Miracle-dz/UniFAR-FTUs huggingface dataset:
The Death-inducer Obliterator 1 (Dido1) Gene Regulates Embryonic Stem Cell Self-renewal*

Background: Dido1 plays important roles in development. Results: Dido1 inhibition led to ES cell differentiation, and its expression promoted ES cell self-renewal. Conclusion: Dido1 participates in ES cell maintenance and forms feedback and feedforward loops with canonical ES cell factors such as Nanog and Oct4. Significance: Dido1 represents a new factor in the ES cell regulatory circuitry for maintaining self-renewal of ES cells. The regulatory network of factors that center on master transcription factors such as Oct4, Nanog, and Sox2 help maintain embryonic stem (ES) cells and ensure their pluripotency. The target genes of these master transcription factors define the ES cell transcriptional landscape. In this study, we report our findings that Dido1, a target of canonical transcription factors such as Oct4, Sox2, and Nanog, plays an important role in regulating ES cell maintenance. We found that depletion of Dido1 in mouse ES cells led to differentiation, and ectopic expression of Dido1 inhibited differentiation induced by leukemia inhibitory factor withdrawal. We further demonstrated that whereas Nanog and Oct4 could occupy the Dido1 locus and promote its transcription, Dido1 could also target to the loci of pluripotency factors such as Nanog and Oct4 and positively regulate their expression. Through this feedback and feedforward loop, Dido1 is able to regulate self-renewal of mouse ES cells
Adenoviruses-mediated RNA interference targeting cytosolic phospholipase A2α attenuates focal ischemic brain damage in mice

Cerebral ischemia injury is a clinical, frequently occurring disease, which causes a heavy burden on society and families. It has been demonstrated that cytosolic phospholipase A2α (cPLA2α) is significant in neurological injury caused by ischemic brain injury, and inhibition of cPLA2α may reduce stroke injury. In the present study, the role of cPLA2α was investigated in a mouse model of middle cerebral artery occlusion and/or reperfusion (MCAO/R) using an effective cPLA2α inhibitor and adenoviruses-mediated RNA interference. The most effective recombinant adenovirus encoding cPLA2α small interfering RNA (pAd-siRNA-cPLA2α) was constructed and selected. MCAO/R surgery is used to construct the model of focal ischemic brain damage in mice. Adenoviruses-mediated RNA interference targeting cPLA2α was administered by stereotactic surgery 2 h before the MCAO/R. The expression/activity of cPLA2α and cPLA2α-derived injurious lipid mediators was assessed. pAd-siRNA-cPLA2α-treated animals (RNA interference; RNAi group) were compared with pAd-siRNA-control-treated animals (negative group) with regard to neurological deficit, motor function, pathological changes, apoptosis, and infarct volume. The RNAi group animals reduced the expression level of cPLA2α, as determined by western blotting and reverse transcription-quantitative polymerase chain reaction, the improvement of locomotor function was evaluated by rotarod test, and the decrease of apoptosis was evaluated by terminal deoxynucleotidyl transferase dUTP nick end-labeling staining. The decreased infarct areas were evaluated by 2,3,5-triphenyltetrazolium chloride staining. The expression levels of prostaglandin E2, leukotrienes B4, lysophosphatidylcholine and free fatty acids were reduced in the RNAi group when compared with the negative control group. Thus, the data indicates that the expression level of cPLA2α was effectively controlled by pAd-siRNA-cPLA2α treatment. pAd-siRNA-cPLA2α treatment, in reducing the levels of inflammatory factors, neurological deficit and tissue damage, represents an effective potential therapeutic strategy. pAd-siRNA-cPLA2α reduces cPLA2α expression levels with long-term efficacy, thereby improving functional deficits and effectively attenuating ischemic brain damage. Thus, pAd-siRNA-cPLA2α shows potential value for therapeutic evaluation in ischemic brain damage.
RNA-seq Reveals Transcriptomic Differences in Inflamed and Noninflamed Intestinal Mucosa of Crohn's Disease Patients Compared with Normal Mucosa of Healthy Controls

Background: Aberrant gene expression in the gut mucosa might contribute to the initiation and progression of Crohn's disease (CD). RNA sequencing (RNA-seq) provides precise measurements of expression levels of transcripts and their isoforms. The aim of this study was to use RNA-seq to investigate transcriptomic differences and identify significantly differentially expressed transcripts in inflamed and noninflamed intestinal mucosa of CD patients. Methods: RNA-seq was performed on 13 pairs of inflamed and noninflamed intestinal mucosa from 13 CD patients and on sex-matched normal mucosa of 13 healthy controls. Significantly differentially expressed transcripts were validated by immunohistochemistry, quantitative reverse transcriptase polymerase chain reaction, and enzyme-linked immunosorbent assay. Results: RNA-seq revealed genome-wide transcriptomic differences between normal mucosa, noninflamed, and inflamed CD mucosa. Among 950 differentially expressed genes, 19 were up- or downregulated (upregulation: ANGPT2, CHN1, CPXM1, CPZ, CXCL1, FCN3, GJC1, HSD11B1, LZTS1, MEOX1, MMP12, PLA1A, SERPINE1, SGIP1, and TRPC4; downregulation: FAM189A1, PDE6A, SLC38A4, and HMGCS2) with statistical significance (p < 0.01 and q < 0.05). Among them, CXCL1 exhibited the highest fold change between groups. Immunohistochemistry for CXCL1 revealed no expression in normal mucosa, slightly increased expression in noninflamed CD mucosa, and highly increased expression in inflamed CD mucosa. Quantitative reverse transcriptase polymerase chain reaction showed that CXCL1 expression was significantly associated with epithelial damage, increased infiltration of polymorphonuclear leukocytes, and submucosal fibrosis. Serum CXCL1 concentration measured by enzyme-linked immunosorbent assay was better correlated with CD activity index (r = 0.660) than with C-reactive protein (r = 0.204). Conclusions: RNA-seq revealed transcriptomic differences between normal mucosa, noninflamed CD mucosa, and inflamed CD mucosa. Intestinal and serum CXCL1 was substantially increased with CD activity and can be used as a potential biomarker of CD.
Investigation of the effects of carbon-based nanomaterials on A53T alpha-synuclein aggregation using a whole-cell recombinant biosensor

The aggregation of alpha-synuclein (αS), natively unstructured presynaptic protein, is a crucial factor leading to the pathogenesis of Parkinson’s disease (PD) and other related disorders. Recent studies have shown prefibrillar and oligomeric intermediates of αS as toxic to the cells. Herein, split-luciferase complementation assay is used to design a “signal-on” biosensor to monitor oligomerization of A53T αS inside the cells. Then, the effect of carbon-based nanomaterials, such as graphene quantum dots (GQDs) and graphene oxide quantum dots (GOQDs), on A53T αS oligomerization in vitro and in living cells is investigated. In this work, for the first time, it was found that GQDs at a concentration of 0.5 μg/mL can promote A53T αS aggregation by shortening the nucleation process, which is the key rate-determining step of fibrillation, thereby making a signal-on biosensor. While these nanomaterials may cross the blood–brain barrier because of their small sizes, the interaction between αS and GQDs may contribute to PD etiology.
srsLTE: an open-source platform for LTE evolution and experimentation

Testbeds are essential for experimental evaluation as well as for product development. In the context of LTE networks, existing testbed platforms are limited either in functionality and/or extensibility or are too complex to modify and customise. In this work we present srsLTE, an open-source platform for LTE experimentation designed for maximum modularity and code reuse and fully compliant with LTE Release 8. We show the potential of the srsLTE library by extending the baseline code to allow LTE transmissions in the unlicensed bands and coexistence with WiFi. We also expand previous results on this emerging research area by showing how different vendor-specific mechanisms in WiFi cards might affect coexistence.
EFFECT OF THERAPEUTIC GAMMA RADIATION ON DIAMETRAL TENSILE STRENGTH AND MICROHARDNESS OF PHOTO-CURED GLASS IONOMER CEMENTS

Oral cancer patients, receiving gamma radiation as primary or supplementary treatment, commonly have a variety of dental restorations including resin-containing glass ionomer cements. Any interactive effects between the incident therapeutic beam and such materials might be of clinical significance if properties of these materials are adversely affected. In this investigation the effects of gamma radiation at three therapeutic dosage levels on the diametral tensile strength (DTS) and microhardness of three photo-cured glass ionomer restorative cements were determined. It was also the objective of this study to characterize the materials before and after gamma radiation using infrared spectroscopy. The results showed a significant increase in DTS of all investigated materials upon exposure to gamma radiation. Microhardness results for all materials showed, in general, an increase after irradiation. These findings were attributed to an increase in the degree of polymerization of these resin-containing photopolymerizable restorative cements. Infrared analysis of the three materials showed no change in their molecular structure (resin component) as a result of irradiation.
Antimicrobial Surgical Sutures: Recent Developments and Strategies

ABSTRACT Surgical sutures are probably the most widely used medical devices in healthcare applications for wound closure. During their application, sutures may be exposed to microorganisms present in the environment leading to bacterial biofilm formation, and thereon to surgical site infections. The physicochemical characteristics of the polymeric substrate play a major role in directing the behavior of the suture in a biological milieu. In such a context, it is necessary to develop sutures which actively repel and inhibit bacterial adherence and colonization on their surfaces. Drug eluting sutures have been proposed as a solution to this dilemma. Currently, bioactive agents (natural or synthetic) are being incorporated in polymeric materials via various methods including blending and compounding, surface functionalization and conjugation, and coating to render antimicrobial surgical sutures. However, each of these methods has its own pros and cons. Depending upon the nature of the substrate, an appropriate processing technique has to be chosen. In this article, we review the recent state-of-the-art developments and strategies in antimicrobial surgical suture fabrication. The efficacy and mechanism of these sutures in controlling infection is critically analyzed. However, such bioactive agent incorporated sutures have to be tested in clinically randomized trials to accurately gauze their applicability in a surgical setting. Presently, very few antimicrobial surgical sutures are available commercially. Therefore, there is a great scope for market development in this area.
Sequence-based taxonomic framework for the classification of uncultured single-stranded DNA viruses of the family Genomoviridae

With the advent of metagenomics approaches, a large diversity of known and unknown viruses has been identified in various types of environmental, plant, and animal samples. One such widespread virus group is the recently established family Genomoviridae which includes viruses with small (∼2–2.4 kb), circular ssDNA genomes encoding rolling-circle replication initiation proteins (Rep) and unique capsid proteins. Here, we propose a sequence-based taxonomic framework for classification of 121 new virus genomes within this family. Genomoviruses display ∼47% sequence diversity, which is very similar to that within the well-established and extensively studied family Geminiviridae (46% diversity). Based on our analysis, we establish a 78% genome-wide pairwise identity as a species demarcation threshold. Furthermore, using a Rep sequence phylogeny-based analysis coupled with the current knowledge on the classification of geminiviruses, we establish nine genera within the Genomoviridae family. These are Gemycircularvirus (n = 73), Gemyduguivirus (n = 1), Gemygorvirus (n = 9), Gemykibivirus (n = 29), Gemykolovirus (n = 3), Gemykrogvirus (n = 3), Gemykroznavirus (n = 1), Gemytondvirus (n = 1), Gemyvongvirus (n = 1). The presented taxonomic framework offers rational classification of genomoviruses based on the sequence information alone and sets an example for future classification of other groups of uncultured viruses discovered using metagenomics approaches.
Multilayered dense collagen–silk fibroin hybrid: a platform for mesenchymal stem cell differentiation towards chondrogenic and osteogenic lineages

Type I collagen is a major structural and functional protein in connective tissues. However, collagen gels exhibit unstable geometrical properties, arising from extensive cell‐mediated contraction. In an effort to stabilize collagen‐based hydrogels, plastic compression was used to hybridize dense collagen (DC) with electrospun silk fibroin (SF) mats, generating multilayered DC–SF–DC constructs. Seeded mesenchymal stem cell (MSC)‐mediated DC–SF–DC contraction, as well as growth and differentiation under chondrogenic and osteogenic supplements, were compared to those seeded in DC and on SF alone. The incorporation of SF within DC prevented extensive cell‐mediated collagen gel contraction. The effect of the multilayered hybrid on MSC remodelling capacity was also evident at the transcription level, where the expression of matrix metalloproteinases and their inhibitor (MMP1, MMP2, MMP3, MMP13 and Timp1) by MSCs within DC–SF–DC were comparable to those on SF and significantly downregulated in comparison to DC, except for Timp1. Chondrogenic supplements stimulated extracellular matrix production within the construct, stabilizing its multilayered structure and promoting MSC chondrogenic differentiation, as indicated by the upregulation of the genes Col2a1 and Agg and the production of collagen type II. In osteogenic medium there was an upregulation in ALP and OP along with the presence of an apatitic phase, indicating MSC osteoblastic differentiation and matrix mineralization. In sum, these results have implications on the modulation of three‐dimensional collagen‐based gel structural stability and on the stimulation and maintenance of the MSC committed phenotype inherent to the in vitro formation of chondral tissue and bone, as well as on potential multilayered complex tissues. Copyright © 2015 John Wiley & Sons, Ltd.
Increased cost of illness among European patients with type 2 diabetes treated with insulin

Abstract Objectives: To investigate the association between outcomes and different escalating combinations of non-insulin medications vs. insulin. Methods: Data were taken from the 2013 5EU NHWS, a cross-sectional survey including 62,000 respondents across France, Germany, Italy, Spain, and the UK. Costs were estimated from self-reported work impairment and healthcare visits using average wages and unit costs. Respondents taking antihyperglycemic medications (n = 2894) were compared according to treatment type using unadjusted comparisons followed by regression to adjust for confounders. Results: Insulin users had the highest costs and worse outcomes, a pattern that remained after adjustment for a range of sociodemographic and disease characteristics. Incremental direct costs were approximately €800. Incremental indirect costs, applicable only to the employed, were larger than incremental direct costs, but were statistically significant only relative to non-insulin monotherapy. Conclusions: Escalation using oral agents rather than insulin is associated with better quality of life and lower costs, though these relationships may not be causal. Further research is warranted on escalation using oral agents among patients for whom insulin is not required.
Inferring Dynamic User Interests in Streams of Short Texts for User Clustering

User clustering has been studied from different angles. In order to identify shared interests, behavior-based methods consider similar browsing or search patterns of users, whereas content-based methods use information from the contents of the documents visited by the users. So far, content-based user clustering has mostly focused on static sets of relatively long documents. Given the dynamic nature of social media, there is a need to dynamically cluster users in the context of streams of short texts. User clustering in this setting is more challenging than in the case of long documents, as it is difficult to capture the users’ dynamic topic distributions in sparse data settings. To address this problem, we propose a dynamic user clustering topic model (UCT). UCT adaptively tracks changes of each user’s time-varying topic distributions based both on the short texts the user posts during a given time period and on previously estimated distributions. To infer changes, we propose a Gibbs sampling algorithm where a set of word pairs from each user is constructed for sampling. UCT can be used in two ways: (1) as a short-term dependency model that infers a user’s current topic distribution based on the user’s topic distributions during the previous time period only, and (2) as a long-term dependency model that infers a user’s current topic distributions based on the user’s topic distributions during multiple time periods in the past. The clustering results are explainable and human-understandable, in contrast to many other clustering algorithms. For evaluation purposes, we work with a dataset consisting of users and tweets from each user. Experimental results demonstrate the effectiveness of our proposed short-term and long-term dependency user clustering models compared to state-of-the-art baselines.
Intrinsic optical signal imaging of the blood volume changes is sufficient for mapping the resting state functional connectivity in the rodent cortex

Objective. Resting state functional connectivity (RSFC) allows the study of functional organization in normal and diseased brain by measuring the spontaneous brain activity generated under resting conditions. Intrinsic optical signal imaging (IOSI) based on multiple illumination wavelengths has been used successfully to compute RSFC maps in animal studies. The IOSI setup complexity would be greatly reduced if only a single wavelength can be used to obtain comparable RSFC maps. Approach. We used anesthetized mice and performed various comparisons between the RSFC maps based on single wavelength as well as oxy-, deoxy- and total hemoglobin concentration changes. Main results. The RSFC maps based on IOSI at a single wavelength selected for sensitivity to the blood volume changes are quantitatively comparable to the RSFC maps based on oxy- and total hemoglobin concentration changes obtained by the more complex IOSI setups. Moreover, RSFC maps do not require CCD cameras with very high frame acquisition rates, since our results demonstrate that they can be computed from the data obtained at frame rates as low as 5 Hz. Significance. Our results will have general utility for guiding future RSFC studies based on IOSI and making decisions about the IOSI system designs.
Comparison of Branched and Linear Perfluoropolyether Chains Functionalization on Hydrophobic, Morphological and Conductive Properties of Multi-Walled Carbon Nanotubes

The functionalization of multi-walled carbon nanotubes (MW-CNTs) was obtained by generating reactive perfluoropolyether (PFPE) radicals that can covalently bond to MW-CNTs’ surface. Branched and linear PFPE peroxides with equivalent molecular weights of 1275 and 1200 amu, respectively, have been thermally decomposed for the production of PFPE radicals. The functionalization with PFPE chains has changed the wettability of MW-CNTs, which switched their behavior from hydrophilic to super-hydrophobic. The low surface energy properties of PFPEs have been transferred to MW-CNTs surface and branched units with trifluoromethyl groups, CF3, have conferred higher hydrophobicity than linear units. Porosimetry discriminated the effects of PFPE functionalization on meso-porosity and macro-porosity. It has been observed that reactive sites located in MW-CNTs mesopores have been intensively functionalized by branched PFPE peroxide due to its low average molecular weight. Conductivity measurements at different applied pressures have showed that the covalent linkage of PFPE chains, branched as well as linear, weakly modified the electrical conductivity of MW-CNTs. The decomposed portions of PFPE residues, the PFPE chains bonded on carbon nanotubes, and the PFPE fluids obtained by homo-coupling side-reactions were evaluated by mass balances. PFPE-modified MW-CNTs have been characterized by X-ray photoelectron spectroscopy (XPS), scanning electron microscopy (SEM), thermogravimetric analysis (TGA), static contact angle (SCA), surface area, and porosity measurements.
A game theoretic channel allocation scheme for multi-user OFDMA relay system

A game theoretic resource allocation approach is proposed in this paper to distribute the channels in multiuser orthogonal frequency division multiplexing access (OFDMA) relay system. The goal is to maximize the system throughput while considering the fairness of the users. The basic idea is to consider backhaul link and access link together as a bundle. Nash bargaining solution (NBS) is used to distribute subchannels among these bundles. The multi-bundle bargaining algorithm is derived based on the two-bundle bargaining algorithm by grouping the bundles into coalitions. Within each bundle, the backhaul link and access link compete for the resources via the two-band partition algorithm to achieve a maximum data rate with the available resource. Simulation results show that the NBS based resource allocation scheme achieves higher user throughput but comparable user fairness compared with two-hop proportional fairness scheduler and round robin scheduler.