bluuebunny/crossref_metadata_2025_split huggingface dataset:
RNase III CLASH in MRSA uncovers sRNA regulatory networks coupling metabolism to toxin expression
Authors: McKellar Stuart W. , Ivanova Ivayla , Arede Pedro , Zapf Rachel L. , Mercier Noémie , Chu Liang-Cui , Mediati Daniel G. , Pickering Amy C. , Briaud Paul , Foster Robert G. , Kudla Grzegorz , Fitzgerald J. Ross , Caldelari Isabelle , Carroll Ronan K. , Tree Jai J. , Granneman Sander 
Published: June 2022

AbstractMethicillin-resistant Staphylococcus aureus (MRSA) is a bacterial pathogen responsible for significant human morbidity and mortality. Post-transcriptional regulation by small RNAs (sRNAs) has emerged as an important mechanism for controlling virulence. However, the functionality of the majority of sRNAs during infection is unknown. To address this, we performed UV cross-linking, ligation, and sequencing of hybrids (CLASH) in MRSA to identify sRNA-RNA interactions under conditions that mimic the host environment. Using a double-stranded endoribonuclease III as bait, we uncovered hundreds of novel sRNA-RNA pairs. Strikingly, our results suggest that the production of small membrane-permeabilizing toxins is under extensive sRNA-mediated regulation and that their expression is intimately connected to metabolism. Additionally, we also uncover an sRNA sponging interaction between RsaE and RsaI. Taken together, we present a comprehensive analysis of sRNA-target interactions in MRSA and provide details on how these contribute to the control of virulence in response to changes in metabolism.
Cooperative chalcogen bonding interactions in confined sites activate aziridines
Authors: Zhu Haofu , Zhou Pan-Pan , Wang Yao 
Published: June 2022

AbstractThe activation of aziridines typically involves the use of strong Lewis acids or transition metals, and methods relying on weak interactions are rare. Herein, we report that cooperative chalcogen bonding interactions in confined sites can activate sulfonyl-protected aziridines. Among the several possible distinct bonding modes, our experiments and computational studies suggest that an activation mode involving the cooperative Se···O and Se···N interactions is in operation. The catalytic reactions between weakly bonded supramolecular species and nonactivated alkenes are considered as unfavorable approaches. However, here we show that the activation of aziridines by cooperative Se···O and Se···N interactions enables the cycloaddition of weakly bonded aziridine-selenide complex with nonactivated alkenes in a catalytic manner. Thus, weak interactions can indeed enable these transformations and are an alternative to methods relying on strong Lewis acids.
Longitudinal trimodal imaging of midbrain-associated network degeneration in Parkinson’s disease
Authors: Steidel Kenan , Ruppert Marina C. , Greuel Andrea , Tahmasian Masoud , Maier Franziska , Hammes Jochen , van Eimeren Thilo , Timmermann Lars , Tittgemeyer Marc , Drzezga Alexander , Pedrosa David J. , Eggers Carsten 
Published: June 2022

AbstractThe prevailing network perspective of Parkinson’s disease (PD) emerges not least from the ascending neuropathology traceable in histological studies. However, whether longitudinal in vivo correlates of network degeneration in PD can be observed remains unresolved. Here, we applied a trimodal imaging protocol combining 18F-fluorodeoxyglucose (FDG)- and 18F-fluoro-L-Dopa- (FDOPA)-PET with resting-state functional MRI to assess longitudinal changes in midbrain metabolism, striatal dopamine depletion and striatocortical dysconnectivity in 17 well-characterized PD patients. Whole-brain (un)paired-t-tests with focus on midbrain or striatum were performed between visits and in relation to 14 healthy controls (HC) in PET modalities. Resulting clusters of FDOPA-PET comparisons provided volumes for seed-based functional connectivity (FC) analyses between visits and in relation to HC. FDG metabolism in the left midbrain decreased compared to baseline along with caudatal FDOPA-uptake. This caudate cluster exhibited a longitudinal FC decrease to sensorimotor and frontal areas. Compared to healthy subjects, dopamine-depleted putamina indicated stronger decline in striatocortical FC at follow-up with respect to baseline. Increasing nigrostriatal deficits and striatocortical decoupling were associated with deterioration in motor scores between visits in repeated-measures correlations. In summary, our results demonstrate the feasibility of in-vivo tracking of progressive network degeneration using a multimodal imaging approach. Specifically, our data suggest advancing striatal and widespread striatocortical dysfunction via an anterior-posterior gradient originating from a hypometabolic midbrain cluster within a well-characterized and only mild to moderately affected PD cohort during a relatively short period.
Women are credited less in science than men
Authors: Ross Matthew B. , Glennon Britta M. , Murciano-Goroff Raviv , Berkes Enrico G. , Weinberg Bruce A. , Lane Julia I. 
Published: June 2022

AbstractThere is a well-documented gap between the observed number of works produced by women and by men in science, with clear consequences for the retention and promotion of women1. The gap might be a result of productivity differences2–5, or it might be owing to women’s contributions not being acknowledged6,7. Here we find that at least part of this gap is the result of unacknowledged contributions: women in research teams are significantly less likely than men to be credited with authorship. The findings are consistent across three very different sources of data. Analysis of the first source—large-scale administrative data on research teams, team scientific output and attribution of credit—show that women are significantly less likely to be named on a given article or patent produced by their team relative to their male peers. The gender gap in attribution is present across most scientific fields and almost all career stages. The second source—an extensive survey of authors—similarly shows that women’s scientific contributions are systematically less likely to be recognized. The third source—qualitative responses—suggests that the reason that women are less likely to be credited is because their work is often not known, is not appreciated or is ignored. At least some of the observed gender gap in scientific output may be owing not to differences in scientific contribution, but rather to differences in attribution.
A global ensemble of ocean wave climate statistics from contemporary wave reanalysis and hindcasts
Authors: Morim J. , Erikson L. H. , Hemer M. , Young I. , Wang X. , Mori N. , Shimura T. , Stopa J. , Trenham C. , Mentaschi L. , Gulev S. , Sharmar V. D. , Bricheno L. , Wolf J. , Aarnes O. , Perez J. , Bidlot J. , Semedo A. , Reguero B. , Wahl T. 
Published: June 2022

AbstractThere are numerous global ocean wave reanalysis and hindcast products currently being distributed and used across different scientific fields. However, there is not a consistent dataset that can sample across all existing products based on a standardized framework. Here, we present and describe the first coordinated multi-product ensemble of present-day global wave fields available to date. This dataset, produced through the Coordinated Ocean Wave Climate Project (COWCLIP) phase 2, includes general and extreme statistics of significant wave height (Hs), mean wave period (Tm) and mean wave direction (θm) computed across 1980–2014, at different frequency resolutions (monthly, seasonally, and annually). This coordinated global ensemble has been derived from fourteen state-of-the-science global wave products obtained from different atmospheric reanalysis forcing and downscaling methods. This data set has been processed, under a specific framework for consistency and quality, following standard Data Reference Syntax, Directory Structures and Metadata specifications. This new comprehensive dataset provides support to future broad-scale analysis of historical wave climatology and variability as well as coastal risk and vulnerability assessments across offshore and coastal engineering applications.
Macronutrient intake modulates impact of EcoRI polymorphism of ApoB gene on lipid profile and inflammatory markers in patients with type 2 diabetes
Authors: Abaj Faezeh , Koohdani Fariba 
Published: June 2022

AbstractWe sought to examine whether dietary intakes may affect the relationship between ApoB EcoRI and lipid profile, as well as serum inflammatory markers, in patients with type 2 diabetes (T2DM). This current study consisted of 648 diabetic patients. Dietary intake was calculated by a food frequency questionnaire. Biochemical markers (high-density lipoprotein (HDL), total cholesterol (TC), LDL, TG, CRP, IL-18, PGF2α) were measured based on standard protocols. Genotyping of the Apo-B polymorphisms (rs1042031) was conducted by the PCR–RFLP method. The gene-diet interactions were evaluated using GLMs. In comparison to GG homozygotes, A-allele carriers with above the median -CHO intake (≥ 54 percent of total energy) had considerably greater TC and PGF2a concentrations. Furthermore, as compared to GG homozygotes, A-allele carriers with above the median protein intake (≥ 14 percent of total energy) had higher serum levels of TG (P = 0.001), CRP (P = 0.02), TG/HDL (P = 0.005), and LDL/HDL (P = 0.04) ratios. Moreover, A-allele carriers with above the median total fat intake (≥ 35 percent of total calories) had significantly higher TC level (P = 0.04) and LDL/HDL (P = 0.04) ratios compared to GG homozygotes. Furthermore, when compared to GG homozygotes, A-allele carriers who consumed above the median cholesterol (> 196 mg) had greater TG (P = 0.04), TG/HDL (P = 0.01) ratio, and IL-18 (P = 0.02). Furthermore, diabetic patients with the GA, AA genotype who consume above the median cholesterol had lower ghrelin levels (P = 0.01). In terms of LDL/HDL ratio, ApoB EcoRI and dietary intakes of specific fatty acids (≥ 9 percent for SFA and ≥ 12 percent for MUFA) had significant interaction. LDL/HDL ratio is greater in A-allele carriers with above the median SFA intake (P = 0.04), also when they consumed above the median MUFA this association was inverse (P = 0.04). Our study showed that plasma lipid levels in participants carrying the (AA or AG) genotype were found to be more responsive to increasing the percentage of energy derived from dietary fat, CHO, protein, SFA, and cholesterol consumption. Therefore, patients with a higher genetic susceptibility (AA or AG) seemed to have greater metabolic markers with a higher percentage of macronutrient consumption. Also, ApoB EcoRI correlations with metabolic markers might be attenuated with above the median MUFA consumption.
Ellipsoid calculations versus manual tumor delineations for glioblastoma tumor volume evaluation
Authors: Le Fèvre Clara , Sun Roger , Cebula Hélène , Thiery Alicia , Antoni Delphine , Schott Roland , Proust François , Constans Jean-Marc , Noël Georges 
Published: June 2022

AbstractIn glioblastoma, the response to treatment assessment is essentially based on the 2D tumor size evolution but remains disputable. Volumetric approaches were evaluated for a more accurate estimation of tumor size. This study included 57 patients and compared two volume measurement methods to determine the size of different glioblastoma regions of interest: the contrast-enhancing area, the necrotic area, the gross target volume and the volume of the edema area. The two methods, the ellipsoid formula (the calculated method) and the manual delineation (the measured method) showed a high correlation to determine glioblastoma volume and a high agreement to classify patients assessment response to treatment according to RANO criteria. This study revealed that calculated and measured methods could be used in clinical practice to estimate glioblastoma volume size and to evaluate tumor size evolution.
A method of radar echo extrapolation based on dilated convolution and attention convolution
Authors: Shen Xiajiong , Meng Kunying , Zhang Lei , Zuo Xianyu 
Published: June 2022

AbstractThe neural network method can obtain a higher precision of radar echo extrapolation than the traditional method. However, its application in radar echo extrapolation is still in the initial stage of exploration, and there is still much room for improvement in the extrapolation accuracy. To improve the utilization of radar echo information and extrapolation accuracy, this paper proposes a radar echo extrapolation model (ADC_Net) based on dilated convolution and attention convolution. In this model, dilated convolution, instead of the pooling operation, is used to downsample the feature matrix obtained after the standard convolution operation. In doing so, the internal data structure of the feature matrix is retained, and the spatial features of radar echo data from different scales are extracted as well. Besides, the attention convolution module is integrated in the ADC_Net model to improve its sensitivity to the target features in the feature matrix and suppress the interference information. The proposed model is tested in the extrapolation of radar echo images in the next 90 min from five aspects—extrapolated image, POD index, CSI index, FAR index, and HSS index. The experimental results show that the model can effectively improve the accuracy of radar echo extrapolation.
Source analysis and ecological risk assessment of heavy metals in farmland soils around heavy metal industry in Anxin County
Authors: Zhao Guoliang , Ma Ye , Liu Yuzhen , Cheng Jiemin , Wang Xiaofeng 
Published: June 2022

AbstractStudying the pollution status, spatial distribution characteristics, and sources of heavy metals in farmland soil in Anxin County will provide a method basis for the next step of soil remediation. This study investigates the contents of Zn, Cu, Pb, Cd, and Ni in wheat grains and soil samples. Moreover, different methods are used to evaluate soil heavy metal pollution. The results show that the soil in the study area is weakly alkaline. Cu, Zn, and Ni contents in the ground are lower than the risk screening values for soil contamination of agricultural land. In comparison, Cd and Pb contents are higher than the screening value of soil pollution risk of agricultural land, and the proportion of points lower than the control value of soil pollution risk of agricultural land are 64.58% and 16.67%, respectively. The farmland with high Cd and Pb content is mainly distributed near roads and factories and concentrated primarily on 0-20 cm topsoil. The Cd content in wheat grains meets the standard, but 4.17% of the samples are close to 0.1 mg kg−1 (more than 0.09 mg kg−1). The Pb content of 50% of the wheat grain samples exceeds the lead limit in the standard. The evaluation results of the single factor pollution index and geoaccumulation index show that the pollution degree of heavy metals in the soil is Cd > Pb > Cu > Zn > Ni. The potential ecological risk index in the study area is 288.83, and the soil heavy metal pollution is at a moderate-considerable ecological risk level. The average value of Cd's single-factor environmental risk index is 233.51, which belongs to the high environmental risk and is the main influencing factor. Cd and Pb in soil are significantly disturbed by the production activities of heavy metal processing enterprises around the farmland. It is speculated that there are two primary sources of soil heavy metal pollution in the study area. Cd, Pb, Zn, and Cu are mainly industrial and mobile sources, and Ni is primarily agricultural and natural sources.
Top-down control of planktonic ciliates by microcrustacean predators is stronger in lakes than in the ocean
Authors: Lu Xiaoteng , Weisse Thomas 
Published: June 2022

AbstractPlanktonic ciliates are major components of pelagic food webs in both marine and freshwaters. Their population dynamics are controlled ‘bottom-up’ by prey availability and ‘top-down’ by microcrustacean predators. In oceans, copepods are the main ciliate predators while in lakes cladocerans are the typical predators. The efficacy by which these functionally different predators control ciliate population dynamics is debated. We, therefore, investigated experimentally the grazing of three microcrustacean predators with different feeding modes on five freshwater ciliates. We then performed a meta-analysis to assess if our findings can be generalised for aquatic ecosystems. We hypothesized that top-down control is stronger in lakes than in the ocean. We find that: (i) average ingestion rates of marine and freshwater microcrustaceans do not differ; (ii) clearance rates of freshwater cladocerans decrease with ciliate size but increase with ciliate size in freshwater copepods; (iii) clearance rates of the marine microcrustaceans is unrelated to ciliate cell size. These findings have implications for the functioning of freshwater and marine food webs: (i) the ciliate—microcrustacean link is stronger in lakes than in the ocean, and (ii) globally top-down control of ciliates is unlikely in the ocean.
Strain-specific predation of Bdellovibrio bacteriovorus on Pseudomonas aeruginosa with a higher range for cystic fibrosis than for bacteremia isolates
Authors: Saralegui Claudia , Herencias Cristina , Halperin Ana Verónica , de Dios-Caballero Juan , Pérez-Viso Blanca , Salgado Sergio , Lanza Val F. , Cantón Rafael , Baquero Fernando , Prieto M. Auxiliadora , del Campo Rosa 
Published: June 2022

AbstractThis work aimed to evaluate the predatory activity of Bdellovibrio bacteriovorus 109J on clinical isolates of Pseudomonas aeruginosa selected from well-characterized collections of cystic fibrosis (CF) lung colonization (n = 30) and bloodstream infections (BSI) (n = 48) including strains selected by genetic lineage (frequent and rare sequence types), antibiotic resistance phenotype (susceptible and multidrug-resistant isolates), and colony phenotype (mucoid and non-mucoid isolates). The intraspecies predation range (I-PR) was defined as the proportion of susceptible strains within the entire collection. In contrast, the predation efficiency (PE) is the ratio of viable prey cells remaining after predation compared to the initial inoculum. I-PR was significantly higher for CF (67%) than for BSI P. aeruginosa isolates (35%) probably related to an environmental origin of CF strains whereas invasive strains are more adapted to humans. I-PR correlation with bacterial features such as mucoid morphotype, genetic background, or antibiotic susceptibility profile was not detected. To test the possibility of increasing I-PR of BSI isolates, a polyhydroxyalkanoate depolymerase deficient B. bacteriovorus bd2637 mutant was used. Global median I-PR and PE values remained constant for both predators, but 31.2% of 109J-resistant isolates were susceptible to the mutant, and 22.9% of 109J-susceptible isolates showed resistance to predation by the mutant, pointing to a predator–prey specificity process. The potential use of predators in the clinical setting should be based on the determination of the I-PR for each species, and the PE of each particular target strain.
Materials informatics approach using domain modelling for exploring structure–property relationships of polymers
Authors: Hara Koki , Yamada Shunji , Kurotani Atsushi , Chikayama Eisuke , Kikuchi Jun 
Published: June 2022

AbstractIn the development of polymer materials, it is an important issue to explore the complex relationships between domain structure and physical properties. In the domain structure analysis of polymer materials, 1H-static solid-state NMR (ssNMR) spectra can provide information on mobile, rigid, and intermediate domains. But estimation of domain structure from its analysis is difficult due to the wide overlap of spectra from multiple domains. Therefore, we have developed a materials informatics approach that combines the domain modeling (http://dmar.riken.jp/matrigica/) and the integrated analysis of meta-information (the elements, functional groups, additives, and physical properties) in polymer materials. Firstly, the 1H-static ssNMR data of 120 polymer materials were subjected to a short-time Fourier transform to obtain frequency, intensity, and T2 relaxation time for domains with different mobility. The average T2 relaxation time of each domain is 0.96 ms for Mobile, 0.55 ms for Intermediate (Mobile), 0.32 ms for Intermediate (Rigid), and 0.11 ms for Rigid. Secondly, the estimated domain proportions were integrated with meta-information such as elements, functional group and thermophysical properties and was analyzed using a self-organization map and market basket analysis. This proposed method can contribute to explore structure–property relationships of polymer materials with multiple domains.
One anastomosis gastric bypass as a one-stage bariatric surgical procedure in patients with BMI ≥ 50 kg/m2
Authors: Kermansaravi Mohammad , Daryabari Seyed Nooredin , Karami Reza , Setaredan Seyed Amin , Valizadeh Rohollah , Rokhgireh Samaneh , Pazouki Abdolreza 
Published: June 2022

AbstractIn patients with BMI ≥ 50 kg/m2, it is difficult to select an appropriate procedure that can lead to optimum results. This study aims to evaluate mid-term weight loss outcomes in patients with BMI ≥ 50 kg/m2 following one anastomosis gastric bypass (OAGB) as a one-stage procedure. A prospective study was conducted on patients with BMI ≥ 50 kg/m2, aged 18 years and above who had undergone primary OAGB from January 2016 to February 2019 with at least two years follow-ups. A total of 197 patients with BMI ≥ 50 kg/m2 had underwent OAGB. The mean age was 38 years and the mean pre-operative BMI was 53.7 kg/m2. Mean EWL% were 63.7%, 67.8% and 66.2% at one, two and five years after OAGB respectively. The highest level of EWL% was 68.4%, which was achieved in the 18th month following OAGB. OAGB can be performed safely in patients with BMI ≥ 50 kg/m2 as a one-stage procedure with acceptable weight loss outcomes and remission of obesity associated medical problems.
Utility of micro-CT for dating post-cranial fractures of known post-traumatic ages through 3D measurements of the trabecular inner morphology
Authors: Viero Alessia , Biehler-Gomez Lucie , Messina Carmelo , Cappella Annalisa , Giannoukos Konstantinos , Viel Guido , Tagliaro Franco , Cattaneo Cristina 
Published: June 2022

AbstractFracture dating is an issue at the forefront of forensic sciences. While dating fracture is crucial to understanding and verifying the chronology of events in cases of abuse and violent death, its application is the subject of considerable discussion in the scientific community, filled with limitations and difficulties. Current methods for fracture dating are mainly based on a qualitative assessment through macroscopy, microscopy, and imaging and subject to variations depending on the experience of the observer. In this paper, we investigated the potential of quantifiable micro-CT analysis for fracture dating. Five histomorphometric parameters commonly used for the study of the 3D bone trabecular microarchitecture with micro-CT were calculated based on nine fractures of known post-traumatic ages, including the degree of anisotropy, connectivity density, bone volume fraction, trabecular thickness, and trabecular separation. As a result, trends in the evolution of the microarchitecture of the bone relative to age of the callus could be identified, in particular concerning anisotropy, trabecular separation and connectivity density, consistent with the healing bone process. The findings obtained in this pilot study encourage further research in quantifiable parameters of the bone microarchitecture as they could represent useful features for the construction of objective models for fracture dating.