Miracle-dz/UniFAR-FTUs huggingface dataset:
Simian immunodeficiency virus RNA is efficiently encapsidated by human immunodeficiency virus type 1 particles

Packaging of retroviral RNA is attained through the specific recognition of a cis-acting encapsidation site (located near the 5' end of the viral RNA) by components of the Gag precursor protein. Human immunodeficiency virus type 1 (HIV-1) and simian immunodeficiency virus (SIV) are two lentiviruses that lack apparent sequence similarity in their putative encapsidation regions. We used SIV vectors to determine whether HIV-1 particles can recognize the SIV encapsidation site and functionally propagate SIV nucleic acid. SIV nucleic acid was replicated by HIV-1 proteins. Thus, efficient lentivirus pseudotyping can take place at the RNA level. Direct examination of the RNA contents of virus particles indicated that encapsidation of this heterologous RNA is efficient. Characterization of deletion mutants in the untranslated leader region of SIV RNA indicates that only a very short region at the 5' end of the SIV RNA is needed for packaging. Comparison of this region with the corresponding region of HIV-1 reveals that both are marked by secondary structures that are likely to be similar. Thus, it is likely that a similar higher-order RNA structure is required for encapsidation.
Development of an unsupported arm exercise test in patients with chronic obstructive pulmonary disease.

BACKGROUND Unsupported arm exercise tests have been used to evaluate the effects of pulmonary rehabilitation in patients with chronic obstructive pulmonary disease (COPD), but the reliability and validity of these tests are not established. OBJECTIVE We evaluated the test-retest reliability and validity of a 6-minute pegboard and ring test (PBRT) in 27 outpatients with COPD and 30 age-matched controls. METHODS We evaluated a 6-minute PBRT, subject demographics, pulmonary function and disease-specific quality of life questionnaire, and the Pulmonary Functional Status Dyspnea Questionnaire-Modified version in 27 patients with COPD. RESULTS Highly significant correlation coefficients (r = .91, P < .001) were found between test and retest of PBRT scores. Statistically significant correlation coefficients were found between PBRT scores and pulmonary function tests such as FEV1% pred and FVC% pred, and activity domain and subdomain of Pulmonary Functional Status Dyspnea Questionnaire-Modified (P <or= .045). In addition, PBRT scores of healthy subjects were significantly higher than those of COPD subjects (P < .001), and were inversely related to age (P = .031). The FEV1% predicted and gender together accounted for 50% of the variance in the PBRT scores of patients with COPD. CONCLUSION PBRT is a reliable and valid method to assess unsupported arm exercise endurance in patients with COPD.
New advances in ovulation induction

Purpose of review To review recent advances in ovulation induction. Recent findings Aromatase inhibitors can replace clomiphene citrate as ovulation-inducing substances. The most widely used aromatase inhibitor for this purpose is letrozole and the optimal dose is 5 mg daily for 5 days. Compared to clomiphene citrate, it is associated with a thicker endometrium and a better pregnancy rate. It is as effective as gonadotropin but yet less expensive. The overall rates of congenital malformation among newborns conceived after infertility treatment with letrozole or clomiphene citrate are similar. When letrozole is combined with gonadotropin, it leads to lower gonadotropin requirements with pregnancy rates comparable to gonadotropin treatment alone. Another promising aromatase inhibitor is anastrazole. Recent evidence suggests that luteinizing hormone activity in human menopausal gonadotropin modifies follicular development so that fewer intermediate-sized follicles develop. Compared to the use of follicular stimulating hormone only, human menopausal gonadotropin is associated with less ovarian hyperstimulation. Summary Aromatase inhibitors are alternative drugs to clomiphene or gonadotropin for ovulation induction or superovulation.
Modeling Holonic Systems with an Organizational approach

Complex Systems often exhibit hierarchical structures and multiple levels of abstraction, and MultiAgent Systems, even if they have proved their adequacy to model such systems, still remains in their larger part at one or two abstraction levels. It seems uncertain in this context that MAS will be able to catch efficiently the whole complexity of such systems. Holonic Multi-Agent Systems and their intrinsic hierarchical structure appears as a natural alternative. In this paper we propose a generic framework for HMAS modeling based upon an organizational approach. The means to model a compound holon using organizations and how to conciliate in a generic way the holonic structure with problem-dependent behaviors, are detailed. Different aspects related to the holon dynamics : holon creation, members integration and self-organization are also studied.
Preclinical studies to predict the disposition of Apo2L/tumor necrosis factor-related apoptosis-inducing ligand in humans: characterization of in vivo efficacy, pharmacokinetics, and safety.

Apo2L/TRAIL (tumor necrosis factor-related apoptosis-inducing ligand) is a member of the tumor necrosis factor gene family known to induce apoptosis in a number of cancer cell lines and may have broad-spectrum activity against human malignancies. These studies have evaluated the potency of recombinant soluble human Apo2L/TRAIL in a mouse xenograft model and the disposition and safety of Apo2L/TRAIL in rodents and nonhuman primates. Mice with established COLO205 tumors were given daily i.v. injections of Apo2L/TRAIL (30-120 mg/kg/day). Control tumors doubled in size every 2 to 3 days, while time to tumor doubling in the treatment groups was significantly longer and related to dose (14-21 days). For pharmacokinetic studies, Apo2L/TRAIL was given as an i.v. bolus to mice (10 mg/kg), rats (10 mg/kg), cynomolgus monkeys (1, 5, and 50 mg/kg), and chimpanzees (1 and 5 mg/kg). Apo2L/TRAIL was rapidly eliminated from the serum of all species studied. Half-lives were approximately 3 to 5 min in rodents and approximately 23 to 31 min in nonhuman primates. Allometric scaling provided estimates of Apo2L/TRAIL kinetics in humans, suggesting that on a milligram per kilogram basis, doses significantly lower than those used in xenograft studies could be effective in humans. Apo2L/TRAIL clearance was highly correlated with glomerular filtration rate across species, indicating that the kidneys play a critical role in the elimination of this molecule. Safety evaluations in cynomolgus monkeys and chimpanzees revealed no abnormalities associated with Apo2L/TRAIL exposure. In conclusion, these studies have characterized the disposition of Apo2L/TRAIL in rodents and primates and provide information that will be used to predict the pharmacokinetics of Apo2L/TRAIL in humans.
A novel Lagrangian-relaxation to the minimum cost multicommodity flow problem and its application to OSPF traffic engineering

The minimum cost multicommodity flow problem plays a central role in today's operations research theory with applications ranging from transportation and logistics to telecommunications network routing. In this paper, we introduce a novel Lagrangian-relaxation technique, which, given an initial feasible solution, can solve the minimum cost multicommodity flow problem as a sequence of single-commodity flow problems. Our methodology is best suited for OSPF traffic engineering, because it can rapidly improve a given path set towards approximate optimality while simultaneously provides the link weights, which implement the paths as shortest paths.
Supercritical Carbon Dioxide and Its Potential as a Life-Sustaining Solvent in a Planetary Environment

Supercritical fluids have different properties compared to regular fluids and could play a role as life-sustaining solvents on other worlds. Even on Earth, some bacterial species have been shown to be tolerant to supercritical fluids. The special properties of supercritical fluids, which include various types of selectivities (e.g., stereo-, regio-, and chemo-selectivity) have recently been recognized in biotechnology and used to catalyze reactions that do not occur in water. One suitable example is enzymes when they are exposed to supercritical fluids such as supercritical carbon dioxide: enzymes become even more stable, because they are conformationally rigid in the dehydrated state. Furthermore, enzymes in anhydrous organic solvents exhibit a “molecular memory”, i.e., the capacity to “remember” a conformational or pH state from being exposed to a previous solvent. Planetary environments with supercritical fluids, particularly supercritical carbon dioxide, exist, even on Earth (below the ocean floor), on Venus, and likely on Super-Earth type exoplanets. These planetary environments may present a possible habitat for exotic life.
Differences in the Onset and Severity of Symptoms of Malignant Hyperthermia with Different Inhalational Anesthetics

Abstract : Malignant hyperthermia (MH) is an uncommon inherited disorder of skeletal muscle in which commonly used anesthetics can trigger sustained skeletal muscle hypermetabolism in patients who may have had no symptoms previously. The onset and severity of clinical symptoms of MH are variable. Non-clinical studies and case reports have identified differences in the onset and severity of symptoms with the commonly used volatile anesthetics. The purpose of this study was to identify if there is a significant difference in the onset and severity of signs and symptoms of malignant hyperthermia in those MH-susceptible patients who received the different volatile anesthetics. A comparative descriptive research design was used. A retrospective review of the database at the (USUHS) MH muscle biopsy diagnostic center was done. The data collected was used to determine if there was a difference in the onset and severity of signs and symptoms of MH episodes with halothane compared to MH episodes of four other volatile anesthetics. For each of these groups, the following variables were assessed: highest temperature, highest end-tidal carbon dioxide, time from beginning of anesthetic until onset of first MH symptom, time of onset of anesthesia until initial treatment for MH, and the incidence of masseter spasm. Based on results of this study, there was no significant difference among the groups. As much of the pediatric data was excluded, the results may have been skewed. Further studies examining these differences between volatile anesthetics would be extremely valuable in understanding the pathophysiology of malignant hyperthermia.
A Review of Applications of Metabolomics in Cancer

Cancer is a devastating disease that alters the metabolism of a cell and the surrounding milieu. Metabolomics is a growing and powerful technology capable of detecting hundreds to thousands of metabolites in tissues and biofluids. The recent advances in metabolomics technologies have enabled a deeper investigation into the metabolism of cancer and a better understanding of how cancer cells use glycolysis, known as the “Warburg effect,” advantageously to produce the amino acids, nucleotides and lipids necessary for tumor proliferation and vascularization. Currently, metabolomics research is being used to discover diagnostic cancer biomarkers in the clinic, to better understand its complex heterogeneous nature, to discover pathways involved in cancer that could be used for new targets and to monitor metabolic biomarkers during therapeutic intervention. These metabolomics approaches may also provide clues to personalized cancer treatments by providing useful information to the clinician about the cancer patient’s response to medical interventions.
The Socio-Economic Significance of Four Phonetic Characteristics in North American English

This paper uses a least-square regression method that relates per-capita income to four phonetic characteristics (r-dropping, and the so-called "father-bother", "cot-caught" and "pin-pen" mergers), to study the socio-economic significance of those characteristics in North American English. As a result we find a positive and statistically significant relationship between per-capita income and r-dropping, and between per-capita income and the presence of the "cot-caught" merger, and a negative and statistically significant relationship between per-capita income and the "pin-pen" merger. No statistically significant relationship is found, however, between per-capita income and the presence of a "father-bother" merger or split.
An integrated hardware-software approach to flexible transactional memory

There has been considerable recent interest in both hardware andsoftware transactional memory (TM). We present an intermediateapproach, in which hardware serves to accelerate a TM implementation controlled fundamentally by software. Specifically, we describe an alert on update mechanism (AOU) that allows a thread to receive fast, asynchronous notification when previously-identified lines are written by other threads, and a programmable data isolation mechanism (PDI) that allows a thread to hide its speculative writes from other threads, ignoring conflicts, until software decides to make them visible. These mechanisms reduce bookkeeping, validation, and copying overheads without constraining software policy on a host of design decisions. We have used AOU and PDI to implement a hardwareacceleratedsoftware transactional memory system we call RTM. We have also used AOU alone to create a simpler "RTM-Lite". Across a range of microbenchmarks, RTM outperforms RSTM, a publicly available software transactional memory system, by as much as 8.7x (geometric mean of 3.5x) in single-thread mode. At 16 threads, it outperforms RSTM by as much as 5x, with an average speedup of 2x. Performance degrades gracefully when transactions overflow hardware structures. RTM-Lite is slightly faster than RTM for transactions that modify only small objects; full RTM is significantly faster when objects are large. In a strongargument for policy flexibility, we find that the choice between eager (first-access) and lazy (commit-time) conflict detection can lead to significant performance differences in both directions, depending on application characteristics.
Pesticides Surveillance on Surface Waters: Developing a Method for Watersheds Prioritization

The occurrence of pesticides in drinking water is a matter of growing concern in several parts of the world, mainly in developing countries, due to the possible adverse effects on human health and the environment. Pesticides applied in the agriculture, important source of contamination, can persist for several years in soil, be retained in agricultural products, be dispersed by the wind or reach the surface and ground waters (Tomita & Beyruth, 2003). Traces of pesticides can be found, both in soil and water sources, depending on their physical and chemical properties, their application and dose patterns, as well as the local environmental characteristics. In Brazil, pesticide monitoring in surface water, both by water supply operators and health authorities, is still rare and insufficient for assessing health risks, often not accomplishing the legal issues regarding the quality control of raw waters (Brazil, 2004b). Inclusion of the whole set of these parameters in monitoring plans is unusual, mainly due to high costs of the analyses and to necessity of specialized manpower. There is also a lack of data on pesticides use in agriculture, in the several Brazilian regions, as well as of studies that associate their use with presence in water and with health risks. Additionally, low potential of pesticides removal in most of the Brazilian water treatment plants completes the picture of lack of reliable information on health risks associated with pesticides exposure by water ingestion. The lack of data and of financial and material resources to comprehensive pesticide surveillance suggests tracing other alternatives to the evaluation of potentiality of pesticides occurrence in surface water. Thus, the aim of this chapter is to discuss a method for prioritization of surveillance actions of pesticides in surface waters, through multicriteria analysis. In the chapter, firstly we discuss concepts related to the subject. Secondly, the structure of the method is presented and, thirdly, we describe an application in Rio Grande basin, Minas Gerais, Brazil. Finally, we draw some conclusions on the study.
The influence of mode of delivery, hormonal status and postnatal O2 environment on epithelial sodium channel (ENaC) expression in perinatal guinea‐pig lung

We have studied factors that potentially modulate the expression of mRNA coding for subunits of the amiloride‐sensitive sodium channel, αENaC and βENaC, in lungs of vaginally and Caesarean (CS)‐delivered late gestation fetal guinea‐pigs. Expression of αENaC and βENaC mRNAs was developmentally regulated in the late gestation fetus, reaching peak levels at term (68 days post conception, PC) and postnatally, respectively. In animals delivered by CS at 65 days PC and term, αENaC mRNA expression was significantly increased by day 1 post partum, reaching levels greater than those normally achieved in vaginally delivered animals at term. In contrast, βENaC mRNA levels remained significantly lower postnatally in animals delivered by CS at 65 days PC compared with those in vaginally and CS‐delivered animals at term. Plasma cortisol and total triiodothyronine (T3) levels increased towards term, were higher 1 day after vaginal delivery but declined towards pre‐term levels by day 3. Cortisol levels also increased rapidly in the CS‐delivered animals, reaching levels similar to those in vaginally delivered animals at day 1. Plasma T3 levels at days 1 and 3 were significantly lower in animals delivered by CS at 65 days PC. The increase in αENaC mRNA paralleled the increase in plasma cortisol after delivery, but not T3, and inhibition of cortisol synthesis with 2‐methyl‐1,2‐di‐3‐pyridyl‐1‐propanone (metyrapone) after CS delivery suppressed the increase in αENaC mRNA expression. Concomitant with the increase in αENaC mRNA expression after CS delivery at 65 days PC was an increase in the amiloride‐blockable component of lung fluid clearance by day 3 postnatally. We conclude that in late gestation guinea‐pigs delivered by CS there is a significant increase in lung αENaC expression postnatally, which is mediated, in part, by the postnatal rise in cortisol at delivery. This in turn leads to an increase in amiloride‐sensitive lung fluid clearance, which is unrelated to labour.
Epigenetic regulation of insulin resistance in nonalcoholic fatty liver disease: Impact of liver methylation of the peroxisome proliferator–activated receptor γ coactivator 1α promoter

Insulin resistance (IR) and mitochondrial dysfunction play a central role in the pathophysiology of nonalcoholic fatty liver disease (NAFLD). We hypothesized that genetic factors and epigenetic modifications occurring in the liver contribute to the IR phenotype. We specifically examined whether fatty liver and IR are modified by hepatic DNA methylation of the peroxisome proliferator–activated receptor γ coactivator 1α (PPARGC1A) and mitochondrial transcription factor A (TFAM) promoters, and also evaluated whether liver mitochondrial DNA (mtDNA) content is associated with NAFLD and IR. We studied liver biopsies obtained from NAFLD patients in a case–control design. After bisulfite treatment of DNA, we used methylation‐specific polymerase chain reaction (PCR) to assess the putative methylation of three CpG in the PPARGC1A and TFAM promoters. Liver mtDNA quantification using nuclear DNA (nDNA) as a reference was evaluated by way of real‐time PCR. Liver PPARGC1A methylated DNA/unmethylated DNA ratio correlated with plasma fasting insulin levels and homeostasis model assessment of insulin resistance (HOMA‐IR); TFAM methylated DNA/unmethylated DNA ratio was inversely correlated with insulin levels. PPARGC1A promoter methylation was inversely correlated with the abundance of liver PPARGC1A messenger RNA. The liver mtDNA/nDNA ratio was significantly higher in control livers compared with NAFLD livers. mtDNA/nDNA ratio was inversely correlated with HOMA‐IR, fasting glucose, and insulin and was inversely correlated with PPARGC1A promoter methylation. Conclusion: Our data suggest that the IR phenotype and the liver transcriptional activity of PPARGC1A show a tight interaction, probably through epigenetic modifications. Decreased liver mtDNA content concomitantly contributes to peripheral IR. (HEPATOLOGY 2010)
Towards the Development of a Low Cost Airborne Sensing System to Monitor Dust Particles after Blasting at Open-Pit Mine Sites

Blasting is an integral part of large-scale open cut mining that often occurs in close proximity to population centers and often results in the emission of particulate material and gases potentially hazardous to health. Current air quality monitoring methods rely on limited numbers of fixed sampling locations to validate a complex fluid environment and collect sufficient data to confirm model effectiveness. This paper describes the development of a methodology to address the need of a more precise approach that is capable of characterizing blasting plumes in near-real time. The integration of the system required the modification and integration of an opto-electrical dust sensor, SHARP GP2Y10, into a small fixed-wing and multi-rotor copter, resulting in the collection of data streamed during flight. The paper also describes the calibration of the optical sensor with an industry grade dust-monitoring device, Dusttrak 8520, demonstrating a high correlation between them, with correlation coefficients (R2) greater than 0.9. The laboratory and field tests demonstrate the feasibility of coupling the sensor with the UAVs. However, further work must be done in the areas of sensor selection and calibration as well as flight planning.
Combinatorial antibody libraries from survivors of the Turkish H5N1 avian influenza outbreak reveal virus neutralization strategies

The widespread incidence of H5N1 influenza viruses in bird populations poses risks to human health. Although the virus has not yet adapted for facile transmission between humans, it can cause severe disease and often death. Here we report the generation of combinatorial antibody libraries from the bone marrow of five survivors of the recent H5N1 avian influenza outbreak in Turkey. To date, these libraries have yielded >300 unique antibodies against H5N1 viral antigens. Among these antibodies, we have identified several broadly reactive neutralizing antibodies that could be used for passive immunization against H5N1 virus or as guides for vaccine design. The large number of antibodies obtained from these survivors provide a detailed immunochemical analysis of individual human solutions to virus neutralization in the setting of an actual virulent influenza outbreak. Remarkably, three of these antibodies neutralized both H1 and H5 subtype influenza viruses.