Miracle-dz/UniFAR-FTUs huggingface dataset:
NAKED PROTEIN CONFORMATIONS : CYTOCHROME C IN THE GAS PHASE

Ion mobility measurementsl have been used to obtain direct information about the conformers present for naked cytochrome c ions in the gas phase. The relative abundance of compact native-like conformations is negligible. However, a number of well-defined, partially folded conformers that are considerably more diffuse than the native structure are observed. These may be intermediates in the folding process. The results suggest that the gas phase is an environment that will allow access to complementary information about protein conformations and the dynamics of protein folding. ' The development of gentle ionization techniques' has facilitated studies of biological molecules using mass spectrometry. Accurate measurements of molecular weigh& as well as sequence information*. h are becoming commonplace, and recently there have been several attempts to use mass spectrometry to deduce information about the three-dimensional structures of biological molecules. For example, the charge distribution generated by electrospray ionization' (ESI) has been shown to depend on the conformation of the protein in s o l u t i ~ n . ~ . ~ Mass spectrometry has been used to monitor 'W'H isotope exchange for proteins in solution"' as well as in the gas phase. ". " Finally, ion beam scattering experiment^'^. ^^ have shown that protein ions in different charge states have different collision cross sections. The ion mobility measurementsl reported here resolve protein conformers on the basis of their different collision cross sections and provide precise cross sections for the conformers
Sensory curation: theorizing media use for sensory regulation and implications for family media conflict

ABSTRACT Media sensory curation theory, introduced here, complements theories of informational, emotional, and relational media gratifications. Sensory curation theory conceptualizes media devices as tools people use to help maintain sensory regulation by simultaneously capturing and curbing sensory input within built and natural environments. This article explicates the theory and introduces the Child and Adult Media Sensory Curation Inventories (MediaSCIs), separate measures of child and adult media sensory behaviors and preferences. A survey of 789 parents and adult caregivers of children ages 3 to 14 revealed moderate to strong correlations between general sensory processing and media sensory curation, validating the MediaSCIs. Controlling usage time, child media sensory curation strongly predicted problematic child media use and moderately predicted adult–child media conflict, which was four times as frequent among adult–child pairs with high MediaSCI scores than with low MediaSCI scores.
Similarities in spaces of features and concepts: Towards semantic evaluations

The article discusses abstract spaces of concepts and features. Concepts correspond to real-world objects. Concepts are described by their features. The study is devoted to relations in the space of concepts and in the space of features. Of greatest interest is similarity of structures in the concepts and features spaces. There is a direct link between features and concepts. Therefore, similarity may be analyzed through structures of both concepts and features. Authors propose generalized similarity relation, applicable to the developed framework. In addition, similarity of nested sets of the space of features and concepts is discussed. Authors introduce an algorithm, which calculates similarity of two structures of nested structures. Developed semantics leads to the set-theoretic model, which allows to flexibly describe abstract information.
BhbZIP60 from Resurrection Plant Boea hygrometrica Is an mRNA Splicing-Activated Endoplasmic Reticulum Stress Regulator Involved in Drought Tolerance

Adverse environmental conditions cause endoplasmic reticulum (ER) stress in plants. To mitigate ER stress damage, ER associated transcription factors and inositol-requiring enzyme-1 (IRE1)-mediated bZIP60 mRNA splicing are activated in plants. A drought-induced gene, encoding the ortholog of AtbZIP60, was identified in the resurrection plant Boea hygrometrica, termed BhbZIP60. In response to ER stress and dehydration, BhbZIP60 mRNA can be spliced to create a frame shift in the C terminus by the excision of 23b segment in a manner of its ortholog in other plants, thus translocating to the nucleus instead of the cytoplasm. The splicing-activated BhbZIP60 (BhbZIP60S) could function in the same way as its Arabidopsis ortholog by restoring the molecular phenotype of the mutant atbzip60. When overexpressed in Arabidopsis, BhbZIP60S provided transgenic plants with enhanced tolerance to drought, tunicamycin and mannitol stresses with upregulation of the expressions of ER quality control (QC) genes (BiP2, BiP3, CNX1, and sPDI) and abscisic acid (ABA) responsive genes (RD29A, RAB18, and RD17). Furthermore, in the yeast one-hybrid system, BhbZIP60S was capable of interacting with ER stress responsive elements (ERSE and ERSE-II) that exist in the promoters of known ER-QC genes, but not binding to ABA responsive cis-elements (ABREs). Our results demonstrated that drought-induced BhbZIP60 may have a function in drought tolerance via the splicing-activated BhbZIP60S to mediate ER-QC by direct binding to the promoters of ER-QC genes. This study evidently demonstrates the involvement of ER-QC in the drought tolerance of Arabidopsis and the desiccation tolerance of the resurrection plant B. hygrometrica.
Verbs, Semantic Classes and Semantic Roles in the Adesse Project

This paper contains an overall description of ADESSE (http://webs.uvigo.es/adesse/), a project whose main goal is to manually provide definitions and information about semantic roles and semantic class membership for all the verbs in a syntactic database of nearly 160,000 clauses retrieved from a Span-ish corpus of 1,5 million words.
Organizational Climate and Perceived Manager Effectiveness: Influencing Perceived Usefulness of Knowledge Sharing Mechanisms

In this study, we examine how perceptions of organizational climate and manager effectiveness influence individuals’ perceived usefulness of three types of knowledge sharing mechanisms (KSMs): (1) informal personalization KSMs, (2) formal codification KSMs, and (3) formal personalization KSMs. We collected survey data from 1036 employees from five different subsidiaries of an organization to test our hypotheses. We found that having a warm and cooperative climate has a positive influence on individuals’ perceptions of all KSMs. A competitive climate, on the other hand, increases individuals’ preference for using formal codification and personalization mechanisms relative to informal personalization mechanisms. Finally, individuals who perceive their managers to be more effective tend to be more supportive of top-down initiatives provided by senior management; thus, these individuals have a significantly more positive opinion of formal mechanisms compared to informal mechanisms. This study provides an extended and more nuanced perspective of how knowledge sharing can be enabled in different social contexts. The results will help managers to customize a portfolio of knowledge management mechanisms based on the climate of their organizational unit.
Shape-Preserving Parametrization of Genus 0 Surfaces

The parametrization of 3-d meshes can be used in many fields of computer graphics. Mesh-texturing, mesh-retriangulation or 3-d morphing are only few applications for which a mesh parametrization is needed. Because, many polygonal surfaces are manifolds of genus 0 (topological equivalent to a sphere), we can apply a mapping, in which 2-d polar coordinates of a sphere can be directly transformed onto the 3-d coordinates of a polygonal object. In this paper we present a hierarchical mapping algorithm, that preserves the local surface properties. Our method consists of three main-steps. First, the mesh is simplified to a tetrahedron. Next, the tetrahedron will be transformed to a spherical surface in which the previous simplification process will be reversed on the surface of the sphere. Hereby, in every refinement step the new vertices are inserted and the resulting parametrization mesh is optimized to be barycentric. Finally, the resulting barycentric mesh is used as the basis for a shape-preserving optimization process. The efficiency of these method will be shown by using our parametrization algorithm on different 3-d objects.
Seasonal, sexual, and individual variation in endurance and activity metabolism in lizards

GARLAND, THEODORE, JR., AND PAUL L. ELSE. SeasonaL, sexual, and individual variation in endurance and activity metabolism in lizards. Am. J. Physiol. 252 (Regulatory Integrative Comp. Physiol. 2‘1): R439-R449, 1987. -Amphibolurus nuchalis were collected in central Australia during mid(January) and late summer (March). Endurance time at 1 km/h on a motorized treadmill is greater in larger lizards, scaling as MO? Maximal O2 consumption (Vozmax) scales as MO*“; standard metabolic rate (SMR) scales as MO? Factorial aerobic scope thus increases ontogenetically (9.4 at 1 g vs. 15 at 50 g). All organ masses scale allometrically; larger lizards have relatively smaller livers, but larger hearts and thigh muscles. Hematocrit and hemoglobin increase during early ontogeny, but are mass independent in adults. Maximal in vitro catalytic rates were determined for citrate synthase (CS) and pyruvate kinase (PK) in liver, heart, and thigh muscle and for lactate dehydrogenase (LDH) (lactate oxidation) in heart. All enzyme activities (expressed per g tissue) scale positively, except CS in heart. Females exhibit lower SMR and heart CS activity. March animals exhibit elevated endurance, vozrnax, heart LDH, and thigh CS and PK activities. Individual variation in endurance correlates with individual differences in heart LDH and thigh CS and/or PK activities. Individual differences in vozrnax are partly related to variation in hematocrit.
Integration of Light and Temperature in the Regulation of Circadian Gene Expression in Drosophila

Circadian clocks are aligned to the environment via synchronizing signals, or Zeitgebers, such as daily light and temperature cycles, food availability, and social behavior. In this study, we found that genome-wide expression profiles from temperature-entrained flies show a dramatic difference in the presence or absence of a thermocycle. Whereas transcript levels appear to be modified broadly by changes in temperature, there is a specific set of temperature-entrained circadian mRNA profiles that continue to oscillate in constant conditions. There are marked differences in the biological functions represented by temperature-driven or circadian regulation. The set of temperature-entrained circadian transcripts overlaps significantly with a previously defined set of transcripts oscillating in response to a photocycle. In follow-up studies, all thermocycle-entrained circadian transcript rhythms also responded to light/dark entrainment, whereas some photocycle-entrained rhythms did not respond to temperature entrainment. Transcripts encoding the clock components Period, Timeless, Clock, Vrille, PAR-domain protein 1, and Cryptochrome were all confirmed to be rhythmic after entrainment to a daily thermocycle, although the presence of a thermocycle resulted in an unexpected phase difference between period and timeless expression rhythms at the transcript but not the protein level. Generally, transcripts that exhibit circadian rhythms both in response to thermocycles and photocycles maintained the same mutual phase relationships after entrainment by temperature or light. Comparison of the collective temperature- and light-entrained circadian phases of these transcripts indicates that natural environmental light and temperature cycles cooperatively entrain the circadian clock. This interpretation is further supported by comparative analysis of the circadian phases observed for temperature-entrained and light-entrained circadian locomotor behavior. Taken together, these findings suggest that information from both light and temperature is integrated by the transcriptional clock mechanism in the adult fly head.
String Topology: Background and Present State

The data of a "2D field theory with a closed string compactification" is an equivariant chain level action of a cell decomposition of the union of all moduli spaces of punctured Riemann surfaces with each component compactified as a pseudomanifold with boundary. The axioms on the data are contained in the following assumptions. It is assumed the punctures are labeled and divided into nonempty sets of inputs and outputs. The inputs are marked by a tangent direction and the outputs are weighted by nonnegative real numbers adding to unity. It is assumed the gluing of inputs to outputs lands on the pseudomanifold boundary of the cell decomposition and the entire pseudomanifold boundary is decomposed into pieces by all such factorings. It is further assumed that the action is equivariant with respect to the toroidal action of rotating the markings. A main result of compactified string topology is the Theorem (closed strings): Each oriented smooth manifold has a 2D field theory with a closed string compactification on the equivariant chains of its free loop space mod constant loops. The sum over all surface types of the top pseudomanifold chain yields a chain X satisfying the master equation dX + X*X = 0 where * is the sum over all gluings. This structure is well defined up to homotopy. The genus zero parts yields an infinity Lie bialgebra on the equivariant chains of the free loop space mod constant loops. The higher genus terms provide further elements of algebraic structure called a "quantum Lie bialgebra" partially resolving the involutive identity. There is also a compactified discussion and a Theorem 2 for open strings as the first step to a more complete theory. We note a second step for knots.
Deamidation of Cdc42 and Rac by Escherichia coliCytotoxic Necrotizing Factor 1: Activation of c-Jun N-Terminal Kinase in HeLa Cells

ABSTRACT Recently, Escherichia coli cytotoxic necrotizing factor 1 (CNF1) was shown to activate the low-molecular-mass GTPase RhoA by deamidation of Gln63, thereby inhibiting intrinsic and GTPase-activating protein (GAP)-stimulated GTPase activities (G. Schmidt, P. Sehr, M. Wilm, J. Selzer, M. Mann, and K. Aktories, Nature 387:725–729, 1997; G. Flatau, E. Lemichez, M. Gauthier, P. Chardin, S. Paris, C. Fiorentini, and P. Boquet, Nature 387:729–733, 1997). Here we report that in addition to RhoA, Cdc42 and Rac also are targets for CNF1 in vitro and in intact cells. Treatment of HeLa cells with CNF1 induced a transient formation of microspikes and formation of membrane ruffles. CNF1 caused a transient 10- to 50-fold increase in the activity of the c-Jun N-terminal kinase. Tryptic peptides of Cdc42 obtained from CNF1-treated cells by immunoprecipitation exhibited an increase in mass of 1 Da compared to control peptides, indicating the deamidation of glutamine 61 by the toxin. The same increase in mass was observed with the respective peptides obtained from CNF1-modified recombinant Cdc42 and Rac1. Modification of recombinant Cdc42 and Rac1 by CNF1 inhibited intrinsic and GAP-stimulated GTPase activities and retarded binding of 2′(3′)- O-(N -methylanthraniloyl)GDP. The data suggest that recombinant as well as cellular Cdc42 and Rac are substrates for CNF1.
Multimodal interactive machine translation

Interactive machine translation (IMT) [1] is an alternative approach to machine translation, integrating human expertise into the automatic translation process. In this framework, a human iteratively interacts with a system until the output desired by the human is completely generated. Traditionally, interaction has been performed using a keyboard and a mouse. However, the use of touchscreens has been popularised recently. Many touchscreen devices already exist in the market, namely mobile phones, laptops and tablet computers like the iPad. In this work, we propose a new interaction modality to take advantage of such devices, for which online handwritten text seems a very natural way of input. Multimodality is formulated as an extension to the traditional IMT protocol where the user can amend errors by writing text with an electronic pen or a stylus on a touchscreen. Different approaches to modality fusion have been studied. In addition, these approaches have been assessed on the Xerox task. Finally, a thorough study of the errors committed by the online handwritten system will show future work directions.
Inference for dependence competing risks from bivariate exponential model under generalized progressive hybrid censoring with partially observed failure causes

Inference are considered for the dependence competing risks model by using the Marshal-Olkin bivariate exponential distribution. Under generalized progressively hybrid censoring with partially observed failure causes, the maximum likelihood estimators are established, and the approximate confidence intervals are also constructed via the observed Fisher information matrix. Moreover, Bayes estimates and highest probability density credible intervals are presented and the importance sampling technique is used to compute corresponding results. Finally, the numerical analysis is proposed for illustration.
Catering for teachers’ individual teaching differences in China: the case of forming reciprocal coaching circles supported by university-based teacher educators

ABSTRACT Opportunities for high quality teachers’ continuing professional development (CPD) are considered scarce in Asian countries such as China, Vietnam, and Cambodia. In addition, there seem to be few sustainable outcomes of teachers’ CPD. The present study aimed to address English teachers’ dissatisfaction with their own CPD in China. With some university-based teacher educators’ support, reciprocal coaching circles were formed by English teachers, where they identified common teaching problems and worked out practical solutions appropriate for their local contexts collaboratively. The findings suggest multiple benefits, including higher confidence in teaching, an expanded repertoire of teaching strategies, and teachers’ professional communities. Both in-service teachers and university-based teacher educators contribute to reciprocal coaching circles in complimentary ways, with local teachers being the main agent for change and university-based teacher educators being facilitators.
Multiple shift maximum element sequential matrix diagonalisation for parahermitian matrices

A polynomial eigenvalue decomposition of paraher-mitian matrices can be calculated approximately using iterative approaches such as the sequential matrix diagonalisation (SMD) algorithm. In this paper, we present an improved SMD algorithm which, compared to existing SMD approaches, eliminates more off-diagonal energy per step. This leads to faster convergence while incurring only a marginal increase in complexity. We motivate the approach, prove its convergence, and demonstrate some results that underline the algorithm's performance.
MicroRNAs in Human Malignant Gliomas

MicroRNA (miRNA) is a new class of small noncoding RNA molecules that regulate a wide spectrum of gene expression in a posttranscriptional manner. MiRNAs play crucial roles in tumorigenesis, angiogenesis, invasion, and apoptosis for various types of tumor. Recent studies have identified dysregulation of specific miRNAs in malignant gliomas. Global expression profiling of miRNAs has revealed several miRNAs clinically implicated in human glioblastomas. Some miRNAs are clearly associated with clinical outcome and chemo- and radio-therapy resistance in these tumors. Furthermore, miRNAs also regulate specific signaling pathways, including the critical core pathways in glioblastoma. As a result, miRNAs have the potential to affect the responses to molecular-targeted therapies. More recent studies have revealed that miRNAs might be associated with cancer stem cell properties, affecting tumor maintenance and progression. Recent investigation have revealed that miRNAs are not only biological markers with diagnostic implications, but also one of the most promising treatment targets in human glioblastoma. Herein, we summarized the novel insights of miRNAs into human malignant gliomas.
Sonar phishing:pinpointing highly vulnerable victims for social engineering attacks

Targeted social engineering attacks use personal information about an individual to create compelling behavioural hooks which draw the target to interact with a malicious payload or give out valuable information, more successfully than unsophisticated generic attacks [1]. Such attacks can hijack trust by pretending to be friends or trusted authorities [2], or can leverage a user’s personal interests to entice them into responding [3]. Currently, technically adept social engineers are able to craft these personalised attacks by mining the information that the targets themselves make readily available on social networking sites (SNSs), achieving more effective phishing attacks (up to 52% increase [1]). Extracting such information from SNSs and crafting personalised attacks has historically been a manual and skilled process. Current tools go some way to allowing social engineers to perform a large-scale personalised attack across all identified employees of an organisation. Fortunately, carrying out an attack so broadly may undermine its effectiveness and ability to remain undetected. The automated generation of sophisticated social engineering attacks therefore faces a number of restrictions:
A Novel Approach for Automatic Web Page Classification using Feature Intervals

A new web page classification algorithm using weighted voting of feature intervals known as WVFI is proposed in this paper. This classifier first discretizes the web page features using a supervised disctretization algorithm which identifies the number of intervals each feature has to be discretized automatically. Each feature is then made to predict the class of the corresponding feature in the test web page using the class distribution of its intervals. The final class of the test web page is predicted by aggregating the weighted vote of each feature. Experiments done on a benchmarking data set called WebKB has shown good classification accuracy when compared with many of the existing classifiers.
Molecular Mechanism Underlying Aβ Immunotherapy: Implications for the Toxic Action of Aβ Oligomers

Aβ immunotherapy brought us not only hope for but also led to greater attention to the mechanism underlying the clearance of amyloid β (Aβ), which provided fascinating insights into disease-relevant molecules such as toxic Aβ oligomers (AβOs). Accumulated lines of evidence indicate that AβOs play a causative role in the pathogenesis of Alzheimer’s disease (AD), leading to a synaptic failure, which is considered a major cellular mechanism underlying the cognitive deficits in patients with mild cognitive impairment and AD. In this mini review, we focus on recent knowledge of the possible mechanisms underlying the action of the anti-Aβ antibody to clarify the toxic action of AβOs.