bluuebunny/crossref_metadata_2025_split huggingface dataset:
Microbiability and microbiome-wide association analyses of feed efficiency and performance traits in pigs
Authors: Aliakbari Amir , Zemb Olivier , Cauquil Laurent , Barilly Céline , Billon Yvon , Gilbert Hélène 
Published: April 2022

Abstract
Background
The objective of the present study was to investigate how variation in the faecal microbial composition is associated with variation in average daily gain (ADG), backfat thickness (BFT), daily feed intake (DFI), feed conversion ratio (FCR), and residual feed intake (RFI), using data from two experimental pig lines that were divergent for feed efficiency. Estimates of microbiability were obtained by a Bayesian approach using animal mixed models. Microbiome-wide association analyses (MWAS) were conducted by single-operational taxonomic units (OTU) regression and by back-solving solutions of best linear unbiased prediction using a microbiome covariance matrix. In addition, accuracy of microbiome predictions of phenotypes using the microbiome covariance matrix was evaluated.

Results
Estimates of heritability ranged from 0.31 ± 0.13 for FCR to 0.51 ± 0.10 for BFT. Estimates of microbiability were lower than those of heritability for all traits and were 0.11 ± 0.09 for RFI, 0.20 ± 0.11 for FCR, 0.04 ± 0.03 for DFI, 0.03 ± 0.03 for ADG, and 0.02 ± 0.03 for BFT. Bivariate analyses showed a high microbial correlation of 0.70 ± 0.34 between RFI and FCR. The two approaches used for MWAS showed similar results. Overall, eight OTU with significant or suggestive effects on the five traits were identified. They belonged to the genera and families that are mainly involved in producing short-chain fatty acids and digestive enzymes. Prediction accuracy of phenotypes using a full model including the genetic and microbiota components ranged from 0.60 ± 0.19 to 0.78 ± 0.05. Similar accuracies of predictions of the microbial component were observed using models that did or did not include an additive animal effect, suggesting no interaction with the genetic effect.

Conclusions
Our results showed substantial associations of the faecal microbiome with feed efficiency related traits but negligible effects with growth traits. Microbiome data incorporated as a covariance matrix can be used to predict phenotypes of animals that do not (yet) have phenotypic information. Connecting breeding environment between training sets and predicted populations could be necessary to obtain reliable microbiome predictions.
Genome-wide identification and expression analysis of the SWEET gene family in daylily (Hemerocallis fulva) and functional analysis of HfSWEET17 in response to cold stress
Authors: Huang Dong-Mei , Chen Ying , Liu Xiang , Ni Di-An , Bai Lu , Qin Qiao-Ping 
Published: April 2022

Abstract
Background
The Sugars Will Eventually be Exported Transporters (SWEETs) are a newly discovered family of sugar transporters whose members exist in a variety of organisms and are highly conserved. SWEETs have been reported to be involved in the growth and development of many plants, but little is known about SWEETs in daylily (Hemerocallis fulva), an important perennial ornamental flower.

Results
In this study, 19 daylily SWEETs were identified and named based on their homologous genes in Arabidopsis and rice. Phylogenetic analysis classified these HfSWEETs into four clades (Clades I to IV). The conserved motifs and gene structures showed that the HfSWEETs were very conservative during evolution. Chromosomal localization and synteny analysis found that HfSWEETs were unevenly distributed on 11 chromosomes, and there were five pairs of segmentally duplicated events and one pair of tandem duplication events. The expression patterns of the 19 HfSWEETs showed that the expression patterns of most HfSWEETs in different tissues were related to corresponding clades, and most HfSWEETs were up-regulated under low temperatures. Furthermore, HfSWEET17 was overexpressed in tobacco, and the cold resistance of transgenic plants was much higher than that of wild-type tobacco.

Conclusion
This study identified the SWEET gene family in daylily at the genome-wide level. Most of the 19 HfSWEETs were expressed differently in different tissues and under low temperatures. Overexpression further suggests that HfSWEET17 participates in daylily low-temperature response. The results of this study provide a basis for further functional analysis of the SWEET family in daylily.
GLUT4 gene rs5418 polymorphism is associated with increased coronary heart disease risk in a Uygur Chinese population
Authors: Yu Fei , Liu Fen , Li Xiao-Mei , Zhao Qian , Luo Jun-Yi , Zhang Jin-Yu , Yang Yi-Ning 
Published: April 2022

Abstract
Background
To explore possible associations between glucose transporter 4 (GLUT4) genetic polymorphisms in the patients with coronary heart disease (CHD) in Han and Uygur Chinese populations in Xinjiang, China.

Methods
Two GLUT4 polymorphisms (rs5418 and rs5435) were genotyped in 1262 Han (628 CHD patients and 634 healthy controls) and 896 Uyghur (397 CHD patients and 499 healthy controls) Chinese populations.

Results
In the Han Chinese population, there were no significant differences in allelic or genotypic distribution of rs5418 and rs5435 between the CHD and control groups (all P > 0.05). However, in the Uygur population, there were significant differences in genotype and allele distributions for rs5418 between CHD and the control group (all P < 0.05). Binary Logistic regression analysis showed that carriers with the rs5418 A allele had a higher risk of CHD compared to carriers of the rs5418 G allele (OR = 1.33, 95% CI: 1.069–1.649, P = 0.01), after adjustment for gender, age, drinking and smoking behavior, hypertension and diabetes. Furthermore, haploid association analysis of the two SNP loci of the GLUT4 gene showed that the AC haplotype was associated with CHD in the Uygur population (P = 0.001598; OR = 1.36, 95% CI = 1.1228–1.6406).

Conclusions
rs5418 GLUT4 gene variants are associated with CHD in the Uygur Chinese population.
Prognostic value of neutrophile-to-lymphocyte ratio (NLR) and lactate dehydrogenase (LDH) levels for geriatric patients with COVID-19
Authors: Önal Uğur , Gülhan Muhammet , Demirci Neşe , Özden Ahmet , Erol Nazlı , Işık Sema , Gülten Sedat , Atalay Fatma , Çöplü Nilay 
Published: April 2022

Abstract
Aim
In this study it was aimed to evaluate the prognostic factors for the geriatric patients with confirmed COVID-19 in a tertiary-care hospital at Kastamonu region of Turkey.

Method
Patients (≥65-year-old) who had PCR positivity for COVID-19 between March 2020 and April 2020 in our center were recorded retrospectively. A p value less than 0.05 was considered significant. Ethical committee approval was given from the Bolu University with decision number 2020/176.

Results
There were a total of 100 patients (44% female). In-hospital mortality was recorded as 7%. In univariate analysis for 1 month mortality, diabetes mellitus (p = 0.038), leucocyte count (p = 0.005), neutrophile count (p = 0.02), neutrophile-to-lymphocyte ratio (NLR) (p < 0.001), thrombocyte-to-lymphocyte ratio (TLR) (p = 0.001), C-reactive protein (CRP) (p = 0.002), lactate dehydrogenase (LDH) (p = 0.001), sequential organ failure assessment (SOFA) score (p = 0.001) and qSOFA score (p = 0.002) were found as independent risk factors. On admission, one point increase of NLR (p = 0.014, odds ratio (OR) = 1.371, 95% CI = 1.067–1.761) and one point increase of LDH (p = 0.047, OR = 1.011, 95% CI = 1.001–1.023) were associated with mortality on day 30 according to logistic regression analysis. The cut-off values were found as > 7.8 for NLR (83.33% sensitivity, 97.7% specificity) and > 300 U/L for LDH (100% sensitivity, 79.31% specificity) regarding the prediction of 30-day mortality.

Conclusion
In order to improve clinical management and identify the geriatric patients with COVID-19 who have high risk for mortality, NLR and LDH levels on admission might be useful prognostic tools.
SARS-CoV-2-specific immune responses in elderly and immunosuppressed participants and patients with hematologic disease or checkpoint inhibition in solid tumors: study protocol of the prospective, observational CoCo immune study
Authors: Dopfer-Jablonka Alexandra , Steffens Sandra , Müller Frank , Mikuteit Marie , Niewolik Jacqueline , Cossmann Anne , Stankov Metodi V. , Behrens Georg M. N. , Hummers Eva , Heesen Gloria , Schröder Dominik , Roder Sascha , Klawonn Frank , Vahldiek Kai , Hasenkamp Justin , Kallusky Jonathan , Falk Christine S. , Overbeck Tobias R. , Heinemann Stephanie 
Published: April 2022

Abstract
Background
Immunocompromised people (ICP) and elderly individuals (older than 80 years) are at increased risk for severe coronavirus infections. To protect against serious infection with SARS-CoV-2, ICP are taking precautions that may include a reduction of social contacts and participation in activities which they normally enjoy. Furthermore, for these people, there is an uncertainty regarding the effectiveness of the vaccination. The COVID-19 Contact (CoCo) Immune study strives to characterize the immune response to COVID-19 vaccination in immunocompromised, elderly people, and patients with hematological or oncological diseases. The study uses blood-based screenings to monitor the humoral and cellular immune response in these groups after vaccination. Questionnaires and qualitative interviews are used to describe the level of social participation.

Methods
The CoCo Immune Study is a mixed methods prospective, longitudinal, observational study at two large university hospitals in Northern Germany. Starting in March 2021, it monitors anti-SARS-CoV-2 immune responses and collects information on social participation in more than 600 participants, at least 18 years old. Inclusion criteria and subcohorts: Participants with (1) regularly intake of immunosuppressive medication (ICP-cohort) or (2) age ≥ 80 years (80 + -cohort). Additionally, patients with current or former (3) myeloid, (4) lymphatic disease or (5) solid tumor under checkpoint inhibition (3–5: HO-cohort). Exclusion criteria: (1) refusal to give informed consent, (2) contraindication to blood testing, (3) inability to declare consent. Participants complete a questionnaire at four different time points: prior to full vaccination, and 1, 6 and 12 months after completed vaccination. In addition, participants draw blood samples themselves or through a local health care provider and send them with their questionnaires per post at the respective time points after vaccination. Patients of the HO cohort dispense additional blood samples at week 3 to 12 and at month 6 to 9 after 2nd vaccination to gain additional knowledge in B and T cell responses. Selected participants are invited to qualitative interviews about social participation.

Discussion
This observational study is designed to gain insight into the immune response of people with weakened immune systems and to find out how social participation is affected after COVID-19 vaccination.
Trial registration: This study was registered with German Clinical Trial Registry (registration number: DRKS00023972) on 30th December 2020.
Involuntary crying episodes with Susac’s syndrome—a rare presentation of a rare disease: a case report
Authors: Alshaqi O. , Moodie T. , Alchaki A. 
Published: April 2022

Abstract
Background
In this case, we reported the pseudobulbar affect (PBA) in a patient with Susac’s syndrome—a rare condition that was caused by a rare syndrome. Previous case reports of Susac syndrome described psychiatric symptoms such as emotional disturbances or personality changes. Only a few case reports have reported psychiatric disorders in patients with Susac’s syndrome. There were no reported cases of Susac syndrome with PBA as an initial presentation.

Case presentation
Our patient was 56 years old and presented with involuntary crying, left-sided headache, left-sided hearing loss, and tinnitus. Brain MRI showed numerous areas of restricted diffusion and enhancement involving the corpus callosum, bilateral hemispheres, and brainstem. Ophthalmological evaluation showed bilateral branch retinal artery occlusion. She was diagnosed with Susac’s syndrome and PBA. She was treated with cyclophosphamide and dextromethorphan hydrobromide/quinidine sulfate with excellent recovery. This is a 2-year clinical course.

Discussion and conclusions
Recognition of the clinical presentation of Susac’s syndrome and PBA with early diagnosis and treatment are the keys to preventing further disability and impact on patients and their families.
Assessment of Perinatal Depression Risk among internally displaced Yazidi Women in Iraq: a descriptive cross-sectional study
Authors: Seidi Pegah AM , Abas Nazdar Qudrat , Jaff Dilshad , Dunstan Raven , Soltan Lein , Brumwell Amanda , Wilson Michael , Nicholson Thomas , Palmquist Aunchalee E. L. 
Published: April 2022

Abstract
Background
Yazidi survivors of a 2014 genocidal attack by the self-proclaimed Islamic State of Iraq and Syria (ISIS) have complex medical and mental health needs in the perinatal and postpartum period. Few studies have assessed perinatal mental health needs for this population of women who are living in camps for Internally Displaced Persons (IDP) in the Kurdistan Region of Iraq (KRI).

Methods
The specific aim of this formative cross-sectional study was to assess the prevalence of perinatal depressive symptoms, specifically the risk of perinatal depression symptoms, among a purposive sample of Yazidi women living in camps for internally displaced persons in the Kurdistan region of Iraq. One hundred twenty-two pregnant and recently postpartum (<1 year) Yazidi women completed a Kurdish-language version of the Edinburgh Postnatal Depression Scale (EPDS) questionnaire. Pregnant and postpartum participants’ responses were analyzed together, in order to assess an overall combined risk of perinatal mental health issues for the study population. Logistic regression analyses were used to measure the association of participant characteristics with an elevated risk of perinatal depressive symptoms.

Results
Participants were 17-45 years of age (mean 32 years, SD 7.63) Among the 122 women, 67.2% (n=82) were pregnant and 32.8% (n=40) were <1 year postpartum. Overall, 78% (n=95) of participants were at an elevated risk of depression (EPDS >10), and 53% (n=65) of all participants were at risk of moderate to severe depression (EPDS >12). Thoughts of self-harm (EPDS item 10) were reported among 97% (n=118) of participants. Logistic regression analysis indicated that increased risk of perinatal depressive symptoms was significantly associated with reports of health problems during pregnancy (OR=3.22, 95% [CI]:1.08-9.61) and marital status (OR=16.00; 95% [CI]: 0.42-0.50). Age (OR= 0.84; 95% [CI]: 0.75–0.94) and level of education (OR=0.15; 95% [CI]: 0.42-0.50) had protective effects.

Conclusions
Rates of perinatal depressive symptoms risk among internally displaced Yazid pregnant and postpartum women are higher than the general Kurdish-speaking population in Iraq (28.4%). Culturally responsive trauma informed perinatal and postpartum care services, which include both community-based and clinical strategies for perinatal depressive symptoms and suicide prevention for this population, are critically needed.
Innovative mouse models for the tumor suppressor activity of Protocadherin-10 isoforms
Authors: Kleinberger Irene , Sanders Ellen , Staes Katrien , Van Troys Marleen , Hirano Shinji , Hochepied Tino , Lemeire Kelly , Martens Liesbet , Ampe Christophe , van Roy Frans 
Published: April 2022

Abstract
Background
Nonclustered mouse protocadherin genes (Pcdh) encode proteins with a typical single ectodomain and a cytoplasmic domain with conserved motifs completely different from those of classic cadherins. Alternative splice isoforms differ in the size of these cytoplasmic domains. In view of the compelling evidence for gene silencing of protocadherins in human tumors, we started investigations on Pcdh functions in mouse cancer models.

Methods
For Pcdh10, we generated two mouse lines: one with floxed exon 1, leading to complete Pcdh10 ablation upon Cre action, and one with floxed exons 2 and 3, leading to ablation of only the long isoforms of Pcdh10. In a mouse medulloblastoma model, we used GFAP-Cre action to locally ablate Pcdh10 in combination with Trp53 and Rb1 ablation. From auricular tumors, that also arose, we obtained tumor-derived cell lines, which were analyzed for malignancy in vitro and in vivo. By lentiviral transduction, we re-expressed Pcdh10 cDNAs. RNA-Seq analyses were performed on these cell families.

Results
Surprisingly, not only medulloblastomas were generated in our model but also tumors of tagged auricles (pinnae). For both tumor types, ablation of either all or only long isoforms of Pcdh10 aggravated the disease. We argued that the perichondrial stem cell compartment is at the origin of the pinnal tumors. Immunohistochemical analysis of these tumors revealed different subtypes. We obtained several pinnal-tumor derived (PTD) cell lines and analyzed these for anchorage-independent growth, invasion into collagen matrices, tumorigenicity in athymic mice. Re-expression of either the short or a long isoform of Pcdh10 in two PTD lines counteracted malignancy in all assays. RNA-Seq analyses of these two PTD lines and their respective Pcdh10-rescued cell lines allowed to identify many interesting differentially expressed genes, which were largely different in the two cell families.

Conclusions
A new mouse model was generated allowing for the first time to examine the remarkable tumor suppression activity of protocadherin-10 in vivo. Despite lacking several conserved motifs, the short isoform of Pcdh10 was fully active as tumor suppressor. Our model contributes to scrutinizing the complex molecular mechanisms of tumor initiation and progression upon PCDH10 silencing in many human cancers.
Femtosecond laser-assisted in situ keratomileusis with topography-guided or asphericity-adjusted derived data: a comparative contralateral eye study
Authors: Alves Ermano M. , Lyra Adriana F. , Tenório Manuela , Mesquita Natália , Bacelar Carolina , Montenegro Afra , Alves Lucas , Alves Márcio 
Published: April 2022

Abstract
Background
Wavefront-optimized laser-assisted in situ keratomileusis (LASIK) ablation is the most commonly performed procedure in refractive surgery, but new technologies have become available. Our goal was to compare topography-guided (Contoura) and asphericity-guided (Custom-Q) customized ablation treatments for the correction of myopia with or without astigmatism.

Methods
This prospective, randomized, double-blind, contralateral eye study included 60 eyes of 30 patients with myopia or myopic astigmatism requiring femtosecond LASIK (FemtoLASIK) treatment. For each patient, one eye was randomized to undergo Contoura treatment, and the other underwent Custom-Q abaltion. Uncorrected distance visual acuity (UDVA), corrected distance visual acuity (CDVA), manifest refractive spherical equivalent (MRSE), sphere (SPH), cylinder (CYL), 6.0-mm total corneal aberration root mean square (RMS), coma (COMA), trefoil (TREF), and spherical aberration (SA) were measured and analysed after a 1-year follow-up.

Results
The UDVA was − 0.08 ± 0.06 logMAR in Contoura eyes and − 0.08 ± 0.05 logMAR in Custom-Q eyes (p = 0.309) after 12 months. Twenty-five eyes (83%) in the Contoura group and twenty-six eyes (87%) in the Custom-Q group had a UDVA of 20/16 at the end of 12 months, and 100% of eyes in both groups reached a UDVA of 20/25 or better. Ninety and 100% of eyes in the Contoura and Custom-Q groups, respectively, achieved a residual CYL ≤0.50 D (p = 0.237). No statistically significant difference was observed between the surgical techniques in the preoperative to 1-year postoperative changes for any of the parameters evaluated (MRSE, CYL, RMS, DEF, COMA, TREF, and SA).

Conclusions
The Contoura and Custom-Q techniques yielded excellent visual and refractive results, but the evidence did not reveal any clear differences between these two methods after 1 year of follow-up.

Trial registration
ReBEC - Registro Brasileiro de Ensaios Clínicos [Internet]: Rio de Janeiro (RJ): Instituto de Informação Científica e Tecnológica em Saúde (Brazil); 2010 -. Identifier RBR-8rs5kt Myopia and Astigmatism Topography-guided Refractive Surgery by Contoura Method Versus Customized by Asphericity in Contralateral Eyes: A prospective Double blind Randomized Study. Available from https://ensaiosclinicos.gov.br/rg/RBR-8rs5kt
Date of registration: 02/03/2020 (dd/mm/yyyy).
CAAE:96778718.9.0000.5192.
Issuing authority: Plataforma Brasil.
CEP:2.979.279.
Issuing authority: HUOC.
“Association of MTHFR and MS/MTR gene polymorphisms with congenital heart defects in North Indian population (Jammu and Kashmir): a case–control study encompassing meta-analysis and trial sequential analysis”
Authors: Raina Jyotdeep Kour , Panjaliya Rakesh Kumar , Dogra Vikas , Sharma Sushil , Anupriya  , Kumar Parvinder 
Published: April 2022

AbstractBackgroundThe risk of Congenital Heart Defects (CHD) is greatly influenced by variants within the genes involved in folate-homocysteine metabolism. Polymorphism in MTHFR (C677T and G1793A) and MS/MTR (A2756G) genes increases the risk of developing CHD risk, but results are controversial. Therefore, we conducted a case–control association pilot study followed by an up-dated meta-analysis with trial sequential analysis (TSA) to obtain more precise estimate of the associations of these two gene variants with the CHD risk.MethodsFor case–control study, we enrolled 50 CHD patients and 100 unrelated healthy controls. Genotyping was done by PCR–RFLP method and meta-analysis was performed by MetaGenyo online Statistical Analysis System software. For meta-analysis total number of individuals was as follows: forMTHFRC677T 3450 CHD patients and 4447 controls whereas forMSA2756G 697 CHD patients and 777 controls.ResultsResults of the original pilot study suggested lack of association forMTHFRC677T andMSA2756G polymorphism with risk of CHD whereasMTHFRG1793A was significantly associated with the disease. On performing meta-analysis, a significant association was observed withMTHFRC677T polymorphism but not withMSA2756G. Trial sequential Analysis also confirmed the sufficient sample size requirement for findings of meta-analysis.ConclusionsThe results of the meta-analysis suggested a significant role ofMTHFRin increased risk of CHD.