Miracle-dz/UniFAR-FTUs huggingface dataset:
Aestuariibacteraggregatus sp. nov., a moderately halophilic bacterium isolated from seawater of theYellow Sea

A Gram-negative, non-spore-forming, catalase- and oxidase-positive, strictly aerobic, short rod-shaped bacterium with a single, polar ﬂagellum, designated strain WH169 T , was isolated from seawater of the Yellow Sea in China. Buds and prosthecae were formed when the organism was grown at 20 1 C for 12 days on marine 2216E agar. The organism grew optimally at 37 1 C, in pH 7.0–8.0, and in the presence of 4.0–6.0% w/v NaCl. Growth did not occur in a medium without Na 1 or sea salts. Strain WH169 T contained ubiquinone-8 as the predominant respiratory lipoquinone and C 16:1 o 7c and/or C 16:1 o 6c (35.9%), C 16:0 (25.3%) and C 18:1 o 7c (9.7%) as the major fatty acids. The polar lipids consisted of phosphatidylethanolamine, phosphatidylglycerol and an unidentiﬁed phospholipid. The DNA G 1 C content of strain WH169 T was 49.4 mol%. 16S rRNA gene sequence analysis showed that strain WH169 T showed 95.1% sequence similarity to both type strains of the only two species in the genus Aestuariibacter . On the basis of the polyphasic taxonomic evidence presented in this study, it was concluded that strain WH169 T should be classiﬁed as a novel species of Aestuariibacter , for which the name Aestuariibacter aggregatus sp. nov. is proposed, with the type strain WH169 T ( = CGMCC 1.8995 T = LMG 25283 T ). dextrin, turanose, sucrose, glycyl-L -bromosuccinic glutamic acid, L -histidine, hydroxy- L -proline, L -ornithine, L -phenylalanine, urocanic acid, inosine and uridine. It shows weak activity for esterase (C4) and cystine arylamidase; negative for indole and H 2 S produc-tion, nitrate reduction, urease, caseinase, lysine decarbox-ylase, ornithine decarboxylase, tryptophan deaminase, a -chymotrypsin, N -acetyl- b -glucosaminidase, a -fucosidase, a -galactosidase, b -glucuronidase, lipase (C14), utilization of D -fructose, D -mannitol, D -rafﬁnose, D -salicin, D -sorbitol, arabinose, mannose, inositol, L -rhamnose, lactose, L -serine, malate, a -cyclodextrin, N -acetyl- D -galactosamine, adonitol, L -fucose, lactulose, maltose, D -psicose, xylitol, hydroxybuty-ric acid, D -glucuronic acid, itaconic acid, sebacic acid, L -leucine, L -asparagine, succinamic acid, L -phenylalanine, serine, L -threonine, thymidine, putrescine, glycerol and 2,3-butanediol. Acids are produced from D -melezitose, glyco-gen, sucrose and trehalose. No acids are produced from arabinose, xylitol, gentiobiose, D -turanose, D -lyxose, D -taga-tose, fucose, arabitol, D -galactose, D -glucose, D -fructose, D -ribose, D -adonitol, fructose, L -sorbose, dulcitol, D -lactose, inulin, xylose, D -melibiose, D -mannitol, D -rafﬁnose, amygdalin,
Construction and Comprehensive Analysis of a ceRNA Network to Reveal Potential Novel Biomarkers for Triple-Negative Breast Cancer

Background: Triple-negative breast cancer (TNBC) is the most common and aggressive type of breast cancer with an unfavourable outcome worldwide. Novel therapeutic targets are urgently required to explore this malignancy. This study explored the ceRNA network and the important genes for predicting the therapeutic targets. Methods: It identified the differentially expressed genes of mRNAs, lncRNAs and miRNAs between TNBC and non-TNBC samples in four cohorts (TCGA, GSE38959, GSE45827 and GSE65194) to explore the novel therapeutic targets for TNBC. Downstream analyses, including functional enrichment analysis, ceRNA network, protein–protein interaction and survival analysis, were then conducted by bioinformatics analysis. Finally, the potential core protein of the ceRNA network in TNBC was validated by immunohistochemistry. Results: A total of 1,045 lncRNAs and 28 miRNAs were differentially expressed in the TCGA TNBC samples, and the intersections of 282 mRNAs (176 upregulations and 106 downregula-tions) between the GEO and TCGA databases were identified. A ceRNA network composed of 7 lncRNAs, 62 mRNAs, 12 miRNAs and 244 edges specific to TNBC was established. The functional assay showed dysregulated genes, and GO, DO and KEGG enrichment analysis were performed. Survival analysis showed that mRNA LIFR and lncRNA AC124312.3 were significantly correlated with the overall survival of patients with TNBC in the TCGA databases (P < 0.05). Finally, the LIFR protein was validated, and immunohistochemical results showed the upregulated expression of LIFR in TNBC tissues. Conclusion: Thus, our study presents an enhanced understanding of the ceRNA network in TNBC, where the key gene LIFR may be a new promising potential therapeutic target for patients with TNBC.
Effect of X-irradiation on the Functional Status of Lysosomal Enzymes of Mouse Mammary Gland Carcinomas1

SUMMARY The subcellular distribution of various lysosomal hydrolases and mitochondria! cytochrome c oxidase of mammary carcinomas of C3H mice was studied by means of differential centrifugation and zonal ultracentriftigation and in electron histochemical preparations. Tumors that received a single local dose of 500, 1000, or 7000 rad showed an increase in the specific activities of acid hydrolases in the whole homogenates. Under the same conditions, time-and dose-dependent increases in the proportion of absolute unsedimentable activities were observed. These changes appeared not earlier than 6 hr after doses of 7000 rad. Whole homogenates from animals receiving a combined treatment of X-irradiation plus vitamin A showed higher levels of specific acid hydrolases than those from mice treated with radiation alone, and homogenates from mice given X-irradiation plus cortisone showed lower levels of acid-hydrolytic activity than those from irradiated animals. A peak of fast-moving acid hydrolases that precedes the mitochondria! fraction in the high-resolution zonal ultracentrifugation techniques appears clearly enlarged in tumors treated with 1000 rad. These samples also showed a decrease of mitochondrial cytochrome c oxidase. The bio chemical and electron histochemical changes observed indicate an involvement of the lysosome system in regressing mammary carcinomas. The fact that the course of biochemical events in the irradiated tumors is modified by lysosome labilizers or stabilizers is also
PABP-interacting proteins, PAIP1 and PAIP2, affect translation termination

Polyadenylate-binding protein (PABP) stimulates translation termination via interaction of its C-terminal domain with eukaryotic polypeptide chain release factor, eRF3. Additionally, two other proteins, poly(A)-binding protein-interacting protein 1 and 2 (PAIP1 and PAIP2), bind the same domain of PABP and regulate its translation-related activity. To study the biochemistry of eRF3 and PAIP1/2 competition for PABP binding, we quantified the effects of PAIPs on translation termination in the presence or absence of PABP. Our results demonstrated that both PAIP1 and PAIP2 prevented translation termination at premature termination codon (PTC), by controlling PABP activity. Moreover, PAIP1 and PAIP2 inhibited the activity of free PABP on translation termination in vitro. However, after binding the poly(A) tail, PABP became insensitive to suppression by PAIPs and efficiently activated translation termination in the presence of eRF3a. Additionally, we revealed that PAIP1 binds eRF3 in solution, which stabilizes the post-termination complex (postTC). These results indicated that PAIP1 and PAIP2 participate in translation termination and are important regulators of readthrough at PTC.
Reduce the Current Ripple of the PMSM with the Vector Control Method Based on Anti-Saturation than the Sensorless Vector Control Method

: This paper investigates a comparison between the sensorless vector control method based on MRAS (Model Reference Adaptive System) using SVPWM (Space Vector Modulation) and the control method of the PMSM (Permanent Magnet Synchronous Motor) Based on anti-saturation current controller. MRAS algorithm is based on comparison between the estimators. The error between the estimated quantities obtained by the two models is used to estimate the rotor speed that started in order to create an optimum vector control method. This method is compared with vector control based on anti-saturation current control block. That created in order to reduce the ripple in vector control current. These two control method were simulated in MATLAB and after comparing the current THD (Total Harmonic Distortion) of the two methods, it was observed the vector control based on anti-saturation block with shaft encoder has bigger volume, less current ripple and more cost than sensorless method.
SCREENS FOR HIGH PRECISION MEASUREMENTS

Scintillation screens made of various inorganic materials are widely used for transverse beam profile diagnostics at all kinds of accelerators. The monitor principle is based on the particles’ energy loss and its conversion to visible light. The resulting light spot is a direct image of the two-dimensional beam distribution. For large beam sizes standard optical techniques can be applied, while for small beam sizes ded-icated optical arrangements have to be used to prevent for image deformations. In the modern linac based light sources scintillator usage serves as an alternative way to overcome limitations related to coherent OTR emission. Radiation damages and intensity based saturation effects, in depen-dence of the screen material, have to be modelled. In this proceeding, an introduction to the scintillation mechanism in inorganic materials will be given including practical demands and limitations. An overview on actual applications at hadron and electron accelerators will be discussed as sum-mary of the Joint ARIES-ADA Workshop on ‘Scintillation Screens and Optical Technology for transverse Profile Measurements’ held in Krakow, Poland [1].
Deep on Edge: Opportunistic Road Damage Detection with Ofﬁcial City Vehicles

—How can we inspect city conditions at low costs? City infrastructures, such as roads, are elements of great importance in urban lives. Roads require constant inspection and repair due to deterioration, but it is expensive to do so with manual labor. Therefore, these works should be done automatically so that the cost of inspecting or repairing becomes cheap. While there are several works to address these road issues, our study focuses on ofﬁcial city vehicles, especially garbage trucks, to detect damaged lane markings (lines) which is the simplest case of road deterioration. Since our proposed system is implemented on an edge computer, it is easy to attach our system to vehicles. In addition, our system utilizes a camera, and since garbage trucks almost run through the entire area of a city every day, we can constantly obtain road images covering wide areas. Our model, which we call Deep on Edge (DoE), is a deep convolutional neural network which detects damaged lines from images. In our experiments, to evaluate our system, we ﬁrst compared the accuracy of line damage detection of DoE with other baseline methods. Our results show that DoE outperforms previous approaches. Then, we investigate whether our system can detect the line damage on a running car. With this demonstration, we show that our system would be useful in practice.
A comparison of Bayesian and classical testing procedures for the association parameter in a 2x2 contingency table

Bayesian alternatives to classical tests for Fisher’s exact test in 2£2 contingency tables are considered. Point null test versus one-sided hypothesis is tested using the log odds ratio in 2£2 contingency tables. Hierarchical Bayes, empirical Bayes and noninformative Bayes procedures are compared with the appropriate classical procedures, either the p-value in Fisher’s exact test or a randomized test. A conjugate prior at the ﬁrst stage and a noninformative prior at the second stage are used for the hyperparameter(s) in the hierarchical approach. For different testing procedures, the likelihood of making a type I error is chosen to be approximately the same. Then the power of different tests is compared: the larger the power, the better the test. In small samples, the randomized test performs well in comparison with the other methods. For moderate samples, empirical Bayes and randomized test procedures perform better than other approaches
Modelling active zone calcium dynamics at cerebellar mossy fibre boutons

The rate at which signals can be transmitted between single neurons limits the speed of information processing. Cerebellar mossy fibre boutons are able to maintain synchronous neurotransmitter release at very high action potential frequencies, up to ∼ 1 kHz. The neurotransmitter release occurs at the presynaptic active zone and is controlled by highly localised calcium signals. In order to allow reliable, fast synaptic transmission, calcium ions must be cleared from the active zone. However, the exact mechanisms of calcium clearance remain elusive. Despite the recent advances in imaging technology, it is not yet possible to measure localised calcium signals on the nanometre scale. Nevertheless, it is possible to address the impact of localised calcium signals on neurotransmitter release with use of computational modelling. In this study, I established an experimentally constrained model of an active zone of the cerebellar mossy fibre bouton. My simulations revealed that endogenous fixed buffers that have low calcium binding capacity (∼ 15) and low affinity for binding calcium in combination with mobile buffers with high affinity for binding calcium enable rapid clearance of calcium from the active zone during high-frequency firing. Moreover, during high-frequency firing, slow endogenous mobile buffers prevent build-up of the intracellular calcium concentration. The results presented in this work suggest that reduced calcium buffering speeds active zone calcium signalling, thus allowing high rates of synaptic transmission. 87 Pages, 170 References, 20 Figures, 3 Tables, 2 Listings Content of this display-optimised version is identical to submitted print-optimised version.
University of Birmingham Imaging and Analysis of Individual Cavitation Microbubbles around Dental Ultrasonic

Cavitation is a potentially effective and less damaging method of removing bioﬁlm from biomaterial sur- faces. The aim of this study is to characterise individual microbubbles around ultrasonic scaler tips using high speed imaging and image processing. This information will provide improved understanding on the disruption of dental bioﬁlm and give insights into how the instruments can be optimised for ultrasonic cleaning. Individual cavitation microbubbles around ultrasonic scalers were analysed using high speed recordings up to a million frames per second with image processing of the bubble movement. The radius and rate of bubble growth together with the collapse was calculated by tracking multiple points on bub- bles over time. The tracking method to determine bubble speed demonstrated good inter-rater reliability (intra class correlation coefﬁcient: 0.993) and can therefore be a useful method to apply in future studies. The bubble speed increased over its oscillation cycle and a maximum of 27 ms (cid:1) 1 was recorded during the collapse phase. The maximum bubble radii ranged from 40 to 80 m m. Bubble growth was observed when the ultrasonic scaler tip receded from an area and similarly bubble collapse was observed when the tip moved towards an area, corresponding to locations of low pressure around the scaler tip. Previous work shows that this cavitation is involved in bioﬁlm removal. Future experimental work can be based on these ﬁndings by using the protocols developed to experimentally analyse cavitation around various clinical instruments and comparing with theoretical calculations. This will help to determine the main cleaning mechanisms of cavitation and how clinical instruments such as ultrasonic scalers can be optimised.
Interaction between the SH3 domain of Src family kinases and HTLV-1 p13’s proline rich motif: a novel mechanism underlying delivery of Src family kinases to mitochondria

The association of the SH3 domain of Src Family Kinases (SFKs) with protein partners bearing proline rich motifs has been implicated in the regulation of the activity, and recently described as a possible mechanism of relocalization to subcellular compartments, of SFKs. We demonstrate for the first time that p13, an accessory protein encoded by the Human T-cell Leukemia Virus type 1 (HTLV-1), binds the SH3 domain of SFKs via its C-terminal proline rich motif, forming a stable heterodimer that translocates to mitochondria by virtue of its N-terminal mitochondrial localization signal. As a result, the activity of SFKs is dramatically enhanced with subsequent increase in mitochondrial tyrosine phosphorylation and the recognized p13’s ability to insert itself into the inner mitochondrial membrane and to perturb the mitochondrial membrane potential is abolished. Overall, this study, in addition to confirming that the catalytic activity of SFKs is modulated by interactors of their SH3 domain, lead us to hypothesize a general mechanism by which proteins bearing a proline rich motif and a mitochondrial localization signal at the same time may act as carriers of SFKs into mitochondria, thus contributing to regulate mitochondrial functions under various pathophysiological conditions. as Intact mitochondria mitochondrial membranes Western blot analysis with anti-Lyn, anti-p13, anti-AIF and anti-aconitase antibodies, in treatment after
Investigation of Inadequate Users in a Q&A Site Who Use Two or More Accounts for Submitting Questions and Manipulating Evaluations

(cid:151)Some users in a question and answer (Q&A) site use multiple user accounts and attempt to manipulate communications in the site. In order to detect these inadequate multiple account users precisely, it is important to investigate them from various points of view. In this paper, we investigate users suspected of manipulating evaluations of their answers by using two or more accounts for submitting many questions. The results of this study will give us a chance to investigate purposes and behaviors of inadequate multiple account users in a Q&A site.
Linkage Scan of Nicotine Dependence in the UCSF Family Alcoholism Study

Background— Nicotine dependence has been shown to represent a heritable condition, and several research groups have performed linkage analysis to identify genomic regions influencing this disorder though only a limited number of the findings have been replicated. Methods— In the present study, a genome-wide linkage scan for nicotine dependence was conducted in a community sample of 950 probands and 1204 relatives recruited through the UCSF Family Alcoholism Study. A modified version of the Semi-Structured Assessment for the Genetics of Alcoholism (SSAGA) with additional questions that probe nicotine use was used to derive DSM-IV nicotine dependence diagnoses. Results— A locus on chromosome 2q31.1 at 184 centimorgans nearest to marker D2S2188 yielded a LOD score of 3.54 (point-wise empirical p-value = .000012). Additional peaks of interest were identified on chromosomes 2q13, 4p15.33-31, 11q25, and 12p11.23-21. Follow-up analyses were conducted examining the contributions of individual nicotine dependence symptoms to the chromosome 2q31.1 linkage peak as well as examining the relation of this chromosomal region to alcohol dependence. Conclusions— The present report suggests that chromosome 2q31.1 confers risk to the development of nicotine dependence and that this region influences a broad range of nicotine dependence symptoms rather than a specific facet of the disorder. Further, the results show this region is not linked to alcohol dependence in this population, and thus may influence nicotine dependence specifically.
Reliablity and Survivability of Wireless Sensor Network Using Security Adaptation Reference Monitor ( SARM)

—Security has become a key issue for any huge deployment of Wireless Sensor Network (WSN). Moreover, data reliability combined with energy loss minimization is really a challenging task, particularly to maintain survivability of the WSN under attacks such as sinkhole. Therefore, new security mechnisms must be in accordance with energy consumption constraint. This paper proposes to address this task using our Security Adaptation Reference Monitor (SARM) which is an efficient Framework capable of trading-off between security and energy optimization. SARM is based on an autonomic computing security looped system, which fine-tunes security means based on the monitoring of the context including energy consumption aspects. We evaluate SARM in the context of WSN through a simulation tool to verify the performance of overall reliability and energy loss in the presence of sinkhole attackers. The results clearly show that SARM is efficient in terms of reliability, overall network utilization and power consumption.
Congruent Growth of Cu 2 Se Thermoelectric Thin Films Enabled by Using High Ablation Fluence During Pulsed Laser Deposition

: The importance of the laser ablation fluence in congruent growth of Cu 2 Se thermoelectric thin films during pulsed laser deposition was shown in this work. By using a larger laser ablation fluence, a more consistent composition between as-grown thin films and the target material has been realized in the pulsed laser deposition of Cu 2 Se films. This is associated with the enhanced plasma shielding effect, which weakens direct laser-solid interaction when increasing laser fluence. Reducing the ablation fluence can obviously increase the amount of the copper deficiencies, due to more effective laser ablation of Se (higher vapor pressure) than that of Cu when the laser direct lasser-solid interaction becomes more efficient. Apart from tuning the ablation fluence, thermoelectric performances of as-grown Cu 2 Se thin films are further optimized as a function of the used argon background gas pressures. The maximum thermoelectric performance of the Cu 2 Se thin film can be obtained when using the highest ablation fluence (~10 J/cm 2 ) and a low argon background pressure(~10 -1 Pa).
Service Correlation and Constraint Aware Composite Service Composition under QOS Context

: The ability to perform web service discovery and composition automatically and dynamically is essential and has emerged as an important research topic. Automated web service composition deals with the significant increase in the number of available services over time, as well as frequent changes in their definitions. It enables significantly faster responses to user queries for composite services, compared to the manual case. Also, it produces compositions up-to-date with the latest web service definitions, despite the dynamic environment. A significant contribution of the approach concerns the full incorporation of semantics. The utilization of semantic information facilitates discovery and composition. It also permits approximate composition and enables the quality assessment of the produced composite services in terms of accuracy by using AI techniques especially planning. The framework maintains compatibility with the current standards, to ensure interoperability, and it is independent from specific planners. The model devised in this paper focuses on the addition of the OWL-S descriptions of produced composite services in the registry of available services, to explore the possibility to accelerate the composition process. In addition it deals with enhancing the approach with the ability to produce various composite services according to nonfunctional user preferences, dealing with pragmatic knowledge and As web service standards evolve, exploitation of pragmatic knowledge could be possible by extending existing web service description.