Miracle-dz/UniFAR-FTUs huggingface dataset:
Synthesis and assembly of retrovirus Gag precursors into immature capsids in vitro

The assembly of retroviral particles is mediated by the product of the gag gene; no other retroviral gene products are necessary for this process. While most retroviruses assemble their capsids at the plasma membrane, viruses of the type D class preassemble immature capsids within the cytoplasm of infected cells. This has allowed us to determine whether immature capsids of the prototypical type D retrovirus, Mason-Pfizer monkey virus (M-PMV), can assemble in a cell-free protein synthesis system. We report here that assembly of M-PMV Gag precursor proteins can occur in this in vitro system. Synthesized particles sediment in isopycnic gradients to the appropriate density and in thin-section electron micrographs have a size and appearance consistent with those of immature retrovirus capsids. The in vitro system described in this report appears to faithfully mimic the process of assembly which occurs in the host cell cytoplasm, since M-PMV gag mutants defective in in vivo assembly also fail to assemble in vitro. Likewise, the Gag precursor proteins of retroviruses that undergo type C morphogenesis, Rous sarcoma virus and human immunodeficiency virus, which do not preassemble capsids in vivo, fail to assemble particles in this system. Additionally, we demonstrate, with the use of anti-Gag antibodies, that this cell-free system can be utilized for analysis in vitro of potential inhibitors of retrovirus assembly.
Probability Theory

These notes cover the basic definitions of discrete probability theory, and then present some results including Bayes' rule, inclusion-exclusion formula, Chebyshev's inequality, and the weak law of large numbers. 1 Sample spaces and events To treat probability rigorously, we define a sample space S whose elements are the possible outcomes of some process or experiment. For example, the sample space might be the outcomes of the roll of a die, or flips of a coin. To each element x of the sample space, we assign a probability, which will be a non-negative number between 0 and 1, which we will denote by p(x). We require that x∈S p(x) = 1, so the total probability of the elements of our sample space is 1. What this means intuitively is that when we perform our process, exactly one of the things in our sample space will happen. Example. The sample space could be S = {a, b, c}, and the probabilities could be p(a) = 1/2, p(b) = 1/3, p(c) = 1/6. If all elements of our sample space have equal probabilities, we call this the uniform probability distribution on our sample space. For example, if our sample space was the outcomes of a die roll, the sample space could be denoted S = {x 1 , x 2 ,. , x 6 }, where the event x i correspond to rolling i. The uniform distribution, in which every outcome x i has probability 1/6 describes the situation for a fair die. Similarly, if we consider tossing a fair coin, the outcomes would be H (heads) and T (tails), each with probability 1/2. In this situation we have the uniform probability distribution on the sample space S = {H, T }. We define an event A to be a subset of the sample space. For example, in the roll of a die, if the event A was rolling an even number, then A = {x 2 , x 4 , x 6 }. The probability of an event A, denoted by P(A), is the sum of the probabilities of the corresponding elements in the sample space. For rolling an even number, we have P(A) = p(x 2) + p(x 4) + p(x 6) = 1 2 Given an event A of our sample space, there is a complementary event which consists of all points in our sample space that are not …
Secret keys from entangled sensor motes: implementation and analysis

Key management in wireless sensor networks does not only face typical, but also several new challenges. The scale, resource limitations, and new threats such as node capture and compromise necessitate the use of an on-line key generation, where secret keys are generated by the nodes themselves. However, the cost of such schemes is high since their secrecy is based on computational complexity. Recently, several research contributions justified that the wireless channel itself can be used to generate information-theoretic secure keys between two parties. By exchanging sampling messages during movement, a bit string can be derived that is only known to the involved entities. Yet, movement is not the only possibility to generate randomness. The channel response is also strongly dependent on the frequency of the transmitted signal. In our work, we introduce a protocol for key generation based on the frequency-selectivity of channel fading. The great practical advantage of this approach is that we do not rely on node movement as the source of randomness. Thus, the frequent case of a sensor network with static motes is supported. Furthermore, the error correction property of the proposed protocol mitigates the effects of measurement errors and other temporal effects, giving rise to a key agreement rate of over 97%. We show the applicability of our protocol by implementing it on MICAz motes, and evaluate its robustness and secrecy through experiments and analysis.
Controlled release of raloxifene by nanoencapsulation: effect on in vitro antiproliferative activity of human breast cancer cells

Raloxifene hydrochloride (RH) is considered to be an antiproliferative agent of mammary tissue. The aim of this study was to investigate the effect of the encapsulation of RH in polymeric nanocapsules with anionic or cationic surface on its release profile and antiproliferative activity. They were prepared by interfacial deposition of preformed polymer, followed by wide physicochemical characterization. The in vitro RH release was assessed by the dialysis membrane method and the data analyzed by mathematical modeling. The antiproliferative effect on MCF-7 cell viability was investigated by 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide assay as well as by counting viable cells. They had high encapsulation efficiency, low polydispersity, and nanometric mean size. Nanocapsules prepared with Eudragit® RS100 and Eudragit® S100 presented positive and negative zeta potentials, respectively. Drug release studies demonstrated controlled release of RH from anionic nanocapsules, which could be explained due to a stronger interaction of the drug to these nanocapsules and the larger amount of entrapped drug. On the other hand, this control was not observed from cationic nanocapsules due to the larger amount of drug adsorbed onto their surface. MCF-7 cell viability studies and cell counting showed that RH-loaded Eudragit® RS100 nanocapsules promote the best antiproliferative activity after 24 hours of treatment, whereas the best activity was observed for RH-loaded Eudragit® S100 nanocapsules after 72 hours. Furthermore, the combined treatment of these formulations improved the antiproliferative effect during the entire treatment.
Systematic review of the association between exercise tests and patient-reported outcomes in patients with chronic obstructive pulmonary disease

Introduction Chronic obstructive pulmonary disease (COPD) is an increasingly common cause of death worldwide. Its cardinal symptoms include breathlessness and severely reduced exercise capacity. Several patient-reported outcome (PRO) measures are used to assess health-related quality of life (HRQoL), functional performance, and breathlessness in patients with COPD. Exercise testing is employed to measure functional performance objectively, which is generally believed to impact on overall HRQoL. However, the extent to which commonly used laboratory- and field-based exercise test results correlate with PROs has not been systematically assessed. Materials and methods A search of Embase, MedLine, and the Cochrane Library identified primary publications in English that reported data on the correlations (Pearson’s r or Spearman’s ρ) between the outcomes of exercise tests and HRQoL and breathlessness PROs. Studies reporting on the following tests were included: 6-minute walk test (6MWT), 12MWT, incremental and endurance shuttle walk tests, incremental and endurance cycle ergometer tests, and treadmill tests. Results Of 3,205 articles screened, 28 were deemed eligible for inclusion. The most commonly reported HRQoL PRO measure was the St George’s Respiratory Questionnaire (13 studies), and the most commonly reported breathlessness PRO measure was the Baseline Dyspnea Index (six studies). The St George’s Respiratory Questionnaire appears to correlate very weakly to moderately with the 6MWT, and breathlessness PROs appear to be moderately to strongly associated with 6MWT outcomes. Across all studies, the 6MWT was the most commonly reported exercise test. Very few publications reporting associations between other exercise tests and PRO measures were found. Conclusion This review found evidence to support the association of 6MWT outcomes with HRQoL and breathlessness PROs. There were limited data showing correlations with the outcomes of other exercise tests. Further work is required to examine the associations between these PROs and exercise test outcomes.
Pharmacokinetics of trimethoprim in the rat.

The pharmacokinetics of trimethoprim was studied in male Sprague-Dawley rats following the intravenous administration of trimethoprim at a dose of 25 mg/kg. Plasma and tissue levels of trimethoprim, as a function of time, were determined by reversed-phase high-performance liquid chromatography. The disposition of trimethoprim was described by both a two-compartment open model with elimination from a central compartment and a noncompartmental method. For the compartmental analysis, the terminal elimination rate constant, elimination half-life, apparent volume of distribution in the central compartment, apparent volume of distribution in the central compartment based on the area under the plasma concentration-time curve, and volume of distribution at steady state, were determined to be 0.007 min-1, 99 min, 2059 mL/kg, 5729 mL/kg, and 2473 mL/kg, respectively. Noncompartmental pharmacokinetic parameters were obtained by the statistical moment theory. The estimates for mean residence time, clearance, and volume of distribution at steady state of trimethoprim were calculated to be 52 min, 40 mL.min-1kg-1, and 2097 mL, respectively. Tissue distribution of trimethoprim followed a biphasic phenomenon with a maximum concentration at 30 min for heart, lung, spleen, liver, kidney, seminal vesicles, and muscle, and at 45 min for testicles, 20 min for prostate gland, and less than 10 min for brain. The data show that compared with the plasma concentration, higher levels of trimethoprim were found in heart, lung, spleen, liver, kidney, prostate gland, and seminal vesicles; a similar concentration was found for muscle, but lower levels of trimethoprim were found for brain and testicles.
Triaxial Accelerometer-Based Fall Detection Method Using a Self-Constructing Cascade-AdaBoost-SVM Classifier

In this paper, we propose a cascade-AdaBoost-support vector machine (SVM) classifier to complete the triaxial accelerometer-based fall detection method. The method uses the acceleration signals of daily activities of volunteers from a database and calculates feature values. By taking the feature values of a sliding window as an input vector, the cascade-AdaBoost-SVM algorithm can self-construct based on training vectors, and the AdaBoost algorithm of each layer can automatically select several optimal weak classifiers to form a strong classifier, which accelerates effectively the processing speed in the testing phase, requiring only selected features rather than all features. In addition, the algorithm can automatically determine whether to replace the AdaBoost classifier by support vector machine. We used the UCI database for the experiment, in which the triaxial accelerometers are, respectively, worn around the left and right ankles, and on the chest as well as the waist. The results are compared to those of the neural network, support vector machine, and the cascade-AdaBoost classifier. The experimental results show that the triaxial accelerometers around the chest and waist produce optimal results, and our proposed method has the highest accuracy rate and detection rate as well as the lowest false alarm rate.
Role of the Left Atrium in Adaptation of the Heart to Chronic Mitral Regurgitation in Conscious Dogs

The manner in which the left atrium adapts to chronic mitral regurgitation and the role of the adapted left atrium as a modulator of excessive central blood volume were analyzed in seven conscious dogs, instrumented with high-fidelity pressure transducers and ultrasonic dimension gauges for measurement of left atrial and left ventricular pressure and cavity size. After obtaining data in a control situation, mitral regurgitation was produced by transventricular chordal sectioning. Heart rate was matched by right atrial pacing. In the “early” stage (7–14 days), left ventricular end-diastolic and mean left atrial pressures increased from 6 to 16 mm Hg and from 4 to 12 mm Kg, respectively. Both left ventricular end-diastolic segment length and left atrial diameter prior to atrial contraction increased by 7%. In the “late” stage (20–35 days), despite significant decreases in left ventricular filling pressure (11 mm Hg) and left atrial pressure (8 mm Hg), there was a continuous increase in left ventricular end-diastolic dimension (10%) and atrial end-diastolic diameter (10%). After the onset of mitral regurgitation, the left atrium performed greater work with a more enlarged cavity. Left atrial chamber stiffness was progressively decreased. These changes were associated with progressive increase in the left atrial diameter at zero stress, and there was a significant increase in the diameter of the left atrial myocyte. These results indicate that during chronic mitral regurgitation, the left atrium enlarges in size and mass, with a more potent booster action. The left atrial chamber becomes more compliant. Thus, the enlarged left atrium appears to exert an important compensatory mechanism in the case of excessive central blood volume by buffering pressure rise in the atrium and by providing an adequate ventricular filling volume.
The Role of Explicit and Implicit Self-Esteem in Peer Modeling of Palatable Food Intake: A Study on Social Media Interaction among Youngsters

Objective This experimental study investigated the impact of peers on palatable food intake of youngsters within a social media setting. To determine whether this effect was moderated by self-esteem, the present study examined the roles of global explicit self-esteem (ESE), body esteem (BE) and implicit self-esteem (ISE). Methods Participants (N = 118; 38.1% boys; M age 11.14±.79) were asked to play a computer game while they believed to interact online with a same-sex normal-weight remote confederate (i.e., instructed peer) who ate either nothing, a small or large amount of candy. Results Participants modeled the candy intake of peers via a social media interaction, but this was qualified by their self-esteem. Participants with higher ISE adjusted their candy intake to that of a peer more closely than those with lower ISE when the confederate ate nothing compared to when eating a modest (β = .26, p = .05) or considerable amount of candy (kcal) (β = .32, p = .001). In contrast, participants with lower BE modeled peer intake more than those with higher BE when eating nothing compared to a considerable amount of candy (kcal) (β = .21, p = .02); ESE did not moderate social modeling behavior. In addition, participants with higher discrepant or “damaged” self-esteem (i.e., high ISE and low ESE) modeled peer intake more when the peer ate nothing or a modest amount compared to a substantial amount of candy (kcal) (β = −.24, p = .004; β = −.26, p<.0001, respectively). Conclusion Youngsters conform to the amount of palatable food eaten by peers through social media interaction. Those with lower body esteem or damaged self-esteem may be more at risk to peer influences on food intake.
Delay-Aware Period Assignment in Control Systems

We consider the problem of optimal static period assignment for multiple independent control tasks executing on the same CPU. Previous works have assumed that the control performance can be expressed as a function of the sampling rate only. Arguing that the control delay has a large impact on the control performance, in this work we include the control delay in the cost function. The delay is estimated using an approximate response-time analysis. Assuming linear cost functions for the controllers then allows us to solve the optimal period assignment problem analytically. The performance improvements over previous methods are verified in evaluations on synthetic task sets as well as detailed co- simulations of the controllers, the plants, and the scheduler.
Teacher Language in ESL Face-To-Face and Written Electronic Discussions

This repeated-measures, counter-balanced study reports on a comparison of quantity and quality of one teacher's language in face-to-face (FTF) and written electronic (WE) discussions with advanced English as a Subsequent Language (ESL) students. Transcripts from the two types of discussions were compared for complexity of teacher input and the language functions this input served during the discussions. Analyses show that the teacher contributed more words, more t-units, and longer t-units to the FTF discussions, and his contributions were longer, consisting of more t-units. The teacher's input to the FTF discussions, unlike the WE discussion, created inequality in participation in the whole group. In the WE setting, teacher language encouraged interaction with individual students, while in the FTF setting, it tended to promote interaction with the whole group. Categorization and analysis of the language functions used showed statistically significant differences.
The Human ARF Cell Cycle Regulatory Gene Promoter Is a CpG Island Which Can Be Silenced by DNA Methylation and Down-Regulated by Wild-Type p53

ABSTRACT The INK4a/ARF locus encodes two proteins involved in tumor suppression in a manner virtually unique in mammalian cells. Distinct first exons, driven from separate promoters, splice onto a common exon 2 and 3 but utilize different reading frames to produce two completely distinct proteins, both of which play roles in cell cycle control. INK4a, a critical element of the retinoblastoma gene pathway, binds to and inhibits the activities of CDK4 and CDK6, while ARF, a critical element of the p53 pathway, increases the level of functional p53 via interaction with MDM2. Here we clone and characterize the promoter of the human ARF gene and show that it is a CpG island characteristic of a housekeeping gene which contains numerous Sp1 sites. Both ARF and INK4a are coordinately expressed in cells except when their promoter regions become de novo methylated. In one of these situations, ARF transcription could be reactivated by treatment with the DNA methylation inhibitor 5-aza-2′-deoxycytidine, and the reactivation kinetics of ARF and INK4a were found to differ slightly in a cell line in which both genes were silenced by methylation. The ARF promoter was also found to be highly responsive to E2F1 expression, in keeping with previous results at the RNA level. Lastly, transcription from the ARF promoter was down-regulated by wild-type p53 expression, and the magnitude of the effect correlated with the status of the endogenous p53 gene. This finding points to the existence of an autoregulatory feedback loop between p53, MDM2, and ARF, aimed at keeping p53 levels in check.
Microinjection of resveratrol into rostral ventrolateral medulla decreases sympathetic vasomotor tone through nitric oxide and intracellular Ca2+ in anesthetized male rats

AbstractAim:To define the effect of resveratrol (RES) on the central regulation of blood pressure (BP), heart rate (HR), and renal sympathetic nerve activity (RSNA). Methods:RES was microinjected into the rostral ventrolateral medulla (RVLM), and BP, HR, and RSNA were recorded simultaneously in anesthetized rats.Results:A microinjection of RES (20, 40, and 80 μmol/L, 0.2 μL) into the RVLM dose dependently decreased BP, HR and RSNA. Pretreatment with an anti-estrogen tamoxifen (100 μmol/L, 0.2 μL) did not affect the effects of RES. Pretreatment with NG-nitro-L-arginine methyl ester (100 μmol/L, 0.2 μL), an inhibitor of nitric oxide (NO) synthase, could completely abolish the effect of RES. A prior microinjection of Bay K8644 (500 nmol/L, 0.2 μL), an agonist of calcium channels, could also abrogate the effect of RES. Prior administration of a potent inhibitor of tyrosine phosphatase, sodium orthovanadate (1 mmol/L, 0.2 μL), could partially attenuate the inhibitory effect of RES.Conclusion:The results suggest that a microinjection of RES into the RVLM inhibits BP, HR, and RSNA. The effects may be mediated by NO synthesis and a decrease in Ca2+ influx, in which protein tyrosine kinase is involved.
Intercropping Competition between Apple Trees and Crops in Agroforestry Systems on the Loess Plateau of China

Agroforestry has been widely practiced in the Loess Plateau region of China because of its prominent effects in reducing soil and water losses, improving land-use efficiency and increasing economic returns. However, the agroforestry practices may lead to competition between crops and trees for underground soil moisture and nutrients, and the trees on the canopy layer may also lead to shortage of light for crops. In order to minimize interspecific competition and maximize the benefits of tree-based intercropping systems, we studied photosynthesis, growth and yield of soybean (Glycine max L. Merr.) and peanut (Arachis hypogaea L.) by measuring photosynthetically active radiation, net photosynthetic rate, soil moisture and soil nutrients in a plantation of apple (Malus pumila M.) at a spacing of 4 m × 5 m on the Loess Plateau of China. The results showed that for both intercropping systems in the study region, soil moisture was the primary factor affecting the crop yields followed by light. Deficiency of the soil nutrients also had a significant impact on crop yields. Compared with soybean, peanut was more suitable for intercropping with apple trees to obtain economic benefits in the region. We concluded that apple-soybean and apple-peanut intercropping systems can be practical and beneficial in the region. However, the distance between crops and tree rows should be adjusted to minimize interspecies competition. Agronomic measures such as regular canopy pruning, root barriers, additional irrigation and fertilization also should be applied in the intercropping systems.
Diurnal cycle of sea surface winds and temperatures during the 2004 North American Monsoon Experiment

The 2004 North American Monsoon Experiment (NAME) Extended Observing Period (EOP) spanned 1 July 15 August with the objective of exploring the large-scale circulation patterns and their diurnal variation over northwestern Mexico and the southwestern United States, and how they relate to the onset and evolution of the monsoon (Higgins et al. 2006). In this study, high-resolution oceanic surface winds and sea surface temperatures in the morning and afternoon will be used to examine features in the summer of 2004. The diurnal cycle in the Gulf of California (GoC) is especially interesting to study with high-resolution datasets because of the challenges faced in modeling the fine-scale structure and the significance in triggering Gulf Surges and even the North American Monsoon.