bluuebunny/crossref_metadata_2025_split huggingface dataset:
Efficacy of Weight Loss Interventions in United States Active Duty Military Populations: A Systematic Review
Authors: Csizmar Geralyn T , Irwin Melinda 
Published: January 2021

ABSTRACT

Background
Since the beginning of overseas contingency operations, the percent of service members who are considered overweight or obese has tripled to 15% for men and 20% for women. This has implications for national security if the country is unable to staff its military with fit-to-fight individuals. The purpose of this systematic review is to move policy efforts forward by illuminating the efficacy of several lifestyle interventions for active duty service members since 2001. It aims to both identify common aspects of successful interventions and also identify interventions without success so DoD leaders may replace those initiatives.

Materials and Methods
The electronic database PubMed was searched from September 11, 2001 to May 15, 2020. Studies were included if the target population was United States active duty service members from any branch, the study included an intervention, and the measured outcome was weight loss. Seven studies met final inclusion criteria.

Results
Interventions with corresponding weight loss data are summarized in Table III. This review found that there is not a sufficient body of evidence to determine if interventions to aid active duty service members in losing weight are effective.

Conclusion
However, as a collection, the studies could support the notion that military members get the best results when interventions are convenient, modern, personalized, and accessible. More studies are needed, and future studies with larger sample sizes and longer durations would be valuable in determining efficacy of weight loss interventions. Undoubtedly, enrollment and compliance is difficult with military member moves and competing mission requirements. Ideally, the DoD should work to aggregate the efforts in this field, as many initiatives are not captured, shared, and utilized by other installations or other services. Data silos and unpublished or underdeveloped research reactively addresses issues and does not proactively address them. Policy change will need to be nested in further research, as well as consider the food environment on bases and possible prevention efforts.
New star clusters discovered towards the Galactic bulge direction using Gaia DR2
Authors: Ferreira F A , Corradi W J B , Maia F F S , Angelo M S , Santos J F C 
Published: January 2021

ABSTRACT
We report the discovery of 34 new open clusters and candidates as a result of a systematic search carried out in 200 adjacent fields of 1 × 1 deg2 area projected towards the Galactic bulge, using Gaia DR2 data. The objects were identified and characterized by a joint analysis of their photometric, kinematic, and spatial distribution that has been consistently used and proved to be effective in our previous works. The discoveries were validated by cross-referencing the objects position and astrometric parameters with the available literature. Besides their coordinates and astrometric parameters, we also provide sizes, ages, distances, and reddening for the discovered objects. In particular, 32 clusters are closer than 2 kpc from the Sun, which represents an increment of nearly $39{{\ \rm per\ cent}}$ of objects with astrophysical parameters determined in the nearby inner disc. Although these objects fill an important gap in the open clusters distribution along the Sagittarius arm, this arm, traced by known clusters, appears to be interrupted, which may be an artefact due to the incompleteness of the cluster census.
SDSS-IV MaNGA: the ‘G-dwarf problem’ revisited
Authors: Greener Michael J , Merrifield Michael , Aragón-Salamanca Alfonso , Peterken Thomas , Andrews Brett , Lane Richard R 
Published: January 2021

ABSTRACT
The levels of heavy elements in stars are the product of enhancement by previous stellar generations, and the distribution of this metallicity among the population contains clues to the process by which a galaxy formed. Most famously, the ‘G-dwarf problem’ highlighted the small number of low-metallicity G-dwarf stars in the Milky Way, which is inconsistent with the simplest picture of a galaxy formed from a ‘closed box’ of gas. It can be resolved by treating the Galaxy as an open system that accretes gas throughout its life. This observation has classically only been made in the Milky Way, but the availability of high-quality spectral data from SDSS-IV MaNGA and the development of new analysis techniques mean that we can now make equivalent measurements for a large sample of spiral galaxies. Our analysis shows that high-mass spirals generically show a similar deficit of low-metallicity stars, implying that the Milky Way’s history of gas accretion is common. By contrast, low-mass spirals show little sign of a G-dwarf problem, presenting the metallicity distribution that would be expected if such systems evolved as pretty much closed boxes. This distinction can be understood from the differing timescales for star formation in galaxies of differing masses.
Diversification of CD1 Molecules Shapes Lipid Antigen Selectivity
Authors: Paterson Nicole M , Al-Zubieri Hussein , Barber Matthew F 
Published: January 2021

Abstract
Molecular studies of host–pathogen evolution have largely focused on the consequences of variation at protein–protein interaction surfaces. The potential for other microbe-associated macromolecules to promote arms race dynamics with host factors remains unclear. The cluster of differentiation 1 (CD1) family of vertebrate cell surface receptors plays a crucial role in adaptive immunity through binding and presentation of lipid antigens to T-cells. Although CD1 proteins present a variety of endogenous and microbial lipids to various T-cell types, they are less diverse within vertebrate populations than the related major histocompatibility complex (MHC) molecules. We discovered that CD1 genes exhibit a high level of divergence between simian primate species, altering predicted lipid-binding properties and T-cell receptor interactions. These findings suggest that lipid–protein conflicts have shaped CD1 genetic variation during primate evolution. Consistent with this hypothesis, multiple primate CD1 family proteins exhibit signatures of repeated positive selection at surfaces impacting antigen presentation, binding pocket morphology, and T-cell receptor accessibility. Using a molecular modeling approach, we observe that interspecies variation as well as single mutations at rapidly-evolving sites in CD1a drastically alter predicted lipid binding and structural features of the T-cell recognition surface. We further show that alterations in both endogenous and microbial lipid-binding affinities influence the ability of CD1a to undergo antigen swapping required for T-cell activation. Together these findings establish lipid–protein interactions as a critical force of host–pathogen conflict and inform potential strategies for lipid-based vaccine development.
Genome-Scale Profiling Reveals Noncoding Loci Carry Higher Proportions of Concordant Data
Authors: Literman Robert , Schwartz Rachel 
Published: January 2021

AbstractMany evolutionary relationships remain controversial despite whole-genome sequencing data. These controversies arise, in part, due to challenges associated with accurately modeling the complex phylogenetic signal coming from genomic regions experiencing distinct evolutionary forces. Here, we examine how different regions of the genome support or contradict well-established relationships among three mammal groups using millions of orthologous parsimony-informative biallelic sites (PIBS) distributed across primate, rodent, and Pecora genomes. We compared PIBS concordance percentages among locus types (e.g. coding sequences (CDS), introns, intergenic regions), and contrasted PIBS utility over evolutionary timescales. Sites derived from noncoding sequences provided more data and proportionally more concordant sites compared with those from CDS in all clades. CDS PIBS were also predominant drivers of tree incongruence in two cases of topological conflict. PIBS derived from most locus types provided surprisingly consistent support for splitting events spread across the timescales we examined, although we find evidence that CDS and intronic PIBS may, respectively and to a limited degree, inform disproportionately about older and younger splits. In this era of accessible wholegenome sequence data, these results:1) suggest benefits to more intentionally focusing on noncoding loci as robust data for tree inference and 2) reinforce the importance of accurate modeling, especially when using CDS data.
The Evolution of euAPETALA2 Genes in Vascular Plants: From Plesiomorphic Roles in Sporangia to Acquired Functions in Ovules and Fruits
Authors: Zumajo-Cardona Cecilia , Pabón-Mora Natalia , Ambrose Barbara A 
Published: January 2021

Abstract
The field of evolutionary developmental biology can help address how morphological novelties evolve, a key question in evolutionary biology. In Arabidopsis thaliana, APETALA2 (AP2) plays a role in the development of key plant innovations including seeds, flowers, and fruits. AP2 belongs to the AP2/ETHYLENE RESPONSIVE ELEMENT BINDING FACTOR family which has members in all viridiplantae, making it one of the oldest and most diverse gene lineages. One key subclade, present across vascular plants is the euAPETALA2 (euAP2) clade, whose founding member is AP2. We reconstructed the evolution of the euAP2 gene lineage in vascular plants to better understand its impact on the morphological evolution of plants, identifying seven major duplication events. We also performed spatiotemporal expression analyses of euAP2/TOE3 genes focusing on less explored vascular plant lineages, including ferns, gymnosperms, early diverging angiosperms and early diverging eudicots. Altogether, our data suggest that euAP2 genes originally contributed to spore and sporangium development, and were subsequently recruited to ovule, fruit and floral organ development. Finally, euAP2 protein sequences are highly conserved; therefore, changes in the role of euAP2 homologs during development are most likely due to changes in regulatory regions.
RNA polymerase clamp conformational dynamics: long-lived states and modulation by crowding, cations, and nonspecific DNA binding
Authors: Mazumder Abhishek , Wang Anna , Uhm Heesoo , Ebright Richard H , Kapanidis Achillefs N 
Published: January 2021

Abstract
The RNA polymerase (RNAP) clamp, a mobile structural element conserved in RNAP from all domains of life, has been proposed to play critical roles at different stages of transcription. In previous work, we demonstrated using single-molecule Förster resonance energy transfer (smFRET) that RNAP clamp interconvert between three short-lived conformational states (lifetimes ∼ 0.3–0.6 s), that the clamp can be locked into any one of these states by small molecules, and that the clamp stays closed during initial transcription and elongation. Here, we extend these studies to obtain a comprehensive understanding of clamp dynamics under conditions RNAP may encounter in living cells. We find that the RNAP clamp can populate long-lived conformational states (lifetimes &gt; 1.0 s) and can switch between these long-lived states and the previously observed short-lived states. In addition, we find that clamp motions are increased in the presence of molecular crowding, are unchanged in the presence of elevated monovalent-cation concentrations, and are reduced in the presence of elevated divalent-cation concentrations. Finally, we find that RNAP bound to non-specific DNA predominantly exhibits a closed clamp conformation. Our results raise the possibility of additional regulatory checkpoints that could affect clamp dynamics and consequently could affect transcription and transcriptional regulation.
The role and uses of antibodies in COVID-19 infections: a living review
Authors: Scourfield D Oliver , Reed Sophie G , Quastel Max , Alderson Jennifer , Bart Valentina M T , Teijeira Crespo Alicia , Jones Ruth , Pring Ellie , Richter Felix Clemens ,   The Oxford-Cardiff COVID-19 Literature Consortium, Ahern David J , Almuttaqi Hannah , Alonzi Dominic S , Alrubayyi Aljawharah , Alsaleh Ghada , Bart Valentina M T , Batchelor Vicky , Bayliss Rebecca , Berthold Dorothée L , Bezbradica Jelena S , Bharuchq Tehmina , Borrmann Helene , Borsa Mariana , Borst Rowie , Brun Juliane , Burnell Stephanie E A , Capitani Lorenzo , Cavounidis Athena , Chapman Lucy , Chauveau Anne , Cifuentes Liliana , Codd Amy Susan , Compeer Ewoud Bernardus , Coveney Clarissa , Cross Amy , Danielli Sara , Davies Luke C , Dendrou Calliope A , Dimonte Sandra , Peter Durairaj Ruban Rex , Dustin Lynn B , Dyer Arthur , Fielding Ceri , Fischer Fabian , Gallimore Awen , Galloway Sarah , Gammage Anís , Gea-Mallorquí Ester , Godkin Andrew , Hanna Stephanie Jean , Heuberger Cornelia , Hulin-Curtis Sarah , Issa Fadi , Jones Emma , Jones Ruth , Ladell Kristin , Lauder Sarah N , Liddiard Kate , Ligoxygakis Petros , Lu Fangfang , MacLachlan Bruce , Maleki-Toyserkani Shayda , Mann Elizabeth H , Marzeda Anna M , James Matthews Reginald , Mazet Julie M , Milicic Anita , Mitchell Emma , Moon Owen , Nguyen Van Dien , O'Hanlon Miriam , Eléonore Pavillet Clara , Peppa Dimitra , Pires Ana , Pring Eleanor , Quastel Max , Reed Sophie , Rehwinkel Jan , Richmond Niamh , Richter Felix Clemens , Robinson Alice J B , Rodrigues Patrícia R S , Sabberwal Pragati , Sami Arvind , Peres Raphael Sanches , Sattentau Quentin , Schonfeldova Barbora , Scourfield David Oliver , Selvakumar Tharini A , Shepherd Freya R , Shorten Cariad , Simon Anna Katharina , Smith Adrian L , Crespo Alicia Teijeira , Tellier Michael , Thornton Emily , Uhl Lion F K , van Grinsven Erinke , Wann Angus K T , Williams Richard , Wilson Joseph D , Zhou Dingxi , Zhu Zihan , Burnell Stephanie E A 
Published: January 2021

AbstractCoronavirus disease 2019 has generated a rapidly evolving field of research, with the global scientific community striving for solutions to the current pandemic. Characterizing humoral responses towards SARS-CoV-2, as well as closely related strains, will help determine whether antibodies are central to infection control, and aid the design of therapeutics and vaccine candidates. This review outlines the major aspects of SARS-CoV-2-specific antibody research to date, with a focus on the various prophylactic and therapeutic uses of antibodies to alleviate disease in addition to the potential of cross-reactive therapies and the implications of long-term immunity.
A recombineering pipeline to clone large and complex genes in Chlamydomonas
Authors: Emrich-Mills Tom Z , Yates Gary , Barrett James , Girr Philipp , Grouneva Irina , Lau Chun Sing , Walker Charlotte E , Kwok Tsz Kam , Davey John W , Johnson Matthew P , Mackinder Luke C M 
Published: January 2021

Abstract
The ability to clone genes has greatly advanced cell and molecular biology research, enabling researchers to generate fluorescent protein fusions for localization and confirm genetic causation by mutant complementation. Most gene cloning is polymerase chain reaction (PCR)�or DNA synthesis-dependent, which can become costly and technically challenging as genes increase in size, particularly if they contain complex regions. This has been a long-standing challenge for the Chlamydomonas reinhardtii research community, as this alga has a high percentage of genes containing complex sequence structures. Here we overcame these challenges by developing a recombineering pipeline for the rapid parallel cloning of genes from a Chlamydomonas bacterial artificial chromosome collection. To generate fluorescent protein fusions for localization, we applied the pipeline at both batch and high-throughput scales to 203 genes related to the Chlamydomonas CO2 concentrating mechanism (CCM), with an overall cloning success rate of 77%. Cloning success was independent of gene size and complexity, with cloned genes as large as 23 kb. Localization of a subset of CCM targets confirmed previous mass spectrometry data, identified new pyrenoid components, and enabled complementation of mutants. We provide vectors and detailed protocols to facilitate easy adoption of this technology, which we envision will open up new possibilities in algal and plant research.
Comparative genomics of Chlamydomonas
Authors: Craig Rory J , Hasan Ahmed R , Ness Rob W , Keightley Peter D 
Published: January 2021

Abstract
Despite its role as a reference organism in the plant sciences, the green alga Chlamydomonas reinhardtii entirely lacks genomic resources from closely related species. We present highly contiguous and well-annotated genome assemblies for three unicellular C. reinhardtii relatives: Chlamydomonas incerta, Chlamydomonas schloesseri, and the more distantly related Edaphochlamys debaryana. The three Chlamydomonas genomes are highly syntenous with similar gene contents, although the 129.2 Mb C. incerta and 130.2 Mb C. schloesseri assemblies are more repeat-rich than the 111.1 Mb C. reinhardtii genome. We identify the major centromeric repeat in C. reinhardtii as a LINE transposable element homologous to Zepp (the centromeric repeat in Coccomyxa subellipsoidea) and infer that centromere locations and structure are likely conserved in C. incerta and C. schloesseri. We report extensive rearrangements, but limited gene turnover, between the minus mating type loci of these Chlamydomonas species. We produce an eight-species core-Reinhardtinia whole-genome alignment, which we use to identify several hundred false positive and missing genes in the C. reinhardtii annotation and &gt;260,000 evolutionarily conserved elements in the C. reinhardtii genome. In summary, these resources will enable comparative genomics analyses for C. reinhardtii, significantly extending the analytical toolkit for this emerging model system.
Genomic imbalance determines positive and negative modulation of gene expression in diploid maize
Authors: Shi Xiaowen , Yang Hua , Chen Chen , Hou Jie , Hanson Katherine M , Albert Patrice S , Ji Tieming , Cheng Jianlin , Birchler James A 
Published: January 2021

Abstract
Genomic imbalance caused by changing the dosage of individual chromosomes (aneuploidy) has a more detrimental effect than varying the dosage of complete sets of chromosomes (ploidy). We examined the impact of both increased and decreased dosage of 15 distal and 1 interstitial chromosomal regions via RNA-seq of maize (Zea mays) mature leaf tissue to reveal new aspects of genomic imbalance. The results indicate that significant changes in gene expression in aneuploids occur both on the varied chromosome (cis) and the remainder of the genome (trans), with a wider spread of modulation compared with the whole-ploidy series of haploid to tetraploid. In general, cis genes in aneuploids range from a gene-dosage effect to dosage compensation, whereas for trans genes the most common effect is an inverse correlation in that expression is modulated toward the opposite direction of the varied chromosomal dosage, although positive modulations also occur. Furthermore, this analysis revealed the existence of increased and decreased effects in which the expression of many genes under genome imbalance are modulated toward the same direction regardless of increased or decreased chromosomal dosage, which is predicted from kinetic considerations of multicomponent molecular interactions. The findings provide novel insights into understanding mechanistic aspects of gene regulation.
Polycomb Repressive Complex 2 and KRYPTONITE regulate pathogen-induced programmed cell death in Arabidopsis
Authors: Dvořák Tomaštíková Eva , Hafrén Anders , Trejo-Arellano Minerva S , Rasmussen Sheena Ricafranca , Sato Hikaru , Santos-González Juan , Köhler Claudia , Hennig Lars , Hofius Daniel 
Published: January 2021

Abstract
The Polycomb Repressive Complex 2 (PRC2) is well-known for its role in controlling developmental transitions by suppressing the premature expression of key developmental regulators. Previous work revealed that PRC2 also controls the onset of senescence, a form of developmental programmed cell death (PCD) in plants. Whether the induction of PCD in response to stress is similarly suppressed by the PRC2 remained largely unknown. In this study, we explored whether PCD triggered in response to immunity- and disease-promoting pathogen effectors is associated with changes in the distribution of the PRC2-mediated histone H3 lysine 27 trimethylation (H3K27me3) modification in Arabidopsis thaliana. We furthermore tested the distribution of the heterochromatic histone mark H3K9me2, which is established, to a large extent, by the H3K9 methyltransferase KRYPTONITE, and occupies chromatin regions generally not targeted by PRC2. We report that effector-induced PCD caused major changes in the distribution of both repressive epigenetic modifications and that both modifications have a regulatory role and impact on the onset of PCD during pathogen infection. Our work highlights that the transition to pathogen-induced PCD is epigenetically controlled, revealing striking similarities to developmental PCD.
Recognizing humanity: dehumanization predicts neural mirroring and empathic accuracy in face-to-face interactions
Authors: Simon Jeremy C , Gutsell Jennifer N 
Published: January 2021

Abstract
Dehumanization is the failure to recognize the cognitive and emotional complexities of the people around us. While its presence has been well documented in horrific acts of violence, it is also theorized to play a role in everyday life. We measured its presence and effects in face-to-face dyadic interactions between strangers and found that not only was there variance in the extent to which they perceived one another as human, but this variance predicted neural processing and behavior. Specifically, participants showed stronger neural mirroring, indexed by electroencephalography (EEG) mu-suppression, in response to partners they evaluated as more human, suggesting their brains neurally simulated those targets’ actions more. Participants were also marginally more empathically accurate about the emotions of partners deemed more human and performed better with them on a cooperative task. These results suggest that there are indeed differences in our recognition of the humanity of people we meet—demonstrated for the first time in a real, face-to-face interaction—and that this mundane variation affects our ability to neurally simulate, cooperate and empathize.
Brain Activation during Thoughts of One’s Own Death and Its Linear and Curvilinear Correlations with Fear of Death in Elderly Individuals: An fMRI Study
Authors: Hirano Kanan , Oba Kentaro , Saito Toshiki , Yamazaki Shohei , Kawashima Ryuta , Sugiura Motoaki 
Published: January 2021

Abstract
Facing one’s own death and managing the fear of death are important existential issues, particularly in older populations. Although recent functional magnetic resonance imaging (fMRI) studies have investigated brain responses to death-related stimuli, none has examined whether this brain activation was specific to one’s own death or how it was related to dispositional fear of death. In this study, during fMRI, 34 elderly participants (aged, 60–72 years) were presented with either death-related or death-unrelated negative words and asked to evaluate the relevance of these words to the “self” or the “other.” The results showed that only the left supplementary motor area (SMA) was selectively activated during self-relevant judgments of death-related words. Regression analyses of the effect of fear of death on brain activation during death-related thoughts identified a significant negative linear correlation in the right supramarginal gyrus (SMG) and an inverted-U-shaped correlation in the posterior cingulate cortex (PCC) only during self-relevant judgments. Our results suggest potential involvement of the SMA in the existential aspect of thoughts of death. The distinct fear-of-death-dependent responses in the SMG and PCC may reflect fear-associated distancing of the physical self and the processing of death-related thoughts as a self-relevant future agenda, respectively.