bluuebunny/crossref_metadata_2025_split huggingface dataset:
Single-step genomic BLUP with genetic groups and automatic adjustment for allele coding
Authors: Strandén Ismo , Aamand Gert P. , Mäntysaari Esa A. 
Published: June 2022

Abstract
Background
Genomic estimated breeding values (GEBV) by single-step genomic BLUP (ssGBLUP) are affected by the centering of marker information used. The use of a fixed effect called J factor will lead to GEBV that are unaffected by the centering used. We extended the use of a single J factor to a group of J factors.

Results
J factor(s) are usually included in mixed model equations (MME) as regression effects but a transformation similar to that regularly used for genetic groups can be applied to obtain a simpler MME, which is sparser than the original MME and does not need computation of the J factors. When the J factor is based on the same structure as the genetic groups, then MME can be transformed such that coefficients for the genetic groups no longer include information from the genomic relationship matrix. We illustrate the use of J factors in the analysis of a Red dairy cattle data set for fertility.

Conclusions
The GEBV from these analyses confirmed the theoretical derivations that show that the resulting GEBV are allele coding independent when a J factor is used. Transformed MME led to faster computing time than the original regression-based MME.
CoQUAD: a COVID-19 question answering dataset system, facilitating research, benchmarking, and practice
Authors: Raza Shaina , Schwartz Brian , Rosella Laura C. 
Published: June 2022

AbstractBackgroundDue to the growing amount of COVID-19 research literature, medical experts, clinical scientists, and researchers frequently struggle to stay up to date on the most recent findings. There is a pressing need to assist researchers and practitioners in mining and responding to COVID-19-related questions on time.MethodsThis paper introduces CoQUAD, a question-answering system that can extract answers related to COVID-19 questions in an efficient manner. There are two datasets provided in this work: a reference-standard dataset built using the CORD-19 and LitCOVID initiatives, and a gold-standard dataset prepared by the experts from a public health domain. The CoQUAD has a Retriever component trained on the BM25 algorithm that searches the reference-standard dataset for relevant documents based on a question related to COVID-19. CoQUAD also has a Reader component that consists of a Transformer-based model, namely MPNet, which is used to read the paragraphs and find the answers related to a question from the retrieved documents. In comparison to previous works, the proposed CoQUAD system can answer questions related to early, mid, and post-COVID-19 topics.ResultsExtensive experiments on CoQUAD Retriever and Reader modules show that CoQUAD can provide effective and relevant answers to any COVID-19-related questions posed in natural language, with a higher level of accuracy. When compared to state-of-the-art baselines, CoQUAD outperforms the previous models, achieving an exact match ratio score of 77.50% and an F1 score of 77.10%.ConclusionCoQUAD is a question-answering system that mines COVID-19 literature using natural language processing techniques to help the research community find the most recent findings and answer any related questions.
Reciprocal positive effects on parasitemia between coinfecting haemosporidian parasites in house sparrows
Authors: Garcia-Longoria Luz , Magallanes Sergio , Huang Xi , Drews Anna , Råberg Lars , Marzal Alfonso , Bensch Staffan , Westerdahl Helena 
Published: June 2022

Abstract
Background
Hosts are often simultaneously infected with several parasite species. These co-infections can lead to within-host interactions of parasites, including mutualism and competition, which may affect both virulence and transmission. Birds are frequently co-infected with different haemosporidian parasites, but very little is known about if and how these parasites interact in natural host populations and what consequences there are for the infected hosts. We therefore set out to study Plasmodium and Haemoproteus parasites in house sparrows Passer domesticus with naturally acquired infections using a protocol where the parasitemia (infection intensity) is quantified by qPCR separately for the two parasites. We analysed infection status (presence/absence of the parasite) and parasitemia of parasites in the blood of both adult and juvenile house sparrows repeatedly over the season.

Results
Haemoproteus passeris and Plasmodium relictum were the two dominating parasite species, found in 99% of the analyzed Sanger sequences. All birds were infected with both Plasmodium and Haemoproteus parasites during the study period. Seasonality explained infection status for both parasites in the adults: H. passeris was completely absent in the winter while P. relictum was present all year round. Among adults infected with H. passeris there was a positive effect of P. relictum parasitemia on H. passeris parasitemia and likewise among adults infected with P. relictum there was a positive effect of H. passeris parasitemia on P. relictum parasitemia. No such associations on parasitemia were seen in juvenile house sparrows.

Conclusions
The reciprocal positive relationships in parasitemia between P. relictum and H. passeris in adult house sparrows suggests either mutualistic interactions between these frequently occurring parasites or that there is variation in immune responses among house sparrow individuals, hence some individuals suppress the parasitemia of both parasites whereas other individuals suppress neither. Our detailed screening of haemosporidian parasites over the season shows that co-infections are very frequent in both juvenile and adult house sparrows, and since co-infections often have stronger negative effects on host fitness than the single infection, it is imperative to use screening systems with the ability to detect multiple parasites in ecological studies of host-parasite interactions.
Frameshift and wild-type proteins are often highly similar because the genetic code and genomes were optimized for frameshift tolerance
Authors: Wang Xiaolong , Dong Quanjiang , Chen Gang , Zhang Jianye , Liu Yongqiang , Cai Yujia 
Published: June 2022

AbstractFrameshift mutations have been considered of significant importance for the molecular evolution of proteins and their coding genes, while frameshift protein sequences encoded in the alternative reading frames of coding genes have been considered to be meaningless. However, functional frameshifts have been found widely existing. It was puzzling how a frameshift protein kept its structure and functionality while substantial changes occurred in its primary amino-acid sequence. This study shows that the similarities among frameshifts and wild types are higher than random similarities and are determined at different levels. Frameshift substitutions are more conservative than random substitutions in the standard genetic code (SGC). The frameshift substitutions score of SGC ranks in the top 2.0-3.5% of alternative genetic codes, showing that SGC is nearly optimal for frameshift tolerance. In many genes and certain genomes, frameshift-resistant codons and codon pairs appear more frequently than expected, suggesting that frameshift tolerance is achieved through not only the optimality of the genetic code but, more importantly, the further optimization of a specific gene or genome through the usages of codons/codon pairs, which sheds light on the role of frameshift mutations in molecular and genomic evolution.
Integrative analysis of summary data from GWAS and eQTL studies implicates genes differentially expressed in Alzheimer’s disease
Authors: Lee Brian , Yao Xiaohui , Shen Li ,   for the Alzheimer’s Disease Neuroimaging Initiative
Published: June 2022

Abstract
Background
Although genome-wide association studies (GWAS) have successfully located various genetic variants susceptible to Alzheimer’s Disease (AD), it is still unclear how specific variants interact with genes and tissues to elucidate pathologies associated with AD. Summary-data-based Mendelian Randomization (SMR) addresses this problem through an instrumental variable approach that integrates data from independent GWAS and expression quantitative trait locus (eQTL) studies in order to infer a causal effect of gene expression on a trait.

Results
Our study employed the SMR approach to integrate a set of meta-analytic cis-eQTL information from the Genotype-Tissue Expression (GTEx), CommonMind Consortium (CMC), and Religious Orders Study and Rush Memory and Aging Project (ROS/MAP) consortiums with three sets of meta-analysis AD GWAS results.

Conclusions
Our analysis identified twelve total gene probes (associated with twelve distinct genes) with a significant association with AD. Four of these genes survived a test of pleiotropy from linkage (the HEIDI test).Three of these genes – RP11-385F7.1, PRSS36, and AC012146.7 – have not yet been reported differentially expressed in the brain in the context of AD, and thus are the novel findings warranting further investigation.
Overexpression of grape ABA receptor gene VaPYL4 enhances tolerance to multiple abiotic stresses in Arabidopsis
Authors: Ren Chong , Kuang Yangfu , Lin Yanping , Guo Yuchen , Li Huayang , Fan Peige , Li Shaohua , Liang Zhenchang 
Published: June 2022

AbstractBackgroundAbscisic acid (ABA) plays a crucial role in abiotic stress responses. The pyrabactin resistance (PYR)/PYR-like (PYL)/regulatory component of ABA receptor (RCAR) proteins that have been characterized as ABA receptors function as the core components in ABA signaling pathway. However, the functions of grapePYLgenes in response to different abiotic stresses, particularly cold stress, remain less studied.ResultsIn this study, we investigated the expression profiles of grapePYLgenes upon cold treatment and isolated theVaPYL4gene fromVitis amurensis, a cold-hardy grape species. Overexpression ofVaPYL4gene in grape calli andArabidopsisresulted in enhanced cold tolerance. Moreover, plant resistance to drought and salt stress was also improved by overexpressingVaPYL4inArabidopsis. More importantly, we evaluated the contribution ofVaPYL4to plant growth and development after the treatment with cold, salt and drought stress simultaneously. The transgenic plants showed higher survival rates, earlier flowering phenotype, and heavier fresh weight of seedlings and siliques when compared with wild-type plants. Physiological analyses showed that transgenic plants had much lower content of malondialdehyde (MDA) and higher peroxidase (POD) activity. Stress-responsive genes such asRD29A(Responsive to desiccation 29A),COR15A(Cold responsive 15A) andKIN2(Kinase 2) were also significantly up-regulated inVaPYL4-overexpressingArabidopsisplants.ConclusionsOur results show that overexpression ofVaPYL4could improve plant performance upon different abiotic stresses, which therefore provides a useful strategy for engineering future crops to deal with adverse environments.
Gurvits syndrome: a case of acute esophageal necrosis associated with diabetic ketoacidosis
Authors: Kitawaki Daisuke , Nishida Atsushi , Sakai Keitaro , Owaki Yuji , Nishino Kyohei , Noda Yoshika , Imaeda Hirotsugu 
Published: June 2022

Abstract
Background
Acute esophageal necrosis (AEN), commonly referred to as Gurvits syndrome or “black esophagus”, is a rare clinical disease. We present a case of AEN associated with diabetic ketoacidosis (DKA).

Case presentation
A 66-year-old male came to our hospital with coffee-ground emesis, dyspnea, and general malaise. He was treated for type 2 diabetes mellitus using insulin and had not been taking his medication, including insulin, for several days. Laboratory analysis revealed severe hyperglycemia (730 mg/dL), normocytic anemia (hemoglobin level, 7.7 g/dL; mean corpuscular volume, 100.4 fL), high serum potassium (7.6 mEq/L), and a high level of blood urea (98.7 mg/dL). Ketones and glucose were detected in the urine, and serum β-hydroxybutyrate was elevated (2132 µmol/L). Arterial blood gas analysis confirmed metabolic acidosis (pH, 7.29; HCO3, 10.5 mmol/L). Collectively, the patient was diagnosed with DKA and upper gastrointestinal bleeding. The patient’s condition improved with intravenous fluids, and he received intravenous insulin to treat DKA. According to these findings, the patient was diagnosed with DKA and upper gastrointestinal bleeding. The patient underwent esophagogastroduodenoscopy (EGD) which revealed a circumferential necrosis of the middle and distal esophagus, immediately proximal to the gastroesophageal junction. The patient was then treated with an intravenous proton pump inhibitor. The patient continued to improve with conservative treatment and was subsequently discharged in a stable condition. An EGD repeated 14 days after discharge showed complete healing of the necrotic-like mucosal change without stricture formation of the esophagus.

Conclusions
AEN is rare but potentially life-threatening case of upper gastrointestinal bleeding. Therefore, a clinician should be aware of AEN as a potential cause of upper gastrointestinal bleeding in elderly patients with poorly controlled diabetes and significant comorbidities.
Underwater endoscopic mucosal resection for rectal neuroendocrine tumors (with videos): a single center retrospective study
Authors: Shi Haitao , Wang Chuying , Wu Jie , Qin Bin , Jiang Jiong , Liu Na , Song Yahua , Qin Yun , Ma Shiyang 
Published: June 2022

Abstract
Background
Underwater endoscopic mucosal resection (UMER) is a new method of endoscopic resection to completely remove the lesion without submucosal injection. But few attempts have been carried out for rectal neuroendocrine tumors (rectal NETs).

Methods
We retrospectively investigated data on the tumor characteristics and outcomes of patients with ≤ 10 mm rectal NETs who underwent UEMR or endoscopic submucosal dissection (ESD) from January 2019 to June 2021 in our institute.

Results
The endoscopic resection rate was 100% in both UEMR and ESD groups. The histological complete resection rate of the UEMR group (95.5%) was lower than that of the ESD group (96.4%) with no significant difference. The average operation time, hospitalization time and operation cost of UEMR group were less than those of ESD group (P < 0.05). The incidence of postoperative abdominal pain and abdominal distention in the UEMR group was lower than that in the ESD group (P < 0.05). There was no significant difference in the incidence of delayed bleeding and perforation between the two groups. There was no local recurrence or distant metastasis in the two groups during the follow-up period.

Conclusions
Both the UEMR and ESD can effectively treat ≤ 10 mm rectal NETs with invasion depth confined to the mucosa and submucosa. UEMR is superior to ESD in operation time, hospitalization time, operation cost, postoperative abdominal pain and abdominal distention.
Frailty, gaps in care coordination, and preventable adverse events
Authors: Akinyelure Oluwasegun P. , Colvin Calvin L. , Sterling Madeline R. , Safford Monika M. , Muntner Paul , Colantonio Lisandro D. , Kern Lisa M. 
Published: June 2022

Abstract
Background
Older US adults often receive care from multiple ambulatory providers. Seeing multiple providers may be clinically appropriate but creates challenges for communication. Whether frailty is a risk factor for gaps in communication among older adults and subsequent preventable adverse events is unknown.

Methods
We conducted a cross-sectional analysis of community-dwelling US adults ≥ 65 years of age in the REasons for Geographic And Racial Differences in Stroke (REGARDS) study who attended an in-home study examination in 2013–2016 and completed a survey on experiences with healthcare in 2017–2018 (n = 5,024). Using 5 frailty indicators (low body mass index, exhaustion, slow walk, weakness, and history of falls), we characterized participants into 3 mutually exclusive groups: not frail (0 indicators), intermediate-frail (1–2 indicators), and frail (3–5 indicators). We used survey data on self-reported gaps in care coordination and self-reported adverse events that participants attributed to poor communication among providers (a drug-drug interaction, repeat testing, an emergency department visit, or a hospital admission).

Results
Overall, 2,398 (47.7%) participants were not frail, 2,436 (48.5%) were intermediate-frail, and 190 (3.8%) were frail. The prevalence of any gap in care coordination was 37.0%, 40.8%, and 51.1% among participants who were not frail, intermediate-frail and frail, respectively. The adjusted prevalence ratio (PR) for any gap in care coordination among intermediate-frail and frail versus not frail participants was 1.09 (95% confidence interval [95%CI] 1.02–1.18) and 1.34 (95%CI 1.15–1.56), respectively. The prevalence of any preventable adverse event was 7.0%, 11.3% and 20.0% among participants who were not frail, intermediate-frail and frail, respectively. The adjusted PR for any preventable adverse event among those who were intermediate-frail and frail versus not frail was 1.47 (95%CI 1.22–1.77) and 2.24 (95%CI 1.60–3.14), respectively.

Conclusion
Among older adults, frailty is associated with an increased prevalence for self-reported gaps in care coordination and preventable adverse events. Targeted interventions to address patient-reported concerns regarding care coordination among intermediate-frail and frail older adults may be warranted.
Validation of the Dyspnoea-12 and Multidimensional Dyspnea profile among older Swedish men in the population
Authors: Olsson Max , Ekström Magnus 
Published: June 2022

Abstract
Background
The Dyspnoea-12 (D12) and Multidimensional dyspnea profile (MDP) are commonly used instruments for assessing multiple dimensions of breathlessness but have not been validated in older people in the population. The aim of this study was to validate the D12 and MDP in 73-years old men in terms of the instruments’ underlying factor structures, internal consistency, and validity.

Methods
A postal survey was sent out to a population sample of 73-years old men (n = 1,193) in southern Sweden. The two-factor structures were evaluated with confirmatory factor analysis, internal consistency with Cronbach's alpha, and validity using Pearson´s correlations with validated scales of breathlessness, anxiety, depression, fatigue, physical/mental quality of life, body mass index (BMI), and cardiorespiratory disease.

Results
A total 684 men were included. Respiratory and cardiovascular disease were reported by 17% and 38%, respectively. For D12 and MDP, the proposed two-factor structure was not fully confirmed in this population. Internal consistency was excellent for all D12 and MDP domain scores (Cronbach's alpha scores > 0.92), and the instruments’ domains showed concurrent validity with other breathlessness scales, and discriminant validity with anxiety, depression, physical/mental quality of life, BMI, and cardiorespiratory disease.

Conclusions
In a population sample of 73-years old men, the D12 and MDP had good psychometrical properties in terms of reliability and validity, which supports that the instruments are valid for use in population studies of older men.
The impact of three progressively introduced interventions on second wave daily COVID-19 case numbers in Melbourne, Australia
Authors: Saul Allan , Scott Nick , Spelman Tim , Crabb Brendan S. , Hellard Margaret 
Published: June 2022

Abstract
Background
The city of Melbourne, Australia experienced two waves of the COVID-19 epidemic peaking, the first in March and a more substantial wave in July 2020. During the second wave, a series of control measure were progressively introduced that initially slowed the growth of the epidemic then resulted in decreasing cases until there was no detectable local transmission.

Methods
To determine the relative efficacy of the progressively introduced intervention measures, we modelled the second wave as a series of exponential growth and decay curves. We used a linear regression of the log of daily cases vs time, using a four-segment linear spline model corresponding to implementation of the three successive major public health measures. The primary model used all reported cases between 14 June and 15 September 2020 then compared the projection of the model with observed cases predicting future case trajectory up until the 31 October 2020 to assess the use of exponential models in projecting the future course and planning future interventions. The main outcome measures were the exponential daily growth constants, analysis of residuals and estimates of the 95% confidence intervals for the expected case distributions, comparison of predicted daily cases.

Results
The exponential growth/decay constants in the primary analysis were: 0.122 (s.e. 0.004), 0.035 (s.e. 0.005), − 0.037 (s.e. 0.011), and − 0.069 (s.e. 0.003) for the initial growth rate, Stage 3, Stage 3 + compulsory masks and Stage 4, respectively. Extrapolation of the regression model from the 14 September to the 31 October matched the decline in observed cases over this period.

Conclusions
The four-segment exponential model provided an excellent fit of the observed reported case data and predicted the day-to-day range of expected cases. The extrapolated regression accurately predicted the decline leading to epidemic control in Melbourne.
Feasibility of a randomized controlled trial of a proprioceptive and tactile vest intervention for children with challenges integrating and processing sensory information
Authors: Nielsen Ann Natasja , la Cour Karen , Brandt Åse 
Published: June 2022

Abstract
Background
Children with challenges integrating and processing sensory information can have difficulties participating in play and learning activities. One way to support participation is to offer sensory stimulation, such as proprioceptive and tactile stimulation provided by wearing a sensory-stimulating vest. The aim of this study was to investigate the feasibility of the key procedures of a planned full-scale randomized controlled trial (RCT) of a proprioceptive and tactile stimulation vest for children aged 6-12 years who have challenges integrating and processing sensory information. The study focused on the feasibility of the recruitment and information processes, the relevance of the study materials, the usefulness of diaries completed by parents, and use of the following outcome measures: Test of Everyday Attention-Children (TEACh), registration of off-task behaviour, and pulse rate.

Methods
Ten schoolchildren aged 6–12 years (mean 8.4) who had challenges integrating and processing sensory information and sensory-seeking behaviours (based on their Short Sensory Profile scores) participated in the study. Study feasibility was assessed using data from interviews with the participating children, their parents and teachers, and psychologists from the municipal Educational Psychological Counselling Departments.

Results
Recruitment and introductory materials were found to be relevant and non-problematic, while the outcome measurements, diaries, and pulse measurements did not work well, and the tool for registering off-task behaviours needed to be revised. The results indicated that an outcome measure relating to the children’s subjective experiences and closer involvement of teachers in the study could be beneficial.

Conclusion
The aim of the study was to investigate the feasibility of the planned methodology for a full-scale RCT of a proprioceptive and tactile stimulating vests for children with challenges integrating and processing sensory information. We found that a partial redesign of the study is needed before a full-scale RCT is conducted and that this should include outcome measures on the children’s subjective experiences with using the vest.