bluuebunny/crossref_metadata_2025_split huggingface dataset:
Third-generation dual-source computed tomography of the abdomen: comparison of radiation dose and image quality of 80kVp and 80/150kVp with tin filter
Authors: Choi Seung Joon , Park So Hyun , Park Seong Ho , Pak Seong Yong , Choi Jae Won , Ahn Su Joa , Shim Young Sup , Jeong Yu Mi , Kim Bohyun 
Published: March 2020

AbstractObjectiveTo compare the radiation dose, objective and subjective image quality, and diagnostic performances of 80 kVp and 80/150 kVp with tin filter (80/Sn150 kVp) computed tomography (CT) in oncology patients.MethodsOne hundred forty-five consecutive oncology patients who underwent third-generation dual-source dual-energy CT of the abdomen for evaluation of malignant visceral, peritoneal, extraperitoneal, and bone tumor were retrospectively recruited. Two radiologists independently reviewed each observation in 80 kVp CT and 80/Sn150 kVp CT. Modified line-density profile of the tumor and contrast-to-noise ratio (CNR) were measured. Diagnostic confidence, lesion conspicuity, and subjective image quality were calculated and compared between image sets.ResultsModified line-density profile analysis revealed higher attenuation differences between the tumor and the normal tissue in 80 kVp CT than in 80/Sn150 kVp CT (127 vs. 107, P = 0.05). The 80 kVp CT showed increased CNR in the liver (8.0 vs. 7.6) and the aorta (18.9 vs. 16.3) than the 80/Sn150 kVp CT. The 80 kVp CT yielded higher enhancement of organs (4.9 ± 0.2 vs. 4.7 ± 0.4, P < 0.001) and lesion conspicuity (4.9 ± 0.3 vs. 4.8 ± 0.5, P = 0.035) than the 80/Sn150 kVp CT; overall image quality and confidence index were comparable. The effective dose reduced by 45.2% with 80 kVp CT (2.3 mSv ± 0.9) compared to 80/Sn150 kVp CT (4.1 mSv ± 1.5).ConclusionsThe 80 kVp CT performed similar or better than 80/Sn150 kVp CT for abdominal tumor evaluation with 45.2% radiation dose reduction in oncology patients.
HumGut: A comprehensive Human Gut prokaryotic genomes collection filtered by metagenome data
Authors: Hiseni Pranvera , Rudi Knut , Wilson Robert C. , Hegge Finn Terje , Snipen Lars 
Published: March 2020

AbstractBackgroundA major bottleneck in the use of metagenome sequencing for human gut microbiome studies has been the lack of a comprehensive genome collection to be used as a reference database. Several recent efforts have been made to re-construct genomes from human gut metagenome data, resulting in a huge increase in the number of relevant genomes. In this work, we aimed to create a collection of the most prevalent healthy human gut prokaryotic genomes, to be used as a reference database, including both MAGs from the human gut and ordinary RefSeq genomes.ResultsWe screened > 5,700 healthy human gut metagenomes for the containment of > 490,000 publicly available prokaryotic genomes sourced from RefSeq and the recently announced UHGG collection. This resulted in a pool of > 379,000 genomes that were subsequently scored and ranked based on their prevalence in the healthy human metagenomes. The genomes were then clustered at subspecies resolution, and cluster representatives were retained to comprise the HumGut collection. Using the Kraken2 software for classification, we find superior performance in the assignment of metagenomic reads, classifying on average 94.5% of the reads in a metagenome, as opposed to 86% with UHGG and 44% when using standard Kraken2 database. HumGut, half the size of standard Kraken2 database and directly comparable to the UHGG size, outperforms them both.ConclusionsThe HumGut collection contains > 30,000 genomes clustered at subspecies resolution and ranked by human gut prevalence. We demonstrate how metagenomes from IBD-patients map equally well to this collection, indicating this reference is relevant also for studies well outside the metagenome reference set used to obtain HumGut. We believe this is a valuable resource in a field in dire need of method standardization. All data and metadata, as well as helpful code, are available athttp://arken.nmbu.no/~larssn/humgut/.
Self-cutting and integrating CRISPR plasmids (SCIPs) enable targeted genomic integration of genetic payloads for rapid cell engineering
Authors: Bloemberg Darin , Sosa-Miranda Daniela , Nguyen Tina , Weeratna Risini D. , McComb Scott 
Published: March 2020

AbstractSince observations that CRISPR nucleases function in mammalian cells, many strategies have been devised to adapt them for genetic engineering. Here, we investigated self-cutting and integrating CRISPR-Cas9 plasmids (SCIPs) as easy-to-use gene editing tools that insert themselves at CRISPR-guided locations. SCIPs demonstrated similar expression kinetics and gene disruption efficiency in mouse (EL4) and human (Jurkat) cells, with stable integration in 3-6% of transfected cells. Clonal sequencing analysis indicated that integrants showed bi- or mono-allelic integration of entire CRISPR plasmids in predictable orientations and with limited indel formation. Interestingly, including longer homology arms (HAs) (500 bp) in varying orientations only modestly increased knock-in efficiency (∼2-fold). Using a SCIP-payload design (SCIPpay) which liberates a promoter-less sequence flanked by HAs thereby requiring perfect homology-directed repair (HDR) for transgene expression, longer HAs resulted in higher integration efficiency and precision of the payload but did not affect integration of the remaining plasmid sequence. As proofs-of-concept, we used SCIPpay to 1) insert a gene fragment encoding tdTomato into theCD69locus of Jurkat cells, thereby creating a cell line that reports T cell activation, and 2) insert a chimeric antigen receptor (CAR) gene into theTRAClocus. Here, we demonstrate that SCIPs function as simple, efficient, and programmable tools useful for generating gene knock-out/knock-in cell lines and suggest future utility in knock-in site screening/optimization, unbiased off-target site identification, and multiplexed, iterative, and/or library-scale automated genome engineering.
Structural influence of the conserved Hsp40 HPD tripeptide on Hsp70 chaperone function
Authors: Mallapre OO , Bascos NAD 
Published: March 2020

ABSTRACTThe control of Hsp70 functions has been related to the modulation of ATP hydrolysis and substrate capture by Hsp40. Structural and biophysical analyses of Hsp40 variants and their interactions with Hsp70 have identified key residues for this functional control mechanism. Conserved residues in both Hsp40 and Hsp70 have revealed conserved interactions that link Hsp40 binding to the catalytic residues within Hsp70. The current work investigates the effect of documented J-domain dysfunctional mutations (i.e. D35N, H33Q) on the described interaction linkage. Molecular dynamics simulations were used to compare the persistence of individual bond types (i.e. H-bonds, salt bridges, hydrophobic interactions) between Hsp70 and the bound forms of functional and dysfunctional Hsp40 variants. The generated data suggests the involvement of both direct and allosteric effects for the tested mutations. The observed changes relate mutations in the conserved HPD tripeptide of Hsp40 to alterations in the interaction network that induces Hsp70 chaperone functions.STATEMENT OF SIGNIFICANCEThe significance of the work may be summarized as follows. First, the interaction network for the simulated systems were observed to be different from one previously proposed for a disulfide linked complex (9). This may be attributed to altered residue movement and interactions without the restrictions set by the disulfide link. These results support the use ofin silicomethods to refine investigations of molecular contacts, particularly for systems, whose invitrostructural elucidation are difficult to achieve without modifications.Second, key interactions for intermolecular and intramolecular contacts were observed within a short simulation time (0.1 ns) matched those from much longer runs (500 ns) (4). This result highlights the possibility of identifying key interactions with relatively low computational cost.
The cytosolicArabidopsis thalianacysteine desulfurase ABA3 delivers sulfur to the sulfurtransferase STR18
Authors: Selles Benjamin , Moseler Anna , Caubrière Damien , Sun Sheng-Kai , Ziesel Morgane , Dhalleine Tiphaine , Hériché Mathilde , Wirtz Markus , Rouhier Nicolas , Couturier Jérémy 
Published: March 2020

ABSTRACTThe biosynthesis of many sulfur-containing molecules depends on cysteine as a sulfur source. Cysteine desulfurase (CD) and rhodanese (Rhd) domain-containing protein families participate in the trafficking of sulfur for various metabolic pathways in bacteria and human, but their connection is not yet described in plants. The existence of natural chimeric proteins, however, containing both CD and Rhd domains in specific bacterial genera suggests a general interaction between both proteins. We report here the biochemical relationships between two cytosolic proteins fromArabidopsis thaliana, a Rhd domain containing protein, the sulfurtransferase 18 (STR18), and a CD isoform referred to as ABA3, and compare these biochemical features to those of a natural CD-Rhd fusion protein from the bacteriumPseudorhodoferax sp.. We observed that the bacterial enzyme is bifunctional exhibiting both CD and STR activities using L-cysteine and thiosulfate as sulfur donors but preferentially uses L-cysteine to catalyze trans-persulfidation reactions.In vitroactivity assays and mass spectrometry analyses revealed that STR18 stimulates the CD activity of ABA3 by reducing the intermediate persulfide on its catalytic cysteine thereby accelerating the overall transfer reaction. Both proteins interactin plantaand form an efficient sulfur relay system whereby STR18 catalyzes trans-persulfidation reactions from ABA3 to the model acceptor protein roGFP2. In conclusion, the ABA3-STR18 couple likely represents an uncharacterized pathway of sulfur trafficking in the cytosol of plant cells, independent of ABA3 function in molybdenum cofactor maturation.
Incorporation of a nucleoside analog maps genome repair sites in post-mitotic human neurons
Authors: Reid Dylan A. , Reed Patrick J. , Schlachetzki Johannes C.M. , Chou Grace , Chandran Sahaana , Lu Ake T. , McClain Claire A. , Ooi Jean H. , Jones Jeffrey R. , Linker Sara B. , Tsui Enoch C. , Ricciardulli Anthony S. , Lau Shong , Schafer Simon T. , Horvath Steve , Dixon Jesse R. , Hah Nasun , Glass Christopher K. , Gage Fred H. 
Published: March 2020

AbstractNeurons are the longest-living cells in our bodies, becoming post-mitotic in early development upon terminal differentiation. Their lack of DNA replication makes them reliant on DNA repair mechanisms to maintain genome fidelity. These repair mechanisms decline with age, potentially giving rise to genomic dysfunction that may influence cognitive decline and neurodegenerative diseases. Despite this challenge, our knowledge of how genome instability emerges and what mechanisms neurons and other long-lived cells may have evolved to protect their genome integrity over the human life span is limited. Using a targeted sequencing approach, we demonstrate that neurons consolidate much of their DNA repair efforts into well-defined hotspots that protect genes that are essential for their identity and function. Our findings provide a basis to understand genome integrity as it relates to aging and disease in the nervous system.One Sentence SummaryRecurrent DNA repair hotspots in neurons are linked to genes essential for identity and function.
Measurement of the leakage flux in the vicinity of a transformer core
Authors: Duchesne Stéphane , Morganti Fabrice , Shulz Carl , Roger Daniel 
Published: March 2020

Purpose
This study presents a new method for the detection of faults in large transformer cores. It is based on the analysis of leakage flux components in the vicinity of the sheet stack. The purpose of this study is to provide a nondestructive analysis tool for transformer cores during the assembly process to detect accidental defects such as inter-laminar short circuits.

Design/methodology/approach
The different components of the leakage flux allow localization of the fault in the stack and also permit to assess its severity. Out of the many kinds of defects which may appear in a transformer core, this method only detects those which actually cause an increase in the transformer’s global iron losses, which are thus the most detrimental.

Findings
The proposed method allows a more efficient control of the quality of the cores during their manufacturing process. Until now, it was only possible to know the quality of the core when the transformer was fully assembled.

Research limitations/implications
The accuracy of the method depends on the size of the defect and may request many measurements to give usable information.

Practical implications
Controlling iron losses in a core during its construction avoids heavy dismantling operations, both financially and temporally.

Originality/value
This method can help transformer manufacturers optimize their building process. In addition, the method remains effective regardless of the size of the core considered.
Employment and attitudes toward women among Syrian refugees
Authors: Baranik Lisa E. 
Published: March 2020

PurposeThe current study examined employment rates and predictors of employment among Syrian refugees currently living in Lebanon and Jordan. This paper argues that men and women refugees have different experiences seeking out employment after resettlement due to patriarchal structures and attitudes toward women that are present in the Arab Middle East. The goals of this paper were a) to examine employment rates among Syrian refugees, b) to examine predictors of employment among male and female refugees, and c) to examine refugee status as a moderator of the relationship between attitudes toward women and employment status.Design/methodology/approachNationally representative data from the Arab Barometer on 600 refugees and 1400 native-born individuals living in Lebanon and Jordan from 2016–2017 were used.FindingsNative-born individuals living in Lebanon and Jordan were 2.16 times more likely to be employed than refugees. Men living in Lebanon and Jordan were 7.83 times more likely to be employed than women. Finally, refugee status moderated the relationship between attitudes toward women's rights and roles and employment. Among native-born women, a positive attitude toward women's rights and roles predicted employment status, whereas this positive relationship was not found for women refugees. Among refugee men, a positive attitude toward women's rights and roles was linked to a lower likelihood of holding a job.Practical implicationsThese findings suggest that agencies supporting refugees should communicate realistic expectations about employment during resettlement and should address the challenges that women refugees face when seeking employment.Originality/valueThis study is the first study to identify attitudes toward women's rights and roles as a predictor of employment among refugee populations and highlights the unique struggles that refugee women face.
The adoption of electronic records management system (ERMS) in the Yemeni oil and gas sector
Authors: Hawash Burkan , Mokhtar Umi Asma’ , Yusof Zawiyah M. , Mukred Muaadh 
Published: March 2020

Purpose
Identification of factors for electronic records management system (ERMS) adoption is important as it allows organizations to focus their efforts on these factors to ensure success. The purpose of this paper is to identify the factors that influence ERMS adoption in the Yemeni oil and gas (O&G) sector.

Design/methodology/approach
This paper conducts a systematic literature review (SLR) to extract the most common factors that could facilitate successful ERMS adoption. Information technology (IT) experts were asked to rank the extracted factors via an e-mail questionnaire and to recommend specific critical success factors that must be given extra attention to increasing the success of ERMS adoption. Essentially, the proposed methodology is technology-organization-environment (TOE) modeling to examine the important factors influencing decision-makers in the Yemeni O&G sector regarding ERMS adoption.

Findings
This paper identifies factors influencing ERMS adoption based on SLR and an expert-ranking survey. The data that were collected from IT experts were analyzed using the statistical package for the social sciences. The results showed that only 12 out of 20 factors were significant. The experts then added three new factors, resulting in 15 significant factors classified into the three dimensions as follows: technology, organization and environment.

Originality/value
Limited studies have been carried out in the context of the O&G sector, even among developed countries such as Canada, the UK and Australia. These studies have focused on a limited number of factors for ERMS adoption targeting better utilization of human resources, faster and more user-friendly system responses and suitability for organizational ease. This paper explores the factors that may prove useful in adopting of ERMS in the O&G sector of developing countries, similar to Yemen.
Phocine distemper virus uses phocine and other animal SLAMs as a receptor but not human SLAM
Authors: Seki Fumio , Ohishi Kazue , Maruyama Tadashi , Takeda Makoto 
Published: March 2020

AbstractMorbilliviruses use the signaling lymphocyte activation molecule (SLAM) as a receptor to infect their hosts. Seals are almost the only animal species that show apparent infection with phocine distemper virus (PDV). Seal SLAM functioned as a PDV receptor. However, dolphin‐ and dog‐SLAM molecules, but not human SLAM, were also fully functional PDV receptors. These data suggest that the host range of PDV is not simply determined by its SLAM usage. However, human nonsusceptibility to PDV infection may be at least partly attributable to the inability of PDV to use human SLAM as a receptor.
Dexmedetomidine in the prevention of postoperative delirium in elderly patients following non‐cardiac surgery: A systematic review and meta‐analysis
Authors: Shen Qi‐hong , Li Hui‐fang , Zhou Xu‐yan , Yuan Xiao‐zhong 
Published: March 2020

AbstractThe efficacy of dexmedetomidine in the prevention of postoperative delirium (POD) remains ambiguous, however, it has been used to reduce the incidence of delirium in elderly patients. Here, we conducted a meta‐analysis study for assessing the effects of dexmedetomidine on POD among elderly patients following non‐cardiac surgery. A systematic literature search was performed against the PubMed, EMBASE, Cochrane Library, and Web of Science databases, and all relevant literature published till November 30, 2019, were considered. Our analysis included 16 randomised controlled trials conducted with 4534 patients for exploring the effects of dexmedetomidine on POD in elderly patients following non‐cardiac surgery. It was observed that the overall incidence of POD was significantly lower in the dexmedetomidine group than in the control group (risk ratio [RR] 0.51, 95% confidence interval [CI] 0.43–0.61, P < .01). Similar results were obtained from subgroup analysis upon comparison of the placebo (RR 0.52, 95% CI 0.41–0.66, P < .01, moderate quality of evidence), propofol‐treated (RR 0.55, 95% CI 0.38–0.78, P < .01, low quality of evidence), and midazolam‐treated (RR 0.38, 95% CI 0.20–0.71, P < .01, low quality of evidence) groups. Trial sequential analysis revealed that the cumulative z‐value superseded the monitoring boundary and reached the required information size. However, patients who received dexmedetomidine had a higher incidence of bradycardia and hypotension. In conclusion, the meta‐analysis revealed that dexmedetomidine appears to decrease the risk of POD in elderly patients following non‐cardiac surgery. However, as some of the studies were heterogeneous and of low quality, high‐quality trials are necessary for drawing more definitive conclusions.
Hemodialysis patients with less extracellular water overload and smaller cardiac atrial chamber sizes are at greater risk of a fall in blood pressure during dialysis
Authors: Yoowannakul Suree , Vongsanim Surachet , Kotecha Tushar , Fontana Marianna , Davenport Andrew 
Published: March 2020

AbstractIntradialytic hypotension is the most common complication of hemodialysis (HD) treatments. Excessive ultrafiltration results in reduced cardiac preload. We aimed to determine whether a fall in systolic blood pressure during HD was greater in patients starting HD with (a) less overhydration measured by extracellular water (ECW) and (b) lower cardiac preload by cardiac magnetic resonance imaging (MRI). Pre‐HD measurements of ECW and total body water (TBW) were performed using multifrequency bioimpedance (MFBIA). Cardiac chamber sizes and functions were determined by MRI. Twenty‐six patients, 18 males (69.2%), 11 (42.3%) with diabetes, mean age 63.9 ± 15.9 years were studied. Systolic blood pressure (SBP) fell in 15 (57.7%) patients, and either did not change or increased in 9. There was no difference in demographics between groups. Patients with a fall in SBP had lower pre‐HD ECW/TBW (0.400 ± 0.018 vs 0.418 ± 0.021), indexed right ventricular end‐diastolic volume (81.2 ± 37.6 vs 100.8 ± 33.7 mL/m2), and indexed left atrial size (13.7 ± 3.9 vs 18.3 ± 5.0 mL/m2), all P < .05, respectively. There were univariate correlations between the change in SBP and pre‐HD ECW/TBW for the trunk (r = .50, P = .009) and indexed left atrial volume (r = .54, P = .005). A fall in blood pressure occurred more commonly in patients starting HD with lower overhydration as measured by bioimpedance, and those with smaller cardiac chamber sizes. Patients with the lowest ECW/TBW and smallest cardiac chamber sizes had the greatest falls in SBP. This study reinforces the importance of determining physiological target weights and avoiding inappropriately low target weights for HD patients.
In vitro performance of trans‐valve left ventricular assist device installed at aortic valve position
Authors: Okamoto Eiji , Yano Tetsuya , Inoue Yusuke , Shiraishi Yasuyuki , Yambe Tomoyuki , Mitamura Yoshinori 
Published: March 2020

AbstractIn this study, we developed a trans‐valve left ventricular assist device (LVAD) that unites a rear‐impeller axial‐flow blood pump (AFBP) and a polymer membrane valve placed at the aortic valve position. The diameter and length of the rear impeller AFBP was 12 and 63 mm, respectively. The polymer membrane valve was similar to the jelly‐fish valve consisting of a valve leaflet made of silicone rubber (thickness 0.5 mm), valve ring (diameter: 25 mm), and valve spokes. The trans‐valve LVAD was examined in a mock circulation. An implantable pulsatile flow (PF) VAD was connected to an atrial reservoir to simulate the left ventricle (LV), and the Hall valve was worn in the inflow port, and the trans‐valve LVAD was placed in the outflow port as an outflow valve. When the motor rotational speed increased to 26 400 rpm, the mean aortic flow increased from 4.2 to 5.3 L/min, mean aortic pressure increased from 83.4 to 100 mm Hg, and mean motor current of the implantable PF VAD decreased from 1.18 to 0.94 A (unloading effect on LV −21%). The energy equivalent pressure increased from 85.2 to 102 mm Hg, and surplus hemodynamic energy (SHE) decreased by −15.4% from the baseline. In conclusion, the trans‐valve LVAD has an advantage of preserving pulsatility without any complicated mechanism and is a novel and promising LV support device.