bluuebunny/crossref_metadata_2025_split huggingface dataset:
Cardiovascular, renal, and lower limb outcomes in patients with type 2 diabetes after percutaneous coronary intervention and treated with sodium–glucose cotransporter 2 inhibitors vs. dipeptidyl peptidase-4 inhibitors
Authors: Lee Hsin-Fu , Chan Yi-Hsin , Chuang Chi , Li Pei-Ru , Yeh Yung-Hsin , Hsiao Fu-Chih , Peng Jian-Rong , See Lai-Chu 
Published: January 2023

Abstract

Aims
Patients with type 2 diabetes (T2D) who undergo percutaneous coronary intervention (PCI) are at higher risk of adverse cardiovascular and renal events than non-diabetic patients. However, limited evidence is available regarding the cardiovascular, renal, and limb outcomes of patients with T2D after PCI and who were treated with sodium–glucose cotransporter-2 inhibitors (SGLT2i). We compare the specified outcomes in patients with T2D after PCI who were treated with SGLT2i vs. dipeptidyl peptidase-4 inhibitors (DPP4i).

Methods and results
In this nationwide retrospective cohort study, we identified 4248 and 37 037 consecutive patients with T2D who underwent PCI with SGLT2i and DPP4i, respectively, for 1 May 2016–31 December 2019. We used propensity score matching (PSM) to balance the covariates between study groups. After PSM, SGLT2i, and DPP4i were associated with comparable risks of ischaemic stroke, acute myocardial infarction, and lower limb amputation. However, SGLT2i was associated with significantly lower risks of heart failure hospitalization [HFH; 1.35% per year vs. 2.28% per year; hazard ratio (HR): 0.60; P = 0.0001], coronary revascularization (2.33% per year vs. 3.36% per year; HR: 0.69; P = 0.0003), composite renal outcomes (0.10% per year vs. 1.05% per year; HR: 0.17; P &lt; 0.0001), and all-cause mortality (2.27% per year vs. 3.80% per year, HR: 0.60; P &lt; 0.0001) than were DPP4i.

Conclusion
Our data indicated that SGLT2i, compared with DPP4i, were associated with lower risks of HFH, coronary revascularization, composite renal outcomes, and all-cause mortality for patients with T2D after PCI. Further randomized or prospective studies can investigate the effects of SGLT2i in patients with T2D after PCI.
A high-quality chromosome-level genome assembly of rohu carp, Labeo rohita, and its utilization in SNP-based exploration of gene flow and sex determination
Authors: Arick Mark A , Grover Corrinne E , Hsu Chuan-Yu , Magbanua Zenaida , Pechanova Olga , Miller Emma R , Thrash Adam , Youngblood Ramey C , Ezzell Lauren , Alam Md Samsul , Benzie John A H , Hamilton Matthew G , Karsi Attila , Lawrence Mark L , Peterson Daniel G 
Published: January 2023

Abstract
Labeo rohita (rohu) is a carp important to aquaculture in South Asia, with a production volume close to Atlantic salmon. While genetic improvements to rohu are ongoing, the genomic methods commonly used in other aquaculture improvement programs have historically been precluded in rohu, partially due to the lack of a high-quality reference genome. Here we present a high-quality de novo genome produced using a combination of next-generation sequencing technologies, resulting in a 946 Mb genome consisting of 25 chromosomes and 2,844 unplaced scaffolds. Notably, while approximately half the size of the existing genome sequence, our genome represents 97.9% of the genome size newly estimated here using flow cytometry. Sequencing from 120 individuals was used in conjunction with this genome to predict the population structure, diversity, and divergence in three major rivers (Jamuna, Padma, and Halda), in addition to infer a likely sex determination mechism in rohu. These results demonstrate the utility of the new rohu genome in modernizing some aspects of rohu genetic improvement programs.
Joint estimation ofS-wave velocity and damping ratio of the near-surface from active Rayleigh wave surveys processed with a wavefield decomposition approach
Authors: Bergamo Paolo , Maranò Stefano , Fäh Donat 
Published: January 2023

SUMMARYThe use of surface wave measurements to derive an S-wave velocity profile of the subsurface has become a widely applied procedure; however, their potential use to reconstruct the S-wave material damping properties of the subsoil is generally overlooked, due to the difficulties in obtaining consistent surface wave amplitude information from field data and translating them into robust estimates of the dissipative properties of the near-surface. In this work, we adapt a wavefield decomposition technique for the processing of elastic surface wave data to the extraction of the complete set of properties of Rayleigh waves generated by a controlled source and propagating in dissipative geomaterials. Retrieved information includes multimodal phase velocity and ellipticity as well as the frequency-dependent attenuation coefficient. We exploit the key advantages of wavefield decomposition processing (joint interpretation of multicomponent recordings, coupled estimation of wave propagation parameters, modelling of multiple superimposing modes) to maximize the robustness of the retrieval of Rayleigh wave properties, especially of the dissipative ones. For the subsequent interpretation of Rayleigh wave dispersion, ellipticity and attenuation data we implement a joint Monte Carlo inversion yielding a coupled estimate of S-wave velocity and damping ratio profile for the subsurface; we incorporate a series of geophysical constraints to narrow down the searched parameter space to realistic soil models. We apply this processing and inversion scheme to a bespoke synthetic data set and to a field survey for the characterization of a strong motion station; in both cases, we succeed in retrieving Rayleigh wave multimodal dispersion, ellipticity and attenuation curves. From the inversion of data from the simulated seismogram we are able to reconstruct the properties of the synthetic model. As for the real case, we determine an S-wave velocity and damping ratio model for the soil column below the station, through which we are able to model the inelastic earthquake local response observed at the site. Basing on the results obtained for the real case, we argue that one of the advantages brought by our processing method—the possibility to process active Rayleigh wave data acquired by a 2-D array illuminated by different source positions—may play a key role in allowing to retrieve dissipative properties of the near-surface closer to the material damping of the soil materials, and less influenced by scattering determined by possible discontinuities in the subsurface.
The Trinidad and Tobago microzonation project: San Fernando
Authors: Papadopoulos Ilias , Manzano Jevan , Reddock Kafele , Latchman Joan L 
Published: January 2023

SUMMARYThe city of San Fernando is the industrial capital of the twin island nation of Trinidad and Tobago in the West Indies. Situated at the west coast, is in close proximity with the Central Range Fault, a major fault crossing the whole island and continuing offshore. Due to this proximity, but also because of the complex tectonics in the area with deep and shallow earthquakes, a detailed seismic hazard map deemed important. A microzonation study was carried throughout the boundaries of the city, using ambient noise techniques. 1200 single-site records of ambient noise, along with 16 microtremor array measurements were obtained. The results indicate that the alluvium deposits in the river basins along with a small part of reclaimed land appear to have velocities in the range 220–500 m s–1 and thickness from shallow to about 60 m. The marls, which cover the majority of the study area, exhibit shear wave velocities in the range of 700–1600 m s–1, depending on the level of compaction, with thickness that can reach almost 100 m. The hardest formations, Naparima Hill and San Fernando formations, in weathered state they appear with velocities above 1000 m s–1, while their unweathered state reaches 3000 m s–1. A parametric investigation which was conducted as an independent investigation to validate the experimental results, is in good agreement. An empirical susceptibility method to calculate the most vulnerable areas, reveals that areas close to coast and the river banks might experience much higher shaking values.
N-glycosylation on Asn-57 is required for the correct HAI-2 protein folding and protease inhibitory activity
Authors: Huang Nanxi , Wang Qiaochu , Chen Chao-Yang , Hu Je-Ming , Wang Jehng-Kang , Chang Ping-Ying , Johnson Michael D , Lin Chen-Yong 
Published: January 2023

Abstract
Hepatocyte growth factor activator inhibitor (HAI)-2 is an integral membrane Kunitz-type serine protease inhibitor that regulates the proteolysis of matriptase and prostasin in a cell-type selective manner. The cell-type selective nature of HAI-2 function depends largely on whether the inhibitor and potential target enzymes are targeted to locations in close proximity. The N-glycan moiety of HAI-2 can function as a subcellular targeting signal. HAI-2 is synthesized with 1 of 2 different N-glycan modifications: one of oligomannose-type, which largely remains in the endoplasmic reticulum/GA, and another of complex-type, which is targeted toward the apical surface in vesicle-like structures, and could function as an inhibitor of matriptase and prostasin. HAI-2 contains 2 putative N-glycosylation sites, Asn-57 and Asn-94, point mutations of which were generated and characterized in this study. The protein expression profile of the HAI-2 mutants indicates that Asn-57, and not Asn-94, is responsible for the N-glycosylation of both HAI-2 species, suggesting that the form with oligomannose-type N-glycan is the precursor of the form with complex-type N-glycan. Unexpectedly, the vast majority of non-glycosylated HAI-2 is synthesized into multiple disulfide-linked oligomers, which lack protease inhibitory function, likely due to distorted conformations caused by the disarrayed disulfide linkages. Although forced expression of HAI-2 in HAI-2 knockout cells artificially enhances HAI-2 oligomerization, disulfide-linked HAI-2 oligomers can also be observed in unmodified cells. These results suggest that N-glycosylation on Asn-57 is required for folding into a functional HAI-2 with full protease suppressive activity and correct subcellular targeting signal.
Methylenetetrahydrofolate reductase deficiency and high-dose FA supplementation disrupt embryonic development of energy balance and metabolic homeostasis in zebrafish
Authors: Simonian Rebecca , Pannia Emanuela , Hammoud Rola , Noche Ramil R , Cui Xiucheng , Kranenburg Eva , Kubant Ruslan , Ashcraft Paula , Wasek Brandi , Bottiglieri Teodoro , Dowling James J , Anderson G Harvey 
Published: January 2023

Abstract
Folic acid (synthetic folate, FA) is consumed in excess in North America and may interact with common pathogenic variants in methylenetetrahydrofolate reductase (MTHFR); the most prevalent inborn error of folate metabolism with wide-ranging obesity-related comorbidities. While preclinical murine models have been valuable to inform on diet–gene interactions, a recent Folate Expert panel has encouraged validation of new animal models. In this study, we characterized a novel zebrafish model of mthfr deficiency and evaluated the effects of genetic loss of mthfr function and FA supplementation during embryonic development on energy homeostasis and metabolism. mthfr-deficient zebrafish were generated using CRISPR mutagenesis and supplemented with no FA (control, 0FA) or 100 μm FA (100FA) throughout embryonic development (0–5 days postfertilization). We show that the genetic loss of mthfr function in zebrafish recapitulates key biochemical hallmarks reported in MTHFR deficiency in humans and leads to greater lipid accumulation and aberrant cholesterol metabolism as reported in the Mthfr murine model. In mthfr-deficient zebrafish, energy homeostasis was also impaired as indicated by altered food intake, reduced metabolic rate and lower expression of central energy-regulatory genes. Microglia abundance, involved in healthy neuronal development, was also reduced. FA supplementation to control zebrafish mimicked many of the adverse effects of mthfr deficiency, some of which were also exacerbated in mthfr-deficient zebrafish. Together, these findings support the translatability of the mthfr-deficient zebrafish as a preclinical model in folate research.
Identification of potential causal metabolites associated with atopic dermatitis
Authors: Jia Yiming , Wang Rong , Sun Lulu , Guo Daoxia , Shi Mengyao , Zhang Kaixin , Yang Pinni , Wang Yu , Liu Fanghua , Chen Guo-Chong , Zhang Yonghong , Zhu Zhengbao 
Published: January 2023

AbstractAtopic dermatitis is a chronically recurrent dermatologic disease affected by complex pathophysiology with limited therapeutic options. To identify promising biomarkers for atopic dermatitis, we conducted a Mendelian randomization (MR) study to systematically screen blood metabolome for potential causal mediators of atopic dermatitis and further predict target-mediated side effects. We selected 128 unique blood metabolites from three European-descent metabolome genome-wide association studies (GWASs) with a total of 147 827 participants. Atopic dermatitis dataset originated from a large-scale GWAS including 10 788 cases and 30 047 controls of European ancestry. MR analyses were performed to estimate the associations of blood metabolites with atopic dermatitis. We then applied a phenome-wide MR analysis to ascertain potential on-target side effects of metabolite intervention. Three metabolites were identified as potential causal mediators for atopic dermatitis, including docosahexaenoic acid (odds ratio [OR], 0.87; 95% confidence interval [CI], 0.81–0.94; P = 3.45 × 10−4), arachidonate (OR, 0.30; 95% CI, 0.17–0.53; P = 4.09 × 10−5) and 1-arachidonoylglycerophosphoethanolamine (1-arachidonoyl-GPE) (OR, 0.25; 95% CI, 0.12–0.53; P = 2.58 × 10−4). In the phenome-wide MR analysis, docosahexaenoic acid and arachidonate were also identified to have beneficial or detrimental effects on multiple diseases beyond atopic dermatitis, respectively. No adverse side effects were found for 1-arachidonoyl-GPE. In this systematic MR study, docosahexaenoic acid, arachidonate and 1-arachidonoyl-GPE were identified as potential causal and beneficial mediators in the development of atopic dermatitis. Side-effect profiles were characterized to help inform drug target prioritization, and 1-arachidonoyl-GPE was a promising target for prevention and treatment of atopic dermatitis with no predicted adverse side effects.
Tracking integrated ecosystem assessments in the ICES network: a social network analysis of the ICES expert groups
Authors: Fuller Jessica L , Strehlow Harry V , Schmidt Jörn O , Bodin Örjan , Dankel Dorothy J 
Published: January 2023

AbstractThe advice the International Council for the Exploration of the Sea (ICES) provides to its member countries is crucial for the sustainable management of shared marine resources, and the conservation of relevant marine ecosystems. In 2014, ICES made a strategic decision to integrate marine and social sciences in a new type of assessment framework called “integrated ecosystem assessments” (IEA) to deliver advice on societal trade-offs between different policy options. The IEA-focused expert groups formed before and after this period now cover all major ecoregions. To track the progression of IEAs in the ICES network over time, we conducted a social network analysis (SNA) on expert group attendance for the years 2015–2019. The IEA-focused expert groups generally ranked lower in the overall ICES network. Our study shows that some IEA-groups become more connected over time, while others decline. We also evaluated the role of workshops in the ICES network, particularly their role in the development of IEA knowledge. Our study shows that workshops play an important role in ICES network connectivity. The study demonstrates how social network analysis can be used to study an organization such as ICES and determine the effectiveness, or impact, of that organizational function.
Names from Nowhere? Fictitious Country Names in Survey Vignettes Affect Experimental Results
Authors: Majnemer Jacklyn , Meibauer Gustav 
Published: January 2023

Abstract
Using fictitious country names in hypothetical scenarios is widespread in experimental international relations research. We survey sixty-four peer-reviewed articles to find that it is justified by reference to necessary “neutralization” compared to real-world scenarios. However, this neutralization effect has not been independently tested. Indeed, psychology and toponymy scholarship suggest that names entail implicit cues that can inadvertently bias survey results. We use a survey experiment to test neutralization and naming effects. We find not only limited evidence for neutralization, but also little evidence for systematic naming effects. Instead, we find that respondents were often more willing to support using force against fictitious countries than even adversarial real-world countries. Real-world associations may provide a “deterrent” effect not captured by hypothetical scenarios with fictitious country names. In turn, fictionalization may decrease the stakes as experienced by respondents. Researchers should therefore carefully explain rationales for and expected effects of fictitious country names, and test their fictitious names independently.
In vivopharmacokinetic/pharmacodynamic evaluation of cefepime/taniborbactam combination against cefepime-non-susceptible Enterobacterales andPseudomonas aeruginosain a murine pneumonia model
Authors: Abdelraouf Kamilia , Nicolau David P 
Published: January 2023

AbstractBackgroundCefepime/taniborbactam is a cephalosporin/bicyclic boronate β-lactamase inhibitor combination in clinical development for nosocomial pneumonia due to MDR Gram-negative bacteria. A murine pneumonia model was used to characterize cefepime/taniborbactam in vivo pharmacodynamics against Enterobacterales and Pseudomonas aeruginosa strains.MethodsClinical cefepime-non-susceptible Enterobacterales and P. aeruginosa strains expressing serine carbapenemases and/or other cefepime-hydrolysing β-lactamases with cefepime/taniborbactam combination MICs of 0.12–16 mg/L were used. Cefepime and taniborbactam human-simulated regimens equivalent to clinical doses (i.e. 2/0.5 g q8h) were established in the pneumonia model. The in vivo activity of the cefepime human-simulated regimen given alone or concomitantly with escalating taniborbactam exposures against eight Enterobacterales and four P. aeruginosa strains was assessed. Taniborbactam pharmacokinetics were evaluated to determine systemic exposures of regimens used; taniborbactam fAUC0–24/MIC values required for efficacy were estimated using the Hill equation. In addition, the in vivo activity of the cefepime/taniborbactam combination human-simulated regimen was assessed against 18 strains.ResultsAmong Enterobacterales, median taniborbactam fAUC0–24/MIC values associated with stasis and 1 log kill were 0.96 and 4.03, respectively, while for P. aeruginosa, requirements were 1.35 and 3.02 for stasis and 1 log kill, respectively. The cefepime/taniborbactam human-simulated regimen produced &gt;2 log kill in 14/18 strains and &gt;1 log kill in 18/18 strains.ConclusionsCefepime/taniborbactam produced marked in vivo bactericidal activity against cefepime-non-susceptible Enterobacterales and P. aeruginosa isolates with cefepime/taniborbactam MICs up to and including 16 mg/L in the pneumonia model. Assessments of the probability of clinical attainment of the identified targets should be undertaken to support the selected cefepime/taniborbactam dose for treatment of nosocomial pneumonia.
Molecular features and transmission of NDM-producing Enterobacterales in Israeli hospitals
Authors: Adler Amos , Ghosh Hiren , Gross Andrea , Rechavi Amit , Lasnoy Michal , Assous Marc V , Geffen Yuval , Darawshe Basel , Wiener-Well Yonit , Grundmann Hajo , Reuter Sandra 
Published: January 2023

AbstractObjectivesNDM-producing Enterobacterales (NDME) account for 34.9% of new carbapenemase-producing Enterobacterales cases in Israeli hospitals. The goals of this study were to characterize the genomic composition of NDME isolates and mobile genetic elements (MGEs) and to identify NDME transmission events (TEs).MethodsThe study was conducted at the Tel-Aviv Sourasky, Rambam and Sha’are-Zedek Medical Centers (TASMC, RMC and SZMC, respectively). All NDME isolates detected between January 2018 and July 2019 were included.Phylogenetic analysis was based on core-genome SNP distances. Core-genome distance of ≤5 SNPs between isolates from patients with overlapping hospitalization periods was suggestive of a potential TE. MGEs were classified by comparison of the blaNDM gene flanking regions.ResultsThe study included 212 NDME isolates from 203 patients, including 104 isolates from TASMC, 30 isolates from RMC and 78 isolates from SZMC. The majority of isolates (n = 157; 74%) harboured the blaNDM-1 gene, followed by the blaNDM-5 (n = 48) and blaNDM-15 genes (n = 7). The most common NDME species were Klebsiella pneumoniae (n = 67), Escherichia coli (n = 65) and Enterobacter cloacae (n = 45), all showing a highly diverse clonal structure. Most blaNDM-1-harbouring isolates (134/157; 85%) were divided into nine different MGE modules, variably distributed across species and hospitals.The numbers of post-admission acquisition cases (n = 118) that could be linked to other cases by both molecular and epidemiological criteria were 13/58 (24.2%), 3/48 (6.3%) and 4/12 (33.3%) in TASMC, SZMC and RMC, respectively.ConclusionsThe study depicted a complex and diverse population structure, suggesting that NDME had not spread via clonal expansion.
Multiobjective optimization of frozen and freeze-driedLactobacillus delbrueckiisubsp.bulgaricusCFL1 production via the modification of fermentation conditions
Authors: Tovilla Coutiño Maria de L , Passot Stéphanie , Trelea Ioan-Cristian , Ropers Marie-Hélène , Gohon Yann , Fonseca Fernanda 
Published: January 2023

AbstractAimThis study investigates the individual and combined effects of fermentation parameters for improving cell biomass productivity and the resistance to freezing, freeze-drying, and freeze-dried storage of Lactobacillus delbrueckii subsp. bulgaricus CFL1.Methods and ResultsCells were cultivated at different temperatures (42°C and 37°C) and pH values (5.8 and 4.8) and harvested at various growth phases (mid-exponential, deceleration, and stationary growth phases). Specific acidifying activity was determined after fermentation, freezing, freeze-drying, and freeze-dried storage. Multiple regression analyses were performed to identify the effects of fermentation parameters on the specific acidifying activity losses and to generate the corresponding 3D response surfaces. A multiobjective decision approach was applied to optimize biomass productivity and specific acidifying activity. The temperature positively influenced biomass productivity, whereas low pH during growth reduced the loss of specific acidifying activity after freezing and freeze-drying. Furthermore, freeze-drying resistance was favored by increased harvest time.ConclusionsProductivity, and freezing and freeze-drying resistances of L. delbrueckii subsp. bulgaricus CFL1 were differentially affected by the fermentation parameters studied. There was no single fermentation condition that improved both productivity and resistance to freezing and freeze-drying. Thus, Pareto fronts were helpful to optimize productivity and resistance, when cells were grown at 42°C, pH 4.8, and harvested at the deceleration phase.