Miracle-dz/UniFAR-FTUs huggingface dataset:
Feasibility of Detecting Human Immunodeficiency Virus Type 1 Drug Resistance in DNA Extracted from Whole Blood or Dried Blood Spots

ABSTRACT Due to high cost, availability of human immunodeficiency virus type 1 (HIV-1) drug resistance testing in resource-poor settings is still limited. We therefore evaluated the usefulness of viral DNA extracted from either whole blood or dried blood spots (DBS). Samples were collected from 50 patients receiving therapy and 10 therapy-naïve patients. Amplification and sequencing of RNA and DNA was performed using an in-house assay. Protease (PR) and reverse transcriptase (RT) sequences of plasma viral RNA were obtained for 96.6% and 89.7%, respectively, of the 29 patients with a detectable viral load. For cellular viral DNA, useful PR and RT sequences were obtained for 96.6% and 93.1% of the whole-blood-cell samples and for 93.1% and 93.1% of the DBS samples, respectively. For the 31 patients with an undetectable viral load, PR and RT sequences were obtained for 67.7% and 61.3% of the whole-blood-cell DNA preparations and for 54.8% and 58.1% of the DBS DNA preparations, respectively. A good correlation between RNA and DNA sequences was found; most discordances were caused by the detection of mixed amino acids. Of the RT drug-resistant mutations, 13 (38.2%) were seen in RNA only, 6 (17.6%) in DNA only, and 15 (44.1%) in both. Repeated amplification and sequencing of DNA extracts revealed a lack of reproducibility for the detection of drug resistance mutations in a number of samples, indicating a possible founder effect. In conclusion, this study shows the feasibility of genotypic drug resistance testing on whole blood cells or DBS and its possible usefulness for HIV-1 subtyping or examining the overall distribution of drug resistance in a population. For individual patients, RNA sequencing was shown to be superior to DNA sequencing, especially for patients who experienced early treatment failure. The use of DNA extracted from whole blood or DBS for the detection of archived drug resistance mutations deserves further study.
Coded excitation system for improving the penetration of real-time phased-array imaging systems

Based on an analysis of the inherent signal-to-noise ratio (SNR) in medical ultrasound imaging, SNR improvements of 15-20 dB are theoretically possible for real-time phased-array imagers using coded excitation. A very simple coded excitation for phased arrays based on the principles of 'pseudochirp' excitation and equalization filtering is described. This system is capable of SNR improvements of about 15 dB with range sidelobe levels acceptable for many medical imaging applications. Such improvements permit increased operating frequencies, and hence enhanced spatial resolution, for real-time array imagers. Both simulations and measurements are used to demonstrate the efficacy of the method. <<ETX>>
Growth Stunting in Early Life in Relation to the Onset of the Childhood Component of Growth

AIMS Growth stunting is prevalent in developing countries. The prevalence of stunting ranges from 10-80% or more. The critical period for growth faltering in length is between six and 18 months. The aims of this study were 1) to investigate the association between the age at onset of the childhood component and growth stunting in early life; 2) to develop a screening method for identifying any individual infant subject to stunting in early life. MATERIALS & METHODS This community-based longitudinal study was carried out in Lahore, Pakistan. Three studied areas and one local control group were included in the study. There were 425 subjects for whom data were available for determining the age at onset of the childhood component. The onset was defined as an abrupt increase in length velocity. It was determined individually using the infancy-childhood-puberty growth model. RESULTS The medians of the age at onset of childhood component were 15, 13, 10 and 9 months in the periurban, village, urban and control groups, respectively. The onset was significantly related to both length and length velocity during the critical period of stunting. Based on the distribution of individual length increment from 12 to 15 months, 2.0 and 3.0 cm were chosen as the cut-off points to identify a stunting infant. In the normal onset group, 84% of the children were identified as growing normally; in the delayed onset group, 61% were identified as stunting. Using this screening method, 97% of children have a delayed onset if their length increase is below 2 cm from 12 to 15 months; 99% of them have a normal onset if the increase is above 3 cm over the same period. CONCLUSIONS The age at onset of the childhood component can significantly explain the variations in both length and length velocity in early life. The stunting screening method reported here is simple. It can be used in almost any situation, such as a pediatric clinic or community-based survey.
Time course and risk factors of post‐stroke fatigue: a prospective cohort study

Background: Post‐stroke fatigue (PSF) often occurs after stroke and has a negative impact on the rehabilitation process. Several studies focused either on short‐ or on long‐term PSF and their relations with stroke characteristics. However, possible pre‐stroke risk factors such as history of depression, pre‐existent white matter lesions or brain atrophy were usually not taken into account. Therefore, the precise mechanisms underlying PSF remain still unclear. This study was aimed at assessing the possible contributions of (pre‐)stroke factors to both short‐term PSF and its course over time.
Education expansion and decline in cohort quality in Brazil: 1995–2013

ABSTRACT This letter explores whether the expansion of tertiary education in Brazil has caused any significant decline in the average quality of the recent cohorts with higher share of tertiary education. Using Brazil National Household Survey 1995–2013 data, we find evidence shows that the recent cohorts earn a relatively smaller tertiary premium after controlling everything else that also affect the tertiary premium, which indicates the decline in average quality of the recent college graduates.
Thromboxane receptor blockade attenuates the toxic effect of cyclosporine in experimental renal transplantation.

Renal dysfunction, manifested as a dose-dependent reduction in glomerular filtration rate (GFR), is a common complication of cyclosporine A (CyA) administration to laboratory animals and humans. We have recently shown that chronic CyA treatment in normal rats is associated with a selective increase in renal thromboxane A2 (TXA2) synthesis, which may play a role in GFR reduction. The present experiments were designed to investigate whether pharmacological inhibition of TXA2 activity could reduce CyA nephrotoxicity in a rat model of renal transplantation. To discriminate the possible biochemical changes due to rejection episodes from those due to CyA nephrotoxicity, we selected a model of renal isograft free of graft rejection processes. We demonstrated that oral CyA administration for 30 days to rats undergoing renal isograft is associated with the development of renal insufficiency, as indicated by a progressive increase in serum creatinine concentration and reduction in creatinine clearance. In the same animals, a parallel increase in the urinary excretion of TXB2 was found. Combination of the specific thromboxane receptor antagonist GR32191 with CyA treatment partially prevented the deterioration in renal function observed in animals given CyA alone, without modifying the urinary TXB2 excretion. In contrast, renal-isografted rats given GR32191 alone or vehicle alone for 30 days did not show any changes in serum creatinine, creatinine clearance, and urinary TXB2 excretion throughout the experimental period. Mild hypercellularity of the glomerular tuft was observed in isografted kidneys chronically exposed to either CyA or CyA plus GR32191. (ABSTRACT TRUNCATED AT 250 WORDS)
Induction of Glutathione Synthesis and Glutathione Reductase Activity by Abiotic Stresses in Maize and Wheat

The effect of different abiotic stresses (extreme temperatures and osmotic stress) on the synthesis of glutathione and hydroxymethylglutathione, on the ratio of the reduced to oxidised forms of these thiols (GSH/GSSG, hmGSH/hmGSSG), and on the glutathione reductase (GR) activity was studied in maize and wheat genotypes having different sensitivity to low temperature stress. Cold treatment induced a greater increase in total glutathione (TG) content and in GR activity in tolerant genotypes of both species than in sensitive ones. The GSH/GSSG and hmGSH/hmGSSG ratios were increased by this treatment only in the frost-tolerant wheat variety. High-temperature stress increased the TG content and the GSH/GSSG ratio only in the chilling-sensitive maize genotype, but GR activity was greater after this treatment in both maize genotypes. Osmotic stress resulted in a great increase in the TG content in wheat and the GR activity in maize. The amount of total hydroxymethylglutathione increased following all stress treatments. These results indicate the involvement of these antioxidants in the stress responses of wheat and maize.
Nonhuman Primate Models for Evaluation of AIDS Therapy a

Infection of macaque monkeys with simian immunodeficiency virus (SIV) has been established as an excellent animal model system for studying the pathogenesis of an HIV-like virus and for evaluating newly developed antiretroviral drugs and vaccines. Based on their genetic, antigenic, and biologic properties, the simian immunodeficiency viruses are the closest known relatives of the human AIDS viruses, and experimental infection of macaque monkeys results in a disease that is remarkably similar to human AIDS. Infected macaques show diarrhea, weight loss, hematologic abnormalities including lymphopenia and thrombocytopenia, lymphadenopathy/lymphoid hyperplasia that progresses to lymphoid depletion, immunosuppression with marked reduction in CD4+ cells and in the CD4+/CD8+ cell ratio, and opportunistic infections. A majority of such macaques die from an AIDS-like disease within one to three years of infection. An acutely lethal variant of SIV has been identified that results in death in susceptible macaques within 7-12 days of infection. Preliminary prophylactic treatment trials with AZT in macaque monkeys exposed to the acutely lethal SIV variant indicate that some protection is provided when AZT treatment is initiated within 24 hours of virus exposure. Other studies with the more chronic SIV infection model, however, failed to show any prophylactic efficacy of CS-87, AZT, D4T, or FDT.
Rough Neuro-Fuzzy Network Applied to Traffic Flow Breakdown in the City of Sao Paulo

In recent years the market behavior has changed, influenced by several aspects like: increased competitiveness, electronic commerce, environment concerns, among others. The new consumption habits have brought products with a shorter life cycle. These behavior increases the amount of discarded and aimlessly items. Predict the traffic behavior could help to make decision about the routing process, as well as enables the improvement in effectiveness and productivity on its physical distribution. This need motivates the search for technological improvements in the Routing performance in metropolitan areas. The purpose of this paper is to present computational evidence that Artificial Neural Network (ANN) could be use to predict the traffic behavior in a metropolitan area such Sao Paulo (around 16 million inhabitants). The proposed methodology involves the application Rough-Fuzzy Sets to define inference morphology for insert the behavior of Dynamic Routing into a structured rule basis, without human expert aid. The attributes of the traffic parameters are described through membership functions. Rough Sets Theory identifies the attributes that are important, and suggest Fuzzy relations to be inserted on a Rough Neuro Fuzzy Network (RNFN) type Multilayer Perceptron (MLP), in order to get an optimal surface response. To measure the performance of the proposed RNFN, the responses of the unreduced rule basis are compared with the reduced rule basis. The results show that by making use of the RNFN, it is possible to reduce the need for human expert in the construction of the Fuzzy inference mechanism in such flow process like traffic breakdown.
Association of fasting and nonfasting serum triglycerides with cardiovascular disease and the role of remnant-like lipoproteins and small dense LDL

Purpose of review The magnitude of the contribution of serum triglycerides to cardiovascular disease risk and the mechanisms by which triglyceride-rich lipoproteins exert their effect on the vascular wall are largely unknown. Postprandial lipemia likewise has been linked to atherosclerosis, but large prospective studies assessing the magnitude of this association are also lacking. Hypertriglyceridemia is characterized by the presence of cholesterol-rich remnant-like lipoproteins and small dense LDL particles, both of which are believed to contribute to cardiovascular disease risk. Recent findings Several large prospective cohort studies and a meta-analysis have been published recently, investigating the association of fasting and nonfasting serum triglycerides with cardiovascular disease. Fasting triglycerides increase the adjusted hazard ratios for cardiovascular disease risk 1.7× (comparing upper with lower tertile), and nonfasting levels around 2.0×. Measurement of nonfasting triglycerides may be more feasible and more informative, but standardization of a test meal is necessary. For clinical practice, the concentration of the atherogenic lipoprotein subfractions in hypertriglyceridemia may be reflected best by measuring apolipoprotein B. Summary Nonfasting triglyceride levels may replace fasting levels in assessing cardiovascular disease risk once standard reference values have been developed. Several atherogenic lipoprotein subfractions can be measured by including apolipoprotein B in addition to HDL, (nonfasting) triglycerides and LDL cholesterol.
The effect of tibial plateau angle on ground reaction forces 4-17 months after tibial plateau leveling osteotomy in Labrador Retrievers.

OBJECTIVE To assess the relationship between postoperative tibial plateau angle (TPA) and ground reaction forces (GRFs) in Labrador Retrievers at least 4-months after tibial plateau leveling osteotomy (TPLO) surgery. STUDY DESIGN A retrospective longitudinal study. ANIMALS Thirty-two Labrador Retrievers with unilateral cranial cruciate ligament disease that had TPLO and concurrent meniscal surgery. METHODS TPA and GRFs were measured pre- and > or = 4 months postoperatively. Preoperative GRFs, preoperative TPA, duration of injury, postoperative TPA and degree of rotation were each compared with postoperative GRFs using correlation analysis. Dogs were also grouped by postoperative TPA and compared using 1-way analysis of variance (ANOVA). Postoperative function was compared with meniscal release/meniscectomy, patient age, sex, body weight and follow-up time using ANOVA. RESULTS No significant relationship was found between preoperative GRFs, preoperative TPA, duration of injury, postoperative TPA, degree of rotation, or meniscal release/meniscectomy and postoperative function. Mean preoperative GRFs for all dogs were 28.8 +/- 9.5 for peak vertical force (PVF) and 9.3 +/- 3.1 for peak vertical impulse (VI). Mean postoperative GRFs for all dogs were 40.4 +/- 5.0 for PVF and 14.1 +/- 1.9 for VI. CONCLUSIONS No statistically significant relationship was found between postoperative TPA and GRFs after TPLO > or = 4 months after surgery, where the postoperative angle was between 0 and 14 degrees. No significant relationship was found between the preoperative TPA and postoperative function. CLINICAL RELEVANCE Limb function in Labrador Retrievers was not affected by postoperative TPA and re-operation for cases with a postoperative TPA between 0 and 14 degrees is not recommended.
Sensor modeling and data fusion for a safety warning system in hydrogen-based vehicles

This document describes the process of analysis, modeling and compensation through data fusion algorithms of two hydrogen sensors for automotive applications: one is used to detect small leaks (e.g. in pipes ranging from the tank to the engine compartment), while the other has the task of detecting hydrogen concentrations near the explosivity level. Fast and accurate models of the sensors are developed allowing an accurate analysis of the main issues of a practical implementation of the warning system. Such analysis drives the development of effective data fusion techniques to reduce the measure uncertainty (reducing the risk of false alarms or missed detections). The implementation of such techniques on microcontroller-based embedded systems with limited resources in terms of memory and computational power is also addressed.
Microoxic Niches within the Thylakoid Stroma of Air-Grown Chlamydomonas reinhardtii Protect [FeFe]-Hydrogenase and Support Hydrogen Production under Fully Aerobic Environment1[OPEN]

Hydrogen production catalyzed by the extremely anaerobic enzyme [FeFe]-hydrogenase in air-grown microalgae reports on microoxic niches within the thylakoid stroma. Photosynthetic hydrogen production in the microalga Chlamydomonas reinhardtii is catalyzed by two [FeFe]-hydrogenase isoforms, HydA1 and HydA2, both irreversibly inactivated upon a few seconds exposure to atmospheric oxygen. Until recently, it was thought that hydrogenase is not active in air-grown microalgal cells. In contrast, we show that the entire pool of cellular [FeFe]-hydrogenase remains active in air-grown cells due to efficient scavenging of oxygen. Using membrane inlet mass spectrometry, 18O2 isotope, and various inhibitors, we were able to dissect the various oxygen uptake mechanisms. We found that both chlororespiration, catalyzed by plastid terminal oxidase, and Mehler reactions, catalyzed by photosystem I and Flavodiiron proteins, significantly contribute to oxygen uptake rate. This rate is considerably enhanced with increasing light, thus forming local anaerobic niches at the proximity of the stromal face of the thylakoid membrane. Furthermore, we found that in transition to high light, the hydrogen production rate is significantly enhanced for a short duration (100 s), thus indicating that [FeFe]-hydrogenase functions as an immediate sink for surplus electrons in aerobic as well as in anaerobic environments. In summary, we show that an anaerobic locality in the chloroplast preserves [FeFe]-hydrogenase activity and supports continuous hydrogen production in air-grown microalgal cells.
Cyclodextrin-poly(anhydride) nanoparticles as new vehicles for oral drug delivery

Introduction: The oral administration of drugs belonging to Class IV of the Biopharmaceutical Classification System (BCS) represents a major challenge. These drugs display poor aqueous solubility and specific permeability characteristics. Most of these compounds are substrates of the P-glycoprotein and/or the cytochrome P450. Among other types of drug, various anti-cancer drugs also suffer from these drawbacks (i.e., paclitaxel), which limits the possibilities for developing oral treatments. Areas covered: This review discusses the factors that influence the bioavailability of drugs when administered by the oral route, as well as the capabilities of cyclodextrins when associated with nanoparticles. In particular, evidence is given regarding the synergistic effect between cyclodextrins and bioadhesive nanoparticles, on the oral delivery of pharmaceuticals. Expert opinion: This article aims to provide an overview of the multiple gains in incorporating cyclodextrins in poly(anhydride) nanoparticles, including improvement of their bioadhesive capability, the loading of lipophilic drugs and the effect on efflux membrane proteins and cytochrome P450. The combination between bioadhesive nanoparticles and P-gp inhibitors without pharmacological activity (i.e., cyclodextrins) may be useful to promote the oral bioavailability of drugs ascribed to Class IV of the BCS.
Realizing Low-Energy Classification Systems by Implementing Matrix Multiplication Directly Within an ADC

In wearable and implantable medical-sensor applications, low-energy classification systems are of importance for deriving high-quality inferences locally within the device. Given that sensor instrumentation is typically followed by A-D conversion, this paper presents a system implementation wherein the majority of the computations required for classification are implemented within the ADC. To achieve this, first an algorithmic formulation is presented that combines linear feature extraction and classification into a single matrix transformation. Second, a matrix-multiplying ADC (MMADC) is presented that enables multiplication between an analog input sample and a digital multiplier, with negligible additional energy beyond that required for A-D conversion. Two systems mapped to the MMADC are demonstrated: (1) an ECG-based cardiac arrhythmia detector; and (2) an image-pixel-based facial gender detector. The RMS error over all multiplication performed, normalized to the RMS of ideal multiplication results is 0.018. Further, compared to idealized versions of conventional systems, the energy savings obtained are estimated to be 13× and 29×, respectively, while achieving similar level of performance.
Changes in non-target arthropod populations following application of liquid bait formulations of insecticides for control of rangeland grasshoppers

Abstract This study was undertaken to determine the non-target impacts of rangeland grasshopper control using liquid bait formulations of insecticides (canola and corn oil as carriers of carbaryl, diflubenzuron, and malathion). The research was conducted on native rangeland in Wyoming under drought conditions. Three collection methods (pitfall traps, yellow sticky cards, and sweep nets) were used to estimate non-target arthropod densities. The formulated insecticides were applied according to the protocol of reduced agent-area treatments, an application method designed to reduce economic and environmental costs by applying insecticides at low rates with incomplete coverage via alternating treated and untreated swaths). Canola and corn oils are vegetable oils high in linolenic and linoleic acids which function as attractants and phagostimulants for many species of grasshoppers. Crop oil is a biologically inert paraffin-based petroleum product that served as a control. Although all treatments markedly reduced grasshopper population densities, non-target populations were nominally affected. There were no consistent, significant differences in the responses of non-target populations to treatments with the liquid baits (canola and corn oil carriers) relative to those observed with the standard carrier (crop oil). Only one taxonomic group (Formicidae) showed a significant negative response to treatment relative to untreated controls. Logistical and ecological factors associated with grasshopper control methods may account for the nominal effects on non-target taxa. Sweep net and sticky trap sampling were more sensitive to treatment effects and time-by-treatment interactions. Temporal changes in population densities may have made treatment effects difficult to distinguish in several taxonomic groups.