Miracle-dz/UniFAR-FTUs huggingface dataset:
Altered dynamics in Lck SH3 upon binding to the LBD1 domain of Herpesvirus saimiri Tip

The Tip protein from Herpesvirus saimiri interacts with the SH3 domain from the Src‐family kinase Lck via a proline‐containing sequence termed LBD1. Src‐family kinase SH3 domains related to Lck have been shown to be dynamic in solution and partially unfold under physiological conditions. The rate of such partial unfolding is reduced by viral protein binding. To determine if the Lck SH3 domain displayed similar behavior, the domain was investigated with hydrogen exchange and mass spectrometry. Lck SH3 was found to be highly dynamic in solution. While other SH3 domains require as much as 10,000 sec to become totally deuterated, Lck SH3 became almost completely labeled within 200 sec. A partial unfolding event involving 8–10 residues was observed with a half‐life of ∼10 sec. Tip LBD1 binding did not cause gross structural changes in Lck SH3 but globally stabilized the domain and reduced the rate of partial unfolding by a factor of five. The region of partial unfolding in Lck SH3 was found to be similar to that identified for other SH3 domains that partially unfold. Although the sequence conservation between Lck SH3 and other closely related SH3 domains is high, the dynamics do not appear to be conserved.
Conformational equilibrium in the alanine dipeptide in the gas phase and aqueous solution : a comparison of theoretical results

The acetyl and methyl amide blocked alanine amino acid, commonly referred to as the alanine dipeptide, has often been used as a model in theoretical studies of backbone conformational equilibria in proteins. In order to evaluate the solvent effects on the conformational equilibrium of the dipeptide, we have used molecular dynamics simulations with holonomic backbone dihedral angle constraints and thermodynamic perturbation theory to calculate free energy profiles along paths connecting four important conformations of the dipeptide in the gas phase and in water. We found that the extended β conformation is the most stable both in the gas phase and in water
Identification of Novel Bovine Cumulus Cell Molecular Markers Predictive of Oocyte Competence: Functional and Diagnostic Implications1

Abstract The present study was undertaken to discover molecular markers in bovine cumulus cells predictive of oocyte competence and to elucidate their functional significance. Differences in RNA transcript abundance in cumulus cells harvested from oocytes of adult versus prepubertal animals (a model of poor oocyte quality) were identified by microarray analysis. Four genes of interest encoding for the lysosomal cysteine proteinases cathepsins B, S, K, and Z and displaying greater transcript abundance in cumulus cells surrounding oocytes harvested from prepubertal animals were chosen for further investigation. Greater mRNA abundance for such genes in cumulus cells of prepubertal oocytes was confirmed by real-time RT-PCR. Elevated transcript abundance for cathepsins B, S, and Z also was observed in cumulus cells surrounding adult metaphase II oocytes that developed to the blastocyst stage at a low percentage following parthenogenetic activation versus those that developed at a high percentage. Functional significance of cumulus cell cathepsin expression to oocyte competence was confirmed by treatment of cumulus-oocyte complexes during in vitro oocyte maturation with a cell-permeable cysteine proteinase (cathepsin) inhibitor. Inhibitor treatment decreased apoptotic nuclei in the cumulus layer and enhanced development of parthenogenetically activated and in vitro-fertilized adult oocytes to the blastocyst stage. Stimulatory effects of inhibitor treatment during meiotic maturation on subsequent embryonic development were not observed when oocytes were matured in the absence of cumulus cells. The present results support a functional role for cumulus cell cathepsins in compromised oocyte competence and suggest that cumulus cell cathepsin mRNA abundance may be predictive of oocyte quality.
MEDICAL MANAGEMENT OF RADIOLOGICAL CASUALTIES

Victims of radiological terrorism events require prompt diagnosis and treatment of medical and surgical conditions as well as conditions related to radiation exposure. Hospital emergency personnel should triage victims using traditional medical and trauma criteria. Radiation dose can be estimated early post-event using rapid-sort, automated biodosimetry and clinical parameters such as the clinical history, the time to emesis (TE), and lymphocyte depletion kinetics. For TE < 2 h, the effective whole-body dose is at least 3 Gy. If TE < 1 h, the whole-body dose most probably exceeds 4 Gy. Lymphocyte depletion follows dose-dependent, first order kinetics after high-level gamma and criticality incidents. Patient radiation dose can be estimated very effectively from the medical history, serial lymphocyte counts, and TE, and subsequently confirmed with chromosome-aberration bioassay, the current gold standard. These data are effectively analyzed using the Armed Forces Radiobiology Research Institute Biodosimetry Assessment Tool. The medical management of patients with acute, moderate to severe radiation exposure (effective whole-body dose >3 Gy) should emphasize the rapid administration of colony stimulating factors. All of these compounds decrease the duration of radiation-induced neutropenia and stimulate neutrophil recovery, albeit with some variability, in patients who have received myelotoxic chemotherapy, and all have demonstrated benefit in irradiated animals. For those patients developing febrile radiation-induced neutropenia, adherence to the current Infectious Diseases Society of America guidelines for high-risk neutropenia is recommended.
Untangle: A New Ontology for Card Catalog Systems

The ontology used by most card catalog and bibliographic systems is based on a now outdated assumption that users of the systems would be looking for books on shelves, and therefore only books were first-class objects, with people, organizations, etc. as simple attributes. This limited the ability of a user to browse. A new ontology for card catalog systems is proposed that suggests that persons, organizations, conferences, etc., should be first-class objects with attributes and relations of their own, creating a rich space of background information that helps users find what they are looking for. This new ontology has been implemented in a knowledge-based system called Untangle, which demonstrates two key advantages of this rich information space: it enables automatic augmentation of the data through reasoning, and it enables a new paradigm for search that combines querying and browsing.
1 SRA gene knockout protects against diet-induced obesity and improves glucose tolerance The running title : SRA deficiency protects against diet-induced obesity

We have recently shown that the non-coding RNA, steroid receptor RNA activator (SRA), functions as a transcriptional coactivator of PPARγ and promotes adipocyte differentiation in vitro. To assess SRA function in vivo, we have generated a whole mouse Sra1 gene knockout (SRA-/-). Here, we show that the Sra1 gene is an important regulator of adipose tissue mass and function. SRA is expressed at a higher level in adipose tissue than other organs in wild type mice. SRA-/mice are resistant to high fat diet-induced obesity, with decreased fat mass and increased lean content. This lean phenotype of SRA-/mice is associated with decreased expression of a subset of adipocyte marker genes and reduced plasma TNFα levels. The SRA-/mice are more insulin sensitive, as evidenced by reduced fasting insulin, and lower blood glucoses in response to IP glucose and insulin. In addition, the livers of SRA-/mice have fewer lipid droplets after high fat diet feeding, and the expression of lipogenesis-associated genes is decreased. To our knowledge, these data are the first to indicate a functional role for SRA in adipose tissue biology and glucose homeostasis in vivo. Introduction Obesity results from an imbalance between energy intake and expenditure, in http://www.jbc. org/cgi/doi/10.1074/jbc.M114.564658 The latest version is at JBC Papers in Press. Published on March 27, 2014 as Manuscript M114.564658 Copyright 2014 by The American Society for Biochemistry and Molecular Biology, Inc. by gest on Sptem er 6, 2017 hp://w w w . jb.org/ D ow nladed from
On Approximate Algorithms for Distance-Based Queries using R-trees

In modern database applications the similarity or dissimilarity of complex objects is examined by performing distance-based queries (DBQs) on data of high dimensionality. The R-tree and its variations are commonly cited multidimensional access methods that can beused for answering such queries. Although the related algorithms work well for low-dimensional data spaces, their performance degrades as the number of dimensions increases (dimensionality curse). In order to obtain acceptable response time in high-dimensional data spaces, algorithms that obtain approximate solutions can be used. Approximation techniques, like N-consider (based on the tree structure), α-allowance and e-approximate (based on distance), or Time-consider (based on time) can be applied in branch-and-bound algorithms for DBQs inorder to control the trade-off between cost and accuracy of the result. In this paper, we improve previous approximate DBQ algorithms by applying a combination of the approximation techniques in the same query algorithm (hybrid approximation scheme). We investigate the performance of these improvements for one of the most representative DBQs (the K-closest pairs query, K-CPQ) in high-dimensional data spaces, as well as the influence of the algorithmic parameters on the control of the trade-off between the response time and the accuracy of the result. The outcome of the experimental evaluation, using synthetic and real datasets, is the derivation of the outperforming DBQ approximate algorithm for large high-dimensional point datasets.
A technique for the extraction of the connector response in adaptive parasitic antenna arrays

The response of the connector of the radiating elements in antenna arrays greatly influences the behavior of the overall system. In this work we present a novel yet simple procedure for the effective extraction of the connector response. Our method allows the calculation of the exact response of the connector by means of the solution of a linear system of equations obtained from the measurement of the impedance matrix of a test array and its simulated value. Once the connector response has been obtained in a simple test case the connector model can be used in the analysis and synthesis of a wide class of problems.
Apoptosis of Hippocampal Neurons in Organotypic Slice Culture Models: Direct Effect of Bacteria Revisited

Neurons of the hippocampal dentate gyrus selectively undergo programmed cell death in patients suffering from bacterial meningitis and in experimental models of pneumococcal meningitis in infant rats. In the present study, a membrane-based organotypic slice culture system of rat hippocampus was used to test whether this selective vulnerability of neurons of the dentate gyrus could be reproduced in vitro. Apoptosis was assessed by nuclear morphology (condensed and fragmented nuclei), by immunochemistry for active caspase-3 and ΔC-APP, and by proteolytic caspase-3 activity. Co-incubation of the cultures with live pneumococci did not induce neuronal apoptosis unless cultures were kept in partially nutrient-deprived medium. Complete nutrient deprivation alone and staurosporine independently induced significant apoptosis, the latter in a dose-response way. In all experimental settings, apoptosis occurred preferentially in the dentate gyrus. Our data demonstrate that factors released by pneumococci per se failed to induce significant apoptosis in vitro. Thus, these factors appear to contribute to a multifactorial pathway, which ultimately leads to neuronal apoptosis in bacterial meningitis.
Effectiveness and tolerability of tomoxetine in adults with attention deficit hyperactivity disorder.

OBJECTIVE The authors assessed the experimental noradrenergic compound tomoxetine as an alternative treatment for adult attention deficit hyperactivity disorder (ADHD). METHOD They conducted a double-blind, placebo-controlled, crossover study of tomoxetine in 22 adults with well-characterized ADHD. RESULTS Treatment with tomoxetine at an average oral dose of 76 mg/day was well tolerated. Drug-specific improvement in ADHD symptom was highly significant overall and sufficiently robust to be detectable in a parallel-groups comparison restricted to the first 3 weeks of the protocol. Eleven of 21 patients showed improvement after receiving tomoxetine, compared with only two of 21 patients who improved after receiving placebo. Significant tomoxetine-associated improvement was noted on neuropsychological measures of inhibitory capacity from Stroop tests. CONCLUSIONS This preliminary study showed that tomoxetine was effective in treating adult ADHD and was well tolerated. These promising results provide support for further studies of tomoxetine over an extended period of treatment.
Analysis and Design of a Double-Stator Flux-Switching Permanent Magnet Machine Using Ferrite Magnet in Hybrid Electric Vehicles

A double-stator flux-switching permanent magnet (DS-FSPM) machine using ferrite is proposed to replace an interior permanent magnet synchronous motor (IPMSM) on hybrid electric vehicles. A conventional FSPM machine is designed, and its torque characteristic is analyzed by a frozen permeability method. It is verified that magnetic saturation causes the reduction of flux linkage generated by PM and leads to the deterioration of electromagnetic torque. A DS-FSPM machine is effective for magnetic saturation because of its unique structure and makes the improvement of efficiency and power density. The proposed DS-FSPM machine achieves distinct performance enhancement compared with an IPMSM, even by utilizing ferrite PM.
Continuous blood cell separation using a dielectrophoretic virtual pillar array

We present continuous blood cell separation using a virtual pillar array induced by negative dielectrophoretic forces. The present cell separation method reduces particle clogging caused by microstructures. Experimental study verifies the clogging-free size-dependent blood cell separation feasibility using diluted whole blood. The separation positions of red blood cells (RBCs) and white blood cells (WBCs) are measured as 17.3plusmn150 mum and 585plusmn62 mum, respectively, at the conditions of the 20Vpp(peak-to-peak voltage) 500 kHz square wave input signal, the net flow rate of 0.2 muml/min, and the buffer conductivity of 0.5 S/m. Therefore, the present method has potential to apply in biological separations where we suffer due to the clogging.
Learning the professional jargon of nursing during change of shift report

Nurses discuss their patients in sequence during change of shift report. Guided by the patient record, this orderly progression of facts and words takes place repeatedly at specific time intervals and imposes order on the easily disordered events of patient units. The amount of information shared by reporting nurses increases when the acuity level of patients is high and when patients are recently admitted to patient units. Shift report functions as a forum for the socialization of nurses into the role of the nurse. During shift report, nurses express worries, complain, warn about possible errors, acknowledge errors, and set standards of nursing care. Using the language of nursing and telling "war stories" of their nursing experiences, nurses gently guide inexperienced nurses. Change of shift report is a nursing ritual that allows the hidden commitment of nurses to continuous coverage and responsibility for patients visible through the professional jargon of nursing.
Work Overload and Turnover Intention of Junior Auditors in Greater Jakarta, Indonesia

This paper aims to analyze how work overload influences turnover intentions of newly hired junior auditors in public accounting offices. Job satisfaction, work related stress and work life conflicts are used as mediating variables between work overload and turnover intention. This study employed 141 auditors from several accounting firms operating in the Greater Jakarta region. The sample was selected using purposive sampling. Three mediation hypotheses were tested using Structural Equation Modeling (SEM). The results show that work overload has a significant effect on increasing turnover intention through both job satisfaction and work related stress. In comparison, work overload does not influence turnover intention through work life balance. This may be due to the nature of the respondents, in which a majority of the newly hired accountants employed in this study are unmarried.
Coreference Resolution System Not Only for Czech

The paper introduces Treex CR, a coreference resolution (CR) system not only for Czech. As its name suggests, it has been implemented as an integral part of the Treex NLP framework. The main feature that distinguishes it from other CR systems is that it operates on the tectogrammatical layer, a representation of deep syntax. This feature allows for natural handling of elided expressions, e.g. unexpressed subjects in Czech as well as generally ignored English anaphoric expression – relative pronouns and zeros. The system implements a sequence of mention ranking models specialized at particular types of coreferential expressions (relative, reflexive, personal pronouns etc.). It takes advantage of rich feature set extracted from the data linguistically preprocessed with Treex. We evaluated Treex CR on Czech and English datasets and compared it with other systems as well as with modules used in Treex so far.
Automatic segment erection system for shield tunnels

Shield tunnelling is now the practice most frequently used in the tunnelling of urban areas. This paper discusses an automatic segment erection system developed for the unmanned implementation of the shield method. The system is composed of a segment erection robot and an automatic segment feeder; the former assembles segments which prevent the collapse of the rock mass and form a tunnel wall, and the latter supplies segments to the robot. It has been difficult to automate the erection steps because the segment pieces are very heavy. So, segment erection has been a problem in the development of an unmanned shield method. The robot reported here has overcome this difficulty, being able to position and join, with high accuracy, a segment in relation to segments already installed. This system was used in shield tunnelling on the largest scale yet seen in the world.
Advantages of having a lateralized brain

Brain lateralization is common among vertebrates. However, despite its implications for higher–order cognitive functions, almost no empirical evidence has been provided to show that it may confer any advantage to the functioning of the brain. Here, we show in the domestic chick (Gallus gallus domesticus) that cerebral lateralization is associated with an enhanced ability to perform two tasks simultaneously: finding food and being vigilant for predators. This finding suggests that cerebral lateralization enhances brain efficiency in cognitive tasks that demand the simultaneous but different use of both hemispheres.
Test Generation for Path Delay Faults Using Binary Decision Diagrams

A new test generation technique for path delay faults in circuits employing scan/hold type flip-flops is presented. Reduced ordered binary decision diagrams (ROBDDs) are used to represent Boolean functions realized by all signals in the circuit, as well as to represent the constraints to be satisfied by the delay fault test. Two faults are considered for each path in the circuit. For each fault, a pair of constraint functions, corresponding to the two time frames that constitute a transition, is evaluated. If the constraint function in the second time frame is non-null, robust-hazard-free-test generation for the delay fault is attempted. A robust test thus generated belongs either to the class of fully transitional path (FTP) tests or to the class of single input transition (SIT) tests. If a robust test cannot be found, the existence of a non-robust test is checked. Boolean algebraic manipulation of the constraint functions guarantees that if neither robust nor non-robust tests exist, the fault is undetectable. In its present form the method is applicable to all circuits that are amenable to analysis using ROBDDs. An implementation of this technique is used to analyze delay fault testability of ISCAS '89 benchmark circuits. These results show that the algebraic technique is one to two orders of magnitude faster than previously reported methods based on branch-and-bound algorithms. >
Carboxylated and Uncarboxylated Forms of Osteocalcin Directly Modulate the Glucose Transport System and Inflammation in Adipocytes

Abstract Osteocalcin is secreted by osteoblasts and improves insulin sensitivity in vivo, although mechanisms remain unclear. We tested the hypothesis that osteocalcin directly modulates cell biology in insulin-targeted peripheral tissues. In L-6 myocytes, osteocalcin stimulated glucose transport both in the absence (basal) and presence of insulin. Similarly, in primary cultured adipocytes, both carboxylated and uncarboxylated osteocalcin increased basal and insulin-stimulated glucose transport as well as insulin sensitivity. Osteocalcin also increased basal and insulin-stimulated glucose oxidation, though there was no effect on fatty acid synthesis or lipolysis. In primary-cultured adipocytes, both forms of osteocalcin suppressed secretion of tumor necrosis factor alpha into the media; however, only carboxylated osteocalcin suppressed interleukin 6 release, and neither form of osteocalcin modulated monocyte chemoattractant protein-1 secretion. Both carboxylated and uncarboxylated osteocalcin increased secretion of adiponectin and the anti-inflammatory cytokine interleukin 10. In conclusion, both carboxylated and uncarboxylated osteocalcin directly increase glucose transport in adipocytes and muscle cells, while suppressing proinflammatory cytokine secretion and stimulating interleukin 10 and adiponectin release. Thus, these results provide a mechanism for the insulin-sensitizing effects of osteocalcin and help elucidate the role that bone plays in regulating systemic metabolism.
Expression of Baculovirus Late and Very Late Genes Depends on LEF-4, a Component of the Viral RNA Polymerase Whose Guanyltransferase Function Is Essential

ABSTRACT Baculovirus lef-4 encodes one subunit of the viral RNA polymerase. Here, we demonstrate the essential nature of LEF-4 by RNA interference and bacmid knockout technology. Silencing of LEF-4 in wild-type virus-infected cells suppressed expression of structural genes, while early expression was unaffected, demonstrating its essential role in late gene expression. After transfection of insect cells with lef-4 mutant bacmid, no viral progeny was produced, further defining its central role in infection. Cotransfection with wild-type lef-4 plasmid restored normal replication, but plasmid encoding a guanyltransferase-deficient version failed to rescue. These results emphasize the importance of the mRNA capping function of LEF-4.
Radar Performance Degradation due to the Presence of Wind Turbines

Wind turbines located in the vicinity of a radar system may affect the system's detection and tracking capability. A description of adverse effects is given in the paper for both primary and secondary radar. In order to judge the consequence of the shadowed volume cast by a wind turbine, results of radar performance analyses are presented. It is shown that radar performance may be significantly degraded when a low-RCS target deliberately seeks a shaded volume. Suggestions to alleviate the problem are given.