bluuebunny/crossref_metadata_2025_split huggingface dataset:
Certification of diamond HPHT-plates for their use as substrates for CVD-synthesis
Authors: Martynova T V , Polushin N I , Laptev A I , Maslov A L , Markova I Y 
Published: February 2021

Abstract
Incoming control of substates and gases is very important part of technological chain. The properties of diamond layer on substrates with different misorientation angles may differ considerably, therefore, determining the deviation of diamond growth plane (100) from the direction [100] is important. Also, in order to select diamond substrates that are most suitable for synthesis of pure quality crystal, it is required to determine the content of impurities in them and the roughness of their surface. In this research, HPHT-plates of one lot were examined using Fourier transform infrared spectrometry, high-resolution diffractometry and scanning probe microscopy in order to classify them according to the studied parameters. Further the classified diamond substrates were used to synthesize diamond layers. Ardis 300 was used for deposition of monocrystalline diamond; synthesis was carried out from a methane-hydrogen plasma with 3% methane at a temperature of 1100 °C, a pressure of 26.7 kPa and a power of 3800 W. The studies have shown that certification of diamond HPHT-plates allows to select substrates for the synthesis of pure quality monocrystalline diamonds.
Identification and distinct regulation of three di/tripeptide transporters in Aspergillus oryzae
Authors: Tanaka Mizuki , Ito Keisuke , Matsuura Tomomi , Kawarasaki Yasuaki , Gomi Katsuya 
Published: February 2021

ABSTRACT
The uptake of di/tripeptides is mediated by the proton-dependent oligopeptide transporter (POT) family. In this study, 3 POT family transporters, designated PotA, PotB, and PotC were identified in Aspergillus oryzae. Growth comparison of deletion mutants of these transporter genes suggested that PotB and PotC are responsible for di/tripeptide uptake. PotA, which had the highest sequence similarity to yeast POT (Ptr2), contributed little to the uptake. Nitrogen starvation induced potB and potC expression, but not potA expression. When 3 dipeptides were provided as nitrogen sources, the expression profiles of these genes were different. PrtR, a transcription factor that regulates proteolytic genes, was involved in regulation of potA and potB but not in potC expression. Only potC expression levels were dramatically reduced by disruption of ubrA, an orthologue of yeast ubiquitin ligase UBR1 responsible for PTR2 expression. Expression of individual POT genes is apparently controlled by different regulatory mechanisms.
Heterogeneity-aware and communication-efficient distributed statistical inference
Authors: Duan Rui , Ning Yang , Chen Yong 
Published: February 2021

SummaryIn multicentre research, individual-level data are often protected against sharing across sites. To overcome the barrier of data sharing, many distributed algorithms, which only require sharing aggregated information, have been developed. The existing distributed algorithms usually assume the data are homogeneously distributed across sites. This assumption ignores the important fact that the data collected at different sites may come from various subpopulations and environments, which can lead to heterogeneity in the distribution of the data. Ignoring the heterogeneity may lead to erroneous statistical inference. We propose distributed algorithms which account for the heterogeneous distributions by allowing site-specific nuisance parameters. The proposed methods extend the surrogate likelihood approach (Wang et al. 2017; Jordan et al. 2018) to the heterogeneous setting by applying a novel density ratio tilting method to the efficient score function. The proposed algorithms maintain the same communication cost as existing communication-efficient algorithms. We establish a nonasymptotic risk bound for the proposed distributed estimator and its limiting distribution in the two-index asymptotic setting, which allows both sample size per site and the number of sites to go to infinity. In addition, we show that the asymptotic variance of the estimator attains the Cramér–Rao lower bound when the number of sites is smaller in rate than the sample size at each site. Finally, we use simulation studies and a real data application to demonstrate the validity and feasibility of the proposed methods.
Intravenous Artesunate for the Treatment of Severe Imported Malaria: Implementation, Efficacy, and Safety in 1391 Patients
Authors: Roussel Camille , Ndour Papa Alioune , Kendjo Eric , Larréché Sébastien , Taieb Aida , Henry Benoît , Lebrun-Vignes Bénédicte , Chambrion Charlotte , Argy Nicolas , Houzé Sandrine , Mouri Oussama , Courtin David , Angoulvant Adela , Delacour Hervé , Gay Frédérick , Siriez Jean-Yves , Danis Martin , Bruneel Fabrice , Bouchaud Olivier , Caumes Eric , Piarroux Renaud , Thellier Marc , Jauréguiberry Stéphane , Buffet Pierre ,   the FRench Artesunate Working Group
Published: February 2021

Abstract

Background
Intravenous artesunate is the World Health Organization–recommended first-line treatment for severe malaria worldwide, but it is still not fully licensed in Europe. Observational studies documenting its safety and efficacy in imported malaria are thus essential.

Methods
We prospectively collected clinical and epidemiological features of 1391 artesunate-treated patients among 110 participant centers during the first 7 years (2011–2017) of a national program implemented by the French Drug Agency.

Results
Artesunate became the most frequent treatment for severe malaria in France, rising from 9.9% in 2011 to 71.4% in 2017. Mortality was estimated at 4.1%. Treatment failure was recorded in 27 patients, but mutations in the Kelch-13 gene were not observed. Main reported adverse events (AEs) were anemia (136 cases), cardiac events (24, including 20 episodes of conduction disorders and/or arrhythmia), and liver enzyme elevation (23). Mortality and AEs were similar in the general population and in people with human immunodeficiency virus, who were overweight, or were pregnant, but the only pregnant woman treated in the first trimester experimented a hemorrhagic miscarriage. The incidence of post-artesunate–delayed hemolysis (PADH) was 42.8% when specifically assessed in a 98-patient subgroup, but was not associated with fatal outcomes or sequelae. PADH was twice as frequent in patients of European compared with African origin.

Conclusions
Artesunate was rapidly deployed and displayed a robust clinical benefit in patients with severe imported malaria, despite a high frequency of mild to moderate PADH. Further explorations in the context of importation should assess outcomes during the first trimester of pregnancy and collect rare but potentially severe cardiac AEs.
Mastery of everyday life and social support needs in older vulnerable women with myocardial infarction and their relatives: a qualitative study
Authors: Pedersen Maria , Støier Louise , Egerod Ingrid , Overgaard Dorthe 
Published: February 2021

Abstract

Aims
The Danish public healthcare system provides a comprehensive cardiac rehabilitation (CR) programme, but attendance rates are low among older vulnerable women. Effective interventions enabling increased CR attendance are warranted. Knowledge about everyday life and social support needs is crucial to the development of effective CR interventions in this group. To explore mastery of everyday life and social support needs in older, vulnerable women with myocardial infarction (MI) and their relatives.

Methods and results
A qualitative explorative design using semi-structured individual or dyadic interviews with patients (n = 21) and their relatives (n = 13) and applying thematic analysis. Five themes captured mastery of everyday life and social support needs. ‘The Big Picture’ suggesting that comorbidities dwarfed the impact of MI. ‘Blaming the Doctor’ illustrated issues of distrust and treatment delay. ‘Rehabilitation Barriers’ explained why these vulnerable patients failed to participate in CR. ‘Caregiver Concerns’ described relatives dual roles as supporters and supported. ‘Finding their Way’ indicated how patients were assisted by peer support to negotiate the trajectory.

Conclusion
The study offers a basis for the development of CR interventions customized to this group of patients. Interventions should target patients with multimorbidity, low motivation for lifestyle changes, and transportation issues. Peer support is suggested for this group of patients where relatives are also apt to be vulnerable.
The Phenotype of mes-2, mes-3, mes-4 and mes-6, Maternal-Effect Genes Required for Survival of the Germline in Caenorhabditis elegans, Is Sensitive to Chromosome Dosage
Authors: Garvin Carol , Holdeman Richard , Strome Susan 
Published: February 2021

Abstract
Mutations in mes-2, mes-3, mes-4, and mes-6 result in maternal-effect sterility: hermaphrodite offspring of mes/mes mothers are sterile because of underproliferation and death of the germ cells, as well as an absence of gametes. Mutant germ cells do not undergo programmed cell death, but instead undergo a necrotic-type death, and their general poor health apparently prevents surviving germ cells from forming gametes. Male offspring of mes mothers display a significantly less severe germline phenotype than their hermaphrodite siblings, and males are often fertile. This differential response of hermaphrodite and male offspring to the absence of mes+ product is a result of their different X chromosome compositions; regardless of their sexual phenotype, XX worms display a more severe germline phenotype than XO worms, and XXX worms display the most severe phenotype. The sensitivity of the mutant phenotype to chromosome dosage, along with the similarity of two MES proteins to chromatin-associated regulators of gene expression in Drosophila, suggest that the essential role of the mes genes is in control of gene expression in the germline. An additional, nonessential role of the mes genes in the soma is suggested by the surprising finding that mutations in the mes genes, like mutations in dosage compensation genes, feminize animals whose male sexual identity is somewhat ambiguous. We hypothesize that the mes genes encode maternally supplied regulators of chromatin structure and gene expression in the germline and perhaps in somatic cells of the early embryo, and that at least some of their targets are on the X chromosomes.
Characterization of the Germinal and Somatic Activity of the Arabidopsis Transposable Element Tag1
Authors: Liu Dong , Crawford Nigel M 
Published: February 2021

Abstract
Tag1 is an autonomous transposon of Arabidopsis thaliana. The excision behavior of Tag1 during reproductive and vegetative development was examined using CaMV 35S-Tag1-GUS constructs. Germinal reversion frequencies varied from 0 to 27% and correlated with Tag1 copy number. Southern blot and somatic sector analyses indicated that each revertant was derived from an independent excision event, and approximately 75% of the revertants had new Tag1 insertions. Revertants were obtained with similar frequencies from the male and female parents. In flowers, small somatic sectors were observed in siliques, carpels, petals and sepals while stemlike organs (filaments and pedicels) had larger sectors. No sectors encompassing entire flowers or inflorescences were observed, however, indicating that excision occurs late in flower development and rarely in inflorescence meristems. Late excision was also observed during vegetative development with 99.8% of leaves showing small sectors encompassing no more than 20 cells. Roots and cotyledons, however, showed larger sectors that included entire lateral roots and cotyledons. These results indicate that Tag1 can excise in the embryo and all the organs of the plant with the timing of excision being restricted to late stages of vegetative and reproductive development in the shoot.
Genetic Variation Within and Among Populations of Arabidopsis thaliana
Authors: Bergelson Joy , Stahl Eli , Dudek Scott , Kreitman Martin 
Published: February 2021

Abstract
We investigated levels of nucleotide polymorphism within and among populations of the highly self-fertilizing Brassicaceous species, Arabidopsis thaliana. Four-cutter RFLP data were collected at one mitochondrial and three nuclear loci from 115 isolines representing 11 worldwide population collections, as well as from seven commonly used ecotypes. The collections include multiple populations from North America and Eurasia, as well as two pairs of collections from locally proximate sites, and thus allow a hierarchical geographic analysis of polymorphism. We found no variation at the mitochondrial locus Nad5 and very low levels of intrapopulation nucleotide diversity at Adh, Dhs1, and Gpa1. Interpopulation nucleotide diversity was also consistently low among the loci, averaging 0.0014. gst, a measure of population differentiation, was estimated to be 0.643. Interestingly, we found no association between geographical distance between populations and genetic distance. Most haplotypes have a worldwide distribution, suggesting a recent expansion of the species or long-distance gene flow. The low level of polymorphism found in this study is consistent with theoretical models of neutral mutations and background selection in highly self-fertilizing species.
The lacI Gene as a Target for Mutation in Transgenic Rodents and Escherichia coli
Authors: de Boer Johan G , Glickman Barry W 
Published: February 2021

Abstract
The lacI gene has been used extensively for the recovery and analysis of mutations in bacteria with various DNA repair backgrounds and after exposure to a wide variety of mutagens. This has resulted in a large database of information on mutational mechanisms and specificity of many mutagens, as well as the effect of DNA repair background on mutagenicity. Most importantly, knowledge about the mutational sensitivity of the lacI gene is now available, yielding information about mutable nucleotides. This popularity and available knowledge resulted in the use of the lacI gene in transgenic rodents for the study of mutagenesis in mammals, where it resides in ~40 repeated copies. As the number of sequenced mutations recovered from these animals increases, we are able to analyze the sites at which mutations have been recovered in great detail and to compare the recovered sites between bacteria and transgenic animals. The nucleotides that code for the DNA-binding domain are nearly saturated with base substitutions. Even after determining the sequences of ~10,000 mutations recovered from the animals, however, new sites and new changes are still being recovered. In addition, we compare the nature of deletion mutations between bacteria and animals. Based on the nature of deletions in the animals, we conclude that each deletion occurs in a single copy of the gene.
Signatures of Population Expansion in Microsatellite Repeat Data
Authors: Kimmel Marek , Chakraborty Ranajit , King J Patrick , Bamshad Michael , Watkins W Scott , Jorde Lynn B 
Published: February 2021

Abstract
To examine the signature of population expansion on genetic variability at microsatellite loci, we consider a population that evolves according to the time-continuous Moran model, with growing population size and mutations that follow a general asymmetric stepwise mutation model. We present calculations of expected allele-size variance and homozygosity at a locus in such a model for several variants of growth, including stepwise, exponential, and logistic growth. These calculations in particular prove that population bottleneck followed by growth in size causes an imbalance between allele size variance and heterozygosity, characterized by the variance being transiently higher than expected under equilibrium conditions. This effect is, in a sense, analogous to that demonstrated before for the infinite allele model, where the number of alleles transiently increases after a stepwise growth of population. We analyze a set of data on tetranucleotide repeats that reveals the imbalance expected under the assumption of bottleneck followed by population growth in two out of three major racial groups. The imbalance is strongest in Asians, intermediate in Europeans, and absent in Africans. This finding is consistent with previous findings by others concerning the population expansion of modern humans, with the bottleneck event being most ancient in Africans, most recent in Asians, and intermediate in Europeans. Nevertheless, the imbalance index alone cannot reliably estimate the time of initiation of population expansion.
Chromosome 14 Contains Determinants That Regulate Susceptibility to Theiler's Virus–Induced Demyelination in the Mouse
Authors: Bureau J-F , Drescher K M , Pease L R , Vikoren T , Delcroix M , Zoecklein L , Brahic M , Rodriguez M 
Published: February 2021

AbstractTheiler's murine encephalomyelitis virus causes a chronic demyelinating disease in susceptible strains of mice that is similar to human multiple sclerosis. Several nonmajor histocompatibility complex–linked genes have been implicated as determinants of susceptibility or resistance to either demyelination or virus persistence. In this study, we used linkage analysis of major histocompatibility complex identical H-2d (DBA/2J × B10.D2) F2 intercross mice to identify loci associated with susceptibility to virus-induced demyelinating disease. In a 20-cM region on chromosome 14, we identified four markers, D14Mit54, D14Mit60, D14Mit61, and D14Mit90 that are significantly associated with demyelination. Because two peaks were identified, one near D14Mit54 and one near D14Mit90, it is possible that two loci in this region are involved in controlling demyelination.
Estimating Within-Locus Nonadditive Coefficient and Discriminating Dominance Versus Overdominance as the Genetic Cause of Heterosis
Authors: Deng Hong-Wen 
Published: February 2021

Abstract
Testing (over)dominance as the genetic cause of heterosis and estimating the (over)dominance coefficient (h) are related. Using simulations, we investigate the statistical properties of Mukai's approach, which is intended to estimate the average (h¯) of hi across loci by regression of outcrossed progeny on the sum of the two corresponding homozygous parents. A new approach for estimating h¯ is also developed, utilizing data on families formed by multiple selfed genotypes from each outcrossed parent, thus not requiring constructing homozygotes. Assuming constant mutation effects, h can be estimated accurately by both approaches under dominance. When rare alleles have low frequencies at any polymorphic locus, Mukai's approach can estimate h accurately under over(under)dominance. Therefore, the (over)dominance hypothesis for heterosis can be tested by estimating h, under either dominance or overdominance at all genomic loci. However, this is invalid with more plausible mixed dominance and overdominance at different loci. Estimating the variance of hi across loci is also investigated. In self-compatible outcrossing populations with mutations of variable effects and lethals, our new approach is better than Mukai's, not only because of not requiring homozygotes but also because of the better statistical performance reflected by the smaller mean square errors of the estimates.
A DNA Methyltransferase Homolog With a Chromodomain Exists in Multiple Polymorphic Forms in Arabidopsis
Authors: Henikoff Steven , Comai Luca 
Published: February 2021

Abstract
Chromodomains are thought to mediate protein-protein interactions between chromatin components. We have detected a chromodomain embedded within the catalytic region of a predicted Arabidopsis DNA methyltransferase that is diverged from other eukaryotic enzymes. The 791 residue “chromomethylase” (CMT1) is encoded by a floral transcript that is spliced from 20 exons and is present at only ~1/10−7 of total mRNA. Genomic sequencing reveals an ancient haplotype split at CMT1 between Col-0 + Metz and the other ecotypes examined. In the Col-0 + Metz haplotype, alternative mRNA processing at intron 13 truncates the coding region. In Ler, RLD, and No-0, similar truncation is caused by insertion of an intact retrotransposon, Evelknievel, which is present as a single copy in Ler and RLD and is currently methylated and inactive. Evelknievel is found at this site on a single branch that connects the Ler, RLD, and No-0 ecotypes but is absent from the genomes of all other ecotypes examined. A stop codon within exon 6 of the Metz ecotype confirms that CMT1 is nonessential. Nevertheless, comparison to CMT1 of Cardaminopsis arenosa, an outcrossing relative, indicates conservation for DNA methyltransferase function. We discuss how allelic diversity of CMT1 may reflect loosened selective constraints in a self-fertilizing species such as Arabidopsis thaliana.
Social Contact Mode and 15-Year Episodic Memory Trajectories in Older Adults With and Without Hearing Loss: Findings From the English Longitudinal Study of Ageing
Authors: Rafnsson Snorri Bjorn , Maharani Asri , Tampubolon Gindo 
Published: February 2021

Abstract

Objectives
Frequent social contact benefits cognition in later life although evidence is lacking on the potential relevance of the modes chosen by older adults, including those living with hearing loss, for interacting with others in their social network.

Method
11,418 participants in the English Longitudinal Study of Ageing provided baseline information on hearing status and social contact mode and frequency of use. Multilevel growth curve models compared episodic memory (immediate and delayed recall) at baseline and longitudinally in participants who interacted frequently (offline only or offline and online combined), compared to infrequently, with others in their social network.

Results
Frequent offline (B = 0.23; SE = 0.09) and combined offline and online (B = 0.71; SE = 0.09) social interactions predicted better episodic memory after adjustment for multiple confounders. We observed positive, longitudinal associations between combined offline and online interactions and episodic memory in participants without hearing loss (B = 0.50, SE = 0.11) but not with strictly offline interactions (B = 0.01, SE = 0.11). In those with hearing loss, episodic memory was positively related to both modes of engagement (offline only: B = 0.79, SE = 0.20; combined online and offline: B = 1.27, SE = 0.20). Sensitivity analyses confirmed the robustness of these findings.

Discussion
Supplementing conventional social interactions with online communication modes may help older adults, especially those living with hearing loss, sustain, and benefit cognitively from, personal relationships.