bluuebunny/crossref_metadata_2025_split huggingface dataset:
Characterization of GMB-1, a novel metallo-β-lactamase (MBL) found in three different Enterobacterales species
Authors: Schauer Jennifer , Gatermann Sören G , Eisfeld Jessica , Hans Jörg Berthold , Ziesing Stefan , Schlüter Dirk , Pfennigwerth Niels 
Published: February 2022

Abstract

Objectives
To identify novel carbapenem resistance mechanisms and their potential to spread among clinical isolates.

Methods
Four clinical isolates of Citrobacter freundii, Serratia marcescens and Raoultella planticola (n = 2) from one hospital in Central Germany were sent to the German National Reference Centre for Multidrug-resistant Gram-negative Bacteria for carbapenemase detection. Phenotypic tests indicated the presence of a metallo-β-lactamase (MBL), but PCR for various MBL genes could not identify any. Using WGS data, a putative bla gene was identified. Its carbapenemase activity was verified by heterologous expression in an Escherichia coli cloning strain, with subsequent MIC determination by broth microdilution, as well as by in vitro hydrolysis assays using purified enzyme.

Results
WGS indicated the presence of a putative β-lactamase with 48% amino acid identity to the subclass B1 MBL SPM-1. MIC studies confirmed that the novel enzyme formed a functional MBL, which was therefore designated as GMB-1 (German MBL). In vitro hydrolysis assays showed a lack of activity not only against aztreonam but also against ertapenem. WGS revealed that in all three species the blaGMB-1 gene was located on the chromosome as part of a genetic island with multiple ISs.

Conclusions
The finding of GMB-1 once again shows that novel carbapenemases continue to emerge and make their way into clinically relevant species. The occurrence of GMB-1 in three different species demonstrates the extraordinary mobility of such genetic islands and their potential to spread carbapenemase genes into diverse genetic environments.
Pre-Clinical Safety and Efficacy Evaluation of a Herbal Nanoemulsion-Based Formulation for Treating Inflammatory Bowel Disease
Authors: Alshahrani Ali , Ali Abuzer 
Published: February 2022

Abstract

Background
Inflammatory bowel disease (IBD) is a chronic autoimmune sickness that affects the gastrointestinal tract (GIT). Currently available treatment regimens have various adverse effects and create a financial burden.

Objective
This paper presents the development of an oral liquid formulation containing a nanoemulsion (NE) of herbal extracts for the treatment of IBD.

Methods
A NE-based formulation was prepared and characterized. Stability studies based on the physical appearance, viscosity, pH, total microbial count, and assay were performed. The antioxidant activity of the individual extract, mixture, and formulation was compared by the DPPH method. In order to assess both the efficacy and the safety of the formulation, a TNBS-induced colitis model was used.

Results
A herbal extract of fennel, anise, chamomile, linseed, and pomegranate fruit peel was used as the oil phase, PEG as a surfactant, Tween 80 as a co-surfactant, and benzalkonium chloride (0.001% w/v) as a preservative in the NE. Average particle size, PDI, viscosity, and pH were 283 nm, 0.33, 48 cp, and 5.9, respectively. Assay of the product by standard marker anethole was 99.6%. It was established that the formulation remains stable at least for 6 months. The antioxidant activity of the combined extract was higher than the individual extracts. The colon mucosa damage index (CMDI) from the formulation was negligible and similar to that of the control group.

Conclusion
The results suggest that it is worthwhile developing the NE of herbal extracts for treating IBD. Additionally, the benefit of selecting a multi-herb extract for NE formulation is demonstrated by the antioxidant activity of the combined extracts.

Highlights
This study revealed that the NE of the herbal extract is a promising approach for IBD treatment. A patent related to the work is published in the Indian Official Journal of the Patent Office (14/2021).
Hand compartment syndrome due to extravasation of contrast medium. A technical error. A report of a case and review of the literature
Authors: Papatheodorou Nikolaos , Keskinis Anthimos , Georgoulas Paraskevas , Tilkeridis Konstantinos , Botaitis Sotirios , Perente Sempachedin , Kougioumtzi Ioanna 
Published: February 2022

Abstract
The extravasation of contrast agents is one of the most common and remarkable complications during a computed tomography (CT) scan. The clinical manifestations are commonly minimal, leading to mild symptoms. However, in rare cases of high-volume extravasation, the complications are extremely threatening. Compartment syndrome of the hand and the forearm leads to critical dysfunction and upper limb necrosis. This article reported an unusual case of hand compartment syndrome following extravasation of iodinated contrast agent from a peripheral venous catheter, during a CT angiography, and its surgical treatment. Moreover, a literature review regarding all published similar surgically treated cases was conducted.
Coronary artery aneurysm, ectasia and stenosis in a 53-year-old man with HIV infection
Authors: Kashyap Abhishek , Abramov Dmitry , Bharadwaj Aditya , Rabkin Miriam , Rabkin David G 
Published: February 2022

Abstract
The impact of long-standing human immunodeficiency virus infection (HIV) and potent anti-retroviral therapy on the coronary circulation is unknown; however, scattered reports are emerging of coronary aneurysms in this population. We report what we believe to be the first described case of both coronary stenosis and coronary artery aneurysms in a person living with HIV and discuss management options.
The Auto-X Attributes of the Father and the Son in Origen
Authors: Miller Micah M 
Published: February 2022

Abstract
This article attempts to address whether or not Origen considers the relationship between the Father and Son to be hierarchical by analysing Origen’s use of auto-X attributes of the Father and Son. Through this analysis, this article will demonstrate that Origen believes the Son to be dependent on the Father for his being and his attributes, a relationship that ranks the Son below the Father. The first section of the article will examine the auto-X attributes of the Father, arguing that Origen’s use of the prefix auto- makes the Son dependent on the Father and, therefore, ranked below him. The second section of the article will analyse the auto-X attributes of the Son. I will follow the work of several scholars who maintain that Origen uses auto-X language of the Son to denote his relationship to creation, not his relationship to the Father. However, I will add to this previous scholarship by providing a more complete analysis of Origen’s use of auto-X language of the Son and by arguing that scholars have not recognized the hierarchical relationship this language indicates.
Intrinsic alignments in IllustrisTNG and their implications for weak lensing: Tidal shearing and tidal torquing mechanisms put to the test
Authors: Zjupa Jolanta , Schäfer Björn Malte , Hahn Oliver 
Published: February 2022

ABSTRACT
Accurate measurements of the cosmic shear signal require a separation of the true weak gravitational lensing signal from intrinsic shape correlations of galaxies. These ‘intrinsic alignments’ of galaxies originate from galaxy formation processes and are expected to be correlated with the gravitational field through tidal processes affecting the galaxies, such as tidal shearing for elliptical galaxies and tidal torquing for spiral galaxies. In this study, we use morphologically selected samples of elliptical and spiral galaxies from the illustrisTNG simulation at z = 0 and z = 1 to test the commonly employed linear (tidal shearing) and quadratic (tidal torquing) models for intrinsic alignments. We obtain local measurements of the linear and quadratic alignment parameters, including corrections for large-scale anisotropies of the cosmologically small simulation volume, and study their dependence on galaxy and environmental properties. We find a significant alignment signal for elliptical galaxies (linear model), that increases with mass and redshift. Spiral galaxies (quadratic model), on the other hand, exhibit a significant signal only for the most massive objects at z = 1. We show the quadratic model for spiral galaxies to break down at its fundamental assumptions, and simultaneously obtain a significant signal of spiral galaxies to align according to the linear model. We use the derived alignment parameters to compute intrinsic alignment spectra and estimate the expected contamination in the weak lensing signal obtained by Euclid.
The impact of dust on the sizes of galaxies in the Epoch of Reionization
Authors: Marshall Madeline A , Wilkins Stephen , Di Matteo Tiziana , Roper William J , Vijayan Aswin P , Ni Yueying , Feng Yu , Croft Rupert A C 
Published: February 2022

ABSTRACT
We study the sizes of galaxies in the Epoch of Reionization using a sample of ${\sim 100\, 000}$ galaxies from the BlueTides cosmological hydrodynamical simulation from z = 7 to 11. We measure the galaxy sizes from stellar mass and luminosity maps, defining the effective radius as the minimum radius that could enclose the pixels containing 50 per cent of the total mass/light in the image. We find an inverse relationship between stellar mass and effective half-mass radius, suggesting that the most massive galaxies are more compact and dense than lower mass galaxies, which have flatter mass distributions. We find a mildly negative relation between intrinsic far-ultraviolet luminosity and size, while we find a positive size–luminosity relation when measured from dust-attenuated images. This suggests that dust is the predominant cause of the observed positive size–luminosity relation, with dust preferentially attenuating bright sightlines resulting in a flatter emission profile and thus larger measured effective radii. We study the size–luminosity relation across the rest-frame ultraviolet and optical, and find that the slope decreases at longer wavelengths; this is a consequence of the relation being caused by dust, which produces less attenuation at longer wavelengths. We find that the far-ultraviolet size–luminosity relation shows mild evolution from z = 7 to 11, and galaxy size evolves with redshift as R ∝ (1 + z)−m, where m = 0.662 ± 0.009. Finally, we investigate the sizes of z = 7 quasar host galaxies, and find that while the intrinsic sizes of quasar hosts are small relative to the overall galaxy sample, they have comparable sizes when measured from dust-attenuated images.
Astrometric star-cluster membership probability: application to the case of M 37 with Gaia EDR3
Authors: Griggio M , Bedin L R 
Published: February 2022

ABSTRACT
In this work, starting from the well-accepted relations in literature, we introduce a new formalism to compute the astrometric membership probabilities for sources in star clusters, and we provide an application to the case of the open cluster M 37. The novelty of our approach is a refined – and magnitude-dependent – modelling of the parallax distribution of the field stars. We employ the here-derived list of members to estimate the cluster’s mean systemic astrometric parameters, which are based on the most recent Gaia’s catalogue (EDR3).
The implication of long non-coding RNA expression profile in rheumatoid arthritis: Correlation with treatment response to tumor necrosis factor inhibitor
Authors: Wang Qiubo , Huang Xuan , Shao Yang , Liu Qingyang , Shen Jin , Xia Jinjun , Zhang Zhiqian , Wang Chunxin 
Published: February 2022

ABSTRACT

Objective
This study aimed to investigate the linkage of long non-coding RNA (lncRNA) expression profile with etanercept response in rheumatoid arthritis (RA) patients.

Methods
Peripheral blood mononuclear cell (PBMC) samples were collected from 80 RA patients prior to etanercept treatment. Samples from eight responders and eight non-responders at week 24 (W24) were proposed to RNA-sequencing, then 10 candidate lncRNAs were sorted and their PBMC expressions were validated by reverse transcription quantitative chain reaction (RT-qPCR) in 80 RA patients. Subsequently, clinical response by lncRNA (CRLnc) prediction model was established.

Results
RNA-sequencing identified 254 up-regulated and 265 down-regulated lncRNAs in W24 responders compared with non-responders, which were enriched in immune or joint related pathways such as B-cell receptor signaling, osteoclast differentiation and T-cell receptor signaling pathways, etc. By reverse transcription quantitative chain reaction (RT-qPCR) validation: Two lncRNAs were correlated with W4 response, three lncRNAs were correlated with W12 response, seven lncRNAs were correlated with W24 response. Subsequently, to construct and validate CRLnc prediction model, 80 RA patients were randomly divided into test set (n = 40) and validation set (n = 40). In the test set, lncRNA RP3-466P17.2 (OR = 9.743, P = .028), RP11-20D14.6 (OR = 10.935, P = .007), RP11-844P9.2 (OR = 0.075, P = .022), and TAS2R64P (OR = 0.044, P = .016) independently related to W24 etanercept response; then CRLnc prediction model integrating these four lncRNAs presented a good value in predicting W24 etanercept response (Area Under Curve (AUC): 0.956, 95%CI: 0.896–1.000). However, in the validation set, the CRLnc prediction model only exhibited a certain value in predicting W24 etanercept response (AUC: 0.753, 95%CI: 0.536–0.969).

Conclusions
CRLnc prediction model is potentially a useful tool to instruct etanercept treatment in RA patients.
Number needed to treat and cost per responder of Janus kinase inhibitors approved for the treatment of moderate-to-severe rheumatoid arthritis in Japan
Authors: Atsumi Tatsuya , Asakura Eri , Doi Michio , Sawant Ruta , Kawaguchi Isao , Sasaki Nobuhito , Liew Danny 
Published: February 2022

ABSTRACT

Objective
This study evaluated the effectiveness and cost-effectiveness of baricitinib, tofacitinib, and upadacitinib regimens, compared to conventional synthetic disease-modifying antirheumatic drug (csDMARD) alone, among Japanese patients with moderate-to-severe rheumatoid arthritis (RA) inadequately responsive to csDMARD, measured in terms of number needed to treat (NNT) and cost per responder (CPR).

Methods
Efficacy data were derived from two recent network meta-analyses among global and Japanese population. The cost perspective was that of the Japanese Health Service. Both NNT and CPR were based on disease activity score for 28 joints with C-reactive protein (DAS28-CRP) remission and American College of Rheumatology (ACR) 20/50/70 at 12 and 24 weeks.

Results
Over 12 weeks, the median NNT and the median CPR to achieve DAS28-CRP remission were 4.3 and JPY 1,799,696 [USD 16,361], respectively, for upadacitinib 15 mg + csDMARD. The equivalent results were 6.0 and JPY 2,691,684 [USD 24,470] for baricitinib 4 mg + csDMARD and 5.6 and JPY 2,507,152 [USD 22,792] for tofacitinib 5 mg + csDMARD. Similar rankings were observed at 24 weeks and for other outcomes.

Conclusions
Upadacitinib 15 mg was associated with the lowest NNT and CPR among the three Janus kinase inhibitors used in treatment regimens for Japanese patients with moderate-to-severe RA inadequately responsive to csDMARD.
Material research from the viewpoint of functional motifs
Authors: Jiang Xiao-Ming , Deng Shuiquan , Whangbo Myung-Hwan , Guo Guo-Cong 
Published: February 2022

Abstract
As early as 2001, the need for the ‘functional motif theory’ was pointed out, to assist the rational design of functional materials. The properties of materials are determined by their functional motifs and how they are arranged in the materials. Uncovering functional motifs and their arrangements is crucial in understanding the properties of materials and rationally designing new materials of desired properties. The functional motifs of materials are the critical microstructural units (e.g. constituent components and building blocks) that play a decisive role in generating certain material functions, and can not be replaced with other structural units without the loss, or significant suppression, of relevant functions. The role of functional motifs and their arrangement in materials, with representative examples, is presented. The microscopic structures of these examples can be classified into six types on a length scale smaller than ∼10 nm with maximum subatomic resolution, i.e. crystal, magnetic, aperiodic, defect, local and electronic structures. Functional motif analysis can be employed in the function-oriented design of materials, as elucidated by taking infrared non-linear optical materials as an example. Machine learning is more efficient in predicting material properties and screening materials with high efficiency than high-throughput experimentation and high-throughput calculations. In order to extract functional motifs and find their quantitative relationships, the development of sufficiently reliable databases for material structures and properties is imperative.
Computed Tomography Texture Analysis for Predicting Clinical Outcomes in Patients With Metastatic Renal Cell Carcinoma Treated With Immune Checkpoint Inhibitors
Authors: Park Hyo Jung , Qin Lei , Bakouny Ziad , Krajewski Katherine M , Van Allen Eliezer M , Choueiri Toni K , Shinagare Atul B 
Published: February 2022

Abstract

Background
The treatment responses of immune checkpoint inhibitors in metastatic renal cell carcinoma (mRCC) vary, requiring reliable prognostic biomarkers. We assessed the prognostic ability of computed tomography (CT) texture analysis in patients with mRCC treated with programmed death receptor-1 (PD-1)/programmed death ligand-1 (PD-L1) inhibitors.

Materials and Methods
Sixty-eight patients with mRCC treated with PD-1/PD-L1 inhibitors between 2012 and 2019 were revaluated. Using baseline and first follow-up CT, baseline and follow-up texture models were developed to predict overall survival (OS) and progression-free survival (PFS) using least absolute shrinkage and selection operator Cox-proportional hazards analysis. Patients were divided into high-risk or low-risk group, and the survival difference was assessed using Kaplan-Meier and log-rank test. Multivariable Cox models were constructed by including only the clinical variables (clinical models) and by combining the clinical variables and the texture models (combined clinical-texture models), and their predictive performance was evaluated using Harrell’s C-index.

Results
The baseline texture models distinguished longer- and shorter-term survivors for both OS (median, 60.1 vs. 17.0 months; P = .048) and PFS (5.2 vs. 2.8 months; P = .003). The follow-up texture models distinguished longer- and shorter-term overall survivors (40.3 vs. 15.2 months; P = .008) but not for PFS (5.0 vs. 3.6 months; P = .25). The combined clinical-texture model outperformed the clinical model in both predicting the OS (C-index, 0.70 vs. 0.63; P = .03) and PFS (C-index, 0.63 vs. 0.55; P = .04).

Conclusion
CT texture analysis performed at baseline and early after starting PD-1/PD-L1 inhibitors is associated with clinical outcomes of patients with mRCC.
Aureochromes maintain polyunsaturated fatty acid content in Nannochloropsis oceanica
Authors: Poliner Eric , Busch Andrea W U , Newton Linsey , Kim Young Uk , Clark Rachel , Gonzalez-Martinez Sofía C , Jeong Byeong-Ryool , Montgomery Beronda L , Farré Eva M 
Published: February 2022

Abstract
Nannochloropsis oceanica, like other stramenopile microalgae, is rich in long-chain polyunsaturated fatty acids (LC-PUFAs) such as eicosapentaenoic acid (EPA). We observed that fatty acid desaturases (FADs) involved in LC-PUFA biosynthesis were among the strongest blue light-induced genes in N. oceanica CCMP1779. Blue light was also necessary for maintaining LC-PUFA levels in CCMP1779 cells, and growth under red light led to a reduction in EPA content. Aureochromes are stramenopile-specific proteins that contain a light–oxygen–voltage (LOV)-sensing domain that associates with a flavin mononucleotide and is able to sense blue light. These proteins also contain a basic leucine zipper DNA-binding motif and can act as blue light-regulated transcription factors by associating with an E-box like motif, which we found enriched in the promoters of blue light-induced genes. We demonstrated that, in vitro, two CCMP1779 aureochromes were able to absorb blue light. Moreover, the loss or reduction of the expression of any of the three aureochrome genes led to a decrease in the blue light-specific induction of several FADs in CCMP1779. EPA content was also significantly reduced in NoAUREO2 and NoAUREO4 mutants. Taken together, our results indicate that aureochromes mediate blue light-dependent regulation of LC-PUFA content in N. oceanica CCMP1779 cells.
Can biochemical traits bridge the gap between genomics and plant performance? A study in rice under drought
Authors: Melandri Giovanni , Monteverde Eliana , Riewe David , AbdElgawad Hamada , McCouch Susan R , Bouwmeester Harro 
Published: February 2022

Abstract
The possibility of introducing metabolic/biochemical phenotyping to complement genomics-based predictions in breeding pipelines has been considered for years. Here we examine to what extent and under what environmental conditions metabolic/biochemical traits can effectively contribute to understanding and predicting plant performance. In this study, multivariable statistical models based on flag leaf central metabolism and oxidative stress status were used to predict grain yield (GY) performance for 271 indica rice (Oryza sativa) accessions grown in the field under well-watered and reproductive stage drought conditions. The resulting models displayed significantly higher predictability than multivariable models based on genomic data for the prediction of GY under drought (Q2 = 0.54–0.56 versus 0.35) and for stress-induced GY loss (Q2 = 0.59–0.64 versus 0.03–0.06). Models based on the combined datasets showed predictabilities similar to metabolic/biochemical-based models alone. In contrast to genetic markers, models with enzyme activities and metabolite values also quantitatively integrated the effect of physiological differences such as plant height on GY. The models highlighted antioxidant enzymes of the ascorbate–glutathione cycle and a lipid oxidation stress marker as important predictors of rice GY stability under drought at the reproductive stage, and these stress-related variables were more predictive than leaf central metabolites. These findings provide evidence that metabolic/biochemical traits can integrate dynamic cellular and physiological responses to the environment and can help bridge the gap between the genome and the phenome of crops as predictors of GY performance under drought.
Pre-release Risk Assessments: Pilot Study of a Novel Tool in One Police Station in the North East of England
Authors: Lyall Alicia , Austin Helena , Alder Ross , Wild Georgina , Reid Keith , McKinnon Iain 
Published: February 2022

Abstract
Research in police custody risk assessment and health screening has historically been focused on detainees arrival in custody with much less emphasis on pre-release risk assessment (PRRA). This research aimed to evaluate a modified PRRA piloted in one police station in the North East of England for two weeks in March/April 2019 against College of Policing’s Authorised Professional Practice (APP) guidance. A controlled before and after study design was conducted. During the intervention phase, custody suite (A) piloted the modified PRRA whilst control custody suite (B) continued to use standard PRRA. Randomised, anonymised custody records were analysed; 300 records were taken from each suite during the intervention phase, and a further 300 from each suite during the period preceding intervention. PRRA records were scored against criteria derived from the College of Policing’s APP guidance. Improvements were seen in seven outcomes with greatest effects observed in recording risks associated with mental health, physical health and substance misuse.