bluuebunny/crossref_metadata_2025_split huggingface dataset:
Genome‐wide scan for runs of homozygosity in Asian wild boars and Anqing six‐end‐white pigs
Authors: Wu Xudong , Zhou Ren , Wang Yuanlang , Zhang Wei , Zheng Xianrui , Zhao Guiying , Zhang Xiaodong , Yin Zongjun , Ding Yueyun 
Published: September 2022

AbstractInbreeding and loss of genetic diversity are serious problems in local Chinese pig breeds. Runs of homozygosity (ROHs) are contiguous lengths of homozygous genotypes that can provide information on inbreeding levels, mating schemes, selection pressure, and genetic events. The Anqing six‐end‐white (AQ) pig, an important autochthonous pig breed bred in the Anhui province of China, plays a key role in the local pig industry. In recent decades, AQ pigs have become a closed breed with a small population size in conservation farms, raising the issue of inbreeding decline. In this study, we used 10× resequencing to detect the whole genome of 24 AQ pigs and six Asian wild boars (AWBs). We used the Plink software to analyze the homozygosity of the genome and the distribution of ROHs in the genome based on the resequencing data. We obtained 935.04 Gb of raw data from the resequencing results and more than 45 822 239 SNPs. Additionally, we identified 28 702 ROHs. Compared with AWB, AQ pigs had higher ROH numbers, longer ROH rates, and higher FROH values, which revealed that artificial selection influenced ROH distribution and genome inbreeding level. A total of 307 and 205 ROH islands were identified in the AQ pigs and AWBs respectively. The genes of ROH islands in AQ pigs were mainly enriched in immune biological processes. Our findings provide a useful reference for developing breeding programs to maintain genetic diversity and germplasm resources in AQ pigs.
De novo assembly of a wild swan goose (Anser cygnoides) genome
Authors: Zhang Yonghong , Ni Hongyu , Xie Hengli , Yin Yijing , Zheng Jinlei , Dong Liping , Diao Jizhe , Yan Shouqing , Yang Yuwei , Sun Hao , Sun Xueqi 
Published: September 2022

AbstractThe swan goose (Anser cygnoides) is the ancestor of the Chinese domestic goose. A previous study reported a scaffold‐level genome version for a Chinese indigenous goose breed, and this assembly was used as the swan goose's reference genome. To date, there is still a lack of a chromosome‐level genome for the swan goose. Here, we reported a de novo assembly of the genome of a wild swan goose using an integrated strategy that combines Illumina Hiseq, Oxford Nanopore and chromosome conformation capture (Hi‐C) sequencing. A total of 134.6 Gb Nanopore data with sequencing coverage of 110.33 and 69.45 Gb Illumina data with coverage of 56.93 were obtained. The genome assembly size was 1153.41 Mb, with a contig N50 of 22.75 Mb. The total size and N50 length of our assembly were larger than the previously reported scaffold‐level genome version. In addition, whole‐genome sequencing data of 10 geese were mapped to the previous and the current assemblies. On average, 97.88 and 93.18% of the reads were properly mapped and paired into our and the previous assemblies. This high‐quality chromosome‐level swan goose genome could provide a valuable resource for the utilisation of goose studies and breeding.
Mitochondrial fission factor (MFF) frameshift variant in Bullmastiffs with mitochondrial fission encephalopathy
Authors: Christen Matthias , Gutierrez‐Quintana Rodrigo , Vandenberghe Helene , Kaczmarska Adriana , Penderis Jacques , José‐López Roberto , Rupp Angie , Griffiths Ian R. , Jagannathan Vidhya , Leeb Tosso 
Published: September 2022

AbstractFamilial cerebellar ataxia with hydrocephalus in Bullmastiffs was described almost 40 years ago as a monogenic autosomal recessive trait. We investigated two young Bullmastiffs showing similar clinical signs. They developed progressive gait and behavioural abnormalities with an onset at around 6 months of age. Neurological assessment was consistent with a multifocal brain disease. Magnetic resonance imaging of the brain showed intra‐axial bilateral symmetrical focal lesions localised to the cerebellar nuclei. Based on the juvenile age, nature of neurological deficits and imaging findings, an inherited disorder of the brain was suspected. We sequenced the genome of one affected Bullmastiff. The data were compared with 782 control genomes of dogs from diverse breeds. This search revealed a private homozygous frameshift variant in the MFF gene in the affected dog, XM_038574000.1:c.471_475delinsCGCTCT, that is predicted to truncate 55% of the wild type MFF open reading frame, XP_038429928.1: p.(Glu158Alafs*14). Human patients with pathogenic MFF variants suffer from ‘encephalopathy due to defective mitochondrial and peroxisomal fission 2’. Archived samples from two additional affected Bullmastiffs related to the originally described cases were obtained. Genotypes in a cohort of four affected and 70 unaffected Bullmastiffs showed perfect segregation with the disease phenotype. The available data together with information from previous disease reports allow classification of the investigated MFF frameshift variant as pathogenic and probably causative defect of the observed neurological phenotype. In analogy to the human phenotype, we propose to rename this disease ‘mitochondrial fission encephalopathy (MFE)’.
Copy number variation association studies for sheep tail‐relevant traits in Hulunbuir sheep
Authors: Li Mianyan , Yin Chang , Zhao Fuping , Liu Yang 
Published: September 2022

AbstractTail type is an important trait that influences meat quality and consumer purchasing attitudes. As a novel genetic marker, the study of genomic copy number variations (CNVs) provides a new research method to study the genetic mechanisms underlying trait formation. In the present paper, we conducted CNV‐based association studies for sheep tail type and growth traits in Hulunbuir sheep. A total of 167 CNVs and 288 individuals were analyzed at the marker and individual level, respectively. Association studies of 10 traits were carried out using two mixed linear models. We found that three, one and one CNV loci were significantly associated with tail type, tail length and tail fat weight, respectively, which together contained a total of 52 candidate genes. Out of these genes, five have been documented to be associated with fat metabolism in sheep. Our findings provide a reference for further studies on fat deposition in sheep as well as a theoretical basis for breeding Hulunbuir sheep with the required tail type.
Farm support and market distortion: Evidence from India
Authors: Narayanan Abhinav , Tomar Shekhar 
Published: September 2022

AbstractThis paper studies market distortions due to farm support policies. Using a recently implemented Price Deficiency Payments (PDP) policy in India, we examine how PDP affects farm‐gate prices and crop supply. We document a new channel, the fall in reservation price of farmers under PDP, behind the decline in farm‐gate prices. This impact depends on the magnitude of the deficiency payments and can lead to a supply glut and price crash. Empirically, the scheme led to a 4% decrease in farm‐gate prices and a 51% increase in market arrivals for black‐gram, a crop with a high magnitude of PDP. Using bid‐level data on crop auctions, we rule out collusion among the market participants, another potential channel for price crash under PDP. The effects of the policy are transitory and disappear after the policy is withdrawn. In terms of welfare effects, this scheme is associated with a monetary loss of INR 1 billion. We discuss an alternate payment scheme that can reduce such losses. In summary, our results extend the current understanding of PDP schemes and contribute to the optimal design of such policies.
Arthralgia induced by endocrine therapy with or without cyclin‐dependent kinase 4/6 inhibitors in breast cancer: A systematic review and meta‐analysis
Authors: Takatsuka Daiki , Sawaki Masataka , Hattori Masaya , Yoshimura Akiyo , Kotani Haruru , Kataoka Ayumi , Horisawa Nanae , Ozaki Yuri , Endo Yuka , Nozawa Kazuki , Iwata Hiroji 
Published: September 2022

AbstractCyclin‐dependent kinase 4/6 inhibitors (CDK4/6i) in combination with endocrine therapy (ET) have been approved for breast cancer (BC) treatment. Several trials suggested that arthralgia was reduced in patients treated with ET plus CDK4/6i compared with that in those with ET‐alone. We aimed to compare arthralgia rates in BC patients treated with/without CDK4/6i. We reviewed randomized controlled phase II/III trials investigating CDK4/6i with ET in hormone receptor‐positive and epidermal growth factor 2‐negative BC. Publications were retrieved from PubMed from January 2014 to April 2021. We compared arthralgia rates between patients who were administered ET plus CDK4/6i (CDK4/6i group) and those treated with ET‐alone (control group). We reviewed 12 trials that reported data on adverse effects for arthralgia. These trials included 17,440 patients (9255 in the CDK4/6i group and 8185 in the control group). The arthralgia rate in the CDK4/6i group was significantly lower than that in the control group (27.6% vs. 34.8%, p < .001), especially in early BC (28.8% vs. 37.3%, p < .001). These suggested that the arthralgia rate in patients treated with ET plus CDK4/6i was lower than that in patients treated with ET‐alone and that CDK4/6i may decrease the arthralgia rate in BC patients treated with ET, especially in early BC.
The status of anti‐ovarian antibody immunoassays: Valid or invalid, in or out?
Authors: Pires Eusebio S. , Parikh Firuza R. 
Published: September 2022

AbstractThere has been a paradign shift in the status of immunoassays. There used to be a time where immunoassays had a very narrow role in clinical medicine, but that is not the case in today‘s world. Immunoassays have taken a central role in helping us better understand and treat human diseases. The literature around anti‐ovarian antibodies (AOA) immunoassay testings have been conflicting. Researchers challenged the specificity of the reported assays, but a systematic study was never elucidated on what/who the trouble maker was in rendering these tests so nonspecific. Attempts were made by our group in Mumbai, India, to throw light on the culprit behind the nonspecificity casative factor in the immunoassays and a method to overcome this was reported and published. This review highlights the stories back five and a half decades to date, to demonstrate where the status of AOA testing was, is and will be.
Occurrence of ventricular septal perforation in patients with permanent left bundle branch pacing followed up using echocardiographic and computed tomography images
Authors: Li Qiaoyuan , Dai Wenlong , Fang Dongping , Ma Weili , Lin Cancan , Lu Chunshan , He Dongfang , Liu Xu , Guo Chengjun 
Published: September 2022

AbstractObjectiveTo explore short‐term changes after left bundle branch pacing (LBBP) using echocardiography and computed tomography (CT), especially for postoperative ventricular septal perforation.MethodsBetween January and September 2019, 33 patients with atrioventricular block underwent LBBP at Beijing Anzhen Hospital. All the patients were evaluated using electrocardiography, pacing, parameters and echocardiographic measurements, including for major complications, during the 1, 3, 6, 12 and 24‐month follow‐up. Interval perforations were examined during a 1‐month follow‐up echocardiogram and CT.ResultsLeft bundle branch pacing was successfully performed in 100% (33/33) of patients. The mean seizure threshold was stable and unchanged postoperatively at the 1, 3, 6, 12 and 24‐month follow‐up. The paced QRS duration of the LBBP was 119.72 ± 2.53 ms and <130 ms in all patients. Unipolar impedance during the procedure was higher than 500 Ω (662.00 ± 181.50 Ω). No ventricular septal perforation occurred at the end of the procedure. At the 1‐month follow‐up, two patients reported transthoracic echocardiography, with CT revealing septal lead perforation. Through CT, two other patients were found to have septal lead perforation, and echocardiography indicated that the pacing lead had penetrated the interventricular septum and entered the left subendocardium. At the 1, 3, 6, 12 and 24‐month follow‐up, these four patients exhibited no significant increase in pacing threshold or impedance (p > .05). No ventricular thrombus or stroke was detected.ConclusionPermanent LBBP is safe and feasible in patients with bradycardia. Echocardiography and/or CT can more accurately evaluate changes in cardiac structure and function after LBBP.
Evaluating the effect of online surgical education on intraoperative cholangiogram interpretation: a pilot study
Authors: Kaldas Peter , Suthakaran Reshi , Weinberg Laurence , Lee Dong‐Kyu , Al‐Habbal Yahya 
Published: September 2022

AbstractBackgroundWeb‐based educational tools can support practitioners in their early years of surgical training. Such tools may be an alternative platform to meet the changing needs in surgical training and professional development and may help explain complex surgical principles providing a structured learning platform that is relevant in the day‐to‐day surgical operating room setting. We investigated the impact of an online surgical education initiative on inter‐observer variability and accuracy of IOC interpretation.MethodsA convenience sample of seven surgical observers evaluated 100 IOCs before and after an online surgical series to evaluate their interpretation. The online video series characterized IOCs using nine key elements. The seven observers were surgical trainees of varying experience, from first‐year surgical trainees to surgical fellows, within a metropolitan hospital in Melbourne, Australia.ResultsInter‐observer variability improved within six of nine key elements following the online tutorial. The accuracy of three out of these interpretations also significantly improved following the tutorial. Inter‐observer agreement of proximal biliary opacification improved from moderate (kappa (κ) = 0.491) to good (κ = 0.725), with an improvement in accuracy from 95% to 99% (P = 0.009). Similarly, inter‐observer agreements of cystic duct leaks dramatically improved from no agreement (κ = −0.089) to moderate agreement (κ = 0.548), with detection rates improving from 67% to 82% (P < 0.05).ConclusionThrough an innovative pilot online surgical education, inter‐observer agreement and overall accuracy in the key elements of IOC interpretation improved. A larger multicenter study evaluating the effect of online surgical education on intraoperative cholangiogram interpretation is justified.
Mechanical intestinal obstruction in underweight, elderly women due to an incarcerated obturator hernia
Authors: Sun Ke‐kang , Wu Yong‐you 
Published: September 2022

AbstractBackgroundObturator hernia is an infrequent pelvic hernia observed in elderly, emaciated and multiparous women. It often presents with nonspecific clinical symptoms, making it difficult to diagnose.MethodsWe conducted a retrospective descriptive study on 11 patients admitted to our hospital for obturator hernia from 2009 to 2020.ResultsAll the patients were diagnosed with intestinal obstruction due to incarcerated obturator hernia preoperatively. Eight patients underwent laparotomy with low midline incision. Laparoscopic approach was tried on the other three patients with two patients converting to open surgery because of inadequate visualization, and only one patient received laparoscopic repair. Of the 10 patients receiving laparotomy, seven cases received obturator hernia repair with a match and three cases were subjected to bowel resection (two cases intestinal necrosis and one case intestinal perforation). Simple peritoneal closure was performed on the three contaminated cases. One patient died of septic shock and multiple organ failure.ConclusionThe emergent computed tomography allow for early and precise diagnosis of incarcerated obturator hernia. Laparotomy with low midline incision is commonly used to manage obturator hernia in an emergency, whereas laproscopic approach may only apply to some selected cases.
Teachers' behaviour and children's academic achievement: Evidence of gene–environment interactions
Authors: Guimond Fanny‐Alexandra , Brendgen Mara , Vitaro Frank , Dionne Ginette , Boivin Michel 
Published: September 2022

AbstractBackgroundChildren's academic achievement is considerably influenced by genetic factors, which rarely operate independently of environmental influences such as teachers' behaviour. Praise and punitive discipline are commonly used management strategies by teachers. However, their effects on the genetic expression of children's academic achievement are still unclear.AimsThis study examined potential gene–environment interactions in the associations between children's estimated genetic disposition for academic achievement and teachers' use of praise and punitive discipline in predicting academic achievement.SampleThe participants were 165 twin pairs in sixth grade (M = 12.1 years).MethodsTeachers reported on children's academic achievement, as well as on their own behaviour.ResultsMultilevel regression analyses showed significant interactions between children's estimated genetic disposition for academic achievement and teachers' use of praise and punitive discipline, respectively, in predicting academic achievement. These interactions indicated an enhancement process, suggesting that genetically advantaged children are those most likely to benefit from regular praise and infrequent punishments from their teacher. Moreover, genetically advantaged children were not more (nor less) likely to receive praise or punishments than other students. However, students from underprivileged backgrounds were less likely to receive praise from their teachers.ConclusionsThe results emphasize the importance of teachers' regular use of praise and infrequent punitive discipline to help genetically advantaged children reach their full potential. Future studies should investigate other protective factors of the school environment that might reduce the role of genetic influences that undermine disadvantaged youth's academic achievement.
‘It's not my greengrocer, it's someone from the medical profession’: A qualitative study regarding acceptability of deceptive and open‐label placebo prescribing in France
Authors: Druart Leo , Vauthrin Oriana , Pinsault Nicolas , Locher Cosima , Blease Charlotte 
Published: September 2022

AbstractObjectivesTo explore participants' views regarding clinical use of deceptive placebo (DP) and open‐label placebo (OLP) treatments.DesignQualitative thematic analysis.MethodsWe conducted eight semi‐structured interviews with healthy participants in an experimental trial comparing the efficacy of OLP and DP (Clinical trials n°NCT03934138). Interviewees' opinions were solicited following administration of placebos during the trial. Interviews were analysed using data‐driven analysis.ResultsWe identified three themes. First, participants considered trust central in judging a placebo treatment to be acceptable. They expressed the importance of an implicit trust both in their health care professionals' (HCPs') competency as well as in the profession at large. A second theme was the perception of how placebo treatments might solve health problems. Acceptability of both types of placebo treatments was dependent on the perception patients had about the treatment solving their problem and/or doubts regarding the effectiveness of placebos The third theme encompassed perceived risks associated with placebo prescribing. Some comments viewed placebos positively as facilitating reduced medication intake. However, participants also identified the potential of placebos to generate adverse side effects.ConclusionsTreatment acceptability by patients is a pre‐requisite, alongside effectiveness, to harness OLPs in clinical care. Our study identified the importance of trust in HCPs prescribing placebos, the clinical effectiveness of placebos and the potential risks of these interventions in assessing their acceptability. Future research is needed to explore the contexts in which placebos might be used, and how best to communicate information about placebo interventions.
Impact of darolutamide on local symptoms: pre‐planned and post hoc analyses of the ARAMIS trial
Authors: Shore Neal D. , Stenzl Arnulf , Pieczonka Christopher , Klaassen Zachary , Aronson William J. , Karsh Lawrence , Ryan Charles J. , Ortiz Jorge , Srinivasan Shankar , Mohamed Ateesha F. , Verholen Frank 
Published: September 2022

ObjectiveTo assess, the effect of darolutamide (a structurally distinct androgen receptor inhibitor) on urinary and bowel symptoms, using data from the phase III ARAMIS trial (NCT02200614) that showed darolutamide significantly reduced the risk of metastasis and death versus placebo.Patients and MethodsPatients with non‐metastatic castration‐resistant prostate cancer (nmCRPC) were randomised 2:1 to darolutamide (n = 955) or placebo (n = 554). Local symptom control was assessed by first prostate cancer‐related invasive procedures and post hoc analyses of time to deterioration in quality of life (QoL) using total urinary and bowel symptoms, and individual questions for these symptoms from the European Organisation for Research and Treatment of Cancer Quality of Life Questionnaire Prostate Cancer Module subscales and Functional Assessment of Cancer Therapy‐Prostate prostate cancer subscale. Prostate‐specific antigen (PSA) responses were correlated with urinary and bowel adverse events (AEs).ResultsFewer patients receiving darolutamide (4.7%) versus placebo (9.6%) underwent invasive procedures, and time to first procedure was prolonged with darolutamide (hazard ratio 0.42, 95% confidence interval 0.28–0.62). Darolutamide significantly (P < 0.01) delayed worsening of QoL for total urinary and bowel symptoms versus placebo, mostly attributed by individual symptoms of urinary frequency, associated pain, and interference with daily activities. AEs of urinary retention and dysuria were less frequent with darolutamide, and greater PSA response (≥90%, ≥50% and <90%, <50%) among darolutamide‐treated patients was associated with lower incidences of urinary retention (2.2%, 4.2%, 5.1%) and dysuria (0.5%, 3.2%, 5.1%), respectively.ConclusionsDarolutamide demonstrated a positive impact on local disease recurrence and symptom control in patients with nmCRPC, delayed time to deterioration in QoL related to urinary and bowel symptoms, and a favourable safety profile showing similar incidence of urinary‐ and bowel‐related AEs compared with placebo.