bluuebunny/crossref_metadata_2025_split huggingface dataset:
Signature of Geochemistry on Density‐Driven CO Mixing in Sandstone Aquifers
Authors: Erfani Hamidreza , Babaei Masoud , Niasar Vahid 
Published: February 2020

AbstractDensity‐driven mixing resulting from CO
injection into aquifers leads to the CO
entrapment mechanism of solubility trapping. Crucially, the coupled flow‐geochemistry and effects of geochemistry on density‐driven mixing process for “sandstone rocks” have not been adequately addressed. Often, there are conflicting remarks in the literature as to whether geochemistry promotes or undermines dissolution‐driven convection in sandstone aquifers. Against this backdrop, we simulate density‐driven mixing in sandstone aquifers by developing a 2‐D modified stream function formulation for multicomponent reactive convective‐diffusive CO
mixing. Two different cases corresponding to laboratory and field scales are studied to investigate the effect of rock‐fluid interaction on density‐driven mixing and the role of mineralization in carbon storage over the project life time. A complex sandstone mineralogical assemblage is considered, and solid‐phase reactions are assumed to be kinetic to study the length‐ and time‐scale dependency of the geochemistry effects. The study revealed nonuniform impact of rock‐fluid and fluid‐fluid interaction in early‐ and late‐time stages of the process. The results show that for moderate Rayleigh (Ra) numbers, rock‐fluid interactions adversely affect solubility trapping while improving the total carbon captured through mineral trapping. Simulation results in the range of 1,500 <
< 55,000 in the field‐scale model showed more pronounced impact of geochemistry for higher
numbers, as geochemistry stimulates the convective instabilities and improves the total sequestered carbon. This study gives new insights into the effect of rock‐fluid interactions on density‐driven mixing and solubility trapping in sandstone aquifers to improve estimation of the carbon storage capacity in deep saline aquifers.
UHRF1-repressed 5’-hydroxymethylcytosine is essential for the male meiotic prophase I
Authors: Pan Hongjie , Jiang Ning , Sun Shenfei , Jiang Hanwei , Xu Jianze , Jiang Xiaohua , Gao Qian , Li Liang , Wu Haili , Zheng Huajun , Qi Qi , Li Tianqi , Zhang Meixing , Zhang Lingling , Wan Xiaofeng , Lin Xinhua , Wong Jiemin , Shi Qinghua , Li Runsheng 
Published: February 2020

Abstract5’-hydroxymethylcytosine (5hmC), an important 5’-cytosine modification, is altered highly in order in male meiotic prophase. However, the regulatory mechanism of this dynamic change and the function of 5hmC in meiosis remain largely unknown. Using a knockout mouse model, we showed that UHRF1 regulated male meiosis. UHRF1 deficiency led to failure of meiosis and male infertility. Mechanistically, the deficiency of UHRF1 altered significantly the meiotic gene profile of spermatocytes. Uhrf1 knockout induced an increase of the global 5hmC level. The enrichment of hyper-5hmC at transcriptional start sites (TSSs) was highly associated with gene downregulation. In addition, the elevated level of the TET1 enzyme might have contributed to the higher 5hmC level in the Uhrf1 knockout spermatocytes. Finally, we reported Uhrf1, a key gene in male meiosis, repressed hyper-5hmC by downregulating TET1. Furthermore, UHRF1 facilitated RNA polymerase II (RNA-pol2) loading to promote gene transcription. Thus our study demonstrated a potential regulatory mechanism of 5hmC dynamic change and its involvement in epigenetic regulation in male meiosis.
Salmonella Typhimurium biofilm disruption by a human antibody that binds a pan-amyloid epitope on curli
Authors: Tursi Sarah A. , Puligedda Rama Devudu , Szabo Paul , Nicastro Lauren K. , Miller Amanda L. , Qiu Connie , Gallucci Stefania , Relkin Norman R. , Buttaro Bettina A. , Dessain Scott K. , Tükel Çagla 
Published: February 2020

AbstractBacterial biofilms, especially those associated with implanted medical devices, are difficult to eradicate. Curli amyloid fibers are important components of the biofilms formed by the Enterobacteriaceae family. Here, we show that a human monoclonal antibody with pan-amyloid-binding activity (mAb 3H3) can disrupt biofilms formed by Salmonella enterica serovar Typhimurium in vitro and in vivo. The antibody disrupts the biofilm structure, enhancing biofilm eradication by antibiotics and immune cells. In mice, 3H3 injections allow antibiotic-mediated clearance of catheter-associated S. Typhimurium biofilms. Thus, monoclonal antibodies that bind a pan-amyloid epitope have potential to prevent or eradicate bacterial biofilms.
Structure of the human cation–chloride cotransporter NKCC1 determined by single-particle electron cryo-microscopy
Authors: Yang Xiaoyong , Wang Qinzhe , Cao Erhu 
Published: February 2020

AbstractThe secondary active cation–chloride cotransporters (CCCs) utilize the existing Na+ and/or K+ gradients to move Cl− into or out of cells. NKCC1 is an intensively studied member of the CCC family and plays fundamental roles in regulating trans-epithelial ion movement, cell volume, chloride homeostasis and neuronal excitability. Here, we report a cryo-EM structure of human NKCC1 captured in a partially loaded, inward-open state. NKCC1 assembles into a dimer, with the first ten transmembrane (TM) helices harboring the transport core and TM11-TM12 helices lining the dimer interface. TM1 and TM6 helices break α-helical geometry halfway across the lipid bilayer where ion binding sites are organized around these discontinuous regions. NKCC1 may harbor multiple extracellular entryways and intracellular exits, raising the possibility that K+, Na+, and Cl− ions may traverse along their own routes for translocation. NKCC1 structure provides a blueprint for further probing structure–function relationships of NKCC1 and other CCCs.
Efficiency fluctuations and noise induced refrigerator-to-heater transition in information engines
Authors: Paneru Govind , Dutta Sandipan , Sagawa Takahiro , Tlusty Tsvi , Pak Hyuk Kyu 
Published: February 2020

AbstractUnderstanding noisy information engines is a fundamental problem of non-equilibrium physics, particularly in biomolecular systems agitated by thermal and active fluctuations in the cell. By the generalized second law of thermodynamics, the efficiency of these engines is bounded by the mutual information passing through their noisy feedback loop. Yet, direct measurement of the interplay between mutual information and energy has so far been elusive. To allow such examination, we explore here the entire phase-space of a noisy colloidal information engine, and study efficiency fluctuations due to the stochasticity of the mutual information and extracted work. We find that the average efficiency is maximal for non-zero noise level, at which the distribution of efficiency switches from bimodal to unimodal, and the stochastic efficiency often exceeds unity. We identify a line of anomalous, noise-driven equilibrium states that defines a refrigerator-to-heater transition, and test the generalized integral fluctuation theorem for continuous engines.
Single-cell sperm transcriptomes and variants from fathers of children with and without autism spectrum disorder
Authors: Tomoiaga Delia , Aguiar-Pulido Vanessa , Shrestha Shristi , Feinstein Paul , Levy Shawn E. , Mason Christopher E. , Rosenfeld Jeffrey A. 
Published: February 2020

AbstractThe human sperm is one of the smallest cells in the body, but also one of the most important, as it serves as the entire paternal genetic contribution to a child. Investigating RNA and mutations in sperm is especially relevant for diseases such as autism spectrum disorders (ASD), which have been correlated with advanced paternal age. Historically, studies have focused on the assessment of bulk sperm, wherein millions of individual sperm are present and only high-frequency variants can be detected. Using 10× Chromium single-cell sequencing technology, we assessed the transcriptome from >65,000 single spermatozoa across six sperm donors (scSperm-RNA-seq), including two who fathered multiple children with ASD and four fathers of neurotypical children. Using RNA-seq methods for differential expression and variant analysis, we found clusters of sperm mutations in each donor that are indicative of the sperm being produced by different stem cell pools. Finally, we have shown that genetic variations can be found in single sperm.
Pharmacological tools to mobilise mesenchymal stromal cells into the blood promote bone formation after surgery
Authors: Fellous Tariq G. , Redpath Andia N. , Fleischer Mackenzie M. , Gandhi Sapan , Hartner Samantha E. , Newton Michael D. , François Moïra , Wong Suet-Ping , Gowers Kate H. C. , Fahs Adam M. , Possley Daniel R. , Bonnet Dominique , Urquhart Paula , Nicolaou Anna , Baker Kevin C. , Rankin Sara M. 
Published: February 2020

AbstractTherapeutic approaches requiring the intravenous injection of autologous or allogeneic mesenchymal stromal cells (MSCs) are currently being evaluated for treatment of a range of diseases, including orthopaedic injuries. An alternative approach would be to mobilise endogenous MSCs into the blood, thereby reducing costs and obviating regulatory and technical hurdles associated with development of cell therapies. However, pharmacological tools for MSC mobilisation are currently lacking. Here we show that β3 adrenergic agonists (β3AR) in combination with a CXCR4 antagonist, AMD3100/Plerixafor, can mobilise MSCs into the blood in mice and rats. Mechanistically we show that reversal of the CXCL12 gradient across the bone marrow endothelium and local generation of endocannabinoids may both play a role in this process. Using a spine fusion model we provide evidence that this pharmacological strategy for MSC mobilisation enhances bone formation.
Resource use by individual Drosophila suzukii reveals a flexible preference for oviposition into healthy fruits
Authors: Kienzle Renate , Groß Lara B. , Caughman Shelby , Rohlfs Marko 
Published: February 2020

AbstractThe invasive pest fruit fly Drosophila suzukii is thought to be a specialist on healthy, i.e. unwounded, non-fermenting fruits. Morphological (sharp ovipositor) and neurophysiological/behavioural adaptations have been suggested to contribute to distinct adult feeding (wounded/microbe-laden fruits) and reproductive (healthy fruits) sites. We tested whether (1) variation in the overall availability of fruits, (2) variation in fruit type (healthy, wounded, fermenting), and (3) the relative abundance of different fruit types are ecological determinants of D. suzukii egg-laying decisions. Even though individual flies reduced their reproductive output when resource availability (blueberries) was low, a significantly higher proportion of eggs was allocated to healthy fruits, relative to wounded and fermenting fruits. However, the preference for healthy over wounded fruits declined continuously with a decrease in the relative abundance of healthy fruits and the overall reproductive output did not change. Under laboratory conditions, D. suzukii larvae achieved a higher developmental success on wounded than on healthy blueberries, but suffered less from density-dependent competition in healthy fruits. These data suggest that D. suzukii, despite showing an egg-laying preference for healthy fruits, also uses wounded/fermenting fruits as egg-laying sites, and that it may thrive well in windfall fruits.
iLoF: An intelligent Lab on Fiber Approach for Human Cancer Single-Cell Type Identification
Authors: Paiva Joana S. , Jorge Pedro A. S. , Ribeiro Rita S. R. , Balmaña Meritxell , Campos Diana , Mereiter Stefan , Jin Chunsheng , Karlsson Niclas G. , Sampaio Paula , Reis Celso A. , Cunha João P. S. 
Published: February 2020

AbstractWith the advent of personalized medicine, there is a movement to develop “smaller” and “smarter” microdevices that are able to distinguish similar cancer subtypes. Tumor cells display major differences when compared to their natural counterparts, due to alterations in fundamental cellular processes such as glycosylation. Glycans are involved in tumor cell biology and they have been considered to be suitable cancer biomarkers. Thus, more selective cancer screening assays can be developed through the detection of specific altered glycans on the surface of circulating cancer cells. Currently, this is only possible through time-consuming assays. In this work, we propose the “intelligent” Lab on Fiber (iLoF) device, that has a high-resolution, and which is a fast and portable method for tumor single-cell type identification and isolation. We apply an Artificial Intelligence approach to the back-scattered signal arising from a trapped cell by a micro-lensed optical fiber. As a proof of concept, we show that iLoF is able to discriminate two human cancer cell models sharing the same genetic background but displaying a different surface glycosylation profile with an accuracy above 90% and a speed rate of 2.3 seconds. We envision the incorporation of the iLoF in an easy-to-operate microchip for cancer identification, which would allow further biological characterization of the captured circulating live cells.
A preliminary study on the potential of Nanopore MinION and Illumina MiSeq 16S rRNA gene sequencing to characterize building-dust microbiomes
Authors: Nygaard Anders B. , Tunsjø Hege S. , Meisal Roger , Charnock Colin 
Published: February 2020

AbstractThere is a growing awareness of the importance of indoor microbiomes for human health. Given their complexity, these microbiomes can only be adequately surveyed using high throughput sequencing techniques. Oxford Nanopore’s MinION is the newest third generation sequencing technology on the market. With its many advantages such as portability, user friendliness, simplicity, speed of sequencing and long read length, the technology is now an actual contender to established sequencing platforms. MinION’s main disadvantage is a relatively low read accuracy compared to several other platforms, although this is constantly improving. The present study, which appears to be the first of its kind, provides the results of a preliminary analysis of the microbial communities in indoor environments based on 16S rRNA gene amplicon sequencing, using both the Oxford Nanopore Technologies (ONT) MinIOn and the Illumina MiSeq DNA sequencers. At the level of family and above, there was no significant difference between the microbial compositions as revealed by the two platforms. However, at the genus, and particularly at the species level, the ONT MinION reported greater taxonomic resolution than Illumina MiSeq.
Intestinal intermediate filament polypeptides in C. elegans: Common and isotype-specific contributions to intestinal ultrastructure and function
Authors: Geisler Florian , Coch Richard A. , Richardson Christine , Goldberg Martin , Bevilacqua Carlo , Prevedel Robert , Leube Rudolf E. 
Published: February 2020

AbstractThe abundance and diversity of intermediate filaments (IFs) in the C. elegans intestine indicate important contributions to intestinal function and organismal wellbeing. Fluorescent IF reporters localize below the actin-rich brush border and are highly enriched in the lumen-enveloping endotube, which is attached to the C. elegans apical junction. Mapping intestinal viscoelasticity by contact-free Brillouin microscopy reveals that the IF-rich endotube is positioned at the interface between the stiff brush border and soft cytoplasm suggesting a mechanical buffering function to deal with the frequent luminal distortions occurring during food intake and movement. In accordance, depletion of IFB-2, IFC-2 and IFD-2 leads to intestinal lumen dilation although depletion of IFC-1, IFD-1 and IFP-1 do not. Ultrastructural analyses of loss of function mutants further show that IFC-2 mutants have a rarefied endotube and IFB-2 mutants lack an endotube altogether. Remarkably, almost all IFB-2- and IFC-2-deficient animals develop to fertile adults. But developmental retardation, reduced brood size, altered survival and increased sensitivity to microbial toxin, osmotic and oxidative stress are seen in both mutants albeit to different degrees. Taken together, we propose that individual intestinal IF polypeptides contribute in different ways to endotube morphogenesis and cooperate to cope with changing environments.
Novel Strain of the Chronic Wasting Disease Agent Isolated From Experimentally Inoculated Elk With LL132 Prion Protein
Authors: Moore Jo , Tatum Trudy , Hwang Soyoun , Vrentas Catherine , West Greenlee M. Heather , Kong Qingzhong , Nicholson Eric , Greenlee Justin 
Published: February 2020

AbstractChronic wasting disease (CWD) is a fatal, progressive disease that affects cervid species, including Rocky mountain elk (Cervus elaphus nelsoni). There are 2 allelic variants in the elk prion protein gene: L132 (leucine) and M132 (methionine). Following experimental oral challenge with the CWD agent incubation periods are longest in LL132 elk, intermediate in ML132 elk, and shortest in MM132 elk. In order to ascertain whether such CWD-infected elk carry distinct prion strains, groups of Tg12 mice that express M132 elk prion protein were inoculated intracranially with brain homogenate from individual CWD-infected elk of various genotypes (LL132, LM132, or MM132). Brain samples were examined for microscopic changes and assessment of the biochemical properties of disease-associated prion protein (PrPSc). On first passage, mice challenged with LL132 elk inoculum had prolonged incubation periods and greater PrPSc fibril stability compared to mice challenged with MM132 or LM132 inoculum. On second passage, relative incubation periods, western blot profiles, and neuropathology were maintained. These results suggest that the CWD prion isolated from LL132 elk is a novel CWD strain and that M132 PrPC is able to propagate some biophysical properties of the L132 PrPSc conformation.
Towards standardisation of contact and contactless electrical measurements of CVD graphene at the macro-, micro- and nano-scale
Authors: Melios Christos , Huang Nathaniel , Callegaro Luca , Centeno Alba , Cultrera Alessandro , Cordon Alvaro , Panchal Vishal , Arnedo Israel , Redo-Sanchez Albert , Etayo David , Fernandez Montserrat , Lopez Alex , Rozhko Sergiy , Txoperena Oihana , Zurutuza Amaia , Kazakova Olga 
Published: February 2020

AbstractGraphene has become the focus of extensive research efforts and it can now be produced in wafer-scale. For the development of next generation graphene-based electronic components, electrical characterization of graphene is imperative and requires the measurement of work function, sheet resistance, carrier concentration and mobility in both macro-, micro- and nano-scale. Moreover, commercial applications of graphene require fast and large-area mapping of electrical properties, rather than obtaining a single point value, which should be ideally achieved by a contactless measurement technique. We demonstrate a comprehensive methodology for measurements of the electrical properties of graphene that ranges from nano- to macro- scales, while balancing the acquisition time and maintaining the robust quality control and reproducibility between contact and contactless methods. The electrical characterisation is achieved by using a combination of techniques, including magneto-transport in the van der Pauw geometry, THz time-domain spectroscopy mapping and calibrated Kelvin probe force microscopy. The results exhibit excellent agreement between the different techniques. Moreover, we highlight the need for standardized electrical measurements in highly controlled environmental conditions and the application of appropriate weighting functions.
Plasma microRNA profiles: identification of miR-1229-3p as a novel chemoresistant and prognostic biomarker in gastric cancer
Authors: Nishibeppu Keiji , Komatsu Shuhei , Imamura Taisuke , Kiuchi Jun , Kishimoto Takuma , Arita Tomohiro , Kosuga Toshiyuki , Konishi Hirotaka , Kubota Takeshi , Shiozaki Atsushi , Fujiwara Hitoshi , Okamoto Kazuma , Otsuji Eigo 
Published: February 2020

AbstractThis study aimed to explore novel microRNAs in plasma for predicting chemoresistance in adjuvant chemotherapy for patients with gastric cancer (GC). We used the Toray 3D-Gene microRNA array-based approach to compare preoperative plasma microRNA levels between GC patients with and without recurrences after curative gastrectomy. All patients underwent adjuvant chemotherapy with S-1, an oral fluoropyrimidine. Of 2566 candidates, six candidate microRNAs (miR-1229-3p, 1249-5p, 762, 711, 1268a and 1260b), which were highly expressed in the preoperative plasma of patients with subsequent recurrences, were selected. In a large-scale validation analysis by quantitative RT-PCR, we focused on high plasma levels of miR-1229-3p, which was an independent poor prognostic factor for recurrence free survival (P = 0.009, HR = 3.71). Overexpression of miR-1229-3p in GC cells induced significant chemoresistance to 5-fluorouracil (5-FU), up-regulation of thymidylate synthase (TS) and dihydroprimidine dehydrogenase (DPD) and down-regulation of SLC22A7 both in vitro and in vivo. Intraperitoneal injection of miR-1229-3p in mice induced significant chemoresistance to 5-FU, accompanied by high levels of miR-1229-3p in plasma and tumor tissue. These findings suggest that plasma miR-1229-3p might be a clinically useful biomarker for predicting chemoresistance to S-1 and selecting other or combined intensive chemotherapy regimens in GC patients.
Global distribution patterns and niche modelling of the invasive Kalanchoe × houghtonii (Crassulaceae)
Authors: Herrando-Moraira Sonia , Vitales Daniel , Nualart Neus , Gómez-Bellver Carlos , Ibáñez Neus , Massó Sergi , Cachón-Ferrero Pilar , González-Gutiérrez Pedro A. , Guillot Daniel , Herrera Ileana , Shaw Daniel , Stinca Adriano , Wang Zhiqiang , López-Pujol Jordi 
Published: February 2020

AbstractInvasive alien species are currently considered one of the main threats to global biodiversity. One of the most rapidly expanding invasive plants in recent times is Kalanchoe × houghtonii (Crassulaceae), an artificial hybrid created in the 1930s in the United States by experimental crossings between K. daigremontiana and K. tubiflora, two species endemic to Madagascar. Thanks to its large colonizing capacity (mainly derived from the production of asexual plantlets), K. × houghtonii soon escaped from cultivation and quickly spread in many parts of the world. However, its actual range is not well known due to the lack of a formal description until recent times (2006) and its strong morphological resemblance with one of its parentals (K. daigremontiana). The present study was aimed, in the first instance, to delimit the present distribution area of K. × houghtonii at the global scale by gathering and validating all its occurrences and to track its colonization history. Currently, K. × houghtonii can be found on all continents except Antarctica, although it did not reach a global distribution until the 2000s. Its potential distribution, estimated with MaxEnt modelling software, is mainly centered in subtropical regions, from 20° to 40° of both northern and southern latitudes, mostly in areas with a high anthropogenic activity. Unexpectedly, concomitant to a poleward migration, future niche models suggest a considerable reduction of its range by up to one-third compared to the present, which might be related with the Crassulaceaean Acid Metabolism (CAM) of K. × houghtonii. Further research may shed light as to whether a decrease in potential habitats constitutes a general pattern for Crassulaceae and CAM plants.