bluuebunny/crossref_metadata_2025_split huggingface dataset:
A NEW METHOD FOR ESTIMATING THE EFFECTIVE POPULATION SIZE FROM ALLELE FREQUENCY CHANGES
Authors: Pollak Edward 
Published: January 2021

ABSTRACT
A new procedure is proposed for estimating the effective population size, given that information is available on changes in frequencies of the alleles at one or more independently segregating loci and the population is observed at two or more separate times. Approximate expressions are obtained for the variances of the new statistic, as well as others, also based on allele frequency changes, that have been discussed in the literature. This analysis indicates that the new statistic will generally have a smaller variance than the others. Estimates of effective population sizes and of the standard errors of the estimates are computed for data on two fly populations that have been discussed in earlier papers. In both cases, there is evidence that the effective population size is very much smaller than the minimum census size of the population.
EGG-LAYING DEFECTIVE MUTANTS OF THE NEMATODE CAENORHABDITIS ELEGANS
Authors: Trent Carol , Tsung Nancy , Horvitz H Robert 
Published: January 2021

ABSTRACT
We have isolated 145 fertile mutants of C. elegans that are defective in egg laying and have characterized 59 of them genetically, behaviorally and pharmacologically. These 59 mutants define 40 new genes called egl, for egg-lay ing abnormal. Most of the other mutants are defective in previously identified genes. The egl mutants differ with respect to the severity of their egg-laying defects and the presence of behavioral or morphological pleiotropies. We have defined four distinct categories of mutants based on their responses to the pharmacological agents serotonin and imipramine, which stimulate egg laying by wild-type hermaphrodites. These drugs test the functioning of the vulva, the vulval and uterine muscles and the hermaphrodite-specific neurons (HSNs), which innervate the vulval muscles. Mutants representing 14 egl genes fail to respond to serotonin and to imipramine and are likely to be defective in the functioning of the vulva or the vulval and uterine muscles. Four mutants (representing four different genes) lay eggs in response to serotonin but not to imipramine and appear to be egg-laying defective because of defects in the HSNs; three of these four were selected specifically for these drug responses. Mutants representing seven egl genes lay eggs in response to serotonin and to imipramine. One egl mutant responds to imipramine but not to serotonin. The remaining egl mutants show variable or intermediate responses to the drugs. Two of the HSN-defective mutants, egl-1 and her-1(n695), lack HSN cell bodies and are likely to be expressing the normally male-specific program of HSN cell death. Whereas egl-1 animals appear to be defective specifically in HSN development, her-1(n695) animals exhibit multiple morphological pleiotropies, displaying partial transformation of the sexual phenotype of many cells and tissues. At least two of the egl mutants appear to be defective in the processing of environmental signals that modulate egg laying and may define new components of the neural circuitry that control egg laying.
LINKAGE OF A KNOWN CHLOROPLAST GENE MUTATION TO THE UNIPARENTAL GENOME OF CHLAMYDOMONAS REINHARDII
Authors: Mets Laurens J , Geist Lois J 
Published: January 2021

ABSTRACT
Data are presented that associate three new markers with the uniparental linkage group in Chlamydomonas reinhardii. One of these, mutant 10-6C, is a genetic marker for the structural gene of the large subunit of ribulose bisphosphate carboxylase. These results provide the first direct link between the uniparental gene map and the physical map of chloroplast DNA. The other two markers, Dr2 (DCMU resistant) and 8-36C (deficient in photosystem II activity), map to a single locus. The data suggest that mixing in zygotic chloroplasts may not be complete so that input genomes do not have equal opportunities to recombine. The data are not compatible with simple linear or circular maps but can be explained on the basis of the known physical structure of chloroplast DNA.
MITOCHONDRIAL DNA EVOLUTION IN MICE
Authors: Ferris Stephen D , Sage Richard D , Prager Ellen M , Ritte Uzi , Wilson Allan C 
Published: January 2021

ABSTRACT
This study extends knowledge of mitochondrial DNA (mtDNA) diversity in mice to include 208 animals belonging to eight species in the subgenus Mus. Highly purified mtDNA from each has been subjected to high-resolution restriction mapping with respect to the known sequence of one mouse mtDNA. Variation attributed to base substitutions was encountered at about 200 of the 300 cleavage sites examined, and a length mutation was located in or near the displacement loop. The variability of different functional regions in this genome was as follows, from least to most: ribosomal RNA, transfer RNA, known proteins, displacement loop and unidentified reading frames.—Phylogenetic analysis confirmed the utility of the Sage and Marshall revision of mouse classification, according to which there are at least four species of commensal mice and three species of aboriginal mice in the complex that was formerly considered to be one species. The most thoroughly studied of these species is Mus domesticus, the house mouse of Western Europe and the Mediterranean region, which is the mitochondrial source of all 50 of the laboratory strains examined and of the representatives of wild house mice introduced by Europeans to North and South America during the past few hundred years.—The level of mtDNA variation among wild representatives of (M. musculus) and several other mammalian species. By contrast, among the many laboratory strains that are known or suspected to stem from the pet mouse trade, there is little interstrain variation, most strains having the "old inbred" type of domesticus mtDNA, whose frequency in the 145 wild mice examined is low, about 0.04. Also notable is the apparent homogeneity of mtDNA in domesticus races that have fixed six or more fused chromosomes and the close relationship of some of these mtDNAs to those of karyotypically normal mice.—In addition, this paper discusses fossil and other evidence for the view that in mice, as in many other mammals, the average rate of point mutational divergence in mtDNA is 2-4% per million years. From this, it is estimated that the commensal association between mice and our ancestors began more than a million years ago, i.e., at an early stage in the evolution of Homo erectus.
HOMOLOGOUS RECOMBINATION BETWEEN EPISOMAL PLASMIDS AND CHROMOSOMES IN YEAST
Authors: Falco S Carl , Rose Mark , Botstein David 
Published: January 2021

ABSTRACT
We have observed genetic recombination between ura3 - mutations (among them extensive deletions) carried on "episomal" (i.e., 2μ DNA-containing) plasmids and other ura3 - alleles present at the normal chromosomal URA3 locus. The recombination frequency found was comparable to the level observed for classical mitotic recombination but was relatively insensitive to sunlamp radiation, which strongly stimulates mitotic recombination. Three equally frequent classes could be distinguished among the recombinants. Two of these are the apparent result of gene conversions (or double crossovers) which leave the URA3 + allele on the chromosome (class I) or on the plasmid (class II). The third class is apparently due to a single crossover that results in the integration of the plasmid into a chromosome. Plasmid-chromosome recombination can be useful in fine structure genetic mapping, since recombination between a chromosomal point mutation and a plasmid-borne deletion mutation only 25 base pairs distant was easily detected.
A RAPID CHROMOSOME-MAPPING METHOD FOR CLONED FRAGMENTS OF YEAST DNA
Authors: Falco S Carl , Botstein David 
Published: January 2021

ABSTRACT
A rapid and generally applicable method is described for mapping a cloned yeast DNA segment to the chromosome(s) from which it originated. The method is based upon the recent finding that the integration into a yeast chromosome of a segment of the 2μ plasmid DNA results, in heterozygous diploids, in the specific loss of genetic information from the chromosome into which the 2μ DNA was integrated (Falco et al. 1982). After verification of the accuracy of the method using several genes whose position was known in advance, the method was used to locate the yeast actin gene, which lies on the left arm of chromosome VI, about 50 cM distal to CDC4.
Imaging strategies to interpret 3-D noisy audio-magnetotelluric data acquired in Gyeongju, South Korea: data processing and inversion
Authors: Uhm Janghwan , Heo Junyeong , Min Dong-Joo , Oh Seokhoon , Chung Ho-Joon 
Published: January 2021

SUMMARY
The largest earthquake recorded in South Korea occurred in Gyeongju on 2016 September 12. Since then, understanding the geological structures near the Gyeongju earthquake's epicentre has been demanded. As a preliminary step to understand the geological structures around the epicentre, a 3-D audio-magnetotelluric (AMT) survey was conducted. These 3-D AMT data were imaged through data processing and inversion. However, because the AMT data acquired in Gyeongju were very noisy, conventional imaging procedures did not yield reliable results. To obtain a reliable model inverted from such noisy data, we propose various imaging strategies: an additional data processing technique using the Nyquist diagram after conventional data processing and several inversion strategies related to the selection of data, the weighting of the data, the constraints on the model parameter vector and the Lagrange multiplier used for the regularization. By applying the additional data processing step and several inversion strategies, we were able to successfully invert the noisy field data. The inversion results verify that the data-screening procedure applying the Nyquist diagram remarkably improves the results compared with those obtained using only conventional data processing. The imaging strategies proposed in this case study can be used to image noisy MT/AMT field data for other regions.
NMR and MD simulations reveal the impact of the V23D mutation on the function of yeast oligosaccharyltransferase subunit Ost4
Authors: Chaudhary Bharat P , Zoetewey David L , McCullagh Martin J , Mohanty Smita 
Published: January 2021

Abstract
Asparagine-linked glycosylation, also known as N-linked glycosylation, is an essential and highly conserved co- and post-translational protein modification in eukaryotes and some prokaryotes. In the central step of this reaction, a carbohydrate moiety is transferred from a lipid-linked donor to the side-chain of a consensus asparagine in a nascent protein as it is synthesized at the ribosome. Complete loss of oligosaccharyltransferase (OST) function is lethal in eukaryotes. This reaction is carried out by a membrane-associated multisubunit enzyme, OST, localized in the endoplasmic reticulum. The smallest subunit, Ost4, contains a single membrane-spanning helix that is critical for maintaining the stability and activity of OST. Mutation of any residue from Met18 to Ile24 of Ost4 destabilizes the enzyme complex, affecting its activity. Here, we report solution nuclear magnetic resonance structures and molecular dynamics (MD) simulations of Ost4 and Ost4V23D in micelles. Our studies revealed that while the point mutation did not impact the structure of the protein, it affected its position and solvent exposure in the membrane mimetic environment. Furthermore, our MD simulations of the membrane-bound OST complex containing either WT or V23D mutant demonstrated disruption of most hydrophobic helix–helix interactions between Ost4V23D and transmembrane TM12 and TM13 of Stt3. This disengagement of Ost4V23D from the OST complex led to solvent exposure of the D23 residue in the hydrophobic pocket created by these interactions. Our study not only solves the structures of yeast Ost4 subunit and its mutant but also provides a basis for the destabilization of the OST complex and reduced OST activity.
A home visit-based early childhood stimulation programme in Brazil—a randomized controlled trial
Authors: Brentani Alexandra , Walker Susan , Chang-Lopez Susan , Grisi Sandra , Powell Christine , Fink Günther 
Published: January 2021

Abstract
Home visiting programmes are increasingly recognized as one of the most effective interventions to improve child health and development in low-income settings. However, the best platforms to deliver such programmes remain unclear. We conducted a randomized controlled trial to test the relative effectiveness of child development agents (CDAs) and community health workers (CHWs) as two possible delivery platforms for early childhood development (ECD) focused home visiting intervention in São Paulo, Brazil. A total of 900 children aged 9–15 months were screened for potential study inclusion between January and March 2015. Children who did not attend crèches at enrolment were included in the trial. Children were randomly assigned to control or to receive biweekly home visits either through a CHW in the areas covered by the Brazilian Family Health Strategy (FHS) or by a newly hired cadre of CDAs in the areas not covered by the FHS. The primary study outcome was children’s development (cognition, motor, language and social emotional skills) assessed after 12 months of intervention with the PRIDI and Caregiver-Reported Early Development Instruments tools. A total of 826 mother-child dyads were enrolled in the trial. In intention-to-treat analysis, neither intervention arm improved study outcomes. In per-protocol (PP) analysis, the CDA programme resulted in a 0.22 standard deviation increase in children’s development (95% confidence interval [0.01–0.43]). The results presented in this study suggest that home visiting programmes have the potential to improve child development among poor urban families in Brazil. However, delivering home visiting interventions through already active CHWs may not be feasible in the Brazilian context and coordination across sectors is essential to effective ECD policies.
Health Promotion Glossary 2021
Authors: Nutbeam Don , Muscat Danielle M 
Published: January 2021

Lay summary
The Health Promotion Glossary 2021 is designed to help clarify the meaning and relationship between terms commonly used in health promotion. This is the first full review and revision of the Glossary in over 20 years. It reflects the continued evolution and development of concepts since the 1998 Glossary, providing an updated overview of the many ideas which are central to contemporary health promotion.
The aim of the Glossary is to facilitate communication among the professions and sectors working in health promotion. The list of terms in the Glossary is not intended to be either exhaustive or exclusive, and draws upon the wide range of disciplines from which health promotion has its origins. The definitions should not be regarded as ‘the final word’ on the terms included. Definitions by their very nature are restrictive, often representing summaries of complex ideas and actions. The use of terms will often be context-specific, and influenced by different social, cultural and economic conditions in countries and communities. Despite these obvious restrictions, the glossary has been assembled to enable as wide an audience as possible to understand the basic ideas and concepts which are central to the development of health promotion.
Modeling the immune response toSalmonelladuring typhoid
Authors: Dhingra Divy , Marathe Sandhya Amol , Sharma Nandita , Marathe Amol , Chakravortty Dipshikha 
Published: January 2021

AbstractSeveral facets of the host immune response to Salmonella infection have been studied independently at great depths to understand the progress and pathogenesis of Salmonella infection. The circumstances under which a Salmonella-infected individual succumbs to an active disease, evolves as a persister or clears the infection are not understood in detail. We have adopted a system-level approach to develop a continuous-time mechanistic model. We considered key interactions of the immune system state variables with Salmonella in the mesenteric lymph node to determine the final disease outcome deterministically and exclusively temporally. The model accurately predicts the disease outcomes and immune response trajectories operational during typhoid. The results of the simulation confirm the role of anti-inflammatory (M2) macrophages as a site for persistence and relapsing infection. Global sensitivity analysis highlights the importance of both bacterial and host attributes in influencing the disease outcome. It also illustrates the importance of robust phagocytic and anti-microbial potential of M1 macrophages and dendritic cells (DCs) in controlling the disease. Finally, we propose therapeutic strategies for both antibiotic-sensitive and antibiotic-resistant strains (such as IFN-γ therapy, DC transfer and phagocytic potential stimulation). We also suggest prevention strategies such as improving the humoral response and macrophage carrying capacity, which could complement current vaccination schemes for enhanced efficiency.
Embodied Theodicy: From Conceptual to Bodily Engagements with Suffering
Authors: Winfield Taylor Paige 
Published: January 2021

AbstractThis article leverages ethnographic research on spiritual journeys to expand traditional definitions of theodicy. Embodied theodicy builds upon embodiment literature to demonstrate how bodily experiences have real emotional consequences—they have the potential to change how individuals make sense of their suffering. Whereas in some cases the bodily experience of pain leads to suffering, in others, pain provides individuals with perspective on their suffering and helps them overcome it. Data from two spiritual journeys, El Camino de Santiago and a Vipassana meditation retreat, introduce three models of embodied theodicy: pain as purifier, pain as teacher, and pain as solidarity. Embodied theodicy bridges the meaning-making concerns of classical and neoclassical literature with the embodiment theories of poststructuralists and contemporary scholars.
Baseline integrase drug resistance mutations and conserved regions across HIV-1 clades in Cameroon: implications for transition to dolutegravir in resource-limited settings
Authors: Semengue Ezechiel Ngoufack Jagni , Armenia Daniele , Inzaule Seth , Santoro Maria Mercedes , Dambaya Béatrice , Takou Désiré , Teto Georges , Nka Alex Durand , Yagai Bouba , Fabeni Lavinia , Chenwi Collins , Angong Beloumou Grâce , Djupsa Ndjeyep Sandrine Claire , Colizzi Vittorio , Perno Carlo-Federico , Ceccherini-Silberstein Francesca , Fokam Joseph 
Published: January 2021

Abstract

Background
Transition to dolutegravir-based regimens in resource-limited settings (RLS) requires prior understanding of HIV-1 integrase variants and conserved regions. Therefore, we evaluated integrase drug resistance mutations (DRMs) and conserved regions amongst integrase strand transfer inhibitor (INSTI)-naive patients harbouring diverse HIV-1 clades in Cameroon.

Methods
A cross-sectional study was conducted amongst 918 INSTI-naive patients from Cameroon (89 ART-naive and 829 ART-experienced patients). HIV-1 sequences were interpreted regarding INSTI-DRMs using the Stanford HIVdb v8.9-1 and the 2019 IAS–USA list. Amino acid positions with &lt;1% variability were considered as highly conserved. Subtyping was performed by phylogeny.

Results
Overall prevalence (95% CI) of INSTI-DRMs was 0.8% (0.4–1.7), with 0.0% (0.0–4.0) amongst ART-naive versus 0.9% (0.5–1.9) amongst ART-experienced patients; P = 0.44. Accessory mutations (95% CI) were found in 33.8% (30.9–37.0), with 38.2% (28.1–49.1) amongst ART-naive versus 33.4% (30.4–36.7) amongst ART-experienced patients; P = 0.21. Of 288 HIV-1 integrase amino acid positions, 58.3% were highly conserved across subtypes in the following major regions: V75–G82, E85–P90, H114–G118, K127–W132, E138–G149, Q168–L172, T174–V180, W235–A239 and L241–D253. Wide genetic diversity was found (37 clades), including groups M (92.3%), N (1.4%), O (6.2%) and P (0.1%). Amongst group M, CRF02_AG was predominant (47.4%), with a significantly higher frequency (95% CI) of accessory mutations compared with non-AG [41.4% (36.8–46.0) versus 27.1% (23.3–31.2) respectively; P &lt; 0.001].

Conclusions
The low baseline of INSTI-DRMs (&lt;1%) in Cameroon suggests effectiveness of dolutegravir-based regimens. In spite of high conservation across clades, the variability of accessory mutations between major circulating strains underscores the need for monitoring the selection of INSTI-DRMs while scaling up dolutegravir-based regimens in RLS.
Prevalence of Vibrio mimicus in Fish, Fishery Products, and Environment of South West Coast of Kerala, India
Authors: Nilavan Ezhil , Vaiyapuri Murugadas , Sadanandan Sheela Greeshma , Nadella Ranjit Kumar , Thandapani Muthulakshmi , Kumar Abhay , Mothadaka Mukteswar Prasad 
Published: January 2021

Abstract

Background
Vibrio mimicus is a seafood-borne bacterium involved in incidences of human infections following consumption of raw or undercooked seafood. Regular monitoring of seafood for V.mimicus is necessary for risk assessment and to establish mitigation measures.

Method
During the period 2017–2020, a total of 250 samples comprising finfish, shellfish, water, ice, and sediment samples were collected from fish markets, fish landing centers, and fish farms in the Ernakulum district on the Southwest coast of Kerala, India. V. mimicus was isolated using enrichment in alkaline peptone water for 18 h followed by plating on thiosulfate citrate bile salts sucrose agar and then incubated at 37°C for 18–24 h. The presumptive V. mimicus isolates were confirmed by biochemical characterization and molecularly with vmh gene-specific for V. mimicus.

Results
The study revealed that the prevalence of V. mimicus is 5.6% in the total of samples screened. The highest occurrence was observed in brackish water fish (19%) followed by freshwater fish (18%) and marine fish (2%) samples. The study points out the risk of brackish water fishes as potential carriers of this pathogen. This requires preventive measures to mitigate health hazards associated with V. mimicus entering into the seafood production chain.
Positive Learning or Deviant Interviewing? Mechanisms of Experience on Interviewer Behavior
Authors: Kosyakova Yuliya , Olbrich Lukas , Sakshaug Joseph W , Schwanhäuser Silvia 
Published: January 2021

Abstract
Interviewer (mis)behavior has been shown to change with interviewers’ professional experience (general experience) and experience gained during the field period (survey experience). We extend this study by using both types of experiences to analyze interviewer effects on a core quality indicator: interview duration. To understand whether the effect of interviewer experience on duration is driven by increased efficiency or deviant behavior—both mechanisms of shorter interview durations—we additionally examine the triggering rate of filter questions to avoid burdensome follow-up questions and response differentiation over the field period. Using multilevel models and data from a large-scale survey on a special and difficult-to-interview population of refugees in Germany, we find that interview duration decreases with increasing survey experience, particularly among the generally inexperienced interviewers. However, this effect is not found for the triggering rate and response differentiation. The results are robust to different sample and model specifications. We conclude that the underlying mechanism driving interview duration is related to increasing efficiency, and not deviant behavior.