bluuebunny/crossref_metadata_2025_split huggingface dataset:
Using egg production longitudinal recording to study the genetic background of resilience in purebred and crossbred laying hens
Authors: Bedere Nicolas , Berghof Tom V. L. , Peeters Katrijn , Pinard-van der Laan Marie-Hélène , Visscher Jeroen , David Ingrid , Mulder Han A. 
Published: April 2022

Abstract
Background
There is growing interest in using genetic selection to obtain more resilient farm animals (i.e. that are minimally affected by disturbances or rapidly recover from them). The aims of this study were to: (i) estimate the genetic parameters of resilience indicator traits based on egg production data, (ii) assess whether these traits are genetically correlated in purebreds and crossbreds, and (iii) assess the genetic correlations of these traits with egg production (EP) as total number of eggs between 25 and 83 weeks. Purebred hens (33,825 from a White Leghorn (WA) line and 34,397 from a Rhode Island (BD) line were housed in individual cages, while crossbred hens were housed in collective cages of 6 to 8 paternal half-sibs (12,852 WA and 3898 BD crossbred groups, where the name of the group refers to the line used as the sire). Deviations of a hen’s weekly egg production from the average of the corresponding batch were calculated. Resilience indicator traits investigated were the natural logarithm of the variance (LNVAR), the skewness (SKEW), and the lag-one autocorrelation (AUTO-R) of these deviations.

Results
In both purebred lines, EP was estimated to be lowly heritable (WA: 0.11 and BD: 0.12). Resilience indicators were also estimated to be lowly heritable in both lines (LNVAR: 0.10 and 0.12, SKEW: 0.04 and 0.02, AUTO-R: 0.06 and 0.08 in WA and BD, respectively). In both crossbred groups, EP, AUTO-R, and SKEW were estimated to be less heritable than in purebreds (EP: $$h^{2}$$

h
2

≤ 0.07; and resilience indicator traits: $$h^{2}$$

h
2

≤ 0.03), while LNVAR had an $$h^{2}$$

h
2

estimate that was similar to or higher in crossbreds ($$h^{2}$$

h
2

ranged from 0.13 to 0.21) than in purebreds. In both purebreds and crossbreds, resilience indicator traits were estimated to have favorable genetic correlations with EP and between each other. For all traits and in both lines, estimates of genetic correlations between purebreds and crossbreds ($$r_{pc}$$

r

pc

) differed from 1 and ranged from 0.16 to 0.63.

Conclusions
These results show that selection for resilience based on EP data can be considered in breeding programs for layers. Genetic improvement of resilience in crossbreds can be achieved by using information on purebreds, but would be greatly enhanced by the integration of information on crossbreds in breeding programs.
Integrative analysis of mutated genes and mutational processes reveals novel mutational biomarkers in colorectal cancer
Authors: Dashti Hamed , Dehzangi Iman , Bayati Masroor , Breen James , Beheshti Amin , Lovell Nigel , Rabiee Hamid R. , Alinejad-Rokny Hamid 
Published: April 2022

Abstract
Background
Colorectal cancer (CRC) is one of the leading causes of cancer-related deaths worldwide. Recent studies have observed causative mutations in susceptible genes related to colorectal cancer in 10 to 15% of the patients. This highlights the importance of identifying mutations for early detection of this cancer for more effective treatments among high risk individuals. Mutation is considered as the key point in cancer research. Many studies have performed cancer subtyping based on the type of frequently mutated genes, or the proportion of mutational processes. However, to the best of our knowledge, combination of these features has never been used together for this task. This highlights the potential to introduce better and more inclusive subtype classification approaches using wider range of related features to enable biomarker discovery and thus inform drug development for CRC.

Results
In this study, we develop a new pipeline based on a novel concept called ‘gene-motif’, which merges mutated gene information with tri-nucleotide motif of mutated sites, for colorectal cancer subtype identification. We apply our pipeline to the International Cancer Genome Consortium (ICGC) CRC samples and identify, for the first time, 3131 gene-motif combinations that are significantly mutated in 536 ICGC colorectal cancer samples. Using these features, we identify seven CRC subtypes with distinguishable phenotypes and biomarkers, including unique cancer related signaling pathways, in which for most of them targeted treatment options are currently available. Interestingly, we also identify several genes that are mutated in multiple subtypes but with unique sequence contexts.

Conclusion
Our results highlight the importance of considering both the mutation type and mutated genes in identification of cancer subtypes and cancer biomarkers. The new CRC subtypes presented in this study demonstrates distinguished phenotypic properties which can be effectively used to develop new treatments. By knowing the genes and phenotypes associated with the subtypes, a personalized treatment plan can be developed that considers the specific phenotypes associated with their genomic lesion.
Exogenously applied spermidine alleviates hypoxia stress in Phyllostachys praecox seedlings via changes in endogenous hormones and gene expression
Authors: Gao Jianshuang , Zhuang Shunyao , Zhang Yuhe , Qian Zhuangzhuang 
Published: April 2022

Abstract
Background
Hypoxia stress is thought to be one of the major abiotic stresses that inhibits the growth and development of higher plants. Phyllostachys pracecox is sensitive to oxygen and suffers soil hypoxia during cultivation; however, the corresponding solutions to mitigate this stress are still limited in practice. In this study, Spermidine (Spd) was tested for regulating the growth of P. praecox seedlings under the hypoxia stress with flooding.

Results
A batch experiment was carried out in seedlings treated with 1 mM and 2 mM Spd under flooding for eight days. Application of 1 mM and 2 mM Spd could alleviate plant growth inhibition and reduce oxidative damage from hypoxia stress. Exogenous Spd significantly (P < 0.05) increased proline, soluble protein content, catalase (CAT), superoxide dismutase (SOD), and S-adenosylmethionine decarboxylase (SAMDC) activity, enhanced abscisic acid (ABA) and indole-3-acetic acid (IAA) content, and reduced ethylene emission, hydrogen peroxide (H2O2), superoxide radical (O2·−) production rate, ACC oxidase (ACO) and ACC synthase (ACS) to protect membranes from lipid peroxidation under flooding. Moreover, exogenous Spd up-regulated the expression of auxin-related genes auxin responsive factor1 (ARF1), auxin1 protein (AUX1), auxin2 protein (AUX2), auxin3 protein (AUX3) and auxin4 protein (AUX4), and down-regulated the expression of ethylene-related ACO and ACS genes during flooding.

Conclusion
The results indicated that exogenous Spd altered hormone concentrations and the expression of hormone-related genes, thereby protecting the bamboo growth under flooding. Our data suggest that Spd can be used to reduce hypoxia-induced cell damage and improve the adaptability of P. praecox to flooding stress.
A clinical study of genetic testing to guide the dosing of warfarin after heart valve replacement
Authors: Zhang Fan , Zhang Congcong , Gu Chengxiong , Yu Yang , Li Jingxing 
Published: April 2022

Abstract
Objective
To explore the role of genetic testing of VKORC1 and CYP2C9 in determining the dosage of warfarin after aortic valve replacement.

Methods
A total of 172 patients receiving warfarin after aortic valve replacement were divided into a control group (n = 86) and an experimental (n = 86) group based on acceptance of genetic testing. In the experimental group, three loci of VKORC1 and CYP2C9 were tested by polymerase chain reaction-restriction fragment length polymorphism technique, and the initial dose of warfarin was determined based on the genetic testing results and warfarin oral-dose table recommended by U.S. Food and Drug Administration (FDA). In the control group, warfarin (3 mg per night) was used as the initial dose. The international normalized ratio (INR) of each patient was continuously monitored after medication. The percentages of patients meeting the target INR in the two groups at specific time points and at 3-month follow-up after discharge from the hospital were monitored, and the incidence of various adverse events was compared between the groups.

Results
Based on the results of genetic testing, 68 patients received 3–4 mg/d (79.1%), 10 patients received 0.5–2 mg/d (11.6%), and eight patients received 5–7 mg/d (9.3%) as the initial dosages of warfarin in the experimental group. The percentages of the patients meeting the target INR on the third and sixth day of postoperative medication were 45.3% and 73.3%, respectively, in the experimental group, and 29.8% and 58.3%, respectively, in the control group. The INR critical values during hospitalization occurred in 2.3% in the experimental group and in 7.1% in the control group, while the percentage of the patients meeting the target INR after 3 months was 86.1% in the experimental group and 83.1% in the control group.

Conclusion
Genetic testing may guide the selection of the initial dose of warfarin after heart valve replacement to rapidly achieve a stable dose.
Trajectories of physical frailty and cognitive impairment in older adults in United States nursing homes
Authors: Yuan Yiyang , Lapane Kate L. , Tjia Jennifer , Baek Jonggyu , Liu Shao-Hsien , Ulbricht Christine M. 
Published: April 2022

Abstract
Background
U.S. nursing homes provide long-term care to over 1.2 million older adults, 60% of whom were physically frail and 68% had moderate or severe cognitive impairment. Limited research has examined the longitudinal experience of these two conditions in older nursing home residents.

Methods
This national longitudinal study included newly-admitted non-skilled nursing care older residents who had Minimum Data Set (MDS) 3.0 (2014–16) assessments at admission, 3 months, and 6 months (n = 266,001). Physical frailty was measured by FRAIL-NH and cognitive impairment by the Brief Interview for Mental Status. Separate sets of group-based trajectory models were fitted to identify the trajectories of physical frailty and trajectories of cognitive impairment, and to estimate the association between older residents’ characteristics at admission with each set of trajectories. A dual trajectory model was used to quantify the association between the physical frailty trajectories and cognitive impairment trajectories.

Results
Over the course of the first six months post-admission, five physical frailty trajectories [“Consistently Frail” (prevalence: 53.0%), “Consistently Pre-frail” (29.0%), “Worsening Frailty” (7.6%), “Improving Frailty” (5.5%), and “Consistently Robust” (4.8%)] and three cognitive impairment trajectories [“Consistently Severe Cognitive Impairment” (35.5%), “Consistently Moderate Cognitive Impairment” (31.8%), “Consistently Intact/Mild Cognitive Impairment” (32.7%)] were identified. One in five older residents simultaneously followed the trajectories of “Consistently Frail” and “Consistently Severe Cognitive Impairment”. Characteristics associated with higher odds of the “Improving Frailty”, “Worsening Frailty”, “Consistently Pre-frail” and “Consistently Frail” trajectories included greater at-admission cognitive impairment, age ≥ 85 years, admitted from acute hospitals, cardiovascular/metabolic diagnoses, neurological diagnoses, hip or other fractures, and presence of pain. Characteristics associated with higher odds of the “Consistently Moderate Cognitive Impairment” and “Consistently Severe Cognitive Impairment” included worse at-admission physical frailty, neurological diagnoses, hip fracture, and receipt of antipsychotics.

Conclusions
Findings provided information regarding the trajectories of physical frailty, the trajectories of cognitive impairment, the association between the two sets of trajectories, and their association with residents’ characteristics in older adults’ first six months post-admission to U.S. nursing homes. Understanding the trajectory that the residents would most likely follow may provide information to develop a comprehensive care approach tailored to their specific healthcare goals.
A study on the current state and equity level of social participation ability among older adults in Henan Province, China
Authors: Ren Weicun , Chen Dongming , Tarimo Clifford Silver , Tian Qingfeng , Wu Jian , Wang Yinying , Li Shangying 
Published: April 2022

Abstract
Background
The social participation ability among older adults (SPAOA) plays an important role in enhancing their quality of life and utilization of medical services. This study aimed to evaluate the current state and equity level of SPAOA in Henan Province, China, as well as explore the factors associated with the current state and equity level of SPAOA.

Methods
This study analyzed data from the “2019 Henan Provincial Older Adults Ability Assessment Survey”, which included 4,593 older people (over 60 years old). The relationships among the SPAOA indicators were explored using the Structural Equation Model (SEM). The Dynamic Material Element Analysis (DMA) and Logistic Regression (LR) were used to examine the current state of SPAOA and its associated factors. The equity level of SPAOA and its correlated factors were determined using the concentration index and T Theil index.

Results
SPAOA received an overall score of 91.89 ± 9.83. Daily living, perception ability and mental state were positively correlated with SPAOA (r = 0.13, 0.83, 0.11, all P < 0.05). Results of LR indicated that the most significant predictors of SPAOA were age, education level, pre-retirement occupation, and income (all P < 0.05). The concentration index of SPAOA based on age and income were -0.0058 and 0.0096, respectively. SPAOA had a total T Theil index of 0.030–0.031, and the contribution rate of the difference within the group was greater than 94%.

Conclusions
While the overall level of SPAOA has been demonstrated to be outstanding, persons with a higher educational level and income are likely to benefit the most. The observed unequal distribution of SPAOA is primarily related to disparities in age or income within the group. To better serve older adults and improve their position and equity in terms of social participation ability, policymakers could emphasize older males with little income who live in urban areas, as well as unhealthy older females who live in rural residences.
The role and diagnostic accuracy of serology for COVID-19
Authors: Kundu Debasree , Gautam Priyanka , Dayanand Divya , Gunasekaran Karthik , Manesh Abi , Sebastian Merylin , Abhilash Kundavaram P. P. , Zachariah Anand , George Tina , Sathyendra Sowmya , Hansdak Samuel G. , Abraham O. C. , Iyadurai Ramya , Thangakunam Balamugesh , Gupta Richa , Karthik Rajiv , Moorthy Mahesh , Varghese George M. 
Published: April 2022

Abstract
Background
The role and performance of various serological tests for the diagnosis of COVID-19 are unclear. This study aimed to evaluate the performance of seven commercially available serological assays for SARS-CoV-2 antibodies by testing COVID-19 cases and controls.

Methods
Adult patients with fever for > 5 days, admitted to a tertiary-care teaching hospital in South India, were enrolled prospectively between June and December 2020. SARS-CoV-2 RT-PCR confirmed patients were classified as cases, and patients with febrile illness with laboratory-confirmed alternative diagnosis and healthy participants were controls. All participants were tested with SCoV-2 Detect™ IgM ELISA kit and SCoV-2 Detect™ IgG ELISA kit (InBios International, Seattle, USA) (Inbios), SARS-CoV-2 Total and SARS-CoV-2 IgG (Siemens Healthcare Diagnostics Inc., Tarrytown, USA) (Siemens), Roche Elecsys® Anti-SARS-CoV-2 (Roche Diagnostics, Rotkreuz, Switzerland) (Roche), Abbott SARS-CoV-2 IgG (Abbott Diagnostics, IL, USA) (Abbott), and Liaison® SARS-CoV-2 S1/S2 IgG (DiaSorinS.p.A., Saluggia, Italy) (Liaison). The sensitivities, specificities, positive predictive values (PPV), negative predictive values (NPV), and accuracies were compared.

Results
There were 303 participants: 153 cases and 150 controls. ELISA detecting anti-S protein antibody was more sensitive (88.9% for IgG and 86.3% for IgM) than the CLIAs (82.4% for total antibodies and 76.5–85.6% for IgG). Among CLIAs, Roche IgG was most sensitive (85.6%) followed by Abbott (83%) and Liaison (83%). Abbot had the best PPV (88.8%) and was more specific (89.3%) than Liaison (82%) and Roche (82%). Siemens IgG was less sensitive (76.5%) than Siemens Total (82.4%). The specificity of all the serological assays was modest (75–90%). Antibody test positivity increased with the duration of illness reaching 90% after 10 days of illness. When cases were compared against pre-pandemic controls, the IgG gave excellent specificity (98–100%). For seroprevalence studies, InBios IgG had the best accuracy (90.8%) with 88.9% sensitivity and 97.6% specificity.

Conclusion
The serological assays are important adjuncts for the diagnosis of COVID-19 in patients with persistent symptoms, especially in the second week of illness. The value of serological diagnostic tests is limited in the first week of illness and they provide additional value in seroprevalence studies. The diagnostic accuracy of the ELISA and CLIA platforms were comparable.
Duration of delayed graft function and its impact on graft outcomes in deceased donor kidney transplantation
Authors: Budhiraja Pooja , Reddy Kunam S , Butterfield Richard J , Jadlowiec Caroline C , Moss Adyr A. , Khamash Hassan A , Kodali Lavanya , Misra Suman S , Heilman Raymond L 
Published: April 2022

Abstract
Background
There is controversy regarding the impact of delayed graft function (DGF) on kidney transplant outcomes. We hypothesize that the duration of DGF, rather than DGF itself, is associated with long-term kidney graft function.

Methods
We analyzed all deceased donor kidney transplants (DDKT) done at our center between 2008 to 2020. We determined factors associated with DGF duration. DGF duration was assessed at three 14-day intervals: < 14 DGF days, 14–27 DGF days, > 28 DGF days.
We studied the impact of DGF duration on survival and graft function and resource utilization, including hospital length of stay and readmissions.

Results
1714 DDKT recipients were included, 59.4% (n = 1018) had DGF. The median DGF duration was 10 days IQR (6,15). The majority of recipients (95%) had resolution of DGF within 28 days. Donor factors associated with DGF days were longer cold ischemia time, donor on inotropes, older age, donation after circulatory death, higher terminal creatinine, and hypertension. Recipient factors associated with increased DGF duration included male sex, length on dialysis before transplant, and higher body mass index. There were no differences in acute rejection events or interstitial fibrosis progression by 4 months when comparing DGF days. The median length of stay was 3 days. However, readmissions increased with increasing DGF duration. Death-censored graft survival was not associated with the length of DGF except when DGF lasted > 28 days.

Conclusions
Inferior graft survival was observed only in recipients of DDKT with DGF lasting beyond 28 days. DGF lasting < 28 days had no impact on graft survival. Duration of DGF, rather than DGF itself, is associated with graft survival.

Trial Registration
Retrospective study approved by Mayo Clinic IRB number ID: 20-011561.
Non-invasive brain stimulation combined with psychosocial intervention for depression: a systematic review and meta-analysis
Authors: He Jiali , Tang Yiling , Lin Jingxia , Faulkner Guy , Tsang Hector W. H. , Chan Sunny H. W. 
Published: April 2022

Abstract
Objectives
This review investigates the efficacy and safety of non-invasive brain stimulation (NIBS) combined with psychosocial intervention on depressive symptoms.

Materials and methods
We systematically searched five electronic databases from their inception to June 2021: PubMed, Embase, PsycINFO, Web of Science, and Medline. Randomized or non-randomized clinical trials in which NIBS plus psychosocial intervention was compared to control conditions in people with depressive symptoms were included.

Results
A total of 17 eligible studies with 660 participants were included. The meta-analysis results showed that NIBS combined with psychosocial therapy had a positive effect on moderate to severe depression ([SMD = − 0.46, 95%CI (− 0.90, − 0.02), I2 = 73%, p < .01]), but did not significantly improve minimal to mild depression ([SMD = − 0.12, 95%CI (− 0.42, 0.18), I2 = 0%, p = .63]). Compared with NIBS alone, the combination treatment had a significantly greater effect in alleviating depressive symptoms ([SMD = − 0.84, 95%CI (− 1.25, − 0.42), I2 = 0%, p = .93]). However, our results suggested that the pooled effect size of ameliorating depression of NIBS plus psychosocial intervention had no significant difference compared with the combination of sham NIBS [SMD = − 0.12, 95%CI (− 0.31, 0.07), I2 = 0%, p = .60] and psychosocial intervention alone [SMD = − 0.97, 95%CI (− 2.32, 0.38), I2 = 72%, p = .01].

Conclusion
NIBS when combined with psychosocial intervention has a significant positive effect in alleviating moderately to severely depressive symptoms. Further well-designed studies of NIBS combined with psychosocial intervention on depression should be carried out to consolidate the conclusions and explore the in-depth underlying mechanism.
“It’s changed my life not to have the continual worry of being warm” – health and wellbeing impacts of a local fuel poverty programme: a mixed-methods evaluation
Authors: Sawyer Alexandra , Sherriff Nigel , Bishop David , Darking Mary , Huber Jörg W. 
Published: April 2022

Abstract
Background
Living in a cold home and being fuel poor can contribute to adverse physical and mental health. Energy efficiency interventions are considered the simplest ways of tackling fuel poverty and preventing associated negative health, wellbeing, and socio-economic consequences. The overall aim of the current study was to provide a greater understanding of the impact of a locally administered programme, which funded the installation of major heating/insulation measures in areas of high fuel poverty, on the health and wellbeing of beneficiaries of the programme.

Methods
A mixed-methods approach to explore the health and wellbeing impacts of a fuel poverty programme in East Sussex that took place between October 2016 and March 2018. Beneficiaries completed the Warwick-Edinburgh Mental Wellbeing Scale before and after any heating/insulation work had been completed in their home. Beneficiaries were also asked to retrospectively rate their health pre- and post-installation. Interviews with 23 beneficiaries of the programme were conducted to explore in-depth the impact of the programme on people’s health and wellbeing and the wider social determinants of health.

Results
A major heating/insulation measure was installed in 149 homes. The majority of measures installed were boilers (57.7%) and new central heating systems (32.2%). Self-rated health and wellbeing were significantly higher post-installation. Interviewees described clear examples of the positive impacts on physical health and wellbeing such as fewer chest infections, reduced pain, feeling less anxious and depressed, and generally feeling happier and more relaxed. Interviews also highlighted broader areas of impact such as reduced social isolation and increased use of domestic space. Many of the beneficiaries also reported a reduction in their energy bills since their new heating systems had been installed.

Conclusions
The findings from the evaluation suggest that the installation of major heating or insulation measures such as new boilers have substantial benefits for the health and wellbeing of beneficiaries. The findings also suggest that the programme had a positive impact on wider determinants of health including reduction in stress and isolation that are likely to be part of the pathways between fuel poverty interventions and mental and physical health outcomes.