bluuebunny/crossref_metadata_2025_split huggingface dataset:
C. elegans germ granules require both assembly and localized regulators for mRNA repression
Authors: Aoki Scott Takeo , Lynch Tina R. , Crittenden Sarah L. , Bingman Craig A. , Wickens Marvin , Kimble Judith 
Published: February 2021

AbstractCytoplasmic RNA–protein (RNP) granules have diverse biophysical properties, from liquid to solid, and play enigmatic roles in RNA metabolism. Nematode P granules are paradigmatic liquid droplet granules and central to germ cell development. Here we analyze a key P granule scaffolding protein, PGL-1, to investigate the functional relationship between P granule assembly and function. Using a protein–RNA tethering assay, we find that reporter mRNA expression is repressed when recruited to PGL-1. We determine the crystal structure of the PGL-1 N-terminal region to 1.5 Å, discover its dimerization, and identify key residues at the dimer interface. Mutations of those interface residues prevent P granule assembly in vivo, de-repress PGL-1 tethered mRNA, and reduce fertility. Therefore, PGL-1 dimerization lies at the heart of both P granule assembly and function. Finally, we identify the P granule-associated Argonaute WAGO-1 as crucial for repression of PGL-1 tethered mRNA. We conclude that P granule function requires both assembly and localized regulators.
Sequential cocatalyst decoration on BaTaO2N towards highly-active Z-scheme water splitting
Authors: Wang Zheng , Luo Ying , Hisatomi Takashi , Vequizo Junie Jhon M. , Suzuki Sayaka , Chen Shanshan , Nakabayashi Mamiko , Lin Lihua , Pan Zhenhua , Kariya Nobuko , Yamakata Akira , Shibata Naoya , Takata Tsuyoshi , Teshima Katsuya , Domen Kazunari 
Published: February 2021

AbstractOxynitride photocatalysts hold promise for renewable solar hydrogen production via water splitting owing to their intense visible light absorption. Cocatalyst loading is essential for activation of such oxynitride photocatalysts. However, cocatalyst nanoparticles form aggregates and exhibit weak interaction with photocatalysts, which prevents eliciting their intrinsic photocatalytic performance. Here, we demonstrate efficient utilization of photoexcited electrons in a single-crystalline particulate BaTaO2N photocatalyst prepared with the assistance of RbCl flux for H2 evolution reactions via sequential decoration of Pt cocatalyst by impregnation-reduction followed by site-selective photodeposition. The Pt-loaded BaTaO2N photocatalyst evolves H2 over 100 times more efficiently than before, with an apparent quantum yield of 6.8% at the wavelength of 420 nm, from a methanol aqueous solution, and a solar-to-hydrogen energy conversion efficiency of 0.24% in Z-scheme water splitting. Enabling uniform dispersion and intimate contact of cocatalyst nanoparticles on single-crystalline narrow-bandgap particulate photocatalysts is a key to efficient solar-to-chemical energy conversion.
Cross-cancer evaluation of polygenic risk scores for 16 cancer types in two large cohorts
Authors: Graff Rebecca E. , Cavazos Taylor B. , Thai Khanh K. , Kachuri Linda , Rashkin Sara R. , Hoffman Joshua D. , Alexeeff Stacey E. , Blatchins Maruta , Meyers Travis J. , Leong Lancelote , Tai Caroline G. , Emami Nima C. , Corley Douglas A. , Kushi Lawrence H. , Ziv Elad , Van Den Eeden Stephen K. , Jorgenson Eric , Hoffmann Thomas J. , Habel Laurel A. , Witte John S. , Sakoda Lori C. 
Published: February 2021

AbstractEven distinct cancer types share biological hallmarks. Here, we investigate polygenic risk score (PRS)-specific pleiotropy across 16 cancers in European ancestry individuals from the Genetic Epidemiology Research on Adult Health and Aging cohort (16,012 cases, 50,552 controls) and UK Biobank (48,969 cases, 359,802 controls). Within cohorts, each PRS is evaluated in multivariable logistic regression models against all other cancer types. Results are then meta-analyzed across cohorts. Ten positive and one inverse cross-cancer associations are found after multiple testing correction. Two pairs show bidirectional associations; the melanoma PRS is positively associated with oral cavity/pharyngeal cancer and vice versa, whereas the lung cancer PRS is positively associated with oral cavity/pharyngeal cancer, and the oral cavity/pharyngeal cancer PRS is inversely associated with lung cancer. Overall, we validate known, and uncover previously unreported, patterns of pleiotropy that have the potential to inform investigations of risk prediction, shared etiology, and precision cancer prevention strategies.
CTCF loss has limited effects on global genome architecture in Drosophila despite critical regulatory functions
Authors: Kaushal Anjali , Mohana Giriram , Dorier Julien , Özdemir Isa , Omer Arina , Cousin Pascal , Semenova Anastasiia , Taschner Michael , Dergai Oleksandr , Marzetta Flavia , Iseli Christian , Eliaz Yossi , Weisz David , Shamim Muhammad Saad , Guex Nicolas , Lieberman Aiden Erez , Gambetta Maria Cristina 
Published: February 2021

AbstractVertebrate genomes are partitioned into contact domains defined by enhanced internal contact frequency and formed by two principal mechanisms: compartmentalization of transcriptionally active and inactive domains, and stalling of chromosomal loop-extruding cohesin by CTCF bound at domain boundaries. While Drosophila has widespread contact domains and CTCF, it is currently unclear whether CTCF-dependent domains exist in flies. We genetically ablate CTCF in Drosophila and examine impacts on genome folding and transcriptional regulation in the central nervous system. We find that CTCF is required to form a small fraction of all domain boundaries, while critically controlling expression patterns of certain genes and supporting nervous system function. We also find that CTCF recruits the pervasive boundary-associated factor Cp190 to CTCF-occupied boundaries and co-regulates a subset of genes near boundaries together with Cp190. These results highlight a profound difference in CTCF-requirement for genome folding in flies and vertebrates, in which a large fraction of boundaries are CTCF-dependent and suggest that CTCF has played mutable roles in genome architecture and direct gene expression control during metazoan evolution.
Immune microenvironment and intrinsic subtyping in hormone receptor-positive/HER2-negative breast cancer
Authors: Griguolo Gaia , Dieci Maria Vittoria , Paré Laia , Miglietta Federica , Generali Daniele Giulio , Frassoldati Antonio , Cavanna Luigi , Bisagni Giancarlo , Piacentini Federico , Tagliafico Enrico , Cagossi Katia , Ficarra Guido , Prat Aleix , Conte Pierfranco , Guarneri Valentina 
Published: February 2021

AbstractLittle is known regarding the interaction between immune microenvironment and tumor biology in hormone receptor (HR)+/HER2− breast cancer (BC). We here assess pretreatment gene-expression data from 66 HR+/HER2− early BCs from the LETLOB trial and show that non-luminal tumors (HER2-enriched, Basal-like) present higher tumor-infiltrating lymphocyte levels than luminal tumors. Moreover, significant differences in immune infiltrate composition, assessed by CIBERSORT, were observed: non-luminal tumors showed a more proinflammatory antitumor immune infiltrate composition than luminal ones.
Intermittent theta burst stimulation for negative symptoms of schizophrenia—A double-blind, sham-controlled pilot study
Authors: Bation Rémy , Magnin Charline , Poulet Emmanuel , Mondino Marine , Brunelin Jérôme 
Published: February 2021

AbstractOptimal noninvasive brain stimulation parameters for the treatment of negative symptoms of schizophrenia remain unclear. Here, we aimed to investigate the clinical and biological effects of intermittent theta burst transcranial magnetic stimulation (iTBS) in patients with treatment-resistant negative symptoms of schizophrenia (NCT00875498). In a randomized sham-controlled 2-arm study, 22 patients with schizophrenia and treatment-resistant negative symptoms received 20 sessions of either active (n = 12) or sham (n = 10) iTBS. Sessions were delivered twice a day on 10 consecutive working days. Negative symptom severity was assessed 5 times using the Scale for the Assessment of Negative Symptoms (SANS): before iTBS, after iTBS, and 1, 3, and 6 months after iTBS. As a secondary objective, we explored the acute effects of iTBS on functional connectivity of the left dorsolateral prefrontal cortex (DLPFC) using seed-based resting-state functional connectivity MRI (rsFC fMRI) images acquired before and after iTBS. Active iTBS over the left DLPFC significantly decreased negative symptoms severity compared to sham iTBS (F(3,60) = 3.321, p = 0.026). Post hoc analyses revealed that the difference between groups was significant 6 months after the end of stimulation sessions. Neuroimaging revealed an increase in rsFC between the left DLPFC and a brain region encompassing the right lateral occipital cortex and right angular gyrus and a right midbrain region that may encompass dopamine neuron cell bodies. Thus, iTBS over the left DLPFC can alleviate negative symptoms of schizophrenia. The effect might be driven by significant modulation of dopamine transmission.
Comparative transcriptome analysis of Rheum australe, an endangered medicinal herb, growing in its natural habitat and those grown in controlled growth chambers
Authors: Mala Deep , Awasthi Supriya , Sharma Nitesh Kumar , Swarnkar Mohit Kumar , Shankar Ravi , Kumar Sanjay 
Published: February 2021

AbstractRheum australeis an endangered medicinal herb of high altitude alpine region of Himalayas and is known to possess anti-cancerous properties. Unlike many herbs of the region,R. australehas broad leaves. The species thrives well under the environmental extremes in its niche habitat, therefore an understanding of transcriptome ofR. australeto environmental cues was of significance. Since, temperature is one of the major environmental variables in the niche ofR. australe, transcriptome was studied in the species growing in natural habitat and those grown in growth chambers maintained at 4 °C and 25 °C to understand genes associated with different temperatures. A total of 39,136 primarily assembled transcripts were obtained from 10,17,74,336 clean read, and 21,303 unigenes could match to public databases. An analysis of transcriptome by fragments per kilobase of transcript per million, followed by validation through qRT-PCR showed 22.4% up- and 22.5% down-regulated common differentially expressed genes in the species growing under natural habitat and at 4 °C as compared to those at 25 °C. These genes largely belonged to signaling pathway, transporters, secondary metabolites, phytohormones, and those associated with cellular protection, suggesting their importance in imparting adaptive advantage toR. australein its niche.
Patterns and processes of pathogen exposure in gray wolves across North America
Authors: Brandell Ellen E. , Cross Paul C. , Craft Meggan E. , Smith Douglas W. , Dubovi Edward J. , Gilbertson Marie L. J. , Wheeldon Tyler , Stephenson John A. , Barber-Meyer Shannon , Borg Bridget L. , Sorum Mathew , Stahler Daniel R. , Kelly Allicia , Anderson Morgan , Cluff H. Dean , MacNulty Daniel R. , Watts Dominique E. , Roffler Gretchen H. , Schwantje Helen , Hebblewhite Mark , Beckmen Kimberlee , Fenton Heather , Hudson Peter J. 
Published: February 2021

AbstractThe presence of many pathogens varies in a predictable manner with latitude, with infections decreasing from the equator towards the poles. We investigated the geographic trends of pathogens infecting a widely distributed carnivore: the gray wolf (Canis lupus). Specifically, we investigated which variables best explain and predict geographic trends in seroprevalence across North American wolf populations and the implications of the underlying mechanisms. We compiled a large serological dataset of nearly 2000 wolves from 17 study areas, spanning 80° longitude and 50° latitude. Generalized linear mixed models were constructed to predict the probability of seropositivity of four important pathogens: canine adenovirus, herpesvirus, parvovirus, and distemper virus—and two parasites: Neospora caninum and Toxoplasma gondii. Canine adenovirus and herpesvirus were the most widely distributed pathogens, whereas N. caninum was relatively uncommon. Canine parvovirus and distemper had high annual variation, with western populations experiencing more frequent outbreaks than eastern populations. Seroprevalence of all infections increased as wolves aged, and denser wolf populations had a greater risk of exposure. Probability of exposure was positively correlated with human density, suggesting that dogs and synanthropic animals may be important pathogen reservoirs. Pathogen exposure did not appear to follow a latitudinal gradient, with the exception of N. caninum. Instead, clustered study areas were more similar: wolves from the Great Lakes region had lower odds of exposure to the viruses, but higher odds of exposure to N. caninum and T. gondii; the opposite was true for wolves from the central Rocky Mountains. Overall, mechanistic predictors were more informative of seroprevalence trends than latitude and longitude. Individual host characteristics as well as inherent features of ecosystems determined pathogen exposure risk on a large scale. This work emphasizes the importance of biogeographic wildlife surveillance, and we expound upon avenues of future research of cross-species transmission, spillover, and spatial variation in pathogen infection.
The assessment of the usability of selected instrumental techniques for the elemental analysis of biomedical samples
Authors: Planeta Karolina , Kubala-Kukus Aldona , Drozdz Agnieszka , Matusiak Katarzyna , Setkowicz Zuzanna , Chwiej Joanna 
Published: February 2021

AbstractThe fundamental role of major, minor and trace elements in different physiological and pathological processes occurring in living organism makes that elemental analysis of biomedical samples becomes more and more popular issue. The most often used tools for analysis of the elemental composition of biological samples include Flame and Graphite Furnace Atomic Absorption Spectroscopy (F-AAS and GF-AAS), Inductively Coupled Plasma Optical Emission Spectroscopy (ICP-OES) and Inductively Coupled Plasma Mass Spectrometry (ICP-MS). Each of these techniques has many advantages and limitations that should be considered in the first stage of planning the measurement procedure. Their reliability can be checked in the validation process and the precision, trueness and detection limits of elements belong to the most frequently determined validation parameters. The main purpose of this paper was the discussion of selected instrumental techniques (F-AAS, GF-AAS, ICP-OES and ICP-MS) in term of the achieved validation parameters and the usefulness in the analysis of biological samples. The focus in the detailed literature studies was also put on the methods of preparation of the biomedical samples. What is more based on the own data the usefulness of the total reflection X-ray fluorescence spectroscopy for the elemental analysis of animal tissues was examined. The detection limits of elements, precision and trueness for the technique were determined and compared with the literature data concerning other of the discussed techniques of elemental analysis. Reassuming, the following paper is to serve as a guide and comprehensive source of information concerning the validation parameters achievable in different instrumental techniques used for the elemental analysis of biomedical samples.
Continuous versus discrete quantity discrimination in dune snail (Mollusca: Gastropoda) seeking thermal refuges
Authors: Bisazza Angelo , Gatto Elia 
Published: February 2021

AbstractThe ability of invertebrates to discriminate quantities is poorly studied, and it is unknown whether other phyla possess the same richness and sophistication of quantification mechanisms observed in vertebrates. The dune snail, Theba pisana, occupies a harsh habitat characterised by sparse vegetation and diurnal soil temperatures well above the thermal tolerance of this species. To survive, a snail must locate and climb one of the rare tall herbs each dawn and spend the daytime hours in an elevated refuge position. Based on their ecology, we predicted that dune snails would prefer larger to smaller groups of refuges. We simulated shelter choice under controlled laboratory conditions. Snails’ acuity in discriminating quantity of shelters was comparable to that of mammals and birds, reaching the 4 versus 5 item discrimination, suggesting that natural selection could drive the evolution of advanced cognitive abilities even in small-brained animals if these functions have a high survival value. In a subsequent series of experiments, we investigated whether snails used numerical information or based their decisions upon continuous quantities, such as cumulative surface, density or convex hull, which co-varies with number. Though our results tend to underplay the role of these continuous cues, behavioural data alone are insufficient to determine if dune snails were using numerical information, leaving open the question of whether gastropod molluscans possess elementary abilities for numerical processing.
Maize intercropping in the milpa system. Diversity, extent and importance for nutritional security in the Western Highlands of Guatemala
Authors: Lopez-Ridaura Santiago , Barba-Escoto Luis , Reyna-Ramirez Cristian A. , Sum Carlos , Palacios-Rojas Natalia , Gerard Bruno 
Published: February 2021

AbstractWe present an assessment of the extent, diversity, and nutritional contribution of the milpa through a quantitative analysis of data from a survey conducted in 989 small scale farm households in the Western Highlands of Guatemala (WHG). The milpa is a traditional agricultural system in which maize is intercropped with other species, such as common beans, faba beans, squashes or potatoes. Our study shows that more than two-thirds of the 1,205 plots recorded were under the milpa system, with a great diversity of crop combinations. As shown with the 357 plots for which specific yields were available, milpa systems present higher total productivity than monocropped maize, expressed as total energy yield of the harvested crops in the respective system, and were also better at providing the recommended daily allowances of fourteen essential nutrients, based on a Potential Nutrient Adequacy (PNA) indicator. Maize-bean-potato, maize-potato, and maize-bean-faba intercrops had the highest PNAs, and monocropped maize, the lowest. These results support the implementation of milpa systems tailored to different agro-ecologies in order to improve nutrition in the WHG and a variety of similar regions.
Bayesian Network Analysis reveals resilience of the jellyfish Aurelia aurita to an Irish Sea regime shift
Authors: Mitchell Emily G. , Wallace Margaret I. , Smith V. Anne , Wiesenthal Amanda A. , Brierley Andrew S. 
Published: February 2021

AbstractRobust time-series of direct observations of jellyfish abundance are not available for many ecosystems, leaving it difficult to determine changes in jellyfish abundance, the possible causes (e.g. climate change) or the consequences (e.g. trophic cascades). We sought an indirect ecological route to reconstruct jellyfish abundance in the Irish Sea: since zooplankton are jellyfish prey, historic variability in zooplankton communities may provide proxies for jellyfish abundance. We determined the Bayesian ecological network of jellyfish–zooplankton dependencies using jellyfish- and zooplankton-abundance data obtained using nets during a 2-week cruise to the Irish Sea in 2008. This network revealed that Aurelia aurita abundance was dependent on zooplankton groups Warm Temperate and Temperate Oceanic as defined by previous zooplankton ecology work. We then determined historic zooplankton networks across the Irish Sea from abundance data from Continuous Plankton Recorder surveys conducted between 1970 and 2000. Transposing the 2008 spatial dependencies onto the historic networks revealed that Aurelia abundance was more strongly dependent over time on sea surface temperature than on the zooplankton community. The generalist predatory abilities of Aurelia may have insulated this jellyfish over the 1985 regime shift when zooplankton composition in the Irish Sea changed abruptly, and also help explain its globally widespread distribution.
Enhanced Ca2+ influx in mechanically distorted erythrocytes measured with 19F nuclear magnetic resonance spectroscopy
Authors: Kuchel Philip W. , Romanenko Konstantin , Shishmarev Dmitry , Galvosas Petrik , Cox Charles D. 
Published: February 2021

AbstractWe present the first direct nuclear magnetic resonance (NMR) evidence of enhanced entry of Ca2+ ions into human erythrocytes (red blood cells; RBCs), when these cells are mechanically distorted. For this we loaded the RBCs with the fluorinated Ca2+ chelator, 1,2-bis(2-amino-5-fluorophenoxy)ethane-N,N,N′,N′-tetraacetic acid (5FBAPTA), and recorded 19F NMR spectra. The RBCs were suspended in gelatin gel in a special stretching/compression apparatus. The 5FBAPTA was loaded into the cells as the tetraacetoxymethyl ester; and 13C NMR spectroscopy with [1,6-13C]d-glucose as substrate showed active glycolysis albeit at a reduced rate in cell suspensions and gels. The enhancement of Ca2+ influx is concluded to be via the mechanosensitive cation channel Piezo1. The increased rate of influx brought about by the activator of Piezo1, 2-[5-[[(2,6-dichlorophenyl)methyl]thio]-1,3,4-thiadiazol-2-yl]-pyrazine (Yoda1) supported this conclusion; while the specificity of the cation-sensing by 5FBAPTA was confirmed by using the Ca2+ ionophore, A23187.
Field evaluation of hermetic and synthetic pesticide-based technologies in smallholder sorghum grain storage in hot and arid climates
Authors: Mubayiwa Macdonald , Mvumi Brighton M. , Stathers Tanya , Mlambo Shaw , Nyabako Tinashe 
Published: February 2021

AbstractField evaluation of six grain storage technologies under hot and arid conditions (32–42 °C; rainfall < 450 mm/year) in two locations in Zimbabwe were conducted over two storage seasons. The treatments included three hermetic technologies (Purdue Improved Crop Storage bags, GrainPro Super Grainbags, metal silos); three synthetic pesticide-based treatments; and an untreated control, all using threshed sorghum grain. Sampling was at eight-week intervals for 32 weeks. Highly significant differences (p < 0.01) occurred between hermetic and non-hermetic treatments regarding grain damage, weight loss, insect pest populations, and grain moisture content; with the hermetic containers exhibiting superior grain protection. Weight losses were low (< 3%) in hermetic treatments compared to pesticide-based treatments (3.7 to 14.2%).Tribolium castaneumdeveloped in metal silos, deltamethrin-incorporated polypropylene bags and a pesticide treatment containing deltamethrin 0.13% and fenitrothion 1% whileSitotroga cerealelladeveloped in a pesticide treatment containing pirimiphos-methyl 0.16% + thiamethoxam 0.036%. Mechanisms of survival and development of these pests in the tested treatments and under similar climatic conditions need further elucidation. These hermetic technologies can be successfully used by smallholder farmers in developing countries as alternatives to synthetic pesticides for protecting stored-sorghum grain under hot and arid climatic conditions to attain household food security. To our knowledge, this is the first published study on modern hermetic storage of sorghum grain under typical smallholder storage conditions and involving stakeholders.