Miracle-dz/UniFAR-FTUs huggingface dataset:
Endothelial progenitor cell-conditioned medium promotes angiogenesis and is neuroprotective after spinal cord injury

Endothelial progenitor cells secrete a variety of growth factors that inhibit inflammation, promote angiogenesis and exert neuroprotective effects. Therefore, in this study, we investigated whether endothelial progenitor cell-conditioned medium might have therapeutic effectiveness for the treatment of spinal cord injury using both in vitro and in vivo experiments. After primary culture of bone marrow-derived macrophages, lipopolysaccharide stimulation was used to classically activate macrophages to their proinflammatory phenotype. These cells were then treated with endothelial progenitor cell-conditioned medium or control medium. Polymerase chain reaction was used to determine mRNA expression levels of related inflammatory factors. Afterwards, primary cultures of rat spinal cord neuronal cells were prepared and treated with H2O2 and either endothelial progenitor cell-conditioned medium or control medium. Hoechst 33258 and propidium iodide staining were used to calculate the proportion of neurons undergoing apoptosis. Aortic ring assay was performed to assess the effect of endothelial progenitor cell-conditioned medium on angiogenesis. Compared with control medium, endothelial progenitor cell-conditioned medium mitigated the macrophage inflammatory response at the spinal cord injury site, suppressed apoptosis, and promoted angiogenesis. Next, we used a rat model of spinal cord injury to examine the effects of the endothelial progenitor cell-conditioned medium in vivo. The rats were randomly administered intraperitoneal injection of PBS, control medium or endothelial progenitor cell-conditioned medium, once a day, for 6 consecutive weeks. Immunohistochemistry was used to observe neuronal morphology. Terminal deoxynucleotidyl transferase-mediated dUTP nick-end labeling assay was performed to detect the proportion of apoptotic neurons in the gray matter. The Basso, Beattie and Bresnahan Locomotor Rating Scale was used to evaluate the recovery of motor function of the bilateral hind limbs after spinal cord injury. Compared with the other two groups, the number of axons was increased, cavities in the spinal cord were decreased, the proportion of apoptotic neurons in the gray matter was reduced, and the Basso, Beattie and Bresnahan score was higher in the endothelial progenitor cell-conditioned medium group. Taken together, the in vivo and in vitro results suggest that endothelial progenitor cell-conditioned medium suppresses inflammation, promotes angiogenesis, provides neuroprotection, and promotes functional recovery after spinal cord injury.
ntiproliferative activity , antioxidant capacity and chemical omposition of extracts from the leaves and stem of Chresta phaerocephala arissa

In this study, antiproliferative and antioxidant activities of crude extracts (hexane, ethyl acetate and methanol) from leaves and stem of Chresta sphaerocephala DC. , Asteraceae, were investigated. Antiproliferative activity was tested in vitro against ten human cancer cells and against VERO (no cancer cell). Antioxidant activities were determined using DPPH and ORAC-FL assays and the total phenolic content was estimated by Folin–Ciocalteu method. Hexane and ethyl acetate extracts (leaves and stem) exhibited antiproliferative activity against cancer cell lines with total growth inhibition (TGI) between 50.40 and 250 g/ml. For VERO cell, TGI values were >250 g/ml for all extracts, except to hexane extract of the stem (TGI 80.92 g/ml). In an initial evaluation, ethyl acetate and methanol extracts (leaves and stem) lavonoids ntiproliferative and antioxidant activities have shown levels of phenolic compounds between 6.94 and 30.96 mg GAE/kg in Folin–Ciocalteu assay, DPPH free-radical scavenging activity with SC50 in the range of 75.22 and 400 g/ml and antioxidant capacity between 290.08 and 1088 mol TE/g of extract in ORAC-FL assay. HPLC-DAD and ESI-MS analysis allowed the identification of flavonoids in the methanol extract from the leaves of C. sphaerocephala. Three steroids and nine triterpenoids were identified in the bioactive hexane extracts using HRGC. ileira © 2015 Sociedade Bras
TcpRT: Instrument and Diagnostic Analysis System for Service Quality of Cloud Databases at Massive Scale in Real-time

Smooth end-to-end performance of mission-critical database system is essential to the stability of applications deployed on the cloud. It's a challenge for cloud database vendors to detect any performance degradation in real-time and locate the root cause quickly in sophisticated network environment. Cloud databases vendors tend to favor a multi-tier distributed architecture to achieve multi-tenant management, scalability and high-availability, which may further complicate the problem. This paper presents TcpRT, the instrument and diagnosis infrastructure in Alibaba Cloud RDS that achieves real-time anomaly detection. We wrote a Linux kernel module to collect trace data of each SQL query, designed to be efficient with minimal overhead, it adds tracepoints in callbacks of TCP congestion control kernel module, that is totally transparent to database processes. In order to reduce the amount of data significantly before sending it to backend, raw trace data is aggregated. Aggregated trace data is then processed, grouped and analyzed in a distributed streaming computing platform. By utilizing a self-adjustable Cauchy distribution statistical model from historical performance data for each DB instance, anomalous events can be automatically detected in databases, which eliminates manually configuring thresholds by experience. A fault or hiccup occurred in any network component that is shared among multiple DB instances (e.g. hosted on the same physical machine or uplinked to the same pair of TOR switches) may cause large-scale service quality degradations. The ratio of anomalous DB instances vs networks components is being calculated, which helps pinpoint the faulty component. TcpRT has been deployed in production at Alibaba Cloud for the past 3 years, collects over 20 million raw traces per second, and processes over 10 billion locally aggregated results in the backend per day, and managed to have within 1% performance impact on DB system. We present case studies of typical scenarios where TcpRT helps to solve various problems occurred in production system.
New insights into the high-pressure polymorphism of SiO 2 cristobalite

Single-crystal X-ray diVraction experiments with SiO2 -cristobalite reveal that the well-known reversible displacive phase transition to cristobalite-II, which occurs at approximately 1.8 GPa, can be suppressed by rapid pressure increase, leading to an overpressurized metastable state, persisting to pressure as high as 10 GPa. In another, slow pressure increase experiment, the monoclinic highpressure phase-II was observed to form at »1.8 GPa, in agreement with earlier in situ studies, and its crystal structure has been unambiguously determined. Single-crystal data have been used to reWne the structure models of both phases over the range of pressure up to the threshold of formation of cristobalite X-I at »12 GPa, providing important constraints on the feasibility of the two competing silica densiWcation models proposed in the literature, based on quantum mechanical calculations. Preliminary diVraction data obtained for cristobalite X-I reveal a monoclinic unit cell that contradicts the currently assumed model.
Tuning ITAM multiplicity on T cell receptors can control potency and selectivity to ligand density

Modeling the responses of synthetic receptors in T cells identifies new ways to optimize CAR–T cell activity. ITAM abundance increases receptor potency T cells transduce extracellular signals by phosphorylating immunoreceptor tyrosine-based activation motifs (ITAMs) within the T cell receptor complex. Why this complex contains more ITAMs than any other immune receptor remains unclear. James engineered drug-responsive synthetic receptors that varied in ITAM abundance to determine how ITAM frequency influenced T cell signaling at the single-cell level. The experimental data fit computational models predicting that increasing ITAM number influenced the efficiency of signal transduction, but not the signal amplitude. Application of these results to human CAR–T cells identified strategies to improve the specificity of these cancer therapeutics. The T cell antigen receptor (TCR) recognizes peptides from pathogenic proteins bound in the major histocompatibility complex (MHC). To convert this binding event into downstream signaling, the TCR complex contains immunoreceptor tyrosine-based activation motifs (ITAMs) that act as docking sites for the cytoplasmic tyrosine kinase ZAP-70. Unique among antigen receptors, the TCR complex uses 10 ITAMs to transduce peptide-MHC binding to the cell interior. Using synthetic, drug-inducible receptor-ligand pairs, it was found that greater ITAM multiplicity primarily enhanced the efficiency with which ligand binding was converted into an intracellular signal. This manifested as an increase in the fraction of cells that became activated in response to antigen, and a more synchronous initiation of TCR-proximal signaling, rather than direct amplification of the intracellular signals. Exploiting these findings, the potency and selectivity of chimeric antigen receptors targeted against cancer were substantially enhanced by modulating the number of encoded ITAMs.
Models of Trachoma Transmission and Their Policy Implications: From Control to Elimination

Abstract Despite great progress in eliminating trachoma from the majority of worldwide districts, trachoma control seems to have stalled in some endemic districts. Can mathematical models help suggest the way forward? We review specific achievements of models in trachoma control in the past. Models showed that, even with incomplete coverage, mass drug administration could eliminate disease through a spillover effect, somewhat analogous to how incomplete vaccine campaigns can eliminate disease through herd protection. Models also suggest that elimination can always be achieved if enough people are treated often enough with an effective enough drug. Other models supported the idea that targeting ages at highest risk or continued improvements in hygiene and sanitation can contribute meaningfully to trachoma control. Models of intensive targeting of a core group may point the way to final eradication even in areas with substantial transmission and within-community heterogeneity.
HHU at SemEval-2018 Task 12: Analyzing an Ensemble-based Deep Learning Approach for the Argument Mining Task of Choosing the Correct Warrant

This paper describes our participation in the SemEval-2018 Task 12 Argument Reasoning Comprehension Task which calls to develop systems that, given a reason and a claim, predict the correct warrant from two opposing options. We decided to use a deep learning architecture and combined 623 models with different hyperparameters into an ensemble. Our extensive analysis of our architecture and ensemble reveals that the decision to use an ensemble was suboptimal. Additionally, we benchmark a support vector machine as a baseline. Furthermore, we experimented with an alternative data split and achieved more stable results.
Soft Palate Pleomorphic Adenoma of a Minor Salivary Gland: An Unusual Presentation

Approximately 10% of pleomorphic adenomas occur in the minor salivary glands with the palate being the most common site. Pleomorphic adenomas account for the majority of palatal tumours; however, minor salivary gland tumours have a higher risk of malignancy compared to tumours of the major salivary glands, so appropriate diagnostic evaluation should be prompt. We present a case of a 52-year-old man with a longstanding history of a soft palate pleomorphic adenoma which required excision under general anaesthetic via a mandibular swing approach. As well as the surgical approach to access this tumour; this case is unique as it is the largest soft palate pleomorphic adenoma reported in the literature. We discuss the appropriate preoperative investigations and airway considerations for this patient, as well as the factors to consider when planning operative management of palatal tumours.
Modelling and simulation of the hybrid system PV-wind with MATLAB/SIMULINK

This paper present a hybrid system connected to the DC load. The hybrid system is composed by a photovoltaic generator (Kaneka GSA060), a wind turbine generator (Air X 600 W) constituted by a turbine and a permanent magnet synchronous generator, a three phase uncontrolled rectifier converter and a DC-DC boost power converter dedicated for each source and controlled by a command based on the method of Perturb and Observe. The aim of the control is to extract the maximum power of each source from the proposed system for different variation of the input parameters (radiation and wind speed). Our system is modulates with MATLAB/SIMULINK environment.
Effect of Biochar Amendment on Bioavailability and Accumulation of Cadmium and Trace Elements in Brassica chinensis L. (Chinese Cabbage)

This study aims to investigate the potential use of maize stalk (MS), bamboo (BB) and cow manure (CM) derived biochar as a soil amendment on the cadmium (Cd) and trace metals (Mn, Zn, Fe) accumulation by two Cd accumulator cultivars; low (Aijiaoheiye 333) (AJ) and high (Zhouyeheiyoudonger) (ZH) of Brassica chinensis L. The effect of different biochar (4% w/w) on both cultivars grown on artificially Cd contaminated Alfisol soil was studied. All selected biochar decreased the bioavailability of Cd in soil and its phytoavailability for both cultivars of B. chinensis L. followed the order: MS > CM > BB. In particular, with increase soil pH MS biochar significantly reduced Cd bioavailability in soil by 54% and accumulation in shoots of AJ and ZH cultivars by 35% and 41%, as soil amendment. These results indicated the effectiveness of biochar by reducing the availability and phytotoxicity of Cd, while enhanced shoot dry biomass by promoting microbial activity and availability of essential trace metals.
Isolation and characterization of bacteriophages with therapeutic potential

The concerning spread of antibiotic resistant bacteria has directed the spotlight upon bacteriophages, in short phages, as potential candidates for therapeutic purposes. Far for being a novelty, phage therapy has been widely used in the 20s and 30s in western countries until the discovery of antibiotics, which, coupled with a lack of knowledge of phage biology at that time, let to the replacement of phage therapy by antibiotics. On the other side of the planet, the Georgian Eliava Institute has been using phages for treating bacterial diseases since short after phage discovery a century ago. Georgian pharmacies commonly sell phage cocktails from the Institute without the need of a doctor’s prescription. A thorough characterisation of the cocktail is though required for it to be accepted as pharmaceutical in the European Union. The potential to investigate the genetic material of microbial communities directly from the environment through metagenomics, allows for genomic characterisation of these cocktail. Furthermore, metagenomics analyses may lead to the discovery of novel phages with therapeutic potential, opening up a promising new horizon for phage therapy. This thesis is divided into five parts, each assigned a chapter. Chapter 1 provides the reader with an introduction to phage biology, history and metagenomics. Here, the main bioinformatics methods used throughout the studies of the following chapters are also presented and briefly described. Chapter 2 presents the paper ”HostPhinder: A Phage Host Prediction Tool” published in May 2016. The tool predicts the bacterial host of a given phage based on co-occurrent k-mers between a query sequence and reference phage genomes with known host. HostPhinder’s accuracy in predicting the host species and genus of an evaluation set was higher than 74% and 81%, respectively. The tool can be applied to identify the host of phage sequences found for instance in metagenomes allowing for a first step characterisation. Chapter 3 presents the paper ”Metagenomic analysis of therapeutic PYO phage cocktails from 1997 to 2014” submitted in October 2017 and currently under peer-revision. In this study, the compositions of 3 batches of a Georgian cocktail from 1997 to 2014 was compared by means of Next Generation Sequencing (NGS) and metagenomic analysis. Thirty and 29 phage draft genomes were found in the cocktails from 1997 and 2014, respectively. One of them was present in both sample and did not resemble any known phage genomes, strongly suggesting its novelty. Phage representatives of all bacterial targets supposedly targeted by the cocktail’s were found, as predicted using HostPhinder. A comparison between cocktails from 1997, 2000, and 2014 showed a closer composition
A Microsatellite DNA Marker Developed for Identifying Disease-resistant Population of Giant Black Tiger Shrimp, Penaeus monodon

White spot disease caused by white spot syndrome virus (WSSV) poses major problems that result in huge economic losses each year in shrimp aquaculture throughout the world. In the present study, microsatellite-based DNA fingerprints have been compared between naturally occurring WSSV disease-resistant and susceptible populations of giant black tiger shrimp, Penaeus monodon, to find DNA markers. For the first time, we report here a microsatellite locus, which, after amplification by polymerase chain reaction, provides a highly statistically significant DNA fingerprint of 71 bp, only in disease susceptible populations but not in disease-resistant shrimp populations, whereas a 317 bp band is common in both. The absence of the former DNA marker will be very useful to identify disease-resistant broodstock of P. monodon for marker-assisted selection in breeding programs to generate disease-free shrimps (P. monodon) in the aquaculture industry.
TALEN-Mediated FLAG-Tagging of Endogenous Histone Methyltransferase DOT1L

Histone modification including H3 lysine 79 methylation (H3K79me) plays a key role during gene transcription and DNA damage repair. DOT1L, the sole methyltransferase for three states of H3K79me, is implicated in leukemia, co-lorectal cancer, and dilated cardiomyopathy. However, understanding of DOT1L and H3K79me in these pathways and disease pathogenesis has been limited due to the difficulty of working with DOT1L protein. For instance, locus-specific or genome-wide binding sites of DOT1L revealed by chromatin immunoprecipitation (ChIP)-based methods are necessary for inferring its functions, but high-quality ChIP-grade antibodies are currently not available. Herein we have developed a knock-in approach to tag endogenous DOT1L with 3 × Flag at its C-terminal domain to follow functional analyses. The knock-in was facilitated by using TALENs to induce a targeted double-strand break at the endogenous DOTIL to stimulate local homologous recombination at that site. The single cell colonies with successful knock-in were isolated and verified by different methods. We also demonstrated that tagged DOT1L maintains its normal function in terms of methylation and that the engineered cells would be very useful for further studies.
Zero-Shot Dual Machine Translation

Neural Machine Translation (NMT) systems rely on large amounts of parallel data. This is a major challenge for low-resource languages. Building on recent work on unsupervised and semi-supervised methods, we present an approach that combines zero-shot and dual learning. The latter relies on reinforcement learning, to exploit the duality of the machine translation task, and requires only monolingual data for the target language pair. Experiments show that a zero-shot dual system, trained on English-French and English-Spanish, outperforms by large margins a standard NMT system in zero-shot translation performance on Spanish-French (both directions). The zero-shot dual method approaches the performance, within 2.2 BLEU points, of a comparable supervised setting. Our method can obtain improvements also on the setting where a small amount of parallel data for the zero-shot language pair is available. Adding Russian, to extend our experiments to jointly modeling 6 zero-shot translation directions, all directions improve between 4 and 15 BLEU points, again, reaching performance near that of the supervised setting.
Rapid thermal annealing of graphene-metal contact

High quality graphene-metal contacts are desirable for high-performance graphene based electronics. Process related factors result large variation in the contact resistance. A post-processing method is needed to improve graphene-metal contacts. In this letter, we studied rapid thermal annealing (RTA) of graphene-metal contacts. We present results of a systematic investigation of device scaling before and after RTA for various metals. The results reveal that RTA provides a convenient technique to reduce contact resistance, thus to obtain reproducible device operation.
Twitter User Geolocation Using Deep Multiview Learning

Predicting the geographical location of users on social networks like Twitter is an active research topic with plenty of methods proposed so far. Most of the existing work follows either a content-based or a network-based approach. The former is based on user-generated content while the latter exploits the structure of the network of users. In this paper, we propose a more generic approach, which incorporates not only both content-based and network-based features, but also other available information into a unified model. Our approach, named Multi-Entry Neural Network (MENET), leverages the latest advances in deep learning and multiview learning. A realization of MENET with textual, network and metadata features results in an effective method for Twitter user geolocation, achieving the state of the art on two well-known datasets.
Iron stress and genetic response in cyanobacteria : fur genes from Synechococcus PCC 7942 and Anabaena PCC 7120

Fur (Ferric uptake regulator) est une proteine d'union a l'ADN qui reprime la transcription des promoteurs regules par le fer, utilise sous forme Fe 2+ comme cofacteur. Chez les bacteries Gram negatif, fur controle l'expression des toxines et des facteurs de virulence lors de stress ferrique. Le fer est un element fondamental qui limite la croissance et la proliferation du phytoplancton. Nous avons clone le gene fur de la cyanobacterie Synechococcus PCC 7942, en appliquant la technique de la reaction en chaine de la polymerase (PCR). Le fragment d'ADN exprime une proteine de la famille de Fur qui conserve les motifs principaux trouves dans cette famille. La proteine Fur de Synechococcus a ete produite avec succes, avec un rendement important de l'ordre de 15 % du contenu total des proteines. De plus, une autre proteine Fur a ete identifiee dans une cyanobacterie filamenteuse fixative d'azote : Anabaena PCC 7120.