bluuebunny/crossref_metadata_2025_split huggingface dataset:
Unraveling genomic associations with feed efficiency and body weight traits in chickens through an integrative approach
Authors: Moreira Gabriel Costa Monteiro , Poleti Mirele Daiana , Pértille Fábio , Boschiero Clarissa , Cesar Aline Silva Mello , Godoy Thaís Fernanda , Ledur Mônica Corrêa , Reecy James M. , Garrick Dorian J. , Coutinho Luiz Lehmann 
Published: November 2019

Abstract

Background
Feed efficiency and growth rate have been targets for selection to improve chicken production. The incorporation of genomic tools may help to accelerate selection. We genotyped 529 individuals using a high-density SNP chip (600 K, Affymetrix®) to estimate genomic heritability of performance traits and to identify genomic regions and their positional candidate genes associated with performance traits in a Brazilian F2 Chicken Resource population. Regions exhibiting selection signatures and a SNP dataset from resequencing were integrated with the genomic regions identified using the chip to refine the list of positional candidate genes and identify potential causative mutations.

Results
Feed intake (FI), feed conversion ratio (FC), feed efficiency (FE) and weight gain (WG) exhibited low genomic heritability values (i.e. from 0.0002 to 0.13), while body weight at hatch (BW1), 35 days-of-age (BW35), and 41 days-of-age (BW41) exhibited high genomic heritability values (i.e. from 0.60 to 0.73) in this F2 population. Twenty unique 1-Mb genomic windows were associated with BW1, BW35 or BW41, located on GGA1–4, 6–7, 10, 14, 24, 27 and 28. Thirty-eight positional candidate genes were identified within these windows, and three of them overlapped with selection signature regions. Thirteen predicted deleterious and three high impact sequence SNPs in these QTL regions were annotated in 11 positional candidate genes related to osteogenesis, skeletal muscle development, growth, energy metabolism and lipid metabolism, which may be associated with body weight in chickens.

Conclusions
The use of a high-density SNP array to identify QTL which were integrated with whole genome sequence signatures of selection allowed the identification of candidate genes and candidate causal variants. One novel QTL was detected providing additional information to understand the genetic architecture of body weight traits. We identified QTL for body weight traits, which were also associated with fatness in the same population. Our findings form a basis for further functional studies to elucidate the role of specific genes in regulating body weight and fat deposition in chickens, generating useful information for poultry breeding programs.
The role of nitric oxide during embryonic wound healing
Authors: Abaffy Pavel , Tomankova Silvie , Naraine Ravindra , Kubista Mikael , Sindelka Radek 
Published: November 2019

AbstractBackgroundThe study of the mechanisms controlling wound healing is an attractive area within the field of biology, with it having a potentially significant impact on the health sector given the current medical burden associated with healing in the elderly population. Healing is a complex process and includes many steps that are regulated by coding and noncoding RNAs, proteins and other molecules. Nitric oxide (NO) is one of these small molecule regulators and its function has already been associated with inflammation and angiogenesis during adult healing.ResultsOur results showed that NO is also an essential component during embryonic scarless healing and acts via a previously unknown mechanism. NO is mainly produced during the early phase of healing and it is crucial for the expression of genes associated with healing. However, we also observed a late phase of healing, which occurs for several hours after wound closure and takes place under the epidermis and includes tissue remodelling that is dependent on NO. We also found that the NO is associated with multiple cellular metabolic pathways, in particularly the glucose metabolism pathway. This is particular noteworthy as the use of NO donors have already been found to be beneficial for the treatment of chronic healing defects (including those associated with diabetes) and it is possible that its mechanism of action follows those observed during embryonic wound healing.ConclusionsOur study describes a new role of NO during healing, which may potentially translate to improved therapeutic treatments, especially for individual suffering with problematic healing.
Unraveling the genetic architecture for carbon and nitrogen related traits and leaf hydraulic conductance in soybean using genome-wide association analyses
Authors: Steketee Clinton J. , Sinclair Thomas R. , Riar Mandeep K. , Schapaugh William T. , Li Zenglu 
Published: November 2019

Abstract

Background
Drought stress is a major limiting factor of soybean [Glycine max (L.) Merr.] production around the world. Soybean plants can ameliorate this stress with improved water-saving, sustained N2 fixation during water deficits, and/or limited leaf hydraulic conductance. In this study, carbon isotope composition (δ13C), which can relate to variation in water-saving capability, was measured. Additionally, nitrogen isotope composition (δ15N) and nitrogen concentration that relate to nitrogen fixation were evaluated. Decrease in transpiration rate (DTR) of de-rooted soybean shoots in a silver nitrate (AgNO3) solution compared to deionized water under high vapor pressure deficit (VPD) conditions was used as a surrogate measurement for limited leaf hydraulic conductance. A panel of over 200 genetically diverse soybean accessions genotyped with the SoySNP50K iSelect BeadChips was evaluated for the carbon and nitrogen related traits in two field environments (Athens, GA in 2015 and 2016) and for transpiration response to AgNO3 in a growth chamber. A multiple loci linear mixed model was implemented in FarmCPU to perform genome-wide association analyses for these traits.

Results
Thirty two, 23, 26, and nine loci for δ13C, δ15N, nitrogen concentration, and transpiration response to AgNO3, respectively, were significantly associated with these traits. Candidate genes that relate to drought stress tolerance enhancement or response were identified near certain loci that could be targets for improving and understanding these traits. Soybean accessions with favorable breeding values were also identified. Low correlations were observed between many of the traits and the genetic loci associated with each trait were largely unique, indicating that these drought tolerance related traits are governed by different genetic loci.

Conclusions
The genomic regions and germplasm identified in this study can be used by breeders to understand the genetic architecture for these traits and to improve soybean drought tolerance. Phenotyping resources needed, trait heritability, and relationship to the target environment should be considered before deciding which of these traits to ultimately employ in a specific breeding program. Potential marker-assisted selection efforts could focus on loci which explain the greatest amount of phenotypic variation for each trait, but may be challenging due to the quantitative nature of these traits.
Insight into transketolase of Pyropia haitanensis under desiccation stress based on integrative analysis of omics and transformation
Authors: Shi Jianzhi , Wang Wenlei , Lin Yinghui , Xu Kai , Xu Yan , Ji Dehua , Chen Changsheng , Xie Chaotian 
Published: November 2019

AbstractBackgroundPyropia haitanensis, distributes in the intertidal zone, can tolerate water losses exceeding 90%. However, the mechanisms enablingP. haitanensisto survive harsh conditions remain uncharacterized. To elucidate the mechanism underlyingP. haitanensisdesiccation tolerance, we completed an integrated analysis of its transcriptome and proteome as well as transgenicChlamydomonas reinhardtiicarrying aP. haitanensisgene.ResultsP. haitanensisrapidly adjusted its physiological activities to compensate for water losses up to 60%, after which, photosynthesis, antioxidant systems, chaperones, and cytoskeleton were activated to response to severe desiccation stress. The integrative analysis suggested that transketolase (TKL) was affected by all desiccation treatments. TransgenicC. reinhardtiicells overexpressedPhTKLgrew better than the wild-type cells in response to osmotic stress.ConclusionP. haitanensisquickly establishes acclimatory homeostasis regarding its transcriptome and proteome to ensure its thalli can recover after being rehydrated. Additionally,PhTKLis vital forP. haitanensisdesiccation tolerance. The present data may provide new insights for the breeding of algae and plants exhibiting enhanced desiccation tolerance.
Low pH effects on reactive oxygen species and methylglyoxal metabolisms in Citrus roots and leaves
Authors: Long An , Huang Wei-Lin , Qi Yi-Ping , Yang Lin-Tong , Lai Ning-Wei , Guo Jiu-Xin , Chen Li-Song 
Published: November 2019

AbstractBackgroundLimited data are available on the responses of reactive oxygen species (ROS) and methylglyoxal (MG) metabolisms to low pH in roots and leaves. In China, quite a few ofCitrusare cultivated in acidic soils (pH < 5.0). ‘Xuegan’ (Citrus sinensis) and ‘Sour pummelo’ (Citrus grandis) (C. sinensiswere more tolerant to low pH thanC. grandis) seedlings were irrigated daily with nutrient solution at a pH of 2.5, 3 or 5 for nine months. Thereafter, we examined low pH effects on growth, and superoxide anion production rate (SAP), malondialdehyde (MDA), MG, antioxidants, and enzymes related to ROS and MG detoxification in roots and leaves in order to (a) test the hypothesis that low pH affected ROS and MG metabolisms more in roots than those of leaves, and (b) understand the roles of ROS and MG metabolisms inCitruslow pH-tolerance and -toxicity.ResultsCompared with control, most of the physiological parameters related to ROS and MG metabolisms were greatly altered at pH 2.5, but almost unaffected at pH 3. In addition to decreased root growth, many fibrous roots became rotten and died at pH 2.5. pH 2.5-induced changes in SAP, the levels of MDA, MG and antioxidants, and the activities of most enzymes related to ROS and MG metabolisms were greater in roots than those of leaves. Impairment of root ascorbate metabolism was the most serious, especially inC. grandisroots. pH 2.5-induced increases in MDA and MG levels in roots and leaves, decreases in the ratios of ascorbate/(ascorbate+dehydroascorbate) in roots and leaves and of reduced glutathione/(reduced+oxidized glutathione) in roots were greater inC. grandisthan those inC. sinensis.ConclusionsLow pH affected MG and ROS metabolisms more in roots than those in leaves. The most seriously impaired ascorbate metabolism in roots was suggested to play a role in low pH-induced root death and growth inhibition. Low pH-treatedC. sinensisroots and leaves had higher capacity to maintain a balance between ROS and MG production and their removal via detoxification systems than low pH-treatedC. grandisones, thus contribute to the higher acid-tolerance ofC. sinensis.
Creating and disseminating a home-based cardiac rehabilitation program: experience from the Veterans Health Administration
Authors: Wakefield Bonnie J. , Drwal Kariann , Paez Monica , Grover Sara , Franciscus Carrie , Reisinger Heather Schacht , Kaboli Peter J. , El Accaoui Ramzi 
Published: November 2019

Abstract

Background
Cardiac rehabilitation (CR) programs provide significant benefit for people with cardiovascular disease. Despite these benefits, such services are not universally available. We designed and evaluated a national home-based CR (HBCR) program in the Veterans Health Administration (VHA). The primary aim of the study was to examine barriers and facilitators associated with site-level implementation of HBCR.

Methods
This study used a convergent parallel mixed-methods design with qualitative data to analyze the process of implementation, quantitative data to determine low and high uptake of the HBCR program, and the integration of the two to determine which facilitators and barriers were associated with adoption. Data were drawn from 16 VHA facilities, and included semi-structured interviews with multiple stakeholders, document analysis, and quantitative analysis of CR program attendance codes. Qualitative data were analyzed using the Consolidated Framework for Implementation Research codes including three years of document analysis and 22 interviews.

Results
Comparing high and low uptake programs, readiness for implementation (leadership engagement, available resources, and access to knowledge and information), planning, and engaging champions and opinion leaders were key to success. High uptake sites were more likely to seek information from the external facilitator, compared to low uptake sites. There were few adaptations to the design of the program at individual sites.

Conclusion
Consistent and supportive leadership, both clinical and administrative, are critical elements to getting HBCR programs up and running and sustaining programs over time. All sites in this study had external funding to develop their program, but high adopters both made better use of those resources and were able to leverage existing resources in the setting. These data will inform broader policy regarding use of HBCR services.
Prevalence of left ventricular diastolic dysfunction by cardiac magnetic resonance imaging in thalassemia major patients with normal left ventricular systolic function
Authors: Chinprateep Benjaporn , Ratanasit Nithima , Kaolawanich Yodying , Karaketklang Khemajira , Saiviroonporn Pairash , Viprakasit Vip , Krittayaphong Rungroj 
Published: November 2019

Abstract

Background
The leading cause of mortality of thalassemia major patients is iron overload cardiomyopathy. Early diagnosis with searching for left ventricular diastolic dysfunction before the systolic dysfunction ensued might yield better prognosis. This study aimed to define the prevalence of the left ventricular diastolic dysfunction (LVDD) in thalassemia major patients with normal left ventricular systolic function and the associated factors.

Methods
Adult thalassemia major patients with normal left ventricular systolic function who were referred for cardiac T2* at Siriraj Hospital – Thailand’s largest national tertiary referral center – during the October 2014 to January 2017 study period. Left ventricular diastolic function was defined by mitral valve filling parameters and left atrial volume index using CMR. Patients with moderate to severe valvular heart disease, pericardial disease, or incomplete data were excluded. Baseline characteristics, comorbid diseases, current medication, and laboratory results were recorded and analyzed.

Results
One hundred and sixteen patients were included, with a mean age of 27.5 ± 13.5 years, 57.8% were female, and 87.9% were transfusion dependent. Proportions of homozygous beta-thalassemia and beta-thalassemia hemoglobin E were 12.1 and 87.9%, respectively. The baseline hematocrit was 26.3 ± 3.3%. The prevalence of LVDD was 20.7% (95% CI: 13.7–29.2%). Cardiac T2* was abnormal in 7.8% (95% CI: 3.6–14.2%). Multivariate analysis revealed age, body surface area, homozygous beta-thalassemia, splenectomy, heart rate, and diastolic blood pressure to be significantly associated with LVDD.

Conclusions
LVDD already exists from the early stages of the disease before the abnormal heart T2 * is detected. Homozygous beta-thalassemia and splenectomy were strong predictors of LVDD. These data may increase awareness of the disease, especially in the high risk groups.
Determinants of suboptimal long-term secondary prevention of acute myocardial infarction: the structural interview method and physical examinations
Authors: Sakalaki Maria , Barywani Salim , Rosengren Annika , Björck Lena , Fu Michael 
Published: November 2019

Abstract

Background
Secondary prevention after an acute myocardial infarction (AMI) reduces morbidity and mortality, but suboptimal secondary prevention of cardiovascular disease is common. Therefore, the present study aimed to identify potential underlying factors for suboptimal secondary prevention 2 years after an AMI event.

Methods
Patients aged 18–85 years at the time of their index AMI and hospitalized between July 2010 and December 2011, were identified retrospectively and consecutively from hospital discharge records. All patients who agreed to participate underwent a structured interview, physical examinations and laboratory analysis 2 years after their index AMI. The secondary preventive goals included are; blood pressure < 140/90 mmHg, LDL < 1.8 mmol/L, HbA1c < 48 mmol/mol, regular physical activity that causes sweating at least twice a week, non-smoking and BMI < 25 kg/m2. Multivariable and univariable logistic regression models were applied to identify independent predictors of different secondary prevention achievements.

Results
Of the 200 patients (mean age 63.3 ± 9.7 years) included in the study, 159 (80%) were men. No common determinants were found in patients who failed to achieve at least six secondary prevention guideline-directed goals. For individual secondary prevention goals, several determinants were defined. Patients born in Sweden were less likely to achieve optimal lipid control [odds ratio (OR) 0.28 (95% confidence interval, CI 0.12–0.63)]. Younger (≤ 65 years) [OR 0.24 (95% CI 0.07–0.74)] and unemployed patients [OR 0.23 (95% CI 0.06–0.82)] were less likely to be non-smokers. Patients with diabetes mellitus [OR 0.21 (95% CI 0.04–0.98)] or with a walking aid [OR 0.23 (95% CI 0.07–0.71)] were less likely to achieve an optimal body mass index (BMI < 25). Living alone was an independent predictor of achieving regular physical activity [OR 1.94 (95% CI 1.02–3.69)].

Conclusion
Long-term secondary prevention remained suboptimal 2 years after an AMI. Causes are likely multifactorial, with no single determinant for all six guideline-recommended preventive goals. Therefore a tailored comprehensive assessment should be requested and updated and treatment of risk factors should be applied.
Association between abnormal myocardial scintigraphy findings and long-term outcomes for elderly patients 85 years or older: a retrospective cohort study
Authors: Kato Takao , Okano Mitsumasa , Haruna Yoshizumi , Inoko Moriaki 
Published: November 2019

Abstract

Background
Normal findings of cardiac scintigraphy predict good outcomes. However, a paucity of the data exists for elderly patients 85 years or older. In the present study, we aimed to demonstrate the association between the abnormal findings of cardiac scintigraphy and the risk of all cause death in patients 85 years or older.

Methods
We enrolled 143 consecutive patients 85 years or older with known or suspected coronary artery disease who underwent stress scintigraphy under adenosine or an exercise test and a 99mTechnetium (Tc)-labeled tracer or thallium 201 (201Tl), dual tracer rest scintigraphy using 201Tl and 123I-β-methyl iodophenyl pentadecanoic acid (123I-BMIPP), or 123I-BMIPP single tracer scintigraphy. Ischemia was defined by an induced perfusion abnormality according to a provocation test with recovery at rest or decreased uptake of 123I-BMIPP despite normal perfusion at rest. Infarction was defined by perfusion abnormalities assessed by images at rest on 201Tl or 99mTc-labeled tracer. We defined these findings as abnormal when at least one of these aforementioned characteristics was observed.

Results
Patients in the abnormal findings group (N = 62) were more likely to have undergone prior coronary angiography and to have decreased ejection fraction than those in the normal findings group (N = 81). The median follow-up duration was 797 days (interquartile range, 635–1045 days), with follow-up rates of 90% at 1 year and 73% at 2 years. The 2-year mortality rate were significantly higher in the abnormal findings group than in the normal findings group (26.8% vs. 10.9%; p = 0.01). The risk of abnormal findings relative to normal findings remained significant for the mortality (adjusted hazard ratio, 5.99; 95% CI, 1.37–42.8; P = 0.015).

Conclusion
Abnormal myocardial scintigraphy findings were associated with the increased risk for mortality, even for patients 85 years or older.
Risk factors for peritonitis in patients on continuous ambulatory peritoneal dialysis who undergo colonoscopy: a retrospective multicentre study
Authors: Gweon Tae-Geun , Jung Sung Hoon , Kim Sang Woo , Lee Kang-Moon , Cheung Dae Young , Lee Bo-In , Choi Hwang 
Published: November 2019

AbstractBackgroundColonoscopy is associated with a risk of peritonitis in patients on peritoneal dialysis. However, no study has yet described the risk factors in play.MethodsThis was a retrospective multicentre study. The medical records of patients on continuous ambulatory peritoneal dialysis (CAPD) who underwent colonoscopy from January 2003 to December 2012 were analysed. We recorded demographic characteristics, colonoscopic factors, use of prophylactic antibiotics, and development of peritonitis. Colonoscopy-related peritonitis was defined as peritonitis developing within 1 week after colonoscopy. Demographic and clinical characteristics were compared between patients who did and those who did not develop peritonitis.ResultsDuring the study period, 236 patients on CAPD underwent colonoscopy, of whom 9 (3.8%) developed peritonitis. The rates of polypectomy/endoscopic mucosal resection were significantly higher in the peritonitis group than in the no peritonitis group (66.7 vs. 23.4%,p = 0.009). Prophylactic antibiotics were prescribed before colonoscopy in 65 patients; none developed peritonitis. No patient who developed peritonitis received prophylactic antibiotics (p = 0.067).ConclusionsAdvanced procedures including polypectomy or endoscopic mucosal resection increase colonoscopy-related peritonitis in patients on CAPD. Randomized controlled trials to investigate whether prophylactic antibiotics are needed to prevent peritonitis in all CAPD patients are warranted.