bluuebunny/crossref_metadata_2025_split huggingface dataset:
Down-regulated lncRNA SBF2-AS1 inhibits tumorigenesis and progression of breast cancer by sponging microRNA-143 and repressing RRS1
Authors: Xia Wenfei , Liu Yun , Cheng Teng , Xu Tao , Dong Menglu , Hu Xiaopeng 
Published: January 2020

Abstract
Background
Recently, the roles of long non-coding RNAs (lncRNAs) and microRNAs (miRNAs) in human diseases have been unveiled, this research was conducted to explore the impacts of lncRNA SET-binding factor 2-antisense RNA1 (SBF2-AS1), miR-143 and resistance to ralstonia solanacearum 1 (RRS1) on breast cancer (BC) development.

Methods
The expression of SBF2-AS1, miR-143 and RRS1 in BC tissues, as well as in MDA-MB-231 and MCF-7 cell lines were assessed. Subsequently, the cells were transfected with miR-143 mimics or/and silenced or overexpressed SBF2-AS1 plasmids, and their negative controls. Then the proliferation, colony formation ability, cell cycle arrest, apoptosis, invasion and migration of the cells were assessed through gain- and loss-of-function experiments. Furthermore, the tumor growth, ki-67 expression and apoptosis in vivo were observed by subcutaneous tumorigenesis in nude mice. Binding relation between SBF2-AS1 and miR-143, and that between miR-143 and RRS1 were confirmed.

Results
SBF2-AS1 and RRS1 were amplified, while miR-143 was reduced in BC tissues and cells. Reduced SBF2-AS1 and elevated miR-143 could repress the proliferation, invasion and migration via restraining RRS1 expression. Moreover, knockdown of SBF2-AS1 up-regulated miR-143 to promote the apoptosis of BC cells by downregulating RRS1, resulting in a prohibitive effect on the tumorigenesis and progression of BC. Results of in vivo experiments indicated that the inhibited SBF2-AS1 and overexpressed miR-143 could restrict BC cell proliferation and promote apoptosis, and decelerate tumor growth in xenografts.

Conclusion
We have discovered in this study that down-regulated SBF2-AS1 could inhibit tumorigenesis and progression of BC by up-regulation miR-143 and repressing RRS1, which provides basic therapeutic considerations for a novel target against BC.
Sublingual microcirculation does not reflect red blood cell transfusion thresholds in the intensive care unit—a prospective observational study in the intensive care unit
Authors: Scheuzger Jonas , Zehnder Anna , Meier Vera , Yeginsoy Desirée , Flükiger Julian , Siegemund Martin 
Published: January 2020

Abstract
Purpose
Hemoglobin (Hb) transfusion thresholds are established in intensive care units. A restrictive transfusion threshold (Hb 70–75 g/l) is recommended in septic patients, and a liberal transfusion threshold (Hb 90 g/l) for cardiogenic shock. It is unclear whether these historically adopted transfusion thresholds meet the challenges of individual patients.

Methods
We evaluated microvascular flow index (MFI) and proportion of perfused vessels (PPV) in the sublingual microcirculation with CytoCam-IDF microscopy and near-infrared spectroscopy (NIRS). A study team-independent, treating intensivist assigned a total of 64 patients to 1 of 2 two transfusion thresholds, 43 patients to the Hb 75 g/l threshold and 21 patients to the Hb 90 g/l threshold, at a surgical intensive care unit. We performed microcirculatory measurements 1 h before and 1 h after transfusion of 1 unit of red blood cells.

Results
Microcirculatory flow variables correlated negatively with pre-transfusion flow variables (ΔMFI: ρ = − 0.821, p <  0.001; ΔPPV: ρ = − 0.778, p <  0.001). Patients with good initial microcirculation (cutoffs: MFI > 2.84, PPV > 88%) showed a deteriorated microcirculation after red blood cell transfusion. An impaired microcirculation improved after transfusion. At both transfusion thresholds, approximately one third of the patients showed an initially impaired microcirculation. In contrast, one third in every group had good microcirculation above the cutoff variables and did not profit from the transfusion.

Conclusion
The data suggest that the established transfusion thresholds and other hemodynamic variables do not reflect microcirculatory perfusion of patients. Blood transfusion at both thresholds 75 g/l and 90 g/l hemoglobin can either improve or harm the microcirculatory blood flow, questioning the concept of arbitrary transfusion thresholds.
Performance difference of graph-based and alignment-based hybrid error correction methods for error-prone long reads
Authors: Wang Anqi , Au Kin Fai 
Published: January 2020

AbstractThe error-prone third-generation sequencing (TGS) long reads can be corrected by the high-quality second-generation sequencing (SGS) short reads, which is referred to as hybrid error correction. We here investigate the influences of the principal algorithmic factors of two major types of hybrid error correction methods by mathematical modeling and analysis on both simulated and real data. Our study reveals the distribution of accuracy gain with respect to the original long read error rate. We also demonstrate that the original error rate of 19% is the limit for perfect correction, beyond which long reads are too error-prone to be corrected by these methods.
cis-regulatory variation modulates susceptibility to enteric infection in the Drosophila genetic reference panel
Authors: Frochaux Michael V. , Bou Sleiman Maroun , Gardeux Vincent , Dainese Riccardo , Hollis Brian , Litovchenko Maria , Braman Virginie S. , Andreani Tommaso , Osman Dani , Deplancke Bart 
Published: January 2020

AbstractBackgroundResistance to enteric pathogens is a complex trait at the crossroads of multiple biological processes. We have previously shown in theDrosophilaGenetic Reference Panel (DGRP) that resistance to infection is highly heritable, but our understanding of how the effects of genetic variants affect different molecular mechanisms to determine gut immunocompetence is still limited.ResultsTo address this, we perform a systems genetics analysis of the gut transcriptomes from 38 DGRP lines that were orally infected withPseudomonas entomophila. We identify a large number of condition-specific, expression quantitative trait loci (local-eQTLs) with infection-specific ones located in regions enriched for FOX transcription factor motifs. By assessing the allelic imbalance in the transcriptomes of 19 F1 hybrid lines from a large round robin design, we independently attribute a robustcis-regulatory effect to only 10% of these detectedlocal-eQTLs. However, additional analyses indicate that manylocal-eQTLs may act intransinstead. Comparison of the transcriptomes of DGRP lines that were either susceptible or resistant toPseudomonas entomophilainfection revealsnutcrackeras the only differentially expressed gene. Interestingly, we find thatnutcrackeris linked to infection-specific eQTLs that correlate with its expression level and to enteric infection susceptibility. Further regulatory analysis reveals one particular eQTL that significantly decreases the binding affinity for the repressor Broad, driving differential allele-specificnutcrackerexpression.ConclusionsOur collective findings point to a large number of infection-specificcis-andtrans-acting eQTLs in the DGRP, including one common non-coding variant that lowers enteric infection susceptibility.
Enteric infection induces Lark-mediated intron retention at the 5′ end of Drosophila genes
Authors: Bou Sleiman Maroun , Frochaux Michael Vincent , Andreani Tommaso , Osman Dani , Guigo Roderic , Deplancke Bart 
Published: January 2020

Abstract
Background
RNA splicing is a key post-transcriptional mechanism that generates protein diversity and contributes to the fine-tuning of gene expression, which may facilitate adaptation to environmental challenges. Here, we employ a systems approach to study alternative splicing changes upon enteric infection in females from classical Drosophila melanogaster strains as well as 38 inbred lines.

Results
We find that infection leads to extensive differences in isoform ratios, which results in a more diverse transcriptome with longer 5′ untranslated regions (5′UTRs). We establish a role for genetic variation in mediating inter-individual splicing differences, with local splicing quantitative trait loci (local-sQTLs) being preferentially located at the 5′ end of transcripts and directly upstream of splice donor sites. Moreover, local-sQTLs are more numerous in the infected state, indicating that acute stress unmasks a substantial number of silent genetic variants. We observe a general increase in intron retention concentrated at the 5′ end of transcripts across multiple strains, whose prevalence scales with the degree of pathogen virulence. The length, GC content, and RNA polymerase II occupancy of these introns with increased retention suggest that they have exon-like characteristics. We further uncover that retained intron sequences are enriched for the Lark/RBM4 RNA binding motif. Interestingly, we find that lark is induced by infection in wild-type flies, its overexpression and knockdown alter survival, and tissue-specific overexpression mimics infection-induced intron retention.

Conclusion
Our collective findings point to pervasive and consistent RNA splicing changes, partly mediated by Lark/RBM4, as being an important aspect of the gut response to infection.
Plant hormone induced enrichment of Chlorella sp. omega-3 fatty acids
Authors: Sivaramakrishnan Ramachandran , Incharoensakdi Aran 
Published: January 2020

AbstractBackgroundOmega-3 fatty acids have various health benefits in combating against neurological problems, cancers, cardiac problems and hypertriglyceridemia. The main dietary omega-3 fatty acids are obtained from marine fish. Due to the pollution of marine environment, recently microalgae are considered as the promising source for the omega-3 fatty acid production. However, the demand and high production cost associated with microalgal biomass make it necessary to implement novel strategies in improving the biomass and omega-3 fatty acids from microalgae.ResultsFour plant hormones zeatin, indole acetic acid (IAA), gibberellic acid (GBA) and abscisic acid (ABA) were investigated for their effect on the production of biomass and lipid in isolatedChlorellasp. The cells showed an increase of the biomass and lipid content after treatments with the plant hormones where the highest stimulatory effect was observed in ABA-treated cells. On the other hand, IAA showed the highest stimulatory effect on the omega-3 fatty acids content, eicosapentaenoic acid (EPA) (23.25%) and docosahexaenoic acid (DHA) (26.06%). On the other hand, cells treated with ABA had highest lipid content suitable for the biodiesel applications. The determination of ROS markers, antioxidant enzymes, and fatty acid biosynthesis genes after plant hormones treatment helped elucidate the mechanism underlying the improvement in biomass, lipid content and omega-3 fatty acids. All four plant hormones upregulated the fatty acid biosynthesis genes, whereas IAA particularly increased omega-3-fatty acids as a result of the upregulation of omega-3 fatty acid desaturase.ConclusionsThe contents of omega-3 fatty acids, the clinically important compounds, were considerably improved in IAA-treated cells. The highest lipid content obtained from ABA-treated biomass can be used for biodiesel application according to its biodiesel properties. The EPA and DHA enriched ethyl esters are an approved form of omega-3 fatty acids by US Food and Drug Administration (FDA) which can be utilized as the therapeutic treatment for the severe hypertriglyceridemia.
A dockerized framework for hierarchical frequency-based document clustering on cloud computing infrastructures
Authors: Kotouza Maria Th. , Psomopoulos Fotis E. , Mitkas Pericles A. 
Published: January 2020

AbstractScalable big data analysis frameworks are of paramount importance in the modern web society, which is characterized by a huge number of resources, including electronic text documents. Document clustering is an important field in text mining and is commonly used for document organization, browsing, summarization and classification. Hierarchical clustering methods construct a hierarchy structure that, combined with the produced clusters, can be useful in managing documents, thus making the browsing and navigation process easier and quicker, and providing only relevant information to the users’ queries by leveraging the structure relationships. Nevertheless, the high computational cost and memory usage of baseline hierarchical clustering algorithms render them inappropriate for the vast number of documents that must be handled daily. In this paper, we propose a new scalable hierarchical clustering framework, which uses the frequency of the topics in the documents to overcome these limitations. Our work consists of a binary tree construction algorithm that creates a hierarchy of the documents using three metrics (Identity, Entropy, Bin Similarity), and a branch breaking algorithm which composes the final clusters by applying thresholds to each branch of the tree. The clustering algorithm is followed by a meta-clustering module which makes use of graph theory to obtain insights in the leaf clusters’ connections. The feature vectors representing each document derive from topic modeling. At the implementation level, the clustering method has been dockerized in order to facilitate its deployment on cloud computing infrastructures. Finally, the proposed framework is evaluated on several datasets of varying size and content, achieving significant reduction in both memory consumption and computational time over existing hierarchical clustering algorithms. The experiments also include performance testing on cloud resources using different setups and the results are promising.
Secure VM management with strong user binding in semi-trusted clouds
Authors: Inokuchi Keisuke , Kourai Kenichi 
Published: January 2020

AbstractIn Infrastructure-as-a-Service (IaaS) clouds, remote users access provided virtual machines (VMs) via the management server. The management server is managed by cloud operators, but not all the cloud operators are trusted in semi-trusted clouds. They can execute arbitrary management commands to users’ VMs and redirect users’ commands to malicious VMs. We call the latter attack the VM redirection attack. The root cause is that the binding of remote users to their VMs is weak. In other words, it is difficult to enforce the execution of only users’ management commands to their VMs. In this paper, we propose UVBond for strongly binding users to their VMs to address this issue. UVBond boots user’s VM by decrypting its encrypted disk inside the trusted hypervisor. Then it issues a VM descriptor to securely identify that VM. To bridge the semantic gap between high-level management commands and low-level hypercalls, UVBond uses hypercall automata, which accept the sequences of hypercalls issued by commands. We have implemented UVBond in Xen and created hypercall automata for various management commands. Using UVBond, we confirmed that a VM descriptor and hypercall automata prevented insider attacks and that the overhead was not large in remote VM management.
Research on retention forestry in Northern Europe
Authors: Gustafsson Lena , Hannerz Mats , Koivula Matti , Shorohova Ekaterina , Vanha-Majamaa Ilkka , Weslien Jan 
Published: January 2020

AbstractRetention approaches in forest management are today common in several North European countries, integrated into the clearcutting practice as a way to promote biodiversity and maintain ecosystem functions. Individual green trees and retention patches (tree groups) are retained at final harvest, and deadwood is left at site or created. Here, we review research on retention in Sweden, Finland, Norway, the Baltic States, and NW Russia, with special focus on biodiversity. Following the first publication in 1994, about 180 peer-reviewed articles have been published. We present results from a systematic search of the retention literature, separated into the following topics: buffer zones, retention patches, high stumps, other types of deadwood, European aspenPopulus tremula, and cost-efficiency. Russian literature is synthesized separately since studies from this region have so far almost exclusively been published in the Russian language. Furthermore, we describe six ongoing large-scale, replicated experiments with varying retention levels, five in Finland and one in Sweden, and summarize their main results. Among main conclusions for practice from the literature and experiments are that retention patches as large as 0.5 ha and 10-m-wide buffers to watercourses are not enough to maintain pre-harvest species composition but survival of forest species is still larger than on conventional clearcuts. Deadwood on clearcuts may present important habitats to saproxylic species, including rare and red-listed ones and a prioritization of tree species per stand is recommended. We identify several important future research directions including switch of focus towards the landscape as well as the species population level. Surveys in parts of European Russia where retention has been unintentionally implemented already for a century would indicate possible future trajectories of biodiversity and their drivers in other regions of Northern Europe. A stronger link to ecological theory would help in study designs and in the formulation of predicted outcomes.
Evaluation of Out-of-Plane Response of R/C Structural Wall Boundary Edges Detailed with Maximum Code-Prescribed Longitudinal Reinforcement Ratio
Authors: Chrysanidis Theodoros A. 
Published: January 2020

AbstractOne type of failure of reinforced concrete seismic walls is out-of-plane buckling. This type of failure appears at the compressive cycle of loading during the cyclic seismic loading. This work is mainly experimental and tries to investigate the influence of the mechanical factor of tensile deformation on the behavior of seismic walls and particularly on the phenomenon of lateral buckling. Five test specimens are constructed simulating the confined boundary regions of structural walls. They are reinforced using the maximum longitudinal reinforcement ratio (4.02%) prescribed by modern seismic and concrete codes for boundary ends. Apart from the investigation of the factor of elongation degree, this method tries to examine if the detailing of walls using maximum allowable reinforced ratio for longitudinal reinforcement inhibits the appearance of transverse buckling. Each prism specimen was strained under different tensile deformation. Degrees of elongation used were equal to 0‰, 10‰, 20‰, 30‰ and 50‰. After the first tensile cycle of loading, a second compression loading cycle was applied on each specimen, till their failure. Thus, nine experiments were carried out in total-two for each specimen apart from the first specimen which suffered zero elongation. Empirical equations are derived trying to estimate the ultimate bearing capacity and the normalized axial deformation at failure for the different tensile degrees.
Co-expression network analysis predicts a key role of microRNAs in the adaptation of the porcine skeletal muscle to nutrient supply
Authors: Mármol-Sánchez Emilio , Ramayo-Caldas Yuliaxis , Quintanilla Raquel , Cardoso Tainã Figueiredo , González-Prendes Rayner , Tibau Joan , Amills Marcel 
Published: January 2020

AbstractBackgroundThe role of non-coding RNAs in the porcine muscle metabolism is poorly understood, with few studies investigating their expression patterns in response to nutrient supply. Therefore, we aimed to investigate the changes in microRNAs (miRNAs), long intergenic non-coding RNAs (lincRNAs) and mRNAs muscle expression before and after food intake.ResultsWe measured the miRNA, lincRNA and mRNA expression levels in thegluteus mediusmuscle of 12 gilts in a fasting condition (AL-T0) and 24 gilts fedad libitumduring either 5 h. (AL-T1,N = 12) or 7 h. (AL-T2,N = 12) prior to slaughter. The small RNA fraction was extracted from muscle samples retrieved from the 36 gilts and sequenced, whereas lincRNA and mRNA expression data were already available. In terms of mean and variance, the expression profiles of miRNAs and lincRNAs in the porcine muscle were quite different than those of mRNAs. Food intake induced the differential expression of 149 (AL-T0/AL-T1) and 435 (AL-T0/AL-T2) mRNAs, 6 (AL-T0/AL-T1) and 28 (AL-T0/AL-T2) miRNAs and none lincRNAs, while the number of differentially dispersed genes was much lower. Among the set of differentially expressed miRNAs, we identified ssc-miR-148a-3p, ssc-miR-22-3p and ssc-miR-1, which play key roles in the regulation of glucose and lipid metabolism. Besides, co-expression network analyses revealed several miRNAs that putatively interact with mRNAs playing key metabolic roles and that also showed differential expression before and after feeding. One case example was represented by seven miRNAs (ssc-miR-148a-3p, ssc-miR-151-3p, ssc-miR-30a-3p, ssc-miR-30e-3p, ssc-miR-421-5p, ssc-miR-493-5p and ssc-miR-503) which putatively interact with thePDK4mRNA, one of the master regulators of glucose utilization and fatty acid oxidation.ConclusionsAs a whole, our results evidence that microRNAs are likely to play an important role in the porcine skeletal muscle metabolic adaptation to nutrient availability.
Predicting high-cost care in a mental health setting
Authors: Colling Craig , Khondoker Mizanur , Patel Rashmi , Fok Marcella , Harland Robert , Broadbent Matthew , McCrone Paul , Stewart Robert 
Published: January 2020

BackgroundThe density of information in digital health records offers new potential opportunities for automated prediction of cost-relevant outcomes.AimsWe investigated the extent to which routinely recorded data held in the electronic health record (EHR) predict priority service outcomes and whether natural language processing tools enhance the predictions. We evaluated three high priority outcomes: in-patient duration, readmission following in-patient care and high service cost after first presentation.MethodWe used data obtained from a clinical database derived from the EHR of a large mental healthcare provider within the UK. We combined structured data with text-derived data relating to diagnosis statements, medication and psychiatric symptomatology. Predictors of the three different clinical outcomes were modelled using logistic regression with performance evaluated against a validation set to derive areas under receiver operating characteristic curves.ResultsIn validation samples, the full models (using all available data) achieved areas under receiver operating characteristic curves between 0.59 and 0.85 (in-patient duration 0.63, readmission 0.59, high service use 0.85). Adding natural language processing-derived data to the models increased the variance explained across all clinical scenarios (observed increase inr2= 12–46%).ConclusionsEHR data offer the potential to improve routine clinical predictions by utilising previously inaccessible data. Of our scenarios, prediction of high service use after initial presentation achieved the highest performance.