bluuebunny/crossref_metadata_2025_split huggingface dataset:
The pan-genome of Saccharomyces cerevisiae
Authors: Li Gang , Ji Boyang , Nielsen Jens 
Published: October 2019

ABSTRACT
Understanding genotype–phenotype relationship is fundamental in biology. With the benefit from next-generation sequencing and high-throughput phenotyping methodologies, there have been generated much genome and phenome data for Saccharomyces cerevisiae. This makes it an excellent model system to understand the genotype–phenotype relationship. In this paper, we presented the reconstruction and application of the yeast pan-genome in resolving genotype–phenotype relationship by a machine learning-assisted approach.
Complete Genome Sequence of the Biocontrol Agent Bacillus velezensis UFLA258 and Its Comparison with Related Species: Diversity within the Commons
Authors: Silva Fabíola de Jesus , Ferreira Larissa Carvalho , Campos Vicente Paulo , Cruz-Magalhães Valter , Barros Aline Ferreira , Andrade Jackeline Pereira , Roberts Daniel P , de Souza Jorge Teodoro 
Published: October 2019

Abstract
In this study, the full genome sequence of Bacillus velezensis strain UFLA258, a biological control agent of plant pathogens was obtained, assembled, and annotated. With a comparative genomics approach, in silico analyses of all complete genomes of B. velezensis and closely related species available in the database were performed. The genome of B. velezensis UFLA258 consisted of a single circular chromosome of 3.95 Mb in length, with a mean GC content of 46.69%. It contained 3,949 genes encoding proteins and 27 RNA genes. Analyses based on Average Nucleotide Identity and Digital DNA–DNA Hybridization and a phylogeny with complete sequences of the rpoB gene confirmed that 19 strains deposited in the database as Bacillus amyloliquefaciens were in fact B. velezensis. In total, 115 genomes were analyzed and taxonomically classified as follows: 105 were B. velezensis, 9 were B. amyloliquefaciens, and 1 was Bacillus siamensis. Although these species are phylogenetically close, the combined analyses of several genomic characteristics, such as the presence of biosynthetic genes encoding secondary metabolites, CRISPr/Cas arrays, Average Nucleotide Identity and Digital DNA–DNA Hybridization, and other information on the strains, including isolation source, allowed their unequivocal classification. This genomic analysis expands our knowledge about the closely related species, B. velezensis, B. amyloliquefaciens, and B. siamensis, with emphasis on their taxonomical status.
Resolving Phylogenetic Relationships within Passeriformes Based on Mitochondrial Genes and Inferring the Evolution of Their Mitogenomes in Terms of Duplications
Authors: Mackiewicz Paweł , Urantówka Adam Dawid , Kroczak Aleksandra , Mackiewicz Dorota 
Published: October 2019

AbstractMitochondrial genes are placed on one molecule, which implies that they should carry consistent phylogenetic information. Following this advantage, we present a well-supported phylogeny based on mitochondrial genomes from almost 300 representatives of Passeriformes, the most numerous and differentiated Aves order. The analyses resolved the phylogenetic position of paraphyletic Basal and Transitional Oscines. Passerida occurred divided into two groups, one containing Paroidea and Sylvioidea, whereas the other, Passeroidea and Muscicapoidea. Analyses of mitogenomes showed four types of rearrangements including a duplicated control region (CR) with adjacent genes. Mapping the presence and absence of duplications onto the phylogenetic tree revealed that the duplication was the ancestral state for passerines and was maintained in early diverged lineages. Next, the duplication could be lost and occurred independently at least four times according to the most parsimonious scenario. In some lineages, two CR copies have been inherited from an ancient duplication and highly diverged, whereas in others, the second copy became similar to the first one due to concerted evolution. The second CR copies accumulated over twice as many substitutions as the first ones. However, the second CRs were not completely eliminated and were retained for a long time, which suggests that both regions can fulfill an important role in mitogenomes. Phylogenetic analyses based on CR sequences subjected to the complex evolution can produce tree topologies inconsistent with real evolutionary relationships between species. Passerines with two CRs showed a higher metabolic rate in relation to their body mass.
Quantitative and Qualitative Role of Antagonistic Heterogeneity in Genetics of Blood Lipids
Authors: Kulminski Alexander M , Loika Yury , Nazarian Alireza , Culminskaya Irina 
Published: October 2019

Abstract
Prevailing strategies in genome-wide association studies (GWAS) mostly rely on principles of medical genetics emphasizing one gene, one function, one phenotype concept. Here, we performed GWAS of blood lipids leveraging a new systemic concept emphasizing complexity of genetic predisposition to such phenotypes. We focused on total cholesterol, low- and high-density lipoprotein cholesterols, and triglycerides available for 29,902 individuals of European ancestry from seven independent studies, men and women combined. To implement the new concept, we leveraged the inherent heterogeneity in genetic predisposition to such complex phenotypes and emphasized a new counter intuitive phenomenon of antagonistic genetic heterogeneity, which is characterized by misalignment of the directions of genetic effects and the phenotype correlation. This analysis identified 37 loci associated with blood lipids but only one locus, FBXO33, was not reported in previous top GWAS. We, however, found strong effect of antagonistic heterogeneity that leaded to profound (quantitative and qualitative) changes in the associations with blood lipids in most, 25 of 37 or 68%, loci. These changes suggested new roles for some genes, which functions were considered as well established such as GCKR, SIK3 (APOA1 locus), LIPC, LIPG, among the others. The antagonistic heterogeneity highlighted a new class of genetic associations emphasizing beneficial and adverse trade-offs in predisposition to lipids. Our results argue that rigorous analyses dissecting heterogeneity in genetic predisposition to complex traits such as lipids beyond those implemented in current GWAS are required to facilitate translation of genetic discoveries into health care.
ADAMTS9 and ADAMTS20 are differentially affected by loss of B3GLCT in mouse model of Peters plus syndrome
Authors: Holdener Bernadette C , Percival Christopher J , Grady Richard C , Cameron Daniel C , Berardinelli Steven J , Zhang Ao , Neupane Sanjiv , Takeuchi Megumi , Jimenez-Vega Javier C , Uddin Sardar M Z , Komatsu David E , Honkanen Robert , Dubail Johanne , Apte Suneel S , Sato Takashi , Narimatsu Hisashi , McClain Steve A , Haltiwanger Robert S 
Published: October 2019

Abstract
Peters plus syndrome (MIM #261540 PTRPLS), characterized by defects in eye development, prominent forehead, hypertelorism, short stature and brachydactyly, is caused by mutations in the β3-glucosyltransferase (B3GLCT) gene. Protein O-fucosyltransferase 2 (POFUT2) and B3GLCT work sequentially to add an O-linked glucose β1-3fucose disaccharide to properly folded thrombospondin type 1 repeats (TSRs). Forty-nine proteins are predicted to be modified by POFUT2, and nearly half are members of the ADAMTS superfamily. Previous studies suggested that O-linked fucose is essential for folding and secretion of POFUT2-modified proteins and that B3GLCT-mediated extension to the disaccharide is essential for only a subset of targets. To test this hypothesis and gain insight into the origin of PTRPLS developmental defects, we developed and characterized two mouse B3glct knockout alleles. Using these models, we tested the role of B3GLCT in enabling function of ADAMTS9 and ADAMTS20, two highly conserved targets whose functions are well characterized in mouse development. The mouse B3glct mutants developed craniofacial and skeletal abnormalities comparable to PTRPLS. In addition, we observed highly penetrant hydrocephalus, white spotting and soft tissue syndactyly. We provide strong genetic and biochemical evidence that hydrocephalus and white spotting in B3glct mutants resulted from loss of ADAMTS20, eye abnormalities from partial reduction of ADAMTS9 and cleft palate from loss of ADAMTS20 and partially reduced ADAMTS9 function. Combined, these results provide compelling evidence that ADAMTS9 and ADAMTS20 were differentially sensitive to B3GLCT inactivation and suggest that the developmental defects in PTRPLS result from disruption of a subset of highly sensitive POFUT2/B3GLCT targets such as ADAMTS20.
Inherited variants at 3q13.33 and 3p24.1 are associated with risk of diffuse large B-cell lymphoma and implicate immune pathways
Authors: Kleinstern Geffen , Yan Huihuang , Hildebrandt Michelle A T , Vijai Joseph , Berndt Sonja I , Ghesquières Hervé , McKay James , Wang Sophia S , Nieters Alexandra , Ye Yuanqing , Monnereau Alain , Brooks-Wilson Angela R , Lan Qing , Melbye Mads , Jackson Rebecca D , Teras Lauren R , Purdue Mark P , Vajdic Claire M , Vermeulen Roel C H , Giles Graham G , Cocco Pier Luigi , Birmann Brenda M , Kraft Peter , Albanes Demetrius , Zeleniuch-Jacquotte Anne , Crouch Simon , Zhang Yawei , Sarangi Vivekananda , Asmann Yan , Offit Kenneth , Salles Gilles , Wu Xifeng , Smedby Karin E , Skibola Christine F , Slager Susan L , Rothman Nathaniel , Chanock Stephen J , Cerhan James R 
Published: October 2019

Abstract
We previously identified five single nucleotide polymorphisms (SNPs) at four susceptibility loci for diffuse large B-cell lymphoma (DLBCL) in individuals of European ancestry through a large genome-wide association study (GWAS). To further elucidate genetic susceptibility to DLBCL, we sought to validate two loci at 3q13.33 and 3p24.1 that were suggestive in the original GWAS with additional genotyping. In the meta-analysis (5662 cases and 9237 controls) of the four original GWAS discovery scans and three replication studies, the 3q13.33 locus (rs9831894; minor allele frequency [MAF] = 0.40) was associated with DLBCL risk [odds ratio (OR) = 0.83, P = 3.62 × 10−13]. rs9831894 is in linkage disequilibrium (LD) with additional variants that are part of a super-enhancer that physically interacts with promoters of CD86 and ILDR1. In the meta-analysis (5510 cases and 12 817 controls) of the four GWAS discovery scans and four replication studies, the 3p24.1 locus (rs6773363; MAF = 0.45) was also associated with DLBCL risk (OR = 1.20, P = 2.31 × 10−12). This SNP is 29 426-bp upstream of the nearest gene EOMES and in LD with additional SNPs that are part of a highly lineage-specific and tumor-acquired super-enhancer that shows long-range interaction with AZI2 promoter. These loci provide additional evidence for the role of immune function in the etiology of DLBCL, the most common lymphoma subtype.
PAICS deficiency, a new defect of de novo purine synthesis resulting in multiple congenital anomalies and fatal outcome
Authors: Pelet Anna , Skopova Vaclava , Steuerwald Ulrike , Baresova Veronika , Zarhrate Mohammed , Plaza Jean-Marc , Hnizda Ales , Krijt Matyas , Souckova Olga , Wibrand Flemming , Andorsdóttir Guðrið , Joensen Fróði , Sedlak David , Bleyer Anthony J , Kmoch Stanislav , Lyonnet Stanislas , Zikanova Marie 
Published: October 2019

AbstractWe report for the first time an autosomal recessive inborn error of de novo purine synthesis (DNPS)—PAICS deficiency. We investigated two siblings from the Faroe Islands born with multiple malformations resulting in early neonatal death. Genetic analysis of affected individuals revealed a homozygous missense mutation in PAICS (c.158A&gt;G; p.Lys53Arg) that affects the structure of the catalytic site of the bifunctional enzyme phosphoribosylaminoimidazole carboxylase (AIRC, EC 4.1.1.21)/phosphoribosylaminoimidazole succinocarboxamide synthetase (SAICARS, EC 6.3.2.6) (PAICS). The mutation reduced the catalytic activity of PAICS in heterozygous carrier and patient skin fibroblasts to approximately 50 and 10% of control levels, respectively. The catalytic activity of the corresponding recombinant enzyme protein carrying the mutation p.Lys53Arg expressed and purified from E. coli was reduced to approximately 25% of the wild-type enzyme. Similar to other two known DNPS defects—adenylosuccinate lyase deficiency and AICA-ribosiduria—the PAICS mutation prevented purinosome formation in the patient’s skin fibroblasts, and this phenotype was corrected by transfection with the wild-type but not the mutated PAICS. Although aminoimidazole ribotide (AIR) and aminoimidazole riboside (AIr), the enzyme substrates that are predicted to accumulate in PAICS deficiency, were not detected in patient’s fibroblasts, the cytotoxic effect of AIr on various cell lines was demonstrated. PAICS deficiency is a newly described disease that enhances our understanding of the DNPS pathway and should be considered in the diagnosis of families with recurrent spontaneous abortion or early neonatal death.
Bone morphogenetic protein 1 cleaves the linker region between ligand-binding repeats 4 and 5 of the LDL receptor and makes the LDL receptor non-functional
Authors: Strøm Thea Bismo , Bjune Katrine , Leren Trond P 
Published: October 2019

AbstractThe cell-surface low-density lipoprotein receptor (LDLR) internalizes low-density lipoprotein (LDL) by receptor-mediated endocytosis and plays a key role in the regulation of plasma cholesterol levels. The ligand-binding domain of the LDLR contains seven ligand-binding repeats of approximately 40 residues each. Between ligand-binding repeats 4 and 5, there is a 10-residue linker region that is subject to enzymatic cleavage. The cleaved LDLR is unable to bind LDL. In this study, we have screened a series of enzyme inhibitors in order to identify the enzyme that cleaves the linker region. These studies have identified bone morphogenetic protein 1 (BMP1) as being the cleavage enzyme. This conclusion is based upon the use of the specific BMP1 inhibitor UK 383367, silencing of the BMP1 gene by the use of siRNA or CRISPR/Cas9 technology and overexpression of wild-type BMP1 or the loss-of-function mutant E214A-BMP1. We have also shown that the propeptide of BMP1 has to be cleaved at RSRR120↓ by furin-like proprotein convertases for BMP1 to have an activity towards the LDLR. Targeting BMP1 could represent a novel strategy to increase the number of functioning LDLRs in order to lower plasma LDL cholesterol levels. However, a concern by using BMP1 inhibitors as cholesterol-lowering drugs could be the risk of side effects based on the important role of BMP1 in collagen assembly.
Disentangling the influence of fishing, demography, and environment on population dynamics of Iberian Peninsula waters fish stocks
Authors: Quinzán M , Castro J , Massutí E , Rueda L , Hidalgo M 
Published: October 2019

AbstractOverexploitation and climate change are increasingly causing unanticipated changes in marine ecosystems such as higher variability in fish recruitment or shifts in species dominance and distribution that alter the productivity of fish stocks. This study analyses how external and internal drivers influence population dynamics of hake (Merluccius merluccius), white anglerfish (Lophius piscatorius), four-spot megrim (Lepidorhombus boscii), and horse mackerel (Trachurus trachurus) of Iberian Peninsula waters of the Northeast Atlantic across different spatiotemporal scales. Available spawning stock biomass and recruitment have been used as biological data, whereas fishing mortality, demographic data as well as climatic and oceanographic data have been used as drivers. The obtained results indicate that population dynamics of these species are mainly driven by oceanographic variability at regional scale along with fishing pressure and demographic factors, while the impact of large-scale climate indices was minimal. The identified variables represent relevant oceanographic regional processes candidate to be potentially integrated into the stock assessment models and management procedures of these important fishery resources.
Review of Heat and Mass Transfer Enhancement Techniques and Current Advancement for Adsorption Heating/Cooling Systems
Authors: Mat Wajid Norhayati , Mompuouo Blaise , Omer Siddig , Riffat Saffa B 
Published: October 2019

Abstract
Adsorption heating/cooling became an alternative to vapour compression system due to low ozone depletion potential (ODP) and global warming potential (GWP). However, more investigation is required due their low efficiency when compared to conventional heating/cooling systems. This review emphasizes on the mathematical modelling simplification and heat transfer enhancement method that applied by many researchers to improve the performance of adsorption heating and cooling technologies. Various techniques investigated by many researchers on solving low thermal conductivity and the different methods for enhancing heat and mass transfer in the adsorbed bed/pipe also discussed. Common techniques used to enhance heat and mass transfer in the adsorbed bed/pipe include the fin type adsorbent tube/ heat exchanger, amalgamated adsorbent bed with a metal foam, consolidated adsorbent, adsorbent coating and adsorbent with multi cooling tubes. Other than that, recent advancements in adsorption cooling/heating systems also discussed in this review.
The Non-selfadjoint Approach to the Hao–Ng Isomorphism
Authors: Katsoulis Elias G , Ramsey Christopher 
Published: October 2019

Abstract
In an earlier work, the authors proposed a non-selfadjoint approach to the Hao–Ng isomorphism problem for the full crossed product, depending on the validity of two conjectures stated in the broader context of crossed products for operator algebras. By work of Harris and Kim, we now know that these conjectures in the generality stated may not always be valid. In this paper we show that in the context of hyperrigid tensor algebras of $\mathrm{C}^*$-correspondences, each one of these conjectures is equivalent to the Hao–Ng problem. This is accomplished by studying the representation theory of non-selfadjoint crossed products of C$^*$-correspondence dynamical systems; in particular we show that there is an appropriate dilation theory. A large class of tensor algebras of $\mathrm{C}^*$-correspondences, including all regular ones, are shown to be hyperrigid. Using Hamana’s injective envelope theory, we extend earlier results from the discrete group case to arbitrary locally compact groups; this includes a resolution of the Hao–Ng isomorphism for the reduced crossed product and all hyperrigid $\mathrm{C}^*$-correspondences. A culmination of these results is the resolution of the Hao–Ng isomorphism problem for the full crossed product and all row-finite graph correspondences; this extends a recent result of Bedos, Kaliszewski, Quigg, and Spielberg.
Measure Rigidity for Horospherical Subgroups of Groups Acting on Trees
Authors: Ciobotaru Corina , Finkelshtein Vladimir , Sert Cagri 
Published: October 2019

Abstract
We prove analogues of some of the classical results in homogeneous dynamics in nonlinear setting. Let $G$ be a closed subgroup of the group of automorphisms of a biregular tree and $\Gamma \leq G$ a discrete subgroup. For a large class of groups $G$, we give a classification of the probability measures on $G/\Gamma $ invariant under horospherical subgroups. When $\Gamma $ is a cocompact lattice, we show the unique ergodicity of the horospherical action. We prove Hedlund’s theorem for geometrically finite quotients. Finally, we show equidistribution of large compact orbits.
Antibiotic use in pregnancy: knowledge, attitudes and practices among pregnant women in Cape Town, South Africa
Authors: Bulabula Andre N H , Dramowski Angela , Mehtar Shaheen 
Published: October 2019

Abstract

Objectives
To establish the knowledge, attitudes and practices (KAP) regarding antibiotic use and self-medication among pregnant women.

Methods
We conducted a KAP survey of 301 pregnant women hospitalized at a tertiary hospital obstetric service in Cape Town, South Africa in November and December 2017, using an interviewer-administered 12 item questionnaire. We stratified analysis of attitudes and practices by participants’ mean knowledge score (K-score) group (<6 versus ≥6 out of 7 questions). Multivariate models were built to identify independent predictors of antibiotic self-medication and K-score.

Results
The mean age of pregnant women was 29 (SD 6.1) years, 44/247 (17.8%) were nulliparous, 69/247 (27.9%) were HIV-infected, 228/247 (92.3%) had completed secondary school and 78/247 (31.6%) reported a monthly household income in the lowest category of ≤50–100 US dollars (USD). The mean K-score was 6.1 (SD 1.02) out of 7 questions. Sixteen percent of the cohort reported antibiotic self-medication, with higher rates among pregnant women with K-score <6 [18/48 (37.5%) versus 32/253 (12.6%); P < 0.001]. The monthly household income category of >500 USD (the highest category) was the only predictor of antibiotic self-medication behaviour [adjusted OR = 6.4 (95% CI 1.2–35.2), P = 0.03].

Conclusions
Higher antibiotic knowledge scores are associated with lower rates of antibiotic self-medication, whereas higher household income is correlated with increasing self-medication behaviours. Education of pregnant women regarding the potential dangers of antibiotic self-medication and stricter enforcement of existing South African antibiotic prescribing and dispensing regulations are needed.
Risk of Cold-Hardy Apple Cultivars for Injury From the Brown Marmorated Stink Bug (Hemiptera: Pentatomidae)
Authors: Shanovich Hailey N , Burkness Eric C , Koch Robert L 
Published: October 2019

Abstract
An invasive species, the brown marmorated stink bug, Halyomorpha halys (Stål) (Hemiptera: Pentatomidae), has emerged as a serious pest of orchard crops in the United States with the highest economic losses to date in Mid-Atlantic apple, Malus domestica Borkh. (Rosales: Rosaceae). If populations continue to grow and spread in the Midwest, H. halys has the potential to become a significant apple pest in the region. The purpose of this study was to assess the risk for injury from H. halys to several popular cold-hardy apple cultivars (Haralson, Honeycrisp, and Zestar!) grown in the Midwestern United States utilizing both field no-choice tests and laboratory choice tests at multiple timings. Results from the field no-choice tests revealed a greater risk for Honeycrisp from H. halys injury compared with Zestar! in mid-August. Results from the laboratory choice tests revealed a greater risk for injury by H. halys for Honeycrisp compared with Zestar! at all timings tested and a greater risk for Haralson compared with Honeycrisp at a later timing. These results echo previous findings in that relative maturity of the fruit seems to play a role in determining the risk of an apple cultivar to H. halys injury. These results also serve as the first assessment of the potential impact of H. halys on different cold-hardy apple cultivars, which will help guide growers in cultivar selection and identifying which apple cultivars should be prioritized for scouting and management efforts.