Miracle-dz/UniFAR-FTUs huggingface dataset:
Role of the Specific Amino Acid Sequence of the Membrane-Spanning Domain of Human Immunodeficiency Virus Type 1 in Membrane Fusion

ABSTRACT Fusion between cell and virus membranes mediated by gp41 initiates the life cycle of human immunodeficiency virus type 1. In contrast to the many studies that have elucidated the structure-function relationship of the ectodomain, the study of the membrane-spanning domain (MSD) has been rather limited. In particular, the role that the MSD's specific amino acid sequences may have in membrane fusion as well as other gp41 functions is not well understood. The MSD of gp41 contains well-conserved glycine residues that form the GXXXG motif (G, glycine; X, other amino acid residues), a motif often found at the helix-helix interface of membrane spanning α-helices. Here we examined the role that the specific amino acid sequence of the gp41 MSD has in gp41 function, particularly in membrane fusion, by making two types of MSD mutants: (i) glycine substitution mutants in which glycine residues of the MSD were mutated to alanine or leucine residues, and (ii) replacement mutants in which the entire MSD was replaced with one derived from glycophorin A or from vesicular stomatitis virus G. The substitution of glycines did not affect gp41 function. MSD-replacement mutants, however, showed severely impaired fusion activity. The assay using the Env expression vector revealed defects in membrane fusion after CD4 binding steps in the MSD-replacement mutants. In addition, the change in Env processing was noted for MSD-replacement mutants. These results suggest that the MSD of gp41 has a relatively wide but not unlimited tolerance for mutations and plays a critical role in membrane fusion as well as in other steps of Env biogenesis.
De novo assembly and comparative analysis of the Ceratodon purpureus transcriptome

The bryophytes are a morphologically and ecologically diverse group of plants that have recently emerged as major model systems for a variety of biological processes. In particular, the genome sequence of the moss, Physcomitrella patens, has significantly enhanced our understanding of the evolution of developmental processes in land plants. However, to fully explore the diversity within bryophytes, we need additional genomic resources. Here, we describe analyses of the transcriptomes of a male and a female isolate of the moss, Ceratodon purpureus, generated using the 454 FLX technology. Comparative analyses between C. purpureus and P. patens indicated that this strategy generated nearly complete coverage of the protonemal transcriptome. An analysis of the overlap in gene sets between C. purpureus and P. patens provides new insights into the evolution of gene family composition across the land plants. In spite of the overall transcriptomic similarity between the two species, Ka/Ks analysis of P. patens and C. purpureus suggests considerable physiological and developmental divergence. Additionally, while the codon usage was very similar between these two mosses, C. purpureus genes showed a slightly greater codon usage bias than P. patens genes potentially because of the contrasting mating system of the two species. Finally, we found evidence of a genome doubling ~65–76 MYA that likely coincided with the contemporaneous polyploidy event inferred for P. patens but postdates the divergence of P. patens and C. purpureus. The powerful laboratory tools now available for C. purpureus will enable the research community to fully exploit these genomic resources.
Older Adults’ Television Viewing from a Life-Span Perspective: Past Research and Future Challenges

This chapter overviews research on older adults television viewing and discusses the assumptions and empirical findings in terms of a life-span perspective. The life-span perspective emphasizes that gains and losses jointly occur in later life. Selection and compensation constitute two central strategies in gerontological models of how people adapt to gains and losses. With regard to television viewing, selection means that people can choose television viewing over other activities for reaching goals in high-priority domains because television viewing is appropriate given environmental demands and individual motivations, skills, and capacities. Compensation means that people can use television viewing as a substitute for diminished abilities or activities. This chapter reviews available literature in three sections: time use, social functions, and content preferences. A large share ofprevious research on older adults television viewing appears to be biased toward compensation, whereas research in this field insufficiently considered selection strategies.
Colonization of Campylobacter spp. in Broiler Chickens and Laying Hens Reared in Tropical Climates with Low-Biosecurity Housing

ABSTRACT The onset and prevalence of Campylobacter colonization in broilers and layers at commercial farms with low biosecurity in tropical climates were tested. Despite the presence of positive animals at the same farms, the broiler flocks tested negative until, on average, 21 days. Prelaying flocks showed a higher prevalence than laying flocks.
Cryptic recombination in the ever‐young sex chromosomes of Hylid frogs

Sex chromosomes are expected to evolve suppressed recombination, which leads to degeneration of the Y and heteromorphism between the X and Y. Some sex chromosomes remain homomorphic, however, and the factors that prevent degeneration of the Y in these cases are not well understood. The homomorphic sex chromosomes of the European tree frogs (Hyla spp.) present an interesting paradox. Recombination in males has never been observed in crossing experiments, but molecular data are suggestive of occasional recombination between the X and Y. The hypothesis that these sex chromosomes recombine has not been tested statistically, however, nor has the X‐Y recombination rate been estimated. Here, we use approximate Bayesian computation coupled with coalescent simulations of sex chromosomes to quantify X‐Y recombination rate from existent data. We find that microsatellite data from H. arborea, H. intermedia and H. molleri support a recombination rate between X and Y that is significantly different from zero. We estimate that rate to be approximately 105 times smaller than that between X chromosomes. Our findings support the notion that very low recombination rate may be sufficient to maintain homomorphism in sex chromosomes.
Black engineering students’ motivation for PhD attainment: passion plus purpose

Purpose Much of the extant research, practice and policy in engineering education has focused on the limited persistence, waning interest and lack of preparation among Black students to continue beyond the post-secondary engineering pipeline. However, this research suggests that many Black PhD students persist and succeed in engineering, fueled by various motivational strengths. To better understand the motivations of Black students in engineering doctoral programs, this study aims to explore the factors that influence their decision to enroll in either an engineering or a computing doctoral program. Design/methodology/approach This paper uses an intrinsic and extrinsic motivational framework to investigate the inspiration of 44 Black engineering doctoral students in PhD engineering programs in 11 engineering schools across the country. Findings Results show that the participants’ motivation to pursue a PhD in engineering comes from several distinct factors, including the following: an unyielding passion for their particular discipline, a sense of responsibility to serve marginalized peoples and society, a path toward autonomy, pre-PhD mentorship and research opportunities and family and prior work experience. Research limitations/implications Based on this study’s findings, a reconceptualization of graduate engineering education that incorporates the importance of “being Black” and its relationships with motivating and, potentially, retaining Black science, technology, engineering and mathematics (STEM) students is also offered. Originality/value This paper seeks to expose particular constructs and behaviors surrounding Black students’ motivation to learn and achieve in engineering at the highest academic levels, offering a more nuanced perspective than currently is found in traditional engineering education literature.
KIC 7668647: a 14 day beaming sdB+WD binary with a pulsating subdwarf

The recently discovered subdwarf B (sdB) pulsator KIC 7668647 is one of the 18 pulsating sdB stars detected in the Kepler field. It features a rich g-mode frequency spectrum, with a few low-amplitude p-modes at short periods. This makes it a promising target for a seismic study aiming to constrain the internal structure of this star, and of sdB stars in general. We use new ground-based lowresolution spectroscopy, and the near-continuous 2.88 year Kepler light curve, to reveal that KIC 7668647 consists of a subdwarf B star with an unseen white-dwarf companion with an orbital period of 14.2 d. An orbit with a radial-velocity amplitude of 39 km s −1 is consistently determined from the spectra, from the orbital Doppler beaming seen by Kepler at 163 ppm, and from measuring the orbital light-travel delay of 27 s by timing of the many pulsations seen in the Kepler light curve. The white dwarf has a minimum mass of 0.40 M� . We use our high signal-to-noise average spectra to study the atmospheric parameters of the sdB star, and find that nitrogen and iron have abundances close to solar values, while helium, carbon, oxygen and silicon are underabundant relative to the solar mixture. We use the full Kepler Q06–Q17 light curve to extract 132 significant pulsation frequencies. Period-spacing relations
A hybrid adaptive blind equalization algorithm for QAM signals in wireless communications

A hybrid adaptive channel equalization technique for quadrature amplitude modulation (QAM) signals is proposed. The proposed algorithm, which is referred to as the modified constant modulus algorithm (MCMA), minimizes an error cost function that includes both amplitude and phase of the equalizer output. In addition to the amplitude-dependent term that is provided by the conventional constant modulus algorithm (CMA), the cost function includes an additive signal constellation matched error (CME) term. This term can be designed to satisfy a set of desirable properties. The MCMA is compared with the CMA for blind equalization. The performance is measured for wireless channels using both transient and steady-state behavior of the mean square error (MSE). It is shown that MCMA is superior and more robust in low signal-to-noise ratio (SNR) environments. Simulation results demonstrate that using MCMA improves adaptive channel equalization by increasing the convergence rate and decreasing the steady-state mean square error.
Validation of an ontological medical decision support system for patient treatment using a repository of patient data

In this article, we begin by presenting OMeD, a medical decision support system, and argue for its value over purely probabilistic approaches that reason about patients for time-critical decision scenarios. We then progress to present Holmes, a Hybrid Ontological and Learning MEdical System which supports decision making about patient treatment. This system is introduced in order to cope with the case of missing data. We demonstrate its effectiveness by operating on an extensive set of real-world patient health data from the CDC, applied to the decision-making scenario of administering sleeping pills. In particular, we clarify how the combination of semantic, ontological representations, and probabilistic reasoning together enable the proposal of effective patient treatments. Our focus is thus on presenting an approach for interpreting medical data in the context of real-time decision making. This constitutes a comprehensive framework for the design of medical recommendation systems for potential use by medical professionals and patients both, with the end result being personalized patient treatment. We conclude with a discussion of the value of our particular approach for such diverse considerations as coping with misinformation provided by patients, performing effectively in time-critical environments where real-time decisions are necessary, and potential applications facilitating patient information gathering.
POLITECNICO DI TORINO Repository ISTITUZIONALE

—In this paper, we conduct a detailed study of the YouTube CDN with a view to understanding the mechanisms and policies used to determine which data centers users download video from. Our analysis is conducted using week-long datasets simultaneously collected from the edge of ﬁve networks - two university campuses and three ISP networks - located in three different countries. We employ state-of-the-art delay-based geolo-cation techniques to ﬁnd the geographical location of YouTube servers. A unique aspect of our work is that we perform our analysis on groups of related YouTube ﬂows. This enables us to infer key aspects of the system design that would be difﬁcult to glean by considering individual ﬂows in isolation. Our results reveal that while the RTT between users and data centers plays a role in the video server selection process, a variety of other factors may inﬂuence this selection including load-balancing, diurnal effects, variations across DNS servers within a network, limited availability of rarely accessed video, and the need to alleviate hot-spots that may arise due to popular video content.
Model-Based FDI Schemes For Robot Manipulators Using Soft Computing Techniques

While modern control methods were becoming widespread, in addition to demanded repeatability and accuracy specifications, reliability and detection and isolation of probable faults have become an obligation for automatic control systems. In the early 70’s, first studies were appeared on this subject. While the first studies on fault detection and isolation (FDI) were implemented for supervisory of chemical processes, following studies were extended to systems like air and spacecrafts, automobiles, nuclear reactors, turbines and HVACs with high reliability mandatories after especially aircraft accidents with high mortality. In 1991, with extending and increasing studies, IFAC SAFEPROCESS comittee was founded and in 1993, this comittee issued some definitions about fault types, fault detection and isolation, fault diagnosis and fault tolerant control (FTC) (Isermann & Balle, 1997). Robots are accepted as an assistant subsystem or an individual part of a complex system in most applications. In addition to applications like serial product lines in which they can work harder, faster and with higher accuracy than humans, they are assigned to missions like waste treatment in nuclear reactors, data and sample collection, maintenance in space and underwater tasks which can be very risky for humans. As a consequence, a fault in one product line may cause a pause in all connected lines even in flexible automation systems or a developing and undetected fault may cause abortion of a whole space or underwater mission with big money costs, it may even cause harm to humans. With the increase of these events in real-life applications and with 90’s, studies on robot reliability and fault detection and diagnosis in robotics have become common. In addition to these studies, NASA and US Army issued some standards on robots and on the reliability and fault possibilities of robotparts (Cavallaro & Walker, 1994). This study is focused on model-based FDI schemes, how they can be applied to robot manipulators, how soft computing techniques can be used in these schemes and three different FDI schemes are proposed. Soft computing techniques which can overcome the difficulties of schemes using analytical methods for nonlinear systems are used as modelling, fault isolator and fault function approximator tools in the proposed schemes. In the following section, a literature overview on FDI for nonlinear systems and robot 7
Visual and Anticipatory Bias in Three Cortical Eye Fields of the Monkey during an Adaptive Decision-Making Task

To examine the role of three cortical eye fields during internally guided decision-making processes, we recorded neuronal activities in the frontal eye field (FEF), supplementary eye field (SEF), and lateral intraparietal cortex (LIP) using a free-choice delayed saccade task with two synchronized targets. Although the monkeys must perform the task in a time-locked manner, they were free to choose either the receptive field (RF) target or the nonreceptive field (nRF) target to receive reward. In all three areas we found neurons with stronger activation during trials when the monkey was going to make a saccade to the RF target (RF trials) than to the nRF target (nRF trials). Modulation occurred not only during target presentation (visual bias) but also before target presentation (anticipatory bias). The visual bias was evident as an attenuated visual response to the RF stimulus in nRF trials. The anticipatory bias, however, was seen as an enhancement of pretarget activity in the RF trials. We analyzed the activity during the 500 msec before target presentation and found that 22.5% of FEF and 31.3% of LIP neurons and 49.1% of SEF neurons showed higher activity during the RF trials. To more accurately determine when each neuron started to show preferential activity, we used a new inverse interspike interval analysis procedure. Our results suggest that although all three cortical eye fields reflect attentional and intentional aspects of sensorimotor processing, SEF plays an earlier and perhaps more cognitive role in internally guided decision-making processes for saccades.
Regulation of embryonic lung vascular development by vascular endothelial growth factor receptors, Flk‐1 and Flt‐1

The biological effects of vascular endothelial growth factor A (VEGF‐A) are mediated by fetal liver kinase‐1 (Flk‐1) and fms‐like tyrosine kinase‐1 (Flt‐1). In lung tissue, VEGF‐A is diffusely expressed throughout the embryonic stages, whereas the development of vascular endothelial cells is not uniform. Noting the signaling properties of the two receptors, we hypothesized that Flk‐1 and Flt‐1 regulate the embryonic development of lung vasculature. We herein show the spatiotemporal expression and experimental inhibition of Flk‐1 and Flt‐1 of embryonic mouse lung tissue. When Flk‐1 was predominantly expressed (embryonic day [E] 9.5–E13.5), then vascular endothelial cells actively proliferated. When Flt‐1 was enhanced (E14.5–E16.5), these cells less actively proliferated, thereby constituting organized networks. The treatment of cultured lung buds (E11.5) with antisense oligonucleotides complementary to Flk‐1 inhibited branching of capillaries and proliferation of endothelial cells. In contrast, the inhibition of Flt‐1 promoted the branching of capillaries and enhanced proliferation of endothelial cells. Of interest, inhibition of Flt‐1 promoted Flk‐1 expression. These results suggest that the two VEGF‐A receptors regulate pulmonary vascular development by modulating the VEGF‐A signaling. Anat Rec, 290:958–973, 2007. © 2007 Wiley‐Liss, Inc.
Mental Disorders and Reasons for Using Complementary Therapy

Objective: To compare patients with and without mental disorders who seek services from a complementary therapy practitioner with regard to quality of life, reasons for seeking complementary therapies, complaints, and physical conditions. Method: We studied new patients who attended a complementary therapy clinic offering acupuncture treatment between July 1, 1993, and March 31, 1995. We collected data from a self-administered questionnaire and from a physician-conducted psychiatric assessment. Results: Of the 826 new patients at the clinic, 578 (70%) presented with a mental disorder. Patients with a mental disorder perceived their quality of life as poorer and reported greater levels of stress than did those without a mental disorder. However, the groups did not differ in their self-reported reasons for seeking complementary therapies, in their complaints, or in their physical conditions. Among patients with a mental disorder, the major reasons for choosing complementary therapies were personal preference, interest, or belief in complementary therapies (44.3%) and perceiving complementary therapies as a last resort (30.7%). Most patients with a mental disorder saw a complementary practitioner for musculoskeletal and connective-tissue disorders (44.1%), fatigue (26.6%), and headache (15.2%). The most frequent physical illnesses among patients with a mental disorder were diseases of the musculoskeletal system and connective tissue (42.6%). Conclusion: Like their counterparts without a mental disorder, individuals with a mental disorder use complementary therapies because of personal beliefs. The wide use of complementary therapies among individuals with a mental disorder may be ascribed to a poor quality of life and high levels of distress.
Millimeter wave power density in aqueous biological samples

Power density distribution inside a water sample placed between two parallel lossy dielectric plates (Polystyrene) was calculated using Fresnel equations for the frequency range of 42.25–53.57 GHz. Due to the multiple internal reflections from the sample boundaries, the distribution of the power density within the thin sample is more uniform than that within a semi‐infinite medium. The power density in a sample depends on the thicknesses of the sample and the adjacent dielectric plates. For the given frequency range the sample thickness optimal for power density uniformity varies between 0.28 and 0.33 mm. The front plate has a significant effect on the magnitude of the power density within the sample but little effect on the power density distribution. The thicker the rear plate, the greater is the non uniformity of the power density distribution within the sample. Based on the calculated data, we determined the dimension of an exposure chamber providing the optimal power density distribution uniformity for mm‐wave irradiation. Bioelectromagnetics 22:288–291, 2001. © 2001 Wiley‐Liss, Inc.
A Mode-Preserving Perfectly Matched Layer for Optical Waveguides

For numerical simulation of wave propagation in optical waveguides, we develop a mode-preserving boundary condition for the popular perfectly matched layer (PML) which truncates the unbounded transverse plane. The method is particularly useful for single mode longitudinally varying wave-guiding structures and it is easy to use for step-index planar waveguides. With this boundary condition, accurate numerical solutions can be obtained in a much smaller computational window. Numerical results based on the beam propagation method for a tapered waveguide are used to demonstrate the capacity of this boundary condition.