Miracle-dz/UniFAR-FTUs huggingface dataset:
Biological Crystallography Structural Basis for Type Vi Secreted Peptidoglycan Dl-endopeptidase Function, Specificity and Neutralization in Serratia Marcescens

Some Gram-negative bacteria target their competitors by exploiting the type VI secretion system to extrude toxic effector proteins. To prevent self-harm, these bacteria also produce highly specific immunity proteins that neutralize these antagonistic effectors. Here, the peptidoglycan endo-peptidase specificity of two type VI secretion-system-associated effectors from Serratia marcescens is characterized. These small secreted proteins, Ssp1 and Ssp2, cleave between-d-glutamic acid and l-meso-diaminopimelic acid with different specificities. Ssp2 degrades the acceptor part of cross-linked tetratetrapeptides. Ssp1 displays greater promiscuity and cleaves monomeric tripeptides, tetrapeptides and pentapeptides and dimeric tetratetra and tetrapenta muro-peptides on both the acceptor and donor strands. Functional assays confirm the identity of a catalytic cysteine in these endopeptidases and crystal structures provide information on the structure–activity relationships of Ssp1 and, by comparison , of related effectors. Functional assays also reveal that neutralization of these effectors by their cognate immunity proteins, which are called resistance-associated proteins (Raps), contributes an essential role to cell fitness. The structures of two immunity proteins, Rap1a and Rap2a, responsible for the neutralization of Ssp1 and Ssp2-like endopeptidases, respectively, revealed two distinct folds, with that of Rap1a not having previously been observed. The structure of the Ssp1–Rap1a complex revealed a tightly bound heteromeric assembly with two effector molecules flanking a Rap1a dimer. A highly effective steric block of the Ssp1 active site forms the basis of effector neutralization. Comparisons with Ssp2–Rap2a orthologues suggest that the specificity of these immunity proteins for neutralizing effectors is fold-dependent and that in cases where the fold is conserved sequence differences contribute to the specificity of effector– immunity protein interactions.
Imatinib Attenuates Diabetes-Associated Atherosclerosis

Objective—Diabetes is associated with accelerated atherosclerosis, the major factor contributing to increased mortality and morbidity in the diabetic population. The molecular mechanisms by which diabetes promotes atherosclerosis are not fully understood. Platelet-derived growth factor has been shown to play a major role in the pathology of vascular diseases, but whether it plays a role in atherosclerosis associated with diabetes remains unknown. The aims of this study were to assess whether platelet-derived growth factor–dependent pathways are involved in the development of diabetes-induced atherosclerosis and to determine the effects of platelet-derived growth factor receptor antagonism on this disorder. Methods and Results—Diabetes was induced by injection of streptozotocin in 6-week-old apolipoprotein E knockout mice. Diabetic animals received treatment with a tyrosine kinase inhibitor that inhibits platelet-derived growth factor action, imatinib (STI-571, 10 mg/kg per day), or no treatment for 20 weeks. Nondiabetic apolipoprotein E knockout mice served as controls. Induction of diabetes was associated with a 5-fold increase in plaque area in association with an increase in aortic platelet-derived growth factor-B expression and platelet-derived growth factor-β receptor phosphorylation as well as other prosclerotic and proinflammatory cytokines. Imatinib treatment prevented the development of atherosclerotic lesions and diabetes-induced inflammatory cytokine overexpression in the aorta. Conclusions—Tyrosine kinase inhibition with imatinib appears to be a novel therapeutic option to retard the development of atherosclerosis, specifically in the context of diabetes.
Inference on Multivariate ARCH Processes with Large Sizes

The covariance matrix is formulated in the framework of a linear multivariate ARCH process with long memory, where the natural cross product structure of the covariance is generalized by adding two linear terms with their respective parameter. The residuals of the linear ARCH process are computed using historical data and the (inverse square root of the) covariance matrix. Simple measure of qualities assessing the independence and unit magnitude of the residual distributions are proposed. The salient properties of the computed residuals are studied for three data sets of size 54, 55 and 330. Both new terms introduced in the covariance help in producing uncorrelated residuals, but the residual magnitudes are very different from unity. The large sizes of the inferred residuals are due to the limited information that can be extracted from the empirical data when the number of time series is large, and denotes a fundamental limitation to the inference that can be achieved.
Social Networks Data Mining Using Visual Analytics

Internet-based social networks are facilities (typically web sites) where people can form online communities, connect to each other and share information. This paper explores the area of applying visual analytics to represent data and underlying relationships in social networks – more specifically, on the Twitter micro-blogging service. Networks of this kind can be treated as graphs, where each node corresponds to a user or a specific piece of information and edges connect such nodes representing relationships. Visualizing graphs is a vast research area in its own right, with numerous applications in science and engineering. In this assignment we are using readily-available software to visualize parts of the network, via filtering or other operations, in order to be able to draw conclusions. Social networks are an excellent candidate to apply visual analytics to, due to their exponential growth when new users join.
The role of fibroblast growth factor receptor 2 (FGFR2) in differentiation of bovine spermatogonial stem cells (SCC)

The receptors 1 and 2 of fibroblast growth factor (FGFR1 and FGFR2, respectively) have been observed in all types of testicular cells. Culture on extracellular matrix (ECM) has been observed to lead to initiation of differentiation in spermatogonial stem cells (SSCs). The present study was carried out to investigate whether FGFR1 and FGFR2 play a role in SSCs differentiation. Following isolation, bovine testicular cells were cultured on ECM-coated or uncoated (control) plates for 12 days. The gene expression of THY1, cKIT, FGFR1 and FGFR2 was evaluated using quantitative real-time polymerase chain reaction (PCR). Results related to the gene expression of markers of with undifferentiated (THY1) and differentiated (cKIT) spermatogonia implicated stimulation of self-renewal and differentiation in cells cultured on ECM-coated and uncoated plates, respectively (p < 0.05). Concomitantly, the expression of FGFR2 increased during culture in the ECM group (p < 0.05), whereas it did not change in the control group (p > 0.05). As a result, the gene expression of FGFR2 was greater in the ECM than control group (p < 0.05). Nevertheless, FGFR1 expression did not change during culture in the control and ECM groups (p > 0.05). In conclusion, the present study revealed the potential role of FGFR2 in differentiation of SSCs during culture on ECM.
No Effect of a Video-Based Awareness Program on the Rate of Soccer Injuries

Background The injury rate in soccer is high, and effective injury prevention methods are needed. Purpose To test the effect of a video-based awareness program on the incidence of acute injuries in soccer. Study Design Randomized control trial; Level of evidence, 1. Methods Participants were elite male soccer players from the top 2 divisions in Iceland. Fifteen of 20 teams completed thestudy: 7 intervention teams (127 players) and 8 control teams (144 players) chosen by random. Just before the start of the 2000soccer season, the intervention teams were visited with an intervention program. The program included a 15-minutepresentation with information on the injury risk of playing elite soccer, typical injuries, and their mechanisms. Then the players workedtogether in pairs and analyzed video sequences to develop preventive strategies. The 12 video sequences were selected fromthe previous Icelandic soccer season, representing 3 typical injury mechanisms that accounted for more than half of all incidentsrecorded. During the season, team physical therapists prospectively recorded all acute injuries, and coaches recorded trainingexposure on a special form. Injury incidence was compared between groups and between the 1999 and 2000 seasons for teamsthat participated in both seasons. Results No difference was observed in injury incidence between the intervention (6.6 ± 0.7 injuries per 1000 player hours) andcontrol groups (6.6 ± 0.7 injuries per 1000 player hours). Furthermore, there was no difference in injury location or type. Conclusion The video-based injury awareness program showed no effect on injury rate.
The need for user models in generating expert system explanation

An explanation facility is an important component of an expert system, but current systems for the most pa r t have neglected the importance of tailoring a system's explanations to the user. This paper explores the role of user modelling in generating expert system explanations, making the claim that individualized user models are essential to produce good explanations when the system users vary in their knowledge of the domain, or in their goals, plans, and preferences. To make this argument, a characterization of explanation, and good explanation is made, leading t o a presentation of how knowledge about the user affects the various aspects of a good explanation. Individualized user models are not only important, it is practical to obtain them. A method for acquiring a model of the user's beliefs implicitly by 'eavesdropping' on the interaction between user and system is presented, along with examples of how this information can be used to tailor an explanation.
Higher type adjunction inequalities for Donaldson invariants.

We prove new adjunction inequalities for embedded surfaces in four-manifolds with non-negative self-intersection number using the Donaldson invariants. These formulas are completely analogous to the ones obtained by Ozsvath and Szabo using the Seiberg-Witten invariants. To prove these relations, we give a fairly explicit description of the structure of the Fukaya-Floer homology of a surface times a circle. As an aside, we also relate the Floer homology of a surface times a circle with the cohomology of some symmetric products of the surface.
Low-Complexity Reduced-Rank Beamforming Algorithms

A reduced-rank framework with set-membership filtering (SMF) techniques is presented for adaptive beamforming problems encountered in radar systems. We develop and analyze stochastic gradient (SG) and recursive least squares (RLS)-type adaptive algorithms, which achieve an enhanced convergence and tracking performance with low computational cost as compared to existing techniques. Simulations show that the proposed algorithms have a superior performance to prior methods, while the complexity is lower.
Fermented dairy food and cardiovascular disease risk

Fermented dairy foods such as yoghurt and cheese are commonly found in the Mediterranean diet. Recent landmark research has confirmed the effect of the Mediterranean diet on reducing the CVD risk, but the relative contributions of fermented dairy foods have not been fully articulated. The present study provides a review of the relationship between fermented dairy foods consumption and CVD risk in the context of the whole diet. Studies show that people who eat healthier diets may be more likely to consume yoghurt, so there is a challenge in attributing separate effects to yoghurt. Analyses from large population studies list yoghurt as the food most negatively associated with the risk of weight gain (a problem that may lead to CVD). There is some suggestion that fermented dairy foods consumption (yoghurt or cheese) may be associated with reduced inflammatory biomarkers associated with the development of CVD. Dietary trials suggest that cheese may not have the same effect on raising LDL-cholesterol levels as butter with the same saturated fat content. The same might be stated for yoghurt. The use of different probiotic cultures and other aspects of study design remain a problem for research. Nevertheless, population studies from a range of countries have shown that a reduced risk of CVD occurs with the consumption of fermented dairy foods. A combination of evidence is necessary, and more research is always valuable, but indications remain that fermented dairy foods such as cheese and yoghurt are integral to diets that are protective against CVD. Disciplines Medicine and Health Sciences | Social and Behavioral Sciences Publication Details Tapsell, L. C. (2015). Fermented dairy food and CVD risk. The British Journal of Nutrition: an international journal of nutritional science, 113 (Suppl. S2), s131-s135. This journal article is available at Research Online: http://ro.uow. edu.au/smhpapers/2896
Design of Automatic Meteorological Data Acquisition System Based on ARM and CAN Bus

Aimed at the current situation that the domestic automatic meteorological data acquisition system is almost based the use of foreign products, a design method of multi-channel meteorological data acquisition system was given which based on ARM and CAN Bus. In the design, it fulfills the acquisition requirements of the analog signals, digital signals and intelligent sensor data through a combination of hardware and software technologies. In order to improve system’s real-time answering capability and multi-task processing capability, it is used “main collector + external bus + sub-collector + sensors + peripheral equipment” in structure design of hardware. At the same time, it is transplanted Linux operating system to improve the reliability and scalability of system. It is translated Linux operating system to embedded processor, and making use of Internet to send meteorological data in Linux operating system. Then the complicated cabling project could be omitted, the data were sent without PC, and in favor of constituting Large-scale meteorological monitoring network
Tumor-Derived Autophagosome Vaccine: Mechanism of Cross-Presentation and Therapeutic Efficacy

Purpose: We previously reported that autophagy in tumor cells plays a critical role in cross-presentation of tumor antigens and that autophagosomes are efficient antigen carriers for cross-priming of tumor-reactive CD8+ T cells. Here, we sought to characterize further the autophagosome-enriched vaccine named DRibble (DRiPs-containing blebs), which is derived from tumor cells after inhibition of protein degradation, and to provide insights into the mechanisms responsible for their efficacy as a novel cancer immunotherapy. Experimental Design: DRibbles were characterized by Western blot and light or transmission electron microscopy. The efficiency of cross-presentation mediated by DRibbles was first compared with that of whole-tumor cells and pure proteins. The mechanisms of antigen cross-presentation by DRibbles were analyzed, and the antitumor efficacy of the DRibble vaccine was tested in 3LL Lewis lung tumors and B16F10 melanoma. Results: The DRibbles sequester both long-lived and short-lived proteins, including defective ribosomal products (DRiP), and damage-associated molecular pattern molecules exemplified by HSP90, HSP94, calreticulin, and HMGB1. DRibbles express ligands for CLEC9A, a newly described C-type lectin receptor expressed by a subset of conventional and plasmacytoid dendritic cells (DC), and cross-presentation was partially CLEC9A dependent. Furthermore, this autophagy-assisted antigen cross-presentation pathway involved both caveolae- and clathrin-mediated endocytosis and endoplasmic reticulum–associated degradation machinery. It depends on proteasome and TAP1, but not lysosome functions of antigen-presenting cells. Importantly, DCs loaded with autophagosome-enriched DRibbles can eradicate 3LL Lewis lung tumors and significantly delay the growth of B16F10 melanoma. Conclusions: These data documented the unique characteristics and potent antitumor efficacy of the autophagosome-based DRibble vaccine. The efficacy of DRibble cancer vaccine will be further tested in clinical trials. Clin Cancer Res; 17(22); 7047–57. ©2011 AACR.
Design and Development of a Programmable Meta Search Engine

To the web user, a Meta Search Engine (MSE) appears much like a regular search engine (SE). MSE, unlike an SE does not have an index. Instead, it dynamically queries multiple search engines; extracts, fuses and re-ranks results and presents to users. Generally, an MSE is developed from scratch even if the focus is on improving fusion ranking, query modification or domain specific search. This paper proposes a programmable MSE with the help of a LISP-like language called T! for interfacing search sources and for modifying fused results. This enables easy construction and deployment of an MSE service. The Programmable-Meta Search Engine (P-MSE) provides, but is not limited to the following new features: construction of a domain specific vertical or general MSE by addition of dynamic web pages as front-end; a tool for fully automated test-run of various fusion algorithms and query modification schemes using a program or script capable of http-querying as front-end on real-time web; a programmable service where account holders can upload scripts and deploy meta search engines. The concept of P-MSE developed here, is showcased by the MSE called SSIR ( S SIR for the S avvy I nformation R etriever).
Framework for the characterization of hotel websites

Nowadays the importance of websites to the tourism and hospitality industries is fundamental. Hotels, for instance, spend a huge amount of money improving their websites to show all the activities and amenities that they can provide. There are studies to evaluate website performance based on functionality, usability and other factors; nevertheless, they are not exhaustive. This paper presents a framework for the characterization of hotel and resort websites, that was applied as a case study to the websites of 5-star hotels and resorts that operate in the tourism region of the Algarve, Portugal. This framework allows us to identify a set of features for the hotel and resort websites characterization. From these features, we propose a set of comprehensive indicators, grouping them into ten fundamental information dimensions, as well as the application of these indicators and information dimensions, which allows obtaining quantitative and qualitative results.
Structure-and-motion pipeline on a hierarchical cluster tree

This papers introduces a novel hierarchical scheme for computing Structure and Motion. The images are organized into a tree with agglomerative clustering, using a measure of overlap as the distance. The reconstruction follows this tree from the leaves to the root. As a result, the problem is broken into smaller instances, which are then separately solved and combined. Compared to the standard sequential approach, this framework has a lower computational complexity, it is independent from the initial pair of views, and copes better with drift problems. A formal complexity analysis and some experimental results support these claims.
All Silicon Data Center, the Energy Perspectives

The energy consumption related to data centers is ever increasing, despite the significant efficiency improvements in the involved technologies and the economic crisis. Pervasive adoption of virtualization, decreasing of PUE as well as new features related to energy-efficiency are not able to stop this growth trend, mainly sustained from the explosion of cloud services in both the fixed and mobile ICT markets. One of the most important factors that contributes to the increase in the data center energy demand is the evolution of data utilization in cloud environments. Big data support is one of the main driver of this process, new data sources continuously produce huge amounts of mostly unstructured data, that should be stored in large centralized storage systems to be accessed by the cloud users and analyzed by the companies in real time. This has a disruptive effect for the energy consumption of the data center hosting the above storage resources, that's why the data need to be stored and analyzed in IOPS intensive style. Flash memory technologies can play a key role in such scenario, since they can reduce dramatically both the storage footprint and energy consumption and increase applications performances bringing appreciable economic benefits. This fundamental efficiency and performance improvement for storage architectures can't be supported by legacy technologies because they are not designed to use flash technologies but rather they are based on energy-hungry legacy mechanical disks. That is limit the energy efficiency and performance delivered by solid state disks (SSD) installed in legacy storage systems, opening the door to the development of new technologies that will be able to fully exploit the potential of flash disks. The aim of this work is presenting a brief survey about the potential of flash technologies for improving the energy efficiency of data center storage systems supporting the incoming Big Data services.
Mefloquine—An Aminoalcohol with Promising Antischistosomal Properties in Mice

Background The treatment and control of schistosomiasis, an often neglected tropical disease that exacerbates poverty, depends on a single drug, praziquantel. The large-scale use of praziquantel might select for drug-resistant parasites, hence there is a need to develop new antischistosomal compounds. Here, we report that the antimalarial drug mefloquine possesses promising antischistosomal properties in mice. Methodology/Principal Findings A single dose of mefloquine (200 or 400 mg/kg) administered orally to mice infected with adult Schistosoma mansoni or adult S. japonicum resulted in high or complete total and female worm burden reductions (72.3%–100%). Importantly, high worm burden reductions were also observed for young developing stages of S. mansoni and S. japonicum harbored in the mouse. Both mefloquine erythro-enantiomers resulted in high and comparable total and female worm burden reductions when given to mice with either a sub-patent or patent S. mansoni infection. Conclusions/Significance Our findings hold promise for the development of a novel antischistosomal drug based on an aminoalcohol functionality. Further in vitro and in vivo studies have been launched to elucidate the possible mechanism of action and to study the effect of mefloquine on S. haematobium and other trematodes. It will be interesting to investigate whether mefloquine, which is widely and effectively used for the treatment of malaria, has an impact on schistosomiasis in areas where both malaria and schistosomiasis co-exist.
A Downlink Max-SINR Precoding for Massive MIMO System

To acquire the maximal array gain and mitigate the impact of pilot contamination, the downlink precoding algorithm on Max-SINR criterion was investigated and improved for Massive MIMO system. The objective function assured to maximize the utilization rate of the transmission power under the condition that SINR is not lower than the desired threshold. The Lagrangian function was deduced according to the objective function. Further SINR computation counted the channel estimation error caused by pilot contamination and its computational complexity was reduced by utilizing the character of Massive MIMO channel. At last the optimal downlink precoding matrix was obtained by KKT conditions. When base station configured 100 antennas and the pilot contamination was severe, numerical results proved that the spectrum efficiency of the proposed algorithm was 1.9 times higher than the popular Massive MIMO precoding --- MF algorithm. The proposed algorithm can effectively mitigate the impact of pilot contamination and achieve high throughput with maximizing gain, and is valuable to Massive MIMO system.