Miracle-dz/UniFAR-FTUs huggingface dataset:
Characterization of acute HIV-1 infection in high-risk Nigerian populations.

BACKGROUND Acute phase of human immunodeficiency virus (HIV) infection (AHI) may account for a significant proportion of HIV-1 transmission. We identified and characterized individuals in Nigeria with AHI. METHODS Individuals were tested using a combination of rapid HIV testing in mobile units and laboratory-based specimen pooling for nucleic acid amplification testing. Genome sequences were characterized. A linear segmented regression model was fit to serial viral load (VL) measurements to characterize early VL profiles. RESULTS Sixteen AHIs were identified from 28 655 persons screened. Specimens were genotyped: 7 (43.8%) were CRF02_AG, 6 (37.5%) were subtype G, 1 (6.3%) was CRF06_cpx, and 2 (12.5%) were unique recombinant forms. No antiretroviral resistance mutations were detected. The mean duration of high VL burden from peak to nadir was 76 days (95% confidence interval [CI], 58-93 days), and the mean rate of viremic control was -0.66 log(10) VL per month. The mean VL at set-point was 4.5 log(10) copies/mL (95% CI, 3.9-5.1 log(10) copies/mL). CONCLUSIONS This study is the first to characterize AHI among Nigerians identified as HIV infected before seroconversion who would be otherwise missed by conventional HIV testing. Infections by HIV subtypes in Nigeria exhibit long periods of high viral burden, which can contribute to increased transmissibility.
A Tightly Controlled Conditional Knockdown System Using the Tol2 Transposon-Mediated Technique

Background Gene knockdown analyses using the in utero electroporation method have helped reveal functional aspects of genes of interest in cortical development. However, the application of this method to analyses in later stages of brain development or in the adult brain is still difficult because the amount of injected plasmids in a cell decreases along with development due to dilution by cell proliferation and the degradation of the plasmids. Furthermore, it is difficult to exclude the influence of earlier knockdown effects. Methodology/Principal Findings We developed a tightly controlled conditional knockdown system using a newly constructed vector, pT2K-TBI-shRNAmir, based on a Tol2 transposon-mediated gene transfer methodology with the tetracycline-inducible gene expression technique, which allows us to maintain a transgene for a long period of time and induce the knockdown of the gene of interest. We showed that expression of the endogenous amyloid precursor protein (APP) was sharply decreased by our inducible, stably integrated knockdown system in PC12 cells. Moreover, we induced an acute insufficiency of Dab1 with our system and observed that radial migration was impaired in the developing cerebral cortex. Such inhibitory effects on radial migration were not observed without induction, indicating that our system tightly controlled the knockdown, without any expression leakage in vivo. Conclusions/Significance Our system enables us to investigate the brain at any of the later stages of development or in the adult by utilizing a knockdown technique with the aid of the in utero electroporation gene transfer methodology. Furthermore, we can perform knockdown analyses free from the influence of undesired earlier knockdown effects.
Activation of the Unfolded Protein Response Occurs at All Stages of Atherosclerotic Lesion Development in Apolipoprotein E–Deficient Mice

Background—Apoptotic cell death contributes to atherosclerotic lesion instability, rupture, and thrombogenicity. Recent findings suggest that free cholesterol (FC) accumulation in macrophages induces endoplasmic reticulum (ER) stress/unfolded protein response (UPR) and apoptotic cell death; however, it is not known at what stage of lesion development the UPR is induced in macrophages or whether a correlation exists between UPR activation, FC accumulation, and apoptotic cell death. Methods and Results—Aortic root sections from apolipoprotein E–deficient (apoE−/−) mice at 9 weeks of age (early-lesion group) or 23 weeks of age (advanced-lesion group) fed a standard chow diet were examined for markers of UPR activation (GRP78, phospho-PERK, CHOP, and TDAG51), apoptotic cell death (TUNEL and cleaved caspase-3), and lipid accumulation (filipin and oil red O). UPR markers were dramatically increased in very early intimal macrophages and in macrophage foam cells from fatty streaks and advanced atherosclerotic lesions. Although accumulation of FC was observed in early-lesion–resident macrophage foam cells, no evidence of apoptotic cell death was observed; however, UPR activation, FC accumulation, and apoptotic cell death were observed in a small percentage of advanced-lesion–resident macrophage foam cells. Conclusions—UPR activation occurs at all stages of atherosclerotic lesion development. The additional finding that macrophage apoptosis did not correlate with UPR activation and FC accumulation in early-lesion–resident macrophages suggests that activation of other cellular mediators and/or pathways are required for apoptotic cell death.
Assisted Feature Engineering and Feature Learning to Build Knowledge-based Agents for Arcade Games

Human knowledge can greatly increase the performance of autonomous agents. Leveraging this knowledge is sometimes neither straightforward nor easy. In this paper, we present an approach for assisted feature engineering and feature learning to build knowledge-based agents for three arcade games within the Arcade Learning Environment. While existing approaches mostly use model-free approaches we aim at creating a descriptive set of features for world modelling and building agents. To this end, we provide (visual) assistance in identifying and modelling features from RAM, we allow for learning features based on labeled game data, and we allow for creating basic agents using the above features. In our evaluation, we compare different methods to learn features from the RAM. We then compare several agents using different sets of manual and learned features with one another and with the state-of-the-art.
Completeness of excision and follow up cytology in patients treated with loop excision biopsy

Aims—To assess the relation between the grade and the status of follow up cytology, the completeness of loop excision biopsies with cervical intraepithelial neoplasia (CIN), and the findings at follow up cytology, as well as the differences between complete and incomplete exclusion, using the odds ratio. Treatment failure was assessed. Methods—1600 women with CIN (290 CIN1, 304 CIN2, 1006 CIN3) were followed for a minimum of six months and a maximum of 10 years. A database was created and comparisons performed. The mean age of the patients was 37 years. Results—Excision was complete in over 84% of loops. Residual disease and recurrence of high grade dyskaryosis was more common in women with CIN 3 than CIN 2 or 1. No high grade dyskaryosis was seen in the fifth follow up smear in patients with CIN 1 and CIN 2. Residual, recurrent, and persistent disease was most common in patients with incompletely excised CIN at ectocervical and endocervical margins and deep margins of resection than in patients with completely excised CIN. The odds ratios were significantly higher in the women who had incomplete excision of CIN at ectocervical, endocervical, both ecto- and endocervical, and deep margins of resection compared with those with apparent complete excision of CIN lesions. One patient developed invasive squamous cell carcinoma 44 months after loop excision which showed CIN 3 invading endocervical crypts and extending to both ectocervical and endocervical margins of resection. Conclusions—At long term follow up, patients with CIN who have residual disease are at increased risk of persistent disease and should therefore be followed up regularly with cytology and colposcopy. The findings support national policy of returning women with treated CIN of any grade to normal recall after five years except for cases of CIN3 where excision was incomplete or equivocal. In these cases follow up with annual smear for 10 years is recommended.
Assessing Students' Satisfaction on the Use of Virtual Learning Environment (VLE): An Input to a Campus-wide E-learning Design and Implementation

Educational institutions have come to realize the potential benefits of using Virtual Learning Environment (VLE). When used correctly, VLE may transform learning experience of students into a more enjoyable, satisfying and effective setting. This paper evaluated students’ satisfaction on the use of VLE as a support technology in teaching students in the Graduate School. Procedures involved in the study include installation of a Modular Object-Oriented Dynamic Learning Environment (MOODLE) package, customizing the VLE and determining the students’ satisfaction. The instrument used for data collection was the developed online questionnaire. A total of 67 Master of Business Administration (MBA) students of Batangas State University (BatStateU) enrolled in the course Management Control and Information System (MCIS) for the period of 2011-2013 served as the respondents of this study. The VLE is found to be effective as a supportive tool to supplement traditional classroom instruction as revealed by satisfied students. Positive attitude is exhibited on the use of VLE regardless of gender. On the other hand, young and experienced users of e-learning platforms tend to be difficult to satisfy with regards to the use of VLE. Keywords: e-learning, virtual learning environment, satisfaction
Advances in the Treatment of Noninfectious Uveitis with Biologics : Anti-TNF and Beyond

All book chapters are Open Access distributed under the Creative Commons Attribution 3.0 license, which allows users to download, copy and build upon published articles even for commercial purposes, as long as the author and publisher are properly credited, which ensures maximum dissemination and a wider impact of our publications. However, users who aim to disseminate and distribute copies of this book as a whole must not seek monetary compensation for such service (excluded OMICS Group representatives and agreed collaborations). After this work has been published by OMICS Group, authors have the right to republish it, in whole or part, in any publication of which they are the author, and to make other personal use of the work. Any republication, referencing or personal use of the work must explicitly identify the original source. Statements and opinions expressed in the book are these of the individual contributors and not necessarily those of the editors or publisher. No responsibility is accepted for the accuracy of information contained in the published chapters. The publisher assumes no responsibility for any damage or injury to persons or property arising out of the use of any materials, instructions, methods or ideas contained in the book.
Hydroxyapatite-Chitosan and Gelatin Based Scaffold for Bone Tissue Engineering

Bone tissue engineering, using a porous scaffold material to induce the formation of bone from the surrounding tissues has some distinct advantages over autografting and allografting, and it is a rapidly growing alternative approach to heal damaged bone tissue. The current study focuses on fabrication and characterization of hydroxyapatite and natural biopolymer composite for improved bone repair and regeneration. The porous composite scaffold containing hydroxyapatite (HAp), chitosan and gelatin having 3D network of interconnected pores with an average pore size of 150 μm was fabricated using freeze drying method. Glutaraldehyde was used as a cross linker between chitosan and gelatin. Characteristic IR band for (–C=N–) group observed in IR study of the prepared scaffold indicated the crosslinking ability of glutaraldehyde with chitosan and gelatin. Total porosity in the scaffold varied between 60 and 70% as determined by Archimedes principle and depended on the solids loading of the scaffold. Microstructural analysis using field emission scanning electron microscopy (FESEM) showed an interconnected porous network in the scaffold where HAp nanoparticles were found to be dispersed in the biopolymer matrix. Thick bone like apatite layer deposition was observed on the surface of the scaffold on immersing it into simulated body fluid (SBF) at 37°C for 7 days. The developed scaffold exhibited a compressive strength of 1.75 MPa which is close to the lower limit of compressive strength of spongy bone. These types of composite scaffolds find application as efficient biomaterial for natural bone tissue regeneration and bone tissue engineering.
Biological sulphate reduction with primary sewage sludge in an upflow anaerobic sludge bed (UASB) reactor - Part 2: Modification of simple wet chemistry analytical procedures to achieve COD and S mass balances

The use of the conventional COD method to measure sulphide proved to be problematic due to the loss of hydrogen sulphide (H2S) during sample handling. For calibration of models based on mass balances, and operation of full-scale systems, it was imperative to develop simple wet chemistry analytical procedures for the accurate measurement of parameters like sulphide, COD, alkalinities and VFA in order to monitor BSR systems and achieve 100% COD and S mass balances. Three different analytical methods were investigated to minimise the loss of un-dissociated H 2 S. Method 1, which is the recommended Standard Methods COD test method, resulted in poor S mass balance (64-75%) due to loss of H 2 S during sample handling, mainly vacuum filtration. Method 2, in which 3 drops of 10 M NaOH are added immediately upon effluent sample collec tion to raise the pH to > 10 and converting un-dissociated H 2 S species into the HS- species resulted in minimal sulphide loss during sample vacuum filtration, dilution, mixing and standing. Method 3, in which a polyelectrolyte is added to the effluent sample to coagulate the organic particles with centrifugation for solid-liquid separation instead of vacuum filtration. Results from Method 3 showed an improvement in the S mass balance with respect to Method 1 - 91% against 75% without a long sample standing period and 88% against 65% with a long sample standing period. However, S mass balance with Method 3 was still relatively low when compared with Method 2 (86 to 91% against 92 to 95%). Therefore, Method 2 was the best simple wet chemistry analytical procedure to accurately measure ST (= H2S + HS ) and achieve close to 100% COD and S mass balances. The effects of S T loss were also investigated on the total and subsystem alkalinities as determined with the 5-pH point titration method. By testing standard solutions with known carbonate, acetate and sulphide species and upflow anaerobic sludge bed (UASB) reactor effluent samples, it was found that the total alkalinity concentration is not affected by H 2 S (and CO 2 ) loss as the subsystem alkalinities re-speciate due to a change in pH; and to obtain accurate H 2 CO 3 * alk and volatile fatty acid (VFA) concentrations, accurate sulphide concentrations are required, i.e. those obtained from Method 2.
Effects of leukotriene D4 nasal challenge on bronchial responsiveness and inflammation in asthmatic patients with allergic rhinitis.

BACKGROUND In asthmatic patients with allergic rhinitis (AR), increased cysteinyl leukotrienes (CysLTs) production in the secretion of nasal mucosa has been associated with greater bronchial hyperresponsiveness (BHR) after nasal allergen challenge. However, the role of CysLTs in eliciting BHR after nasal allergen challenge has not been evaluated. The aim of this study is to evaluate the effect of LTD4 nasal challenge on BHR and inflammation in asthmatic patients with AR. METHODS In this self-controlled study, fifteen eligible consecutively recruited subjects underwent methacholine (Mch) bronchial provocation test before and 30 minutes after LTD4 nasal provocation test. The cumulative concentration of LTD4 inducing a 60% increase in nasal airway resistance (PC60NAR) was calculated. The mean values of cumulative doses inducing a 20% decrease in forced expiratory flow in one second (PD20FEV1) for Mch before and after nasal challenge were compared. Fractional exhaled nitric oxide (FeNO), differential inflammatory cell counts in nasal lavage and induced sputum before and after nasal challenge were compared. RESULTS House dust mites were the major allergens accounting for 10/15 (66.7%) of asthmatic patients with AR. The PC60NAR for LT was (8.39±3.48)×10-3 mg·mL-1. The PD20FEV1 before and after nasal challenge was 3.05±3.81 and 2.70±3.81 µmol, respectively (P=0.45). The percentages of eosinophils were (38.36±23.14)% and (45.70±24.86)% in nasal lavage, and (17.51±11.05)% and (24.29±16.52)% in induced sputum before and 24 hours after nasal challenge. The neutrophil counts were (60.64±23.14)% and (53.30±24.46)% in nasal lavage, and (53.83±23.27)% and (56.19±22.28)% in induced sputum before and 24 hours after nasal challenge. The values of FeNO were 40 [35] and 43 [30] ppb before and 24 hours after nasal challenge. No severe adverse effects were reported during the tests. CONCLUSIONS Although most asthmatic patients with AR were sensitive to LTD4 nasal challenge, LTD4 nasal provocation tests do not confer any major effect on BHR. LTD4 might not play a vital role in eliciting bronchial responsiveness induced by nasal allergen challenge.
Experimental determination of the PTW 60019 microDiamond dosimeter active area and volume.

PURPOSE Small field output correction factors have been studied by several research groups for the PTW 60019 microDiamond (MD) dosimeter, by comparing the response of such a device with both reference dosimeters and Monte Carlo simulations. A general good agreement is observed for field sizes down to about 1 cm. However, evident inconsistencies can be noticed when comparing some experimental results and Monte Carlo simulations obtained for smaller irradiation fields. This issue was tentatively attributed by some authors to unintentional large variations of the MD active surface area. The aim of the present study is a nondestructive experimental determination of the MD active surface area and active volume. METHODS Ten MD dosimeters, one MD prototype, and three synthetic diamond samples were investigated in the present work. 2D maps of the MD response were recorded under scanned soft x-ray microbeam irradiation, leading to an experimental determination of the device active surface area. Profiles of the device responses were measured as well. In order to evaluate the MD active volume, the thickness of the diamond sensing layer was independently evaluated by capacitance measurements and alpha particle detection experiments. The MD sensitivity, measured at the PTW calibration laboratory, was also used to calculate the device active volume thickness. RESULTS An average active surface area diameter of (2.19 ± 0.02) mm was evaluated by 2D maps and response profiles of all the MDs. Average active volume thicknesses of (1.01 ± 0.13) μm and (0.97 ± 0.14) μm were derived by capacitance and sensitivity measurements, respectively. The obtained results are well in agreement with the nominal values reported in the manufacturer dosimeter specifications. A homogeneous response was observed over the whole device active area. Besides the one from the device active volume, no contributions from other components of the housing nor from encapsulation materials were observed in the 2D response maps. CONCLUSIONS The obtained results demonstrate the high reproducibility of the MD fabrication process. The observed discrepancies among the output correction factors reported by several authors for MD response in very small fields are very unlikely to be ascribed to unintentional variations of the device active surface area and volume. It is the opinion of the authors that the role of the volume averaging as well as of other perturbation effects should be separately investigated instead, both experimentally and by Monte Carlo simulations, in order to better clarify the behaviour of the MD response in very small fields.
Object Reacquisition and Tracking in Large-Scale Smart Camera Networks

Object reacquisition or reidentification is the process of matching objects between images taken from separate cameras. In this paper, we present our work on feature based object reidentification performed on autonomous embedded smart cameras and applied to traffic scenarios. We present a novel approach based on PCA-SIFT features and a vocabulary tree. By building unique object signatures from visual features, reidentification can be done efficiently coevally minimizing the communication overhead between separate camera nodes. Applied to large-scale traffic scenarios, important parameters including travel time, travel time variability, section density, and partial dynamic origin/destination demands can be obtained. The proposed approach works on spatially separated, un-calibrated, non-overlapping cameras, is highly scalable and solely based on appearance-based optical features. The entire system is implemented and evaluated with regard to a typical embedded smart camera platform featuring one single Texas Instruments trade fixed-point DSP.
Classifying tumor event attributes in radiology reports

Radiology reports contain vital diagnostic information that characterizes patient disease progression. However, information from reports is represented in free text, which is difficult to query against for secondary use. Automatic extraction of important information, such as tumor events using natural language processing, offers possibilities in improved clinical decision support, cohort identification, and retrospective evidence‐based research for cancer patients. The goal of this work was to classify tumor event attributes: negation, temporality, and malignancy, using biomedical ontology and linguistically enriched features. We report our results on an annotated corpus of 101 hepatocellular carcinoma patient radiology reports, and show that the improved classification improves overall template structuring. Classification performances for negation identification, past temporality classification, and malignancy classification were at 0.94, 0.62, and 0.77 F1, respectively. Incorporating the attributes into full templates led to an improvement of 0.72 F1 for tumor‐related events over a baseline of 0.65 F1. Improvement of negation, malignancy, and temporality classifications led to significant improvements in template extraction for the majority of categories. We present our machine‐learning approach to identifying these several tumor event attributes from radiology reports, as well as highlight challenges and areas for improvement.