bluuebunny/crossref_metadata_2025_split huggingface dataset:
P-Element Insertion Alleles of Essential Genes on the Third Chromosome of Drosophila melanogaster Correlation of Physical and Cytogenetic Maps in Chromosomal Region 86E-87F
Authors: Deák Peter , Omar Mahmoud M , Saunders Robert D C , Pál Margit , Komonyi Orbán , Szidonya János , Maróy Péter , Zhang Yong , Ashburner Michael , Benos Panayiotis , Savakis Charalambos , Siden-Kiamos Inga , Louis Christos , Bolshakov Viacheslav N , Kafatos Fotis C , Madueno Encarnación , Modolell Juan , Glover David M 
Published: January 2021

Abstract
We have established a collection of 2460 lethal or semi-lethal mutant lines using a procedure thought to insert single P elements into vital genes on the third chromosome of Drosophila melanogaster. More than 1200 randomly selected lines were examined by in situ hybridization and 90% found to contain single insertions at sites that mark 89% of all lettered subdivisions of the Bridges' map. A set of chromosomal deficiencies that collectively uncover ~25% of the euchromatin of chromosome 3 reveal lethal mutations in 468 lines corresponding to 145 complementation groups. We undertook a detailed analysis of the cytogenetic interval 86E-87F and identified 87 P-element-induced mutations falling into 38 complementation groups, 16 of which correspond to previously known genes. Twenty-one of these 38 complementation groups have at least one allele that has a P-element insertion at a position consistent with the cytogenetics of the locus. We have rescued P elements and flanking chromosomal sequences from the 86E-87F region in 35 lines with either lethal or genetically silent P insertions, and used these as probes to identify cosmids and P1 clones from the Drosophila genome projects. This has tied together the physical and genetic maps and has linked 44 previously identified cosmid contigs into seven “super-contigs” that span the interval. STS data for sequences flanking one side of the P-element insertions in 49 lines has identified insertions in the αγ element at 87C, two known transposable elements, and the open reading frames of seven putative single copy genes. These correspond to five known genes in this interval, and two genes identified by the homology of their predicted products to known proteins from other organisms.
Haldane's Rule and X-chromosome Size in Drosophila
Authors: Turelli Michael , Begun David J 
Published: January 2021

Abstract
The “dominance theory” of Haldane's rule postulates that hybrids of the heterogametic sex are more likely to be inviable or sterile than the homogametic sex because some of the epistatic incompatibilities contributing to postzygotic isolation behave as X-linked partial recessives. When this is true, pairs of taxa with relatively large X chromosomes should require less divergence time, on average, to produce Haldane's rule than pairs with smaller Xs. Similarly, if the dominance theory is correct and if the X chromosome evolves at a similar rate to the autosomes, the size of the X should not influence the rate at which homogametic hybrids become inviable or sterile. We use Drosophila data to examine both of these predictions. As expected under the dominance theory, pairs of taxa with large X chromosomes (~40% of the nuclear genome) show Haldane's rule for sterility at significantly smaller genetic distances than pairs with smaller X chromosomes (~20% of the genome). As also predicted, the genetic distances between taxa that exhibit female inviability/sterility show no differences between “large X” vs. “small X” pairs. We present some simple mathematical models to relate these data to the dominance theory and alternative hypotheses involving faster evolution of the X vs. the autosomes and/or faster evolution of incompatibilities that produce male-specific vs. female-specific sterility. Although the data agree qualitatively with the predictions of the dominance theory, they depart significantly from the quantitative predictions of simple models of the dominance theory and the other hypotheses considered. These departures probably stem from the many simplifying assumptions needed to tractably model epistatic incompatibilities and to analyze heterogeneous data from many taxa.
The Autosomal Chorion Locus of the Medfly Ceratitis capitata. I. Conserved Synteny, Amplification and Tissue Specificity but Sequence Divergence and Altered Temporal Regulation
Authors: Vlachou Dina , Konsolalti Mary , Tolias Peter P , Kafatos Fotis C , Komitopoulou Katia 
Published: January 2021

Abstract
We report the isolation, full sequence characterization, amplification and expression properties of medfly chorion genes corresponding to the autosomal chorion locus of Drosophila. These genes are found adjacent to the paramyosin gene and are organized in the same order and tandem orientation as their Drosophila homologues, although they are spaced further apart. They show substantial sequence divergence from their Drosophila homologues, including novel peptide repeats and a new spacing of the tyrosines, which are known to be cross-linked in Dipteran chorion. The genes are amplified and expressed during oogenesis, as in Drosophila. Three of them are expressed in the same relative temporal order as in Drosophila but the fourth gene, the homologue of s15, shows a clear shift to an earlier expression period. This is the first known instance of changed temporal regulation in dipteran chorion genes.
The Sampling Distribution of Disease-Associated Alleles
Authors: Slatkin Montgomery , Rannala Bruce 
Published: January 2021

Abstract
A theory is developed that provides the sampling distribution of low frequency alleles at a single locus under the assumption that each allele is the result of a unique mutation. The numbers of copies of each allele is assumed to follow a linear birth-death process with sampling. If the population is of constant size, standard results from theory of birth-death processes show that the distribution of numbers of copies of each allele is logarithmic and that the joint distribution of numbers of copies of k alleles found in a sample of size n follows the Ewens sampling distribution. If the population from which the sample was obtained was increasing in size, if there are different selective classes of alleles, or if there are differences in penetrance among alleles, the Ewens distribution no longer applies. Likelihood functions for a given set of observations are obtained under different alternative hypotheses. These results are applied to published data from the BRCA1 locus (associated with early onset breast cancer) and the factor VIII locus (associated with hemophilia A) in humans. In both cases, the sampling distribution of alleles allows rejection of the null hypothesis, but relatively small deviations from the null model can account for the data. In particular, roughly the same population growth rate appears consistent with both data sets.
Nucleotide Sequence Evolution at the κ-Casein Locus: Evidence for Positive Selection Within the Family Bovidae
Authors: Ward Todd J , Honeycutt Rodney L , Derr James N 
Published: January 2021

Abstract
κ-Casein is a mammalian milk protein involved in a number of important physiological processes. In the gut, the ingested protein is split into an insoluble peptide (para κ-casein) and a soluble hydrophilic glycopeptide (caseinomacropeptide). Caseinomacropeptide is responsible for increased efficiency of digestion, prevention of neonate hypersensitivity to ingested proteins, and inhibition of gastric pathogens. Variation within this peptide has significant effects associated with important traits such as milk production. The nucleotide sequences for regions of κ-casein exon and intron four were determined for representatives of the artiodactyl family Bovidae. The pattern of nucleotide substitution in κ-casein sequences for distantly related bovid taxa demonstrates that positive selection has accelerated their divergence at the amino acid sequence level. This selection has differentially influenced the molecular evolution of the two Kcasein split peptides and is focused within a 34-codon region of caseinomacropeptide.
The Self-Regulation of Healthy Aging: Goal-Related Processes in Three Domains
Authors: Hennecke Marie , Brandstätter Veronika , Oettingen Gabriele 
Published: January 2021

Abstract
As people age, they experience typical age-graded challenges and opportunities, for example, their own retirement, changes in their social networks, or a decline in health condition. The extent to which people successfully process, respond to, and act on these challenges and opportunities is highly important for their health, at the core of which the WHO sees the possibility of “doing what one has reason to value.” In this article, we posit that individuals can play an active role in determining whether they can, in response to these age-graded influences, continue doing what they have reason to value, and that they can do so by deploying the self-regulatory processes of goal setting (including reengagement in new goals after disengaging from a previous goal), goal pursuit, and goal disengagement. We discuss the role of these self-regulatory processes in three important goal domains: work/retirement, interpersonal relationships, and health. Across these domains, we consider typical challenges and opportunities including the increased availability of daily time in old age, the long past that lies behind older adults, and their limited future time perspective. Finally, we derive open research questions that may be studied to better understand how the very old may self-regulate their response to age-graded influences.
Middle–Late Permian magnetostratigraphy and the onset of the Illawarra Reversals in the northeastern Parana Basin, South America
Authors: Aragão Marcela , Scardia Giancarlo 
Published: January 2021

SUMMARYRecent compilations of the Illawarra Reversals show remarkable differences in the onset age (265 Ma versus 269 Ma) and the magnetic polarity pattern, hampering the establishment of a reference geomagnetic timescale for the Middle–Late Permian. The Parana Basin hosts a 7-km-thick, discontinuous sedimentary succession spanning the Palaeozoic to the Mesozoic, including the Gondwana 1 supersequence which extends from Late Carboniferous to the Triassic or Jurassic. We provide the magnetostratigraphy of the middle and upper Permian part of this sequence of a ca. 300-m-long core, pertaining to the Passa Dois Group and the Piramboia Formation. Sample demagnetization of NRM revealed two magnetic overprints ascribed to the Brunhes chron and to the emplacement of Parana Large Igneous Province in the Early Cretaceous, respectively. Stable, dual polarity characteristic components (ChRM) were isolated at temperatures higher than 450 °C and interpreted as a primary detrital magnetic remanence (DRM), acquired during or soon after sediment deposition. Available U-Pb dating on volcanic zircons from the literature provided independent chronologic constraints for our magnetostratigraphy. A total of 8 reverse polarity intervals were identified, the lowermost of which (up to 110 m thick) correlates to the Kiaman Superchron. The overlying Illawarra is dominated by a reverse polarity magnetization with thin (4–5 m thick) normal polarity intervals. This pattern agrees with the Illawarra sequence from the Karoo Basin and other proposed timescales for the Permian. The onset of the Illawarra reversals is interpolated to ca. 270 Ma, close to the age of 269 Ma from the Karoo Basin. Combined magnetostratigraphy and geochronology yielded sediment accumulation rates of ca. 8 m Myr–1 for the Passa Dois Group in the northeastern (marginal) sector of the Parana Basin, indicating that Serra Alta and Teresina Formations span 279–274 Ma and 274–254 Ma, respectively.
The interaction between mantle plumes and lithosphere and its surface expressions: 3-D numerical modelling
Authors: Wang Yongming , Li Mingming 
Published: January 2021

SUMMARY
The rise of mantle plumes to the base of the lithosphere leads to observable surface expressions, which provide important information about the deep mantle structure. However, the process of plume–lithosphere interaction and its surface expressions remain not well understood. In this study, we perform 3-D spherical numerical simulations to investigate the relationship between surface observables induced by plume–lithosphere interaction (including dynamic topography, geoid anomaly and melt production rate) and the physical properties of plume and lithosphere (including plume size, plume excess temperature, plume viscosity, and lithosphere viscosity and thickness). We find that the plume-induced surface expressions have strong spatial and temporal variations. Before reaching the base of the lithosphere, the rise of a plume head in the deep mantle causes positive and rapid increase of dynamic topography and geoid anomaly at the surface but no melt production. The subsequent impinging of a plume head at the base of the lithosphere leads to further increase of dynamic topography and geoid anomaly and causes rapid increase of melt production. After reaching maximum values, these plume-induced observables become relatively stable and are more affected by the plume conduit. In addition, whereas the geoid anomaly and dynamic topography decrease from regions above the plume centre to regions above the plume edge, the melt production always concentrates at the centre part of the plume. We also find that the surface expressions have different sensitivities to plume and lithosphere properties. The dynamic topography significantly increases with the plume size, plume excess temperature and plume viscosity. The geoid anomaly also increases with the size and excess temperature of the plume but is less sensitive to plume viscosity. Compared to the influence of plume properties, the dynamic topography and geoid anomaly are less affected by lithosphere viscosity and thickness. The melt production significantly increases with plume size, plume excess temperature and plume viscosity, but decreases with lithosphere viscosity and thickness.
Double-difference seismic attenuation tomography method and its application to The Geysers geothermal field, California
Authors: Guo Hao , Thurber Clifford 
Published: January 2021

SUMMARY
Knowledge of attenuation structure is important for understanding subsurface material properties. We have developed a double-difference seismic attenuation (DDQ) tomography method for high-resolution imaging of 3-D attenuation structure. Our method includes two main elements, the inversion of event-pair differential ${t^*}$ ($d{t^*}$) data and 3-D attenuation tomography with the $d{t^*}$ data. We developed a new spectral ratio method that jointly inverts spectral ratio data from pairs of events observed at a common set of stations to determine the $d{t^*}$ data. The spectral ratio method cancels out instrument and site response terms, resulting in more accurate $d{t^*}$ data compared to absolute ${t^*}$ from traditional methods using individual spectra. Synthetic tests show that the inversion of $d{t^*}$ data using our spectral ratio method is robust to the choice of source model and a moderate degree of noise. We modified an existing velocity tomography code so that it can invert $d{t^*}$ data for 3-D attenuation structure. We applied the new method to The Geyser geothermal field, California, which has vapour-dominated reservoirs and a long history of water injection. A new Qp model at The Geysers is determined using P-wave data of earthquakes in 2011, using our updated earthquake locations and Vp model. By taking advantage of more accurate $d{t^*}$ data and the cancellation of model uncertainties along the common paths outside of the source region, the DDQ tomography method achieves higher resolution, especially in the earthquake source regions, compared to the standard tomography method using ${t^*}$ data. This is validated by both the real and synthetic data tests. Our Qp and Vp models show consistent variations in a normal temperature reservoir that can be explained by variations in fracturing, permeability and fluid saturation and/or steam pressure. A prominent low-Qp and Vp zone associated with very active seismicity is imaged within a high temperature reservoir at depths below 2 km. This anomalous zone is likely partially saturated with injected fluids.
Residual Malaria Transmission in Select Countries of Asia-Pacific Region: Old Wine in a New Barrel
Authors: Hii Jeffrey , Hustedt John , Bangs Michael J 
Published: January 2021

Abstract

Background
Despite substantial reductions in malaria burden and improvement in case management, malaria remains a major public health challenge in the Asia-Pacific region. Residual malaria transmission (RMT) is the fraction of total transmission that persists after achievement of full operational coverage with effective insecticide-treated bed nets (ITNs)/long-lasting insecticidal nets (LLINs) and/or indoor residual spray interventions. There is a critical need to standardize and share best practices for entomological, anthropological, and product development investigative protocols to meet the challenges of RMT and elimination goals.

Methods
A systematic review was conducted to describe when and where RMT is occurring, while specifically targeting ownership and usage of ITN/LLINs, indoor residual spray application, insecticide susceptibility of vectors, and human and vector biting behavior, with a focus on nighttime activities.

Results
Sixty-six publications from 1995 to present met the inclusion criteria for closer review. Associations between local vector control coverage and use with behaviors of human and mosquito vectors varied by locality and circumstance. Consequently, the magnitude of RMT is insufficiently studied and analyzed with sparse estimates of individual exposure in communities, insufficient or incomplete observations of ITN/LLIN use, and the local human population movement into and from high-risk areas.

Conclusions
This review identified significant gaps or deficiencies that require urgent attention, namely, developing standardized procedures and methods to estimate risk exposure beyond the peridomestic setting, analytical approaches to measure key human-vector interactions, and seasonal location-specific agricultural or forest use calendars, and establishing the collection of longitudinal human and vector data close in time and location.
Uropathogenic Escherichia coli Virulence Factor α-Hemolysin Reduces Histone Acetylation to Inhibit Expression of Proinflammatory Cytokine Genes
Authors: Zhang Zhengguo , Wang Ming , Zhang Yu , Zhang Yiming , Bartkuhn Marek , Markmann Melanie , Hossain Hamid , Chakraborty Trinad , Hake Sandra B , Jia Zhankui , Meinhardt Andreas , Bhushan Sudhanshu 
Published: January 2021

Abstract
Urinary tract infections are common and costly diseases affecting millions of people. Uropathogenic Escherichia coli (UPEC) is a primary cause of these infections and has developed multiple strategies to avoid the host immune response. Here, we dissected the molecular mechanisms underpinning UPEC inhibition of inflammatory cytokine in vitro and in vivo. We found that UPEC infection simulates nuclear factor-κB activation but does not result in transcription of cytokine genes. Instead, UPEC-mediated suppression of the metabolic enzyme ATP citrate lyase results in decreased acetyl-CoA levels, leading to reduced H3K9 histone acetylation in the promotor region of CXCL8. These effects were dependent on the UPEC virulence factor α-hemolysin and were reversed by exogenous acetate. In a murine cystitis model, prior acetate supplementation rapidly resolved UPEC-elicited immune responses and improved tissue recovery. Thus, upon infection, UPEC rearranges host cell metabolism to induce chromatin remodeling processes that subvert expression of host innate immune response genes.
Reporting antimicrobial susceptibilities and resistance phenotypes inStaphylococcusspp.: a nationwide proficiency study
Authors: Fernández-Cuenca Felipe , López-Hernández Inmaculada , Cercenado Emilia , Conejo Carmen , Tormo Nuria , Gimeno Concha , Pascual Alvaro 
Published: January 2021

AbstractObjectivesTo evaluate the proficiency of microbiology laboratories in Spain in antimicrobial susceptibility testing (AST) of Staphylococcus spp.Materials and methodsEight Staphylococcus spp. with different resistance mechanisms were selected: six Staphylococcus aureus (CC-01/mecA, CC-02/mecC, CC-03/BORSA, CC-04/MLSBi, CC-06/blaZ and CC-07/linezolid resistant, cfr); one Staphylococcus epidermidis (CC-05/linezolid resistant, 23S rRNA mutation); and one Staphylococcus capitis (CC-08/daptomycin non-susceptible). Fifty-one laboratories were asked to report: (i) AST system used; (ii) antimicrobial MICs; (iii) breakpoints used (CLSI or EUCAST); and (iv) clinical category. Minor, major and very major errors (mEs, MEs and VMEs, respectively) were determined.ResultsThe greatest MIC discrepancies found were: (i) by AST method: 19.4% (gradient diffusion); (ii) by antimicrobial agent: daptomycin (21.3%) and oxacillin (20.6%); and (iii) by isolate: CC-07/cfr (48.0%). The greatest error rates were: (i) by AST method: gradient diffusion (4.3% and 5.1% VMEs, using EUCAST and CLSI, respectively); (ii) by breakpoint: 3.8% EUCAST and 2.3% CLSI; (iii) by error type: mEs (0.8% EUCAST and 1.0% CLSI), MEs (1.8% EUCAST and 0.7% CLSI) and VMEs (1.2% EUCAST and 0.6% CLSI); (iii) by antimicrobial agent: VMEs (4.7% linezolid and 4.3% oxacillin using EUCAST); MEs (14.3% fosfomycin, 9.1% tobramycin and 5.7% gentamicin using EUCAST); and mEs (22.6% amikacin using EUCAST).ConclusionsClinical microbiology laboratories should improve their ability to determine the susceptibility of Staphylococcus spp. to some antimicrobial agents to avoid reporting false-susceptible or false-resistant results. The greatest discrepancies and errors were associated with gradient diffusion, EUCAST breakpoints and some antimicrobials (mEs for aminoglycosides; MEs for fosfomycin, aminoglycosides and oxacillin; and VMEs for linezolid and oxacillin).
A Reference Genome Assembly of Simmental Cattle, Bos taurus taurus
Authors: Heaton Michael P , Smith Timothy P L , Bickhart Derek M , Vander Ley Brian L , Kuehn Larry A , Oppenheimer Jonas , Shafer Wade R , Schuetze Fred T , Stroud Brad , McClure Jennifer C , Barfield Jennifer P , Blackburn Harvey D , Kalbfleisch Theodore S , Davenport Kimberly M , Kuhn Kristen L , Green Richard E , Shapiro Beth , Rosen Benjamin D 
Published: January 2021

Abstract
Genomics research has relied principally on the establishment and curation of a reference genome for the species. However, it is increasingly recognized that a single reference genome cannot fully describe the extent of genetic variation within many widely distributed species. Pangenome representations are based on high-quality genome assemblies of multiple individuals and intended to represent the broadest possible diversity within a species. A Bovine Pangenome Consortium (BPC) has recently been established to begin assembling genomes from more than 600 recognized breeds of cattle, together with other related species to provide information on ancestral alleles and haplotypes. Previously reported de novo genome assemblies for Angus, Brahman, Hereford, and Highland breeds of cattle are part of the initial BPC effort. The present report describes a complete single haplotype assembly at chromosome-scale for a fullblood Simmental cow from an F1 bison–cattle hybrid fetus by trio binning. Simmental cattle, also known as Fleckvieh due to their red and white spots, originated in central Europe in the 1830s as a triple-purpose breed selected for draught, meat, and dairy production. There are over 50 million Simmental cattle in the world, known today for their fast growth and beef yields. This assembly (ARS_Simm1.0) is similar in length to the other bovine assemblies at 2.86 Gb, with a scaffold N50 of 102 Mb (max scaffold 156.8 Mb) and meets or exceeds the continuity of the best Bos taurus reference assemblies to date.