bluuebunny/crossref_metadata_2025_split huggingface dataset:
Evidence for Inversion Polymorphism Related to Sympatric Host Race Formation in the Apple Maggot Fly,Rhagoletis pomonella
Authors: Feder Jeffrey L , Roethele Joseph B , Filchak Kenneth , Niedbalski Julie , Romero-Severson Jeanne 
Published: April 2021

AbstractEvidence suggests that the apple maggot, Rhagoletis pomonella (Diptera: Tephritidae) is undergoing sympatric speciation (i.e., divergence without geographic isolation) in the process of shifting and adapting to a new host plant. Prior to the introduction of cultivated apples (Malus pumila) in North America, R. pomonella infested the fruit of native hawthorns (Crataegus spp.). However, sometime in the mid-1800s the fly formed a sympatric race on apple. The recently derived apple-infesting race shows consistent allele frequency differences from the hawthorn host race for six allozyme loci mapping to three different chromosomes. Alleles at all six of these allozymes correlate with the timing of adult eclosion, an event dependent on the duration of the overwintering pupal diapause. This timing difference differentially adapts the univoltine fly races to an ∼3- to 4-week difference in the peak fruiting times of apple and hawthorn trees, partially reproductively isolating the host races. Here, we report finding substantial gametic disequilibrium among allozyme and complementary DNA (cDNA) markers encompassing the three chromosomal regions differentiating apple and hawthorn flies. The regions of disequilibrium extend well beyond the previously characterized six allozyme loci, covering substantial portions of chromosomes 1, 2, and 3 (haploid n = 6 in R. pomonella). Moreover, significant recombination heterogeneity and variation in gene order were observed among single-pair crosses for each of the three genomic regions, implying the existence of inversion polymorphism. We therefore have evidence that genes affecting diapause traits involved in host race formation reside within large complexes of rearranged genes. We explore whether these genomic regions (inversions) constitute coadapted gene complexes and discuss the implications of our findings for sympatric speciation in Rhagoletis.
Experimental Prediction of the Natural Evolution of Antibiotic Resistance
Authors: Barlow Miriam , Hall Barry G 
Published: April 2021

Abstract
The TEM family of β-lactamases has evolved to confer resistance to most of the β-lactam antibiotics, but not to cefepime. To determine whether the TEM β-lactamases have the potential to evolve cefepime resistance, we evolved the ancestral TEM allele, TEM-1, in vitro and selected for cefepime resistance. After four rounds of mutagenesis and selection for increased cefepime resistance each of eight independent populations reached a level equivalent to clinical resistance. All eight evolved alleles increased the level of cefepime resistance by a factor of at least 32, and the best allele improved by a factor of 512. Sequencing showed that alleles contained from two to six amino acid substitutions, many of which were shared among alleles, and that the best allele contained only three substitutions.
Conjugational Hyperrecombination Achieved by Derepressing the LexA Regulon, Altering the Properties of RecA Protein and Inactivating Mismatch Repair in Escherichia coli K-12
Authors: Lanzov Vladislav A , Bakhlanova Irina V , Clark Alvin J 
Published: April 2021

Abstract
The frequency of recombinational exchanges (FRE) that disrupt co-inheritance of transferred donor markers in Escherichia coli Hfr by F- crosses differs by up to a factor of two depending on physiological factors and culture conditions. Under standard conditions we found FRE to be 5.01 ± 0.43 exchanges per 100-min units of DNA length for wild-type strains of the AB1157 line. Using these conditions we showed a cumulative effect of various mutations on FRE. Constitutive SOS expression by lexA gene inactivation (lexA71::Tn5) and recA gene mutation (recA730) showed, respectively, ∼4- and 7-fold increases of FRE. The double lexA71 recA730 combination gave an ∼17-fold increase in FRE. Addition of mutS215::Tn10, inactivating the mismatch repair system, to the double lexA recA mutant increased FRE to ∼26-fold above wild-type FRE. Finally, we showed that another recA mutation produced as much SOS expression as recA730 but increased FRE only 3-fold. We conclude that three factors contribute to normally low FRE under standard conditions: repression of the LexA regulon, the properties of wild-type RecA protein, and a functioning MutSHL mismatch repair system. We discuss mechanisms by which the lexA, recA, and mutS mutations may elevate FRE cumulatively to obtain hyperrecombination.
Crossover Interference in Saccharomyces cerevisiae Requires a TID1/RDH54- and DMC1-Dependent Pathway
Authors: Shinohara Miki , Sakai Kazuko , Shinohara Akira , Bishop Douglas K 
Published: April 2021

Abstract
Two RecA-like recombinases, Rad51 and Dmc1, function together during double-strand break (DSB)-mediated meiotic recombination to promote homologous strand invasion in the budding yeast Saccharomyces cerevisiae. Two partially redundant proteins, Rad54 and Tid1/Rdh54, act as recombinase accessory factors. Here, tetrad analysis shows that mutants lacking Tid1 form four-viable-spore tetrads with levels of interhomolog crossover (CO) and noncrossover recombination similar to, or slightly greater than, those in wild type. Importantly, tid1 mutants show a marked defect in crossover interference, a mechanism that distributes crossover events nonrandomly along chromosomes during meiosis. Previous work showed that dmc1Δ mutants are strongly defective in strand invasion and meiotic progression and that these defects can be partially suppressed by increasing the copy number of RAD54. Tetrad analysis is used to show that meiotic recombination in RAD54-suppressed dmc1Δ cells is similar to that in tid1; the frequency of COs and gene conversions is near normal, but crossover interference is defective. These results support the proposal that crossover interference acts at the strand invasion stage of recombination.
Normal Synaptonemal Complex and Abnormal Recombination Nodules in Two Alleles of the Drosophila Meiotic Mutant mei-W68
Authors: Carpenter Adelaide T C 
Published: April 2021

Abstract
The meiotic phenotypes of two mutant alleles of the mei-W68 gene, 1 and L1, were studied by genetics and by serial-section electron microscopy. Despite no or reduced exchange, both mutant alleles have normal synaptonemal complex. However, neither has any early recombination nodules; instead, both exhibit high numbers of very long (up to 2 μm) structures here named “noodles.” These are hypothesized to be formed by the unchecked extension of identical but much shorter structures ephemerally seen in wild type, which may be precursors of early recombination nodules. Although the mei-W68L1 allele is identical to the mei-W681 allele in both the absence of early recombination nodules and a high frequency of noodles (i.e., it is amorphic for the noodle phene), it is hypomorphic in its effects on exchange and late recombination nodules. The differential effects of this allele on early and late recombination nodules are consistent with the hypothesis that Drosophila females have two separate recombination pathways—one for simple gene conversion, the other for exchange.
Dominance of Mutations Affecting Viability inDrosophila melanogaster
Authors: Fry James D , Nuzhdin Sergey V 
Published: April 2021

AbstractThere have been several attempts to estimate the average dominance (ratio of heterozygous to homozygous effects) of spontaneous deleterious mutations in Drosophila melanogaster, but these have given inconsistent results. We investigated whether transposable element (TE) insertions have higher average dominance for egg-to-adult viability than do point mutations, a possibility suggested by the types of fitness-depressing effects that TEs are believed to have. If so, then variation in dominance estimates among strains and crosses would be expected as a consequence of variation in TE activity. As a first test, we estimated the average dominance of all mutations and of copia insertions in a set of lines that had accumulated spontaneous mutations for 33 generations. A traditional regression method gave a dominance estimate for all mutations of 0.17, whereas average dominance of copia insertions was 0.51; the difference between these two estimates approached significance (P = 0.08). As a second test, we reanalyzed Ohnishi’s (1974) data on dominance of spontaneous and EMS-induced mutations. Because a considerable fraction of spontaneous mutations are caused by TE insertions, whereas EMS induces mainly point mutations, we predicted that average dominance would decline with increasing EMS concentration. This pattern was observed, but again fell short of formal significance (P = 0.07). Taken together, however, the two results give modest support for the hypothesis that TE insertions have greater average dominance in their viability effects than do point mutations, possibly as a result of deleterious effects of expression of TE-encoded genes.
Strand Invasion and DNA Synthesis From the Two 3′ Ends of a Double-Strand Break in Mammalian Cells
Authors: McCulloch Richard D , Read Leah R , Baker Mark D 
Published: April 2021

Abstract
Analysis of the crossover products recovered following transformation of mammalian cells with a sequence insertion (“ends-in”) gene-targeting vector revealed a novel class of recombinant. In this class of recombinants, a single vector copy has integrated into an ectopic genomic position, leaving the structure of the cognate chromosomal locus unaltered. Thus, in this respect, the recombinants resemble simple cases of random vector integration. However, the important difference is that the two paired 3′ vector ends have acquired endogenous, chromosomal sequences flanking both sides of the vector-borne double-strand break (DSB). In some cases, copying was extensive, extending &gt;16 kb into nonhomologous flanking DNA. The results suggest that mammalian homologous recombination events can involve strand invasion and DNA synthesis by both 3′ ends of the DSB. These DNA interactions are a central, predicted feature of the DSBR model of recombination.
The Distribution of Fitness Effects Among Beneficial Mutations
Authors: Orr H Allen 
Published: April 2021

Abstract
We know little about the distribution of fitness effects among new beneficial mutations, a problem that partly reflects the rarity of these changes. Surprisingly, though, population genetic theory allows us to predict what this distribution should look like under fairly general assumptions. Using extreme value theory, I derive this distribution and show that it has two unexpected properties. First, the distribution of beneficial fitness effects at a gene is exponential. Second, the distribution of beneficial effects at a gene has the same mean regardless of the fitness of the present wild-type allele. Adaptation from new mutations is thus characterized by a kind of invariance: natural selection chooses from the same spectrum of beneficial effects at a locus independent of the fitness rank of the present wild type. I show that these findings are reasonably robust to deviations from several assumptions. I further show that one can back calculate the mean size of new beneficial mutations from the observed mean size of fixed beneficial mutations.
Patterns of Cell Division and the Risk of Cancer
Authors: Frank Steven A , Iwasa Yoh , Nowak Martin A 
Published: April 2021

Abstract
Epidermal and intestinal tissues divide throughout life to replace lost surface cells. These renewing tissues have long-lived basal stem cell lineages that divide many times, each division producing one stem cell and one transit cell. The transit cell divides a limited number of times, producing cells that move up from the basal layer and eventually slough off from the surface. If mutation rates are the same in stem and transit divisions, we show that minimal cancer risk is obtained by using the fewest possible stem divisions subject to the constraints imposed by the need to renew the tissue. In this case, stem cells are a necessary risk imposed by the constraints of tissue architecture. Cairns suggested that stem cells may have lower mutation rates than transit cells do. We develop a mathematical model to study the consequences of different stem and transit mutation rates. Our model shows that stem cell mutation rates two or three orders of magnitude less than transit mutation rates may favor relatively more stem divisions and fewer transit divisions, perhaps explaining how renewing tissues allocate cell divisions between long stem and short transit lineages.
Social Determinants of Shingles Vaccination in the United States
Authors: Vogelsang Eric M , Polonijo Andrea N 
Published: April 2021

Abstract

Objective
Only about one-third of older adults in the United States are vaccinated against shingles, contributing to approximately 1 million shingles cases annually. This study examines how sociodemographic characteristics, health behaviors, and self-rated health are associated with shingles vaccine uptake.

Method
Data come from the 2017 wave of the Behavioral Risk Factor Surveillance System survey, using a subset of older adults aged 60-plus (N = 208,301). Logistic regression models test (a) for associations between individual-level sociodemographic characteristics and vaccine uptake and (b) whether health behaviors and self-rated health moderate these associations.

Results
Black and Hispanic older adults have almost 50% lower odds of shingles vaccination, compared to non-Hispanic Whites. Abstaining from alcohol, being employed, living with children, and having poor self-rated health are also associated with lower uptake. Unmarried (vs married) individuals have lower odds of vaccination that are explained by broad differences in health behavior.

Discussion
Our study contributes to understanding how shingles vaccination coverage systematically differs among social groups. In doing so, it provides guidance for public health interventions to increase uptake. This line of research is increasingly salient in a world facing novel virus threats and antivaccine social movements.
Modelling quasi-periodic signals in geodetic time-series using Gaussian processes
Authors: Koulali A , Clarke P J 
Published: April 2021

SUMMARY
Seasonal signals in geodetic time-series have long been recognized to be associated with environmental phenomena such as polar motion, atmospheric loading, groundwater loading and other hydrological processes. Modelling these periodic signals is crucial for the geophysical interpretation of these time-series. The most common approach used for resolving seasonal (annual and semi-annual) signals is their approximation by sinusoidal functions with constant amplitudes. However, because of their environmental source, seasonal signals are likely to be quasi-periodic. In this study, we investigate a Gaussian process (GP) to model quasi-periodic signals in geodetic time-series, a flexible method that allows capturing the variability structure in the data using covariance functions. We use the Markov Chain Monte Carlo method to evaluate the posterior probability density function. To test its effectiveness, we apply this method to a synthetic time-series in the presence of time-correlated noise. We find that the GP model provides a better fit to the time-series, resulting in time-series residuals with fewer systematic effects. We use the GP model to estimate the secular velocity of selected GPS sites from Antarctica and Alaska, as well as an example of Gravity Recovery and Climate Experiment time-series. The Bayesian aspect of the GP model allows inferring the linear velocity ensemble in the vicinity of the true solution while taking into account the quasi-periodic systematics in the time-series.
Early cusp tear of the second-generation Trifecta valve with Glide Technology
Authors: Morisaki Akimasa , Takahashi Yosuke , Nishimura Shinsuke , Shibata Toshihiko 
Published: April 2021

Abstract
We herein report a case of early cusp tear of the second-generation Trifecta valve with Glide Technology. A 69-year-old woman underwent aortic valve replacement with a Trifecta valve with Glide Technology and partial arch replacement for severe aortic valve stenosis caused by a bicuspid valve and ascending aortic and aortic arch aneurysms 2 years previously. During follow-up, she suddenly developed dyspnoea and a heart murmur. Echocardiography revealed severe aortic valve regurgitation caused by structural valve deterioration. We performed re-aortic valve replacement with a mechanical valve through re-median sternotomy. Intraoperative examination revealed a bottom tear of the left coronary cusp without infection or pannus formation.
Potential Aphid Population Regulation by Aphidius colemani (Hymenoptera: Aphidiidae) in Response to Host Density, Parasitoid Density, and Age
Authors: Khatri Diwas , He Xiong Z , Wang Qiao 
Published: April 2021

Abstract
Aphidius colemani Viereck is an important parasitoid of green peach aphid [Myzus persicae (Sulzer)], a serious pest of greenhouse crops. Augmentation of natural enemies is the most used approach to biological control of greenhouse pests. Yet, the optimal release time, rate, and age of natural enemies are often unclear. Here we tested the influence of population density of both A. colemani and M. persicae, as well as parasitoid age, on parasitism and sex allocation. We aim is to provide information for cost-effective aphid biological control programs. We show that 1) parasitoid females increased parasitism and produced more female-biased offspring with an increase of aphid density, 2) a moderate increase of parasitoid release rate elevated parasitism and daughter production when aphid density was high, 3) parasitism rate declined with an increase of aphid density but the moderate increase of parasitoid release rate eased the decline rate, and 4) 3-d-old parasitoids parasitized more aphids than younger ones but parasitoid age had no effect on daughter production. These findings suggest that A. colemani females can adjust their ability to regulate the aphid population in response to aphid population dynamics. In augmentative programs, a moderate increase of parasitoid release when aphid density is high could achieve effective control and a release of 3-d-old parasitoids could lead to a better control outcome.
Production of D-lactic acid containing polyhydroxyalkanoate polymers in yeast Saccharomyces cerevisiae
Authors: Ylinen Anna , Maaheimo Hannu , Anghelescu-Hakala Adina , Penttilä Merja , Salusjärvi Laura , Toivari Mervi 
Published: April 2021

Abstract
Polyhydroxyalkanoates (PHAs) provide biodegradable and bio-based alternatives to conventional plastics. Incorporation of 2-hydroxy acid monomers into polymer, in addition to 3-hydroxy acids, offers possibility to tailor the polymer properties. In this study, poly(D-lactic acid) (PDLA) and copolymer P(LA-3HB) were produced and characterized for the first time in the yeast Saccharomyces cerevisiae. Expression of engineered PHA synthase PhaC1437Ps6–19, propionyl-CoA transferase Pct540Cp, acetyl-CoA acetyltransferase PhaA, and acetoacetyl-CoA reductase PhaB1 resulted in accumulation of 3.6% P(LA-3HB) and expression of engineered enzymes PhaC1Pre and PctMe resulted in accumulation of 0.73% PDLA of the cell dry weight (CDW). According to NMR, P(LA-3HB) contained D-lactic acid repeating sequences. For reference, expression of PhaA, PhaB1, and PHA synthase PhaC1 resulted in accumulation 11% poly(hydroxybutyrate) (PHB) of the CDW. Weight average molecular weights of these polymers were comparable to similar polymers produced by bacterial strains, 24.6, 6.3, and 1 130 kDa for P(LA-3HB), PDLA, and PHB, respectively. The results suggest that yeast, as a robust and acid tolerant industrial production organism, could be suitable for production of 2-hydroxy acid containing PHAs from sugars or from 2-hydroxy acid containing raw materials. Moreover, the wide substrate specificity of PHA synthase enzymes employed increases the possibilities for modifying copolymer properties in yeast in the future.
Revised points and disputed matters in the eighth edition of the TNM staging system for gastric cancer
Authors: Kumagai Koshi , Sano Takeshi 
Published: April 2021

Abstract
The American Joint Committee on Cancer and the Union for International Cancer Control have now released the eighth edition of the cancer staging system, which incorporates some major revisions concerning gastric cancer. First, grouping of pathological stages has been revised in accordance with a proposal from the International Gastric Cancer Association. That revision was based on analysis of survival of more than 25 000 patients worldwide who had undergone curative gastrectomy without neoadjuvant therapy. Stratification of survival in Stage III subgroups has been improved by subdividing N3 into N3a and N3b. Second, a simplified grouping of clinical stages that differs completely from grouping of pathological stages has been proposed. Pre-treatment depth of tumour invasion is now categorized as T1/T2, T3/T4a or T4b, and lymph node status is simply categorized as N0 or N+. Additionally, a ‘yp-stage’ for specimens resected after neoadjuvant therapy has been newly proposed. These clinical and post-neoadjuvant stages were considered useful now that neoadjuvant chemotherapy is increasingly being administered to patients with potentially resectable gastric cancer. Third, staging of oesophagogastric junction tumours has been modified; Siewert type 3 tumours are now classified as gastric tumours and are staged according to the gastric, rather than the oesophageal, system. More appropriate staging of gastric cancers treated with neoadjuvant therapy, and/or new staging systems incorporating variables other than T/N/M, such as biological or genomic markers, are likely future developments.
Environmental and behavioral factors influencing individual variation in spatial use by Guiana dolphins (Sotalia guianensis)
Authors: de Moura Stephane P G , Cantor Mauricio , Broadhurst Matt K , Domit Camila 
Published: April 2021

AbstractMarine apex predators, such as coastal dolphins, are key components of ecosystem function and dynamics; understanding their spatial use therefore is important for conservation planning. Here, we describe spatial use of the threatened Guiana dolphin, Sotalia guianensis, within a mosaic of protected areas at their southern range in the Paranaguá estuarine complex (PEC), Brazil. Based on environmental characteristics and S. guianensis population densities, individual photo-identification surveys were focused on two sectors of the northern mouth of the PEC between 2013 and 2015. We photo-identified 107 individuals and recorded 351 groups of Guiana dolphins; nearly 50% of which contained calves. Group sizes were small (mean ± SD: Sector 1 = 3.4 ± 2.7; Sector 2 = 3.6 ± 2.0) and ranged from 1 to 30 individuals. Clustering algorithms were applied to resighted, photo-identified Guiana dolphins to classify individuals as “residents” (sighted in 87% of surveys, n = 11) and “transients” (two clusters; 62%, n = 22; 95%, n = 72). All individuals predominantly were observed foraging (90% in Sector 1 and 76% in Sector 2), but spatial use by transient individuals differed from the residents in terms of environmental (slope, water depth, and rainfall) and behavioral factors (presence of calves and foraging behavior). Compared to transients, resident dolphins ranged over smaller areas, typically more suitable for feeding, calf caring, and more protected from predators and vessels. Because resident Guiana dolphins exhibit small home ranges, they are particularly vulnerable to local anthropogenic activities and habitat loss. These characteristics imply a strong need for regionalized management plans to reduce negative impacts and to maintain the ecological functionality of the species.