bluuebunny/crossref_metadata_2025_split huggingface dataset:
The Saint-Ursanne earthquakes of 2000 revisited: evidence for active shallow thrust-faulting in the Jura fold-and-thrust belt
Authors: Lanza Federica , Diehl Tobias , Deichmann Nicholas , Kraft Toni , Nussbaum Christophe , Schefer Senecio , Wiemer Stefan 
Published: January 2022

AbstractThe interpretation of seismotectonic processes within the uppermost few kilometers of the Earth’s crust has proven challenging due to the often significant uncertainties in hypocenter locations and focal mechanisms of shallow seismicity. Here, we revisit the shallow seismic sequence of Saint-Ursanne of March and April 2000 and apply advanced seismological analyses to reduce these uncertainties. The sequence, consisting of five earthquakes of which the largest one reached a local magnitude (ML) of 3.2, occurred in the vicinity of two critical sites, the Mont Terri rock laboratory and Haute-Sorne, which is currently evaluated as a possible site for the development of a deep geothermal project. Template matching analysis for the period 2000–2021, including data from mini arrays installed in the region since 2014, suggests that the source of the 2000 sequence has not been persistently active ever since. Forward modelling of synthetic waveforms points to a very shallow source, between 0 and 1 km depth, and the focal mechanism analysis indicates a low-angle, NNW-dipping, thrust mechanism. These results combined with geological data suggest that the sequence is likely related to a backthrust fault located within the sedimentary cover and shed new light on the hosting lithology and source kinematics of the Saint-Ursanne sequence. Together with two other more recent shallow thrust faulting earthquakes near Grenchen and Neuchâtel in the north-central portion of the Jura fold-and-thrust belt (FTB), these new findings provide new insights into the present-day seismotectonic processes of the Jura FTB of northern Switzerland and suggest that the Jura FTB is still undergoing seismically active contraction at rates likely < 0.5 mm/yr. The shallow focal depths provide indications that this low-rate contraction in the NE portion of the Jura FTB is at least partly accommodated within the sedimentary cover and possibly decoupled from the basement.
LncRNA HCG18 promotes osteosarcoma growth by enhanced aerobic glycolysis via the miR-365a-3p/PGK1 axis
Authors: Pan Xiaohui , Guo Jin , Liu Canjun , Pan Zhanpeng , Yang Zhicheng , Yao Xiang , Yuan Jishan 
Published: January 2022

Abstract
Background
Osteosarcoma (OS) is a common primary bone malignancy. Long noncoding RNA HCG18 is known to play an important role in a variety of cancers. However, its role in OS and relevant molecular mechanisms are unclear.

Methods
Real-time quantitative PCR was performed to determine the expression of target genes. Function experiments showed the effects of HCG18 and miR-365a-3p on OS cell growth.

Results
HCG18 expression was increased in OS cell lines. Moreover, in vitro and in vivo experiments demonstrated that HCG18 knockdown inhibited OS cell proliferation. Mechanistically, HCG18 was defined as a competing endogenous RNA by sponging miR-365a-3p, thus elevating phosphoglycerate kinase 1 (PGK1) expression by directly targeting its 3ʹUTR to increase aerobic glycolysis.

Conclusion
HCG18 promoted OS cell proliferation via enhancing aerobic glycolysis by regulating the miR-365a-3p/PGK1 axis. Therefore, HCG18 may be a potential target for OS treatment.
Development of a remote learning educational model for international Emergency Medicine trainees in the era of COVID-19
Authors: Ciano Joseph D. , Acerra John , Tang Aimee 
Published: January 2022

Abstract
Background
The COVID-19 pandemic has pressured post-graduate medical education programs to shift from traditional in-person teaching to remote teaching and learning. Remote learning in medical education has been described in the literature mostly in the context of local in-country teaching. International remote medical education poses unique challenges for educators, especially in low-middle income countries (LMICs) who need continued Emergency Medicine (EM) specialty development. Our objective is to describe the development and implementation of our remote educational curriculum for EM trainees in West Bengal, India, and to assess trainee satisfaction with our remote learning curriculum.

Methods
Our curriculum was developed by adapting remote learning techniques used in Western post-graduate medical education, conducting literature searches on remote learning modalities, and through collaboration with local faculty in India. We assessed resident satisfaction in our curriculum with feedback surveys and group discussions.

Results
The remote educational curriculum had overall high trainee satisfaction ratings for weekly livestream video lectures and throughout our monthly educational modules (median ratings 9-10 out of a 10-point Likert scale). Qualitative feedback regarding specific lecture topics and educational modules were also received.

Conclusions
International remote education in LMICs poses a unique set of challenges to medical educators. Residents in our study reported high satisfaction with the curriculum, but there is a lack of clarity regarding how a remote curriculum may impact academic and clinical performance. Future studies are needed to further evaluate the efficacy and academic and clinical implications of remote medical education in LMICs.
Influence of citrate and PEG coatings on the bioaccumulation of TiO2 and CeO2 nanoparticles following dietary exposure in rainbow trout
Authors: Connolly Mona , Hernández-Moreno David , Conde Estefanía , Garnica Alicia , Navas José M. , Torrent Fernando , Rucandio Isabel , Fernandez-Cruz María L. 
Published: January 2022

Abstract
Background
This study was conducted to provide much needed information on the potential of low solubility, highly biodurable nanoparticles (NPs) (TiO2 and CeO2 NPs), to bioaccumulate in fish and to investigate the relationship between an engineered nanomaterials surface coating, uptake and biokinetics in vivo. Rainbow trout (Oncorhynchus mykiss) were fed diets spiked with uncoated or surface coated (polyethylene glycol (PEG) or citrate (CIT)) TiO2 and CeO2 NPs (100 mg NPs/kg feed) for 10 days and thereafter fish were allowed to depurate for 42 days. Special care was taken to measure the real dispersed and actual administered concentrations, taking into consideration any potential losses from leaching, and to characterise the form (size, aggregation state, charge) of the NPs to which the fish were exposed.

Results
The coatings had an influence on levels of uptake and distributions. Most notably a higher uptake of PEG and CIT coated TiO2 and CeO2 NPs compared to fish exposed to uncoated materials was observed. The elimination of any Ti from tissues was rapid during the first day of depuration, whereas Ce levels remained in fish tissues (stomach, intestine and liver) with differences in depuration and redistribution of the three types of CeO2 NPs. However, no bioaccumulation potential for both tested metal oxide NPs in fish irrespective of coatings is expected according to BMF values < 1.

Conclusions
Distinct uptake, distribution and depuration kinetics in rainbow trout have been evidenced for different metal oxide NPs (TiO2 and CeO2 NPs). Coatings influenced uptake and in some cases led to slower depuration and distinct distributions, but do not make the uncoated NPs studied bioaccumulative (BMF > 1).

Graphical Abstract
Quantifying the impacts of climate variation, damming, and flow regulation on river thermal dynamics: a case study of the Włocławek Reservoir in the Vistula River, Poland
Authors: Yang Rui , Wu Shiqiang , Wu Xiufeng , Ptak Mariusz , Li Xudong , Sojka Mariusz , Graf Renata , Dai Jiangyu , Zhu Senlin 
Published: January 2022

Abstract
Background
River damming inevitably reshapes water thermal conditions that are important to the general health of river ecosystems. Although a lot of studies have addressed the damming’s thermal impacts, most of them just assess the overall effects of climate variation and human activities on river thermal dynamics. Less attention has been given to quantifying the impact of climate variation, damming and flow regulation, respectively. In addition, for rivers that have already faced an erosion problem in downstream channels, an adjustment of the hydroelectric power plant operation manner is expected, which reinforces the need for understanding of flow regulation’s thermal impact. To fill this gap, an air2stream-based approach is proposed and applied at the Włocławek Reservoir in the Vistula River in Poland.

Results
In the years of 1952–1983, downstream river water temperature rose by 0.31 ℃ after damming. Meanwhile, the construction of dam increased the average annual water temperature by 0.55 ℃, while climate change oppositely made it decreased by 0.26 ℃. In addition, for the seasonal impact of damming, autumn was the most affected season with the warming reached 1.14 ℃, and the least affected season was winter when water temperature experienced a warming of 0.1 ℃. The absolute values of seasonal average temperature changes due to flow regulation were less than 0.1 ℃ for all the seasons.

Conclusions
The impacts of climate variation, damming, and flow regulation on river water temperatures can be evaluated reasonably on the strength of the proposed methodology. Climate variation and damming led to general opposite impacts on the downstream water temperature at the Włocławek Reservoir before 1980s. It is noted that the climate variation impact showed an opposite trend compared to that after 1980s. Besides, flow regulation below dam hardly affected downstream river water temperature variation. This study extends the current knowledge about impacts of climate variation and hydromorphological conditions on river water temperature, with a study area where river water temperature is higher than air temperature throughout a year.
scDIOR: single cell RNA-seq data IO software
Authors: Feng Huijian , Lin Lihui , Chen Jiekai 
Published: January 2022

Abstract
Background
Single-cell RNA sequencing is becoming a powerful tool to identify cell states, reconstruct developmental trajectories, and deconvolute spatial expression. The rapid development of computational methods promotes the insight of heterogeneous single-cell data. An increasing number of tools have been provided for biological analysts, of which two programming languages- R and Python are widely used among researchers. R and Python are complementary, as many methods are implemented specifically in R or Python. However, the different platforms immediately caused the data sharing and transformation problem, especially for Scanpy, Seurat, and SingleCellExperiemnt. Currently, there is no efficient and user-friendly software to perform data transformation of single-cell omics between platforms, which makes users spend unbearable time on data Input and Output (IO), significantly reducing the efficiency of data analysis.

Results
We developed scDIOR for single-cell data transformation between platforms of R and Python based on Hierarchical Data Format Version 5 (HDF5). We have created a data IO ecosystem between three R packages (Seurat, SingleCellExperiment, Monocle) and a Python package (Scanpy). Importantly, scDIOR accommodates a variety of data types across programming languages and platforms in an ultrafast way, including single-cell RNA-seq and spatial resolved transcriptomics data, using only a few codes in IDE or command line interface. For large scale datasets, users can partially load the needed information, e.g., cell annotation without the gene expression matrices. scDIOR connects the analytical tasks of different platforms, which makes it easy to compare the performance of algorithms between them.

Conclusions
scDIOR contains two modules, dior in R and diopy in Python. scDIOR is a versatile and user-friendly tool that implements single-cell data transformation between R and Python rapidly and stably. The software is freely accessible at https://github.com/JiekaiLab/scDIOR.
Lerna: transformer architectures for configuring error correction tools for short- and long-read genome sequencing
Authors: Sharma Atul , Jain Pranjal , Mahgoub Ashraf , Zhou Zihan , Mahadik Kanak , Chaterji Somali 
Published: January 2022

AbstractBackgroundSequencing technologies are prone to errors, making error correction (EC) necessary for downstream applications. EC tools need to be manually configured for optimal performance. We find that the optimal parameters (e.g.,k-mer size) are both tool- and dataset-dependent. Moreover, evaluating the performance (i.e., Alignment-rate or Gain) of a given tool usually relies on a reference genome, but quality reference genomes are not always available. We introduceLernafor the automated configuration ofk-mer-based EC tools.Lernafirst creates a language model (LM) of the uncorrected genomic reads, and then, based on this LM, calculates a metric called theperplexity metricto evaluate the corrected reads for different parameter choices. Next, it finds the one that produces the highest alignment ratewithoutusing a reference genome. The fundamental intuition of our approach is that the perplexity metric is inversely correlated with the quality of the assembly after error correction. Therefore,Lernaleverages the perplexity metric for automated tuning ofk-mer sizes without needing a reference genome.ResultsFirst, we show that the bestk-mer value can vary for different datasets, even for the same EC tool. This motivates our design that automatesk-mer size selection without using a reference genome. Second, we show the gains of our LM using its component attention-based transformers. We show the model’s estimation of the perplexity metric before and after error correction. The lower the perplexity after correction, the better thek-mer size. We also show that the alignment rate and assembly quality computed for the corrected reads are stronglynegativelycorrelated with the perplexity, enabling the automated selection ofk-mer values for better error correction, and hence, improved assembly quality. We validate our approach on both short and long reads. Additionally, we show that our attention-based models have significant runtime improvement for the entire pipeline—18$$\times$$×faster than previous works, due to parallelizing the attention mechanism and the use of JIT compilation for GPU inferencing.ConclusionLerna improvesde novogenome assembly by optimizing EC tools. Our code is made available in a public repository at:https://github.com/icanforce/lerna-genomics.
RNA-combine: a toolkit for comprehensive analyses on transcriptome data from different sequencing platforms
Authors: Dong Xuemin , Dong Shanshan , Pan Shengkai , Zhan Xiangjiang 
Published: January 2022

AbstractBackgroundUnderstanding the transcriptome has become an essential step towards the full interpretation of the biological function of a cell, a tissue or even an organ. Many tools are available for either processing, analysing transcriptome data, or visualizing analysis results. However, most existing tools are limited to data from a single sequencing platform and only several of them could handle more than one analysis module, which are far from enough to meet the requirements of users, especially those without advanced programming skills. Hence, we still lack an open-source toolkit that enables both bioinformatician and non-bioinformatician users to process and analyze the large transcriptome data from different sequencing platforms and visualize the results.ResultsWe present a Linux-based toolkit, RNA-combine, to automatically perform the quality assessment, downstream analysis of the transcriptome data generated from different sequencing platforms, including bulk RNA-seq (Illumina platform), single cell RNA-seq (10x Genomics) and Iso-Seq (PacBio) and visualization of the results. Besides, this toolkit is implemented with at least 10 analysis modules more than other toolkits examined in this study. Source codes of RNA-combine are available on GitHub:https://github.com/dongxuemin666/RNA-combine.ConclusionOur results suggest that RNA-combine is a reliable tool for transcriptome data processing and result interpretation for both bioinformaticians and non-bioinformaticians.
Prediction of trehalose-metabolic pathway and comparative analysis of KEGG, MetaCyc, and RAST databases based on complete genome of Variovorax sp. PAMC28711
Authors: Shrestha Prasansah , Kim Min-Su , Elbasani Ermal , Kim Jeong-Dong , Oh Tae-Jin 
Published: January 2022

Abstract
Background
Metabolism including anabolism and catabolism is a prerequisite phenomenon for all living organisms. Anabolism refers to the synthesis of the entire compound needed by a species. Catabolism refers to the breakdown of molecules to obtain energy. Many metabolic pathways are undisclosed and many organism-specific enzymes involved in metabolism are misplaced. When predicting a specific metabolic pathway of a microorganism, the first and foremost steps is to explore available online databases. Among many online databases, KEGG and MetaCyc pathway databases were used to deduce trehalose metabolic network for bacteria Variovorax sp. PAMC28711. Trehalose, a disaccharide, is used by the microorganism as an alternative carbon source.

Results
While using KEGG and MetaCyc databases, we found that the KEGG pathway database had one missing enzyme (maltooligosyl-trehalose synthase, EC 5.4.99.15). The MetaCyc pathway database also had some enzymes. However, when we used RAST to annotate the entire genome of Variovorax sp. PAMC28711, we found that all enzymes that were missing in KEGG and MetaCyc databases were involved in the trehalose metabolic pathway.

Conclusions
Findings of this study shed light on bioinformatics tools and raise awareness among researchers about the importance of conducting detailed investigation before proceeding with any further work. While such comparison for databases such as KEGG and MetaCyc has been done before, it has never been done with a specific microbial pathway. Such studies are useful for future improvement of bioinformatics tools to reduce limitations.
Evaluation of CRISPR gene-editing tools in zebrafish
Authors: Uribe-Salazar José M. , Kaya Gulhan , Sekar Aadithya , Weyenberg KaeChandra , Ingamells Cole , Dennis Megan Y. 
Published: January 2022

AbstractBackgroundZebrafish have practical features that make them a useful model for higher-throughput tests of gene function using CRISPR/Cas9 editing to create ‘knockout’ models. In particular, the use of G0mosaic mutants has potential to increase throughput of functional studies significantly but may suffer from transient effects of introducing Cas9 via microinjection. Further, a large number of computational and empirical tools exist to design CRISPR assays but often produce varied predictions across methods leaving uncertainty in choosing an optimal approach for zebrafish studies.MethodsTo systematically assess accuracy of tool predictions of on- and off-target gene editing, we subjected zebrafish embryos to CRISPR/Cas9 with 50 different guide RNAs (gRNAs) targeting 14 genes. We also investigate potential confounders of G0-based CRISPR screens by assaying control embryos for spurious mutations and altered gene expression.ResultsWe compared our experimental in vivo editing efficiencies in mosaic G0embryos with those predicted by eight commonly used gRNA design tools and found large discrepancies between methods. Assessing off-target mutations (predicted in silico and in vitro) found that the majority of tested loci had low in vivo frequencies (< 1%). To characterize if commonly used ‘mock’ CRISPR controls (larvae injected with Cas9 enzyme or mRNA with no gRNA) exhibited spurious molecular features that might exacerbate studies of G0mosaic CRISPR knockout fish, we generated an RNA-seq dataset of various control larvae at 5 days post fertilization. While we found no evidence of spontaneous somatic mutations of injected larvae, we did identify several hundred differentially-expressed genes with high variability between injection types. Network analyses of shared differentially-expressed genes in the ‘mock’ injected larvae implicated a number of key regulators of common metabolic pathways, and gene-ontology analysis revealed connections with response to wounding and cytoskeleton organization, highlighting a potentially lasting effect from the microinjection process that requires further investigation.ConclusionOverall, our results provide a valuable resource for the zebrafish community for the design and execution of CRISPR/Cas9 experiments.
Admission pattern, treatment outcomes, and associated factors for children admitted to pediatric intensive care unit of Tikur Anbessa specialized hospital, 2021: a retrospective cross-sectional study
Authors: Seifu Ashenafi , Eshetu Oliyad , Tafesse Dawit , Hailu Seyoum 
Published: January 2022

Abstract
Background
Assessement of the pattern of admission and treatment outcomes of critically ill pediatrics admitted to pediatric intensive care units (PICU) in developing countries is crucial. In these countries with resource limitations, it may help to identify priorities for resource mobilization that may improve patient service quality. The PICU mortality rate varies globally, depending on the facilities of the intensive care unit, availability of experties, and admission patterns. This study assessed the admission pattern, treatment outcomes, and associated factors for children admitted to the PICU.

Methods
A retrospective cross-sectional study was implemented on 406 randomly selected pediatrics patients admitted to the PICU of Tikur Anbessa Specialized Hospital from 1-Oct-2018 to 30-Sept-2020. The data were collected with a pretested questionnaire. A normality curve was used to check for data the distribution. Both bivariable and multivariable analyses were used to see association of variables. A variable with a p-value of < 0.2 in the bivariable model was a candidate for multivariate analysis. The strength of association was shown by an adjusted odds ratio (AOR) with a 95% Confidence interval (CI), and a p-value of < 0.05 was considered statistically significant. Frequency, percentage,and tables were used to present the data.

Results
A total of 361 (89% response rate) patient charts were studied, 197 (54.6%) were male, and 164(45.4%) were female. The most common pattern for admission was a septic shock (27.14%), whereas the least common pattern was Asthma 9(2.50%). The mortality rate at the pediatric intensive care unit was 43.8%. Moreover, mechanical ventilation need (AOR = 11.2, 95%CI (4.3–28.9), P < 0.001), need for inotropic agents (AOR = 10.7, 95%CI (4.1–27.8), P < 0.001), comorbidity (AOR =8.4, 95%CI (3.5–20.5), P < 0.001), length of PICU stay from 2 to 7 days (AOR = 7.3, 95%CI (1.7–30.6), P = 0.007) and severe GCS (< 8) (AOR = 10.5, 95%CI (3.8–29.1), P < 0.001) were independent clinical outcome predictors (mortality).

Conclusion
The mortality rate at the PICU was 43.8%. Septic shock, and meningitis were the common cause of death and the largest death has happened in less than 7 days of admission.