Miracle-dz/UniFAR-FTUs huggingface dataset:
Development of a Simple Assay Protocol for High-Throughput Screening of Mycobacterium tuberculosis Glutamine Synthetase for the Identification of Novel Inhibitors

Mycobacterium tuberculosis glutamine synthetase (GS) is an essential enzyme involved in the pathogenicity of the organism. The screening of a compound library using a robust high-throughput screening (HTS) assay is currently thought to be the most efficient way of getting lead molecules, which are potent inhibitors for this enzyme. The authors have purified the enzyme to a >90% level from the recombinant Escherichia coli strain YMC21E, and it was used for partial characterization as well as standardization experiments. The results indicated that the Kmof the enzyme for L-glutamine and hydroxylamine were 60 mM and 8.3 mM, respectively. The Km for ADP, arsenate, and Mn2+ were 2 [. proportional]M, 5 [. proportional]M, and 25 [. proportional]M, respectively. When the components were adjusted according to their Km values, the activity remained constant for at least 3 h at both 25° C and 37° C. The Z′ factor determined in microplate format indicated robustness of the assay. When the signal/noise ratios were determined for different assay volumes, it was observed that the 200-[. proportional]l volume was found to be optimum. The DMSO tolerance of the enzyme was checked up to 10%, with minimal inhibition. The IC50 value determined for L-methionine S-sulfoximine on the enzyme activity was 3 mM. Approximately 18,000 small molecules could be screened per day using this protocol by a Beckman Coulter HTS setup.
Toxicology and human health assessment of decabromodiphenyl ether

We evaluated the available pharmacokinetic data and human and animal toxicity data for 2,2′,3,3′,4,4′,5,5′,6,6′-decabromodiphenyl ether (BDE-209) (CASRN 1163-19-5) with the objective of deriving a reference dose (RfD) based on the best available science. The available studies for deriving an RfD were first screened using the Klimisch criteria and further evaluated using the United States Environmental Protection Agency’s general assessment factors for data quality and relevance (i.e., soundness, applicability and utility, clarity and completeness, uncertainty and variability, and evaluation and review). The chronic 2-year dietary feeding study conducted by the United States National Toxicology Program (, Technical Report Series No. 309) was selected for RfD derivation. Hepatocellular degeneration in male rats was chosen as the critical endpoint in the development of an RfD. For dose-response characterization, we applied benchmark-dose modeling to animal data and determined a point of departure (the 95% lower confidence limit for a 10% increase in hepatocellular degeneration) of 419 mg/kg-day for oral exposures. Based on the similar pharmacokinetic characteristics of BDE-209 across species, this value was converted to a human equivalence dose of 113 mg/kg-day by applying a dosimetric adjustment factor based on body weight scaling to the ¾ power. An oral RfD of 4 mg/kg-day was calculated by using a composite uncertainty factor of 30, which consisted of 10 for intraspecies uncertainty, 3 for interspecies uncertainty (i.e., 3 for toxicodynamics × 1 for toxicokinetics), and 1 for deficiencies with the database. We consider the RfD to be adequately protective of sensitive subpopulations, including women, their fetuses, children, and people with hepatocellular diseases.
An Evaluation of the Google Chrome Extension Security Architecture

Vulnerabilities in browser extensions put users at risk by providing a way for website and network attackers to gain access to users' private data and credentials. Extensions can also introduce vulnerabilities into the websites that they modify. In 2009, Google Chrome introduced a new extension platform with several features intended to prevent and mitigate extension vulnerabilities: strong isolation between websites and extensions, privilege separation within an extension, and an extension permission system. We performed a security review of 100 Chrome extensions and found 70 vulnerabilities across 40 extensions. Given these vulnerabilities, we evaluate how well each of the security mechanisms defends against extension vulnerabilities. We find that the mechanisms mostly succeed at preventing direct web attacks on extensions, but new security mechanisms are needed to protect users from network attacks on extensions, website metadata attacks on extensions, and vulnerabilities that extensions add to websites. We propose and evaluate additional defenses, and we conclude that banning HTTP scripts and inline scripts would prevent 47 of the 50 most severe vulnerabilities with only modest impact on developers.
Circulating microRNA Profiling Needs Further Refinement Before Clinical Use in Patients With Aortic Stenosis

Background Aortic stenosis (AS) is a progressive condition leading to heart failure and death without treatment. No medical therapy currently exists for AS, and a major management challenge is deciding on the correct timing of aortic valve replacement. MicroRNAs (miRNAs) are short noncoding RNAs that are stable in the circulation. We wished to use miRNAs as biomarkers of disease in AS. Methods and Results We performed microarray-based whole miRNome profiling of 24 participants with AS and 27 control participants. After adjustment for age and multiple testing, we identified 4 miRNAs significantly different between groups. These findings were then examined using quantitative polymerase chain reaction in a larger validation cohort of 101 controls and 94 participants with AS, stratified in a prespecified analysis by presence of coexisting coronary artery disease (CAD). We obtained mixed results for miR-22-3p, miR-24-3p, miR-382-5p, and miR-451a in the validation cohort, with differing associations according to CAD status. miR-21-5p was increased in AS patients without CAD, but there was no difference between groups with CAD. Conclusion Despite holding great promise, circulating miRNA profiling requires further refinement before translation into clinical use as a biomarker in aortic stenosis.
STUDY OF THE STATUS OF TUBERCULOSIS CONTROL PROGRAM BASED ON THE IMPLEMENTATION OF THE DIRECTLY OBSERVED TREATMENT SHORT-COURSE STRATEGY (DOTS)

Introduction: Ascendant trend of tuberculosis in the world introduces this disease to be one of the most important infectious diseases in the world. So that every year, 9 million people are afflicted to active TB and about 5.1 million people die of the disease. As the HIV contaminated cases are increased, emergence and spread field of Multidrug-resistant tuberculosis (MDR-TB) bacilli has been provided. Objective: This study aimed to assess the Tuberculosis Control Program from 2005 to 2012 to determine the overall situation of disease epidemiology and prioritized strategies in disease control program within the south of Tehran. Materials and Methods: This cross-sectional study was extracted and analyzed retrospectively on the basis of records of all TB patients in TB health center and TB software in south Tehran in 2005-2012 years. Results: From the total population under protection of health center of south Tehran, 99% are urban and 1% are rural. During 2005-2012, 1242 TB cases have been registered and they were treated by DOTS method. There were 553 cases of new smear-positive pulmonary TB (44%), 222 cases of smear-negative pulmonary TB (18%) and 336 cases of extra-pulmonary tuberculosis (27%), 26 cases of recurrence (2%) and 11 cases of MDR (0.9%). Smear-positive pulmonary tuberculosis has included 67.4% of all tuberculosis patients. Conclusions: The results showed that, in accordance with TB worldwide statistics, at the health center of south Tehran, pulmonary TB is the most common form of the disease (67.4%). The incidence of smear-positive tuberculosis and all forms of TB cases has been an ascending trend over the period between 2005 and 2012.
Evasion of the Immune Response by Trypanosoma cruzi during Acute Infection

Trypanosoma cruzi is the etiologic agent of Chagas disease, a neglected tropical disease that affects millions of people mainly in Latin America. To establish a life-long infection, T. cruzi must subvert the vertebrate host’s immune system, using strategies that can be traced to the parasite’s life cycle. Once inside the vertebrate host, metacyclic trypomastigotes rapidly invade a wide variety of nucleated host cells in a membrane-bound compartment known as the parasitophorous vacuole, which fuses to lysosomes, originating the phagolysosome. In this compartment, the parasite relies on a complex network of antioxidant enzymes to shield itself from lysosomal oxygen and nitrogen reactive species. Lysosomal acidification of the parasitophorous vacuole is an important factor that allows trypomastigote escape from the extremely oxidative environment of the phagolysosome to the cytoplasm, where it differentiates into amastigote forms. In the cytosol of infected macrophages, oxidative stress instead of being detrimental to the parasite, favors amastigote burden, which then differentiates into bloodstream trypomastigotes. Trypomastigotes released in the bloodstream upon the rupture of the host cell membrane express surface molecules, such as calreticulin and GP160 proteins, which disrupt initial and key components of the complement pathway, while others such as glycosylphosphatidylinositol-mucins stimulate immunoregulatory receptors, delaying the progression of a protective immune response. After an immunologically silent entry at the early phase of infection, T. cruzi elicits polyclonal B cell activation, hypergammaglobulinemia, and unspecific anti-T. cruzi antibodies, which are inefficient in controlling the infection. Additionally, the coexpression of several related, but not identical, epitopes derived from trypomastigote surface proteins delays the generation of T. cruzi-specific neutralizing antibodies. Later in the infection, the establishment of an anti-T. cruzi CD8+ immune response focused on the parasite’s immunodominant epitopes controls parasitemia and tissue infection, but fails to completely eliminate the parasite. This outcome is not detrimental to the parasite, as it reduces host mortality and maintains the parasite infectivity toward the insect vectors.
Growth performance, length – weight relationship and condition factor of Clarias gariepinus fed Anisophyllea laurina seed meal substitute

Length-weight relationships are of significance as an important tool for the assessment of the growth pattern of fish species and the condition in which they grow. This study evaluates the biological parameters (’a, b, and r 2 ’) as well as length-weight relationship and condition factor of 150 specimens of Clarias gariepinus fed dietary inclusion of Anisophyllea laurina seed meal. The values of the regression coefficient ‘b’ obtained for the length-weight relationship for the five treatments were 3.3, 3.03, 3.0, 2.9 and 2.7 with corresponding coefficient of determination (R 2 ) values of 0.8313, 0.9517, 0.9629, 0.9223, and 0.8726. T4 and T5 exhibited a negative allometric growth pattern. In addition, T1, T2 and T3 demonstrated isometric growth and displayed the ideal shape of fish. The regression equation for the LWR was (W=32.72+ 0.32), revealing a significant correlation between the variables. The coefficient of determination shows a significant relationship (r 2 = 0.95) between length and weight of T2 and T3 (25% and 50% ASM inclusions) and other treatments. The species are found to be in a good condition as shown by the condition factor which was k >1. In conclusion, the results revealed that Anisophyllea laurina seed meal could serve as substitute source of vital nutrient and antioxidant ingredients with health benefits at 25% and 50% levels. Keywords: Isometric growth; regression coefficient; correlation of determination; antioxidant
Measuring Tibial Artery Blood Flow Following a Moderate Fire and Air Vacuum Cupping Treatment

Background: Cupping therapy has become an increasingly popular method of alternative medicine. However, no quantitative measures on the effects of cupping therapy on blood flow and lymphatic drainage have been examined. Purpose: The purpose of this study was to determine the effects of both fire and air vacuum cupping applied at a moderate intensity on skin temperature and blood flow of the tibial artery. The research questions that guided this study included: Does either fire cupping or air vacuum cupping applied at moderate intensity increase blood flow through the tibial artery in a healthy population? Does either method of cupping increase blood flow through the tibial artery more than the other? Study Design: A pre and posttest experimental design was used. Independent variables included both fire and air vacuum cupping and dependent variables were skin surface temperatures and blood flow velocity. Methods: Twenty healthy males (20.70 ± 2.83 years) participated. Blood flow and skin temperatures were measured prior to the intervention. The intervention included either fire or air vacuum cupping for 15 minutes. After the testing period, blood flow and skin temperature were re-measured. Results: Blood flow from fire cupping had a range of change from -62.68ml/min to +298.54ml/min. The four surface temperatures during fire cupping increased 0.14°C ± 0.30°C. Blood flow from air vacuum cupping had a range of change from -120.42ml/min to 304.4ml/min. All four surface temperatures during air vacuum cupping did not change. Conclusions: The results suggest that air vacuum and fire cupping both increased and decreased blood flow. Furthermore, fire cupping decreased the tibial artery blood flow (-3%) while air vacuum cupping increased (5%). It is possible that the inability to accurately control pressures
Living quarters and unmet need for personal care assistance among adults with disabilities.

OBJECTIVES This study used a person-environment (P-E) framework to examine individual capabilities and social and physical environmental attributes for their association with unmet assistance needs in activities of daily living (ADLs). Analyses were replicated among five ADLs (bathing, dressing, transferring, toileting, eating) and test the relative risk of apartment dwellers compared to those living in houses. METHODS Data were obtained from the National Health Interview Survey, Supplement on Disability Followback Survey. Analyses consisted of a nationally representative sample of aged and nonaged adults with one or more ADL limitations. RESULTS Slightly less than 1 in 5 subjects with a specific ADL limitation had unmet needs for that ADL. This was true across all ADLs. The likelihood of unmet ADL assistance increased with the number of ADL limitations and other health status indicators. It was at least 50% higher among those living in apartments than in houses and higher among Hispanics. There were no differences by age or gender. DISCUSSION The P-E framework postulates that individuals seek settings matched to their capabilities, but findings suggest that many are at risk for adaptation at any one time. Specific risk factors are identified. Selection factors like preferences, expectations, and adaptation options available have not been directly measured.
Application of Support Vector Machines for Damage Detection in Structures

Support vector machines (SVMs) are a set of supervised learning methods that have recently been applied for structural damage detection due to their ability to form an accurate boundary from a small amount of training data. During training, they require data from the undamaged and damaged structure. The unavailability of data from the damaged structure is a major challenge in such methods due to the irreversibility of damage. Recent methods create data for the damaged structure from finite element models. In this thesis we propose a new method to derive the dataset representing the damage structure from the dataset measured on the undamaged structure without using a detailed structural finite element model. The basic idea is to reduce the values of a copy of the data from the undamaged structure to create the data representing the damaged structure. The performance of the method in the presence of measurement noise, ambient base excitation, wind loading is investigated. We find that SVMs can be used to detect small amounts of damage in the structure in the presence of noise. The ability of the method to detect damage at different locations in a structure and the effect of measurement location on the sensitivity of the method has been investigated. An online structural health monitoring method has also been proposed to use the SVM boundary, trained on data measured from the damaged structure, as an indicator of the structural health condition.
Optimal Linear Combinations of Neural Networks 1

Neural network (NN)-based modeling often involves trying multiple networks with diierent architectures and training parameters in order to achieve acceptable model accuracy. Typically, one of the trained NNs is chosen as best, while the rest are discarded. Hashem and Schmeiser 25] proposed using optimal linear combinations of a number of trained neural networks instead of using a single best network. Combining the trained networks may help integrate the knowledge acquired by the component networks and thus improve model accuracy. In this paper, we discuss and extend the idea of optimal linear combinations (OLCs) of neural networks and derive closed-form expressions for four cases of OLCs. We present two algorithms for selecting the component networks for the combination to improve the generalization ability of OLCs. Our experimental results demonstrate signiicant improvements in model accuracy as a result of using OLCs, as compared to the best network.
Global evolutionary isolation measures can capture key local conservation species in Nearctic and Neotropical bird communities

Understanding how to prioritize among the most deserving imperilled species has been a focus of biodiversity science for the past three decades. Though global metrics that integrate evolutionary history and likelihood of loss have been successfully implemented, conservation is typically carried out at sub-global scales on communities of species rather than among members of complete taxonomic assemblages. Whether and how global measures map to a local scale has received little scrutiny. At a local scale, conservation-relevant assemblages of species are likely to be made up of relatively few species spread across a large phylogenetic tree, and as a consequence there are potentially relatively large amounts of evolutionary history at stake. We ask to what extent global metrics of evolutionary history are useful for conservation priority setting at the community level by evaluating the extent to which three global measures of evolutionary isolation (evolutionary distinctiveness (ED), average pairwise distance (APD) and the pendant edge or unique phylogenetic diversity (PD) contribution) capture community-level phylogenetic and trait diversity for a large sample of Neotropical and Nearctic bird communities. We find that prioritizing the most ED species globally safeguards more than twice the total PD of local communities on average, but that this does not translate into increased local trait diversity. By contrast, global APD is strongly related to the APD of those same species at the community level, and prioritizing these species also safeguards local PD and trait diversity. The next step for biologists is to understand the variation in the concordance of global and local level scores and what this means for conservation priorities: we need more directed research on the use of different measures of evolutionary isolation to determine which might best capture desirable aspects of biodiversity.
Determination Of Association Of Pigmentary Glaucoma With Pigment Dispersion Syndrome.

BACKGROUND Pigment Dispersion Syndrome (PDS) is an autosomal dominant disorder of white males between 20 to 40 years of age characterized by deposition of pigment on the lens, zonules of lens, trabecular meshwork and corneal endothelium (Krukenberg's spindle) in addition to radial, spoke like transillumination defects in the mid peripheral iris. This study was conducted to determine the frequency of occurrence of Pigmentary Glaucoma in patients with Pigment Dispersion Syndrome (PDS). METHODS This longitudinal follow up study included patients presenting with Krukenberg's spindle on the endothelial side of cornea and pigmentation of angle of anterior chamber seen on slit lamp examination and gonioscopy. RESULTS Seventy-two cases of PDS were included in the study, amongst them 63 (87.50%) were males. Mean age was 35.00±6.54 years (range 24-46 years). Forty-seven (65.28%) patients had an IOP in the range of 10-14 mmHg, 22 (30.56%) patients had an IOP in the range of 15-18 mmHg and 3 (4.17%) patients developed an IOP of greater than 19 mmHg. Fundoscopy showed myopic degeneration in 49 (68.06%) patients and optic disc cupping in 3 (4.17%) patients. Four (5.56%) patients had refractive error between +1D to +3D, 9 (12.50%) patients had refractive error between -1D to -4D, 21 (29.17%) patients had refractive error between -5 D to -8 D and 38 (52.78%) patients had refractive error between -9 D to -12 D. Our study showed that one patient having PDS developed glaucoma at 5 years of follow up and three patients developed glaucoma at 14 years of follow up. CONCLUSIONS On the basis of this study we conclude that early onset primary open angle glaucoma associated with PDS or Juvenile glaucoma associated with PDS might have been mistaken as Pigmentary Glaucoma in Pakistani patients and a distinct entity in the form of Pigmentary Glaucoma may be non-existent.
BIRDS: A Bare-Metal Recovery Systemfor Instant Restoration of Data Services

We propose Birds: a bare-metal recovery system for instant restoration of data services, focusing on a general-purpose automatic backup-and-recovery approach to protect data and resume data services from scratch instantly after disasters. We design BIRDS to possess two appealing features: full automation in the backup-and-recovery process, and instant data service resumption after disasters. BIRDS achieves the former one with automatic whole system replication and restoration, by taking the backup process outside of the protected system with the help of a novel non-intrusive light-weight physical to virtual conversion method. The latter one is enabled by a novel pipelined parallel recovery mechanism, which allows data services being instantly resumed while data recovery between the backup data center and the production site is still in progress. We implemented a BIRDS prototype and evaluated it using standard benchmarks. We show that BIRDS outperforms existing disaster recovery techniques by the means of recovery efficiency while introducing relatively small runtime overhead. Furthermore, BIRDS can be directly applied to any existing system in a plug-and-protect fashion without requiring re-installation or any modification of the existing system.