bluuebunny/crossref_metadata_2025_split huggingface dataset:
Last-minute cancellation of adult patients scheduled for cardiothoracic surgery in a large Dutch tertiary care centre
Authors: Scheenstra Bart , Princée Anouk M A , Imkamp Maike S V , Kietselaer Bas , Ganushchak Yuri M , van’t Hof Arnoud W J , Maessen Jos G 
Published: April 2021

Abstract

OBJECTIVES
Unanticipated cancellation of a surgical procedure is a common problem, causing distress to the patient and increases in healthcare costs. However, limited evidence exists on the effects of last-minute cancellations of cardiothoracic surgical procedures in particular. The goal of this study was to gain insight into the prevalence of and the reasons for last-minute cancellations and to examine whether cancellation is associated with adverse medical outcomes.

METHODS
Patients who were scheduled for elective cardiothoracic surgical procedures between January 2017 and June 2019 were evaluated. The reasons for the cancellations were assigned to the categories medically related or process related. We examined the differences in patient characteristics between those designated as no cancellation, medically related cancellations and process-related cancellations. Lastly, we examined the outcomes of patients who experienced a last-minute cancellation of a scheduled operation.

RESULTS
A total of 2111 patients were included; of these, 301 (14.3%) had last-minute cancellations. In 78 (26%) cases, the cancellations were attributable to medical reasons (e.g. infection, comorbidities); 215 (71%) of the cancellations were process related (e.g. another patient in more urgent need of surgery, lack of staff). Almost 99% of the operations with a process-related cancellation were rescheduled compared to only 71.8% of the medically related cancelled operations (P &lt; 0.001). Patients with a medically related cancellation had significantly higher 1-year mortality than patients who had no cancellation (unadjusted hazard ratio 2.50; 95% confidence interval, 1.30–4.78; P = 0.006); after adjustment for the EuroSCORE II, this effect remained significant.

CONCLUSIONS
Last-minute cancellations were commonly seen in our cohort, and the reasons for cancellation were significantly related to adverse medical outcomes.
Soil microbial interconnections along ecological restoration gradients of lowland forests after slash-and-burn agriculture
Authors: Lin Qiang , Dini-Andreote Francisco , Li Lingjuan , Umari Ruma , Novotny Vojtech , Kukla Jaroslav , Heděnec Petr , Frouz Jan 
Published: April 2021

ABSTRACTMicrobial interconnections in soil are pivotal to ecosystem services and restoration. However, little is known about how soil microbial interconnections respond to slash-and-burn agriculture and to the subsequent ecosystem restoration after the practice. Here, we used amplicon sequencing and co-occurrence network analyses to explore the interconnections within soil bacterial and fungal communities in response to slash-and-burn practice and a spontaneous restoration (spanning ca. 60 years) of tropical forests after the practice, in Papua New Guinea. We found significantly higher complexity and greater variations in fungal networks than in those of bacteria, despite no significant changes observed in bacterial or fungal networks across successional stages. Within most successional stages, bacterial core co-occurrences (co-occurrences consistently present across all sub-networks in a stage) were more frequent than those of fungi, indicating higher stability of interconnections between bacteria along succession. The stable interconnections occurred frequently between bacterial taxa (i.e. Sporosarcina, Acidimicrobiale and Bacillaceae) and between ectomycorrhizal fungi (Boletaceae and Russula ochroleuca), implying important ecological roles of these taxa in the ecosystem restoration. Collectively, our results provide new insight into microbial interconnections in response to slash-and-burn agriculture and the subsequent ecosystem restoration, thus promoting a better understanding of microbial roles in ecosystem services and restoration.
Correlations between maximum reductive dechlorination rates and specific biomass parameters in Dehalococcoides mccartyi consortia enriched on chloroethenes PCE, TCE and cis-1,2-DCE
Authors: Matturro B , Majone M , Aulenta F , Rossetti S 
Published: April 2021

ABSTRACT
One of the challenges to implementing the modeling of the biological reductive dechlorination (RD) process is the evaluation of biological parameters that represent the abundance/activity levels of the microorganisms involved in the biodegradation of chloroethenes. Here we report a combined analysis of kinetic and specific biomass parameters conducted on three dechlorinating consortia enriched on PCE, TCE and cis-1,2-DCE. In these consortia, Dehalococcoides mccartyi (Dhc) represented ≥70% of the bacterial population identified via 16S rRNA gene amplicon sequencing. Quantitative biomolecular methods were used to generate specific biomass parameters targeting either the Dhc population (16S rRNA genes or cells) or specific genes encoding RD process-involved reductive dehalogenases. The correlation factor between the abundance of active Dhc cells or tceA gene copies and maximum RD rates allowed to predict an increment of 7E+09 of active Dhc cells or 5E+09 tceA gene copies/L under controlled conditions. Diversely, the utilization of gene transcripts as biomass parameters for RD modeling did not provide reliable correlations with kinetic performances. This study provides valuable insights for further modeling of the RD process through the utilization of specific biomass parameters.
Expansion of EasyClone-MarkerFree toolkit for Saccharomyces cerevisiae genome with new integration sites
Authors: Babaei Mahsa , Sartori Luisa , Karpukhin Alexey , Abashkin Dmitrii , Matrosova Elena , Borodina Irina 
Published: April 2021

ABSTRACT
Biotechnological production requires genetically stable recombinant strains. To ensure genomic stability, recombinant DNA is commonly integrated into the genome of the host strain. Multiple genetic tools have been developed for genomic integration into baker's yeast Saccharomyces cerevisiae. Previously, we had developed a vector toolkit EasyClone-MarkerFree for stable integration into eleven sites on chromosomes X, XI, and XII of S. cerevisiae. The markerless integration was enabled by CRISPR-Cas9 system. In this study, we have expanded the kit with eight additional intergenic integration sites located on different chromosomes. The integration efficiency into the new sites was above 80%. The expression level of green fluorescence protein (gfp) for all eight sites was similar or above XI-2 site from the original EasyClone-MarkerFree toolkit. The cellular growth was not affected by the integration into any of the new eight locations. The eight-vector expansion kit is available from AddGene.
Effects of kinship correction on inflation of genetic interaction statistics in commonly used mouse populations
Authors: Tyler Anna L , El Kassaby Baha , Kolishovski Georgi , Emerson Jake , Wells Ann E , Mahoney J Matthew , Carter Gregory W 
Published: April 2021

AbstractIt is well understood that variation in relatedness among individuals, or kinship, can lead to false genetic associations. Multiple methods have been developed to adjust for kinship while maintaining power to detect true associations. However, relatively unstudied are the effects of kinship on genetic interaction test statistics. Here, we performed a survey of kinship effects on studies of six commonly used mouse populations. We measured inflation of main effect test statistics, genetic interaction test statistics, and interaction test statistics reparametrized by the Combined Analysis of Pleiotropy and Epistasis (CAPE). We also performed linear mixed model (LMM) kinship corrections using two types of kinship matrix: an overall kinship matrix calculated from the full set of genotyped markers, and a reduced kinship matrix, which left out markers on the chromosome(s) being tested. We found that test statistic inflation varied across populations and was driven largely by linkage disequilibrium. In contrast, there was no observable inflation in the genetic interaction test statistics. CAPE statistics were inflated at a level in between that of the main effects and the interaction effects. The overall kinship matrix overcorrected the inflation of main effect statistics relative to the reduced kinship matrix. The two types of kinship matrices had similar effects on the interaction statistics and CAPE statistics, although the overall kinship matrix trended toward a more severe correction. In conclusion, we recommend using an LMM kinship correction for both main effects and genetic interactions and further recommend that the kinship matrix be calculated from a reduced set of markers in which the chromosomes being tested are omitted from the calculation. This is particularly important in populations with substantial population structure, such as recombinant inbred lines in which genomic replicates are used.
Spermiogenesis Initiation in Caenorhabditis elegans Involves a Casein Kinase 1 Encoded by the spe-6 Gene
Authors: Muhlrad Paul J , Ward Samuel 
Published: April 2021

Abstract
Immature spermatids from Caenorhabditis elegans are stimulated by an external activation signal to reorganize their membranes and cytoskeleton to form crawling spermatozoa. This rapid maturation, termed spermiogenesis, occurs without any new gene expression. To better understand this signal transduction pathway, we isolated suppressors of a mutation in the spe-27 gene, which is part of the pathway. The suppressors bypass the requirement for spe-27, as well as three other genes that act in this pathway, spe-8, spe-12, and spe-29. Eighteen of the suppressor mutations are new alleles of spe-6, a previously identified gene required for an early stage of spermatogenesis. The original spe-6 mutations are loss-of-function alleles that prevent major sperm protein (MSP) assembly in the fibrous bodies of spermatocytes and arrest development in meiosis. We have isolated the spe-6 gene and find that it encodes a predicted protein-serine/threonine kinase in the casein kinase 1 family. The suppressor mutations appear to be reduction-of-function alleles. We propose a model whereby SPE-6, in addition to its early role in spermatocyte development, inhibits spermiogenesis until the activation signal is received. The activation signal is transduced through SPE-8, SPE-12, SPE-27, and SPE-29 to relieve SPE-6 repression, thus triggering the formation of crawling spermatozoa.
Drosophila melanogaster Importin α1 and α3 Can Replace Importin α2 During Spermatogenesis but Not Oogenesis
Authors: Mason D Adam , Fleming Robert J , Goldfarb David S 
Published: April 2021

Abstract
Importin α’s mediate the nuclear transport of many classical nuclear localization signal (cNLS)-containing proteins. Multicellular animals contain multiple importin α genes, most of which fall into three conventional phylogenetic clades, here designated α1, α2, and α3. Using degenerate PCR we cloned Drosophila melanogaster importin α1, α2, and α3 genes, demonstrating that the complete conventional importin α gene family arose prior to the split between invertebrates and vertebrates. We have begun to analyze the genetic interactions among conventional importin α genes by studying their capacity to rescue the male and female sterility of importin α2 null flies. The sterility of α2 null males was rescued to similar extents by importin α1, α2, and α3 transgenes, suggesting that all three conventional importin α’s are capable of performing the important role of importin α2 during spermatogenesis. In contrast, sterility of α2 null females was rescued only by importin α2 transgenes, suggesting that it plays a paralog-specific role in oogenesis. Female infertility was also rescued by a mutant importin α2 transgene lacking a site that is normally phosphorylated in ovaries. These rescue experiments suggest that male and female gametogenesis have distinct requirements for importin α2.
Genetic Control of Cuticle Formation During Embryonic Development ofDrosophila melanogaster
Authors: Ostrowski Stephen , Dierick Herman A , Bejsovec Amy 
Published: April 2021

AbstractThe embryonic cuticle of Drosophila melanogaster is deposited by the epidermal epithelium during stage 16 of development. This tough, waterproof layer is essential for maintaining the structural integrity of the larval body. We have characterized mutations in a set of genes required for proper deposition and/or morphogenesis of the cuticle. Zygotic disruption of any one of these genes results in embryonic lethality. Mutant embryos are hyperactive within the eggshell, resulting in a high proportion reversed within the eggshell (the “retroactive” phenotype), and all show poor cuticle integrity when embryos are mechanically devitellinized. This last property results in embryonic cuticle preparations that appear grossly inflated compared to wild-type cuticles (the “blimp” phenotype). We find that one of these genes, krotzkopf verkehrt (kkv), encodes the Drosophila chitin synthase enzyme and that a closely linked gene, knickkopf (knk), encodes a novel protein that shows genetic interaction with the Drosophila E-cadherin, shotgun. We also demonstrate that two other known mutants, grainy head (grh) and retroactive (rtv), show the blimp phenotype when devitellinized, and we describe a new mutation, called zeppelin (zep), that shows the blimp phenotype but does not produce defects in the head cuticle as the other mutations do.
The bereft Gene, a Potential Target of the Neural Selector Gene cut, Contributes to Bristle Morphogenesis
Authors: Hardiman Kirsten E , Brewster Rachel , Khan Shaema M , Deo Monika , Bodmer Rolf 
Published: April 2021

Abstract
The neural selector gene cut, a homeobox transcription factor, is required for the specification of the correct identity of external (bristle-type) sensory organs in Drosophila. Targets of cut function, however, have not been described. Here, we study bereft (bft) mutants, which exhibit loss or malformation of a majority of the interommatidial bristles of the eye and cause defects in other external sensory organs. These mutants were generated by excising a P element located at chromosomal location 33AB, the enhancer trap line E8-2-46, indicating that a gene near the insertion site is responsible for this phenotype. Similar to the transcripts of the gene nearest to the insertion, reporter gene expression of E8-2-46 coincides with Cut in the support cells of external sensory organs, which secrete the bristle shaft and socket. Although bft transcripts do not obviously code for a protein product, its expression is abolished in bft deletion mutants, and the integrity of the bft locus is required for (interommatidial) bristle morphogenesis. This suggests that disruption of the bft gene is the cause of the observed bristle phenotype. We also sought to determine what factors regulate the expression of bft and the enhancer trap line. The correct specification of individual external sensory organ cells involves not only cut, but also the lineage genes numb and tramtrack. We demonstrate that mutations of these three genes affect the expression levels at the bft locus. Furthermore, cut overexpression is sufficient to induce ectopic bft expression in the PNS and in nonneuronal epidermis. On the basis of these results, we propose that bft acts downstream of cut and tramtrack to implement correct bristle morphogenesis.
Larger Genetic Differences Within Africans Than Between Africans and Eurasians
Authors: Yu Ning , Chen Feng-Chi , Ota Satoshi , Jorde Lynn B , Pamilo Pekka , Patthy Laszlo , Ramsay Michele , Jenkins Trefor , Shyue Song-Kun , Li Wen-Hsiung 
Published: April 2021

Abstract
The worldwide pattern of single nucleotide polymorphism (SNP) variation is of great interest to human geneticists, population geneticists, and evolutionists, but remains incompletely understood. We studied the pattern in noncoding regions, because they are less affected by natural selection than are coding regions. Thus, it can reflect better the history of human evolution and can serve as a baseline for understanding the maintenance of SNPs in human populations. We sequenced 50 noncoding DNA segments each ∼500 bp long in 10 Africans, 10 Europeans, and 10 Asians. An analysis of the data suggests that the sampling scheme is adequate for our purpose. The average nucleotide diversity (π) for the 50 segments is only 0.061% ± 0.010% among Asians and 0.064% ± 0.011% among Europeans but almost twice as high (0.115% ± 0.016%) among Africans. The African diversity estimate is even higher than that between Africans and Eurasians (0.096% ± 0.012%). From available data for noncoding autosomal regions (total length = 47,038 bp) and X-linked regions (47,421 bp), we estimated the π-values for autosomal regions to be 0.105, 0.070, 0.069, and 0.097% for Africans, Asians, Europeans, and between Africans and Eurasians, and the corresponding values for X-linked regions to be 0.088, 0.042, 0.053, and 0.082%. Thus, Africans differ from one another slightly more than from Eurasians, and the genetic diversity in Eurasians is largely a subset of that in Africans, supporting the out of Africa model of human evolution. Clearly, one must specify the geographic origins of the individuals sampled when studying π or SNP density.
Sequence Variation and Haplotype Structure Surrounding the Flowering Time Locus FRI in Arabidopsis thaliana
Authors: Hagenblad Jenny , Nordborg Magnus 
Published: April 2021

Abstract
Linkage disequilibrium in highly selfing organisms is expected to extend well beyond the scale of individual genes. The pattern of polymorphism in such species must thus be studied over a larger scale. We sequenced 14 short (0.5-1 kb) fragments from a 400-kb region surrounding the flowering time locus FRI in a sample of 20 accessions of Arabidopsis thaliana. The distribution of allele frequencies, as quantified by Tajima’s D, varies considerably over the region and is incompatible with a standard neutral model. The region is characterized by extensive haplotype structure, with linkage disequilibrium decaying over 250 kb. In particular, recombination is evident within 35 kb of FRI in a haplotype associated with a functionally important allele. This suggests that A. thaliana may be highly suitable for linkage disequilibrium mapping.
A Molecular Cytogenetic Map of Sorghum Chromosome 1: Fluorescence in Situ Hybridization Analysis With Mapped Bacterial Artificial Chromosomes
Authors: Islam-Faridi M N , Childs K L , Klein P E , Hodnett G , Menz M A , Klein R R , Rooney W L , Mullet J E , Stelly D M , Price H J 
Published: April 2021

Abstract
We used structural genomic resources for Sorghum bicolor (L.) Moench to target and develop multiple molecular cytogenetic probes that would provide extensive coverage for a specific chromosome of sorghum. Bacterial artificial chromosome (BAC) clones containing molecular markers mapped across sorghum linkage group A were labeled as probes for fluorescence in situ hybridization (FISH). Signals from single-, dual-, and multiprobe BAC-FISH to spreads of mitotic chromosomes and pachytene bivalents were associated with the largest sorghum chromosome, which bears the nucleolus organizing region (NOR). The order of individual BAC-FISH loci along the chromosome was fully concordant to that of marker loci along the linkage map. In addition, the order of several tightly linked molecular markers was clarified by FISH analysis. The FISH results indicate that markers from the linkage map positions 0.0-81.8 cM reside in the short arm of chromosome 1 whereas markers from 81.8-242.9 cM are located in the long arm of chromosome 1. The centromere and NOR were located in a large heterochromatic region that spans ∼60% of chromosome 1. In contrast, this region represents only 0.7% of the total genetic map distance of this chromosome. Variation in recombination frequency among euchromatic chromosomal regions also was apparent. The integrated data underscore the value of cytological data, because minor errors and uncertainties in linkage maps can involve huge physical regions. The successful development of multiprobe FISH cocktails suggests that it is feasible to develop chromosome-specific “paints” from genomic resources rather than flow sorting or microdissection and that when applied to pachytene chromatin, such cocktails provide an especially powerful framework for mapping. Such a molecular cytogenetic infrastructure would be inherently cross-linked with other genomic tools and thereby establish a cytogenomics system with extensive utility in development and application of genomic resources, cloning, transgene localization, development of plant “chromonomics,” germplasm introgression, and marker-assisted breeding. In combination with previously reported work, the results indicate that a sorghum cytogenomics system would be partially applicable to other gramineous genera.
The Correlation Between Relatives on the Supposition of Genomic Imprinting
Authors: Spencer Hamish G 
Published: April 2021

Abstract
Standard genetic analyses assume that reciprocal heterozygotes are, on average, phenotypically identical. If a locus is subject to genomic imprinting, however, this assumption does not hold. We incorporate imprinting into the standard quantitative-genetic model for two alleles at a single locus, deriving expressions for the additive and dominance components of genetic variance, as well as measures of resemblance among relatives. We show that, in contrast to the case with Mendelian expression, the additive and dominance deviations are correlated. In principle, this correlation allows imprinting to be detected solely on the basis of different measures of familial resemblances, but in practice, the standard error of the estimate is likely to be too large for a test to have much statistical power. The effects of genomic imprinting will need to be incorporated into quantitative-genetic models of many traits, for example, those concerned with mammalian birthweight.
Analysis of Multilocus Zygotic Associations
Authors: Yang Rong-Cai 
Published: April 2021

AbstractWhile nonrandom associations between zygotes at different loci (zygotic associations) frequently occur in Hardy-Weinberg disequilibrium populations, statistical analysis of such associations has received little attention. In this article, we describe the joint distributions of zygotes at multiple loci, which are completely characterized by heterozygosities at individual loci and various multilocus zygotic associations. These zygotic associations are defined in the same fashion as the usual multilocus linkage (gametic) disequilibria on the basis of gametic and allelic frequencies. The estimation and test procedures are described with details being given for three loci. The sampling properties of the estimates are examined through Monte Carlo simulation. The estimates of three-locus associations are not free of bias due to the presence of two-locus associations and vice versa. The power of detecting the zygotic associations is small unless different loci are strongly associated and/or sample sizes are large (&gt;100). The analysis of zygotic associations not only offers an effective means of packaging numerous genic disequilibria required for a complete characterization of multilocus structure, but also provides opportunities for making inference about evolutionary and demographic processes through a comparative assessment of zygotic association vs. gametic disequilibrium for the same set of loci in nonequilibrium populations.