bluuebunny/crossref_metadata_2025_split huggingface dataset:
Coprophagy prevention alters microbiome, metabolism, neurochemistry, and cognitive behavior in a small mammal
Authors: Bo Ting-Bei , Zhang Xue-Ying , Kohl Kevin D , Wen Jing , Tian Shuang-Jie , Wang De-Hua 
Published: July 2020

Abstract
Many small mammals engage in coprophagy, or the behavior of consuming feces, as a means to meet nutritional requirements when feeding on low-quality foods. In addition to nutritional benefits, coprophagy may also help herbivores retain necessary gut microbial diversity and function, which may have downstream physiological effects, such as maintaining energy balance and cognitive function. Here, we used collars to prevent Brandt’s vole (Lasiopodomys brandtii) from engaging in coprophagy and monitored changes in microbial community structure, energy metabolism, and cognitive performance. In this research, we found that coprophagy prevention decreased alpha diversity of the gut microbiota, and altered proportions of microbial taxa such as Bacteroidetes, Firmicutes, and Oscillospira. Preventing coprophagy resulted in a reduced body mass, and increased food intake. Importantly, coprophagy prevention decreased vole cognitive behavior and altered levels of neurotransmitters in brain. Daily acetate administration was able to reverse some of the coprophagy prevention-induced changes in microbiota composition, metabolism, neurochemistry, and cognitive behavior. These findings identify the functional importance of coprophagy behavior and interactions between the gut microbiota, energy metabolism, and neurological function. Our results suggest that coprophagy contributes to stabilizing the gut microbiota, promoting microbial metabolism, maintaining host energy balance and, consequently, altering cognitive performance.
Multi-parent populations in crops: a toolbox integrating genomics and genetic mapping with breeding
Authors: Scott Michael F. , Ladejobi Olufunmilayo , Amer Samer , Bentley Alison R. , Biernaskie Jay , Boden Scott A. , Clark Matt , Dell’Acqua Matteo , Dixon Laura E. , Filippi Carla V. , Fradgley Nick , Gardner Keith A. , Mackay Ian J. , O’Sullivan Donal , Percival-Alwyn Lawrence , Roorkiwal Manish , Singh Rakesh Kumar , Thudi Mahendar , Varshney Rajeev Kumar , Venturini Luca , Whan Alex , Cockram James , Mott Richard 
Published: July 2020

AbstractCrop populations derived from experimental crosses enable the genetic dissection of complex traits and support modern plant breeding. Among these, multi-parent populations now play a central role. By mixing and recombining the genomes of multiple founders, multi-parent populations combine many commonly sought beneficial properties of genetic mapping populations. For example, they have high power and resolution for mapping quantitative trait loci, high genetic diversity and minimal population structure. Many multi-parent populations have been constructed in crop species, and their inbred germplasm and associated phenotypic and genotypic data serve as enduring resources. Their utility has grown from being a tool for mapping quantitative trait loci to a means of providing germplasm for breeding programmes. Genomics approaches, including de novo genome assemblies and gene annotations for the population founders, have allowed the imputation of rich sequence information into the descendent population, expanding the breadth of research and breeding applications of multi-parent populations. Here, we report recent successes from crop multi-parent populations in crops. We also propose an ideal genotypic, phenotypic and germplasm ‘package’ that multi-parent populations should feature to optimise their use as powerful community resources for crop research, development and breeding.
Astrocytic Ca2+ signaling is reduced during sleep and is involved in the regulation of slow wave sleep
Authors: Bojarskaite Laura , Bjørnstad Daniel M. , Pettersen Klas H. , Cunen Céline , Hermansen Gudmund Horn , Åbjørsbråten Knut Sindre , Chambers Anna R. , Sprengel Rolf , Vervaeke Koen , Tang Wannan , Enger Rune , Nagelhus Erlend A. 
Published: July 2020

AbstractAstrocytic Ca2+ signaling has been intensively studied in health and disease but has not been quantified during natural sleep. Here, we employ an activity-based algorithm to assess astrocytic Ca2+ signals in the neocortex of awake and naturally sleeping mice while monitoring neuronal Ca2+ activity, brain rhythms and behavior. We show that astrocytic Ca2+ signals exhibit distinct features across the sleep-wake cycle and are reduced during sleep compared to wakefulness. Moreover, an increase in astrocytic Ca2+ signaling precedes transitions from slow wave sleep to wakefulness, with a peak upon awakening exceeding the levels during whisking and locomotion. Finally, genetic ablation of an important astrocytic Ca2+ signaling pathway impairs slow wave sleep and results in an increased number of microarousals, abnormal brain rhythms, and an increased frequency of slow wave sleep state transitions and sleep spindles. Our findings demonstrate an essential role for astrocytic Ca2+ signaling in regulating slow wave sleep.
Utilizing ion leaching effects for achieving high oxygen-evolving performance on hybrid nanocomposite with self-optimized behaviors
Authors: Guan Daqin , Ryu Gihun , Hu Zhiwei , Zhou Jing , Dong Chung-Li , Huang Yu-Cheng , Zhang Kaifeng , Zhong Yijun , Komarek Alexander C. , Zhu Ming , Wu Xinhao , Pao Chih-Wen , Chang Chung-Kai , Lin Hong-Ji , Chen Chien-Te , Zhou Wei , Shao Zongping 
Published: July 2020

AbstractIon leaching from pure-phase oxygen-evolving electrocatalysts generally exists, leading to the collapse and loss of catalyst crystalline matrix. Here, different from previous design methodologies of pure-phase perovskites, we introduce soluble BaCl2 and SrCl2 into perovskites through a self-assembly process aimed at simultaneously tuning dual cation/anion leaching effects and optimizing ion match in perovskites to protect the crystalline matrix. As a proof-of-concept, self-assembled hybrid Ba0.35Sr0.65Co0.8Fe0.2O3-δ (BSCF) nanocomposite (with BaCl2 and SrCl2) exhibits the low overpotential of 260 mV at 10 mA cm-2 in 0.1 M KOH. Multiple operando spectroscopic techniques reveal that the pre-leaching of soluble compounds lowers the difference of interfacial ion concentrations and thus endows the host phase in hybrid BSCF with abundant time and space to form stable edge/face-sharing surface structures. These self-optimized crystalline structures show stable lattice oxygen active sites and short reaction pathways between Co–Co/Fe metal active sites to trigger favorable adsorption of OH− species.
Marked T cell activation, senescence, exhaustion and skewing towards TH17 in patients with COVID-19 pneumonia
Authors: De Biasi Sara , Meschiari Marianna , Gibellini Lara , Bellinazzi Caterina , Borella Rebecca , Fidanza Lucia , Gozzi Licia , Iannone Anna , Lo Tartaro Domenico , Mattioli Marco , Paolini Annamaria , Menozzi Marianna , Milić Jovana , Franceschi Giacomo , Fantini Riccardo , Tonelli Roberto , Sita Marco , Sarti Mario , Trenti Tommaso , Brugioni Lucio , Cicchetti Luca , Facchinetti Fabio , Pietrangelo Antonello , Clini Enrico , Girardis Massimo , Guaraldi Giovanni , Mussini Cristina , Cossarizza Andrea 
Published: July 2020

AbstractThe immune system of patients infected by SARS-CoV-2 is severely impaired. Detailed investigation of T cells and cytokine production in patients affected by COVID-19 pneumonia are urgently required. Here we show that, compared with healthy controls, COVID-19 patients’ T cell compartment displays several alterations involving naïve, central memory, effector memory and terminally differentiated cells, as well as regulatory T cells and PD1+CD57+ exhausted T cells. Significant alterations exist also in several lineage-specifying transcription factors and chemokine receptors. Terminally differentiated T cells from patients proliferate less than those from healthy controls, whereas their mitochondria functionality is similar in CD4+ T cells from both groups. Patients display significant increases of proinflammatory or anti-inflammatory cytokines, including T helper type-1 and type-2 cytokines, chemokines and galectins; their lymphocytes produce more tumor necrosis factor (TNF), interferon-γ, interleukin (IL)-2 and IL-17, with the last observation implying that blocking IL-17 could provide a novel therapeutic strategy for COVID-19.
ctDNA applications and integration in colorectal cancer: an NCI Colon and Rectal–Anal Task Forces whitepaper
Authors: Dasari Arvind , Morris Van K. , Allegra Carmen J. , Atreya Chloe , Benson Al B. , Boland Patrick , Chung Ki , Copur Mehmet S. , Corcoran Ryan B. , Deming Dustin A. , Dwyer Andrea , Diehn Maximilian , Eng Cathy , George Thomas J. , Gollub Marc J. , Goodwin Rachel A. , Hamilton Stanley R. , Hechtman Jaclyn F. , Hochster Howard , Hong Theodore S. , Innocenti Federico , Iqbal Atif , Jacobs Samuel A. , Kennecke Hagen F. , Lee James J. , Lieu Christopher H. , Lenz Heinz-Josef , Lindwasser O. Wolf , Montagut Clara , Odisio Bruno , Ou Fang-Shu , Porter Laura , Raghav Kanwal , Schrag Deborah , Scott Aaron J. , Shi Qian , Strickler John H. , Venook Alan , Yaeger Rona , Yothers Greg , You Y. Nancy , Zell Jason A. , Kopetz Scott 
Published: July 2020

AbstractAn increasing number of studies are describing potential uses of circulating tumour DNA (ctDNA) in the care of patients with colorectal cancer. Owing to this rapidly developing area of research, the Colon and Rectal–Anal Task Forces of the United States National Cancer Institute convened a panel of multidisciplinary experts to summarize current data on the utility of ctDNA in the management of colorectal cancer and to provide guidance in promoting the efficient development and integration of this technology into clinical care. The panel focused on four key areas in which ctDNA has the potential to change clinical practice, including the detection of minimal residual disease, the management of patients with rectal cancer, monitoring responses to therapy, and tracking clonal dynamics in response to targeted therapies and other systemic treatments. The panel also provides general guidelines with relevance for ctDNA-related research efforts, irrespective of indication.
Enhancing droplet-based single-nucleus RNA-seq resolution using the semi-supervised machine learning classifier DIEM
Authors: Alvarez Marcus , Rahmani Elior , Jew Brandon , Garske Kristina M. , Miao Zong , Benhammou Jihane N. , Ye Chun Jimmie , Pisegna Joseph R. , Pietiläinen Kirsi H. , Halperin Eran , Pajukanta Päivi 
Published: July 2020

AbstractSingle-nucleus RNA sequencing (snRNA-seq) measures gene expression in individual nuclei instead of cells, allowing for unbiased cell type characterization in solid tissues. We observe that snRNA-seq is commonly subject to contamination by high amounts of ambient RNA, which can lead to biased downstream analyses, such as identification of spurious cell types if overlooked. We present a novel approach to quantify contamination and filter droplets in snRNA-seq experiments, called Debris Identification using Expectation Maximization (DIEM). Our likelihood-based approach models the gene expression distribution of debris and cell types, which are estimated using EM. We evaluated DIEM using three snRNA-seq data sets: (1) human differentiating preadipocytes in vitro, (2) fresh mouse brain tissue, and (3) human frozen adipose tissue (AT) from six individuals. All three data sets showed evidence of extranuclear RNA contamination, and we observed that existing methods fail to account for contaminated droplets and led to spurious cell types. When compared to filtering using these state of the art methods, DIEM better removed droplets containing high levels of extranuclear RNA and led to higher quality clusters. Although DIEM was designed for snRNA-seq, our clustering strategy also successfully filtered single-cell RNA-seq data. To conclude, our novel method DIEM removes debris-contaminated droplets from single-cell-based data fast and effectively, leading to cleaner downstream analysis. Our code is freely available for use athttps://github.com/marcalva/diem.
A quaternary ammonium silane antimicrobial triggers bacterial membrane and biofilm destruction
Authors: Daood Umer , Matinlinna Jukka P. , Pichika Malikarjuna Rao , Mak Kit-Kay , Nagendrababu Venkateshbabu , Fawzy Amr S. 
Published: July 2020

AbstractTo study the antimicrobial effects of quaternary ammonium silane (QAS) exposure on Streptococcus mutans and Lactobacillus acidophilus bacterial biofilms at different concentrations. Streptococcus mutans and Lactobacillus acidophilus biofilms were cultured on dentine disks, and incubated for bacterial adhesion for 3-days. Disks were treated with disinfectant (experimental QAS or control) and returned to culture for four days. Small-molecule drug discovery-suite was used to analyze QAS/Sortase-A active site. Cleavage of a synthetic fluorescent peptide substrate, was used to analyze inhibition of Sortase-A. Raman spectroscopy was performed and biofilms stained for confocal laser scanning microscopy (CLSM). Dentine disks that contained treated dual-species biofilms were examined using scanning electron microscopy (SEM). Analysis of DAPI within biofilms was performed using CLSM. Fatty acids in bacterial membranes were assessed with succinic-dehydrogenase assay along with time-kill assay. Sortase-A protein underwent conformational change due to QAS molecule during simulation, showing fluctuating alpha and beta strands. Spectroscopy revealed low carbohydrate intensities in 1% and 2% QAS. SEM images demonstrated absence of bacterial colonies after treatment. DAPI staining decreased with 1% QAS (p < 0.05). Fatty acid compositions of dual specie biofilm increased in both 1% and 2% QAS specimens (p < 0.05). Quaternary ammonium silane demonstrated to be a potent antibacterial cavity disinfectant and a plaque inhibitor and can be of potential significance in eliminating caries-forming bacteria.
Validating earliest rice farming in the Indonesian Archipelago
Authors: Deng Zhenhua , Hung Hsiao-chun , Carson Mike T. , Oktaviana Adhi Agus , Hakim Budianto , Simanjuntak Truman 
Published: July 2020

AbstractPreserved ancient botanical evidence in the form of rice phytoliths has confirmed that people farmed domesticated rice (Oryza sativa) in the interior of Sulawesi Island, Indonesia, by at least 3,500 years ago. This discovery helps to resolve a mystery about one of the region’s major events in natural and cultural history, by documenting when rice farming spread into Indonesia, ultimately from a source in mainland China. At the Minanga Sipakko site in Sulawesi, preserved leaf and husk phytoliths of rice show the diagnostic morphology of domesticated varieties, and the discarded husks indicate on-site processing of the crops. The phytoliths were contained within an undisturbed, subsurface archaeological layer of red-slipped pottery, a marker for an evidently sudden cultural change in the region that multiple radiocarbon results extend back to 3,500 years ago. The results from Minanga Sipakko allow factual evaluation of previously untested hypotheses about the timing, geographic pattern, and cultural context of the spread of rice farming into Indonesia, as well as the contribution of external immigrants in this process.
A sea-level monopole in the equatorial Indian Ocean
Authors: Thandlam Venugopal , T.V.S Udaya Bhaskar , Hasibur Rahaman , Luca Paolo De , Sahlée Erik , Rutgersson Anna , M Ravichandran , S.S.V.S Ramakrishna 
Published: July 2020

AbstractIn this study, we show the relationship between sea-level anomalies (SLA) and upper-ocean parameters in the Equatorial Indian Ocean (EIO). This work also focuses on the variability of SLA obtained from satellite altimeter data in different spatial and temporal scales and its relationship with computed ocean heat content (OHC), dynamic height (DH), and thermocline depth (20 °C isotherm: D20) during 1993–2015. SLA showed low Pearson’s correlation coefficient (CC) with upper-ocean parameters over central EIO resembling a “Monopole” pattern. The Array for Real-time Geostrophic Oceanography (ARGO) in situ profile data in the central EIO also confirmed this. SLA over this monopole showed low correlations with all parameters as compared with eastern and western EIO. These findings show a clear signature of a persisting sea-level monopole in the central EIO. Oscillating SLA over western and eastern EIO during summer and winter monsoon months is found to be responsible for locking this monopole in the central EIO. Both SLA and OHC increased in EIO during 2006–2015 compared with 1993–2005. The month of January showed different east–west trends at different times. This trend during 1993–2015 is neutral, but it shifted from negative during 1993–2005 to positive during 2006–2015.
Bias-controlled plasmon switching in lithium-doped graphene on dielectric model Al2O3 substrate
Authors: Despoja Vito , Jakovac Josip , Golenić Neven , Marušić Leonardo 
Published: July 2020

AbstractGraphene doped by lithium atoms supports a strong Dirac plasmon, a weak acoustic plasmon and a strong interband plasmon Li(π + σ). Here we demonstrate that applying a positive or negative bias on the lithium-doped graphene causes the appearance (‘switching ON’) or disappearance (‘switching OFF’) of the Li(π + σ) plasmon and the ‘conversion’ of the Dirac plasmon into a strong acoustic plasmon. This has two important consequences: 1. bias-controlled UV optical activity of the Li-doped graphene and 2. bias-controlled position of the 2D plasmon centroid. These effects turn out to be very robust and independent of the details of the experimental setup, which means that they should be easily experimentally verified, and very attractive for potential applications.
Structure of a DNA polymerase abortive complex with the 8OG:dA base pair at the primer terminus
Authors: Batra Vinod K. , Wilson Samuel H. 
Published: July 2020

AbstractAdenine frequently pairs with the Hoogsteen edge of an oxidized guanine base (8OG) causing G to T transversions. The (syn)8OG:dA base pair is indistinguishable from the cognant base pair and can be extended by DNA polymerases with reduced efficiency. To examine the structural basis of this reduced efficiency, we sought to obtain the structure of the “product” complex of DNA polymerase (pol) β with the (syn)8OG:dA base pair at the primer terminus by soaking the binary complex crystals with a hydrolysable dCTP analogue complementary to the template base G. Crystallographic refinement of the structure revealed that the adenine of the (syn)8OG:dA base pair had been expelled from the primer terminus and a dCMP was inserted opposite 8OG in a reverse orientation; another uninserted molecule of the analogue was bound to the templating base G. This leads to an abortive complex that could form the basis of oxidatively-induced pol β stalling.
The orphan nuclear receptor Nurr1 is responsive to non-steroidal anti-inflammatory drugs
Authors: Willems Sabine , Kilu Whitney , Ni Xiaomin , Chaikuad Apirat , Knapp Stefan , Heering Jan , Merk Daniel 
Published: July 2020

AbstractNuclear receptor related 1 (Nurr1) is an orphan ligand-activated transcription factor and considered as neuroprotective transcriptional regulator with great potential as therapeutic target for neurodegenerative diseases. However, the collection of available Nurr1 modulators and mechanistic understanding of Nurr1 are limited. Here, we report the discovery of several structurally diverse non-steroidal anti-inflammatory drugs as inverse Nurr1 agonists demonstrating that Nurr1 activity can be regulated bidirectionally. As chemical tools, these ligands enable unraveling the co-regulatory network of Nurr1 and the mode of action distinguishing agonists from inverse agonists. In addition to its ability to dimerize, we observe an ability of Nurr1 to recruit several canonical nuclear receptor co-regulators in a ligand-dependent fashion. Distinct dimerization states and co-regulator interaction patterns arise as discriminating factors of Nurr1 agonists and inverse agonists. Our results contribute a valuable collection of Nurr1 modulators and relevant mechanistic insights for future Nurr1 target validation and drug discovery.
Identification of novel activators of the metal responsive transcription factor (MTF-1) using a gene expression biomarker in a microarray compendium
Authors: Jackson Abigail C , Liu Jie , Vallanat Beena , Jones Carlton , Nelms Mark D , Patlewicz Grace , Corton J Christopher 
Published: July 2020

Abstract
Environmental exposure to metals is known to cause a number of human toxicities including cancer. Metal-responsive transcription factor 1 (MTF-1) is an important component of metal regulation systems in mammalian cells. Here, we describe a novel method to identify chemicals that activate MTF-1 based on microarray profiling data. MTF-1 biomarker genes were identified that exhibited consistent, robust expression across 10 microarray comparisons examining the effects of metals (zinc, nickel, lead, arsenic, mercury, and silver) on gene expression in human cells. A subset of the resulting 81 biomarker genes was shown to be altered by knockdown of the MTF1 gene including metallothionein family members and a zinc transporter. The ability to correctly identify treatment conditions that activate MTF-1 was determined by comparing the biomarker to microarray comparisons from cells exposed to reference metal activators of MTF-1 using the rank-based Running Fisher algorithm. The balanced accuracy for prediction was 93%. The biomarker was then used to identify organic chemicals that activate MTF-1 from a compendium of 11 725 human gene expression comparisons representing 2582 chemicals. There were 700 chemicals identified that included those known to interact with cellular metals, such as clioquinol and disulfiram, as well as a set of novel chemicals. All nine of the novel chemicals selected for validation were confirmed to activate MTF-1 biomarker genes in MCF-7 cells and to lesser extents in MTF1-null cells by qPCR and targeted RNA-Seq. Overall, our work demonstrates that the biomarker for MTF-1 coupled with the Running Fisher test is a reliable strategy to identify novel chemical modulators of metal homeostasis using gene expression profiling.
Oxidation of polyunsaturated fatty acids to produce lipid mediators
Authors: Christie William W. , Harwood John L. 
Published: July 2020

AbstractThe chemistry, biochemistry, pharmacology and molecular biology of oxylipins (defined as a family of oxygenated natural products that are formed from unsaturated fatty acids by pathways involving at least one step of dioxygen-dependent oxidation) are complex and occasionally contradictory subjects that continue to develop at an extraordinarily rapid rate. The term includes docosanoids (e.g. protectins, resolvins and maresins, or specialized pro-resolving mediators), eicosanoids and octadecanoids and plant oxylipins, which are derived from either the omega-6 (n-6) or the omega-3 (n-3) families of polyunsaturated fatty acids. For example, the term eicosanoid is used to embrace those biologically active lipid mediators that are derived from C20 fatty acids, and include prostaglandins, thromboxanes, leukotrienes, hydroxyeicosatetraenoic acids and related oxygenated derivatives. The key enzymes for the production of prostanoids are prostaglandin endoperoxide H synthases (cyclo-oxygenases), while lipoxygenases and oxidases of the cytochrome P450 family produce numerous other metabolites. In plants, the lipoxygenase pathway from C18 polyunsaturated fatty acids yields a variety of important products, especially the jasmonates, which have some comparable structural features and functions. Related oxylipins are produced by non-enzymic means (isoprostanes), while fatty acid esters of hydroxy fatty acids (FAHFA) are now being considered together with the oxylipins from a functional perspective. In all kingdoms of life, oxylipins usually act as lipid mediators through specific receptors, have short half-lives and have functions in innumerable biological contexts.