Miracle-dz/UniFAR-FTUs huggingface dataset:
A Systematic Review of In vitro and In vivo Activities of Anti-Toxoplasma Drugs and Compounds (2006–2016)

The currently available anti-Toxoplasma agents have serious limitations. This systematic review was performed to evaluate drugs and new compounds used for the treatment of toxoplasmosis. Data was systematically collected from published papers on the efficacy of drugs/compounds used against Toxoplasma gondii (T. gondii) globally during 2006–2016. The searched databases were PubMed, Google Scholar, Science Direct, ISI Web of Science, EBSCO, and Scopus. One hundred and eighteen papers were eligible for inclusion in this systematic review, which were both in vitro and in vivo studies. Within this review, 80 clinically available drugs and a large number of new compounds with more than 39 mechanisms of action were evaluated. Interestingly, many of the drugs/compounds evaluated against T. gondii act on the apicoplast. Therefore, the apicoplast represents as a potential drug target for new chemotherapy. Based on the current findings, 49 drugs/compounds demonstrated in vitro half-maximal inhibitory concentration (IC50) values of below 1 μM, but most of them were not evaluated further for in vivo effectiveness. However, the derivatives of the ciprofloxacin, endochin-like quinolones and 1-[4-(4-nitrophenoxy) phenyl] propane-1-one (NPPP) were significantly active against T. gondii tachyzoites both in vitro and in vivo. Thus, these compounds are promising candidates for future studies. Also, compound 32 (T. gondii calcium-dependent protein kinase 1 inhibitor), endochin-like quinolones, miltefosine, rolipram abolish, and guanabenz can be repurposed into an effective anti-parasitic with a unique ability to reduce brain tissue cysts (88.7, 88, 78, 74, and 69%, respectively). Additionally, no promising drugs are available for congenital toxoplasmosis. In conclusion, as current chemotherapy against toxoplasmosis is still not satisfactory, development of well-tolerated and safe specific immunoprophylaxis in relaxing the need of dependence on chemotherapeutics is a highly valuable goal for global disease control. However, with the increasing number of high-risk individuals, and absence of a proper vaccine, continued efforts are necessary for the development of novel treatment options against T. gondii. Some of the novel compounds reviewed here may represent good starting points for the discovery of effective new drugs. In further, bioinformatic and in silico studies are needed in order to identify new potential toxoplasmicidal drugs.
Object recognition from 3D blurred images

This paper presents a novel approach for 3D object recognition and classification. The originality of this approach is the combination of statistical reasoning, feature learning and expertise knowledge from the application. It is based on 2D processing of images alternating with 3D validation of class characteristics for recognition. Classification is based on iterative refinement of hypotheses. An application is presented for pollen grain observed with light microscopy for allergy prevention.
Broad activation of the ubiquitin–proteasome system by Parkin is critical for mitophagy

Parkin, an E3 ubiquitin ligase implicated in Parkinson's disease, promotes degradation of dysfunctional mitochondria by autophagy. Using proteomic and cellular approaches, we show that upon translocation to mitochondria, Parkin activates the ubiquitin–proteasome system (UPS) for widespread degradation of outer membrane proteins. This is evidenced by an increase in K48-linked polyubiquitin on mitochondria, recruitment of the 26S proteasome and rapid degradation of multiple outer membrane proteins. The degradation of proteins by the UPS occurs independently of the autophagy pathway, and inhibition of the 26S proteasome completely abrogates Parkin-mediated mitophagy in HeLa, SH-SY5Y and mouse cells. Although the mitofusins Mfn1 and Mfn2 are rapid degradation targets of Parkin, we find that degradation of additional targets is essential for mitophagy. These results indicate that remodeling of the mitochondrial outer membrane proteome is important for mitophagy, and reveal a causal link between the UPS and autophagy, the major pathways for degradation of intracellular substrates.
Towards image retrieval for eight percent of color-blind men

About 8% of men (but not women) are suffering from color blindness. The objective of this work was to investigate the problem of image retrieval based on color cooccurrence features when comparing normal vision and three kinds of color blindness (dichromasia): protanopia, deuteranopia, and tritanopia. Original database comprises 12000 images that were also converted into three dichromatic versions using the Vischeck simulation tool. Results of 48000 queries were used to study influence of color blindness on retrieval results. Principal component analysis, multidimensional scaling, hierarchical clustering, support vector machines, and statistical methods were employed for investigating feature space distortions associated with color blindness.
The price of truthfulness for pay-per-click auctions

We analyze the problem of designing a truthful pay-per-click auction where the click-through-rates (CTR) of the bidders are unknown to the auction. Such an auction faces the classic explore/exploit dilemma: while gathering information about the click through rates of advertisers, the mechanism may loose revenue; however, this gleaned information may prove valuable in the future for a more profitable allocation. In this sense, such mechanisms are prime candidates to be designed using multi-armed bandit techniques. However, a naive application of multi-armed bandit algorithms would not take into account the strategic considerations of the players -- players might manipulate their bids (which determine the auction's revenue) in a way as to maximize their own utility. Hence, we consider the natural restriction that the auction be truthful. The revenue that we could hope to achieve is the expected revenue of a Vickrey auction that knows the true CTRs, and we define the truthful regret to be the difference between the expected revenue of the auction and this Vickrey revenue. This work sharply characterizes what regret is achievable, under a truthful restriction. We show that this truthful restriction imposes statistical limits on the achievable regret -- the achievable regret is Θ(T2/3), while for traditional bandit algorithms (without the truthful restriction) the achievable regret is Θ(T1/2) (where T is the number of rounds). We term the extra T1/6 factor, the `price of truthfulness'.
Gene activation, apolipoprotein A-I/high density lipoprotein, atherosclerosis prevention and longevity.

Recent studies in man and human apolipoprotein A-I transgenic animals emphasize the significance of apolipoprotein A-I and high density lipoprotein in antiatherogenesis. Several drugs and other compounds, e.g. phenobarbital, gemfibrozil, fenofibrate, prednisone, estrogen and alcohol, induce apolipoprotein A-I synthesis. They commonly produce serum lipoprotein patterns typical of a low risk of coronary heart disease, and many of them have been found to prevent atherogenesis, reduce coronary heart disease mortality and increase survival. These compounds act against atherosclerosis by using one or several mechanisms that include overexpression of the apolipoprotein A-I gene with an increase in serum apolipoprotein A-I and high density lipoprotein and promotion of reverse cholesterol transport, upregulation of the low density lipoprotein receptor gene with a decrease in serum apolipoprotein B and low density lipoprotein, maintenance of endothelial cell function and protection against thrombosis. They have been found to raise high density lipoprotein cholesterol and apolipoprotein A-I together with a decrease in cholesterol ester transfer protein activity, and to induce hepatic cholesterol 7 alpha-hydroxylase and cholesterol and bile acid elimination from the body. By raising the activities of apolipoprotein A-I/high density lipoprotein-associated paraoxonase and other antioxidative enzymes, the inducers have the capacity to prevent atherogenesis in arterial walls through inhibition of the oxidative modification of low density lipoprotein. Other antiatherogenic vascular actions of high density lipoprotein include interference with low density lipoprotein aggregation and uptake by endothelial cells, and competition with low density lipoprotein for endothelial-localized low density lipoprotein receptors. Apolipoprotein A-I/high density lipoprotein beneficially enhances fibrinolysis, decreases platelet aggregation, increases prostacyclin production and stabilization and prevents atherogenic immune and inflammatory responses. This gene activation or microsomal induction can prevent atherosclerosis and is a basis for tailoring effective new agents and optimal non-invasive therapy against atherosclerotic vascular disease to promote health and enhance longevity.
Olfactory neurons express a unique glycosylated form of the neural cell adhesion molecule (N-CAM)

mAb-based approaches were used to identify cell surface components involved in the development and function of the frog olfactory system. We describe here a 205-kD cell surface glycoprotein on olfactory receptor neurons that was detected with three mAbs: 9-OE, 5-OE, and 13- OE. mAb 9-OE immunoreactivity, unlike mAbs 5-OE and 13-OE, was restricted to only the axons and terminations of the primary sensory olfactory neurons in the frog nervous system. The 9-OE polypeptide(s) were immunoprecipitated and tested for cross-reactivity with known neural cell surface components including HNK-1, the cell adhesion molecule L1, and the neural cell adhesion molecule (N-CAM). These experiments revealed that 9-OE-reactive molecules were not L1 related but were a subset of the 200-kD isoforms of N-CAM. mAb 9-OE recognized epitopes associated with N-linked carbohydrate residues that were distinct from the polysialic acid chains present on the embryonic form of N-CAM. Moreover, 9-OE N-CAM was a heterogeneous population consisting of subsets both with and without the HNK-1 epitope. Thus, combined immunohistochemical and immunoprecipitation experiments have revealed a new glycosylated form of N-CAM unique to the olfactory system. The restricted spatial expression pattern of this N-CAM glycoform suggests a possible role in the unusual regenerative properties of this sensory system.
Sensitivity analysis of blind separation of speech mixtures

Author: Savaskan Bulek Title: Sensitivity Analysis of Blind Separation of Speech Mixtures Institution: Florida Atlantic University Dissertation Advisor: Dr. Nurgun Erdol Degree: Doctor of Philosophy Year: 2010 Blind source separation (BSS) refers to a class of methods by which multiple sensor signals are combined with the aim of estimating the original source signals. Independent component analysis (ICA) is one such method that effectively resolves static linear combinations of independent non-Gaussian distributions. We propose a method that can track variations in the mixing system by seeking a compromise between adaptive and block methods by using mini-batches. The resulting permutation indeterminacy is resolved based on the correlation continuity principle. Methods employing higher order cumulants in the separation criterion are susceptible to outliers in the finite sample case. We propose a robust method based on low-order non-integer moments by exploiting the Laplacian model of speech signals. We study separation methods for even (over)-determined linear convolutive mixtures in the frequency domain based on joint diagonalization of matrices employing time-varying second order statistics. We investigate the sources affecting the sensitivity of the solution under the finite sample case such as the set size, overlap
Fatty acid production in genetically modified cyanobacteria

To avoid costly biomass recovery in photosynthetic microbial biofuel production, we genetically modified cyanobacteria to produce and secrete fatty acids. Starting with introducing an acyl–acyl carrier protein thioesterase gene, we made six successive generations of genetic modifications of cyanobacterium Synechocystis sp. PCC6803 wild type (SD100). The fatty acid secretion yield was increased to 197 ± 14 mg/L of culture in one improved strain at a cell density of 1.0 × 109 cells/mL by adding codon-optimized thioesterase genes and weakening polar cell wall layers. Although these strains exhibited damaged cell membranes at low cell densities, they grew more rapidly at high cell densities in late exponential and stationary phase and exhibited less cell damage than cells in wild-type cultures. Our results suggest that fatty acid secreting cyanobacteria are a promising technology for renewable biofuel production.
Assessment the Photo-neutron Contamination of IMRT and 3D-Conformal Techniques Using Thermo-luminescent Dosimeter (TLD)

The aim of the study is to evaluate the dependence of photo-neutron production on field size, depth in phantom and distance from isocenter and also to calculate the equivalent neutron doses for PTV and OARs of IMRT and 3DCRT techniques using TLD (600/700). The Linac Siemens Oncor installed at Nasser Institute, Cairo, Egypt. TLDs, Neutron Monitor, Ionization chamber were provided by NIS, the duration of the study was from November 2017 to July 2018. 5 prostate cancer cases were selected treated with high energy beam (15MV) Linear accelerator using 3DCRT and IMRT treatment plans. The OARs were bladder, rectum and femur. Once the plans were completed, there were copied from the planning system onto the RW3 slab phantom in which pairs of TLD chips (600/700) were placed at the exact site of PTV and OARs. The results showed that: The measured photo-neutron decreases from 0.2 mSv/Gy to 0.09 mSv/Gy as increases field sizes from 2x2 cm2 to 20x20 cm2. The measured photo-neutron was maximum at dmax =0.15 mSv/Gy and decreases gradually as increases the depth in phantom reaches to 0.07 mSv/Gy at 10cm depth in phantom. The measured photo-neutron decreases from 1.5 mSv/Gy to 0.02 mSv/Gy when measured at isocenter and at 100cm along the patient couch. Using 3DCRT for PTV and OARs were ranging from 0.027 to 0.39 mSv per photon Gy and for IMRT were 0.135 to 2.34 mSv per photon Gy. In conclusion the photo-neutron production is decreases as increases field size and distance from isocenter along patient couch while increases with depth in phantom up to dmax and decreases gradually as increases depth in phantom. IMRT requires longer beam-on time than 3DCRT leading to worse OARs sparing and increase the production of photo-neutrons than 3DCRT.
Power Semiconductor Trends in Electric Drive Systems

Nowadays lots of big brands (like Tesla, Nissan, Audi etc.) deal with electric cars and electric drive systems. The first brand deals with only electric drive systems and everyone know this name. These cars are more environmentally friendly, because those operate only with electric energy (this article does not deal with the source of electric energy). The design of electric drive systems is very difficult and complicated task: the electric, thermal and mechanical parameters are very important during the design process. The task is given: it must be designed to reach the most efficient drive system with a low cost. This article deals with the current semiconductor trends and properties, investigates the current electric car drive systems (semiconductor design perspective) and deals with the future trends.
Environment, lifestyle and male infertility.

Our understanding of the importance of environmental and lifestyle factors on sperm count and fertility is constrained by the extreme variation in sperm count between men and between ejaculates. The factors responsible for this variation provide a key to understanding what factors actually affect the sperm count. The relative importance of the various factors and the pathways via which they affect sperm count are discussed. The most important are Sertoli cell number, ejaculatory frequency, season, factors affecting scrotal heating (e.g. the time spent seated), a past history of reproductive tract disorders and ageing. The possible role of other environmental factors commonly supposed to affect sperm count (exposure to pesticides or endocrine disruptors) is discussed, although the evidence for a major influence of such factors is lacking. It is suggested that lifestyle changes, especially in the time spent seated, will exert an adverse effect on sperm production in a progressively larger group of men over the next decade.
The inhibitory microcircuit of the substantia nigra provides feedback gain control of the basal ganglia output

Dysfunction of the basal ganglia produces severe deficits in the timing, initiation, and vigor of movement. These diverse impairments suggest a control system gone awry. In engineered systems, feedback is critical for control. By contrast, models of the basal ganglia highlight feedforward circuitry and ignore intrinsic feedback circuits. In this study, we show that feedback via axon collaterals of substantia nigra projection neurons control the gain of the basal ganglia output. Through a combination of physiology, optogenetics, anatomy, and circuit mapping, we elaborate a general circuit mechanism for gain control in a microcircuit lacking interneurons. Our data suggest that diverse tonic firing rates, weak unitary connections and a spatially diffuse collateral circuit with distinct topography and kinetics from feedforward input is sufficient to implement divisive feedback inhibition. The importance of feedback for engineered systems implies that the intranigral microcircuit, despite its absence from canonical models, could be essential to basal ganglia function. DOI: http://dx.doi. org/10.7554/eLife.02397. 001
Analysis of Computational Time of Simple Estimation of Distribution Algorithms

Estimation of distribution algorithms (EDAs) are widely used in stochastic optimization. Impressive experimental results have been reported in the literature. However, little work has been done on analyzing the computation time of EDAs in relation to the problem size. It is still unclear how well EDAs (with a finite population size larger than two) will scale up when the dimension of the optimization problem (problem size) goes up. This paper studies the computational time complexity of a simple EDA, i.e., the univariate marginal distribution algorithm (UMDA), in order to gain more insight into EDAs complexity. First, we discuss how to measure the computational time complexity of EDAs. A classification of problem hardness based on our discussions is then given. Second, we prove a theorem related to problem hardness and the probability conditions of EDAs. Third, we propose a novel approach to analyzing the computational time complexity of UMDA using discrete dynamic systems and Chernoff bounds. Following this approach, we are able to derive a number of results on the first hitting time of UMDA on a well-known unimodal pseudo-boolean function, i.e., the LeadingOnes problem, and another problem derived from LeadingOnes, named BVLeadingOnes. Although both problems are unimodal, our analysis shows that LeadingOnes is easy for the UMDA, while BVLeadingOnes is hard for the UMDA. Finally, in order to address the key issue of what problem characteristics make a problem hard for UMDA, we discuss in depth the idea of ¿margins¿ (or relaxation). We prove theoretically that the UMDA with margins can solve the BVLeadingOnes problem efficiently.
Combining Language Model with Sentiment Analysis for Opinion Retrieval of Blog-Post

This paper describes our participation in Blog Opinion Retrieval task this year. We conduct experiments on “FirteX” platform that is developed by our lab. Language Model is used to retrieve related blog unit. Interactive Knowledge is adopted to expand query for retrieve blog unit include opinion. Then we introduce a novel extracting technology to extract text from retrieved blog-post. Finally, Lexicon based method is used to rerank the document by opinion.
CAPSim: simulation and code generation based on the CAPS

Situational Aware (SiA) Cyber-Physical Systems (CPS) harmoniously integrate computational and physical parts for being aware of what is happening in the surroundings, and utilizing this data to decide and act accordingly. In this tool demo, we present our architecture-driven simulating tool named CAPSim. This tool enables cyber-physical systems designers and architects to simulate the software architecture, hardware conffiguration, and physical space views for a situational aware CPS, for being able to evaluate the energy consumption and data traffic under different conditions.
Towards a Better Approximation for Sparsest Cut?

We give a new (1 + ε)-approximation for SPARSEST CUT problem on graphs where small sets expand significantly more than the sparsest cut (expansion of sets of size n/r exceeds that of the sparsest cut by a factor √log n log r, for some small r; this condition holds for many natural graph families). We give two different algorithms. One involves Guruswami-Sinop rounding on the level-r Lasserre relaxation. The other is combinatorial and involves a new notion called Small Set Expander Flows (inspired by the expander flows of [1]) which we show exists in the input graph. Both algorithms run in time 2O(r)poly(n). We also show similar approximation algorithms in graphs with genus g with an analogous local expansion condition. This is the first algorithm we know of that achieves (1 + ε)-approximation on such general family of graphs.
Methods of the International Tobacco Control (ITC) Four Country Survey

This paper outlines the design features, data collection methods and analytic strategies of the International Tobacco Control (ITC) Four Country Survey, a prospective study of more than 2000 longitudinal respondents per country with yearly replenishments. This survey possesses unique features that sets it apart among surveys on tobacco use and cessation. One of these features is the use of theory-driven conceptual models. In this paper, however, the focus is on the two key statistical features of the survey: longitudinal and “quasi-experimental” designs. Although it is often possible to address the same scientific questions with a cross-sectional or a longitudinal study, the latter has the major advantage of being able to distinguish changes over time within individuals from differences among people at baseline (that is, differences between age and cohort effects). Furthermore, quasi-experiments, where countries not implementing a given new tobacco control policy act as the control group to which the country implementing such a policy will be compared, provide much stronger evidence than observational studies on the effects of national-level tobacco control policies. In summary, application of rigorous research methods enables this survey to be a rich data resource, not only to evaluate policies, but also to gain new insights into the natural history of smoking cessation, through longitudinal analyses of smoker behaviour.