bluuebunny/crossref_metadata_2025_split huggingface dataset:
DNA methylation and miRNA-1296 act in concert to mediate spatiotemporal expression of KPNA7 during bovine oocyte and early embryonic development
Authors: Wang Lei , Hand Jacqelyn M. , Fu Liyuan , Smith George W. , Yao Jianbo 
Published: December 2019

Abstract
Background
Epigenetic regulation of oocyte-specific maternal factors is essential for oocyte and early embryonic development. KPNA7 is an oocyte-specific maternal factor, which controls transportation of nuclear proteins important for early embryonic development. To elucidate the epigenetic mechanisms involved in the controlled expression of KPNA7, both DNA methylation associated transcriptional silencing and microRNA (miRNA)-mediated mRNA degradation of KPNA7 were examined.

Results
Comparison of DNA methylation profiles at the proximal promoter of KPNA7 gene between oocyte and 6 different somatic tissues identified 3 oocyte-specific differentially methylated CpG sites. Expression of KPNA7 mRNA was reintroduced in bovine kidney-derived CCL2 cells after treatment with the methylation inhibitor, 5-aza-2′-deoxycytidine (5-Aza-CdR). Analysis of the promoter region of KPNA7 gene in CCL2 cells treated with 5-Aza-CdR showed a lighter methylation rate in all the CpG sites. Bioinformatic analysis predicted 4 miRNA-1296 binding sites in the coding region of KPNA7 mRNA. Ectopic co-expression of miRNA-1296 and KPNA7 in HEK293 cells led to reduced expression of KPNA7 protein. Quantitative real time PCR (RT-qPCR) analysis revealed that miRNA-1296 is expressed in oocytes and early stage embryos, and the expression reaches a peak level in 8-cell stage embryos, coincident with the time of embryonic genome activation and the start of declining of KPNA7 expression.

Conclusions
These results suggest that DNA methylation may account for oocyte-specific expression of KPNA7, and miRNA-1296 targeting the coding region of KPNA7 is a potential mechanism for KPNA7 transcript degradation during the maternal-to-zygotic transition.
CRISPR elements provide a new framework for the genealogy of the citrus canker pathogen Xanthomonas citri pv. citri
Authors: Jeong Kwanho , Muñoz-Bodnar Alejandra , Arias Rojas Nathalia , Poulin Lucie , Rodriguez-R Luis Miguel , Gagnevin Lionel , Vernière Christian , Pruvost Olivier , Koebnik Ralf 
Published: December 2019

Abstract
Background
Xanthomonads are an important clade of Gram-negative bacteria infecting a plethora of economically important host plants, including citrus. Knowledge about the pathogen’s diversity and population structure are prerequisite for epidemiological surveillance and efficient disease management. Rapidly evolving genetic loci, such as Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR), are of special interest to develop new molecular typing tools.

Results
We analyzed CRISPR loci of 56 Xanthomonas citri pv. citri strains of world-wide origin, a regulated pathogen causing Asiatic citrus canker in several regions of the world. With one exception, 23 unique sequences built up the repertoire of spacers, suggesting that this set of strains originated from a common ancestor that already harbored these 23 spacers. One isolate originating from Pakistan contained a string of 14 additional, probably more recently acquired spacers indicating that this genetic lineage has or had until recently the capacity to acquire new spacers. Comparison of CRISPR arrays with previously obtained molecular typing data, such as amplified fragment length polymorphisms (AFLP), variable-number of tandem-repeats (VNTR) and genome-wide single-nucleotide polymorphisms (SNP), demonstrated that these methods reveal similar evolutionary trajectories. Notably, genome analyses allowed to generate a model for CRISPR array evolution in X. citri pv. citri, which provides a new framework for the genealogy of the citrus canker pathogen.

Conclusions
CRISPR-based typing will further improve the accuracy of the genetic identification of X. citri pv. citri outbreak strains in molecular epidemiology analyses, especially when used concomitantly with another genotyping method.
Microarray and metabolome analysis of hepatic response to fasting and subsequent refeeding in zebrafish (Danio rerio)
Authors: Jia Jirong , Qin Jingkai , Yuan Xi , Liao Zongzhen , Huang Jinfeng , Wang Bin , Sun Caiyun , Li Wensheng 
Published: December 2019

Abstract
Background
Compensatory growth refers to the phenomenon in which organisms grow faster after the improvement of an adverse environment and is thought to be an adaptive evolution to cope with the alleviation of the hostile environment. Many fish have the capacity for compensatory growth, but the underlying cellular mechanisms remain unclear. In the present study, microarray and nontargeted metabolomics were performed to characterize the transcriptome and metabolome of zebrafish liver during compensatory growth.

Results
Zebrafish could regain the weight they lost during 3 weeks of fasting and reach a final weight similar to that of fish fed ad libitum when refed for 15 days. When refeeding for 3 days, the liver displayed hyperplasia accompanied with decreased triglyceride contents and increased glycogen contents. The microarray results showed that when food was resupplied for 3 days, the liver TCA cycle (Tricarboxylic acid cycle) and oxidative phosphorylation processes were upregulated, while DNA replication and repair, as well as proteasome assembly were also activated. Integration of transcriptome and metabolome data highlighted transcriptionally driven alterations in metabolism during compensatory growth, such as altered glycolysis and lipid metabolism activities. The metabolome data also implied the participation of amino acid metabolism during compensatory growth in zebrafish liver.

Conclusion
Our study provides a global resource for metabolic adaptations and their transcriptional regulation during refeeding in zebrafish liver. This study represents a first step towards understanding of the impact of metabolism on compensatory growth and will potentially aid in understanding the molecular mechanism associated with compensatory growth.
Analysis of reporting completeness in exercise cancer trials: a systematic review
Authors: Meneses-Echavez Jose Francisco , Rodriguez-Prieto Indira , Elkins Mark , Martínez-Torres Javier , Nguyen Lien , Bidonde Julia 
Published: December 2019

Abstract
Background
Exercise is an effective therapeutic intervention for cancer survivors. Concerns about the completeness of reporting of exercise interventions have been raised in the literature, but without any formal analysis. This study aimed to evaluate the completeness of reporting of exercise interventions for cancer survivors in a large sample of randomized clinical trials (RCTs).

Methods
We developed a pre-defined protocol. We searched MEDLINE, EMBASE, and CENTRAL for exercise trials in oncology between 2010 and 2017. Pairs of independent researchers screened the records, extracted study characteristics, and assessed 16 items on the TIDieR checklist (i.e., the 12 items, with item 5 divided into two and item 8 divided into four). For each of these items, the percentage of interventions in the included studies that reported the item was calculated.

Results
We included 131 RCTs reporting 138 interventions in the analysis. Breast cancer was the most common type of cancer (69, 50%), and aerobic exercise was the most studied exercise modality (43, 30%) followed by combined aerobic and resistance training (40, 28%). Completeness of reporting ranged from 42 to 96% among the TIDieR items; none of the items was fully reported. ‘Intervention length’ was the most reported item across interventions (133, 96%), followed by ‘rationale’ (131, 95%), whereas ‘provider’ (58, 42%) and ‘how well (planned)’ (63, 46%) were the two least reported items. Half of the TIDieR items were completely reported in 50 to 70% of the interventions, and only four items were reported in more than 80% of the interventions (Items 2 and 8a to c). The seven items deemed to be core for replication (Items 3 to 9) exhibited a mean reporting of 71%, ranging from 42 to 96%.

Conclusion
Exercise training interventions for cancer survivors are incompletely reported across RCTs published between 2010 and 2017. The reporting of information about the provider, materials, and modifications require urgent improvements. Stronger reporting will enhance usability of trial reports by both healthcare providers and survivors, and will help to reduce research waste.
General practitioners referring patients to specialists in tertiary healthcare: a qualitative study
Authors: Tzartzas Konstantinos , Oberhauser Pierre-Nicolas , Marion-Veyron Régis , Bourquin Céline , Senn Nicolas , Stiefel Friedrich 
Published: December 2019

AbstractBackgroundThere is a large and unexplained variation in referral rates to specialists by general practitioners, which calls for investigations regarding general practitioners’ perceptions and expectations during the referral process. Our objective was to describe the decision-making process underlying referral of patients to specialists by general practitioners working in a university outpatient primary care center.MethodsTwo focus groups were conducted among general practitioners (10 residents and 8 chief residents) working in the Center for Primary Care and Public Health (Unisanté) of the University of Lausanne, in Switzerland. Focus group data were analyzed with thematic content analysis. A feedback group of general practitioners validated the results.ResultsParticipating general practitioners distinguished two kinds of situations regarding referral: a) “clear-cut situations”, in which the decision to refer or not seems obvious and b) “complex cases”, in which they hesitate to refer or not. Regarding the “complex cases”, they reported various types of concerns: a) about the treatment, b) about the patient and the doctor-patient relationship and c) about themselves. General practitioners evoked numerous reasons for referring, including non-medical factors such as influencing patients’ emotions, earning specialists’ esteem or sharing responsibility. They also explained that they seek validation by colleagues and postpone referral so as to relieve some of the decision-related distress.ConclusionsGeneral practitioners’ referral of patients to specialists cannot be explained in biomedical terms only. It seems necessary to take into account the fact that referral is a sensitive topic for general practitioners, involving emotionally charged interactions and relationships with patients, colleagues, specialists and supervisors. The decision to refer or not is influenced by multiple contextual, personal and clinical factors that dynamically interact and shape the decision-making process.
Irritable bowel syndrome-like symptoms and health related quality of life two years after Roux-en-Y gastric bypass - a prospective cohort study
Authors: Blom-Høgestøl Ingvild Kristine , Aasbrenn Martin , Chahal-Kummen Monica , Brunborg Cathrine , Eribe Inger , Kristinsson Jon , Farup Per G. , Mala Tom 
Published: December 2019

Abstract
Background
Irritable bowel syndrome (IBS) is prevalent in patients with morbid obesity. After Roux-en-Y gastric bypass (RYGB) chronic abdominal pain is common, however the etiology is largely unknown. We aimed to study the change in the prevalence of IBS-like symptoms 2 years after RYGB and possible preoperative predictors of such symptoms. Secondly, to evaluate changes in symptoms of constipation and diarrhea, and Health related quality of life (HRQoL).

Methods
Patients with morbid obesity were included at two obesity centers in South-Eastern Norway. IBS was diagnosed according to the Rome III criteria. Predictors were evaluated in a multivariable logistic regression analysis.

Results
Of 307 participants operated with RYGB, 233 (76%) completed the study questionnaires. Preoperatively 27/233 participants (12%) had IBS, 2 years after RYGB 61/233 (26%) had IBS-like symptoms (p < 0.001). Eleven participants with IBS preoperatively (41%) did not report such symptoms after RYGB. New onset IBS-like symptoms was identified in 45/206 (22%) after RYGB. Fibromyalgia, low LDL levels, high vitamin B1 levels and IBS before RYGB were independent preoperative predictors of IBS-like symptoms at the follow-up visit. Symptom scores for constipation preoperatively and 2 year after RYGB were 1.5 (0.9) and 1.8 (1.2), and for diarrhea 1.4 (0.9) and 1.8 (1.1), respectively (p < 0.001). We observed a significant improvement in the physical component score for all participants. However, participants with new onset IBS-like symptoms had a significant worsening of the mental component score.

Conclusions
The prevalence of IBS-like symptoms doubled 2 years after RYGB, and these symptoms were associated with reduced HRQoL. Preoperative IBS and fibromyalgia were strong predictors of postoperative IBS-like symptoms.
Clinical impact of the perioperative management of oral anticoagulants in bleeding after colonic endoscopic mucosal resection
Authors: Ono Shoko , Ishikawa Marin , Matsuda Kana , Tsuda Momoko , Yamamoto Keiko , Shimizu Yuichi , Sakamoto Naoya 
Published: December 2019

Abstract
Background
Heparin bridging therapy (HBT) is indeed related to a high frequency of bleeding after endoscopic mucosal resection (EMR). In this study, our aim was to investigate clinical impact of management of oral anticoagulants without HBT in bleeding after colonic EMR.

Methods
From data for patients who underwent consecutive colonic EMR, the relationships of patient factors and procedural factors with the risk of bleeding were analysed. Our management of antithrombotic agents was based on the shortest cessation as follows: the administration of warfarin was generally continued within the therapeutic range, and direct oral anticoagulants (DOACs) were not administered on the day of the procedure. We calculated bleeding risks after EMR in patients who used antithrombotic agents and evaluated whether perioperative management of anticoagulants without HBT was beneficial for bleeding.

Results
A total of 1734 polyps in 825 EMRs were analysed. Bleeding occurred in 4.0% of the patients and 1.9% of the polyps. The odds ratios for bleeding using multivariate logistic regression analysis were 3.67 in patients who used anticoagulants and 4.95 in patients who used both anticoagulants and antiplatelet agents. In patients with one-day skip of DOACs, bleeding occurred in 6.5% of the polyps, and there were no significant differences in bleeding risk between HBT and continuous warfarin or one-day skip DOACs.

Conclusions
The use of oral anticoagulants was related to bleeding after colonic EMR, and perioperative management of oral anticoagulants based on the shortest cessation without HBT would be clinically acceptable.
Depressive symptoms in long term care facilities in Western Canada: a cross sectional study
Authors: Hoben Matthias , Heninger Abigail , Holroyd-Leduc Jayna , Knopp-Sihota Jennifer , Estabrooks Carole , Goodarzi Zahra 
Published: December 2019

Abstract
Background
The main objective is to better understand the prevalence of depressive symptoms, in long-term care (LTC) residents with or without cognitive impairment across Western Canada. Secondary objectives are to examine comorbidities and other factors associated with of depressive symptoms, and treatments used in LTC.

Methods
11,445 residents across a random sample of 91 LTC facilities, from 09/2014 to 05/2015, were stratified by owner-operator model (private for-profit, public or voluntary not-for-profit), size (small: < 80 beds, medium: 80–120 beds, large > 120 beds), location (Calgary and Edmonton Health Zones, Alberta; Fraser and Interior Health Regions, British Columbia; Winnipeg Health Region, Manitoba).
Random intercept generalized linear mixed models with depressive symptoms as the dependent variable, cognitive impairment as primary independent variable, and resident, care unit and facility characteristics as covariates were used. Resident variables came from the Resident Assessment Instrument – Minimum Data Set (RAI-MDS) 2.0 records (the RAI-MDS version routinely collected in Western Canadian LTC). Care unit and facility variables came from surveys completed with care unit or facility managers.

Results
Depressive symptoms affects 27.1% of all LTC residents and 23.3% of LTC resident have both, depressive symptoms and cognitive impairment. Hypertension, urinary and fecal incontinence were the most common comorbidities. Cognitive impairment increases the risk for depressive symptoms (adjusted odds ratio 1.65 [95% confidence interval 1.43; 1.90]). Pain, anxiety and pulmonary disorders were also significantly associated with depressive symptoms. Pharmacologic therapies were commonly used in those with depressive symptoms, however there was minimal use of non-pharmacologic management.

Conclusions
Depressive symptoms are common in LTC residents –particularly in those with cognitive impairment. Depressive symptoms are an important target for clinical intervention and further research to reduce the burden of these illnesses.
The need for improved cognitive, hearing and vision assessments for older people with cognitive impairment: a qualitative study
Authors: Wolski Lucas , Leroi Iracema , Regan Jemma , Dawes Piers , Charalambous Anna Pavlina , Thodi Chryssoula , Prokopiou Juliana , Villeneuve Roxane , Helmer Catherine , Yohannes Abebaw Mengistu , Himmelsbach Ines 
Published: December 2019

Abstract
Background
Hearing and vision (sensory) impairments are highly prevalent in people with dementia (PwD) and exacerbate the impact of living with dementia. Assessment of sensory or cognitive function may be difficult if people have concurrent dual or triple impairments. Most standard cognitive assessment tests are heavily dependent on having intact hearing and vision, and impairments in these domains may render the assessments unreliable or even invalid. Likewise, dementia may impede on the accurate reporting of symptoms that is required for most hearing and vision assessments. Thus, there is an urgent need for hearing, vision and cognitive assessment strategies to be adapted to ensure that appropriate management and support can be provided.

Objective
To explore the perspectives of PwD and the care partners regarding the need for accurate hearing, vision and cognitive assessments.

Methods
We conducted focus groups and semi-structured interviews regarding the clinical assessment for cognitive, hearing and visual impairment. Participants (n = 18) were older adults with mild to moderate dementia and a sensory impairment as well as their care partners (e.g. a family member) (n = 15) at three European sites. The qualitative material was analysed according to Mayring’s summative content analysis approach.

Results
Participants reported that hearing, vision and cognitive assessments were not appropriate to the complex needs of PwD and sensory comorbidity and that challenges in communication with professionals and conveying unmet needs and concerns by PwD were common in all three types of clinical assessments. They felt that information about and guidance regarding support for the condition was not adequate in the assessments and that information sharing among the professionals regarding the concurrent problems was limited. Professionals were reported as being concerned only with problems related to their own discipline and had limited regard for problems in other domains which might impact on their own assessments.

Conclusions
The optimal assessment and support for PwD with multiple impairments, more comprehensive, yet easy to understand, information regarding these linked to conditions and corrective device use is needed. Communication among health care professionals relevant to hearing, vision and cognition needs to be improved.
Development and validation of elder-friendly urban spaces questionnaire (EFUSQ)
Authors: Lak Azadeh , Aghamolaei Reihaneh , Baradaran Hamid R. , Myint Phyo K. 
Published: December 2019

Abstract
Background
Considering the lack of specific measurement tools to study elders’ perceptions in outdoor spaces, the study objectives were to derive and validate a questionnaire that assesses the essential features of elderly-friendly urban spaces.

Methods
We used closed-ended questions in two phases. In the first qualitative phase, a preliminary questionnaire was defined using grounded theory. In the second phase, the psychometric properties of the elderly-friendly urban spaces were examined through validity and reliability indices.

Results
The findings of the first phase led to a preliminary item extraction and questionnaire with 15 major domains based on three dimensions: place function, place preferences, and process. In the second phase, a 48-item questionnaire, based on three dimensions, in addition to personal characteristics, was introduced.

Conclusions
The Elderly-Friendly Urban Spaces Questionnaire (EFUSQ) can be adopted in various communities in understanding of how to create age-friendly urban spaces to promote active aging.
Elimination of hepatitis C virus in Germany: modelling the cost-effectiveness of HCV screening strategies
Authors: Krauth Christian , Rossol Siegbert , Ortsäter Gustaf , Kautz Achim , Krüger Kathrin , Herder Babette , Stahmeyer Jona Theodor 
Published: December 2019

Abstract
Background
Chronic hepatitis C is a major public health burden. With new interferon-free direct-acting agents (showing sustained viral response rates of more than 98%), elimination of HCV seems feasible for the first time. However, as HCV infection often remains undiagnosed, screening is crucial for improving health outcomes of HCV-patients. Our aim was to assess the long-term cost-effectiveness of a nationwide screening strategy in Germany.

Methods
We used a Markov cohort model to simulate disease progression and examine long-term population outcomes, HCV associated costs and cost-effectiveness of HCV screening. The model divides the total population into three subpopulations: general population (GEP), people who inject drugs (PWID) and HIV-infected men who have sex with men (MSM), with total infection numbers being highest in GEP, but new infections occurring only in PWIDs and MSM. The model compares four alternative screening strategies (no/basic/advanced/total screening) differing in participation and treatment rates.

Results
Total number of HCV-infected patients declined from 275,000 in 2015 to between 125,000 (no screening) and 14,000 (total screening) in 2040. Similarly, lost quality adjusted life years (QALYs) were 320,000 QALYs lower, while costs were 2.4 billion EUR higher in total screening compared to no screening. While incremental cost-effectiveness ratio (ICER) increased sharply in GEP and MSM with more comprehensive strategies (30,000 EUR per QALY for total vs. advanced screening), ICER decreased in PWIDs (30 EUR per QALY for total vs. advanced screening).

Conclusions
Screening is key to have an efficient decline of the HCV-infected population in Germany. Recommendation for an overall population screening is to screen the total PWID subpopulation, and to apply less comprehensive advanced screening for MSM and GEP.