bluuebunny/crossref_metadata_2025_split huggingface dataset:
Full scale, microscopically resolved tomographies of sandstone and carbonate rocks augmented by experimental porosity and permeability values
Authors: Esteves Ferreira Matheus , Rodrigues Del Grande Mariana , Neumann Barros Ferreira Rodrigo , Ferreira da Silva Ademir , Nogueira Pereira da Silva Márcio , Tirapu-Azpiroz Jaione , Lucas-Oliveira Everton , de Araújo Ferreira Arthur Gustavo , Soares Renato , B. Eckardt Christian , J. Bonagamba Tito , Steiner Mathias 
Published: June 2023

AbstractWe report a dataset containing full-scale, 3D images of rock plugs augmented by petrophysical lab characterization data for application in digital rock and capillary network analysis. Specifically, we have acquired microscopically resolved tomography datasets of 18 cylindrical sandstone and carbonate rock samples having lengths of 25.4 mm and diameters of 9.5 mm. Based on the micro-tomography data, we have computed porosity-values for each imaged rock sample. For validating the computed porosity values with a complementary lab method, we have measured porosity for each rock sample by using standard petrophysical characterization techniques. Overall, the tomography-based porosity values agree with the measurement results obtained from the lab, with values ranging from 8% to 30%. In addition, we provide for each rock sample the experimental permeabilities, with values ranging from 0.4 mD to above 5D. This dataset will be essential for establishing, benchmarking, and referencing the relation between porosity and permeability of reservoir rock at pore scale.
Unified real-time environmental-epidemiological data for multiscale modeling of the COVID-19 pandemic
Authors: Badr Hamada S. , Zaitchik Benjamin F. , Kerr Gaige H. , Nguyen Nhat-Lan H. , Chen Yen-Ting , Hinson Patrick , Colston Josh M. , Kosek Margaret N. , Dong Ensheng , Du Hongru , Marshall Maximilian , Nixon Kristen , Mohegh Arash , Goldberg Daniel L. , Anenberg Susan C. , Gardner Lauren M. 
Published: June 2023

AbstractAn impressive number of COVID-19 data catalogs exist. However, none are fully optimized for data science applications. Inconsistent naming and data conventions, uneven quality control, and lack of alignment between disease data and potential predictors pose barriers to robust modeling and analysis. To address this gap, we generated a unified dataset that integrates and implements quality checks of the data from numerous leading sources of COVID-19 epidemiological and environmental data. We use a globally consistent hierarchy of administrative units to facilitate analysis within and across countries. The dataset applies this unified hierarchy to align COVID-19 epidemiological data with a number of other data types relevant to understanding and predicting COVID-19 risk, including hydrometeorological data, air quality, information on COVID-19 control policies, vaccine data, and key demographic characteristics.
LDLR gene’s promoter region hypermethylation in patients with familial hypercholesterolemia
Authors: Zorzo R. A. , Suen V. M. M. , Santos J. E. , Silva-Jr W. A. , Suazo V. K. , Honorato A. L. S. C. , Santos R. D. , Jannes C. E. , Pereira A. , Krieger J. E. , Liberatore-Jr R. D. R. 
Published: June 2023

AbstractFamilial hypercholesterolemia (FH) is characterized by high low-density lipoprotein cholesterol (LDL-C) levels and a high risk of early coronary heart disease. Structural alterations in theLDLR,APOB, andPCSK9genes were not found in 20–40% of patients diagnosed using the Dutch Lipid Clinic Network (DCLN) criteria. We hypothesized that methylation in canonical genes could explain the origin of the phenotype in these patients. This study included 62 DNA samples from patients with a clinical diagnosis of FH according to the DCLN criteria, who previously tested negative for structural alterations in the canonical genes, and 47 DNA samples from patients with normal blood lipids (control group). All DNA samples were tested for methylation in the CpG islands of the three genes. The prevalence of FH relative to each gene was determined in both groups and the respective prevalence ratios (PRs) were calculated. The methylation analysis ofAPOBandPCSK9was negative in both groups, showing no relationship between methylation in these genes and the FH phenotype. Asthe LDLRgene has two CpG islands, we analyzed each island separately. The analysis ofLDLR-island1 showed PR = 0.982 (CI 0.33–2.95; χ2 = 0.001; p = 0.973), also suggesting no relationship between methylation and the FH phenotype. Analysis ofLDLR-island2 showed a PR of 4.12 (CI 1.43–11.88; χ2 = 13,921; p = 0.00019), indicating a possible association between methylation on this island and the FH phenotype.
Decomposing solar and geomagnetic activity and seasonal dependencies to examine the relationship between GPS loss of lock and ionospheric turbulence
Authors: Lovati Giulia , De Michelis Paola , Consolini Giuseppe , Pezzopane Michael , Pignalberi Alessio , Berrilli Francesco 
Published: June 2023

AbstractIonospheric irregularities are plasma density variations that occur at various altitudes and latitudes and whose size ranges from a few meters to a few hundred kilometers. They can have a negative impact on the Global Navigation Satellite Systems (GNSS), on their positioning accuracy and even cause a signal loss of lock (LoL), a phenomenon for which GNSS receivers can no longer track the satellites’ signal. Nowadays, the study of plasma density irregularities is important because many of the crucial infrastructures of our society rely on the efficient operation of these positioning systems. It was recently discovered that, of all possible ionospheric plasma density fluctuations, those in a turbulent state and characterized by extremely high values of the Rate Of change of the electron Density Index appear to be associated with the occurrence of LoL events. The spatial distributions of this class of fluctuations at mid and high latitudes are reconstructed for the first time using data collected on Swarm satellites between July 15th, 2014 and December 31st, 2021, emphasizing their dependence on solar activity, geomagnetic conditions, and season. The results unequivocally show that the identified class of plasma fluctuations exhibits spatio-temporal behaviours similar to those of LoL events.
How transform fault shear influences where detachment faults form near mid-ocean ridges
Authors: Schierjott Jana C. , Ito Garrett , Behn Mark D. , Tian Xiaochuan , Morrow Thomas , Kaus Boris J. P. , Escartín Javier 
Published: June 2023

AbstractOceanic detachment faults represent an end-member form of seafloor creation, associated with relatively weak magmatism at slow-spreading mid-ocean ridges. We use 3-D numerical models to investigate the underlying mechanisms for why detachment faults predominantly form on the transform side (inside corner) of a ridge-transform intersection as opposed to the fracture zone side (outside corner). One hypothesis for this behavior is that the slipping, and hence weaker, transform fault allows for the detachment fault to form on the inside corner, and a stronger fracture zone prevents the detachment fault from forming on the outside corner. However, the results of our numerical models, which simulate different frictional strengths in the transform and fracture zone, do not support the first hypothesis. Instead, the model results, combined with evidence from rock physics experiments, suggest that shear-stress on transform fault generates excess lithospheric tension that promotes detachment faulting on the inside corner.
Dengue virus infection during window period of consecutive outbreaks in Nepal and assessment of clinical parameters
Authors: Rauniyar Ramanuj , Prajapati Sabita , Manandhar Binod , Bastola Anup , Chalise Bimal Sharma , Shrestha Srijan , Khanal Chetana , Thapa Machchhendra , Napit Rajindra , Bajracharya Anup Muni , Shrestha Shova , Adhikari Anurag , Das Manandhar Krishna 
Published: June 2023

AbstractNepal is an endemic country for dengue infection with rolling of every 3 year’s clear cyclic outbreaks with exponential growth since 2019 outbreak and the virus gearing towards the non-foci temperate hill regions. However, the information regarding circulating serotype and genotype is not frequent. This research discusses on the clinical features, diagnosis, epidemiology, circulating serotype and genotype among 61 dengue suspected cases from different hospitals of Nepal during the window period 2017–2018 between the two outbreaks of 2016 and 2019. E-gene sequences from PCR positive samples were subjected to phylogenetic analysis under time to most recent common ancestor tree using Markov Chain Monte Carlo (MCMC) and BEAST v2.5.1. Both evolution and genotypes were determined based on the phylogenetic tree. Serotyping by Real-time PCR and Nested PCR showed the co-circulation of all the 3 serotypes of dengue in the year 2017 and only DENV-2 in 2018. Genotype V for DENV-1 and Cosmopolitan Genotype IVa for DENV-2 were detected. The detected Genotype V of DENV-1 in Terai was found close to Indian genotype while Cosmopolitan IVa of DENV-2 found spreading to geographically safe hilly region (now gripped to 9 districts) was close to South-East Asia. The genetic drift of DENV-2 is probably due to climate change and rapid viral evolution which could be a representative model for high altitude shift of the infection. Further, the increased primary infection indicates dengue venturing to new populations. Platelets count together with Aspartate transaminase and Aalanine transaminase could serve as important clinical markers to support clinical diagnosis. The study will support future dengue virology and epidemiology in Nepal.
Comprehensive RNA-Seq-based study and metabolite profiling to identify genes involved in podophyllotoxin biosynthesis in Linum album Kotschy ex Boiss. (Linaceae)
Authors: Danaeipour Zahra , Garoosi Ghasemali , Tohidfar Masoud , Bakhtiarizadeh Mohammad Reza , Mirjalili Mohammad Hossein 
Published: June 2023

AbstractLinum albumis a well-known rich source of anticancer compounds, i.e., podophyllotoxin (PTOX) and other lignans. These compounds play an important role in the plant’s defensive system. The RNA-Seq data of flax (L. usitatissimum) were analyzed under various biotic and abiotic stresses to comprehend better the importance of lignans in plant defense responses. Then, the association between the lignan contents and some related gene expressions was experimented with HPLC and qRT-PCR, respectively. Transcriptomic profiling showed a specific expression pattern in different organs, and just the commonly regulated geneEP3was detected with a significant increase under all stresses. The in silico analysis of the PTOX biosynthesis pathway identified a list of genes, including laccase (LAC11), lactoperoxidase (POD), 4-coumarate-CoA ligase (4CL), and secoisolariciresinol dehydrogenase (SDH). These genes increased significantly under individual stresses. The HPLC analysis showed that the measured lignan contents generally increased under stress. In contrast, a quantitative expression of the genes involved in this pathway using qRT-PCR showed a different pattern that seems to contribute to regulating PTOX content in response to stress. Identified modifications of critical genes related to PTOX biosynthesis in response to multiple stresses can provide a baseline for improving PTOX content inL. album.
Three-dimensional growth and biomechanical risk progression of abdominal aortic aneurysms under serial computed tomography assessment
Authors: Siika Antti , Bogdanovic Marko , Liljeqvist Moritz Lindquist , Gasser T. Christian , Hultgren Rebecka , Roy Joy 
Published: June 2023

AbstractGrowth of abdominal aortic aneurysms (AAAs) is often described as erratic and discontinuous. This study aimed at describing growth patterns of AAAs with respect to maximal aneurysm diameter (Dmax) and aneurysm volume, and to characterize changes in the intraluminal thrombus (ILT) and biomechanical indices as AAAs grow. 384 computed tomography angiographies (CTAs) from 100 patients (mean age 70.0, standard deviation, SD = 8.5 years, 22 women), who had undergone at least three CTAs, were included. The mean follow-up was 5.2 (SD = 2.5) years. Growth of Dmax was 2.64 mm/year (SD = 1.18), volume 13.73 cm3/year (SD = 10.24) and PWS 7.3 kPa/year (SD = 4.95). For Dmax and volume, individual patients exhibited linear growth in 87% and 77% of cases. In the tertile of patients with the slowest Dmax-growth (< 2.1 mm/year), only 67% belonged to the slowest tertile for volume-growth, and 52% and 55% to the lowest tertile of PWS- and PWRI-increase, respectively. The ILT-ratio (ILT-volume/aneurysm volume) increased with time (2.6%/year, p < 0.001), but when adjusted for volume, the ILT-ratio was inversely associated with biomechanical stress. In contrast to the notion that AAAs grow in an erratic fashion most AAAs displayed continuous and linear growth. Considering only change in Dmax, however, fails to capture the biomechanical risk progression, and parameters such as volume and the ILT-ratio need to be considered.
Efficacy of atosiban for repeated implantation failure in frozen embryo transfer cycles
Authors: Li Xiufang , Du Yanbo , Han Xu , Wang Huidan , Sheng Yan , Lian Fang , Lian Qingfeng 
Published: June 2023

AbstractAtosiban was commonly added to improve pregnancy outcomes of patients with repeated embryo implantation failure (RIF). In this study, we aimed to investigate the effect of atosiban before transferring the frozen-thawed embryo to RIF patients. This retrospective study was conducted in the Hospital for Reproductive Medicine affiliated to Shandong University from August 2017 to June 2021. A total of 1774 women with a history of RIF undergoing frozen embryo transfer (FET) were included in this study. All the participants were classified into atosiban or control group: Group A included 677 patients who were administered atosiban intravenously 30 min prior to FET with a dose of 37.5 mg; Group B included 1097 patients who received no atosiban before the transfer. There were no significant differences observed in the live birth rate (LBR) (39.73% vs. 39.02%, P = 0.928) between the two groups. Other secondary outcomes including biochemical pregnancy rate, clinical pregnancy rate, implantation rate, clinical miscarriage rate and preterm birth rate were similar between the two groups (all P > 0.05). However, subgroup analysis demonstrated significantly higher preterm birth rates in the control group compared with the atosiban group (0 versus 3.0%, P = 0.024) in the natural FET cycles. Atosiban may not improve pregnancy outcomes of RIF patients in FET cycles. However, the effects of Atosiban on pregnancy outcomes should be assessed in clinical trials with larger sample sizes.
A nomogram for predicting cancer-specific survival in patients with uterine clear cell carcinoma: a population-based study
Authors: Cheng Wen-li , Wang Rui-min , Zhao Yi , Chen Juan 
Published: June 2023

AbstractUterine clear cell carcinoma (UCCC) is a relatively rare endometrial cancer. There is limited information on its prognosis. This study aimed to develop a predictive model predicting the cancer-specific survival (CSS) of UCCC patients based on data from the Surveillance, Epidemiology, and End Results (SEER) database between 2000 and 2018. A total of 2329 patients initially diagnosed with UCCC were included in this study. Patients were randomized into training and validation cohorts (7:3). Multivariate Cox regression analysis identified that age, tumor size, SEER stage, surgery, number of lymph nodes detected, lymph node metastasis, radiotherapy and chemotherapy were independent prognostic factors for CSS. Based on these factors, a nomogram for predicting the prognosis of UCCC patients was constructed. The nomogram was validated using concordance index (C-index), calibration curves, and decision curve analyses (DCA). The C-index of the nomograms in the training and validation sets are 0.778 and 0.765, respectively. Calibration curves showed good consistency of CSS between actual observations and nomogram predictions, and DCA showed that the nomogram has great clinical utility. In conclusion, a prognostic nomogram was firstly established for predicting the CSS of UCCC patients, which can help clinicians make personalized prognostic predictions and provide accurate treatment recommendations.
Knocking out alpha-synuclein in melanoma cells downregulates L1CAM and decreases motility
Authors: Gajendran Nithya , Rajasekaran Santhanasabapathy , Witt Stephan N. 
Published: June 2023

AbstractThe Parkinson’s disease (PD) associated protein, alpha-synuclein (α-syn/SNCA), is highly expressed in aggressive melanomas. The goal of this study was to reveal possible mechanism(s) of α-syn involvement in melanoma pathogenesis. Herein, we asked whether α-syn modulates the expression of the pro-oncogenic adhesion molecules L1CAM and N-cadherin. We used two human melanoma cell lines (SK-MEL-28, SK-MEL-29), SNCA-knockout (KO) clones, and two human SH-SY5Y neuroblastoma cell lines. In the melanoma lines, loss of α-syn expression resulted in significant decreases in the expression of L1CAM and N-cadherin and concomitant significant decreases in motility. On average, there was a 75% reduction in motility in the four SNCA-KOs tested compared to control cells. Strikingly, comparing neuroblastoma SH-SY5Y cells that have no detectable α-syn to SH-SY5Y cells that stably express α-syn (SH/+αS), we found that expressing α-syn increased L1CAM and single-cell motility by 54% and 597%, respectively. The reduction in L1CAM level in SNCA-KO clones was not due to a transcriptional effect, rather we found that L1CAM is more efficiently degraded in the lysosome in SNCA-KO clones than in control cells. We propose that α-syn is pro-survival to melanoma (and possibly neuroblastoma) because it promotes the intracellular trafficking of L1CAM to the plasma membrane.
Comprehensive analysis of the coding and non-coding RNA transcriptome expression profiles of hippocampus tissue in tx-J animal model of Wilson's disease
Authors: Wang Dan , Xie Daojun , Zhang Juan , Cai Biao , Yang Bo , Zhou Lei , Huang Xiaofeng 
Published: June 2023

AbstractWilson's disease (WD) is an autosomal recessive disorder with a genetic basis. The predominant non-motor symptom of WD is cognitive dysfunction, although the specific genetic regulatory mechanism remains unclear. Tx-J mice, with an 82% sequence homology of the ATP7B gene to the human gene, are considered the most suitable model for WD. This study employs deep sequencing to investigate the differences in RNA transcript profiles, both coding and non-coding, as well as the functional characteristics of the regulatory network involved in WD cognitive impairment. The cognitive function of tx-J mice was evaluated using the Water Maze Test (WMT). Long non-coding RNA (lncRNA), circular RNA (circRNA), and messenger RNA (mRNA) profiles were analyzed in the hippocampal tissue of tx-J mice to identify differentially expressed RNAs (DE-RNAs). Subsequently, the DE-RNAs were used to construct protein–protein interaction (PPI) networks, as well as DE-circRNAs and lncRNAs-associated competing endogenous RNA (ceRNA) expression networks, and coding-noncoding co-expression (CNC) networks. To elucidate their biological functions and pathways, the PPI and ceRNA networks were subjected to Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis. A total of 361 differentially expressed mRNAs (DE-mRNAs), comprising 193 up-regulated and 168 down-regulated mRNAs, 2627 differentially expressed long non-coding RNAs (DE-lncRNAs), consisting of 1270 up-regulated and 1357 down-regulated lncRNAs, and 99 differentially expressed circular RNAs (DE-circRNAs), consisting of 68 up-regulated and 31 down-regulated circRNAs, were observed in the tx-J mice group when compared to the control mice group. Gene Ontology (GO) and pathway analyses revealed that DE-mRNAs were enriched in cellular processes, calcium signaling pathways, and mRNA surveillance pathways. In contrast, the DE-circRNAs-associated competing endogenous RNA (ceRNA) network was enriched for covalent chromatin modification, histone modification, and axon guidance, whereas the DE-lncRNAs-associated ceRNA network was enriched for dendritic spine, regulation of cell morphogenesis involved in differentiation, and mRNA surveillance pathway. The study presented the expression profiles of lncRNA, circRNA, and mRNA in the hippocampal tissue of tx-J mice. Furthermore, the study constructed PPI, ceRNA, and CNC expression networks. The findings are significant in comprehending the function of regulatory genes in WD associated with cognitive impairment. These results also offer valuable information for the diagnosis and treatment of WD.
Simultaneous determination of 2-(3-hydroxy-5-phosphonooxymethyl-2-methyl-4-pyridyl)-1,3-thiazolidine-4-carboxylic acid and main plasma aminothiols by HPLC–UV based method
Authors: Piechocka Justyna , Wyszczelska-Rokiel Monika , Głowacki Rafał 
Published: June 2023

AbstractThe report presents the first method for simultaneous determination of plasma 2-(3-hydroxy-5-phosphonooxymethyl-2-methyl-4-pyridyl)-1,3-thiazolidine-4-carboxylic acid (HPPTCA), an adduct of cysteine (Cys) and active form of vitamin B6 pyridoxal 5′-phosphate (PLP), as well as total low molecular-weight thiols content, including Cys, homocysteine (Hcy), cysteinyl-glycine (Cys-Gly), and glutathione (GSH). The assay is based on high performance liquid chromatography coupled with ultraviolet detection (HPLC–UV) and involves disulfides reduction with tris(2-carboxyethyl)phosphine (TCEP), derivatization with 2-chloro-1-methylquinolinium tetrafluoroborate (CMQT) followed by sample deproteinization with perchloric acid (PCA). The chromatographic separation of obtained stable UV-absorbing derivatives is achieved on ZORBAX SB-C18 (150 × 4.6 mm, 5.0 µm) column using gradient elution with eluent consisted of 0.1 mol/L trichloroacetic acid (TCA), pH 1.7 and acetonitrile (ACN), delivered at a flow rate 1 mL/min. Under these conditions, the analytes are separated within 14 min at room temperature, and quantified by monitoring at 355 nm. Regarding HPPTCA, the assay linearity was demonstrated within a 1–100 µmol/L in plasma and the lowest concentration on the calibration curve was recognized as the limit of quantification (LOQ). The accuracy ranged from 92.74 to 105.57% and 95.43 to 115.73%, while precision varied from 2.48 to 6.99% and 0.84 to 6.98% for intra- and inter-day measurements, respectively. The utility of the assay was proved by application to plasma samples delivered by apparently healthy donors (n = 18) in which the HPPTCA concentration ranged from 19.2 to 65.6 µmol/L. The HPLC–UV assay provides complementary tool for routine clinical analysis, facilitating further studies on the role of aminothiols and HPPTCA in living systems.
Synthesis of substituted pyridines with diverse functional groups via the remodeling of (Aza)indole/Benzofuran skeletons
Authors: Vaithegi Kannan , Yi Sihyeong , Lee Ji Hyae , Varun Begur Vasanthkumar , Park Seung Bum 
Published: June 2023

AbstractSubstituted pyridines with diverse functional groups are important structural motifs found in numerous bioactive molecules. Several methodologies for the introduction of various bio-relevant functional groups to pyridine have been reported, but there is still a need for a single robust method allowing the selective introduction of multiple functional groups. This study reports a ring cleavage methodology reaction for the synthesis of 2-alkyl/aryl 3-electron-withdrawing groups (esters, sulfones, and phosphonates) 5-aminoaryl/phenol pyridines via the remodeling of 3-formyl (aza)indoles/benzofurans. Totally ninety-three 5-aminoaryl pyridines and thirty-three 5-phenol pyridines were synthesized showing the robustness of the developed methodology. The application of this methodology further provided a privileged pyridine scaffold containing biologically relevant molecules and direct drug/natural product conjugation with ethyl 2-methyl nicotinate.