Miracle-dz/UniFAR-FTUs huggingface dataset:
The First Endogenous Herpesvirus, Identified in the Tarsier Genome, and Novel Sequences from Primate Rhadinoviruses and Lymphocryptoviruses

Herpesviridae is a diverse family of large and complex pathogens whose genomes are extremely difficult to sequence. This is particularly true for clinical samples, and if the virus, host, or both genomes are being sequenced for the first time. Although herpesviruses are known to occasionally integrate in host genomes, and can also be inherited in a Mendelian fashion, they are notably absent from the genomic fossil record comprised of endogenous viral elements (EVEs). Here, we combine paleovirological and metagenomic approaches to both explore the constituent viral diversity of mammalian genomes and search for endogenous herpesviruses. We describe the first endogenous herpesvirus from the genome of the Philippine tarsier, belonging to the Roseolovirus genus, and characterize its highly defective genome that is integrated and flanked by unambiguous host DNA. From a draft assembly of the aye-aye genome, we use bioinformatic tools to reveal over 100,000 bp of a novel rhadinovirus that is the first lemur gammaherpesvirus, closely related to Kaposi's sarcoma-associated virus. We also identify 58 genes of Pan paniscus lymphocryptovirus 1, the bonobo equivalent of human Epstein-Barr virus. For each of the viruses, we postulate gene function via comparative analysis to known viral relatives. Most notably, the evidence from gene content and phylogenetics suggests that the aye-aye sequences represent the most basal known rhadinovirus, and indicates that tumorigenic herpesviruses have been infecting primates since their emergence in the late Cretaceous. Overall, these data show that a genomic fossil record of herpesviruses exists despite their extremely large genomes, and expands the known diversity of Herpesviridae, which will aid the characterization of pathogenesis. Our analytical approach illustrates the benefit of intersecting evolutionary approaches with metagenomics, genetics and paleovirology.
The Global DNA Methylation Surrogate LINE-1 Methylation Is Correlated with MGMT Promoter Methylation and Is a Better Prognostic Factor for Glioma

Gliomas are the most frequently occurring primary brain tumor in the central nervous system of adults. Glioblastoma multiformes (GBMs, WHO grade 4) have a dismal prognosis despite the use of the alkylating agent, temozolomide (TMZ), and even low grade gliomas (LGGs, WHO grade 2) eventually transform to malignant secondary GBMs. Although GBM patients benefit from promoter hypermethylation of the O 6-methylguanine-DNA methyltransferase (MGMT) that is the main determinant of resistance to TMZ, recent studies suggested that MGMT promoter methylation is of prognostic as well as predictive significance for the efficacy of TMZ. Glioma-CpG island methylator phenotype (G-CIMP) in the global genome was shown to be a significant predictor of improved survival in patients with GBM. Collectively, we hypothesized that MGMT promoter methylation might reflect global DNA methylation. Additionally in LGGs, the significance of MGMT promoter methylation is still undetermined. In the current study, we aimed to determine the correlation between clinical, genetic, and epigenetic profiles including LINE-1 and different cancer-related genes and the clinical outcome in newly diagnosed 57 LGG and 54 GBM patients. Here, we demonstrated that (1) IDH1/2 mutation is closely correlated with MGMT promoter methylation and 1p/19q codeletion in LGGs, (2) LINE-1 methylation levels in primary and secondary GBMs are lower than those in LGGs and normal brain tissues, (3) LINE-1 methylation is proportional to MGMT promoter methylation in gliomas, and (4) higher LINE-1 methylation is a favorable prognostic factor in primary GBMs, even compared to MGMT promoter methylation. As a global DNA methylation marker, LINE-1 may be a promising marker in gliomas.
A New Autonomy-Supportive Way of Teaching That Increases Conceptual Learning: Teaching in Students' Preferred Ways

We tested the educational utility of “teaching in students' preferred ways” as a new autonomy-supportive way of teaching to enhance students' autonomy and conceptual learning. A pilot test first differentiated preferred versus nonpreferred ways of teaching. In the main study, a hired teacher who was blind to the purpose of the study taught 63 college-age participants in small groups the same 48-minute lesson in one of these two different ways, and we assessed participants' perceived autonomy support, autonomy-need satisfaction, engagement (self-report and rater scored), and conceptual learning (self-report and rater scored). Multilevel analyses showed that participants randomly assigned to receive a preferred way of teaching perceived the teacher as more autonomy supportive and showed significantly greater autonomy-need satisfaction, engagement, and conceptual learning. Mediation analyses using multilevel modeling for clustered data showed that this way of teaching enhanced conceptual learning because it first increased students' autonomy. We conclude that “teaching in students' preferred ways” represents a way of teaching that increases students' autonomy, engagement, and conceptual learning.
Mental health as a function of religious orientation

This dissertation studies the relationship between religious commitment and mental health. It is contended thau the concept of religious orientation has not been utilized sufficiently in previous relevant research. This concept is thus used in an attempt to clarify the vague and confusing relationship that has thus far been shown to exist befcwean religion and mental health. This dissertation proposes that it is not religious commitment as such, hut rather religious orientation, that is important in determining the level of personal adjustment. The Religious Orientation Scale and Personal Orientation Inventory were administered by various Church Ministers from different denominations to voluntary members of their congregations. Two hundred and thirty one unspoilt questionnaires were returned by post, and were analyzed in terms of breakdown across demographic variables as well as the relationship between religous orientation and self-actualization. Using zero-order and partial correlation coefficients, it was determined that significant correlations in the predicted direction exist between religous orientation and the Time Competence and Outer Directed dimensions of self-actualization. On this basis it was concluded that intrinsic orientation is associated with a self-actualizing mode of being, while an extrinsic orientation is associated with a non self-actualizing mode of beJ.iv
tRNA acceptor stem and anticodon bases form independent codes related to protein folding

Significance The universal genetic code is the earliest point to which we can trace biological inheritance. Earlier work hinted at a relationship between the codon bases and the physical properties of the 20 amino acids that dictate the 3D conformations of proteins in solution. Here, we show that acceptor stems and anticodons, which are at opposite ends of the tRNA molecule, code, respectively, for size and polarity. These two distinct properties of the amino acid side-chains jointly determine their preferred locations in folded proteins. The early appearance of an acceptor stem code based on size, β-branching, and carboxylate groups might have favored the appearance of antiparallel peptides that have been suggested to have a special affinity for RNA. Aminoacyl-tRNA synthetases recognize tRNA anticodon and 3′ acceptor stem bases. Synthetase Urzymes acylate cognate tRNAs even without anticodon-binding domains, in keeping with the possibility that acceptor stem recognition preceded anticodon recognition. Representing tRNA identity elements with two bits per base, we show that the anticodon encodes the hydrophobicity of each amino acid side-chain as represented by its water-to-cyclohexane distribution coefficient, and this relationship holds true over the entire temperature range of liquid water. The acceptor stem codes preferentially for the surface area or size of each side-chain, as represented by its vapor-to-cyclohexane distribution coefficient. These orthogonal experimental properties are both necessary to account satisfactorily for the exposed surface area of amino acids in folded proteins. Moreover, the acceptor stem codes correctly for β-branched and carboxylic acid side-chains, whereas the anticodon codes for a wider range of such properties, but not for size or β-branching. These and other results suggest that genetic coding of 3D protein structures evolved in distinct stages, based initially on the size of the amino acid and later on its compatibility with globular folding in water.
Hexaaquamagnesium(II) bis{[2-(1-phenyl-1H-tetrazol-5-yl)sulfanyl]acetate}

The asymmetric unit of the title compound, [Mg(H2O)6](C9H7N4O2S)2, contains one-half of a [Mg(H2O)6]2+ cation ( symmetry) and one uncoordinated 2-[(1-phenyl-1H-tetrazol-5-yl)sulfanyl]acetate anion. The MgII cation is coordinated by six water molecules, exhibiting a slightly distorted octahedral coordination. A two-dimensional network parallel to (001) is formed via extensive hydrogen-bonding interactions involving the water molecules as donors and the tetrazole N and carboxylate O atoms of the anion as acceptors. The shortest distance between two adjacent parallel benzene rings is 3.315 (2) Å. The dihedral angle between the benzene ring and the tetrazole ring is 40.98 (2)°.
Choosing the Right Type of Rotation in PCA and EFA

Question: In Chapter 7 of the 2008 book on heritage language learning that you co-edited with Kimi Kondo-Brown, there is a study (Lee & Kim, 2008) comparing the attitudes of 111 Korean heritage language learners. On page 167 of that book, a principal components analysis (with varimax rotation) describes the relation of examining 16 purported reasons for studying Korean with four broader factors. Several questions come to mind. What is a principal components analysis? How does principal components analysis differ from factor analysis? What guidelines do researchers need to bear in mind when selecting “factors”? And finally, what is a varimax rotation and why is it applied?
The Persuasiveness of Synthetic Speech versus Human Speech

Is computer-synthesized speech as persuasive as the human voice when presenting an argument? After completing an attitude pretest, 193 participants were randomly assigned to listen to a persuasive appeal under three conditions: a high-quality synthesized speech system (DECtalk Express), a low-quality synthesized speech system (Monologue), and a tape recording of a human voice. Following the appeal, participants completed a posttest attitude survey and a series of questionnaires designed to assess perceptions of speech qualities, perceptions of the speaker, and perceptions of the message. The human voice was generally perceived more favorably than the computer-synthesized voice, and the speaker was perceived more favorably when the voice was a human voice than when it was computer synthesized. There was, however, no evidence that computerized speech, as compared with the human voice, affected persuasion or perceptions of the message. Actual or potential applications of this research include issues that should be considered when designing synthetic speech systems.
Leatherdyke Boys and Their Daddies: How to Have Sex without Women or Men

Contemporary queer theory sees gender as a regulatory construct, a site of shifting power relations. Although queer theorists have made many claims about the power of queerly gendered bodies and performativities to disrupt enforced normative sex/gender systems, theory lags far behind community discourses here. In sexual-minority communities, such as queer leather communities, there are rich and subtly nuanced discourses of gendered pleasure, practice, desire, and subjectivity. These community discourses sometimes reflect rich and subtly nuanced embodiments of gender that resist and exceed any simple categorization into female, male, woman, man, and thus into homosexual, bisexual, or heterosexual.1 Further, queer theory has tended to neglect "the implications of an enforced sex/gender system for people who live outside it," as Ki Namaste has argued with regard to queer theory's erasure of transgendered subjectivity.2 When transgendered subjects participate in minority communities organized around radical sexual practice, new and theoretically interesting configurations of sex, gender, and sexuality arise. In this paper, I will theorize the genderings of U.S. leatherdyke boys and their leatherdyke daddies. I am especially concerned to explore how leatherdyke genderplay functions as a means for gender interrogation, solidification, resistance, destabilization, and reconfiguration. From this investigation, I will draw some tentative conclusions about multiple gender statuses already available in the United States.
Changes in parental emotional support and psychological control during the transition to adulthood: direct and indirect associations with educational, occupational, and financial adjustment through mental health symptoms

Young adulthood is a critical period during which advances in educational, occupational, and financial adjustment set the stage for lifelong economic capital, health, and wellbeing. Greater understanding of the factors that contribute to positive and negative adjustment in young adulthood is warranted. This longitudinal study highlights the important role of parents by investigating (1) changes in the emotional quality of parentyouth relationships during adolescence and the transition to adulthood, (2) whether such changes relate to young adults’ adjustment outcomes in three age-salient domains, and (3) whether the effects of changes in parental relationships are associated with young adults’ adjustment outcomes through the intervening effects of mental health symptoms. Specifically, I examined direct and indirect associations between changes in mother and father emotional support (ES) and psychological control (PC) and young adults’ educational, occupational, and financial outcomes through youths’ depressive and anxiety symptoms. Sex and SES group differences were also examined. Participants were 545 youth from a medium-sized Canadian city. They were assessed at four time points over a
HIV‐disease and bone marrow changes: A study of 60 cases

We report our experience of peripheral blood and bone marrow changes in patients with HIV disease. Abnormalities were most commonly seen in patients with advanced disease. In AIDS group IV patients (CDC classification) anaemia (92%) neutropenia (85%) monocytopenia (75%) and thrombocytopenia (61%) have their highest incidence, the reason being a combination of factors such as infection, myelosuppressive drugs and HIV infection itself. Bone marrow examinations were performed most commonly for microbiological culture (25%) and the investigation of anaemia (16%). Morphological changes in the bone marrow were non‐specific and not pathognomic; however erythroid hypoplasia was found to be a distinctive feature associated with MAI infection. The procedure provided a high yield for microbiological culture, particularly in MAI infection.
Attend Refine Repeat: Active Box Proposal Generation via In-Out Localization

The problem of computing category agnostic bounding box proposals is utilized as a core component in many computer vision tasks and thus has lately attracted a lot of attention. In this work we propose a new approach to tackle this problem that is based on an active strategy for generating box proposals that starts from a set of seed boxes, which are uniformly distributed on the image, and then progressively moves its attention on the promising image areas where it is more likely to discover well localized bounding box proposals. We call our approach AttractioNet and a core component of it is a CNN-based category agnostic object location refinement module that is capable of yielding accurate and robust bounding box predictions regardless of the object category. We extensively evaluate our AttractioNet approach on several image datasets (i.e. COCO, PASCAL, ImageNet detection and NYU-Depth V2 datasets) reporting on all of them state-of-the-art results that surpass the previous work in the field by a significant margin and also providing strong empirical evidence that our approach is capable to generalize to unseen categories. Furthermore, we evaluate our AttractioNet proposals in the context of the object detection task using a VGG16-Net based detector and the achieved detection performance on COCO manages to significantly surpass all other VGG16-Net based detectors while even being competitive with a heavily tuned ResNet-101 based detector. Code as well as box proposals computed for several datasets are available at:: this https URL
Isometric tetanic force measurement method of the tibialis anterior in the rat

Tetanic force measurements of rat tibialis anterior (TA) muscles have been described, but with a variety of stimulation parameters. This study presents a novel functional method of force measurement of the rat TA muscle and describes the optimization of stimulation parameters. Bilateral TA muscles in 10 male Lewis rats were attached to a force transducer after the corresponding hindlimb was fixed. Preload, stimulus intensity, duration, and frequency were optimized for each individual muscle and the isometric maximal tetanic muscle force was measured. The mean left side tetanic force as a percentage of the right was 100.0 ± 4.4% and was statistically equivalent. Large standard deviations between sides (35–50%) were observed in the optimized parameters (preload, stimulus intensity, duration, and frequency). Optimization of the variables affecting isometric tetanic force resulted in reproducible and reliable side‐to‐side measurements of the TA muscle in the rat model. © 2008 Wiley‐Liss, Inc. Microsurgery, 2008.
Using the web for automated translation extraction in cross-language information retrieval

There have been significant advances in Cross-Language Information Retrieval (CLIR) in recent years. One of the major remaining reasons that CLIR does not perform as well as monolingual retrieval is the presence of out of vocabulary (OOV) terms. Previous work has either relied on manual intervention or has only been partially successful in solving this problem. We use a method that extends earlier work in this area by augmenting this with statistical analysis, and corpus-based translation disambiguation to dynamically discover translations of OOV terms. The method can be applied to both Chinese-English and English-Chinese CLIR, correctly extracting translations of OOV terms from the Web automatically, and thus is a significant improvement on earlier work.
Technology Acceptance and Organizational Change: An Integration of Theory

This dissertation uses a sequential mixed method research design to examine a new model of change readiness that focuses on change initiatives involving technology. The model is called the model of technological change. It integrates two models, one from organizational change literature and one from information systems (IS) literature. The model of readiness for change follows the theoretical framework provided by Fishbein and Ajzen in the Theory of Planned Behavior (TPB) to predict behaviors using attitudes formed by beliefs, which are in turn informed by antecedents. The model consists of four classes of antecedents: content, process, context, and individual differences, which predict the five change recipient beliefs. The beliefs are: discrepancy, appropriateness, change efficacy, principal support, and personal valence. These beliefs reflect the attitude called readiness for change and predict various change-related outcomes. The technology acceptance model (TAM) comes from IS literature. The model is commonly used to predict use of a new technology after being implemented in an organization. It too follows the framework of Fishbein and Ajzen’s TPB and matches very closely to the model of readiness for change in terms of its content, except that it has two beliefs that are very different, perceived ease of use and perceived usefulness. These two models are combined and both literatures are examined. Additional theoretical development related to expectancy theory as a process to explain readiness and resistance to change is explored by examining the combination of belief constructs within the integrated model. A smaller hypothesized model consisting of one variable from each of the four antecedent categories is tested. The antecedents include specific ERP subsystem for content, training for process, LMX for context, and core self-evaluation for individual differences. The model includes all
Model-based learning for mobile robot navigation from the dynamical systems perspective

This paper discusses how a behavior-based robot can construct a "symbolic process" that accounts for its deliberative thinking processes using models of the environment. The paper focuses on two essential problems; one is the symbol grounding problem and the other is how the internal symbolic processes can be situated with respect to the behavioral contexts. We investigate these problems by applying a dynamical system's approach to the robot navigation learning problem. Our formulation, based on a forward modeling scheme using recurrent neural learning, shows that the robot is capable of learning grammatical structure hidden in the geometry of the workspace from the local sensory inputs through its navigational experiences. Furthermore, the robot is capable of generating diverse action plans to reach an arbitrary goal using the acquired forward model which incorporates chaotic dynamics. The essential claim is that the internal symbolic process, being embedded in the attractor, is grounded since it is self-organized solely through interaction with the physical world. It is also shown that structural stability arises in the interaction between the neural dynamics and the environmental dynamics, which accounts for the situatedness of the internal symbolic process, The experimental results using a mobile robot, equipped with a local sensor consisting of a laser range finder, verify our claims.