Miracle-dz/UniFAR-FTUs huggingface dataset:
Phylogenetic patterns of enamel microstructure in dinosaur teeth

The tooth enamel microstructure of all the dinosaur taxa that are adequately represented in the American Museum of Natural History collections were analyzed using scanning electron microscopy. This study aims to determine whether or not better sampling within a major nonmammalian amniote (hereafter referred to descriptively as “reptile”) clade will unearth phylogenetic patterns in enamel microstructure in addition to those dictated by tooth function. While interest in reptile enamel microstructure has increased in the past few years, intensive sampling focused on just one monophyletic reptile clade was not previously implemented. This study reveals that phylogenetic constraints play a larger role in shaping enamel microstructure in reptiles than previously thought. Within many monophyletic dinosaur clades the combination of enamel types and enamel features within a tooth—the schmelzmuster—is the same in all the taxa due to their common ancestry, and their schmelzmusters are diagnostic of their respective clades. While distantly related taxa with similar teeth and diets have similar schmelzmusters due to functional constraints, phylogenetic constraints keep those schmelzmusters distinct from one another. An interesting finding of this analysis is that the enamel complexity of a taxon does not necessarily coincide with the position of the taxon on a phylogenetic tree; more derived taxa do not necessarily have more derived enamel and more primitive taxa do not necessarily have more primitive enamel. J. Morphol. © 2005 Wiley‐Liss, Inc.
Task Motivation in Process: A Complex Systems Perspective

While many studies into task-based interaction have been conducted within a cognitive-linguistic perspective, few have been conducted with the aim of investigating learners’ task motivation. Framed within a complex systems approach, the principle objectives of this classroom-based study were to provide a complexity description of task motivation and to identify how various socio-affective and task condition-related elements interact together to influence learner motivation during different types of tasks. The elements include task enjoyment, effort, success expectancy, relevance, emotional state, perceived difficulty, perceived group work dynamic, and specific aspects related to the structure and content of tasks. Participants for the study consisted of 38 Korean intermediate learners of English in a conversation course as part of a TESOL certificate program. Data were collected through questionnaires during the course, at pre- and post-task, and as well, through post-task interviews. Supporting the notion that task motivation functions as a complex system, learners’ motivation decreased as a result of different combinations of socio-affective variables acting together rather than in isolation. Task conditions related to cognitive complexity and topic, furthermore, were shown to function as important control parameters in the shaping of the motivational patterns. De nombreuses études de l’interaction centrée sur les tâches ont déjà été réalisées dans une perspective cognitive-linguistique, mais rares sont celles qui ont eu pour objectif d’examiner la motivation de l’apprenant à l’égard de ses tâches. Réalisée en classe et dans la perspective des systèmes complexes, notre étude avait pour principaux objectifs de produire une description complexe de la motivation à l’égard de la tâche, d’une part, et d’identifier les façons dont différents facteurs socioaffectifs et autres éléments liés aux conditions d’exécution interagissent et influencent la motivation de l’apprenant pendant qu’il exécute ses tâches, d’autre part. Ces facteurs comprennent le plaisir, l’effort et l’espoir de réussite liés à la tâche, sa pertinence, l’état émotionnel du sujet, la difficulté perçue, la dynamique perçue du travail en groupe, ainsi que certains aspects propres à la structure et au contenu de chaque tâche. Le groupe de participants était formé de 38 apprenants coréens inscrits dans un cours intermédiaire de conversation anglaise du programme de certificat TESOL. Les données ont été obtenues au moyen de questionnaires remplis avant, pendant et après les tâches, et d’entrevues réalisées après les tâches. Confirmant l’idée selon laquelle la motivation fonctionne comme un système complexe, la motivation des apprenants a diminué en fonction des différentes combinaisons de variables socioaffectives prises ensemble plutôt que séparément. On a constaté, de plus, que les conditions liées à la complexité cognitive et au thème de la tâche avaient un rôle important comme « paramètres de contrôle » dans la formation des schèmes de motivation.
Towards feature-oriented requirements validation for automotive systems

In the modern automotive industry, feature models have been widely used as a domain-specific requirements model, which can capture commonality and variability of a software product line through a set of features. Product variants can thus be configured by selecting different sets of features from the feature model. For feature-oriented requirements validation, the variability of feature sets often makes the hidden flaws such as behavioral inconsistencies of features, hardly to avoid. In this paper, we present an approach to feature-oriented requirements validation for automotive systems w.r. t. both functional behaviors and non-functional properties. Our approach first starts with the behavioral specification of features and the associated requirements by following a restricted use case modeling approach, and then formalizes such specifications by using a formal yet literate language for analysis. We demonstrate the applicability of our approach through an industrial application of a Vehicle Locking-Unlocking system.
Power and area calibration of switch arbiter for high speed switch control and scheduling in network-on-chip

Network-on-chip (NoC) is being considered as a promising model to overcome the communication bottleneck of future multicore systems. It plays an important role in determining the area and power of the entire chip. As a basic component in on-chip router, arbiter has a large impact on the performance of router. A centralized arbiter called switch arbiter resolves conflicts between the input ports to get the access for the same output port. The design of such power and area efficient switch arbiter for Network on Chip is a major challenge in DSM technology. This paper proposes a novel switch arbiter that reduces power dissipation and consumes less area in comparison to conventional switch arbiter. The novel switch arbiter has been designed using twisted ring counter instead of ring counter to increase its performance. Simulation results have been carried out using Cadence Design Framework with 180nm technology.
The Glutathione System of Peroxide Detoxification Is Less Efficient in Neurons than in Astroglial Cells

Abstract: The ability of neurons to detoxify exogenously applied peroxides was analyzed using neuron‐rich primary cultures derived from embryonic rat brain. Incubation of neurons with H2O2 at an initial concentration of 100 μM (300 nmol/3 ml) led to a decrease in the concentration of the peroxide, which depended strongly on the seeding density of the neurons. When 3 × 106 viable cells were seeded per dish, the half‐time for the clearance by neurons of H2O2 from the incubation buffer was 15.1 min. Immediately after application of 100 μM H2O2 to neurons, glutathione was quickly oxidized. After incubation for 2.5 min, GSSG accounted for 48% of the total glutathione. Subsequent removal of H2O2 caused an almost complete regeneration of the original ratio of GSH to GSSG within 2.5 min. Compared with confluent astroglial cultures, neuron‐rich cultures cleared H2O2 more slowly from the incubation buffer. However, if the differences in protein content were taken into consideration, the ability of the cells to dispose of H2O2 was identical in the two culture types. The clearance rate by neurons for H2O2 was strongly reduced in the presence of the catalase inhibitor 3‐aminotriazol, a situation contrasting with that in astroglial cultures. This indicates that for the rapid clearance of H2O2 by neurons, both glutathione peroxidase and catalase are essential and that the glutathione system cannot functionally compensate for the loss of the catalase reaction. In addition, the protein‐normalized ability of neuronal cultures to detoxify exogenous cumene hydroperoxide, an alkyl hydroperoxide that is reduced exclusively via the glutathione system, was lower than that of astroglial cells by a factor of 3. These results demonstrate that the glutathione system of peroxide detoxification in neurons is less efficient than that of astroglial cells.
Reliability and validity of a brief instrument for assessing post‐traumatic stress disorder

This study examines the psychometric properties of two versions of the PTSD Sympton Scale (PSS). The scale contains 17 items that diagnose PTSD according to DSM-III-R criteria and assess the severity of PTSD symptoms. An interview and self-report version of the PSS were administered to a sample of 118 recent rape and non-sexual assault victims. The results indicate that both versions of the PSS have satisfactory internal consistency, high test-retest reliability, and good concurrent validity. The interview version yielded high interrater agreement when administred separately by two interviewers and excellent convergent validity with the SCID. When used to diagnose PTSD, the self-report version of the PSS was somewhat more conservative than the interview version.
Robust equalizer design for allpass transformed DFT filter banks with LTI property

Allpass transformed filter banks provide a nonuniform frequency resolution and can be used in mobile speech processing systems, e.g., cellular phones or digital hearing aids. The nominal design of such an allpass transformed analysis-synthesis filter bank (AS FB) with near perfect reconstruction (NPR) is achieved by numerical optimization of finite-impulse response (FIR) equalizers in each subchannel. The underlying nominal optimization problem is an equality constrained leasts-quares problem. In a robust design, we take into account coefficient uncertainty in a possible implementation of such a filter bank. We will describe this uncertainty by the choice of two simple set-based worst-case uncertainty models, namely a norm bound error model and a coefficient bound error model. When including these error models, both robust designs can be recast as second-order cone programs (SOCP) and solved efficiently by standard numerical optimization methods. Furthermore, we will provide design examples to show that both robust designs maintain a good overall performance with respect to NPR while offering less sensitivity to quantization errors.
Unusual Bound or Localized States

Abstract We summarize unusual bound or localized states in quantum mechanics. Our guide through these intriguing phenomena is the classical physics of the upside-down pendulum, taking advantage of the analogy between the corresponding Newton’s equation of motion and the time independent Schrödinger equation. We discuss the zero-energy ground state in a three-dimensional, spatially oscillating, potential. Moreover, we focus on the effect of the attractive quantum anti-centrifugal potential that only occurs in a two-dimensional situation.
Comparative Skeletal Muscle Proteomics Using Two-Dimensional Gel Electrophoresis

The pioneering work by Patrick H. O’Farrell established two-dimensional gel electrophoresis as one of the most important high-resolution protein separation techniques of modern biochemistry (Journal of Biological Chemistry 1975, 250, 4007–4021). The application of two-dimensional gel electrophoresis has played a key role in the systematic identification and detailed characterization of the protein constituents of skeletal muscles. Protein changes during myogenesis, muscle maturation, fibre type specification, physiological muscle adaptations and natural muscle aging were studied in depth by the original O’Farrell method or slightly modified gel electrophoretic techniques. Over the last 40 years, the combined usage of isoelectric focusing in the first dimension and sodium dodecyl sulfate polyacrylamide slab gel electrophoresis in the second dimension has been successfully employed in several hundred published studies on gel-based skeletal muscle biochemistry. This review focuses on normal and physiologically challenged skeletal muscle tissues and outlines key findings from mass spectrometry-based muscle proteomics, which was instrumental in the identification of several thousand individual protein isoforms following gel electrophoretic separation. These muscle-associated protein species belong to the diverse group of regulatory and contractile proteins of the acto-myosin apparatus that forms the sarcomere, cytoskeletal proteins, metabolic enzymes and transporters, signaling proteins, ion-handling proteins, molecular chaperones and extracellular matrix proteins.
The simple image processing scheme for document retrieval using date of issue as query

Storing paper-based documents converted into digital image format is one of effective solutions to preserve content in a document. Searching the Document Images stored in a repository by using time as queries is one of importance tasks of document retrieval. This paper presents a simple scheme of image processing to retrieve the documents, which contain the desired date of issue printed in Thai alphabets, from a repository. The procedure of this retrieval scheme consists of 4 stages: image acquisition, pre-processing, zone identification, and pattern recognition. The proposed machine vision scheme gave the excellent result over 365 dummy dates of issue of documents in the tested repository. It is a simple and uncomplex approach for the document image retrieval of Thai government letters, printed in Thai alphabets, using date of issue as query.
Are We There Yet? Grounding Temporal Concepts in Shared Journeys

An understanding of time and temporal concepts is critical for interacting with the world and with other agents in the world. What does a robot need to know to refer to the temporal aspects of events-could a robot gain a grounded understanding of “a long journey,” or “soon? ” Cognitive maps constructed by individual agents from their own journey experiences have been used for grounding spatial concepts in robot languages. In this paper, we test whether a similar methodology can be applied to learning temporal concepts and an associated lexicon to answer the question “how long” did it take to complete a journey. Using evolutionary language games for specific and generic journeys, successful communication was established for concepts based on representations of time, distance, and amount of change. The studies demonstrate that a lexicon for journey duration can be grounded using a variety of concepts. Spatial and temporal terms are not identical, but the studies show that both can be learned using similar language evolution methods, and that time, distance, and change can serve as proxies for each other under noisy conditions. Effective concepts and names for duration provide a first step towards a grounded lexicon for temporal interval logic.
Cellular localization of an Epstein‐Barr virus (EBV)‐associated complement‐fixing antigen in producer and non‐producer lymphoblastoid cell lines

Anti‐complement immunofluorescence (ACIF) was used to study the complementfixing antigens of human lymphoblastoid cell lines. These cell lines carry the Epstein‐Barr virus (EBV) genome although only producer cultures synthetize EBV‐specific antigens (virus capsid antigen, VCA and early antigen, EA) detectable by direct and indirect immunofluorescence, usually in less than 5% of the cells. The ACIF test revealed an antigen localized in the nucleus of the lymphoblastoid cells. In contrast to EA and VCA, this antigen was present in over 90% of the cells of both producer and non‐producer cultures. The antigen was shown to be specific for EBV by comparing the reactions of 52 sera in the ACIF test. Sera giving the nuclear reaction contained antibodies to VCA, EA or antigens detectable by complement fixation tests on cell extracts, but sera without EBV antibodies failed to give the reaction. Weak, equivocal or discordant reactions occurred with six sera with low titres in VCA, EA or complement fixation tests. Cell lines derived by transformation of human and primate lymphocytes by EBV gave the nuclear reaction. Control cells with no known association with EBV were non‐reactive. These included foetal lymphocytes transformed by phytohaemagglutinin, cell lines derived from breast cancer, glioma, normal glia, pleuritis maligna and myeloma, and two marmoset lymphoid lines carrying Herpesvirus saimiri (HVS). In preliminary experiments, the ACIF test was used as a tool to trace the EBV genome at the cellular level. Cells from two Burkitt lymphoma biopsies, one tested after biopsy and one after passaging in nude mice, contained an EBV‐specific antigen. Three clones of cells derived from hybrids of mouse somatic cells and a human lymphoblastoid cell line also contained such an antigen, but the number of reactive cells varied from clone to clone. A fourth clone was non‐reactive.
Thiol changes during epididymal maturation: a link to flagellar angulation in mouse spermatozoa?

Caput epididymal wild‐type spermatozoa and cauda epididymal spermatozoa from mice null for the adenylyl cyclase Adcy10 gene are immotile unless stimulated by a membrane‐permeant cyclic AMP analogue. Both types of spermatozoa exhibit flagellar angulation where the head folds back under these conditions. As sperm proteins undergo oxidation of sulfhydryl groups and the flagellum becomes more stable to external forces during epididymal transit, we hypothesized that ADCY10 is involved in a mechanism regulating flagellar stabilization. Although no differences were observed in global sulfhydryl status between caput and cauda epididymal spermatozoa from wild‐type or Adcy10‐null mice, two‐dimensional fluorescence difference gel electrophoresis was performed to identify specific mouse sperm proteins containing sulfhydryl groups that became oxidized during epididymal maturation. A‐kinase anchor protein 4, fatty acid‐binding protein 9 (FABP9), glutathione S‐transferase mu 5 and voltage‐dependent anion channel 2 exhibited changes in thiol status between caput and cauda epididymal spermatozoa. The level and thiol status of each of these proteins were quantified in wild‐type and Adcy10‐null cauda epididymal spermatozoa. No differences in the abundance of any protein were observed; however, FABP9 in Adcy10‐null cauda epididymal spermatozoa contained fewer disulfide bonds than wild‐type sperm cells. In caput epididymal spermatozoa, FABP9 was detected in the cytoplasmic droplet, principal piece, midpiece, and non‐acrosomal area of the head. However, in cauda epididymal spermatozoa, this protein localized to the perforatorium, post‐acrosomal region and principal piece. Together, these results suggest that thiol changes during epididymal maturation have a role in the stabilization of the sperm flagellum.
Structural basis for assembly of the CBF3 kinetochore complex

Eukaryotic chromosomes contain a specialised region known as the centromere, which forms the platform for kinetochore assembly and microtubule attachment. The centromere is distinguished by the presence of nucleosomes containing the histone H3 variant, CENP‐A. In budding yeast, centromere establishment begins with the recognition of a specific DNA sequence by the CBF3 complex. This in turn facilitates CENP‐ACse4 nucleosome deposition and kinetochore assembly. Here, we describe a 3.6 Å single‐particle cryo‐EM reconstruction of the core CBF3 complex, incorporating the sequence‐specific DNA‐binding protein Cep3 together with regulatory subunits Ctf13 and Skp1. This provides the first structural data on Ctf13, defining it as an F‐box protein of the leucine‐rich‐repeat family, and demonstrates how a novel F‐box‐mediated interaction between Ctf13 and Skp1 is responsible for initial assembly of the CBF3 complex.
Dietary Intake of Vegetables and Fruits and the Modification Effects of GSTM1 and NAT2 Genotypes on Bladder Cancer Risk

We analyzed the association between intakes of vegetables and fruits as defined by the U.S. Department of Agriculture pyramid food groups and bladder cancer risk using data collected in a large case-control study. The study included 884 histologically confirmed bladder cancer cases and 878 healthy controls matched to cases by age (±5 years), gender, and ethnicity. Significant inverse associations were observed for intakes of total vegetables, cruciferous vegetables, orange vegetables, dark green vegetables, and bladder cancer risk. Compared with those in the lowest quartile of total vegetable intake, the odds ratios for the 2nd, 3rd, and 4th quartiles of total vegetable intake were 0.84 [95% confidence interval (95% CI), 0.64-1.10], 0.71 (95% CI, 0.54-0.95), and 0.67 (95% CI, 0.50-0.90), respectively (P for trend = 0.004). Compared with those in the lowest quartile, those in the highest quartile of cruciferous vegetable intake had an odds ratio of 0.69 (95% CI, 0.52-0.92; P for trend = 0.001) and those in the highest quartile of orange vegetable intake had an odds ratio of 0.68 (95% CI, 0.52-0.91; P for trend = 0.006). Furthermore, the protective effect of cruciferous vegetables was more evident in subjects carrying GSTM1-null (odds ratio, 0.43; 95% CI, 0.25-0.73 for the 4th quartile of intake) and NAT2-slow genotypes (odds ratio, 0.56; 95% CI, 0.33-0.97 for the 4th quartile of intake). No association was observed for intakes of total fruits or citrus fruits. Our data strongly support that high vegetable consumption, especially cruciferous vegetable intake, may protect against bladder cancer and that genetic variants of GSTM1 and NAT2 may modify the association. (Cancer Epidemiol Biomarkers Prev 2009;18(7):2090–7)
Impaired Opsonization with C3b and Phagocytosis of Streptococcus pneumoniae in Sera from Subjects with Defects in the Classical Complement Pathway

ABSTRACT Results from studies using mice deficient in specific complement factors and clinical data on patients with an inherited deficiency of the classical complement pathway component C2 suggest that the classical pathway is vital for immunity to Streptococcus pneumoniae. However, the consequences of defects in classical pathway activity for opsonization with C3b and the phagocytosis of different S. pneumoniae serotypes in human serum are not known, and there has not been a systematic analysis of the abilities of sera from subjects with a C2 deficiency to opsonize S. pneumoniae. Hence, to investigate the role of the classical pathway in immunity to S. pneumoniae in more detail, flow cytometry assays of opsonization with C3b and the phagocytosis of three capsular serotypes of S. pneumoniae were performed using human sera depleted of the complement factor C1q or B or sera obtained from C2-deficient subjects. The results demonstrate that, in human serum, the classical pathway is vital for C3b-iC3b deposition onto cells of all three serotypes of S. pneumoniae and seems to be more important than the alternative pathway for phagocytosis. Compared to the results for sera from normal subjects, C3b-iC3b deposition and total anti-S. pneumoniae antibody activity levels in sera obtained from C2−/− subjects were reduced and the efficiency of phagocytosis of all three S. pneumoniae strains was impaired. Anticapsular antibody levels did not correlate with phagocytosis or C3b-iC3b deposition. These data confirm that the classical pathway is vital for complement-mediated phagocytosis of S. pneumoniae and demonstrate why subjects with a C2 deficiency have a marked increase in susceptibility to S. pneumoniae infections.