bluuebunny/crossref_metadata_2025_split huggingface dataset:
Prediction of genomic breeding values based on pre-selected SNPs using ssGBLUP, WssGBLUP and BayesB for Edwardsiellosis resistance in Japanese flounder
Authors: Lu Sheng , Liu Yang , Yu Xijiang , Li Yangzhen , Yang Yingming , Wei Min , Zhou Qian , Wang Jie , Zhang Yingping , Zheng Weiwei , Chen Songlin 
Published: August 2020

Abstract
Background
Edwardsiella tarda causes acute symptoms with ascites in Japanese flounder (Paralichthys olivaceus) and is a major problem for China’s aquaculture sector. Genomic selection (GS) has been widely adopted in breeding industries because it shortens generation intervals and results in the selection of individuals that have great breeding potential with high accuracy. Based on an artificial challenge test and re-sequenced data of 1099 flounders, the aims of this study were to estimate the genetic parameters of resistance to E. tarda in Japanese flounder and to evaluate the accuracy of single-step GBLUP (ssGBLUP), weighted ssGBLUP (WssGBLUP), and BayesB for improving resistance to E. tarda by using three subsets of pre-selected single nucleotide polymorphisms (SNPs). In addition, SNPs that are associated with this trait were identified using a single-SNP genome-wide association study (GWAS) and WssGBLUP.

Results
We estimated a heritability of 0.13 ± 0.02 for resistance to E. tarda in Japanese flounder. One million SNPs at fixed intervals were selected from 4,978,724 SNPs that passed quality controls. GWAS identified significant SNPs on chromosomes 14 and 24. WssGBLUP revealed that the putative quantitative trait loci on chromosomes 1 and 14 contained SNPs that explained more than 1% of the genetic variance. Three 50 k-SNP subsets were pre-selected based on different criteria. Compared with pedigree-based prediction (ABLUP), the three genomic methods evaluated resulted in at least 7.7% greater accuracy of predictions. The accuracy of these genomic prediction methods was almost unchanged when pre-selected trait-related SNPs were used for prediction.

Conclusions
Resistance to E. tarda in Japanese flounder has a low heritability. GWAS and WssGBLUP revealed that the genetic architecture of this trait is polygenic. Genomic prediction of breeding values performed better than ABLUP. It is feasible to implement genomic selection to increase resistance to E. tarda in Japanese flounder with 50 k SNPs. Based on the criteria used here, pre-selection of SNPs was not beneficial and other criteria for pre-selection should be considered.
Rapid size change associated with intra-island evolutionary radiation in extinct Caribbean “island-shrews”
Authors: Woods Roseina , Turvey Samuel T. , Brace Selina , McCabe Christopher V. , Dalén Love , Rayfield Emily J. , Brown Mark J. F. , Barnes Ian 
Published: August 2020

AbstractBackgroundThe Caribbean offers a unique opportunity to study evolutionary dynamics in insular mammals. However, the recent extinction of most Caribbean non-volant mammals has obstructed evolutionary studies, and poor DNA preservation associated with tropical environments means that very few ancient DNA sequences are available for extinct vertebrates known from the region’s Holocene subfossil record. The endemic Caribbean eulipotyphlan family Nesophontidae (“island-shrews”) became extinct ~ 500 years ago, and the taxonomic validity of manyNesophontesspecies and their wider evolutionary dynamics remain unclear. Here we use both morphometric and palaeogenomic methods to clarify the status and evolutionary history ofNesophontesspecies from Hispaniola, the second-largest Caribbean island.ResultsPrincipal component analysis of 65Nesophontesmandibles from late Quaternary fossil sites across Hispaniola identified three non-overlapping morphometric clusters, providing statistical support for the existence of three size-differentiated HispaniolanNesophontesspecies. We were also able to extract and sequence ancient DNA from a ~ 750-year-old specimen ofNesophontes zamicrus, the smallest non-volant Caribbean mammal, including a whole-mitochondrial genome and partial nuclear genes.Nesophontes paramicrus(39-47 g) andN. zamicrus(~ 10 g) diverged recently during the Middle Pleistocene (mean estimated divergence = 0.699 Ma), comparable to the youngest species splits in Eulipotyphla and other mammal groups. Pairwise genetic distance values forN. paramicrusandN. zamicrusbased on mitochondrial and nuclear genes are low, but fall within the range of comparative pairwise data for extant eulipotyphlan species-pairs.ConclusionsOur combined morphometric and palaeogenomic analyses provide evidence for multiple co-occurring species and rapid body size evolution in HispaniolanNesophontes, in contrast to patterns of genetic and morphometric differentiation seen in Hispaniola’s extant non-volant land mammals. Different components of Hispaniola’s mammal fauna have therefore exhibited drastically different rates of morphological evolution. Morphological evolution inNesophontesis also rapid compared to patterns across the Eulipotyphla, and our study provides an important new example of rapid body size change in a small-bodied insular vertebrate lineage. The Caribbean was a hotspot for evolutionary diversification as well as preserving ancient biodiversity, and studying the surviving representatives of its mammal fauna is insufficient to reveal the evolutionary patterns and processes that generated regional diversity.
Comprehensive geriatric assessment in older patients with cancer: an external validation of the multidimensional prognostic index in a French prospective cohort study
Authors: Liuu Evelyne , Hu Chunyun , Valero Simon , Brunet Thomas , Jamet Amelie , Bureau Marie-Laure , Pilotto Alberto , Saulnier Pierre-Jean , Paccalin Marc 
Published: August 2020

Abstract
Background
Older patients with cancer require specific and individualized management. The 3-group Multidimensional Prognostic Index (MPI) based on the Comprehensive Geriatric Assessment (CGA) has shown a predictive interest in terms of mortality. The objective of our study was to assess the prognostic value of MPI for 1-year mortality in an external prospective French cohort of elderly patients with cancer.

Methods
From March 2015 to March 2017 a prospective single-center cohort study enrolled all patients with cancer, aged 75 years and older referred to the geriatric oncology clinic. We used a proportional hazard model for 1-year mortality adjusted for age, sex, tumor sites and metastatic status. C-statistics were used to assess the incremental predictive value of MPI index to these risk factors.

Results
overall, 433 patients underwent CGA with MPI (women 42%; mean age 82.8 ± 4.8 years). The most common tumor sites were prostate (23%), skin (17%), colorectum (15%) and breast (12%); 29% of patients had a metastatic disease; 231 patients (53%) belonged to the “MPI-1” group, 172 (40%) to the “MPI-2” group and 30 patients were classified in the “MPI-3” group. One-year mortality rate was 32% (23% in MPI-1, 41% in MPI-2 and 53% in MPI-3, p = 0.024). All domains of MPI except cognition and living status were significantly associated with mortality at one-year, as well as tumor sites and metastatic status. Higher MPI was associated with a higher mortality risk (adjusted HR 1.56 [95%CI 1.70–2.09] and 1.72 [1.33–2.22] for MPI groups 2 and 3 compared to 1; p < 0.0001).

Conclusions
In addition to established risk factors, MPI improves risk prediction of 1-year mortality. This practical prognostic tool may help to optimize management of these vulnerable patients.
The potential of CBC-derived ratios (monocyte-to-lymphocyte, neutrophil-to-lymphocyte, and platelet-to-lymphocyte) to predict or diagnose incident TB infection in Tanzanian adolescents
Authors: Rees Christiaan A. , Pineros Dwan B. , Amour Maryam , Munseri Patricia , Said Jamila , Magohe Albert , Matee Mecky , Pallangyo Kisali , von Reyn C. Fordham 
Published: August 2020

Abstract
Background
Ratios of different immune cell populations (i.e., monocyte-to-lymphocyte, neutrophil-to-lymphocyte, and platelet-to-lymphocyte ratios) have been studied as a means of predicting future tuberculosis (TB) disease risk or to assist in the diagnosis of incident TB disease. No studies to-date, however, have evaluated the potential of these ratios to predict or assist in the diagnosis of incident TB infection - the first step in the natural history of TB disease.

Methods
In this prospective study, we evaluated the complete blood count (CBC)-derived metrics of monocyte-to-lymphocyte ratio (MLR), neutrophil-to-lymphocyte ratio (NLR), and platelet-to-lymphocyte ratio (PLR) as predictors of future TB infection risk or aids in the diagnosis of TB infection among 145 Tanzanian adolescents enrolled in the DAR-901 vaccine trial, using paired CBCs and interferon-gamma release assays (IGRAs) obtained at 0, 60 and 720 days after study enrollment.

Results
At baseline, there were no significant differences between study participants who remained persistently IGRA negative throughout the study period and those who subsequently converted to IGRA positive with respect to MLR (0.18 vs 0.17, p = 0.10), NLR (0.88 vs 1.02, p = 0.08), or PLR (115 vs 120, p = 0.28). Similarly, no significant differences were noted with respect to MLR, NLR, and PLR between IGRA converters and time-matched negative controls at the time of IGRA conversion. With respect to other blood cell measures, however, there were modest but significant differences between IGRA negatives and IGRA converters with respect to red blood cell count (4.8 vs 4.6 ×  106 cells/mcL, p = 0.008), hemoglobin (12.6 vs 12.3 g/dL, p = 0.01), and hematocrit (38.8 vs 37.8%, p = 0.005).

Conclusions
In contrast to prior studies that have suggested that the ratios of different immune cell populations are associated with development of TB disease, our present findings do not demonstrate an association between these ratios and the development of TB infection. However, decreased red blood cell measures were associated with the subsequent development of TB infection, suggesting either that dysregulation of iron metabolism may play a role in TB pathogenesis or that following TB infection, iron dysregulation may precede IGRA positivity.

Trial registration
Clinicaltrials.gov NCT02712424. Date of registration: March 14, 2016.
Home-based intervention for non-Hispanic black families finds no significant difference in infant size or growth: results from the Mothers & Others randomized controlled trial
Authors: Wasser Heather M. , Thompson Amanda L. , Suchindran Chirayath M. , Goldman Barbara D. , Hodges Eric A. , Heinig Meredith J. , Bentley Margaret E. 
Published: August 2020

Abstract
Background
Non-Hispanic black (NHB) infants are twice as likely as non-Hispanic white infants to experience rapid weight gain in the first 6 months, yet few trials have targeted this population. The current study tests the efficacy of “Mothers & Others,” a home-based intervention for NHB women and their study partners versus an attention-control, on infant size and growth between birth and 15 months.

Methods
Mothers & Others was a two-group randomized controlled trial conducted between November 2013 and December 2017 with enrollment at 28-weeks pregnancy and follow-up at 3-, 6-, 9-, 12-, and 15-months postpartum. Eligible women self-identified as NHB, English-speaking, and 18–39 years. The obesity prevention group (OPG) received anticipatory guidance (AG) on responsive feeding and care practices and identified a study partner, who was encouraged to attend home visits. The injury prevention group (IPG) received AG on child safety and IPG partners only completed study assessments. The primary delivery channel for both groups was six home visits by a peer educator (PE). The planned primary outcome was mean weight-for-length z-score. Given significant differences between groups in length-for-age z-scores, infant weight-for-age z-score (WAZ) was used in the current study. A linear mixed model, using an Intent-To-Treat (ITT) data set, tested differences in WAZ trajectories between the two treatment groups. A non-ITT mixed model tested for differences by dose received.

Results
Approximately 1575 women were screened for eligibility and 430 were enrolled. Women were 25.7 ± 5.3 years, mostly single (72.3%), and receiving Medicaid (74.4%). OPG infants demonstrated lower WAZ than IPG infants at all time points, but differences were not statistically significant (WAZdiff = − 0.07, 95% CI − 0.40 to 0.25, p = 0.659). In non-ITT models, infants in the upper end of the WAZ distribution at birth demonstrated incremental reductions in WAZ for each home visit completed, but the overall test of the interaction was not significant (F2,170 = 1.41, p = 0.25).

Conclusions
Despite rich preliminary data and a strong conceptual model, Mothers & Others did not produce significant differences in infant growth. Results suggest a positive impact of peer support in both groups.

Trial registration
ClinicalTrials.gov, NCT01938118, 09/10/2013.
Exploring patient satisfaction after operative and nonoperative treatment for midshaft clavicle fractures: a focus group analysis
Authors: Tutuhatunewa Eric D. , Stevens Martin , Dams Olivier C. , van Son Jeffrey , Louhanepessy Rebecca D. , Krabbe Paul F. M. , Postma Maarten J. , Diercks Ron L. 
Published: August 2020

Abstract
Background
There is no consensus on the optimal treatment for displaced midshaft clavicle fractures. Several studies indicate superior patient satisfaction in favour of operative reconstruction. It is unknown what drives superior satisfaction in this treatment group. The aim of this study was to explore patient satisfaction and identify contributors to patient satisfaction after operative and nonoperative treatment for displaced midshaft clavicle fractures in adults using a focus group approach.

Methods
Four face-to-face and two web-based focus groups were hosted. A total of 24 participants who were treated nonoperatively (n = 14) or operatively (n = 10) agreed to participate. Participants were selected using purposive sampling, ensuring variation in gender, age, treatment complications and outcomes. A question script was developed to systematically explore patient expectations, attitudes and satisfaction with different dimensions of care. All focus groups were voice-recorded and transcribed at verbatim. Thematic analysis was conducted on all face-to-face and web-based transcripts.

Results
The main emerging themes across treatment groups were; need for more information, functional recovery, speed of recovery and patient-doctor interaction. There was no difference in themes observed between operative and nonoperative focus groups. The lack of information was the most important complaint in dissatisfied patients.

Conclusion
Our study shows that informing patients about their injury, treatment options and expectations for recovery is paramount for overall patient satisfaction after treatment for a displaced midshaft clavicle fracture.

Level of evidence
Level III, focus group study.
The neglected perioperative population of undiagnosed diabetics – a retrospective cohort study
Authors: Teo Wei W. , Ti Lian K. , Lean Lyn L. , Seet Edwin , Paramasivan Ambika , Liu Weiling , Wang Jiexun , Chua Vanessa , Liew Lydia Q. 
Published: August 2020

Abstract
Background
Diabetes is known to increase morbidity and 30-day mortality in adults undergoing non-cardiac surgery, but longer term outcomes are less studied. This study was done to explore how undiagnosed and known diabetes affect 30-day and one-year morbidity and mortality outcomes. The secondary aim was to study the prevalence of undiagnosed diabetics in our perioperative Asian surgical population.

Methods
A retrospective cohort study of 2106 patients aged > 45 years undergoing non-cardiac surgery in a single tertiary hospital was performed. Undiagnosed diabetics were identified (HbA1c ≥6.5% or fasting blood glucose ≥126 mg/dL) and relevant demographic, clinical and surgical data were analyzed to elicit the relationship to adverse outcomes. Univariate analysis was first performed to identify significant variables with p-values ≤0.1, which were then analyzed using multiple logistic regression to calculate the adjusted odds ratio.

Results
The prevalence of undiagnosed diabetes was 7.4%. The mean and median HbA1c of known diabetics were 7.9 and 7.5%, while the mean and median HbA1c for undiagnosed diabetics were 7.2 and 6.8% respectively. 36.4% of known diabetics and 20.5% of undiagnosed diabetics respectively had a random blood glucose > 200 mg/dL. Undiagnosed diabetics had a three-fold increase in 1-year mortality compared to non-diabetics (adjusted OR 3.46(1.80–6.49) p < 0.001) but this relationship was not significant between known and non-diabetics. Compared to non-diabetics, known diabetics were at increased risks of new-onset atrial fibrillation (aOR 2.48(1.01–6.25) p = 0.047), infection (aOR 1.49(1.07–2.07) p = 0.017), 30-day readmission (aOR 1.62(1.17–2.25) p = 0.004) and 30-day mortality (aOR 3.11(1.16–8.56) p = 0.025).

Conclusions
Although undiagnosed diabetics have biochemically less severe disease compared to known diabetics at the point of testing, they are at a one-year mortality disadvantage which is not seen among known diabetics. This worrying trend highlights the importance of identifying and treating diabetes. Congruent to previous studies, known diabetics have higher morbidity and 30-day mortality compared to non-diabetics.
Sharing the initial experience of pan-cancer panel analysis in high-risk renal cell carcinoma in the Korean population
Authors: Suh Jungyo , Jeong Chang Wook , Choi Seongmin , Ku Ja Hyeon , Kim Hyeon Hoe , Kim Kwangsoo , Kwak Cheol 
Published: August 2020

Abstract
Background
This study aimed to assess the feasibility of a pan-cancer panel assay for high-risk renal cell carcinoma (RCC) in the Korean population. We also analyzed the clinical and genetic factors contributing to metastasis in clear cell RCC.

Methods
Thirty-one patients with advanced RCC who underwent radical nephrectomy were analyzed. A 1.8 Mb multi-cancer panel (including 25 RCC-related genes, such as VHL, PBRM1, SETD2, and MET), comprising 181 target genes, 23 fusion genes, and 45 drug target lesions developed by Seoul National University Hospital, was used for this study.

Results
We extracted DNA from 30 of the 31 (96.7%) RCC specimens. Twenty-one patients (average age 63.3 ± 11.3 years) with clear cell RCC, 5 with papillary RCC, 3 with chromophobe RCC, and one patient, each with MiT family translocation carcinoma RCC and succinate dehydrogenase deficiency RCC, were analyzed. The sequencing depth was 430.8 ± 206.6 and 97 mutations (7.3 ± 2.7 mutations per patient) were detected. The most commonly mutated genes were VHL (46%), PBRM1 (30%), and BAP1, NOTCH4, and POLQ (23.33% each). Compared with TNM stage matched data from TCGA of clear cell RCC, VHL and PBRM1 are most common in both cohorts. Univariate and multivariate analyses revealed that tumor size (Hazard ratio = 2.47, p = 0.04) and PBRM1 (Hazard ratio = 28.69, p = 0.05) were related to metastasis in clear cell RCC.

Conclusion
The pan-cancer panel comprised of RCC-related genes is a feasible and promising tool to evaluate genetic alterations in advanced RCC. However, large-scale studies and a focus on the clinical utility of this cancer panels is needed.
Outpatient dental care for people with disabilities under general anaesthesia in Switzerland
Authors: Jockusch Julia , Sobotta Bernhard A. J. , Nitschke Ina 
Published: August 2020

Abstract
Background
Life expectancy of people with permanent disabilities has increased. The dental care of these vulnerable patients is one of the greatest challenges for the dentist and the dental team due to limited or non-existent cooperation and the associated lack of health competence. In order to be able to provide safe and acceptable, quality dental treatment without psychological and physical stress for these patients, it is therefore necessary to resort to sedation or general anaesthesia (GA) under medical supervision. The aim of the analysis is to highlight the need for dental treatment performed under GA for people with disabilities and the associated indications and treatment patterns.

Methods
Ten-year retrospective analysis of outpatient dental care under GA for people with disabilities.

Results
Of all adult patients (n = 221) who attended the GA pre-assessment, 69.7% (n = 154) received dental treatment under GA based on the clinical findings or in cases of suspected pain. Most patients received one GA. A total of 205 dental treatment sessions were performed under GA mostly for conservative (n = 442, 52%) and surgical (n = 389, 45.8%) procedures. Endodontic treatment (n = 19, 2.2%) was rare. The failure rate related to all teeth in need of treatment (n = 850) was 5.1% (n = 43), in most cases due to secondary caries (n = 40; 93.0%). Patients were enrolled in an annual recall for dental examination and prophylaxis without GA. Non-compliant patients for whom oral hygiene was impossible received a periodic GA.

Conclusion
There is a high need of people with disabilities for dental treatment under GA. Main indications for treatment under GA are dental complaints, pain or suspected pain. Dental care can be successful if, for the benefit of patients with special needs, all carers cooperate closely. Caregivers have to be trained in nutrition control as well as in oral hygiene. These factors in conjunction help to prevent dental emergencies.
Effect of different restorative crown design and materials on stress distribution in endodontically treated molars: a finite element analysis study
Authors: Lin Jie , Lin Zhenxiang , Zheng Zhiqiang 
Published: August 2020

Abstract
Background
The purposes of this simulation study were to evaluate the stresses in the roots of endodontically treated molars with extensive coronal tissue loss which were restored by endocrowns (all-in-one core and crown) and traditional crowns with post-cores, during masticatory simulation using finite element analysis.

Methods
A mesio-distal cross-section of a lower right first molar was digitized and used to create 2-dimensional models of the teeth and supporting tissue; different crown designs, viz., endocrown with 2 mm occlusal clearance, endocrown with 4 mm occlusal clearance and post-core crown; different crown materials, viz., zirconia (Zr) and lithia-disilicate reinforced glass ceramic (LDRGC), and different post and core materials, viz., glass fiber (GF), stainless steel (SS) and metal cast (MC). An axial load of 600 N was applied to the central fossa of occlusal surface.

Results
The stress distributions were similar between Zr and LDRGC for periodontal ligament and alveolar bone. The root canal inner wall maximum principal stresses of SS post (70.8 MPa) and MC post (71.4 MPa) were higher than that of GF post (36.0 MPa) and endocrown (2.4 MPa).

Conclusion
The endocrowns reduced stress concentration for the root canal inner wall in comparison with the conventional post-core crown. Molars restored with endocrowns are less prone to root fracture than those with posts.