Miracle-dz/UniFAR-FTUs huggingface dataset:
Reevaluation of Amino Acid Variability of the Human Immunodeficiency Virus Type 1 gp120 Envelope Glycoprotein and Prediction of New Discontinuous Epitopes

ABSTRACT To elucidate the evolutionary mechanisms of the human immunodeficiency virus type 1 gp120 envelope glycoprotein at the single-site level, the degree of amino acid variation and the numbers of synonymous and nonsynonymous substitutions were examined in 186 nucleotide sequences for gp120 (subtype B). Analyses of amino acid variabilities showed that the level of variability was very different from site to site in both conserved (C1 to C5) and variable (V1 to V5) regions previously assigned. To examine the relative importance of positive and negative selection for each amino acid position, the numbers of synonymous and nonsynonymous substitutions that occurred at each codon position were estimated by taking phylogenetic relationships into account. Among the 414 codon positions examined, we identified 33 positions where nonsynonymous substitutions were significantly predominant. These positions where positive selection may be operating, which we call putative positive selection (PS) sites, were found not only in the variable loops but also in the conserved regions (C1 to C4). In particular, we found seven PS sites at the surface positions of the α-helix (positions 335 to 347 in the C3 region) in the opposite face for CD4 binding. Furthermore, two PS sites in the C2 region and four PS sites in the C4 region were detected in the same face of the protein. The PS sites found in the C2, C3, and C4 regions were separated in the amino acid sequence but close together in the three-dimensional structure. This observation suggests the existence of discontinuous epitopes in the protein's surface including this α-helix, although the antigenicity of this area has not been reported yet.
Overview of the NTCIR-8 Community QA Pilot Task (Part I): The Test Collection and the Task

Identifying high-quality content in community-type Q&A (CQA) sites is important. We propose a task in which a computer identifies good answers from such sites. We describe the design of our bestanswer estimation task using Yahoo! Chiebukuro. We also describe a method of constructing the test collection used for our CQA pilot task, the manual assessment method, and assessment results.
Efficacy of Sweet Potato Powder and Added Water as Fat Replacer on the Quality Attributes of Low-fat Pork Patties

The present study was conducted to investigate the efficacy of sweet potato powder (SPP) and water as a fat replacer in low-fat pork patties. Low-fat pork patties were developed by replacing the added fat with combinations of SPP and chilled water. Three different levels of SPP/chilled water viz. 0.5/9.5% (T-1), 1.0/9.0% (T-2), and 1.5/8.5% (T-3) were compared with a control containing 10% animal fat. The quality of low-fat pork patties was evaluated for physico-chemical (pH, emulsion stability, cooking yield, aw), proximate, instrumental colour and textural profile, and sensory attributes. The cooking yield and emulsion stability improved (p<0.05) in all treatments over the control and were highest in T-2. Instrumental texture profile attributes and hardness decreased, whereas cohesiveness increased compared with control, irrespective of SPP level. Dimensional parameters (% gain in height and % decrease in diameter) were better maintained during cooking in the low-fat product than control. The sensory quality attributes juiciness, texture and overall acceptability of T-2 and T-3 were (p<0.05) higher than control. Results concluded that low-fat pork patties with acceptable sensory attributes, improved cooking yield and textural attributes can be successfully developed with the incorporation of a combination of 1.0% SPP and 9.0% chilled water.
Sequence Encoders Enable Large-Scale Lexical Modeling: Reply to Bowers and Davis (2009)

Sibley, Kello, Plaut, and Elman (2008) proposed the sequence encoder as a model that learns fixed-width distributed representations of variable-length sequences. In doing so, the sequence encoder overcomes problems that have restricted models of word reading and recognition to processing only monosyllabic words. Bowers and Davis (in press) recently claimed that the sequence encoder does not actually overcome the relevant problems, and hence is not a useful component of large-scale word reading models. In this reply, it is noted that the sequence encoder has facilitated the creation of large-scale word reading models. The reasons for this success are explained, and stand as counterarguments to claims made by Bowers and Davis.
Religion and happiness: Consensus, contradictions, comments and concerns

The relationship between religion and happiness has been the focus of much research. The present review provides a critical examination of this research and, in particular, focuses on conceptual and methodological concerns. The majority of studies report a positive association between measures of religion and happiness; however, contradictory findings are common. This is exemplified in the literature that has systematically employed the Francis Scale of Attitude toward Christianity alongside two different measures of happiness among a variety of samples. Two opposing conclusions have found consistent support. Research with the Oxford Happiness Inventory has consistently found religiosity to be associated with happiness, while research employing the Depression–Happiness Scale has consistently found no association. It is argued that such contradictions may reflect both conceptual and methodological weaknesses in this literature.
The X-ray to optical-UV luminosity ratio of X-ray selected type 1 AGN in XMM-COSMOS

We present a study of the X-ray to optical properties of a sample of 545 X-ray selected type 1 AGN, from the XMM-COSMOS survey, over a wide range of redshifts (0.04 \textless z \textless 4.25) and X-ray luminosities (40.6 \textless= Log L([2-10]) (keV) \textless= 45.3). About 60% of them are spectroscopically identified type 1 AGN, while the others have a reliable photometric redshift and are classified as type 1 AGN on the basis of their multi-band Spectral Energy Distributions. We discuss the relationship between UV and X-ray luminosity, as parameterized by the alpha(ox) spectral slope, and its dependence on redshift and luminosity. We compare our findings with previous investigations of optically selected broad-line AGN (mostly from SDSS). A highly significant correlation between alpha(ox) and L(2500) angstrom is found, in agreement with previous investigations of optically selected samples. We calculate bolometric corrections, k(bol), for the whole sample using hard X-ray luminosities (L([2-10] keV)), and the Eddington ratios for a subsample of 150 objects for which black hole mass estimates are available. We confirm the trend of increasing bolometric correction with increasing Eddington ratio as proposed in previous works. A tight correlation is found between alpha(ox) and k(bol), which can be used to estimate accurate bolometric corrections using only optical and X-ray data. We find a significant correlation between alpha(ox) and Eddington ratio, in which the ratio between X-ray and optical flux decreases with increasing Eddington ratio.
Obstructive sleep apnoea and urine catecholamines in hypertensive males: a population-based study

Studies addressing the relationship between obstructive sleep apnoea (OSA) and sympathoadrenal activity have been criticized for poor control of factors known to confound sympathetic function, including hypertension. The aim of this study was to investigate the relationship between OSA and urinary catecholamines in a population-based sample of hypertensive males. In 1994, 2,668 males aged 40–79 yrs answered a questionnaire regarding sleep disorders and somatic diseases. Of those who reported hypertension, an age-stratified sample of 116 was selected for monitoring of breathing during sleep and overnight urine analysis. Subjects with OSA, defined as apnoea-hypopnoea index ≥10·h−1, had higher concentrations of urinary normetanephrine (182±57 versus 141±45 µmol·mol−1 creatinine, p<0.001) and metanephrine (70±28 versus 61±28 µmol·mol−1 creatinine, p<0.05) in comparison to subjects without OSA. In a multiple regression analysis, there was an association between variables of sleep-disordered breathing and normetanephrine and metanephrine concentrations, independent of major confounding factors. The authors concluded that, in a population-based sample of hypertensive males, obstructive sleep apnoea is associated with increased urinary concentrations of extraneuronal metabolites of catecholamines independent of major confounding factors, suggesting increased sympathoadrenal activity. Elevated sympathoadrenal activity may explain the increased cardiovascular morbidity associated with obstructive sleep apnoea.
The Development of the Attitude towards Computerized Assessment Scale

Test equivalence can be evaluated in terms of four aspects: psychometric, behavioral, experiential, and individual differences (i.e., relativity of equivalence) (Honaker, 1988). This study examined the psychometric properties of the Attitude Towards Computerized Assessment Scale (ATCAS) designed to assess one of these criteria, namely, experiential equivalence. Specifically, the ATCAS was developed to explore examinees' emotional, perceptual and attitudinal reactions towards computerized relative to conventional testing methods. The validity and reliability of the ATCAS is addressed by presenting research findings from two independent studies. An exploratory factor analysis (EFA) of the intercorrelations of responses on the 13-items comprising the ATCAS was conducted in Study 1 using data from 92 undergraduate psychology students. The results of the EFA yielded two qualitatively different aspects of the individual's perceptions and experience of computer-based testing (CBT): Ease of Use and CBT-Confidence. The second study used data collected from an Australian Defence Force (ADF) sample to further explore and then confirm the factor structure of the ATCAS. The second study was divided into two phases. Based on the responses of 201 ADF applicants, an EFA of the ATCAS supported the presence of the Ease of Use and CBT-Confidence factors. Based on the responses of 331 ADF applicants, a confirmatory factor analysis (CFA) of ATCAS items supported the two-factor model. In studies 1 and 2, internal consistency was evidenced for the ATCAS and its subscales with values ranging from . 76 to . 92. Implications for the study of experiential equivalence are discussed, while areas for future research are also considered.
Symbiont type influences trophic plasticity of a model cnidarian–dinoflagellate symbiosis

ABSTRACT The association between cnidarians and photosynthetic dinoflagellates within the genus Symbiodinium is a prevalent relationship in tropical and subtropical marine environments. Although the diversity of Symbiodinium provides a possible axis for niche diversification, increased functional range and resilience to physical stressors such as elevated temperature, how such diversity relates to the physiological balance between autotrophy and heterotrophy of the host animal remains unknown. Here, we experimentally show interspecific and intraspecific variability of photosynthetic carbon fixation and subsequent translocation by Symbiodinium to the model cnidarian host Aiptasia pallida. By using a clonal anemone line harboring different species of Symbiodinium, we determined that symbiont identity influences trophic plasticity through its density, capacity to fix carbon, quantity of translocated carbon and ultimately the host's capacity to ingest and digest prey. Symbiont carbon translocation and host prey ingestion were positively correlated across symbiont combinations that consisted of different isoclonal lines of Symbiodinium minutum, while a combination with type D4-5 Symbiodinium displayed lower carbon translocation, and prey capture and digestion more similar to Aiptasia lacking symbionts. The absence of a shift toward greater heterotrophy when carbon translocation is low suggests that the metabolic demand of feeding and digestion may overwhelm nutritional stores when photosynthesis is reduced, and amends the possible role of animal feeding in resistance to or recovery from the effects of climate change in more obligate symbioses such as reef-building corals. Summary: Not all cnidarian–dinoflagellate symbioses are equally nutritionally advantageous to the animal as the genetic identity of the symbiont affects the host's feeding capacity.
Public roles and private negotiations: Considering city magazines’ public service and market functions

Editors at city and regional magazines face the same competing loyalties as other local journalists, including sharing information about their cities while considering the interests of their organizations, readers, and advertisers. This study used in-depth interviews with city and regional magazine editors (N = 11) around the country to explore how they navigate public and private interests affecting their work and the implications of these negotiations for their journalistic identity and the perceived functions of their publications in communities. The results shed light on how the editors negotiate a focus on private-service content, which attracts readers and revenue, and public-service content, which serves the magazines’ journalistic role.
Effects of Social Exclusion in Trauma Survivors With Posttraumatic Stress Disorder

Trauma survivors with posttraumatic stress disorder (PTSD) often experience or report social stigmatization and isolation. Williams (2001) provided an experimental paradigm to assess behavioral effects of social exclusion. This paradigm (face-to-face version) has been applied in a 2 2 group experimental condition design. Participants in the PTSD group (N 16) and the nontraumatized control group (N 25) were randomly assigned to an exclusion or inclusion condition. The results showed interaction effects for main psychopathological assessments (depression, anxiety, psychoticism) and expected main effects for the majority of outcome measures (psychopathology, well-being, belonging, and meaningful existence). The research concludes that a general assumption of elevated levels of self-perceived social exclusion in PTSD patients has to be considered in terms of differentiated psychopathological effects of exclusion.
Fighting for Our Lives

The quest for quality education is a part of the ongoing struggle faced by African Americans. Few, if any, teacher education programs design programs that expressly meet the needs of African American students. Although some teacher preparation programs are designed for “urban” education, the significance of African American culture rarely is a feature of such programs. This article addresses the uniqueness of the African American cultural experience and details a variety of pedagogical and programmatic strategies that have been employed to assist teachers in better meeting the needs of African American students.
The Third Circle: On Education and Distance Learning

Has it been demonstrated that distance learning is as effective as face-to-face learning? This paper, proposing a “three circle” model of postsecondary education, argues that measurable competence, though a central component of education, is not in itself an adequate indicator of educational effectiveness. The model, supported by research into educational effects, is discussed in relation to the distinction between semantic memory and episodic memory, and in relation to the role of context in memory. Analysis of a widely-cited summary of 248 studies comparing distance learning and face-to-face learning concludes that these studies, which generally fail to go beyond measurable competence, and fail as well to support the newer interactive technologies commonly associated with distance learning, do not support any transfer of postsecondary education from the classroom to the screen. The limitations of distance learning are discussed in relation to their broader social implications.
Lies, rebukes and social norms

Reflecting upon the lies that are tied to rebukes is a fundamental step in the analysis of interactions between health-care professionals and their clients. Our research focuses on questions that incite people to lie, namely, those for which a lying response avoids a rebuke or a judgment based on some type of behaviour. Our objectives are: 1) to characterize the `question/response' exchange that is interpreted as a `potential rebuke/ lie' exchange, and the questions that may induce lying; 2) to identify the strategies that health-care professionals implement in order to obtain the information they seek when questioning their clients; and 3) to identify themes that refer to behavioural norms that clients might be inclined to lie about. The results are based on the assumption that there are ties between behaviour and speech acts, in this case between the transgression of behavioural norms and lying.
Exploratory nature of, and uncertainty tolerance in, qualitative research

Purpose – This paper seeks to depict an overall picture of an exploratory research journey to exemplify how qualitative studies on little understood phenomena can be done successfully. The paper aims to show how the author adopted an appropriate approach and an apposite methodology to cope with the uncertainty, stress and ambiguity arising during exploratory research.Design/methodology/approach – The paper was developed based on a reflective and narrative approach by the author to highlight the pivotal milestones of the reported research. The paper narrates how the research naturally evolved through seven stages including origination, orientation, exploration, elucidation, consolidation, reflection and culmination.Findings – Dealing with uncertainty and ambiguity is inevitable in exploratory studies. Constant interplay with the data, thorough implementation of the employed methodology and deep involvement with the research context are pivotal elements to achieve success in these studies. Finally, findings.
Neurological suppression of diaphragm electromyographs in hamsters infected with West Nile virus

To address the hypothesis that respiratory distress associated with West Nile virus (WNV) is neurologically caused, electromyographs (EMGs) were measured longitudinally from the diaphragms of alert hamsters infected subcutaneously (s.c.) with WNV. The EMG activity in WNV-infected hamsters was consistently and significantly (P ≤ .001) less than that of sham-infected animals, beginning with suppression at day 3 and continuing to beyond day 17 after viral challenge. Of the tissues known to affect respiration, i.e., lung, diaphragm, cervical spinal cord, brain stem, and the carotid or aortic bodies, foci of WNV-immunoreactive neurons were only observed in the brain stems and some cervical spinal cords from EMG-suppressed animals. To confirm the involvement of the brain stem and spinal cord, WNV was injected directly in the ventrolateral medulla containing respiratory functions using stereotaxic surgery and into the cervical cord at the C4 vertebral level. As with subcutaneous WNV challenge, hamsters developed EMG suppression of the diaphragm within 4 days. Because WNV-positive neurons were only sporadically identified in EMG-suppressed animals as early as day 3, a plausible mechanism of EMG suppression may involve regulation of diaphragm activity via vagal afferents acting on respiratory control system neurons in the brain stem. Brain auditory evoked response (BAER) was performed to determine if generalized brain stem neuropathy was the cause of diaphragmatic EMG suppression. Because deficiencies of BAER were only observed after day 11, which is long after diaphragm EMGs became suppressed, multiple phases of WNV-induced neurological disease are likely. These data establish that WNV infection of hamsters causes electrophysiological suppression of the diaphragm either directly by lesions in the brain stem and cervical spinal cord, or indirectly by altered vagal afferent function. This WNV-induced EMG suppression may be analogous to conditions leading to respiratory distress of WNV-infected human patients.
Life and death in Freud and Heidegger

students’’ (p. 33). Macdonald’s colourful descriptions seem to delight in describing the slicing and dicing of the dead. They appear to repeat on the page what she is critical of: the use of human remains for entertainment. Most importantly, her central argument, that anatomy is a cultural activity which encourages a proprietary attitude toward human remains that allows, even encourages, the use and abuse of human remains across history and countries, is unconvincing. Macdonald links the actions of Jack the Ripper, Gunther von Hagens, the organ scandal at Alder Hey, Burke and Hare, colonialism, racism, dissection, and medical practise today as all driven by this attitude she critiques. Referencing Ruth Richardson, Macdonald writes of a ‘‘fearful symmetry’’ between medicine’s past and its present’’ (p. 188). But this is too sweeping. She fails to distinguish between actions which appear similar (the cutting up of bodies) but which are driven and interpreted through very different social contexts and meanings. To conflate such different periods and actions indiscriminately hints of a psychological essentialism and does a disservice to those medics who are not killers or colonialists.
Modeling intra-label dynamics in connectionist temporal classification

Most sequence processing tasks can be cast as a problem of mapping a sequence of observations into a sequence of labels. This is a very difficult problem since the association between input data sequences and output label sequences is not given at the frame level. Recurrent neural networks (RNNs) equipped with connectionist temporal classification (CTC) are among the best tools devised to handle this problem and have been used to achieve state of the art results in many handwritten and speech recognition tasks. The reason that RNNs are used instead of feedforward networks in combination with CTC is that CTC does not model the dynamics of sequences. Specifically, the long short term memory (LSTM) RNN, which is excellent at memorizing information for a long time, is used in combination with CTC to overcome the limitations of CTC in modeling the dynamics of sequences. In this paper, we propose to model each label with a sequence of hidden sub-labels at the CTC level. The proposed framework allows CTC to learn the intra-label relations which transfers part of the load of learning dynamical sequences from RNN to CTC. Our experiments on handwriting recognition tasks show that the proposed method outperforms standard CTC in terms of accuracy.
Comparative study of Mg/Al- and Zn/Al-layered double hydroxide-perindopril erbumine nanocomposites for inhibition of angiotensin-converting enzyme

The intercalation of a drug active, perindopril, into Mg/Al-layered double hydroxide for the formation of a new nanocomposite, PMAE, was accomplished using a simple ion exchange technique. A relatively high loading percentage of perindopril of about 36.5% (w/w) indicates that intercalation of the active took place in the Mg/Al inorganic interlayer. Intercalation was further supported by Fourier transform infrared spectroscopy, and thermal analysis shows markedly enhanced thermal stability of the active. The release of perindopril from the nanocomposite occurred in a controlled manner governed by pseudo-second order kinetics. MTT assay showed no cytotoxicity effects from either Mg/Al-layered double hydroxide or its nanocomposite, PMAE. Mg/Al-layered double hydroxide showed angiotensin-converting enzyme inhibitory activity, with 5.6% inhibition after 90 minutes of incubation. On incubation of angiotensin-converting enzyme with 0.5 μg/mL of the PMAE nanocomposite, inhibition of the enzyme increased from 56.6% to 70.6% at 30 and 90 minutes, respectively. These results are comparable with data reported in the literature for Zn/Al-perindopril.