Miracle-dz/UniFAR-FTUs huggingface dataset:
Compilation and prevalence of mutations associated with resistance to non-nucleoside reverse transcriptase inhibitors

Background Non-nucleoside reverse transcriptase inhibitors (NNRTIs) are an important component of antiretroviral therapy for HIV type-1 (HIV-1)-infected patients. Development of NNRTI resistance can lead to treatment failure and is conferred by the presence of specific resistance-associated mutations (RAMs) in the reverse transcriptase. In addition to the widely used list of NNRTI RAMs provided by the International AIDS Society-USA HIV-1 Drug Resistance Mutation Group, which were identified on the basis of clinical experience with the approved NNRTIs, a more comprehensive list of NNRTI RAMs is needed to guide the study of baseline and emerging resistance to new NNRTIs. Methods We conducted an extensive review of the existing literature on NNRTI resistance, together with several in vitro and in vivo studies on the mechanism of HIV-1 resistance to approved NNRTIs and to NNRTIs formerly or currently in clinical development. Results In total, 44 NNRTI RAMs were identified. These included V90I, A98G, L100I, K101E/P/Q, K103H/N/S/T, V106A/I/M, V108I, E138G/K/Q, V179D/E/F/G/I, Y181C/ I/V, Y188C/H/L, V189I, G190A/C/E/Q/S, H221Y, P225H, F227C/L, M230I/L, P236L, K238N/T and Y318F. These NNRTI RAMs were observed, either alone or in combination with others, ranging in frequency from 0.02% to 56.96% in a panel of 101,679 NNRTI-resistant isolates submitted to Virco BVBA (Mechelen, Belgium) for routine clinical resistance testing. Phenotypical data from site-directed mutants helped to establish the contribution of each mutation to NNRTI resistance. Conclusions The list of 44 NNRTI RAMs compiled in this study provides a comprehensive overview of mutations that play a role in HIV-1 NNRTI resistance and can be used to guide further in vitro and in vivo research on the mechanisms of HIV-1 NNRTI resistance.
A pseudo-boolean programming approach for CMOL cell assignment

In this paper, we introduce a pseudo-boolean programming approach to CMOL cell assignment. Unlike the SAT-based method, we encode the CMOL cell assignment problem as pseudo-boolean (PB) constraints; and the problem can be solved by using PB solver. The proposed method is tested on ISCAS benchmarks. Experimental results show that the proposed method has small constraints files, and can deal with some circuits while the SAT-based method can't do.
Modeling The Fan Effect Using Dynamically Structured Holographic Memory

Dynamically Structured Holographic Memory (DSHM), a system based on holographic reduced representations, designed for modeling memory is described. A DSHM model of the fan effect (Anderson, 1974) is presented. Comparisons between the DSHM model and an existing ACT-R model (Anderson & Reder, 1999) are made. It is argued that DSHM can be interpreted as providing a lower-level account of several features of ACT-R such as activation, noise, and the ability to make errors.
Effects of mesenchyme on epithelial tissue architecture revealed by tissue recombination experiments between the submandibular gland and lung of embryonic mice

Lung epithelium during morphogenesis maintains a sheet structure of polarized cells lining a lumen, in which E‐cadherin, β‐catenin and tight junctional proteins are localized at the cell–cell contact sites. On the other hand, the submandibular gland epithelium at early stages of development forms a non‐cavitated mass of cells where E‐cadherin/β‐catenin are present on the entire cell surfaces and tight junctional proteins are almost absent or weakly scattered. In the present study, tissue recombination experiments were performed between the two organs to explore roles of mesenchyme in the architectural development of the epithelium. Homotypic recombinants of both submandibular gland and lung showed the tissue architecture as observed in the intact organs. In contrast, 11‐day lung epithelium cultured with 13‐day submandibular mesenchyme formed multilayers of cells with the lumen being less visible. It was accompanied by redistribution of E‐cadherin/β‐catenin along the entire cell surfaces and by an irregular distribution of tight junctional proteins. A similar redistribution of these molecules was observed in 15‐day lung epithelium cultured with the submandibular mesenchyme, although the epithelial sheet structure lining the lumen was formed. On the other hand, the tissue architecture of submandibular gland epithelium was little affected by lung mesenchyme, although the epithelium was flattened and showed branching morphogenesis.
Proximate causes of adaptive growth rates: growth efficiency variation among latitudinal populations of Rana temporaria

In ectothermic organisms, declining season length and lower temperature towards higher latitudes often select for latitudinal variation in growth and development. However, the energetic mechanisms underlying this adaptive variation are largely unknown. We investigated growth, food intake and growth efficiency of Rana temporaria tadpoles from eight populations along a 1500 km latitudinal gradient across Sweden. To gain an insight into the mechanisms of adaptation at organ level, we also examined variation in tadpole gut length. The tadpoles were raised at two temperatures (16 and 20 °C) in a laboratory common garden experiment. We found increased growth rate towards higher latitudes, regardless of temperature treatment. This increase in growth was not because of a higher food intake rate, but populations from higher latitudes had higher growth efficiency, i.e. they were more efficient at converting ingested food into body mass. Low temperature reduced growth efficiency most strongly in southern populations. Relative gut length increased with latitude, and tadpoles at low temperature tended to have longer guts. However, variation in gut length was not the sole adaptive explanation for increased growth efficiency as latitude and body length still explained significant amounts of variation in growth efficiency. Hence, additional energetic adaptations are probably involved in growth efficiency variation along the latitudinal gradient.
PCR Detection of Entamoeba histolytica, Entamoeba dispar, and Entamoeba moshkovskii in Stool Samples from Sydney, Australia

ABSTRACT This study investigated the presence of Entamoeba histolytica, Entamoeba dispar, and Entamoeba moshkovskii in stool samples from a patient population in Sydney, Australia. Stool samples were tested by microscopy and PCR. Five patients were found with E. histolytica infections, while E. dispar and E. moshkovskii were observed in 63 (70.8%) and 55 (61.8%) patients, respectively, by PCR. This is the first study in Australia using molecular techniques to determine the presence of E. histolytica, E. dispar, and E. moshkovskii.
Adaptive Link Aware on-demand Multicast Routing Scheme in MANET

The main objective of this paper is to propose a new multicast routing scheme to adopt with the dynamic topology of MANET at the same time to provide high multicast efficiency and packet delivery ratio. The proposed scheme is named as Link Aware on Demand Multicast Routing (LAOMR) scheme. In this scheme, initially the source node forms the multicast group by announcing itself as a multicast source agent to all the nodes in the network. The nodes which are eager to join in the group are sending the join request to the source node. Then the source node finds the route to reach the multicast group through some intermediate nodes. The intermediate nodes are not interested to hear the multicast message but they are act as the routers to forward the packets to the multicast group. The intermediate nodes are chosen based on the link residual life (LRL) of the nodes. The node which has the highest LRL and closer to the multicast group is selected as the forwarder node. So, the proposed scheme reduces the link failure in the multicast route and increases the multicast efficiency, throughput. The performance is evaluated by using the simulation results obtained from NS2 Simulator.
Pair-instability and super-luminous supernova discoveries

We present the discovery of three super-luminous supernovae (SLSNe) at z= 2−4 as part of our survey to detect ultraviolet-luminous supernova at z > 2. SLSNe are ≥10 times more luminous than normal supernova types, reaching peak luminosities of 1044 erg s−1. A small subset of SLSNe (type SLSN-R) exhibit a slow evolution, and thus enormous integrated energies ( 1051 erg), consistent with the radiative decay of several solar masses of 56Ni. SLSN-R are believed to be the deaths of very massive stars, ∼140 260 M , that are theorized to result in pair-instability supernovae. Two of the high redshift SLSNe presented here are consistent with the behavior of SLSN-R out to the extent in which their light curves are sampled, with the third event being consistent with the more rapid fade of the type II-L SLSN SN 2008es at z = 0.205. SLSNe are extremely rare locally but are expected to have been more common in the early Universe and as members of the first generation of stars to form after the Big Bang, the Population III stars. The high intrinsic luminosity of SLSNe and their detectability using our image-stacking technique out to z ∼ 6 provide the first viable route to detect and study the deaths of massive Population III stars which are expected to form in pristine gas at redshifts as low as z∼ 2.
Driving innovation, leadership and change at Groote Schuur Hospital, Cape Town, South Africa.

Globally, cost-effective and equitable delivery of healthcare is becoming a challenge. In the South African (SA) context, balancing the burden of disease and the patient load within available resources, while still maintaining quality of care, is becoming unsustainable. Our public healthcare services need to support a growing population of uninsured citizens together with immigrants from elsewhere in Africa seeking care, and while the reasons for the problem are both economic and related to health service design and delivery, it is compounded by an ageing population, a rising burden of infectious and chronic diseases and the global shortage of adequately skilled healthcare workers. The leaders of today will need to do something different in order to avoid collapse of the system.
A Novel Demand Response Model with an Application for a Virtual Power Plant

In modern power systems and electricity markets, demand response (DR) programs play an important role enabling the mitigation of critical load periods or price-peaking scenarios, thereby improving system reliability. Price fluctuations, in forward or real-time markets, can be an effective price-based DR mechanism for curtailing or shifting load. However, using dynamic pricing to achieve a desired load profile requires both an accurate demand forecast and knowledge of the price elasticity of demand, which is notoriously difficult to estimate. The limited accuracy of these parameter estimates is the main source of uncertainty limiting appropriate DR implementation. In this paper, we present a novel DR scheme that avoids the need to predict the price elasticity of demand or demand forecast, yet still delivers a significant DR. This is done based on the consumers' submissions of candidate load profiles ranked in the preference order. The load aggregator then performs the final selection of individual load profiles subject to the total system cost minimization. Additionally, the proposed DR model incorporates a fair billing mechanism that is enhanced with an ex post consumer performance tracking scheme implemented in a context of a virtual power plant aggregating load and generation units.
Lead‐Induced Abnormalities of Porphyrin Metabolism The Relationship with Iron Deficiency a

Lead poisoning remains a serious public health problem in this country, particularly for underprivileged urban children. The major source of Pb is household dust,’ containing not only Pb from peeling paint in old buildings but also the deposits of airborne Pb. ’ Epidemiological studies from our laboratory have provided evidence that low-level exposure to Pb results in biochemical toxicity to children. ’ These studies, and the demonstration that neurological damage is possible at a low level of e x p ~ s u r e , ~ have been instrumental in inspiring the Environmental Protection Agency to legislate the progressive reduction of Pb in gasoline. There has been a substantial decrease in the average blood Pb (BPb) in recent years, associated with a reduction in the use of Pb in gasoline.5-* This has greatly reduced the average BPb of all Americans and the frequency of clinically severe childhood Pb poisoning. The situation is greatly improved from the deplorable state that existed in the 1960s. Many children, however, still have an excessive body burden of Pb.9 The HANES study” indicates that 4% of American children 6 months to 5 years old (that is, over 650 000 children) have an excessive body burden of Pb; the percentage rises to 18% among poor urban black children. A simple and accurate fluorometric technique for measurement of erythrocyte protoporphyrin (EP) from a finger puncture was developed by us” in 1972. This method (the EP Test) has become the standard for Pb-poisoning screening12 and has opened the way to a nationwide screening program for childhood Pb poisoning; this program has tested several millions of children and detected hundreds of thousands of unsuspected cases. The initial observations were rapidly It was soon apparent that elevation of EP has greater clinical relevance to childhood Pb poisoning and to neurological toxicity than the BPb level itself. ”-I9 The Center for Disease Control” recommended that children with BPb >30 pg/dl be given medical attention, if they also had an elevated EP. These recommendations have been recently updated to include children with BPb >25 pg/dl, and with elevated EP. ” As our knowledge of the toxic effects of Pb increases, the acceptable body burden decreases. In 1965, Patterson-on purely geophysical considerations-postulated a
Enhanced confocal microscopy imaging of the in-plane switching of cholesteric liquid crystal cells

The recently developed fluorescence confocal polarizing microscopy (FCPM) imaging technique allows 3D images of the director structure in a liquid crystal cell to be resolved with sub-micron resolution. Results are presented on imaging the response of 5-micron pitch cholesteric liquid crystals to an in-plane electric field applied between two silver electrodes. The results show, in exquisite detail, how the application of an in-plane field causes the cholesteric helix to tilt through 90° either within, or immediately adjacent to, the electrode gap depending on the sign of the dielectric anisotropy of the liquid crystal. Furthermore, imaging the cholesteric material above the silver electrodes reveals a previously unreported optical intensity enhancement. This phenomenon is discussed along with its possible benefits to the existing imaging technique. The effects of the point spread function of the system are discussed and a ray optics model is used to produce model data highlighting the influence of this phenomenon on the recorded results.
Vocabulary Coverage in Spanish Textbooks: How Representative is It?

Certainly one of the primary goals in developing materials for second language learners should be to create materials that reflect vocabulary and grammar that these learners are likely to encounter in the “real world”. There is little to be gained from having students memorize long lists of vocabulary in a textbook, if the learners never again encounter these words once they venture out in the “real world”. The goal of this paper is to determine how well Spanish textbooks do in terms of including realistic, frequency-based vocabulary. We will consider this from two different points of view. First, in quantitative terms, we will consider what percentage of the vocabulary in textbooks appears in standard frequency listings of Spanish vocabulary (and vice versa). Second, in qualitative terms, we will consider what type of vocabulary is both over-represented and also under-represented in Spanish textbooks, vis a vis actual frequency data from other sources. Before we can address either question, however, we first need to consider two additional questions. First, where can we go to get reliable frequency data for Spanish? Second, how do we measure the vocabulary that appears in textbooks. We will consider the fist two questions in Sections 2 and 3. In Sections 4 and 5 we will then return to the question of representativeness of vocabulary in Spanish textbooks – from both a quantitative and qualitative point of view. Finally, in a point that we will come back to later in the paper, we should note that this is not a paper on second language acquisition in general, nor the specific issue of vocabulary acquisition. Our focus is strictly the quantitative, corpus-based issue of how vocabulary in Spanish textbooks relates to “real world” language use. Thus this study is only one part of the puzzle, although arguably one of the first pieces needed to create the entire picture.
Phase relations and their petrological implications in the system MgO-SiO 2H 2 OCO 2 at pressures up to lfi ) kbar

A comprehensive model has been developed for phase relations in the system MgO-SiOrHrO-CO, on the basis of Schreinemakers' rules and subsolidus thermodynamic data. The assemblage forsterite plus enstatite can melt in the presence of vapor of any HrO,/CO, ratio at low pressures, in the presence of vapor whose HrOlCO, ratio is bufered by magnesite at intermediate pressures, and at a vapor-absent eutectic at high pressures. Forsterite and HrOCO, vapor cannot coexist at pressures greater than 90 kbar. A thermal maximum is postulated to exist on the reaction Fo * En * V + L at pressures greater than 35 kbar. Thermal maxima on vapor-present melting reactions may be responsible for the eruption of kimberlitic magma from the upper mantle.
Scale‐down of continuous filtration for rapid bioprocess design: Recovery and dewatering of protein precipitate suspensions

The early specification of bioprocesses often has to be achieved with small (tens of millilitres) quantities of process material. If extensive process discovery is to be avoided at pilot or industrial scale, it is necessary that scale‐down methods be created that not only examine the conditions of process stages but also allows production of realistic output streams (i.e., streams truly representative of the large scale). These output streams can then be used in the development of subsequent purification operations. The traditional approach to predicting filtration operations is via a bench‐scale pressure filter using constant pressure tests to examine the effect of pressure on the filtrate flux rate and filter cake dewatering. Interpretation of the results into cake resistance at unit applied pressure (α) and compressibility (n) is used to predict the pressure profile required to maintain the filtrate flux rate at a constant predetermined value. This article reports on the operation of a continuous mode laboratory filter in such a way as to prepare filter cakes and filtrate similar to what may be achieved at the industrial scale. Analysis of the filtration rate profile indicated the filter cake to have changing properties (compressibility) with time. Using the insight gained from the new scale‐down methodology gave predictions of the flux profile in a pilot‐scale candle filter superior to those obtained from the traditional batch filter used for laboratory development. © 2003 Wiley Periodicals, Inc. Biotechnol Bioeng 83: 454–464, 2003.
Re-evaluation of the oxygen diffusion model for predicting minimum contact lens Dk/t values needed to avoid corneal anoxia.

PURPOSE (1) To update Fatt's mathematical model of the distribution of oxygen tension (pO2) across the cornea and contact lens (CL) to include the recent finding that corneal oxygen consumption increases with the acidification that occurs with CL wear. (2) To estimate the minimum transmissibility (CL Dk/t) to avoid epithelial anoxia or to avoid stromal anoxia. METHODS A five-layer static and one-dimensional mathematical model of oxygen diffusion through the cornea based on Fatt's models was used. The relationships between acidosis and increased QO2, and acidosis and CL Dk/t were used to estimate corneal QO2 for a given CL Dk/t. RESULTS (1) Revised model predictions are in agreement with direct tear pO2 measurements beneath CLs in the rabbit. (2) For the human eye, the minimum CL Dk/t for oxygen delivery to the basal epithelial cells was determined to be 23 for the open eye and 89 for the closed eye. To prevent anoxia throughout the entire corneal thickness the Dk/t requirements are 35 for the open eye and 125 for the closed eye. CONCLUSIONS (1) Model predictions of the oxygen distribution beneath contact lenses are significantly lower than previous models that did not include the effect of acidosis on corneal QO2. (2) Minimum Dk/t values that allow oxygen delivery to the basal epithelium are in agreement with the Dk/t needed to avoid corneal edema.
Association of Mx1 gene polymorphism with some economic traits in Meishan pigs

This study was conducted to determine the association of polymorphisms in exon 14 of the Mx1 gene with significant economic traits in Meishan pigs, with the aim of identifying genetic markers of disease resistance. PCR-RFLP analysis of exon 14 of the Mx1 gene was conducted and associations with some cytokine levels (IFN-$\alpha$, IFN-$\gamma$, IL-2, IL-6, IL-10, and IL-12), early body weight (birth weight, 20-day weight, and 40-day weight), and reproductive performance within different parities (total number born, number born alive, number in live weaning litter, birth weight, and weaning weight) were analyzed. The results showed that there were AA, AB, and BB genotypes defined, while a G36T mutation was identified in BB genotype individuals of Meishan pigs. Correlation analysis indicated that the IFN-$\gamma$ levels were significantly higher in the AA genotype than the AB genotype (P < 0.05). However, there were no significant differences in the levels of other cytokines, early body weight, and reproductive performance among the three genotypes. These data indicated that selective molecular breeding practices may enhance the antiviral capability of Meishan pigs without detrimental influences on early body weight, development, and reproductive performance.
Antioxidative and cytoprotective effects of andrographolide against CCl4-induced hepatotoxicity in HepG2 cells

This article describes antioxidative and cytoprotective property of andrographolide, a major active component of the plant Andrographis paniculata (A. paniculata). High yields (2.7%) of andrographolide was isolated from the aerial parts of this plant via silica column chromatography. The purity of the compound was determined by high-performance thin-layer chromatography (HPTLC) and reversed phase high-performance liquid chromatography (HPLC) analysis. The structure was elucidated using techniques such as UV-visible spectrophotometry, elemental analysis, Fourier transform infrared (FT-IR), 1H nuclear magnetic resonance (1H NMR), 13C nuclear magnetic resonance (13C NMR) and mass spectral analysis and the data obtained were comparable with reported results. It was observed that andrographolide exhibited significant antioxidative property (IC50 = 3.2 µg/ml) by its ability to scavenge a stable free radical 1,1-diphenyl-2-picrylhydrazyl (DPPH) as compared to known antioxidants like ascorbic acid, butylated hydroxy toluene (BHT) and the plant extract. The cytoprotective role of andrographolide against carbon tetrachloride (CCl4) toxicity in human hepatoma HepG2 cell line was assessed using trypan blue exclusion test, 3-(4, 5-dimethylthiazol-2-yl)-2, 5-diphenyltetrazolium bromide (MTT) assay, by estimation of various leakage enzymes and by measuring the glutathione levels. The recovery obtained for andrographolide treatment in the presence of CCl4 was two-fold compared to A. paniculata extract for all other related biochemical parameters investigated. The results of the study indicate that andrographolide is a potent inhibitor of CCl4-mediated lipid peroxidation.