Miracle-dz/UniFAR-FTUs huggingface dataset:
Detection of Human Endogenous Retrovirus K (HERV-K) Transcripts in Human Prostate Cancer Cell Lines

Human endogenous retroviruses (HERVs) are transcribed in many cancers including prostate cancer. Human endogenous retrovirus K (HERV-K) of the HML2 subtype is the most recently integrated and most intact retrovirus in the human genome, with many of the viral genomes encoding full- or partial-length viral proteins. To assess transcripts of HERV-K in prostate cancer cell lines and identify the specific HERV-K elements in the human genome that are transcribed, reverse transcriptase-PCR (RT-PCR) and cDNA sequencing were undertaken. Strand-specific RT-PCR, plasmid subcloning, and cDNA sequencing detected the presence of HERV-K(HML2) coding strand transcripts within four prostate cell lines (LNCaP, DU145, PC3, and VCaP). RT-PCR across splice junctions revealed splicing variants for env gene mRNA in three cell lines, two involving previously undescribed alternative splice sites. To determine the HERV-K loci from which the transcripts arose, RepeatMasker was used to compile a list of over 200 HERV-K internal genome segment fragments and over 1,000 HERV-K solo long terminal repeat (LTR) fragments in the human genome. Surprisingly, the sequences identified from internal positions of the viral genome were mostly smaller segments, while the LTRs were relatively intact. Possible reasons for this are discussed. The transcripts in the cell lines tested, arose from several HERV-K loci, with some proviruses being detected in multiple cell lines and others in only one of the four used. In some instances, transcripts from viral antisense strands was also detected. In addition, transcripts from both strands of solo LTRs were detected. These data show that transcripts from HERV-K loci commonly occur in prostate cancer cell lines and that transcription of either strand can occur. They also emphasize the importance of single nucleotide level analysis to identify the specific, individual HERV-K loci that are transcribed, and indicate that HERV-K expression in prostate cancer warrants further study.
Semi-supervised Sentiment Classification using Ranked Opinion Words

This work proposes a semi-supervised sentiment classification method which is based on the co-training framework. The proposed method needs to construct three sentiment classifiers. We use common text features to construct the first classifier. We extract opinion words from consumer reviews, and then we ranked these opinion words according to their importance. We also employ extracted opinion words and the ranked co-occurrence opinion words of the extracted opinion words of each review to get the second sentiment classifier. A third sentiment classifier comes into being using non-opinion text features from each review. Based on co-training semi-supervised learning framework, we use the three sentiment classifiers to iteratively get the final sentiment classifier. Experimental results show that our proposed method has better performance than the Self-learning SVM method and the Naive co-training SVM method.
The Frequency and Impact of Exposure to Potentially Traumatic Events Over the Life Course

We examined the frequency and impact of exposure to potentially traumatic events in a nonclinical sample of older adults (N = 3,575), a population typically underrepresented in epidemiological research concerning the prevalence of traumatic events. Current posttraumatic stress disorder (PTSD) symptom severity and the centrality of events to identity were assessed for events nominated as currently most distressing. Approximately 90% of participants experienced one or more potentially traumatic events. Events that occurred with greater frequency early in the life course were associated with more severe PTSD symptoms compared to events that occurred with greater frequency during later decades. Early life traumas, however, were not more central to identity. Results underscore the differential impact of traumatic events experienced throughout the life course. We conclude with suggestions for further research concerning mechanisms that promote the persistence of posttraumatic stress related to early life traumas and empirical evaluation of psychotherapeutic treatments for older adults with PTSD.
The Relationship between Perfectionism and Anger*

Abstract The aim of the paper is to examine the relationship between perfectionism and anger in university students’ sample. The paper is a survey model composed of 725 students. The data used to determine the individual qualities in the paper are Multidimensional Perfectionism Scale, Multidimensional Anger Scale and ‘Individual Information Inventory’. In this study, it was discovered that social dimensional perfectionism of male students’ perfectionism level is found expressively higher than those of females. In other sub-dimensions, no remarkable differences were found. According to gender, when the feeling of not being taken seriously subdimension considered, it was also discovered that the anger level of female students has been found higher than male students’ and on the other hand concerning the unconcern behavior sub-dimension, anger of male students has been found higher than those of females. The researcher also discovered that there is a positive and significant correlation between students’ perfectionism and anger.
In Vitro Selection of Mutations in the Human Immunodeficiency Virus Type 1 Reverse Transcriptase That Decrease Susceptibility to (−)-β-d-Dioxolane-Guanosine and Suppress Resistance to 3′-Azido-3′-Deoxythymidine

ABSTRACT Human immunodeficiency virus type 1 (HIV-1) isolates resistant to (−)-β-d-dioxolane-guanosine (DXG), a potent and selective nucleoside analog HIV-1 reverse transcriptase (RT) inhibitor, were selected by serial passage of HIV-1LAI in increasing drug concentrations (maximum concentration, 30 μM). Two independent selection experiments were performed. Viral isolates for which the DXG median effective concentrations (EC50s) increased 7.3- and 12.2-fold were isolated after 13 and 14 passages, respectively. Cloning and DNA sequencing of the RT region from the first resistant isolate identified a K65R mutation (AAA to AGA) in 10 of 10 clones. The role of this mutation in DXG resistance was confirmed by site-specific mutagenesis of HIV-1LAI. The K65R mutation also conferred greater than threefold cross-resistance to 2′,3′-dideoxycytidine, 2′,3′-dideoxyinosine, 2′,3′-dideoxy-3′-thiacytidine, 9-(2-phosphonylmethoxyethyl)adenine, 2-amino-6-chloropurine dioxolane, dioxolanyl-5-fluorocytosine, and diaminopurine dioxolane but had only marginal effects on 3′-azido-3′-deoxthymidine (AZT) susceptibility. However, when introduced into a genetic background for AZT resistance (D67N, K70R, T215Y, T219Q), the K65R mutation reversed the AZT resistance. DNA sequencing of RT clones derived from the second resistant isolate identified the L74V mutation, previously reported to cause ddI resistance. The L74V mutation also decreased the AZT resistance when the mutation was introduced into a genetic background for AZT resistance (D67N, K70R, T215Y, T219Q) but to a lesser degree than the K65R mutation did. These findings indicate that DXG and certain 2′,3′-dideoxy compounds (e.g., ddI) can select for the same resistance mutations and thus may not be optimal for use in combination. However, the combination of AZT with DXG or its orally bioavailable prodrug (−)-β-d-2,6-diaminopurine-dioxolane should be explored because of the suppressive effects of the K65R and L74V mutations on AZT resistance.
Annual Review of Golf Coaching 2012

Gary Wiren is most known in the world of golf instruction / coaching / teaching as the author of the PGA Teaching Manual, which was published in 1990, and the originator of the Laws, Principles and Preferences model of golf teaching which has had global influence. As Director of Education for the PGA of America, Wiren was involved in the development of numerous programs including the Professional Golf Management (PGM) Program and the PGA National Academy of Golf for Juniors. From a comprehensive review of published material by or about Wiren, this article shows that he is not only a globally influential educator in golf but also a values-based coach and evidence-based practitioner.
The Relationship between College Zoology Students' Beliefs about Evolutionary Theory and Religion.

An anonymous questionnaire was administered to college zoology students prior to and following a study of evolutionary theory to assess their understanding and acceptance of the credibility of the evidences supporting the theory. A number of misconceptions that students held about the theory were identified. Many did not did have a clear understanding of the differences between a theory and a law, nor did they comprehend Darwin's Theory of Natural Selection. Most of the students surveyed could not correctly identify the mechanisms of speciation. The students were asked to explain whether or not their religious views were reconcilable with evolutionary theory. Beliefs were shown to interfere with the ability to objectively view scientific evidence, especially when they involved deeply ingrained religious teachings which were counter to the information being presented. Those who held strong creationist religious beliefs felt the choice was dichotomous. They accepted a literal Biblical account of creation and rejected the theory of evolution
High-resolution antibody dynamics of vaccine-induced immune responses

Significance The immune system must constantly adapt to combat infections and other challenges. This is accomplished by continuously evolving the antibody repertoire, and by maintaining memory of prior challenges. By using next-generation DNA sequencing technology, we have examined the shear amount of antibody made by individuals during a flu vaccination trial. We demonstrate one of the first characterizations of the fast antibody dynamics through time in multiple individuals responding to an immune challenge. The adaptive immune system confers protection by generating a diverse repertoire of antibody receptors that are rapidly expanded and contracted in response to specific targets. Next-generation DNA sequencing now provides the opportunity to survey this complex and vast repertoire. In the present work, we describe a set of tools for the analysis of antibody repertoires and their application to elucidating the dynamics of the response to viral vaccination in human volunteers. By analyzing data from 38 separate blood samples across 2 y, we found that the use of the germ-line library of V and J segments is conserved between individuals over time. Surprisingly, there appeared to be no correlation between the use level of a particular VJ combination and degree of expansion. We found the antibody RNA repertoire in each volunteer to be highly dynamic, with each individual displaying qualitatively different response dynamics. By using combinatorial phage display, we screened selected VH genes paired with their corresponding VL library for affinity against the vaccine antigens. Altogether, this work presents an additional set of tools for profiling the human antibody repertoire and demonstrates characterization of the fast repertoire dynamics through time in multiple individuals responding to an immune challenge.
Simple Disk-Based Method for Detection of Klebsiella pneumoniae Carbapenemase-Type β-Lactamase by Use of a Boronic Acid Compound

ABSTRACT A disk potentiation method using carbapenems as substrates and 3-aminophenyl boronic acid as an inhibitor was evaluated for the detection of Klebsiella pneumoniae carbapenemase (KPC)-type β-lactamases. When combined with nonsusceptibility to ertapenem, the method was easy to perform and reliably differentiated isolates producing KPC-type β-lactamases from those producing other types of β-lactamases.
Distinct types of ionic modulation of GABA actions in pyramidal cells and interneurons during electrical induction of hippocampal seizure‐like network activity

It has recently been shown that electrical stimulation in normal extracellular fluid induces seizure‐like afterdischarge activity that is always preceded by GABA‐dependent slow depolarization. These afterdischarge responses are synchronous among mature hippocampal neurons and driven by excitatory GABAergic input. However, the differences in the mechanisms whereby the GABAergic signals in pyramidal cells and interneurons are transiently converted from hyperpolarizing to depolarizing (and even excitatory) have remained unclear. To clarify the network mechanisms underlying this rapid GABA conversion that induces afterdischarges, we examined the temporal changes in GABAergic responses in pyramidal cells and/or interneurons of the rat hippocampal CA1 area in vitro. The extents of slow depolarization and GABA conversion were much larger in the pyramidal cell group than in any group of interneurons. Besides GABAA receptor activation, neuronal excitation by ionotropic glutamate receptors enhanced GABA conversion in the pyramidal cells and consequent induction of afterdischarge. The slow depolarization was confirmed to consist of two distinct phases; an early phase that depended primarily on GABAA‐mediated postsynaptic Cl– accumulation, and a late phase that depended on extracellular K+ accumulation, both of which were enhanced by glutamatergic neuron excitation. Moreover, extracellular K+ accumulation augmented each oscillatory response of the afterdischarge, probably by further Cl– accumulation through K+‐coupled Cl– transporters. Our findings suggest that the GABA reversal potential may be elevated above their spike threshold predominantly in the pyramidal cells by biphasic Cl– intrusion during the slow depolarization in GABA‐ and glutamate‐dependent fashion, leading to the initiation of seizure‐like epileptiform activity.
Structural Basis for Inhibiting Β-amyloid Oligomerization by a Non-coded Β-breaker-substituted Endomorphin Analogue

A lzheimer's disease (AD), the most widespread cause of dementia in the elderly population, is the sixth leading cause of death in the United States. 1 Strong genetic, physiological, and biochemical evidence suggests that the β-amyloid polypeptide (Aβ) plays a key role in the pathogenesis of the disease. 2 Although the etiologic role of Aβ in AD is acknowledged, 3 the molecular mechanism of neurotoxicity is still under debate. The occurrence of insoluble Aβ fibrils in AD has long been recognized , yet neuronal damage in AD may occur in the absence of amyloid plaques. Recent studies have demonstrated that non-fibrillar structures, including oligomers (56 kDa), 4,5 amyloid-derived diffusible ligands (ADDLs), 6 and protofibrils, 7 possess neurotoxic properties. Because the process of amyloid assembly is accompanied by a transition of a correctly folded monomer into oligomers and/or fibrils even at low, submicromolar concentrations , a very precise and highly specific process of molecular recognition must occur to enable such well-ordered, supramolecular structures to be formed. 8 Rational drug design approaches for developing inhibitors of Aβ aggregation are hampered by the absence of specific structural information on soluble or fibrillar Aβ, whose amorphic nature precludes using most structural methods. Previous experimental and theoretical studies by our group and others have indicated the apparent role of aromatic residues in the molecular recognition and self-assembly processes that lead to the formation of amyloid fibrils. 9À13 The aromatic amino acid tryptophan has been found to be very important for facilitating proteinÀprotein interactions 14 and was ranked as the amino acid with the highest amyloidogenic propensity. 15 Thus, inhibiting Aβ aggregation using aromatic entities, with an emphasis on tryptophan, is a rational strategy for therapeutic intervention in AD. 16 A number of small aromatic molecules such as short peptides, 17,18 polyphenols, 19 indole derivatives, 20 and quinines 21,22 have been shown to inhibit aggregation of several amyloidogenic peptides. Moreover, conjugating a β-breaker motif to recognition elements has been proposed to hinder amyloid formation. 23 A milestone in the search for proof of this concept was provided by Soto et al., who demonstrated that amyloid formation was inhibited by incorporating proline as a β-breaker element in short peptides bearing a recognition sequence of the amyloidogenic protein. 23 Our approach for breaking amyloidogenic β-sheet structures utilizes α-aminoisobutyric acid (Aib) as a potent β-breaker element. 16,24 This achiral amino acid has two methyl residues attached to the Cα …
Reinforcement Learning Strategies for Clinical Trials in Nonsmall Cell Lung Cancer

Summary Typical regimens for advanced metastatic stage IIIB/IV nonsmall cell lung cancer (NSCLC) consist of multiple lines of treatment. We present an adaptive reinforcement learning approach to discover optimal individualized treatment regimens from a specially designed clinical trial (a “clinical reinforcement trial”) of an experimental treatment for patients with advanced NSCLC who have not been treated previously with systemic therapy. In addition to the complexity of the problem of selecting optimal compounds for first‐ and second‐line treatments based on prognostic factors, another primary goal is to determine the optimal time to initiate second‐line therapy, either immediately or delayed after induction therapy, yielding the longest overall survival time. A reinforcement learning method called Q‐learning is utilized, which involves learning an optimal regimen from patient data generated from the clinical reinforcement trial. Approximating the Q‐function with time‐indexed parameters can be achieved by using a modification of support vector regression that can utilize censored data. Within this framework, a simulation study shows that the procedure can extract optimal regimens for two lines of treatment directly from clinical data without prior knowledge of the treatment effect mechanism. In addition, we demonstrate that the design reliably selects the best initial time for second‐line therapy while taking into account the heterogeneity of NSCLC across patients.
Force Field Feature Extraction for Ear Biometrics

The overall objective in defining feature space is to reduce the dimensionality of the original pattern space, whilst maintaining discriminatory power for classification. To meet this objective in the context of ear biometrics a new force field transformation treats the image as an array of mutually attracting particles that act as the source of a Gaussian force field. Underlying the force field there is a scalar potential energy field, which in the case of an ear takes the form of a smooth surface that resembles a small mountain with a number of peaks joined by ridges. The peaks correspond to potential energy wells and to extend the analogy the ridges correspond to potential energy channels. Since the transform also turns out to be invertible, and since the surface is otherwise smooth, information theory suggests that much of the information is transferred to these features, thus confirming their efficacy. We previously described how field line feature extraction, using an algorithm similar to gradient descent, exploits the directional properties of the force field to automatically locate these channels and wells, which then form the basis of characteristic ear features. We now show how an analysis of the mechanism of this algorithmic approach leads to a closed analytical description based on the divergence of force direction, which reveals that channels and wells are really manifestations of the same phenomenon. We further show that this new operator, with its own distinct advantages, has a striking similarity to the Marr-Hildreth operator, but with the important difference that it is non-linear. As well as addressing faster implementation, invertibility, and brightness sensitivity, the technique is also validated by performing recognition on a database of ears selected from the XM2VTS face database, and by comparing the results with the more established technique of Principal Components Analysis. This confirms not only that ears do indeed appear to have potential as a biometric, but also that the new approach is well suited to their description, being robust especially in the presence of noise, and having the advantages that the ear does not need to be explicitly extracted from the background.
Clearance of Bilirubin from Rat Brain after Reversible Osmotic Opening of the Blood-Brain Barrier

ABSTRACT. : Utilizing multicomponent spectrophotometry, we assayed the bilirubin content of rat cerebral hemispheres. With this assay, we determined the clearance of bilirubin from the rat brain following reversible, osmotic opening of the blood-brain barrier. Clearance was rapid, with a half-time of 1.7 h. This half-time was the same as that for clearance of bilirubin from the serum, suggesting that brain bilirubin was removed by transport or diffusion back into the general circulation. Osmotic opening does not damage brain tissue. Thus, in the undamaged rat brain, bilirubin is rapidly cleared, in contrast to its persistence in autopsy-proven human kernicterus. The potential for clearance of bilirubin from human neonatal brain should be considered, especially in the absence of underlying tissue damage.
Selection procedures for module discovery : exploring evolutionary algorithms for cognitive science

Evolutionary algorithms are playing an increasingly important role as search methods in cognitive science domains. In this study, methodological issues in the use of evolutionary algorithms were investigated via simulations in which procedures were systematically varied to modify the selection pressures on populations of evolving agents. Traditional roulette wheel, tournament, and variations of these selection algorithms were compared on the “needle-in-a-haystack” problem developed by Hinton and Nowlan in their 1987 study of the Baldwin effect. The task is an important one for cognitive science, as it demonstrates the power of learning as a local search technique in smoothing a fitness landscape that lacks gradient information. One aspect that has continued to foster interest in the problem is the observation of residual learning ability in simulated populations even after long periods of time. Effective evolutionary algorithms balance their search effort between broad exploration of the search space and in-depth exploitation of promising solutions already found. Issues discussed include the differential effects of rank and proportional selection, the tradeoff between migration of populations towards good solutions and maintenance of diversity, and the development of measures that illustrate how each selection algorithm affects the search process over generations. We show that both roulette wheel and tournament algorithms can be modified to appropriately balance search between exploration and exploitation, and effectively eliminate residual learning in this problem.
More than just a pretty picture? How sociologists (and other social scientists) can use Pinterest

Between Facebook, Twitter and LinkedIn, academics can be forgiven for struggling to keep up with the social media boom. Deborah Lupton investigates the latest popular platform, Pinterest, and finds it can be more than just a pretty picture. In fact, it has potential to be of great value to sociologists and social scientists.