Miracle-dz/UniFAR-FTUs huggingface dataset:
Specific reverse transcriptase slippage at the HIV ribosomal frameshift sequence: potential implications for modulation of GagPol synthesis

Abstract Synthesis of HIV GagPol involves a proportion of ribosomes translating a U6A shift site at the distal end of the gag gene performing a programmed -1 ribosomal frameshift event to enter the overlapping pol gene. In vitro studies here show that at the same shift motif HIV reverse transcriptase generates -1 and +1 indels with their ratio being sensitive to the relative concentration ratio of dNTPs specified by the RNA template slippage-prone sequence and its 5′ adjacent base. The GGG sequence 3′ adjacent to the U6A shift/slippage site, which is important for ribosomal frameshifting, is shown here to limit reverse transcriptase base substitution and indel ‘errors’ in the run of A’s in the product. The indels characterized here have either 1 more or less A, than the corresponding number of template U’s. cDNA with 5 A’s may yield novel Gag product(s), while cDNA with an extra base, 7 A’s, may only be a minor contributor to GagPol polyprotein. Synthesis of a proportion of non-ribosomal frameshift derived GagPol would be relevant in efforts to identify therapeutically useful compounds that perturb the ratio of GagPol to Gag, and pertinent to the extent in which specific polymerase slippage is utilized in gene expression.
Genes for breakfast: the have-your-cake-and-eat-it-too of bacterial transformation.

Bacterial transformation, in which cells take up and recombine free strands of DNA, is the simplest process thought to have evolved for genetic exchange, i.e., because of the potential benefits of producing progeny with recombinant genotypes. However, two other functions are equally plausible: acquisition of intact DNA strands to use for recombinational repair of DNA damage, and acquisition of the nutrients contained in DNA molecules. Although the recombinant progeny produced by transformation can be beneficial, the success of genes causing transformation is limited by other factors, especially by the genetic quality of DNA derived from dead cells. Our recent experiments in the naturally transformable bacteria Haemophilus influenzae and Bacillus subtilis suggest that the DNA-repair hypothesis is unlikely to be correct. In H. influenzae, transformation does not detectably increase the cells' ability to survive DNA damage. More importantly, we have found that, although competence (the ability to take up DNA) is induced by nutritional limitation in both H. influenzae and B. subtilis, it is not induced by DNA damage in either. Thus we favor the hypothesis that transformation evolved as a nutrient-uptake system, especially because unrelated DNA is abundant in the environments of many naturally transformable bacteria.
Spatial Alignment and Response Hand in Geometric and Motion Illusions

Perception of visual illusions is susceptible to manipulation of their spatial properties. Further, illusions can sometimes affect visually guided actions, especially the movement planning phase. Remarkably, visual properties of objects related to actions, such as affordances, can prime more accurate perceptual judgements. In spite of the amount of knowledge available on affordances and on the influence of illusions on actions (or lack of thereof), virtually nothing is known about the reverse: the influence of action-related parameters on the perception of visual illusions. Here, we tested a hypothesis that the response mode (that can be linked to action-relevant features) can affect perception of the Poggendorff (geometric) and of the Vanishing Point (motion) illusion. We explored the role of hand dominance (right dominant versus left non-dominant hand) and its interaction with stimulus spatial alignment (i.e., congruency between visual stimulus and the hand used for responses). Seventeen right-handed participants performed our tasks with their right and left hands, and the stimuli were presented in regular and mirror-reversed views. It turned out that the regular version of the Poggendorff display generates a stronger illusion compared to the mirror version, and that participants are less accurate and show more variability when they use their left hand in responding to the Vanishing Point. In summary, our results show that there is a marginal effect of hand precision in motion related illusions, which is absent for geometrical illusions. In the latter, attentional anisometry seems to play a greater role in generating the illusory effect. Taken together, our findings suggest that changes in the response mode (here: manual action-related parameters) do not necessarily affect illusion perception. Therefore, although intuitively speaking there should be at least unidirectional effects of perception on action, and possible interactions between the two systems, this simple study still suggests their relative independence, except for the case when the less skilled (non-dominant) hand and arguably more deliberate responses are used.
OpenGUFI: An Extensible Graphical User Flow Interface for an SDN-Enabled Wireless Testbed

In this paper, the authors propose an extensible (Open) Graphical User (Flow) Interface called OpenGUFI. OpenGUFI is a Software-Defined Networking application that provides a visual abstraction of the underlying network. The Visualizer has been implemented and tested in an SDN-enabled Wireless Testbed based on the Odin framework. As a use case a network driven handover between multiple wireless access points is used to explain how the visualizer works. OpenGUFI visualizes the following information: the real-time network topology, associations between the mobile clients and the wireless access points and traffic flows. In addition to that OpenGUFI also provides a control interface via which actions can be triggered within the network. In its current version handovers can be triggered via drag and drop gestures. With the proposed solution, a greater visibility of the wireless network via well-defined open APIs is gained and hence, another service function in the Application Plane is offered.
On the performance of linear optimal filter and Wiener filter for signal detection in liquid ionization calorimeters

The performance of the linear optimal filter (LOF) is compared to the newly reported Wiener filter for signal detection in ATLAS liquid ionization calorimeters. The equivalence between the two methods is established, and further related to the conventional notion of (whitening + matched) filter configuration for optimal signal detection in presence of colored noise. Without arrival time spread, the LOF and Wiener results converge to each other, regardless of the SNR of the calorimeter readout path. In addition, the LOF performance displays a dependence on the pulse arrival time delay-manifested as a non-zero mean and an elevated standard deviation of the amplitude estimation error-due to the truncation of high-order terms in deriving the linear filter. In contrast, once trained with the exact signal statistics of the calorimeter, i.e., the arrival time spread and noise structure, the Wiener filter can always adapt to an optimal, unbiased solution using the same linear FIR filter structure. However, when such prior knowledge is removed, the Wiener outcomes nearly coincide with those of the LOF. All the results are obtained via Monte Carlo simulations of a readout signal-processing chain assuming identical electrical parameters of the ATLAS liquid argon calorimeter system with a sample rate of 80 MSPS. The equivalence between the two approaches is also examined and confirmed using a Gaussian pulse shape and an invertible pulse-shaping function without any finite zeroes on the jω-axis.
Transcutaneous monitoring of carbon dioxide tension after cardiothoracic surgery in infants and children.

UNLABELLED In this prospective investigation, we evaluated the efficacy and accuracy of transcutaneous monitoring of CO2 (TC-CO2) in infants and children after cardiothoracic surgery. Cardiothoracic surgery patients whose ETCO2 and arterial CO2 values did not correlate (gradient > or = 5 mm Hg) during the first postoperative hour underwent placement of the TC electrode (30 of 33 patients). If the TC-CO2 to arterial difference was > or = 5 mm Hg, the TC-CO2 electrode was recalibrated and reapplied on another site. If the discrepancy was still > or =5 mm Hg, the case was considered a clinical failure and no further data were collected (3 of 30 patients). If the arterial to TC gradient was <5 mm Hg, the patient was included in the data collection (27 of 30 patients). One to five sample sets (TC and arterial CO2) were collected from these patients. Statistical analysis included linear regression analysis and Bland-Altman analysis. The cohort for the study included 27 patients ranging in age from 2 days to 9 yr and in weight from 3.2 to 25 kg. A total of 101 sample sets were analyzed. The mean +/- SD absolute difference between the TC-CO2 and arterial CO2 was 1.7 +/- 1.4 mm Hg (range 0-9 mm Hg). The TC-CO2 to arterial CO2 difference was 0-2 mm Hg in 82 of 101 values (81%), 35 mm Hg in 18 of 101 values (18%), and >6 mm Hg in 1 of 101 values (1%). Linear regression analysis revealed a slope of 0.90, an r value of 0.9410, and an r2 value of 0.8854 (P < 0.0001). Bland-Altman analysis revealed a bias of 0.58 mm Hg with a precision of +/- 2.1 mm Hg when comparing the TC-CO2 with the arterial CO2. IMPLICATIONS We conclude that, with certain caveats in mind, including the need to correlate the transcutaneous CO2 with an initial arterial CO2 value, transcutaneous CO2 monitoring can be used to estimate arterial CO2 in most neonates and children after cardiothoracic surgery.
A GA-based method for constructing fuzzy systems directly from numerical data

A method based on the concepts of genetic algorithm (GA) and recursive least-squares method is proposed to construct a fuzzy system directly from some gathered input-output data of the discussed problem. The proposed method can find an appropriate fuzzy system with a low number of rules to approach an identified system under the condition that the constructed fuzzy system must satisfy a predetermined acceptable performance. In this method, each individual in the population is constructed to determine the number of fuzzy rules and the premise part of the fuzzy system, and the recursive least-squares method is used to determine the consequent part of the constructed fuzzy system described by this individual. Finally, three identification problems of nonlinear systems are utilized to illustrate the effectiveness of the proposed method.
Economic thermoregulatory response explains mismatch between thermal physiology and behaviour in newts

ABSTRACT Temperature is an important factor determining distribution and abundance of organisms. Predicting the impact of warming climate on ectotherm populations requires information about species' thermal requirements, i.e. their so-called ‘thermal niche’. The characterization of thermal niche remains a complicated task. We compared the applicability of two indirect approaches, based on reaction norm (aerobic scope curve) and optimality (preferred body temperature) concepts, for indirect estimation of thermal niche while using newts, Ichthyosaura alpestris, as a study system. If the two approaches are linked, then digesting newts should keep their body temperatures close to values maximizing aerobic scope for digestion. After feeding, newts maintained their body temperatures within a narrower range than did hungry individuals. The range of preferred body temperatures was well below the temperature maximizing aerobic scope for digestion. Optimal temperatures for factorial aerobic scope fell within the preferred body temperature range of digesting individuals. We conclude that digesting newts prefer body temperatures that are optimal for the maximum aerobic performance but relative to the maintenance costs. What might be termed the ‘economic’ thermoregulatory response explains the mismatch between thermal physiology and behaviour in this system. Summary: Digesting newts prefer body temperatures that are optimal for aerobic scope not in absolute terms but relative to the minimum oxygen consumption.
An Electrically Large Metallic Cavity Antenna With Circular Polarization for Satellite Applications

An electrically large metallic cavity antenna with circular polarization (CP) is proposed in this letter. The aim is to increase the size of satellite antennas working in the Ku-band and other higher-frequency bands through low cost and easy fabrication. A brass C-band antenna prototype is designed, fabricated, and measured for concept verification. The overall dimensions of the antenna are 0. 67λ<sub>0</sub> × 0. 67λ<sub>0</sub> × 0. 83λ<sub>0</sub> at the working frequency. The resonant mode of the proposed cavity antenna is excited by a coaxial feeding probe, and circular polarization is realized by an inserted perturbation screw. The measured impedance bandwidth for | <i>S</i><sub>11</sub>| ≤ -10 dB and 3-dB axial-ratio bandwidth are 1.02 GHz (6.07-7.09 GHz) and 320 MHz (6.59-6.91 GHz), respectively. The measured gain is 8.5 dBic across the whole 3-dB axial-ratio bandwidth. The measured 3-dB axial-ratio beamwidths at the central frequency are 150<sup>°</sup> and 148<sup>°</sup> in the <i>xoz</i>- and the <i>yoz</i>-planes, respectively, which is wide enough to cover the >; 0-dBi gain beamwidths of 120<sup>°</sup> for practical engineering applications. The measured and the simulated results show good agreement.
Residual energy-based OLSR in mobile ad hoc networks

OLSR is a proactive routing protocol for mobile ad hoc networks (MANETs). OLSR uses a concept of MPR selection mechanism to reduce broadcast packets during a flooding process. MPR nodes use more energy than nonMPR nodes. Thus they easily run out their energy since mobile nodes in MANETs are powered by battery with limited energy. This paper proposes a residual energy-based OLSR protocol named REOLSR2. The REOLSR2 selects MPR nodes based on not only reachability and degree but also residual energy of 1-hop neighbors. The aim is to avoid selecting MPR nodes which has small residual energy and concentrating energy consumption in specific nodes. Simulation results show that the proposed scheme reduces energy consumption and enhances network throughput efficiently.
6LoWPAN based intelligent transport system for surveillance - a model of ubiquitous computing technology

This era of internet of things (IOT) and ubiquitous computing technology demands that their potential be leveraged in all areas of human life. Towards this effort this paper proposes a novel architecture for intelligent transport system (ITS) for surveillance based on 6LoWPAN technology which also combines ubiquitous computing technology. The novelty of the proposed architecture lies in integrating maximum aspects of ITS surveillance into a single architecture. Also the combination of IOT and ubiquitous computing comes as an added advantage to existing ITS.
The nuclear factor YY1 participates in repression of the beta-casein gene promoter in mammary epithelial cells and is counteracted by mammary gland factor during lactogenic hormone induction

Expression of the beta-casein milk protein gene in the mammary epithelial cell line HC11 is primarily regulated at the transcriptional level. A 338-bp segment of promoter sequence 5' of the transcription start site is sufficient to confer inducibility by the lactogenic hormones insulin, glucocorticoid hormone, and prolactin. Positively and negatively acting promoter elements and specific DNA binding proteins have been identified. The binding of the mammary gland factor MGF to a site between -80 and -100 is indispensable for hormonal induction of transcription. Binding of MGF activity to DNA is greatly enhanced by the action of the lactogenic hormones. Repression of transcription in the uninduced state is mediated by a promoter element located adjacent to the MGF binding site at positions -110 to -150. This repressor element consists of two interacting protein binding sites. A nuclear factor that binds specifically to the proximal site between positions -110 and -120 has been characterized and found to be identical with the nuclear factor YY1 (delta, NF-E1). YY1 does not bind to the distal site. The simultaneous mutation in the proximal and the distal sites results in high, hormone-independent transcription. This finding suggests that YY1 plays a functional role in the repression and acts in conjunction with a second DNA binding protein. Comparison of YY1 DNA binding activity in uninduced and hormone-induced cells showed that relief of repression is not mediated by changes in the concentration or binding affinity of YY1. Infection of HC11 cells with a YY1-expressing recombinant retrovirus resulted in overexpression of YY1 but did not suppress hormonal induction. The addition of purified MGF decreased YY1 binding to its DNA recognition site in vitro. This finding indicates that MGF regulates the DNA binding activity of YY1 and thereby may cause the relief of transcriptional repression.
Software engineering occupational stress and knowledge sharing in the context of Global Software Development

The success of a software development project does not only rely on technical support but also depends on human and social factors. The human side of software development has been ignored in the past decade or so, which calls for increasing our efforts to understand this side of software engineering. Human knowledge and creativity is the cornerstone for software development. However, this human knowledge has lesser or no value when it is isolated or individualized; hence knowledge sharing becomes critical for the success of software projects. The dilemma with knowledge sharing is that there are many impediments to it. One such impediment can be occupational stress which has increased after the globalization of software engineering. In the context of Global Software Development (GSD), the objective of this paper is to highlight the impact of software engineering occupational stress on knowledge sharing. To highlight this important relationship a thorough literature survey has been conducted and the results of the survey are presented in this paper.
Virus-Induced Inhibition of CD1d1-Mediated Antigen Presentation: Reciprocal Regulation by p38 and ERK1

A critical component of the host’s innate immune response involves lipid Ag presentation by CD1d molecules to NK T cells. In this study we used murine CD1d1-transfected L (L-CD1) cells to study the effect of viruses on CD1d-mediated Ag presentation to NKT cells and found that an infection with vesicular stomatitis and vaccinia (but not lymphocytic choriomeningitis) virus inhibited murine CD1d1-mediated Ag presentation. This was under the reciprocal control of the MAPKs, p38 and ERK, and was due to changes in the intracellular trafficking of CD1d1. The reciprocal regulation of CD1d1-mediated Ag presentation by MAPK suggests that the targeting of these pathways is a novel means of immune evasion by viruses.
Scrapie Pathogenesis: The Role of Complement C1q in Scrapie Agent Uptake by Conventional Dendritic Cells1

Mice lacking complement components show delayed development of prion disease following peripheral inoculation. The delay could relate to reduced scrapie prion protein (PrPSc) accumulation on follicular dendritic cells (DCs). However conventional DCs (cDCs) play a crucial role in the early pathogenesis of prion diseases and complement deficiency could result in decreased PrPSc uptake by cDCs in the periphery. To explore this possibility, we cultured murine splenic or gut-associated lymph node cDCs with scrapie-infected whole brain homogenate in the presence or absence of complement. Uptake decreased significantly if the serum in the cultures was heat-inactivated. Because heat inactivation primarily denatures C1q, we used serum from C1q−/− mice and showed that PrPSc uptake was markedly decreased. PrPSc internalization was saturable and temperature-dependent, suggesting receptor-mediated uptake. Furthermore, uptake characteristics differed from fluid-phase endocytosis. Immunofluorescence showed colocalization of C1q and PrPSc, suggesting interaction between these molecules. We evaluated the expression of several complement receptors on cDCs and confirmed that cDCs that take up PrPSc express one of the C1q receptors, calreticulin. Our results show that C1q participates in PrPSc uptake by cDCs, revealing a critical role for cDCs in initial prion capture, an event that takes place before the PrPSc accumulation within the follicular DC network.
Central venous saturation is a predictor of reintubation in difficult-to-wean patients*

Objective: To evaluate the predictive value of central venous saturation to detect extubation failure in difficult-to-wean patients. Design: Cohort, multicentric, clinical study. Setting: Three medical-surgical intensive care units. Patients: All difficult-to-wean patients (defined as failure to tolerate the first 2-hr T-tube trial), mechanically ventilated for >48 hrs, were extubated after undergoing a two-step weaning protocol (measurements of predictors followed by a T-tube trial). Extubation failure was defined as the need of reintubation within 48 hrs. Interventions: The weaning protocol evaluated hemodynamic and ventilation parameters, and arterial and venous gases during mechanical ventilation (immediately before T-tube trial), and at the 30th min of spontaneous breathing trial. Measurements and Main Results: Seventy-three patients were enrolled in the study over a 6-mo period. Reintubation rate was 42.5%. Analysis by logistic regression revealed that central venous saturation was the only variable able to discriminate outcome of extubation. Reduction of central venous saturation by >4.5% was an independent predictor of reintubation, with odds ratio of 49.4 (95% confidence interval 12.1–201.5), a sensitivity of 88%, and a specificity of 95%. Reduction of central venous saturation during spontaneous breathing trial was associated with extubation failure and could reflect the increase of respiratory muscles oxygen consumption. Conclusions: Central venous saturation was an early and independent predictor of extubation failure and may be a valuable accurate parameter to be included in weaning protocols of difficult-to-wean patients.
Relative risks of death due to liver disease among Japanese male adults having various statuses for hepatitis B s and e antigen/antibody in serum: A prospective study

Taking advantage of the compulsory annual medical check‐up at the Central Institute of Health, Japan National Railways, hepatitis B seromarkers were tested in male employees at work and their “dead and alive” status was followed for more than 6 years for their prognostic significance. Two prospective studies were carried out. In the first study, two groups (cohorts) of males age 40 to 55 years were tested in 1973 and 1978, respectively, for HBsAg and anti‐HBs. The relative risk of dying from primary liver cancer in HBsAg‐positive carriers (n = 126) as compared to the controls who were negative for both HBsAg and anti‐HBs (n = 5,322) was 30.03 and significantly high, whereas those positive for anti‐HBs (n = 1,470) had no increased risk of dying from primary liver cancer or from other liver diseases. The follow‐up period ranged from 6.5 to 11.5 years, averaging 8.5 years.