bluuebunny/crossref_metadata_2025_split huggingface dataset:
A unifying mechanism for cation effect modulating C1 and C2 productions from CO2 electroreduction
Authors: Shin Seung-Jae , Choi Hansol , Ringe Stefan , Won Da Hye , Oh Hyung-Suk , Kim Dong Hyun , Lee Taemin , Nam Dae-Hyun , Kim Hyungjun , Choi Chang Hyuck 
Published: September 2022

AbstractElectrocatalysis, whose reaction venue locates at the catalyst–electrolyte interface, is controlled by the electron transfer across the electric double layer, envisaging a mechanistic link between the electron transfer rate and the electric double layer structure. A fine example is in the CO2 reduction reaction, of which rate shows a strong dependence on the alkali metal cation (M+) identity, but there is yet to be a unified molecular picture for that. Using quantum-mechanics-based atom-scale simulation, we herein scrutinize the M+-coupling capability to possible intermediates, and establish H+- and M+-associated ET mechanisms for CH4 and CO/C2H4 formations, respectively. These theoretical scenarios are successfully underpinned by Nernstian shifts of polarization curves with the H+ or M+ concentrations and the first-order kinetics of CO/C2H4 formation on the electrode surface charge density. Our finding further rationalizes the merit of using Nafion-coated electrode for enhanced C2 production in terms of enhanced surface charge density.
Angiocrine extracellular vesicles impose mesenchymal reprogramming upon proneural glioma stem cells
Authors: Adnani Lata , Kassouf Jordan , Meehan Brian , Spinelli Cristiana , Tawil Nadim , Nakano Ichiro , Rak Janusz 
Published: September 2022

AbstractGlioblastoma (GBM) is an incurable form of primary astrocytic brain tumor driven by glioma stem cell (GSC) compartment closely associated with the vascular niche. GSC phenotypes are heterogeneous and range from proneural to mesenchymal-like, the latter characterised by greater invasiveness. Here we document the secretory (angiocrine) role of endothelial cells and their derived extracellular vesicles (EVs) as drivers of proneural-to-mesenchymal reprogramming of GSCs. These changes involve activation of matrix metalloproteinases (MMPs) and NFκB, and inactivation of NOTCH, while altering responsiveness to chemotherapy and driving infiltrative growth in the brain. Our findings suggest that EV-mediated angiocrine interactions impact the nature of cellular stemness in GBM with implications for disease biology and therapy.
Transformation of primary sensory cortical representations from layer 4 to layer 2
Authors: Voelcker Bettina , Pancholi Ravi , Peron Simon 
Published: September 2022

AbstractSensory input arrives from thalamus in cortical layer (L) 4, which outputs predominantly to superficial layers. L4 to L2 thus constitutes one of the earliest cortical feedforward networks. Despite extensive study, the transformation performed by this network remains poorly understood. We use two-photon calcium imaging to record neural activity in L2-4 of primary vibrissal somatosensory cortex (vS1) as mice perform an object localization task with two whiskers. Touch responses sparsen and become more reliable from L4 to L2, with nearly half of the superficial touch response confined to ~1 % of excitatory neurons. These highly responsive neurons have broad receptive fields and can more accurately decode stimulus features. They participate disproportionately in ensembles, small subnetworks with elevated pairwise correlations. Thus, from L4 to L2, cortex transitions from distributed probabilistic coding to sparse and robust ensemble-based coding, resulting in more efficient and accurate representations.
A stem cell roadmap of ribosome heterogeneity reveals a function for RPL10A in mesoderm production
Authors: Genuth Naomi R. , Shi Zhen , Kunimoto Koshi , Hung Victoria , Xu Adele F. , Kerr Craig H. , Tiu Gerald C. , Oses-Prieto Juan A. , Salomon-Shulman Rachel E. A. , Axelrod Jeffrey D. , Burlingame Alma L. , Loh Kyle M. , Barna Maria 
Published: September 2022

AbstractRecent findings suggest that the ribosome itself modulates gene expression. However, whether ribosomes change composition across cell types or control cell fate remains unknown. Here, employing quantitative mass spectrometry during human embryonic stem cell differentiation, we identify dozens of ribosome composition changes underlying cell fate specification. We observe upregulation of RPL10A/uL1-containing ribosomes in the primitive streak followed by progressive decreases during mesoderm differentiation. An Rpl10a loss-of-function allele in mice causes striking early mesodermal phenotypes, including posterior trunk truncations, and inhibits paraxial mesoderm production in culture. Ribosome profiling in Rpl10a loss-of-function mice reveals decreased translation of mesoderm regulators, including Wnt pathway mRNAs, which are also enriched on RPL10A/uL1-containing ribosomes. We further show that RPL10A/uL1 regulates canonical and non-canonical Wnt signaling during stem cell differentiation and in the developing embryo. These findings reveal unexpected ribosome composition modularity that controls differentiation and development through the specialized translation of key signaling networks.
SeqCode: a nomenclatural code for prokaryotes described from sequence data
Authors: Hedlund Brian P. , Chuvochina Maria , Hugenholtz Philip , Konstantinidis Konstantinos T. , Murray Alison E. , Palmer Marike , Parks Donovan H. , Probst Alexander J. , Reysenbach Anna-Louise , Rodriguez-R Luis M. , Rossello-Mora Ramon , Sutcliffe Iain C. , Venter Stephanus N. , Whitman William B. 
Published: September 2022

AbstractMost prokaryotes are not available as pure cultures and therefore ineligible for naming under the rules and recommendations of the International Code of Nomenclature of Prokaryotes (ICNP). Here we summarize the development of the SeqCode, a code of nomenclature under which genome sequences serve as nomenclatural types. This code enables valid publication of names of prokaryotes based upon isolate genome, metagenome-assembled genome or single-amplified genome sequences. Otherwise, it is similar to the ICNP with regard to the formation of names and rules of priority. It operates through the SeqCode Registry (https://seqco.de/), a registration portal through which names and nomenclatural types are registered, validated and linked to metadata. We describe the two paths currently available within SeqCode to register and validate names, includingCandidatusnames, and provide examples for both. Recommendations on minimal standards for DNA sequences are provided. Thus, the SeqCode provides a reproducible and objective framework for the nomenclature of all prokaryotes regardless of cultivability and facilitates communication across microbiological disciplines.
A functional selection reveals previously undetected anti-phage defence systems in the E. coli pangenome
Authors: Vassallo Christopher N. , Doering Christopher R. , Littlehale Megan L. , Teodoro Gabriella I. C. , Laub Michael T. 
Published: September 2022

AbstractThe ancient, ongoing coevolutionary battle between bacteria and their viruses, bacteriophages, has given rise to sophisticated immune systems including restriction-modification and CRISPR-Cas. Many additional anti-phage systems have been identified using computational approaches based on genomic co-location within defence islands, but these screens may not be exhaustive. Here we developed an experimental selection scheme agnostic to genomic context to identify defence systems in 71 diverse E. coli strains. Our results unveil 21 conserved defence systems, none of which were previously detected as enriched in defence islands. Additionally, our work indicates that intact prophages and mobile genetic elements are primary reservoirs and distributors of defence systems in E. coli, with defence systems typically carried in specific locations or hotspots. These hotspots encode dozens of additional uncharacterized defence system candidates. Our findings reveal an extended landscape of antiviral immunity in E. coli and provide an approach for mapping defence systems in other species.
Lactococcus lactis engineered to deliver hCAP18 cDNA alleviates DNBS-induced colitis in C57BL/6 mice by promoting IL17A and IL10 cytokine expression
Authors: Noguès Esther Borras , Kropp Camille , Bétemps Laureline , de Sousa Cassiana , Chain Florian , Auger Sandrine , Azevedo Vasco , Langella Philippe , Chatel Jean-Marc 
Published: September 2022

AbstractWith its antimicrobial and immunomodulating properties, the cathelicidin (LL37) plays an important role in innate immune system. Here, we attempted to alleviate chemically induced colitis using a lactococci strain that either directly expressed the precursor to LL37, hCAP18 (LL-pSEC:hCAP18), or delivered hCAP18 cDNA to host cells under the control of the cytomegalovirus promoter (LL-Probi-H1:hCAP18). We also investigated whether the alleviation of symptoms could be explained through modification of the gut microbiota by hCAP18. Mice were administered daily doses of LL-pSEC:hCAP18 or LL-Probi-H1:hCAP18. On day 7, colitis was induced by DNBS. During autopsy, we assessed macroscopic tissue damage in the colon and collected tissue samples for the characterization of inflammation markers and histological analysis. Feces were collected at day 7 for 16S DNA sequencing. We also performed a fecal transplant experiment in which mice underwent colon washing and received feces from Lactococcus lactis-treated mice before DNBS-colitis induction. Treatment with LL-Probi-H1:hCAP18 reduced the severity of colitis symptoms. The protective effects were accompanied by increased levels of IL17A and IL10 in mesenteric lymph node cells. L. lactis administration altered the abundance of Lachnospiraceae and Muribaculaceae. However, fecal transplant from L. lactis-treated mice did not improve DNBS-induced symptoms in recipient mice.
Inhibitors of RNA and protein synthesis cause Glut4 translocation and increase glucose uptake in adipocytes
Authors: Meriin A. B. , Zaarur N. , Bogan J. S. , Kandror K. V. 
Published: September 2022

AbstractInsulin stimulates glucose uptake in adipocytes by triggering translocation of glucose transporter 4-containg vesicles to the plasma membrane. Under basal conditions, these vesicles (IRVs for insulin-responsive vesicles) are retained inside the cell via a “static” or “dynamic” mechanism. We have found that inhibitors of RNA and protein synthesis, actinomycin D and emetine, stimulate Glut4 translocation and glucose uptake in adipocytes without engaging conventional signaling proteins, such as Akt, TBC1D4, or TUG. Actinomycin D does not significantly affect endocytosis of Glut4 or recycling of transferrin, suggesting that it specifically increases exocytosis of the IRVs. Thus, the intracellular retention of the IRVs in adipocytes requires continuous RNA and protein biosynthesis de novo. These results point out to the existence of a short-lived inhibitor of IRV translocation thus supporting the “static” model.
Hydromechanical impact of basement rock on injection-induced seismicity in Illinois Basin
Authors: Bondarenko Nikita , Podladchikov Yury , Makhnenko Roman 
Published: September 2022

AbstractThe common explanation of observed injection-induced microseismicity is based on the measured stress state at the injection interval and the assumption that it remains the same in the vicinity. We argue here that representing the stress state in different geologic formations over the injection site with the single Mohr’s circle is insufficient due to local stratigraphic features and contrast in compressibilities of the involved formations. The role of hydromechanical coupling in the microseismic response is also crucial for the proper assessment of the problem. Thoroughly monitored Illinois Basin Decatur Project revealed the majority of CO2 injection-associated microseismic events being originated in the crystalline basement. Even though basement faults can serve as the conduits for fluid flow—the predicted pressure increase seems to be insufficient to trigger seismicity. To address this issue, accurate laboratory measurements of rock properties from the involved formations are conducted. The pre-injection stress state and its evolution are evaluated with the hydromechanically coupled numerical model. It appears that the presence of an offset in a stiff competent layer affects the stress state in its vicinity. Therefore, both the pre-injection stress state and its evolution during the fluid injection should be addressed during the induced seismicity assessment.
Integrated analysis to study the interplay between post-translational modifications (PTM) in hepatitis C virus proteins and hepatocellular carcinoma (HCC) development
Authors: Ikram Aqsa , Rauff Bisma , Alzahrani Badr , Awan Faryal Mehwish , Obaid Ayesha , Naz Anam , Kakar Salik Javed , Janjua Hussnain Ahmed 
Published: September 2022

AbstractMany PTMs dysregulation is known to be the major cause of many cancers including HCV induced HCC. PTMs of hepatitis C virus (HCV) regions NS3/4A, NS5A and NS5B are crucial for proper protein functions and replication that directly affect the generation of infectious virus particles and completion of its life cycle. In this study, we have performed comprehensive analysis of PTMs within HCV non-structural proteins (NS3/4A, NS5A and NS5B) through bioinformatics analysis to examine post-translational crosstalk between phosphorylation, palmitoylation, methylation, acetylation and ubiquitination sites in selected viral proteins. Our analysis has revealed many highly putative PTMs sites that are also conserved among major genotypes conferring the importance of these sites. We have also analysed viral 3D structures in their modified and unmodified forms to address extent and signatures of structural changes upon PTM. This study provides evidence that PTMs induce significant conformational changes and make viral proteins more stable. To find the potential role of PTMs in HCV induced HCC, docking analysis between selected viral proteins and p38-MAPK has been performed which also confirms their strong association with HCV induced HCC. The major findings proposed that PTMs at specific sites of HCV viral proteins could dysregulate specific pathways that cause the development of HCC.
Mortality in patients with acquired human immunodeficiency virus infection hospitalized in an intensive care unit during the period 2017–2019
Authors: Ruiz Guillermo Ortiz , Herrera Carlos Felipe López , Bohórquez Jorge Andrés Mahecha , Betancur John Edison 
Published: September 2022

AbstractIdentify risk factors associated with mortality in HIV patients admitted to an ICU in the city of Bogotá. Retrospective cohort study of patients treated in an ICU during the years 2017–2019. The analysis included descriptive statistics, association tests, and a logistic regression model. A predictive model of mortality at the time of admission to the ICU was developed. 110 HIV patients were identified. Association was found between a Charlson index ≥ 6 and mortality (OR = 2.3, 95% CI 1.0–5.1) and an increase in mortality in the first 21 days of ICU stay (OR = 2.2, 95% CI 1.0–4.9). In the logistic regression analysis, the absence of highly active antiretroviral therapy (HAART) upon admission to the ICU (OR = 2.5 95% CI 1.0–6.1) and the first 21 days of ICU stay (OR = 2.3 95% CI 1.0–5.4) were associated with an increase in mortality. The predictive mortality model established that mortality was higher in patients admitted to the ICU without having previously received HAART than in those who did receive therapy at the time of admission to the ICU. In patients with HIV admitted to the ICU, the absence of HAART will negatively impact mortality during their hospital stay.
Perception of the non-dominant hand as larger after non-judgmental focus on its details
Authors: Ghaderi Ata , Welch Elisabeth 
Published: September 2022

AbstractWe investigated whether brief non-judgmental focus on the details of one’s non-dominant hand might lead to changes in perception of its size, and if such a change would be related to central coherence, body dissatisfaction, or how much participants liked their hand. After two pilot experiments (N = 28 and N = 30 respectively: Appendix 1), a within-subject experiment (N = 82) was conducted. Subjects were mainly university students. They were asked to rate the size of their non-dominant hand and how much they liked it, and the size of an external object (a X-box controller) on a visual-analog scale before and after focusing on their details for 5 min, as well as the size of another object (a calculator) before and after a 5 min long distraction task. After completing the tasks, they were asked to respond to a brief questionnaire on body dissatisfaction. A s significant interaction between time and factors (non-dominant hand, X-box controller and calculator) emerged (F(2, 78) = 6.41, p = .003). Participants rated their hand as larger after focusing on its details compared to baseline, and this change was significantly larger than those reported for the X-box controller. No significant change in how they liked their hand was observed, and contrary to the pilot experiments, the perceived change in size of the hand was not related to body dissatisfaction. The significant change in reporting of the size of the hand after focusing on its details seems to be an interesting finding, worth further replications.
Modification of the immune response by bacteriophages alters methicillin-resistant Staphylococcus aureus infection
Authors: Suda Tomoya , Hanawa Tomoko , Tanaka Mayuko , Tanji Yasunori , Miyanaga Kazuhiko , Hasegawa-Ishii Sanae , Shirato Ken , Kizaki Takako , Matsuda Takeaki 
Published: September 2022

AbstractThere is an urgent need to develop phage therapies for multidrug-resistant bacterial infections. However, although bacteria have been shown to be susceptible to phage therapy, phage therapy is not sufficient in some cases. PhiMR003 is a methicillin-resistant Staphylococcus aureus phage previously isolated from sewage influent, and it has demonstrated high lytic activity and a broad host range to MRSA clinical isolates in vitro. To investigate the potential of phiMR003 for the treatment of MRSA infection, the effects of phiMR003 on immune responses in vivo were analysed using phiMR003-susceptible MRSA strains in a mouse wound infection model. Additionally, we assessed whether phiMR003 could affect the immune response to infection with a nonsusceptible MRSA strain. Interestingly, wounds infected with both susceptible and nonsusceptible MRSA strains treated with phiMR003 demonstrated decreased bacterial load, reduced inflammation and accelerated wound closure. Moreover, the infiltration of inflammatory cells in infected tissue was altered by phiMR003. While the effects of phiMR003 on inflammation and bacterial load disappeared with heat inactivation of phiMR003. Transcripts of proinflammatory cytokines induced by lipopolysaccharide were reduced in mouse peritoneal macrophages. These results show that the immune modulation occurring as a response to the phage itself improves the clinical outcomes of phage therapy.
Evaluation of different 89Zr-labeled synthons for direct labeling and tracking of white blood cells and stem cells in healthy athymic mice
Authors: Bansal Aditya , Sharma Shalini , Klasen Benedikt , Rösch Frank , Pandey Mukesh K. 
Published: September 2022

AbstractCell based therapies are evolving as an effective new approach to treat various diseases. To understand the safety, efficacy, and mechanism of action of cell-based therapies, it is imperative to follow their biodistribution noninvasively. Positron-emission-tomography (PET)-based non-invasive imaging of cell trafficking offers such a potential. Herein, we evaluated and compared three different ready-to-use direct cell radiolabeling synthons, [89Zr]Zr-DFO-Bn-NCS, [89Zr]Zr-Hy3ADA5-NCS, and [89Zr]Zr-Hy3ADA5-SA for PET imaging-based trafficking of white blood cells (WBCs) and stem cells (SCs) up to 7 days in athymic nude mice. We compared the degree of 89Zr complexation and percentage of cell radiolabeling efficiencies with each. All three synthons, [89Zr]Zr-DFO-Bn-NCS, [89Zr]Zr-Hy3ADA5-NCS, and [89Zr]Zr-Hy3ADA5-SA, were successfully prepared, and used for radiolabeling of WBCs and SCs. The highest cell radiolabeling yield was found for [89Zr]Zr-DFO-Bn-NCS, followed by [89Zr]Zr-Hy3ADA5-NCS, and [89Zr]Zr-Hy3ADA5-SA. In terms of biodistribution, WBCs radiolabeled with [89Zr]Zr-DFO-Bn-NCS or [89Zr]Zr-Hy3ADA5-NCS, were primarily accumulated in liver and spleen, whereas SCs radiolabeled with [89Zr]Zr-DFO-Bn-NCS or [89Zr]Zr-Hy3ADA5-NCS were found in lung, liver and spleen. A high bone uptake was observed for both WBCs and SCs radiolabeled with [89Zr]Zr-Hy3ADA5-SA, suggesting in-vivo instability of [89Zr]Zr-Hy3ADA5-SA synthon. This study offers an appropriate selection of ready-to-use radiolabeling synthons for noninvasive trafficking of WBCs, SCs and other cell-based therapies.
Oligomerization state of the functional bacterial twin-arginine translocation (Tat) receptor complex
Authors: Sharma Ankith , Chowdhury Rajdeep , Musser Siegfried M. 
Published: September 2022

AbstractThe twin-arginine translocation (Tat) system transports folded proteins across bacterial and plastid energy transducing membranes. Ion leaks are generally considered to be mitigated by the creation and destruction of the translocation conduit in a cargo-dependent manner, a mechanism that enables tight sealing around a wide range of cargo shapes and sizes. In contrast to the variable stoichiometry of the active translocon, the oligomerization state of the receptor complex is considered more consistently stable but has proved stubbornly difficult to establish. Here, using a single molecule photobleaching analysis of individual inverted membrane vesicles, we demonstrate that Tat receptor complexes are tetrameric in native membranes with respect to both TatB and TatC. This establishes a maximal diameter for a resting state closed pore. A large percentage of Tat-deficient vesicles explains the typically low transport efficiencies observed. This individual reaction chamber approach will facilitate examination of the effects of stochastically distributed molecules.
Reactivity of aminophenols in forming nitrogen-containing brown carbon from iron-catalyzed reactions
Authors: Al-Abadleh Hind A. , Motaghedi Fatemeh , Mohammed Wisam , Rana Md Sohel , Malek Kotiba A. , Rastogi Dewansh , Asa-Awuku Akua A. , Guzman Marcelo I. 
Published: September 2022

AbstractNitrogen-containing organic carbon (NOC) in atmospheric particles is an important class of brown carbon (BrC). Redox active NOC like aminophenols received little attention in their ability to form BrC. Here we show that iron can catalyze dark oxidative oligomerization of o- and p-aminophenols under simulated aerosol and cloud conditions (pH 1–7, and ionic strength 0.01–1 M). Homogeneous aqueous phase reactions were conducted using soluble Fe(III), where particle growth/agglomeration were monitored using dynamic light scattering. Mass yield experiments of insoluble soot-like dark brown to black particles were as high as 40%. Hygroscopicity growth factors (κ) of these insoluble products under sub- and super-saturated conditions ranged from 0.4–0.6, higher than that of levoglucosan, a prominent proxy for biomass burning organic aerosol (BBOA). Soluble products analyzed using chromatography and mass spectrometry revealed the formation of ring coupling products of o- and p-aminophenols and their primary oxidation products. Heterogeneous reactions of aminophenol were also conducted using Arizona Test Dust (AZTD) under simulated aging conditions, and showed clear changes to optical properties, morphology, mixing state, and chemical composition. These results highlight the important role of iron redox chemistry in BrC formation under atmospherically relevant conditions.