bluuebunny/crossref_metadata_2025_split huggingface dataset:
Real-world evidence data on the monoclonal antibody erenumab in migraine prevention: perspectives of treating physicians in Germany
Authors: Straube Andreas , Stude Philipp , Gaul Charly , Schuh Katrin , Koch Mirja 
Published: November 2021

Abstract
Background
Erenumab, the first-in-class fully human monoclonal antibody targeting the calcitonin gene-related peptide receptor, was shown to be efficacious and safe for the prophylactic treatment of migraine in adults in randomized clinical trials. Large-scale, real-world evidence in multi-centre settings is still needed to confirm these results. Erenumab patient profiles outside clinical trials and physicians’ treatment patterns, as well as data from patients treated in Germany, a severely impacted population, are not published yet.

Methods
TELESCOPE was a multi-centre survey gathering real-world data from 45 German headache centres between July 2019 and December 2019. The project consisted of two parts. In the first part, treating physicians shared their experiences on current erenumab treatment with regard to patient profiles, treatment patterns and treatment responses. In the second part, a retrospective chart review was conducted of 542 migraine patients treated with erenumab for at least three months. Treatment responses focused on various aspects of patients’ quality of life.

Results
The analysis of 542 patients’ charts revealed that three-month treatment with erenumab significantly reduced monthly headaches, migraine and acute medication days. Furthermore, headache intensity and frequency were reduced in over 75 % and accompanying aura in 35 % of patients. The clinical global impression scale revealed a general improvement in 91 % of patients. According to the treating physicians’ professional judgement, 83 % of patients responded to erenumab and 80 % were satisfied with the treatment. Physicians evaluated restricted quality of life, the number of monthly migraine days and previous, prophylactic treatments as the main components of the current patient profile for monoclonal antibody recipients. Based on the assessment of physicians, erenumab reduced migraine symptoms in 65 % and increased quality of life in more than 75 % of their patients.

Conclusions
TELESCOPE confirms positive treatment responses with erenumab shown in clinical trials in a real-world multi-centre setting. The results show consistently positive experiences of physicians utilizing erenumab in clinical practice and underline that therapy with this monoclonal antibody is effective in migraine patients, particular in those, who have failed several prophylactic therapies.
Urosepsis secondary to ureterosciatic hernia corrected with ureteral stent placement: a case report and literature review
Authors: Kakimoto Kohei , Hikone Mayu , Nagai Ko , Yamakawa Jun , Sugiyama Kazuhiro , Hamabe Yuichi 
Published: November 2021

Abstract
Background
Ureterosciatic hernia is a rare type of pelvic floor herniation that occurs through the sciatic foramen. The resulting ureteral obstruction may lead to hydronephrosis and to further complications including urinary tract infection and urosepsis. There have been 30 reported cases of ureterosciatic hernia. Ureteral stenting and surgical repair have been used as treatment options.

Case presentation
We report the case of an 86-year-old woman who was transferred to Tokyo Metropolitan Bokutoh Hospital with symptoms of fever and septic shock. Her computed tomography scan revealed left hydronephrosis and deviation of the left ureter into the sciatic foramen; she was therefore diagnosed with a left ureteral sciatic hernia and admitted in our intensive care unit for further treatment with resuscitative fluids, vasopressors, and antibiotics. Following a retrograde insertion ureteral catheter insertion, ureteral incarceration was relieved, and a double-J ureteral stent was placed in situ. Antibiotic treatment was initiated, and the patient’s hemodynamic status gradually improved.

Conclusions
Although ureterosciatic hernia is a rare disorder, it is associated with serious complications including urinary tract infection with sepsis, which may warrant urgent corrective procedure to relieve the structural obstruction. Treatment may be conservative or surgical, though treatment with ureteral stent placement may be a favorable approach in elderly patients with multiple comorbidities presenting with urosepsis.
Breed of origin of alleles and genomic predictions for crossbred dairy cows
Authors: Eiríksson Jón H. , Karaman Emre , Su Guosheng , Christensen Ole F. 
Published: November 2021

Abstract
Background
In dairy cattle, genomic selection has been implemented successfully for purebred populations, but, to date, genomic estimated breeding values (GEBV) for crossbred cows are rarely available, although they are valuable for rotational crossbreeding schemes that are promoted as efficient strategies. An attractive approach to provide GEBV for crossbreds is to use estimated marker effects from the genetic evaluation of purebreds. The effects of each marker allele in crossbreds can depend on the breed of origin of the allele (BOA), thus applying marker effects based on BOA could result in more accurate GEBV than applying only proportional contribution of the purebreds. Application of BOA models in rotational crossbreeding requires methods for detecting BOA, but the existing methods have not been developed for rotational crossbreeding. Therefore, the aims of this study were to develop and test methods for detecting BOA in a rotational crossbreeding system, and to investigate methods for calculating GEBV for crossbred cows using estimated marker effects from purebreds.

Results
For detecting BOA in crossbred cows from rotational crossbreeding for which pedigree is recorded, we developed the AllOr method based on the comparison of haplotypes in overlapping windows. To calculate the GEBV of crossbred cows, two models were compared: a BOA model where marker effects estimated from purebreds are combined based on the detected BOA; and a breed proportion model where marker effects are combined based on estimated breed proportions. The methods were tested on simulated data that mimic the first four generations of rotational crossbreeding between Holstein, Jersey and Red Dairy Cattle. The AllOr method detected BOA correctly for 99.6% of the marker alleles across the four crossbred generations. The reliability of GEBV was higher with the BOA model than with the breed proportion model for the four generations of crossbreeding, with the largest difference observed in the first generation.

Conclusions
In rotational crossbreeding for which pedigree is recorded, BOA can be accurately detected using the AllOr method. Combining marker effects estimated from purebreds to predict the breeding value of crossbreds based on BOA is a promising approach to provide GEBV for crossbred dairy cows.
Estimates of recent and historical effective population size in turbot, seabream, seabass and carp selective breeding programmes
Authors: Saura María , Caballero Armando , Santiago Enrique , Fernández Almudena , Morales-González Elisabeth , Fernández Jesús , Cabaleiro Santiago , Millán Adrián , Martínez Paulino , Palaiokostas Christos , Kocour Martin , Aslam Muhammad L. , Houston Ross D. , Prchal Martin , Bargelloni Luca , Tzokas Kostas , Haffray Pierrick , Bruant Jean-Sebastien , Villanueva Beatriz 
Published: November 2021

Abstract
Background
The high fecundity of fish species allows intense selection to be practised and therefore leads to fast genetic gains. Based on this, numerous selective breeding programmes have been started in Europe in the last decades, but in general, little is known about how the base populations of breeders have been built. Such knowledge is important because base populations can be created from very few individuals, which can lead to small effective population sizes and associated reductions in genetic variability. In this study, we used genomic information that was recently made available for turbot (Scophthalmus maximus), gilthead seabream (Sparus aurata), European seabass (Dicentrarchus labrax) and common carp (Cyprinus carpio) to obtain accurate estimates of the effective size for commercial populations.

Methods
Restriction-site associated DNA sequencing data were used to estimate current and historical effective population sizes. We used a novel method that considers the linkage disequilibrium spectrum for the whole range of genetic distances between all pairs of single nucleotide polymorphisms (SNPs), and thus accounts for potential fluctuations in population size over time.

Results
Our results show that the current effective population size for these populations is small (equal to or less than 50 fish), potentially putting the sustainability of the breeding programmes at risk. We have also detected important drops in effective population size about five to nine generations ago, most likely as a result of domestication and the start of selective breeding programmes for these species in Europe.

Conclusions
Our findings highlight the need to broaden the genetic composition of the base populations from which selection programmes start, and suggest that measures designed to increase effective population size within all farmed populations analysed here should be implemented in order to manage genetic variability and ensure the sustainability of the breeding programmes.
Genome-wide analysis of Dof transcription factors and their response to cold stress in rice (Oryza sativa L.)
Authors: Liu Jia , Meng Qinglin , Xiang Hongtao , Shi Fengmei , Ma Ligong , Li Yichu , Liu Chunlai , Liu Yu , Su Baohua 
Published: November 2021

Abstract
Background
Rice (Oryza sativa L.) is a food crop for humans worldwide. However, temperature has an effect during the vegetative and reproductive stages. In high-latitude regions where rice is cultivated, cold stress is a major cause of yield loss and plant death. Research has identified a group of plant-specific transcription factors, DNA binding with one zinc fingers (DOFs), with a diverse range of functions, including stress signaling and stress response during plant growth. The aim of this study was to identify Dof genes in two rice subspecies, indica and japonica, and screen for Dof genes that may be involved in cold tolerance during plant growth.

Results
A total of 30 rice Dofs (OsDofs) were identified using bioinformatics and genome-wide analyses and phylogenetically analyzed. The 30 OsDOFs were classified into six subfamilies, and 24 motifs were identified based on protein sequence alignment. The chromosome locations of OsDofs were determined and nine gene duplication events were identified. A joint phylogenetic analysis was performed on DOF protein sequences obtained from four monocotyledon species to examine the evolutionary relationship of DOF proteins. Expression profiling of OsDofs from two japonica cultivars (Longdao5, which is cold-tolerant, and Longjing11, which is cold-sensitive) revealed that OsDof1 and OsDof19 are cold-inducible genes. We examined the seed setting rates in OsDof1- and OsDof19-overexpression and RNAi lines and found that OsDof1 showed a response to cold stress.

Conclusions
Our investigation identified OsDof1 as a potential target for genetic breeding of rice with enhanced cold tolerance.
Exploring the size of reference population for expected accuracy of genomic prediction using simulated and real data in Japanese Black cattle
Authors: Takeda Masayuki , Inoue Keiichi , Oyama Hidemi , Uchiyama Katsuo , Yoshinari Kanako , Sasago Nanae , Kojima Takatoshi , Kashima Masashi , Suzuki Hiromi , Kamata Takehiro , Kumagai Masahiro , Takasugi Wataru , Aonuma Tatsuya , Soma Yuusuke , Konno Sachi , Saito Takaaki , Ishida Mana , Muraki Eiji , Inoue Yoshinobu , Takayama Megumi , Nariai Shota , Hideshima Ryoya , Nakamura Ryoichi , Nishikawa Sayuri , Kobayashi Hiroshi , Shibata Eri , Yamamoto Koji , Yoshimura Kenichi , Matsuda Hironori , Inoue Tetsuro , Fujita Atsumi , Terayama Shohei , Inoue Kazuya , Morita Sayuri , Nakashima Ryotaro , Suezawa Ryohei , Hanamure Takeshi , Zoda Atsushi , Uemoto Yoshinobu 
Published: November 2021

AbstractBackgroundSize of reference population is a crucial factor affecting the accuracy of prediction of the genomic estimated breeding value (GEBV). There are few studies in beef cattle that have compared accuracies achieved using real data to that achieved with simulated data and deterministic predictions. Thus, extent to which traits of interest affect accuracy of genomic prediction in Japanese Black cattle remains obscure. This study aimed to explore the size of reference population for expected accuracy of genomic prediction for simulated and carcass traits in Japanese Black cattle using a large amount of samples.ResultsA simulation analysis showed that heritability and size of reference population substantially impacted the accuracy of GEBV, whereas the number of quantitative trait loci did not. The estimated numbers of independent chromosome segments (Me) and the related weighting factor (w) derived from simulation results and a maximum likelihood (ML) approach were 1900–3900 and 1, respectively. The expected accuracy for trait with heritability of 0.1–0.5 fitted well with empirical values when the reference population comprised > 5000 animals. The heritability for carcass traits was estimated to be 0.29–0.41 and the accuracy of GEBVs was relatively consistent with simulation results. When the reference population comprised 7000–11,000 animals, the accuracy of GEBV for carcass traits can range 0.73–0.79, which is comparable to estimated breeding value obtained in the progeny test.ConclusionOur simulation analysis demonstrated that the expected accuracy of GEBV for a polygenic trait with low-to-moderate heritability could be practical in Japanese Black cattle population. For carcass traits, a total of 7000–11,000 animals can be a sufficient size of reference population for genomic prediction.
Bovine milk somatic cell transcriptomic response to Staphylococcus aureus is dependent on strain genotype
Authors: Niedziela Dagmara A. , Cormican Paul , Foucras Gilles , Leonard Finola C. , Keane Orla M. 
Published: November 2021

Abstract
Background
Mastitis is an economically important disease of dairy cows with Staphylococcus aureus a major cause worldwide. Challenge of Holstein-Friesian cows demonstrated that S. aureus strain MOK124, which belongs to Clonal Complex (CC)151, caused clinical mastitis, while strain MOK023, belonging to CC97, caused mild or subclinical mastitis. The aim of this study was to elucidate the molecular mechanisms of the host immune response utilising a transcriptomic approach. Milk somatic cells were collected from cows infected with either S. aureus MOK023 or MOK124 at 0, 24, 48, 72 and 168 h post-infection (hpi) and analysed for differentially expressed (DE) genes in response to each strain.

Results
In response to MOK023, 1278, 2278, 1986 and 1750 DE genes were found at 24, 48, 72 and 168 hpi, respectively, while 2293, 1979, 1428 and 1544 DE genes were found in response to MOK124 at those time points. Genes involved in milk production (CSN1, CSN10, CSN1S2, CSN2, a-LACTA and PRLR) were downregulated in response to both strains, with a more pronounced decrease in the MOK124 group. Immune response pathways such as NF-κB and TNF signalling were overrepresented in response to both strains at 24 hpi. These immune pathways continued to be overrepresented in the MOK023 group at 48 and 72 hpi, while the Hippo signalling, extracellular matrix interaction (ECM) and tight junction pathways were overrepresented in the MOK124 group between 48 and 168 hpi. Cellular composition analysis demonstrated that a neutrophil response was predominant in response to MOK124, while M1 macrophages were the main milk cell type post-infection in the MOK023 group.

Conclusions
A switch from immune response pathways to pathways involved in maintaining the integrity of the epithelial cell layer was observed in the MOK124 group from 48 hpi, which coincided with the occurrence of clinical signs in the infected animals. The higher proportion of M1 macrophages in the MOK023 group and lack of substantial neutrophil recruitment in response to MOK023 may indicate immune evasion by this strain. The results of this study highlight that the somatic cell transcriptomic response to S. aureus is dependent on the genotype of the infecting strain.
Prevention of alcohol withdrawal seizure recurrence and treatment of other alcohol withdrawal symptoms in the emergency department: a rapid review
Authors: Koh Justin Jek-Kahn , Malczewska Madeline , Doyle-Waters Mary M. , Moe Jessica 
Published: November 2021

Abstract
Background
Patients who experience harms from alcohol and other substance use often seek care in the emergency department (ED). ED visits related to alcohol withdrawal have increased across the world during the COVID-19 pandemic. ED clinicians are responsible for risk-stratifying patients under time and resource constraints and must reliably identify those who are safe for outpatient management versus those who require more intensive levels of care. Published guidelines for alcohol withdrawal are largely limited to the primary care and outpatient settings, and do not provide specific guidance for ED use. The purpose of this review was to synthesize published evidence on the treatment of alcohol withdrawal syndrome in the ED.

Methods
We conducted a rapid review by searching MEDLINE, Embase, and the Cochrane Central Register of Controlled Trials (1980 to 2020). We searched for grey literature on Google and hand-searched the conference abstracts of relevant addiction medicine and emergency medicine professional associations (2015 to 2020). We included interventional and observational studies that reported outcomes of clinical interventions aimed at treating alcohol withdrawal syndrome in adults in the ED.

Results
We identified 13 studies that met inclusion criteria for our review (7 randomized controlled trials and 6 observational studies). Most studies were at high/serious risk of bias. We divided studies based on intervention and summarized evidence narratively. Benzodiazepines decrease alcohol withdrawal seizure recurrence and treat other alcohol withdrawal symptoms, but no clear evidence supports the use of one benzodiazepine over another. It is unclear if symptom-triggered benzodiazepine protocols are effective for use in the ED. More evidence is needed to determine if phenobarbital, with or without benzodiazepines, can be used safely and effectively to treat alcohol withdrawal in the ED. Phenytoin does not have evidence of effectiveness at preventing withdrawal seizures in the ED.

Conclusions
Few studies have evaluated the safety and efficacy of pharmacotherapies for alcohol withdrawal specifically in the ED setting. Benzodiazepines are the most evidence-based treatment for alcohol withdrawal in the ED. Pharmacotherapies that have demonstrated benefit for treatment of alcohol withdrawal in other inpatient and outpatient settings should be evaluated in the ED setting before routine use.
Analysis of multivariate longitudinal substance use outcomes using multivariate mixed cumulative logit model
Authors: Lin Xiaolei , Mermelstein Robin , Hedeker Donald 
Published: November 2021

AbstractBackgroundLongitudinal assessments of usage are often conducted for multiple substances (e.g., cigarettes, alcohol and marijuana) and research interests are often focused on the inter-substance association. We propose a multivariate longitudinal modeling approach for jointly analyzing the ordinal multivariate substance use data.MethodsWe describe how the binary random slope logistic regression model can be extended to the multi-category ordinal outcomes. We also describe how the proportional odds assumption can be relaxed by allowing differential covariate effects on different cumulative logits for multiple outcomes. Data are analyzed from a P01 study that evaluates the usage levels of cigarettes, alcohol and marijuana repeatedly across 8 measurement waves during 7 consecutive years.Results1263 subjects participated in the study with informed consent, among whom 56.6% are females. Males and females show significant differences in terms of the time trend for substance use. Specifically, males showed steeper trends on cigarette and marijuana use over time compared to females, while less so for alcohol. For all three substances, age effects appear to be different for different cumulative logits, indicating the violation of proportional odds assumption.ConclusionsThe multivariate mixed cumulative logit model offers the most flexibility and allows one to examine the inter-substance association when proportional odds assumption is violated.
Evaluating kidney function using a point-of-care creatinine test in Ugandan children with severe malaria: a prospective cohort study
Authors: Batte Anthony , Murphy Kristin J. , Namazzi Ruth , Co Katrina , Opoka Robert O. , Ssenkusu John M. , John Chandy C. , Conroy Andrea L. 
Published: November 2021

Abstract
Background
Acute kidney injury (AKI) disproportionately affects individuals in low-and middle-income countries (LMIC). However, LMIC—particularly countries in sub-Saharan Africa— are under-represented in global AKI research. A critical barrier in diagnosing AKI is access to reliable serum creatinine results. We evaluated the utility of a point-of-care test to measure creatinine and diagnose AKI in Ugandan children with malaria.

Methods
Paired admission creatinine was assessed in 539 Ugandan children 6 months to 4 years of age hospitalized with severe malaria based on blood smear or rapid diagnostic test. Creatinine levels were measured using isotope dilution mass spectrometry (IDMS)-traceable methods. The reference creatinine was measured using the modified Jaffe method by a certified laboratory and the point-of-care testing was conducted using an i-STAT blood analyzer (i-STAT1, with and without adjustment for the partial pressure of carbon dioxide). AKI was defined and staged using the Kidney Disease: Improving Global Outcomes criteria.

Results
The mean age of children was 2.1 years, and 21.6% of children were stunted. Mortality was 7.6% in-hospital. Over the entire range of measured creatinine values (<0.20mg/dL-8.4mg/dL), the correlation between the reference creatinine and adjusted and unadjusted point-of-care creatinine was high with R2 values of 0.95 and 0.93 respectively; however, the correlation was significantly lower in children with creatinine values <1mg/dL (R2 of 0.44 between the reference and adjusted and unadjusted i-STAT creatinine). The prevalence of AKI was 45.5% using the reference creatinine, and 27.1 and 32.3% using the unadjusted and adjusted point-of-care creatinine values, respectively. There was a step-wise increase in mortality across AKI stages, and all methods were strongly associated with mortality (p<0.0001 for all). AKI defined using the reference creatinine measure was the most sensitive to predict mortality with a sensitivity of 85.4% compared to 70.7 and 63.4% with the adjusted and unadjusted point-of-care creatinine values, respectively.

Conclusions
Point-of-care assessment of creatinine in lean Ugandan children <4 years of age underestimated creatinine and AKI compared to the clinical reference. Additional studies are needed to evaluate other biomarkers of AKI in LMIC to ensure equitable access to AKI diagnostics globally.