bluuebunny/crossref_metadata_2025_split huggingface dataset:
A Mixture Model Approach to the Mapping of Quantitative Trait Loci in Complex Populations With an Application to Multiple Cattle Families
Authors: Jansen Ritsert C , Johnson David L , Van Arendonk Johan A M 
Published: February 2021

AbstractA mixture model approach is presented for the mapping of one or more quantitative trait loci (QTLs) in complex populations. In order to exploit the full power of complete linkage maps the simultaneous likelihood of phenotype and a multilocus (all markers and putative QTLs) genotype is computed. Maximum likelihood estimation in our mixture models is implemented via an Expectation-Maximization algorithm: exact, stochastic or Monte Carlo EM by using a simple and flexible Gibbs sampler. Parameters include allele frequencies of markers and QTLs, discrete or normal effects of biallelic or multiallelic QTLs, and homogeneous or heterogeneous residual variances. As an illustration a dairy cattle data set consisting of twenty half-sib families has been reanalyzed. We discuss the potential which our and other approaches have for realistic multiple-QTL analyses in complex populations.
Restriction Fragment Length Polymorphism and Divergence in the Genomic Regions of High and Low Recombination in Self-Fertilizing and Cross-Fertilizing Aegilops Species
Authors: Dvorřák Jan , Luo Ming-Cheng , Yang Zu-Li 
Published: February 2021

Abstract
RFLP was investigated at 52 single-copy gene loci among six species of Aegilops, including both cross-fertilizing and self-fertilizing species. Average gene diversity (H) was found to correlate with the level of outcrossing. No relationship was found between H and the phylogenetic status of a species. In all six species, the level of RFLP at a locus was a function of the position of the locus on the chromosome and the recombination rate in the neighborhood of the locus. Loci in the proximal chromosome regions, which show greatly reduced recombination rates relative to the distal regions, were significantly less variable than loci in the distal chromosome regions in all six species. Variation in recombination rates was also reflected in the haplotype divergence between closely related species; loci in the chromosome regions with low recombination rates were found to be diverged less than those in the chromosome regions with high recombination rates. This relationship was not found among the more distantly related species.
Translation of Some Maize Small Heat Shock Proteins Is Initiated From Internal In-Frame AUGs
Authors: Frappier J Roger H , Walden David B , Atkinson Burr G 
Published: February 2021

Abstract
Etiolated maize radicles (inbred Oh43) subjected to a brief heat shock synthesize a family of small heat shock proteins (≃18 kD) that is composed of at least 12 members. We previously described the cDNA-derived sequence of three maize shsp mRNAs (cMHSP18-1, cMHSP18-3, and cMHSP18-9). In this report, we demonstrate that the mRNA transcribed in vitro from one of these cDNAs (cMHSP 18-9) is responsible for the synthesis of three members of the shsp family, and we suggest that cMHSP18-3 may be responsible for the synthesis of three additional members and cMHSP18-1 for the synthesis of two other members of this family. The fact that these genes do not contain introns, coupled with the observations reported herein, suggest that maize may have established another method of using a single gene to produce a number of different proteins.
Genetic Interaction With vps8-200 Allows Partial Suppression of the Vestigial Vacuole Phenotype Caused by a pep5 Mutation in Saccharomyces cerevisiae
Authors: Woolford Carol A , Bounoutas George S , Frew Sarah E , Jones Elizabeth W 
Published: February 2021

Abstract
pep5 mutants of Saccharomyces cerevisiae accumulate inactive precursors to the vacuolar hydrolases. In addition, they show a vestigial vacuole morphology and a sensitivity to growth on media containing excess divalent cations. This pleiotropic phenotype observed for pep5::TRP1 mutants is partially suppressed by the vps8-200 allele. pep5::TRP1 vps8-200 mutants show near wild-type levels of mature-sized soluble vacuolar hydrolases, growth on zinc-containing medium, and a more “wild-type” vacuolar morphology; however, aminopeptidase I and alkaline phosphatase accumulate as precursors. These data suggest that Pep5p is a bifunctional protein and that the TRP1 insertion does not eliminate function, but results in a shorter peptide that can interact with Vps8-200p, allowing for partial function. vps8 deletion/disruption mutants contain a single enlarged vacuole. This genetic interaction was unexpected, since Pep5p was thought to interact more directly with the vacuole, and Vps8p is thought to play a role in transport between the Golgi complex and the prevacuolar compartment. The data are consistent with Pep5p functioning both at the site of Vps8p function and more closely proximal to the vacuole. They also provide evidence that the three transport pathways to the vacuole either converge or share gene products at late step(s) in the pathway(s).
Characterization of mat A-2, mat A-3 and ΔmatA Mating-Type Mutants of Neurospora crassa
Authors: Ferreira Adlane V-B , An Zhiqiang , Metzenberg Robert L , Glass N Louise 
Published: February 2021

AbstractThe mating-type locus of Neurospora crassa regulates mating identity and entry into the sexual cycle. The mat A idiomorph encodes three genes, mat A-1, mat A-2, and mat A-3. Mutations in mat A-1 result in strains that have lost mating identity and vegetative incompatibility with mat a strains. A strain containing mutations in both mat A-2 and mat A-3 is able to mate, but forms few ascospores. In this study, we describe the isolation and characterization of a mutant deleted for mat (ΔmatA), as well as mutants in either mat A-2 or mat A-3. The ΔmatA strain is morphologically wild type during vegetative growth, but it is sterile and heterokaryon compatible with both mat A and mat a strains. The mat A-2 and mat A-3 mutants are also normal during vegetative growth, mate as a mat A strain, and produce abundant biparental asci in crosses with mat a, and are thus indistinguishable from a wild-type mat A strain. These data and the fact that the mat A-2 mat A-3 double mutant makes few asci with ascospores indicate that MAT A-2 and MAT A-3 are redundant and may function in the same pathway. Analysis of the expression of two genes (sdv-1 and sdv-4) in the various mat mutants suggests that the mat A polypeptides function in concert to regulate the expression of some sexual development genes.
Bayesian Mapping of Multiple Quantitative Trait Loci From Incomplete Inbred Line Cross Data
Authors: Sillanpää Mikko J , Arjas Elja 
Published: February 2021

AbstractA novel fine structure mapping method for quantitative traits is presented. It is based on Bayesian modeling and inference, treating the number of quantitative trait loci (QTLs) as an unobserved random variable and using ideas similar to composite interval mapping to account for the effects of QTLs in other chromosomes. The method is introduced for inbred lines and it can be applied also in situations involving frequent missing genotypes. We propose that two new probabilistic measures be used to summarize the results from the statistical analysis: (1) the (posterior) QTL-intensity, for estimating the number of QTLs in a chromosome and for localizing them into some particular chromosomal regions, and (2) the location wise (posterior) distributions of the phenotypic effects of the QTLs. Both these measures will be viewed as functions of the putative QTL locus, over the marker range in the linkage group. The method is tested and compared with standard interval and composite interval mapping techniques by using simulated backcross progeny data. It is implemented as a software package. Its initial version is freely available for research purposes under the name Multimapper at URL http://www.rni.helsinki.fi/~mjs.
The Roles of the Bacteriophage T4 r Genes in Lysis Inhibition and Fine-Structure Genetics: A New Perspective
Authors: Paddison Patrick , Abedon Stephen T , Dressman Holly Kloos , Gailbreath Katherine , Tracy Julia , Mosser Eric , Neitzel James , Guttman Burton , Kutter Elizabeth 
Published: February 2021

Abstract
Seldom has the study of a set of genes contributed more to our understanding of molecular genetics than has the characterization of the rapid-lysis genes of bacteriophage T4. For example, T4 rII mutants were used to define gene structure and mutagen effects at the molecular level and to help unravel the genetic code. The large-plaque morphology of these mutants reflects a block in expressing lysis inhibition (LIN), the ability to delay lysis for several hours in response to sensing external related phages attacking the cell, which is a unique and highly adaptive attribute of the T4 family of phages. However, surprisingly little is known about the mechanism of LIN, or how the various r genes affect its expression. Here, we review the extensive old literature about the r genes and the lysis process and try to sort out the major players affecting lysis inhibition. We confirm that superinfection can induce lysis inhibition even while infected cells are lysing, suggesting that the signal response is virtually instantaneous and thus probably the result of post-translational regulation. We identify the rI gene as ORF tk.–2, based on sequence analysis of canonical rI mutants. The rI gene encodes a peptide of 97 amino acids (Mr = 11.1 kD; pI = 4.8) that probably is secreted into the periplasmic space. This gene is widely conserved among T-even phage. We then present a model for LIN, postulating that rI is largely responsible for regulating the gpt holin protein in response to superinfection. The evidence suggests that the rIIA and B genes are not directly involved in lysis inhibition; rather, when they are absent, an alternate pathway for lysis develops which depends on the presence of genes from any of several possible prophages and is not sensitive to lysis inhibition.
Paramutation of the r1 Locus of Maize Is Associated With Increased Cytosine Methylation
Authors: Walker Elsbeth L 
Published: February 2021

Abstract
In paramutation two alleles of a gene interact so that one of the alleles is epigenetically silenced. The silenced state is then genetically transmissible for many generations. The large (220 kbp) multigenic complex R-r is paramutable: its level of expression is changed during paramutation. R-r was found to exhibit increases in its level of cytosine methylation (C-methylation) following paramutation. These C-methylation changes are localized to the 5′ portions of the two genes in the complex that are most sensitive to paramutation. These methylation changes flank a small region called σ that is thought to have been derived from a transposon named doppia. A mutant derivative of R-r that has a deletion of the σ region fails to become methylated under conditions in which R-r is heavily methylated. This suggests that the presence of σ sequences at the locus is required for the methylation changes that are observed following paramutation.
How Optimized Is the Translational Machinery in Escherichia coli, Salmonella typhimurium and Saccharomyces cerevisiae?
Authors: Xia Xuhua 
Published: February 2021

Abstract
The optimization of the translational machinery in cells requires the mutual adaptation of codon usage and tRNA concentration, and the adaptation of tRNA concentration to amino acid usage. Two predictions were derived based on a simple deterministic model of translation which assumes that elongation of the peptide chain is rate-limiting. The highest translational efficiency is achieved when the codon recognized by the most abundant tRNA reaches the maximum frequency. For each codon family, the tRNA concentration is optimally adapted to codon usage when the concentration of different tRNA species matches the square-root of the frequency of their corresponding synonymous codons. When tRNA concentration and codon usage are well adapted to each other, the optimal content of all tRNA species carrying the same amino acid should match the square-root of the frequency of the amino acid. These predictions are examined against empirical data from Escherichia coli, Salmonella typhimurium, and Saccharomyces cerevisiae.
Quantitative Trait Locus (QTL) Mapping Using Different Testers and Independent Population Samples in Maize Reveals Low Power of QTL Detection and Large Bias in Estimates of QTL Effects
Authors: Melchinger Albrecht E , Utz H Friedrich , Schön Chris C 
Published: February 2021

AbstractThe efficiency of marker-assisted selection (MAS) depends on the power of quantitative trait locus (QTL) detection and unbiased estimation of QTL effects. Two independent samples (N = 344 and 107) of F2 plants were genotyped for 89 RFLP markers. For each sample, testcross (TC) progenies of the corresponding F3 lines with two testers were evaluated in four environments. QTL for grain yield and other agronomically important traits were mapped in both samples. QTL effects were estimated from the same data as used for detection and mapping of QTL (calibration) and, based on QTL positions from calibration, from the second, independent sample (validation). For all traits and both testers we detected a total of 107 QTL with N = 344, and 39 QTL with N = 107, of which only 20 were in common. Consistency of QTL effects across testers was in agreement with corresponding genotypic correlations between the two TC series. Most QTL displayed no significant QTL × environment nor epistatic interactions. Estimates of the proportion of the phenotypic and genetic variance explained by QTL were considerably reduced when derived from the independent validation sample as opposed to estimates from the calibration sample. We conclude that, unless QTL effects are estimated from an independent sample, they can be inflated, resulting in an overly optimistic assessment of the efficiency of MAS.
Top four types of sentinel events in Saudi Arabia during the period 2016–19
Authors: Altalhi Nasser , Alnaimi Haifa , Chaouali Mafaten , Alahmari Falaa , Alabdulkareem Noor , Alaama Tareef 
Published: February 2021

Abstract

Background
This study discusses the summary, investigation and root causes of the top four sentinel events (SEs) in Saudi Arabia (SA) that occurred between January 2016 and December 2019, as reported by the Ministry of Health (MOH) and private hospitals through the MOH SE reporting system (SERS). It is intended for use by legislators, health-care facilities and the public to shed light on areas that still need improvement to preserve patient safety.

Objectives
The purpose of this study is to review the most common SEs reported by the MOH and private hospitals between the years 2016 and 2019 to assess the patterns and identify risk areas and the common root causes of these events in order to promote country-wide learning and support services that can improve patient safety.

Methods
In this retrospective descriptive study, the data were retrieved from the SERS, which routinely collects records from both MOH and private hospitals in SA. SEs were analyzed by type of event, location, time, patient demographics, outcome and root causes.

Results
There were 727 SEs during this period, 38.4% of which were under the category of unexpected patient death, 19.4% under maternal death, 11.7% under unexpected loss of limb or function and 9.9% under retained instruments or sponge. Common root causes were related to policies and procedures, guidelines, miscommunication between health-care facilities, shortage of staff and lack of competencies.

Conclusion
Given these results, efforts should focus on improving the care of deteriorating patients in general wards, ICU (Intensive Care Units) admission/discharge criteria and maternal, child and surgical safety. The results also highlighted the problem of underreporting of SEs, which needs to be addressed and improved. Linking data sources such as claims and patient complaints databases and electronic medical records to the national reporting system must also be considered to ensure an optimal estimation of the number of events.
The Performance of Friendship: Paschal de L’estocart and His Circle at the University of Basel, 1581–1583
Authors: Latour Melinda 
Published: February 2021

Abstract
In this article, I present new research on the composer Paschal de L’Estocart during his peak years of activity at the University of Basel (1581–3). In addition to discussing two fresh pieces of archival evidence related to L’Estocart found in the Basel archives, I offer new research on the identities of his laudatory contributors. Considering how little biographical information has survived on the composer beyond his published music, the identities of these poetic contributors are a critical piece of evidence that fills in our skeletal knowledge of L’Estocart’s network and the social context of his music. Taken together, this new evidence sheds light on L’Estocart’s active participation in the most elite academic circles in Basel and Geneva, which makes his return to the Catholic world at the end of his life all the more difficult to explain. L’Estocart’s 1583 letter to Zwinger, however, offers a clue that might explain his break from the Reformed faith.
The Retroauricular Incision as an Effective and Safe Alternative Incision for Decompressive Hemicraniectomy
Authors: Dowlati Ehsan , Mortazavi Armin , Keating Gregory , Jha Ribhu Tushar , Felbaum Daniel R , Chang Jason J , Nair Mani N , Mason Robert B , Aulisi Edward F , Armonda Rocco A , Mai Jeffrey C 
Published: February 2021

Abstract

BACKGROUND
The reverse question mark (RQM) incision has been traditionally utilized to perform decompressive hemicraniectomies (DHC) to relieve refractory intracranial hypertension. Alternative incisions have been proposed in the literature but have not been compared directly.

OBJECTIVE
To present the retroauricular (RA) incision as an alternative incision that we hypothesize will increase calvarium exposure to maximize the removal of the hemicranium and will decrease wound-related complications compared to the RQM incision.

METHODS
This study is a retrospective review of all DHCs performed at our institution over a span of 34 mo, stratified based on the type of scalp incision. The surface areas of the cranial defects were calculated, normalizing to their respective skull diameters. For those patients surviving beyond 1 wk, complications were examined from both cohorts.

RESULTS
A total of 63 patients in the RQM group and 43 patients in the RA group were included. The average surface area for the RA and RQM incisions was 117.0 and 107.8 cm2 (P = .0009), respectively. The ratio of average defect size to skull size for RA incision was 0.81 compared to 0.77 for the RQM group (P = .0163). Of those who survived beyond 1 wk, the absolute risk for surgical site complications was 14.0% and 8.3% for RQM and RA group (P = .5201), respectively.

CONCLUSION
The RA incision provides a safe and effective alternative incision to the traditional RQM incision used for DHC. This incision affords a potentially larger craniectomy while mitigating postoperative wound complications.
Development of highly radiopure NaI(Tl) scintillator for PICOLON dark matter search project
Authors: Fushimi K , Kanemitsu Y , Hirata S , Chernyak D , Hazama R , Ikeda H , Imagawa K , Ishiura H , Ito H , Kisimoto T , Kozlov A , Takemoto Y , Yasuda K , Ejiri H , Hata K , Iida T , Inoue K , Koga M , Nakamura K , Orito R , Shima T , Umehara S , Yoshida S 
Published: February 2021

Abstract
Highly radiopure NaI(Tl) was developed to search for particle candidates of dark matter. Optimized methods were combined to reduce various radioactive impurities. $^{40}$K was effectively reduced by the recrystallization method. The progenies of the decay chains of uranium and thorium were reduced by appropriate resins. The concentration of natural potassium in NaI(Tl) crystal was reduced to 20 ppb. Concentrations of alpha-ray emitters were successfully reduced by appropriate resin selection. The present concentrations of the thorium series and $^{226}$Ra were $1.2\pm1.4$$\mu$Bq/kg and $13\pm4$$\mu$Bq/kg, respectively. No significant excess in the concentration of $^{210}$Pb was obtained, and the upper limit was 5.7 $\mu$Bq/kg at 90$\#$ CL. The achieved level of radiopurity of NaI(Tl) crystals makes the construction of a dark matter detector possible.
Gamow–Teller transitions of neutron-rich N = 82,81 nuclei by shell-model calculations
Authors: Shimizu Noritaka , Togashi Tomoaki , Utsuno Yutaka 
Published: February 2021

Abstract
$\beta$ -decay half-lives of neutron-rich nuclei around $N=82$ are key data to understand the $r$-process nucleosynthesis. We performed large-scale shell-model calculations in this region using a newly constructed shell-model Hamiltonian, and successfully described the low-lying spectra and half-lives of neutron-rich $N=82$ and $N=81$ isotones with $Z=42\text{--}49$ in a unified way. We found that their Gamow–Teller strength distributions have a peak in the low excitation energies, which significantly contributes to the half-lives. This peak, dominated by $\nu 0g_{7/2} \to \pi 0g_{9/2}$ transitions, is enhanced on the proton-deficient side because the Pauli-blocking effect caused by occupying the valence proton $0g_{9/2}$ orbit is weakened.
Effects of bacterial cultures, enzymes, and yeast-based feed additive combinations on ruminal fermentation in a dual-flow continuous culture system
Authors: Bennett S L , Arce-Cordero J A , Brandao V L N , Vinyard J R , Agustinho B C , Monteiro H F , Lobo R R , Tomaz L , Faciola A P 
Published: February 2021

Abstract
Bacterial cultures, enzymes, and yeast-derived feed additives are often included in commercial dairy rations due to their effects on ruminal fermentation. However, the effects of these additives when fed together are not well understood. The objective of this study was to evaluate the changes in ruminal fermentation when a dairy ration is supplemented with combinations of bacterial probiotics, enzymes and yeast. Our hypotheses were that ruminal fermentation would be altered, indicated through changes in volatile fatty acid profile and nutrient digestibility, with the inclusion of (1) an additive, (2) yeast, and (3) increasing additive doses. Treatments were randomly assigned to 8 fermenters in a replicated 4 × 4 Latin square with four 10 d experimental periods, consisting of 7 d for diet adaptation and 3 d for sample collection. Basal diets contained 52:48 forage:concentrate and fermenters were fed 106 g of dry matter per day divided equally between two feeding times. Treatments were: control (CTRL, without additives); bacterial culture/enzyme blend (EB, 1.7 mg/d); bacterial culture/enzyme blend with a blend of live yeast and yeast culture (EBY, 49.76 mg/d); and a double dose of the EBY treatment (2×, 99.53 mg/d). The bacterial culture/enzyme blend contained five strains of probiotics (Lactobacillus animalis, Propionibacterium freudenreichii, Bacillus lichenformis, Bacillus subtilis, and Enterococcus faecium) and three enzymes (amylase, hemicellulase, and xylanase). On d 8–10, samples were collected for pH, redox, volatile fatty acids, lactate, ammonia N, and digestibility measurements. Statistical analysis was performed using the GLIMMIX procedure of SAS. Repeated measures were used for pH, redox, VFA, NH3-N, and lactate kinetics data. Orthogonal contrasts were used to test the effect of (1) additives, ADD (CTRL vs. EB, EBY, and 2X); (2) yeast, YEAST (EB vs. EBY, and 2X); and (3) dose, DOSE (EBY vs. 2X). No effects (P &gt; 0.05) were observed for pH, redox, NH3-N, acetate, isobutyrate, valerate, total VFA, acetate:propionate, nutrient digestibility or N utilization. Within the 24 h pool, the molar proportion of butyrate increased (P = 0.03) with the inclusion of additives when compared to the control while the molar proportion of propionate tended to decrease (P = 0.07). In conclusion, the inclusion of bacterial cultures, enzymes and yeast in the diet increased butyrate concentration; but did not result in major changes in ruminal fermentation.