bluuebunny/crossref_metadata_2025_split huggingface dataset:
Estimation of dynamic SNP-heritability with Bayesian Gaussian process models
Authors: Arjas Arttu , Hauptmann Andreas , Sillanpää Mikko J 
Published: March 2020

Abstract

Motivation
Improved DNA technology has made it practical to estimate single-nucleotide polymorphism (SNP)-heritability among distantly related individuals with unknown relationships. For growth- and development-related traits, it is meaningful to base SNP-heritability estimation on longitudinal data due to the time-dependency of the process. However, only few statistical methods have been developed so far for estimating dynamic SNP-heritability and quantifying its full uncertainty.

Results
We introduce a completely tuning-free Bayesian Gaussian process (GP)-based approach for estimating dynamic variance components and heritability as their function. For parameter estimation, we use a modern Markov Chain Monte Carlo method which allows full uncertainty quantification. Several datasets are analysed and our results clearly illustrate that the 95% credible intervals of the proposed joint estimation method (which ‘borrows strength’ from adjacent time points) are significantly narrower than of a two-stage baseline method that first estimates the variance components at each time point independently and then performs smoothing. We compare the method with a random regression model using MTG2 and BLUPF90 software and quantitative measures indicate superior performance of our method. Results are presented for simulated and real data with up to 1000 time points. Finally, we demonstrate scalability of the proposed method for simulated data with tens of thousands of individuals.

Availability and implementation
The C++ implementation dynBGP and simulated data are available in GitHub: https://github.com/aarjas/dynBGP. The programmes can be run in R. Real datasets are available in QTL archive: https://phenome.jax.org/centers/QTLA.

Supplementary information
Supplementary data are available at Bioinformatics online.
Dynamic QoS-Aware Cloud Service Selection Using Best-Worst Method and Timeslot Weighted Satisfaction Scores
Authors: Nawaz Falak , Janjua Naeem Khalid 
Published: March 2020

Abstract
The number of cloud services has dramatically increased over the past few years. Consequently, finding a service with the most suitable quality of service (QoS) criteria matching the user’s requirements is becoming a challenging task. Although various decision-making methods have been proposed to help users to find their required cloud services, some uncertainties such as dynamic QoS variations hamper the users from employing such methods. Additionally, the current approaches use either static or average QoS values for cloud service selection and do not consider dynamic QoS variations. In this paper, we overcome this drawback by developing a broker-based approach for cloud service selection. In this approach, we use recently monitored QoS values to find a timeslot weighted satisfaction score that represents how well a service satisfies the user’s QoS requirements. The timeslot weighted satisfaction score is then used in Best-Worst Method, which is a multi-criteria decision-making method, to rank the available cloud services. The proposed approach is validated using Amazon’s Elastic Compute Cloud (EC2) cloud services performance data. The results show that the proposed approach leads to the selection of more suitable cloud services and is also efficient in terms of performance compared to the existing analytic hierarchy process-based cloud service selection approaches.
Spatial variation in egg polymorphism among cuckoo hosts across 4 continents
Authors: Yang Canchao , Si Xingfeng , Liang Wei , Møller Anders Pape 
Published: March 2020

AbstractAlthough egg color polymorphism has evolved as an effective defensive adaptation to brood parasitism, spatial variations in egg color polymorphism remain poorly characterized. Here, we investigated egg polymorphism in 647 host species (68 families and 231 genera) parasitized by 41 species of Old Word cuckoos (1 family and 11 genera) across Asia, Europe, Africa, and Australia. The diversity of parasitic cuckoos differs among continents, reflecting the continent-specific intensities of parasitic selection pressure on hosts. Therefore, host egg polymorphism is expected to evolve more frequently on continents with higher cuckoo diversity. We identified egg polymorphism in 24.1% of all host species and 47.6% of all host families. The common cuckoo Cuculus canorus utilized 184 hosts (28.4% of all host species). Hosts of the common cuckoo and of Chrysococcyx species were more likely to have polymorphic eggs than hosts parasitized by other cuckoos. Both the number of host species and the host families targeted by the cuckoo species were positively correlated with the frequency of host egg polymorphism. Most host species and most hosts exhibiting egg color polymorphism were located in Asia and Africa. Host egg polymorphism was observed less frequently in Australia and Europe. Our results also suggested that egg polymorphism tends to occur more frequently in hosts that are utilized by several cuckoo species or by generalist cuckoo species. We suggest that selection pressure on hosts from a given continent increases proportionally to the number of cuckoo species, and that this selection pressure may, in turn, favor the evolution of host egg polymorphism.
Identifying the Implementation Conditions Associated With Positive Outcomes in a Successful Nursing Facility Demonstration Project
Authors: Hickman Susan E , Miech Edward J , Stump Timothy E , Fowler Nicole R , Unroe Kathleen T 
Published: March 2020

Abstract

Background and Objectives
To identify the implementation barriers, facilitators, and conditions associated with successful outcomes from a clinical demonstration project to reduce potentially avoidable hospitalizations of long-stay nursing facility residents in 19 Indiana nursing homes.

Research Design and Methods
Optimizing Patient Transfers, Impacting Medical quality, Improving Symptoms—Transforming Institutional Care (OPTIMISTIC) is a multicomponent intervention that includes enhanced geriatric care, transition support, and palliative care. The configurational analysis was used to analyze descriptive and quantitative data collected during the project. The primary outcome was reductions in hospitalizations per 1,000 eligible resident days.

Results
Analysis of barriers, facilitators, and conditions for success yielded a model with 2 solution pathways associated with a 10% reduction in potentially avoidable hospitalizations per 1,000 resident days: (a) lower baseline hospitalization rates and investment of senior management; or (b) turnover by the director of nursing during the observation period. Conditions for success were similar for a 20% reduction, with the addition of increased resident acuity.

Discussion and Implications
Key conditions for successful implementation of the OPTIMISTIC intervention include strong investment by senior leadership and an environment in which baseline hospitalization rates leave ample room for improvement. Turnover in the position of director of nursing also linked to successful implementation; this switch in leadership may represent an opportunity for culture change by bringing in new perspectives and viewpoints. These findings help define the conditions for the successful implementation of the OPTIMISTIC model and have implications for the successful implementation of interventions in the nursing facility more generally.
Old abuses in new markets? Dealing with excessive pricing by a two-sided platform
Authors: Ayata Zeynep 
Published: March 2020

Abstract
Exploitative abuses, especially excessive pricing, have been one of the most debated forms of abuse of dominant position. Unlike exclusionary abuses, they have been prohibited only under certain jurisdictions and on rather rare occasions. In Europe there have been few recent decisions and investigations that have reiterated existing approaches and tests for establishing excessive pricing. The Turkish Competition Authority’s Sahibinden.com decision has come at such a time where the discussion on excessive pricing has been somewhat revived. However, this decision stands out as it is the first one where a competition authority has found prices to be excessive and therefore abusive in the context of a two-sided platform. Competition in platform markets display unique dynamics that may be very different from what may be observed in traditional markets especially in terms of pricing strategies. This article aims to demonstrate, through the Turkish Competition Authority’s recent decision, the difficulties in applying existing tests and criteria on excessive pricing to a two-sided platform. A thorough analysis of this decision demonstrates that competition enforcement in what may be called ‘new’ platform markets necessitates new approaches or adjustments of existing ones.
Factors influencing digital review of pathology test results in an inpatient setting: a cross-sectional study
Authors: Challen Robert , Tsaneva-Atanasova Krasimira , Edwards Tom , Gompels Luke , Dayer Mark , Pitt Martin , Danon Leon 
Published: March 2020

Abstract

Background
Delay or failure to view test results in a hospital setting can lead to delayed diagnosis, risk of patient harm, and represents inefficiency. Factors influencing this were investigated to identify how timeliness and completeness of test review could be improved through an evidence-based redesign of the use of clinical test review software.

Methods
A cross-section of all abnormal hematology and biochemistry results which were published on a digital test review platform over a 3-year period were investigated. The time it took for clinicians to view these results, and the results that were not viewed within 30 days, were analyzed relative to time of the week, the detailed type of test, and an indicator of patient record data quality.

Results
The majority of results were viewed within 90 min, and 93.9% of these results viewed on the digital platform within 30 days. There was significant variation in results review throughout the week, shown to be due to an interplay between technical and clinical workflow factors. Routine results were less likely to be reviewed, as were those with patient record data quality issues.

Conclusion
The evidence suggests that test result review would be improved by stream-lining access to the result platform, differentiating between urgent and routine results, improving handover of responsibility for result review, and improving search for temporary patient records. Altering the timing of phlebotomy rounds and a review of the appropriateness of routine test requests at the weekend may also improve result review rates.
Increased Tau Expression Correlates With IDH Mutation in Infiltrating Gliomas and Impairs Cell Migration
Authors: Nakata Satoshi , Price Antionette , Eberhart Charles , Morris Meaghan 
Published: March 2020

Abstract
Although the microtubule-associated protein tau is well studied in human neurodegeneration, the role of tau in neoplastic brain diseases is not well understood. Recently, studies have shown tau mRNA expression is associated with improved survival in human infiltrating gliomas. However, the biologic basis of this association is largely unexplored. Using 2 independent publicly available mRNA databases, we show that high tau mRNA expression is associated with improved patient survival in infiltrating gliomas. Higher tau protein expression is also associated with improved patient prognosis in infiltrating gliomas by immunohistochemical staining of tissue microarrays. This prognostic association is in part due to higher tau mRNA and protein expression in IDH-mutant infiltrating astrocytomas. Expression of tau in an IDH-wildtype glioblastoma cell line selectively impairs cell migration in assays designed to mimic tumor invasion. These findings suggest that tau expression is not only associated with IDH mutation status but also may contribute to improved patient outcomes by impairing tumor invasion.
The Thomas Mans, their Books, and Jesus College Librarianship
Authors: Hanna Ralph 
Published: March 2020

Abstract
On 21 January 1684/5, Thomas Man, a thirty-year-old Fellow, made a substantial donation of manuscripts to Jesus College, Cambridge. These included a substantial number of books from medieval institutional collections, including at least thirty-one from Durham cathedral priory. The essay ascertains the extent of the donation, a discussion intertwined with that of librarianship at Jesus College. It also offers information about the collection activity of Man’s father, also Thomas, who assembled the collection, and points to several Man books now preserved elsewhere.
The Location of the Fullest Manuscript of the Louth Park Abbey Chronicle, Brutus to 1413
Authors: Smith Trevor Russell 
Published: March 2020

Abstract
This note discusses the Louth Park Abbey Chronicle, which survives in three manuscripts in varying levels of completeness, the fullest of which has changed hands several times since the only edition of the text was produced in 1891. Further study of the text and its two additional manuscripts has been impossible, however, as the fullest manuscript has been untraced since 1987, at the latest. This article examines the provenance of this lost manuscript and identifies its current location.
The Triad in Dispute: Johannes Lippius, His Audiences, and the Disputatio Genre
Authors: Mutch Caleb 
Published: March 2020

AbstractThe reception of Johannes Lippius’s path-breaking conception of the triad chiefly relies upon his treatise Synopsis musicae novae. Yet Lippius first published most of his ideas in texts called “disputations,” whose genre-specific peculiarities have been overlooked. By situating Lippius’s writings within the early-modern university system, this essay reveals an important instance of how demands of audience and genre have shaped music theory and offers tantalizing glimpses of how the oral disputation may have encouraged Lippius to clarify his ideas, particularly in his recasting of the analogy between the triad and the Trinity.
Proteins inform survival-based differences in patients with glioblastoma
Authors: Stetson L C , Ostrom Quinn T , Schlatzer Daniela , Liao Peter , Devine Karen , Waite Kristin , Couce Marta E , Harris Peggy L R , Kerstetter-Fogle Amber , Berens Michael E , Sloan Andrew E , Islam Mohammad M , Rajaratnam Vilashini , Mirza Shama P , Chance Mark R , Barnholtz-Sloan Jill S 
Published: March 2020

Abstract

Background
Improving the care of patients with glioblastoma (GB) requires accurate and reliable predictors of patient prognosis. Unfortunately, while protein markers are an effective readout of cellular function, proteomics has been underutilized in GB prognostic marker discovery.

Methods
For this study, GB patients were prospectively recruited and proteomics discovery using liquid chromatography–mass spectrometry analysis (LC-MS/MS) was performed for 27 patients including 13 short-term survivors (STS) (≤10 months) and 14 long-term survivors (LTS) (≥18 months).

Results
Proteomics discovery identified 11 941 peptides in 2495 unique proteins, with 469 proteins exhibiting significant dysregulation when comparing STS to LTS. We verified the differential abundance of 67 out of these 469 proteins in a small previously published independent dataset. Proteins involved in axon guidance were upregulated in STS compared to LTS, while those involved in p53 signaling were upregulated in LTS. We also assessed the correlation between LS MS/MS data with RNAseq data from the same discovery patients and found a low correlation between protein abundance and mRNA expression. Finally, using LC-MS/MS on a set of 18 samples from 6 patients, we quantified the intratumoral heterogeneity of more than 2256 proteins in the multisample dataset.

Conclusions
These proteomic datasets and noted protein variations present a beneficial resource for better predicting patient outcome and investigating potential therapeutic targets.
Multi-Trait Genome-Wide Association Studies Reveal Loci Associated with Maize Inflorescence and Leaf Architecture
Authors: Rice Brian R , Fernandes Samuel B , Lipka Alexander E 
Published: March 2020

AbstractMaize inflorescence is a complex phenotype that involves the physical and developmental interplay of multiple traits. Given the evidence that genes could pleiotropically contribute to several of these traits, we used publicly available maize data to assess the ability of multivariate genome-wide association study (GWAS) approaches to identify pleiotropic quantitative trait loci (pQTL). Our analysis of 23 publicly available inflorescence and leaf-related traits in a diversity panel of n = 281 maize lines genotyped with 376,336 markers revealed that the two multivariate GWAS approaches we tested were capable of identifying pQTL in genomic regions coinciding with similar associations found in previous studies. We then conducted a parallel simulation study on the same individuals, where it was shown that multivariate GWAS approaches yielded a higher true-positive quantitative trait nucleotide (QTN) detection rate than comparable univariate approaches for all evaluated simulation settings except for when the correlated simulated traits had a heritability of 0.9. We therefore conclude that the implementation of state-of-the-art multivariate GWAS approaches is a useful tool for dissecting pleiotropy and their more widespread implementation could facilitate the discovery of genes and other biological mechanisms underlying maize inflorescence.
NICE public health guidance update
Authors: Fryer Ben , McGuire Hugh , Elliott Lise , Desai Monica , Richardson Judith 
Published: March 2020

Abstract
This article covers recent National Institute for Health and Care Excellence (NICE) guidance relevant to public health, with a focus on indoor air quality. It introduces the evidence behind this guideline, and the actions that need to be taken by a wide range of stakeholders to implement the guidance and help people to achieve good air quality in their homes. It also highlights the inequalities in exposure to poor quality indoor air and identifies groups that are more vulnerable to health impacts.
Influence of Megasphaera elsdenii and feeding strategies on feedlot performance, compositional growth, and carcass parameters of early weaned, beef calves
Authors: DeClerck Jonathan C , Wade Zain E , Reeves Nathan R , Miller Mark F , Johnson Brad J , Ducharme Gary A , Rathmann Ryan J 
Published: March 2020

Abstract
Simmental–Angus calves [n = 135; 72 steers and 63 heifers; body weight (BW) = 212.4 kg ± 36.1] were early weaned (~5 mo) to evaluate multiple feeding regimens (conventional vs. aggressive energy diets ± Megasphaera elsdenii NCIMB 41125 (M. elsdenii culture (MEC); Lactipro Advance; MS Biotec Inc., Wamego, KS) in order to elucidate the optimal development strategy. Objectives were measured by tracking the effects of caloric density and oral drenching of growing phase performance and subsequent carcass traits. The 72-d experiment featured three groups: 1) control (CON), fed exclusively a 35% roughage diet; 2) aggressive (AGR), fed a blend of a 10% and 35% roughage diets; 3) MEC, fed the same diet as AGR and drenched with 50 mL of M. elsdenii NCIMB 41125 on day 1. A subset of calves (n = 45) was equipped with wireless rumination tags (Allflex Flex Tag; SCR Engineers, Ltd; Netanya, Israel), which logged daily rumination and general activity. Skeletal growth variables were assessed by measuring wither and hip height pretrial and posttrial. Ultrasonography provided additional resolution concerning growing phase compositional gain, which was later verified by carcass data collection. Data were analyzed as a nested analysis of variance with BW and gender serving as blocking factors. The increased caloric density of the diets administered to MEC and AGR calves resulted in greater average daily gain and gain:feed values compared with CON even during the first 21 d of diet acclimation (P ≤ 0.05). Additional fiber concentration of CON diets led to increased rumination times in 9 of the 10 wk of trial (P ≤ 0.10). No differences amongst treatments were detected for skeletal variables or ultrasound 12th rib fat. Cattle fed CON diets posted 3.4% inferior BW at the end of the growing period trial and a 3.8% reduction in hot carcass weight (HCW), reinforcing the theory that intensifying caloric intake during the growing phase does not compromise future feedlot performance. Ultrasound marbling scores for MEC-treated cattle were 19° greater than AGR treated cattle (P ≤ 0.05) at the end of the growing phase trial. Nearly the exact same advantage (22°) was observed in the cooler 5 mo later (P = 0.42). Implying MEC metabolically imprinted cattle to favor marbling development. It appears that maximizing dietary caloric density in light-weight calves does not adversely affect the growth curve, while oral dosing of MEC during the growing period may be a precursor for enhanced quality grade.
The energy requirements of performance horses in training
Authors: Ebert Mark , Moore-Colyer Meriel J S 
Published: March 2020

AbstractThe aim of this study was to estimate the energy requirements of performance horses in active, variable training in the field. Sixty horses in England and Switzerland were measured over 2-wk periods and, for 15 of these, the measurement period was extended, ranging from 21 to 42 wk. Energy intake was estimated by measuring daily feed consumption. Energy output was measured using heart rate (HR) monitors during 608 training sessions, relating HR to volume of oxygen (VO₂) and converting VO₂ to energy. Field maintenance requirements were calculated by deducting the marginal energy cost of training from energy input. The mean field maintenance expenditure for performance horses with a normal temperament was found to be 0.118 MJ of metabolizable energy (ME) per kilogram of body weight (BW) per day (SD = 0.008, CI = 0.005, n = 60 horses). This result is between 1.9% (P = 0.086) and 20.9% (P &lt; 0.001) greater than the official guidance found in the United States, France, Germany, and Holland. Heart rate monitoring of training revealed a mean energy expenditure (EE) per ridden session of 0.023 MJ ME (SD = 0.001, CI = 0.001, n = 175 training sessions). The mean daily EE for exercise based on a full week’s training was 0.018 MJ ME/kg BW/d (SD = 0.005, CI = 0.001, n = 60 horses), representing a multiple of maintenance of 15.3%. This implies that the official guidance in the United States and France may overstate expenditure for exercise by 111% and 15%, respectively (P &lt; 0.01). Daily EE between countries and within disciplines was consistent, allowing for the creation of user-friendly tables that can be used in budgeting the energy component of diets.