Miracle-dz/UniFAR-FTUs huggingface dataset:
Helix‐coil transition of PrP106–126: Molecular dynamic study

A set of 34 molecular dynamic (MD) simulations totaling 305 ns of simulation time of the prion protein‐derived peptide PrP106–126 was performed with both explicit and implicit solvent models. The objective of these simulations is to investigate the relative stability of the α‐helical conformation of the peptide and the mechanism for conversion from the helix to a random‐coil structure. At neutral pH, the wild‐type peptide was found to lose its initial helical structure very fast, within a few nanoseconds (ns) from the beginning of the simulations. The helix breaks up in the middle and then unwinds to the termini. The spontaneous transition into the random coil structure is governed by the hydrophobic interaction between His111 and Val122. The A117V mutation, which is linked to GSS disease, was found to destabilize the helix conformation of the peptide significantly, leading to a complete loss of helicity approximately 1 ns faster than in the wild‐type. Furthermore, the A117V mutant exhibits a different mechanism for helix‐coil conversion, wherein the helix begins to break up at the C‐terminus and then gradually to unwind towards the N‐terminus. In most simulations, the mutation was found to speed up the conversion through an additional hydrophobic interaction between Met112 and the mutated residue Val117, an interaction that did not exist in the wild‐type peptide. Finally, the β‐sheet conformation of the wild‐type peptide was found to be less stable at acidic pH due to a destabilization of the His111–Val122, since at acidic pH this histidine is protonated and is unlikely to participate in hydrophobic interaction. Proteins 2001;45:382–396. © 2001 Wiley‐Liss, Inc.
Standard-Compliant LTE-A Uplink Scheduling Scheme With Quality of Service

In this paper, we focus on uplink scheduling with the practical constraints imposed by the Long-Term Evolution/Long-Term Evolution-Advanced (LTE/LTE-A) standard. We consider multimedia traffic generated by mobile users with heterogeneous quality-of-service (QoS) requirements. To tackle the resulting time and frequency problem, we then propose an adaptive and potential aware scheduling scheme (APASS), which is standard compliant and covers a wide range of scheduling objectives. This scheduling scheme is composed of three algorithms, which work jointly to provide an efficient solution. Our performance evaluation shows that the APASS outperforms other state-of-the-art scheduling schemes in terms of user satisfaction and delay.
Testing the inter-relations of factors that may support continued use intention: The case of Facebook

Information systems (IS) may not improve organizational and/or companies’ performance if they are not used by stakeholders. Understanding why people continue or discontinue use of IS is crucial in increasing users’ acceptance. This article aims to analyze what is needed to perpetuate use of Facebook as a social media channel. Factors such as confirmation, perceived usefulness, social influence, satisfaction and attitude were tested for their impact on continued use intention in relation to Facebook. The inter-relations between the aforementioned constructs are tested with empirical data collected from 732 European university students. We found that social influence essentially had no effect within the model, so it seems that intention to continue using Facebook is affected mainly by stakeholders’/users’ attitude toward using this platform. Although we based the research on the IS Continuance Model, this article has extended its dimensions by incorporating (1) social influence and (2) attitude, offering the first investigation of continued use intention in relation to Facebook by testing the inter-relations between the aforementioned factors.
Adenovirus E4-dependent activation of the early E2 promoter is insufficient to promote the early-to-late-phase transition

The adenovirus E4 ORF6/7 protein has been shown to activate the cellular transcription factor E2F. E2F activation leads to activation of the adenovirus early E2 promoter which controls the production of viral DNA replication proteins. In the present study an adenovirus type 5 cDNA mutant, H5ilE4L, was constructed. This mutant is capable of making the ORF6/7 polypeptide but lacks the coding sequences for all other E4 products. H5ilE4L trans activates the early E2 promoter to wild-type levels, but still it is defective for viral DNA replication. A mutant expressing ORF6 in addition to ORF6/7, H5ilE4I, is normal for viral DNA replication. This indicates that activation of the early E2 promoter is insufficient to promote efficient viral DNA replication and that another E4-encoded function is necessary. The ORF6 protein seems to provide this function. We suggest that ORF6/7-induced activation of E2F is not necessary for adenovirus growth in HeLa cells. Rather, this activation might be of importance in the normal, growth-arrested host cell, since E2F has been shown to bind to the promoter regions of a number of immediate-early genes involved in regulation of cell proliferation (M. Mudryj, S. W. Hiebert, and J. R. Nevins, EMBO J. 9:2179-2184, 1990).
Getting the Personal Perspective into View

There is a long-standing concern that psychiatrists have the task of fitting a square peg into a round hole: the empirical generalizations upon which diagnoses are made have seemed too many to overlook something essential about the individual person who is the subject of the diagnosis. This concern prompted a World Psychiatric Association (WPA) workgroup to suggest that a personalized component should be added to patients’ diagnostic assessment (IDGA Workgroup 2003). One might have the following worry about the WPA workgroup’s suggestion: if this personalized component is merely tagged on to the existing diagnostic framework, and diagnoses still rest primarily on empirical generalizations, which are left untouched by this added personalized component, then it is far from clear that anything has really been gained by the addition of the personalized component. Now the hope of integrating a personalized component into diagnostic practice in a meaningful way presumes that we have a reasonably clear understanding of what such a component would amount to in substantive terms. However, the notion of personalization is vague as it stands. In what follows, I suggest a way of conceiving of the personalized component and offer one reason for believing that it is indispensable to psychiatric diagnoses. To begin with, I take it that the integration that is sought after is the integration between the personal and the scientific perspectives 1 There have been at least two motivations for wanting include the personal perspective within the specific context of psychiatric assessments. In what remains, my focus is on the first motivation.
Modeling Rhythmic Interlimb Coordination: Beyond the Haken–Kelso–Bunz Model

Although the Haken-Kelso-Bunz (HKB) model was originally formulated to account for phase transitions in bimanual movements, it evolved, through experimentation and conceptual elaboration, into a fundamental formal construct for the experimental study of rhythmically coordinated movements in general. The model consists of two levels of formalization: a potential defining the stability properties of relative phase and a system of coupled limit cycle oscillators defining the individual limb movements and their interactions. Whereas the empirical validity of the potential is well established, the validity of the formalization in terms of coupled oscillators is questionable, both with regard to the assumption that individual limb movements are limit cycle oscillators with (only) two active degrees of freedom and with regard to the postulated coupling. To remedy these limitations a more elaborate system of coupled oscillators is outlined, comprising two coupled limit cycle oscillators at the neural level, each of which is coupled to a linearly damped oscillator, representing the end-effectors.
Measuring the cost of regression testing in practice: a study of Java projects using continuous integration

Software defects cost time and money to diagnose and fix. Consequently, developers use a variety of techniques to avoid introducing defects into their systems. However, these techniques have costs of their own; the benefit of using a technique must outweigh the cost of applying it. In this paper we investigate the costs and benefits of automated regression testing in practice. Specifically, we studied 61 projects that use Travis CI, a cloud-based continuous integration tool, in order to examine real test failures that were encountered by the developers of those projects. We determined how the developers resolved the failures they encountered and used this information to classify the failures as being caused by a flaky test, by a bug in the system under test, or by a broken or obsolete test. We consider that test failures caused by bugs represent a benefit of the test suite, while failures caused by broken or obsolete tests represent a test suite maintenance cost. We found that 18% of test suite executions fail and that 13% of these failures are flaky. Of the non-flaky failures, only 74% were caused by a bug in the system under test; the remaining 26% were due to incorrect or obsolete tests. In addition, we found that, in the failed builds, only 0.38% of the test case executions failed and 64% of failed builds contained more than one failed test. Our findings contribute to a wider understanding of the unforeseen costs that can impact the overall cost effectiveness of regression testing in practice. They can also inform research into test case selection techniques, as we have provided an approximate empirical bound on the practical value that could be extracted from such techniques. This value appears to be large, as the 61 systems under study contained nearly 3 million lines of test code and yet over 99% of test case executions could have been eliminated with a perfect oracle.
Differential Effects of Four Comprehension-Facilitating Conditions on LD and Normal Elementary-School Readers

Ninety-nine elementary-school learning disabled and normal children were assigned to one of four comprehension-facilitating conditions (word identification and meaning aids, sentence aids, purpose-setting aids, and prior-knowledge aids) to determine their effects on comprehension. Controlling for age, intelligence, prior reading achievement, and pretest comprehension levels, sentence aids were found to be significantly more effective than prior knowledge for both learning disabled and similarly achieving, but younger readers. Moreover, for the same two groups of subjects the average effect of words and sentences (micro-level aids) was significantly higher than the average effect of purpose setting and prior knowledge (macro-level aids). No significant differences were found among the four types of comprehension facilitators for normally achieving readers who were the same age as the learning disabled group.
Reading Effects of IBM’s “Writing to Read” Program: A Review of Evaluations

This article reviews evaluations of IBM’s Writing to Read program in kindergartens and first grades. In Writing to Read (WTR), students rotate through five learning stations to learn and practice phonics, to write stories, and to listen to recorded books. Two of these stations involve computers. Twenty-one studies of Writing to Read in kindergartens found a median effect size of 0.23, but in many cases this effect may be due to comparisons of WTR with nonacademic programs. Across 13 first-grade studies, the median effect size was . 00. Two-year (K-l) implementations and one-year follow-up studies found no consistent achievement effects. The commercial success of WTR is discussed in light of these disappointing findings and of the existence of more effective and far less expensive alternatives
Tracking the hypersensitive dimension in narcissism: Reliability and validity of the Hypersensitive Narcissism Scale

The aim of the study was to assess the reliability and the validity of the Italian translation of the Hypersensitive Narcissism Scale (HSNS) in a sample of consecutively admitted psychiatric outpatients (N = 366) and in an independent sample of non-clinical volunteers (N = 385). In both samples, data from the HSNS had adequate internal consistency, considering its limited length. Consistent with our hypothesis, a two-factor structure explained the HSNS item intercorrelations. Among clinical participants, the HSNS and the Narcissistic Personality Inventory (NPI) showed radically different patterns of correlations with the fourth edition of the Diagnostic and Statistical Manual for Mental Disorders (DSM-IV) Personality Disorder diagnoses. In both samples, the HSNS and the NPI showed distinct and theoretically consistent correlations with temperament and character dimensions. As a whole, these findings seem to support the reliability and the validity of the HSNS as a measure of hypersensitive narcissism. Copyright © 2009 John Wiley & Sons, Ltd.
Bloat is Unnatural: An Analysis of Changes in Variable Chromosome Length Absent Selection Pressure

In this work we provide empirical evidence that shows how a variable-length genetic algorithm (GA) can naturally evolve shorter average size populations. This reduction in chromosome length appears to occur in finite population GAs when 1) selection is absent from the GA (random) or 2) when selection focuses on some other property not influenced by the length of individuals within a population.
Social Goal Orientations, Interpersonal Stress, and Depressive Symptoms Among Early Adolescents in Japan: A Test of the Diathesis-Stress Model Using the Trichotomous Framework of Social Goal Orientations

This longitudinal study investigated whether depression among early adolescents (aged 12-14 years, N = 116; 65 girls) can be predicted by interactions between social goal orientations and interpersonal stress. Based on Kuroda and Sakurai (2001), this study applied Elliot and Harackiewicz’s (1996) trichotomous framework of achievement goals to Dweck and Leggett’s (1988) model of social goals and investigated three types of social goals: social learning goals (to grow through interpersonal experiences), social performance-approach goals (to obtain positive evaluations), and social performance-avoidance goals (to avoid negative evaluations). The results indicated that social learning goals reduced the effects of interpersonal stress, thus protecting against depression, whereas social performance-avoidance goals exacerbated the effects of interpersonal stress, thereby developing depression. Social performance-approach goals neither reduced nor exacerbated the effects of interpersonal stress. The nature and functioning of these goals were discussed.
Why did he do it? attribution of obedience and the phenomenon of dispositional bias

Two studies are reported which demonstrate the influence of perceptual or ‘perspective’ variables in mediating attribution processes. In both studies subjects first observed a re-enactment of Milgram's (1963) experiment of obedience in which a ‘teacher’ obeys an experimenter's request to deliver dangerously high levels of shock. They were then asked to make judgements concerning the magnitude of situational forces acting upon the teacher and also to make inferences about his personality dispositions. Study I showed that passage of time can lead observers to assume more situational control when they were required to think and write about the witnessed re-enactment of the Milgram situation compared with observers who had no time to contemplate or who were prevented from doing so. Study II did not support the notion that focus of attribution is a simple function of what one pays attention to, or a function of the differing perspectives which actors and observers employ. Both of these results seriously challenge Jones and Nisbett's (1972) contention that the differences in attribution tendencies between actors and observers arise from the difference in perspective, Moreover, considerable evidence suggests that changes in situational and dispositional attributions may not follow a simple ‘zero-sum’ model, and that subjects seem to be unwilling to treat the two sources of control as if they were inversely correlated.
A trust based approach for protecting user data in social networks

Social networks are graphs that represent relations among people, institutions, and their activities. We introduce a novel social access control (SAC) strategy inspired by multi-level security (MLS) [1] for protecting data on social networks. In MLS, the data objects and subjects are classified in hierarchical levels based on security clearance and access controlled accordingly. Instead of clearance levels, we use trust levels to annotate objects and subjects. The trust level of an object is specified by the creator. The trust level of a subject is obtained from a trust modeling process [2, 3]. Reading a data object is controlled using the relative trust values of subjects and objects. We describe one aspect of the SAC model that supports the confidentiality of read-only data objects. We performed simulation studies using traces from the flickr.com social network to evaluate the performance of some key primitives used in the SAC design.
Torrenticolid water mites (Acari: Hydrachnidia: Torrenticolidae) from Malaysian Borneo.

New records of water mites of the family Torrenticolidae (Acari: Hydrachnidia) from streams in two mountain ranges in northern Borneo are presented. Aims of this study were to reconstruct phylogenetic relationships of the newly collected torrenticolids using molecular methods, and describe all new species. A fragment of the mtCOI gene was successfully PCR-amplified from 18 torrenticolid specimens and 14 new species are described: Torrenticola (Torrenticola) borneoensis n. sp. , T. (T.) kinabaluensis n. sp. , T. (T.) sabahensis n. sp. , T. (T.) neoindica n. sp. , T. (T.) schilthuizeni n. sp. , Neoatractides (Allotorrenticola) sundaensis n. sp. , N. (Heteratractides) uniscutatus n. sp. , Pseudotorrenticola borneoensis n. sp. , Monatractides (Monatractides) epiales n. sp. , M. (M.) morpheus n. sp. , M. (M.) phantasos n. sp. , M. (M.) phobetor n. sp. , M. (M.) hercules n. sp. and M. (M.) minuta n. sp. Additionally, the first records for Borneo are given for Torrenticola (Megapalpis) cf. pugionirostris (K. Viets, 1939), Monatractides (Monatractides) longiventris (K. Viets, 1939), M. (M.) cf. macroporus (K. Viets, 1935) and M. (M.) oxystomus (K. Viets, 1935). Monatractides tobaensis (K. Viets, 1935) is transferred to the subgenus Vietsclio Pešić & Smit, 2014. A key to the species of Monatractides is presented.
Adaptation and Validation of the Brazilian Version of the Hope Index

The objective of this study was to adapt and gather validity evidence for a Brazilian sample version of the Hope Index and to verify if cultural differences would produce different results than those found in the United States. In this study, we present a set of analyses that together comprise a comprehensive validity argument for the use of a test in a new language or culture. Participants were 844 undergraduate Brazilian students (mean age 21.3 years). A content validity study suggested that new items could be added to the scale. Factor analyses extracted two factors replicating the original instrument structure. The internal consistency was adequate with and without the added items. The results illustrate how different validation procedures can be used to support the use of an adapted version of a test, suggesting that in Brazil, researchers may choose the original adapted version (16 items) or the more emic version (21 items) depending on the objectives of their study. The indication that the Hope Index is valid in a Brazilian sample strengthens the idea that this construct may be universal. The results also stress the importance of conducting content validity studies as part of a cross-cultural adaptation of a test.
Kindergarten and primary school children’s implicit theories of learning to write

This paper studies the process of learning to write from an insider perspective, by adopting the framework of implicit theories of learning. We interviewed 160 children attending kindergarten or primary education in public schools in Argentina (20 children from each of the eight grades from kindergarten to seventh grade). Main questions explored children’s accounts of their learning activity, learning difficulties and awareness of learning in the field of writing. The textual transcriptions of their oral responses were analysed with the lexicometric method. Results indicate an early shift from a direct theory of learning to write to an interpretative one revealing increasing complexity, dynamisation and internalisation of learning agency.
Shear wave group velocity inversion in MR elastography of human skeletal muscle

In vivo quantification of the anisotropic shear elasticity of soft tissue is an appealing objective of elastography techniques because elastic anisotropy can potentially provide specific information about structural alterations in diseased tissue. Here a method is introduced and applied to MR elastography (MRE) of skeletal muscle. With this method one can elucidate anisotropy by means of two shear moduli (one parallel and one perpendicular to the muscle fiber direction). The technique is based on group velocity inversion applied to bulk shear waves, which is achieved by an automatic analysis of wave‐phase gradients on a spatiotemporal scale. The shear moduli are then accessed by analyzing the directional dependence of the shear wave speed using analytic expressions of group velocities in k‐space, which are numerically mapped to real space. The method is demonstrated by MRE experiments on the biceps muscle of five volunteers, resulting in 5.5 ± 0.9 kPa and 29.3 ± 6.2 kPa (P < 0.05) for the medians of the perpendicular and parallel shear moduli, respectively. The proposed technique combines fast steady‐state free precession (SSFP) MRE experiments and fully automated processing of anisotropic wave data, and is thus an interesting MRI modality for aiding clinical diagnosis. Magn Reson Med, 2006. © 2006 Wiley‐Liss, Inc.
The Drosophila kinesin-like protein KLP3A is a midbody component required for central spindle assembly and initiation of cytokinesis

We describe here a new member of the kinesin superfamily in Drosophila, KLP3A (Kinesin-Like-Protein-at-3A). The KLP3A protein localizes to the equator of the central spindle during late anaphase and telophase of male meiosis. Mutations in the KLP3A gene disrupt the interdigitation of microtubules in spermatocyte central spindles. Despite this defect, anaphase B spindle elongation is not obviously aberrant. However, cytokinesis frequently fails after both meiotic divisions in mutant testes. Together, these findings strongly suggest that the KLP3A presumptive motor protein is a critical component in the establishment or stabilization of the central spindle. Furthermore, these results imply that the central spindle is the source of signals that initiate the cleavage furrow in higher cells.