation. At the third month follow-up, blood pressure and renal function were normal.

Discussion
This case suggests that IVUS could be useful for qualifying and treating the subacute renal artery IMH.
Sociodemographic factors associated with secondhand smoke exposure and smoking rules in homes with children
Authors: Arechavala Teresa , Continente Xavier , Pérez-Ríos Mónica , Schiaffino Anna , Fernández Esteve , López María José 
Published: April 2019

Abstract

Background
This study aims to identify sociodemographic characteristics associated with secondhand smoke (SHS) exposure and the adoption of smoking bans in homes with children in Spain

Methods
We performed, in 2016, a cross-sectional study to a representative sample of Spanish households with children under 12 years old. We administered a telephone survey to the parents asking about smoking patterns at home, children’s SHS exposure and sociodemographic characteristics. Poisson regression models with robust variance were built to assess sociodemographic characteristics associated with household SHS exposure and the adoption of smoking rules.

Results
In this study participated 2411 families, 25.8% of which reported exposure at home and 84.4% implemented smoking bans. SHS exposure was associated with having one (aPR = 2.09; 95% CI: 1.43–3.04) or two Spanish parents (aPR = 1.71; 95% CI: 1.24–2.36), lower educational attainment (primary: aPR = 1.74; 95% CI: 1.45–2.10; secondary: aPR = 1.37; 95% CI: 1.17–1.60 compared with university studies), a family structure different from two-parent family (aPR = 1.38; 95% CI: 1.14–1.67) and parents between 31 and 40 years (aPR = 0.75; 95% CI: 0.57–0.99) and 41–50 years (aPR = 0.62; 95% CI: 0.47–0.81) compared with 18- to 30-year-old parents. The adoption of smoking bans was associated with two-parent family (aPR = 1.09; 95% CI: 1.01–1.17), living with non-smokers (aPR = 1.46; 95% CI: 1.31–1.62), parents of foreign origin (aPR = 1.09; 95% CI: 1.04–1.14) and younger children (0–3 years: aPR = 1.05; 95% CI: 1.01–1.09) compared with the oldest children (8–11 years).

Conclusion
The parent’s origin and the family structure were associated with SHS exposure and the adoption of smoking bans at home. Moreover, the number of smokers living at home was relevant for the adoption of smoking bans, and the educational attainment for SHS exposure. These factors should be taken into consideration when designing or implementing smoke-free home programmes.
Emergent surgical treatment for acute thrombosis caused by pulmonary artery kinking after left upper sleeve lobectomy
Authors: Nakajima Daisuke , Oda Hiromi , Chen-Yoshikawa Toyofumi F , Date Hiroshi 
Published: April 2019

AbstractThis is a report on the pulmonary arterioplasty for mechanical stenosis post-left upper sleeve lobectomy. A 64-year-old man had a tumour protruding into the left upper bronchus with a diagnosis of squamous cell carcinoma (cT1cN1M0). Left upper bronchial sleeve lobectomy was performed through posterolateral thoracotomy. On postoperative day 1, he received veno-arterial extracorporeal membrane oxygen support due to sudden pulseless electrical activity. We detected left pulmonary artery (PA) kinking with an impaired blood flow by using pulmonary angiography and immediately performed PA thrombectomy and arterioplasty using rethoracotomy. Following the en bloc removal of a thrombus that had completely occluded the left PA, the redundant PA was resected, and PA reconstruction was performed by direct end-to-end anastomosis. A postoperative contrast-enhanced computed tomography scan showed no signs of PA kinking and no residual thrombus formation. When PA bending and mechanical stenosis are detected after bronchial sleeve lobectomy, resection of the redundant PA is also required to prevent PA thrombosis.
Violent crime among Swedish military veterans after deployment to Afghanistan: a population-based matched cohort study
Authors: Pethrus Carl-Martin , Frisell Thomas , Reutfors Johan , Johansson Kari , Neovius Kristian , Söderling Jonas K , Bruze Gustaf , Neovius Martin 
Published: April 2019

Abstract

Objective
To investigate the incidence of violent crime conviction among Swedish military veterans after deployment to Afghanistan versus non-deployed comparators. The main outcome was first conviction of a violent crime, retrieved from the Swedish National Council for Crime Prevention Register until December 31, 2013.

Methods
This was a cohort study of military veterans identified through personnel registers regarding deployment to Afghanistan between 2002 and 2013 (n = 5894). To each military veteran, up to five non-deployed comparators identified via the Military Service Conscription Register were matched by age, sex, conscription year, cognitive ability, psychological assessment, self-reported mental health, body mass index, antidepressants/anxiolytics prescriptions and self-harm (fully matched comparators; n = 28 895). Multivariable adjustment was made for substance abuse and previous health care visits with psychiatric diagnoses. An additional comparator group matched only for age, sex and conscription year was also used (age-sex-matched comparators; n = 29 410).

Results
During 21 898 person-years of follow-up (median = 3.6 years) there were 26 events among deployed military veterans compared with 98 in non-deployed fully matched comparators [12 vs 9 per 10 000 person-years, adjusted hazard ratio (aHR) 1.36; 95% confidence interval (CI) 0.88–2.10]. Among non-deployed age-sex-matched comparators there were 170 violent crime convictions (16 per 10 000 person-years; aHR 0.85; 95% CI 0.56–1.29). Factors associated with greater risk of violent crime convictions were younger age, lower scores on cognitive ability tests and psychological assessment, and convictions preceding deployment.

Conclusion
The violent crime conviction rate after returning from military deployment to Afghanistan was not different compared with non-deployed comparators in individuals without history of violent crime convictions.
Necrotizing Soft Tissue Infection Staphylococcus aureus but not S. pyogenes Isolates Display High Rates of Internalization and Cytotoxicity Toward Human Myoblasts
Authors: Baude Jessica , Bastien Sylvère , Gillet Yves , Leblanc Pascal , Itzek Andreas , Tristan Anne , Bes Michèle , Duguez Stephanie , Moreau Karen , Diep Binh An , Norrby-Teglund Anna , Henry Thomas , Vandenesch François ,   INFECT Study Group, Arnell Per , Bergey Francois , Martins Dos Santos Vitor A P , Hyldegaard Ole , Nekludov Michael , Norrby-Teglund Anna , Pieper Dietmar , Skrede Steinar , Svensson Mattias , Vandenesch Francois 
Published: April 2019

Abstract

Background
Necrotizing soft tissue infections (NSTIs) caused by group A Streptococcus (GAS) and occasionally by Staphylococcus aureus (SA) frequently involve the deep fascia and often lead to muscle necrosis.

Methods
To assess the pathogenicity of GAS and S. aureus for muscles in comparison to keratinocytes, adhesion and invasion of NSTI-GAS and NSTI-SA isolates were assessed in these cells. Bloodstream infections (BSI-SA) and noninvasive coagulase-negative staphylococci (CNS) isolates were used as controls.

Results
NSTI-SA and BSI-SA exhibited stronger internalization into human keratinocytes and myoblasts than NSTI-GAS or CNS. S. aureus internalization reached over 30% in human myoblasts due to a higher percentage of infected myoblasts (>11%) as compared to keratinocytes (<3%). Higher cytotoxicity for myoblasts of NSTI-SA as compared to BSI-SA was attributed to higher levels of psmα and RNAIII transcripts in NSTI-SA. However, the 2 groups were not discriminated at the genomic level. The cellular basis of high internalization rate in myoblasts was attributed to higher expression of α5β1 integrin in myoblasts. Major contribution of FnbpAB-integrin α5β1 pathway to internalization was confirmed by isogenic mutants.

Conclusions
Our findings suggest a factor in NSTI-SA severity is the strong invasiveness of S. aureus in muscle cells, a property not shared by NSTI-GAS isolates.
Neodermis Formation in Full Thickness Wounds Using an Esterified Hyaluronic Acid Matrix
Authors: Aballay Ariel , Hermans Michel H E 
Published: April 2019

AbstractThe role of the dermis is essential for the proper orchestration of all phases of the normal wound healing process. Wounds with seriously damaged or even absent dermis consistently show seriously impaired wound healing and/or long-term complications such as hypertrophic scarring. Replacing a damaged dermis requires a dermal matrix that is compatible with, or even stimulates, the process of wound healing. Hyaluronic acid (HA), in an esterified form, is among the many matrices that are available. HA has been used in a number of indications, such as ulcers (ie, diabetic foot ulcers and venous leg ulcers), trauma, including burns, and for the repair of contractures and hypertrophic scars. The shorter healing time and the decrease of recurring hypertrophy demonstrate the efficiency of HA-derived matrices. Biopsies, taken up to 12 months post-reconstruction show a neodermis that histologically is largely comparable to normal skin, which probably is a function of HA playing such a pivotal role in normal, unwounded skin, as well as in the process of healing.
Featured Article: Behavior Interventions Addressing Obesity in Rural Settings: The E-FLIP for Kids Trial
Authors: Janicke David M , Lim Crystal S , Perri Michael G , Mathews Anne E , Bobroff Linda B , Gurka Matthew J , Parish Alice , Brumback Babette A , Dumont-Driscoll Marilyn , Silverstein Janet H 
Published: April 2019

Abstract

Objective
To assess the effectiveness of behavioral parent-only (PO) and family-based (FB) interventions on child weight, dietary intake, glycated hemoglobin, and quality of life in rural settings.

Methods
This study was a three-armed, randomized controlled trial. Participants were children (age 8–12 years) with overweight or obesity and their parents. A FB (n = 88), a PO (n = 78) and a health education condition (HEC) (n = 83) each included 20 group contacts over 1 year. Assessment and treatment contacts occurred at Cooperative Extension Service offices. The main outcome was change in child body mass index z-score (BMIz) from baseline to year 2.

Results
Parents in all conditions reported high treatment satisfaction (mean of 3.5 or higher on a 4-point scale). A linear mixed model analysis of change in child BMIz from baseline to year 1 and year 2 found that there were no significant group by time differences in child BMIz (year 2 change in BMIz for FB = −0.03 [−0.1, 0.04], PO = −0.01 [−0.08, 0.06], and HEC = −0.09 [−0.15, −0.02]). While mean attendance across conditions was satisfactory during months 1–4 (69%), it dropped during the maintenance phase (42%). High attendance for the PO intervention was related to greater changes in child BMIz (p < .02). Numerous barriers to participation were reported.

Conclusion
Many barriers exist that inhibit regular attendance at in-person contacts for many families. Innovative delivery strategies are needed that balance treatment intensity with feasibility and acceptability to families and providers to facilitate broad dissemination in underserved rural settings.
ClinicalTrials.gov Identifier: NCT01820338.
Cytokinin inhibits cotton fiber initiation by disrupting PIN3a-mediated asymmetric accumulation of auxin in the ovule epidermis
Authors: Zeng Jianyan , Zhang Mi , Hou Lei , Bai Wenqin , Yan Xingying , Hou Nan , Wang Hongxing , Huang Juan , Zhao Juan , Pei Yan 
Published: April 2019

AbstractAuxin-dependent cell expansion is crucial for initiation of fiber cells in cotton (Gossypium hirsutum), which ultimately determines fiber yield and quality. However, the regulation of this process is far from being well understood. In this study, we demonstrate an antagonistic effect between cytokinin (CK) and auxin on cotton fiber initiation. In vitro and in planta experiments indicate that enhanced CK levels can reduce auxin accumulation in the ovule integument, which may account for the defects in the fiberless mutant xu142fl. In turn, supplementation with auxin can recover fiber growth of CK-treated ovules and mutant ovules. We further found that GhPIN3a is a key auxin transporter for fiber-cell initiation and is polarly localized to the plasma membranes of non-fiber cells, but not to those of fiber cells. This polar localization allows auxin to be transported within the ovule integument while specifically accumulating in fiber cells. We show that CKs antagonize the promotive effect of auxin on fiber cell initiation by undermining asymmetric accumulation of auxin in the ovule epidermis through down-regulation of GhPIN3a and disturbance of the polar localization of the protein.