Miracle-dz/UniFAR-FTUs huggingface dataset:
Protein fragments as models for events in protein folding pathways: protein engineering analysis of the association of two complementary fragments of the barley chymotrypsin inhibitor 2 (CI-2).

Two fragments of chymotrypsin inhibitor-2, CI-2(20-59) and CI-2(60-83), derived from cyanogen bromide cleavage at Met-59, associate to give a native-like structure. We analyze the kinetics and equilibria of association of mutant fragments derived from cleaving mutant proteins at the same methionine residue. The changes in free energy of association have been measured both from isothermal studies of the binding of fragments and from thermal denaturation of the complexes. In general, there is a good correlation between the changes on mutation of the free energy of association of fragments and the changes in free energy of folding of the uncleaved parent protein. The notable exceptions are for residues in regions of the fragments that form nonnative hydrophobic clusters in the isolated fragments; mutation of the hydrophobic residues involved in these clusters decreases the equilibrium constant for formation of the noncovalent complex less than it does the equilibrium constant for folding of intact protein. The dissociated fragments must be destabilized by mutation of those hydrophobic residues, but to a lesser extent than is the complex itself. These clusters are thus less important energetically in the denatured state of the intact protein. The second-order rate constants for the major phase of association change with mutation, similar results being obtained from fluorescence measurements of the regain of tertiary structure and from circular dichroism measurements of the regain of secondary structure. The rate constants for association correlate well, in general, with the rate constants of refolding of the respective uncleaved proteins. (ABSTRACT TRUNCATED AT 250 WORDS)
Activation of epitope‐specific memory cytotoxic T lymphocyte responses by synthetic peptides

Cytotoxic T lymphocytes (CTL) recognize antigens as short peptides selected for presentation by their ability to bind to MHC class I molecules. Polyclonal Epstein–Barr virus (EBV)‐specific memory CTL responses, reactivated from blood lymphocytes of HLA‐A11‐positive individuals by stimulation with the autologous EBV‐transformed lymphoblastoid cell line (LCL), are often dominated by reactivities directed to the peptide epitope IVTDFSVIK (IVT), corresponding to amino acids 416–424 of EBV nuclear antigen‐4 (EBNA4). We now report the selective activation of IVT‐specific CTL by stimulation of lymphocytes with the corresponding synthetic peptide. A more than 10‐fold increase in frequency of CTL clones with this specificity (from 8% to 96%) was obtained when the peptide was presented by HLA‐A11‐transfected T2 cells (T2/A11). Titration of synthetic peptide in cytotoxic assay demonstrated that clones activated under these conditions are as efficient as clones activated by conventional LCL stimulations. Induction of memory CTL responses required low surface density of MHC : peptide complexes, since reactivation was achieved by stimulation with T2/A11 cells pulsed with concentrations of peptide that are suboptimal for induction of target cell lysis. This protocol of activation revealed the presence of IVT‐specific CTL precursors in a donor that failed to mount an IVT‐specific response upon stimulation with the autologous B95.8 virus‐transformed LCL. The results suggest that stimulation with synthetic peptide epitopes can be efficiently used for induction of memory CTL responses, and may be particularly helpful for the selective expansion of subdominant CTL specificities.
Construction of Curriculum Ontology Aiming at Educational Service Support: An Ontology Approach for Knowledge-Intensive Service Systems

The main purpose of this paper is to present a conceptual model of curriculum to support the educational service system using ontological technology, which describes the semantic constraints on curriculum knowledge, and illustrates the characteristics of an knowledge-intensive educational service system. The approach has two major advantages as follows. (A) It provides the conceptualized curriculum service knowledge that is a part of a generic architecture for service-oriented educational systems. (B) It can facilitate the communication between different stakeholders in service system with conceptual level primitives.
ENVIRONMENTAL FACTORS (RH, T) AND THE STRATUM CORNEUM BARRIER FUNCTION TO OCCUPATIONAL CHEMICALS

Skin permeation for the occupational chemicals mainly depends on the Stratum Corneum (SC), which behaves as a barrier against the entrance of any substance applied on it. The hydration state of the SC plays a crucial role for its barrier function and the permeation process, especially for the water-soluble substances. In this work the relationship of the environmental Relative Humidity (RH) and Temperature (T) with the Stratum Corneum Hydration state, was studied and measured in vitro. We found that the SC hydration state is closely related with the environmental values of RH and T. This means that an increase of RH and T, in the working environment, can promote the toxicity hazards from occupational chemicals.
Axonal degeneration stimulates the formation of NG2+ cells and oligodendrocytes in the mouse

Proliferation of the adult NG2‐expressing oligodendrocyte precursor cells has traditionally been viewed as a remyelination response ensuing from destruction of myelin and oligodendrocytes, and not to the axonal pathology that is also a characteristic of demyelinating disease. To better understand the response of the NG2+ cells to the different components of demyelinating pathology, we investigated the response of adult NG2+ cells to axonal degeneration in the absence of primary myelin or oligodendrocyte pathology. Axonal degeneration was induced in the hippocampal dentate gyrus of adult mice by transection of the entorhino‐dentate perforant path projection. The acutely induced degeneration of axons and terminals resulted in a prompt response of NG2+ cells, consisting of morphological transformation, cellular proliferation, and upregulation of NG2 expression days 2–3 after surgery. This was followed by a reduction of cellular NG2 expression to subnormal levels from day 5 to 7 and reappearance of normal appearing NG2+ cells from day 10. Mice that had received repeated injections of bromodeoxyuridine from 24 to 72 h after surgery contained significant numbers of bromodeoxyuridine‐incorporating oligodendrocytes in the areas with axonal degeneration at day 7. The results suggest that axonal degeneration induces a unique sequence of changes of NG2+ cells and that a subpopulation of the newly generated NG2+ cells differentiate into oligodendrocytes. © 2006 Wiley‐Liss, Inc.
Fabrication of graphene devices, issues and prospects

Graphene based devices have seen an enormous amount of published literature since its isolation 6 years ago, however processing issues and wafer size material availability have proven to be the most demanding tasks in fabrication of graphene devices. This work focuses on some of the main technological issues relating to realization of graphene based devices. Solutions and current techniques are shortly presented and discussed.
StartState Configuration Circumstance Temporal Place Whole Elements Possessor Species Instance Quantity Superset Causer Agent CreatorCo-Agent Explanation Attribute Manner Reciprocation Purpose Function Age Time Frequency Duration RelativeTime EndTimeStartTime ClockTimeCxn DeicticTime Path Locus Valu

We present the first corpus annotated with preposition supersenses, unlexicalized categories for semantic functions that can be marked by English prepositions (Schneider et al., 2015). The preposition supersenses are organized hierarchically and designed to facilitate comprehensive manual annotation. Our dataset is publicly released on the web.1
Performance bounds for queues via generating functions

Modern applications, e.g., very large-scale integration (VLSI) manufacturing, give rise to complicated queueing models, often of the re-entrant type. Their complexity, together with implications of their performance, have renewed interest in their performance and the computation of good control (e.g., scheduling) policies. Recent work concentrated on computable (mostly linear) performance bounds. We show that the linear bounds can be obtained naturally, and under weaker assumptions, using generating function techniques. This approach gives rise to a new class of bounds, on performance over busy periods.
Description of two new species of Meharia Chrétien, 1915 (Lepidoptera: Cossidae) from East Africa.

The genus Meharia Chretien, 1915 is a monotypic genus in the subfamily Mehariinae (Yakovlev 2011), clearly differentiated from other taxa in the family Cossidae. The morphological features of the genus are described in detail by Komarov and Zolotuhin (2005), Borth et al. 2011, Saldaitis and Ivinskis (2010) and Yakovlev (2011). Two unknown species of Meharia were collected in Kenya and Malawi and we describe them herein as new. The new species are similar to Meharia acuta Wiltshire 1982 and are distributed in the Arabian Peninsula (Hacker 1999; Yakovlev 2011). All three species have specific tineoid appearance and labial palpi twice as long as the head diameter. Currently, including the two newly described species, the genus Meharia consists of 13 species (Hacker 1999; Hacker et al. 1999, 2001; Yakovlev and Saldaitis 2008; Yakovlev 2011): M. acuta Wiltshire (distributed in Saudi Arabia, Yemen and Oman); M. avicenna Yakovlev (distr. in S Iran); M. fischeri Yakovlev & Saldaitis (distr. in Morocco); M. hackeri Saldaitis, Ivinskis & Yakovlev (distr. on Socotra Island, Yemen); M. incurvariella Chretien (distr. in Algeria and Morocco); M. murphyi Yakovlev & Saldaitis sp. nov. (distr. in Malawi); M. ostrauskasi Ivinskis & Saldaitis sp. nov. (distr. in Kenya); M. philbyi Bradley (distr. across the Arabian peninsula in Saudi Arabia, Yemen and Oman); M . scythica Komarov et Zolotuhin (distr. in the S Volga region, SW Russia: ); M . semilactea (Warren et Rothschild) (distr. in Israel, Jordan, Saudi Arabia, Oman, UAE, Yemen, the Sinai Peninsula, Egypt, N Sudan, Morocco and Mauritania); M. tancredii Sutton (distr. in N. Iran); M. tanganyikae Bradley (distr. in Tanzania); M . yakovlevi Saldaitis & Ivinskis (distr. on Socotra Island, Yemen).
Sumoylation and the Structural Maintenance of Chromosomes (Smc) 5/6 Complex Slow Senescence through Recombination Intermediate Resolution*

Telomeres are repetitive nucleoprotein structures that cap the ends of chromosomes. Without telomerase, telomeres shorten with replication and eventually signal cell cycle arrest (cell senescence). Homologous recombination (HR)-based mechanisms slow senescence, and distinct HR mechanisms support the growth of the rare survivors of senescence. Here, we report novel roles for the post-translational modification of small ubiquitin-like modifier (SUMO) in regulating the rate of senescence in Saccharomyces cerevisiae telomerase mutants. We identify Mms21 as the relevant SUMO E3 ligase and demonstrate that cells lacking Mms21-dependent sumoylation accumulate HR intermediates selectively at telomeres during senescence. One target of Mms21-dependent sumoylation is the cohesin- and condensin-related Smc5-Smc6 complex (Smc5/6). We show that hypomorphic smc5 or smc6 alleles exhibit phenotypes similar to mms21 sumoylation-deficient mutants with regard to senescence and the accumulation of unresolved HR intermediates. Further, we provide evidence that Mms21 and Smc5/6 prevent aberrant recombination between sister telomeres and also globally facilitate resolution of sister chromatid HR intermediates.
Immunoglobulin E‐mediated airway inflammation is active in most patients with asthma

Purpose: To review the role of immunoglobulin E (IgE)‐mediated inflammation in the pathogenesis of asthma, limitations of standard therapies, and IgE as a logical target for therapy with omalizumab aimed at attaining asthma symptom control. Data sources: Review of worldwide scientific literature on the role of IgE‐mediated inflammation in patients with asthma, supplemented with a clinical case study. Conclusions: Clinical trials point to an important role for IgE blocker therapy as an add‐on to current therapy to reduce exacerbations and corticosteroid use and to improve quality of life in patients with moderate‐to‐severe asthma. Omalizumab, a monoclonal antibody that binds IgE, has been shown to be an effective, well‐tolerated treatment in these patients. Implications for practice: A significant number of patients with moderate‐to‐severe asthma do not achieve asthma symptom control, despite adhering to current guidelines–based standards of therapy, including the use of inhaled corticosteroids, &bgr;‐agonists, and leukotriene modifiers. None of these therapies directly addresses IgE‐mediated inflammation. Therefore, patients with persistent symptoms of moderate‐to‐severe asthma should be evaluated and considered for therapy with the IgE blocker omalizumab.
Programming Windows Azure - Programming the Microsoft Cloud

Learn the nuts and bolts of cloud computing with Windows Azure, Microsoft's new Internet services platform. Written by a key member of the product development team, this book shows you how to build, deploy, host, and manage applications using Windows Azure's programming model and essential storage services. Chapters in Programming Windows Azure are organized to reflect the platform's buffet of services. The book's first half focuses on how to write and host application code on Windows Azure, while the second half explains all of the options you have for storing and accessing data on the platform with high scalability and reliability. Lots of code samples and screenshots are available to help you along the way. Learn how to build applications using the Windows Azure toolset Discover how Windows Azure works under the hood, and learn the how and the why behind several features Choose to write application code in . NET or other languages such as C/C++, PHP, or Ruby Understand the various options for managing your service Get up to speed on Azure's storage services, including blobs, queues, and tables Build a secure backup system, and learn about cloud application security, cryptography, and performance
Cannabinoid agonist WIN55,212‐2 induces apoptosis in cerebellar granule cells via activation of the CB1 receptor and downregulation of bcl‐xL gene expression

The endogenous cannabinoid system is involved in the regulation of a number of physiologic effects in both the central and peripheral nervous systems. Its role in the control of neuronal cell proliferation has attracted major attention because of its potential implications for new therapeutic strategies. In the present study, we demonstrated that treatment of cultured cerebellar granule cells with the synthetic cannabinoid WIN55,212‐2, causes cell‐body and nuclear shrinkage, which are hallmarks of neuronal apoptosis, as well as concentration‐dependent decrease in cell viability. Staining with the fluorescent nuclear dye, Hoechst 33258, revealed apoptosis in 27.1% and 58.5% of cells exposed to 1 and 10 μM of WIN55,212‐2, respectively (P < 0.01 and P < 0.001 vs. control respectively) after 36 hr. After 24 hr of exposure to WIN55,212‐2, mRNA levels for the anti‐apoptotic gene bcl‐xL were reduced to 45.6% of those found in control (P < 0.01). These effects were completely reverted when cells were exposed to the synthetic cannabinoid in the presence of the specific CB1‐receptor antagonist, SR141716A (1 μM). Moreover, the pro‐apoptotic effect of 10 μM WIN55,212‐2 could be reduced by the addition to the incubation medium of a cell‐permeant inhibitor of caspase‐1 (50 nM). Finally, WIN55,212‐2 significantly increased caspase‐1 activity after 24 hr. These findings show that the activation of CB1 receptors on cerebellar granule cells induces apoptotic cell death, which is associated with downregulation of the anti‐apoptotic gene, bcl‐xL, and at least in part, activation of caspase‐1. © 2006 Wiley‐Liss, Inc.
Working Paper Series , N . 4 , November 2015 On penalised likelihood and bias reduction

We propose a likelihood function endowed with a penalisation that reduces the bias of the maximum likelihood estimator in regular parametric models. The penalisation hinges on the first two derivatives of the log likelihood and can be computed numerically. The asymptotic properties and the sensitivity to nuisance parameters of the penalised likelihood and derived quantities are addressed. In models for stratified data in a two-index asymptotic setting, the bias of the penalised profile score function is found to be equivalent to the bias of a modified profile score function.
A Study of Suppressing Strong Clutter in Radar Signal Based ICA

It is great difficult to handle the clutter in Radar signal processing. To reduce the influence of clutter, the paper firstly attempts to use FastICA algorithm by separating the target signal and clutter to suppress the strong clutter. The pretreatment of increasing the dimension and dividing the frequency is used before Fast ICA algorithm because of the special radar complex signals. In the same matched filter conditions, Fast ICA algorithm is proved effectively through the increased peak side lobe ratio (PSLR) and signal clutter ratio (SCR).
Impact of hypertension on left ventricular structure in patients with asymptomatic aortic valve stenosis (a SEAS substudy)

Objective Both hypertension and aortic valve stenosis induce left ventricular hypertrophy. However, less is known about the influence of concomitant hypertension on left ventricular structure in patients with aortic valve stenosis. Methods Baseline Doppler echocardiography was performed in 1720 patients with asymptomatic aortic valve stenosis (peak transaortic velocity ≥2.5 m/s and ≤4.0 m/s) recruited in the Simvastatin and Ezetimibe in Aortic Stenosis study at 173 centers in seven European countries. Patients were grouped as normotensive (n = 482) or hypertensive (n = 1238) according to history of hypertension or clinic blood pressure greater than 140 mmHg systolic or greater than 90 mmHg diastolic at baseline visits. Results Hypertensive patients were older, more obese, and included more women (all P < 0.05). Furthermore, the hypertensive group had higher wall thicknesses and left ventricular mass and higher prevalence of left ventricular hypertrophy (40 vs. 25%) and increased relative wall thickness (21 vs. 14%, both P < 0.01). On the basis of aortic valve area and energy loss the degree of aortic valve stenosis did not differ between the groups. In multivariate analysis, hypertension predicted higher left ventricular mass independent of other well known confounders including male sex, circumferential end-systolic stress, body mass index, aortic regurgitation, left ventricular ejection fraction and severity of aortic stenosis (multiple R2 = 0.30, P < 0.001). Conclusion In patients with asymptomatic aortic stenosis, concomitant hypertension significantly influences left ventricular geometry and is associated with higher left ventricular mass, relative wall thickness and higher prevalence of left ventricular hypertrophy.
Serum Ghrelin and Cholesterol Values in Suicide Attempters

In our previous study, we demonstrated that suicide attempters had statistically significant lower leptin and cholesterol levels compared with healthy controls. In keeping with our previous report regarding lower serum cholesterol and leptin levels in suicide attempters compared with healthy controls, the relationship between cholesterol and leptin, and ghrelin, we aimed to evaluate serum total cholesterol and ghrelin levels in suicide attempters. In the present study, 30 patients with suicide attempts (aged 18–47 years) and the same number of healthy controls were compared with regard to serum total cholesterol and ghrelin levels. The mean cholesterol level of the patients was significantly lower than that of the controls. On the other hand, the suicide attempters had significantly higher ghrelin levels compared with the controls. The results suggest that suicide attempts seem to be associated with decreased serum cholesterol and higher ghrelin values.
AGENT-BASED SIMULATION FOR BORDER CROSSING MODELING

The aim of this study is to build a computational model to simulate border crossing. Since the 19th century, many theories have been applied to the study of international migration phenomena. These theories cover sociological, economical, and cultural aspects. All the theories aim at estimating the magnitude of population movements. Multi-Agent Systems (MAS) are presented as a new methodological approach to model and foresee the process of migration. This article discusses how legal aspects can also be treated from a computational point of view. When a migrant reaches the border checkpoint, he/she must deal with the legislation of the destination country, which is applied by the border security police. This interaction at the microlevel between the migrant and the border agent is based on the definition of a behavioral model that includes the migrant's profile, the border officer's profile, and the legislation that rules the border crossing. With this model, the effects at the macrolevel of new policies (which are usually difficult to predict) can be estimated. Changes in legislation or in strictness in applying the existing law at certain borders can influence migration trends; for example, the choice of route. This study presents the main features of the computational model that has been developed to recreate the border-crossing scenario in a Multi-Agent System.
Estimating Snow Leopard Population Abundance Using Photography and Capture–Recapture Techniques

Abstract Conservation and management of snow leopards (Uncia uncia) has largely relied on anecdotal evidence and presence–absence data due to their cryptic nature and the difficult terrain they inhabit. These methods generally lack the scientific rigor necessary to accurately estimate population size and monitor trends. We evaluated the use of photography in capture–mark–recapture (CMR) techniques for estimating snow leopard population abundance and density within Hemis National Park, Ladakh, India. We placed infrared camera traps along actively used travel paths, scent-sprayed rocks, and scrape sites within 16- to 30-km2 sampling grids in successive winters during January and March 2003–2004. We used head-on, oblique, and side-view camera configurations to obtain snow leopard photographs at varying body orientations. We calculated snow leopard abundance estimates using the program CAPTURE. We obtained a total of 66 and 49 snow leopard captures resulting in 8.91 and 5.63 individuals per 100 trap-nights during 2003 and 2004, respectively. We identified snow leopards based on the distinct pelage patterns located primarily on the forelimbs, flanks, and dorsal surface of the tail. Capture probabilities ranged from 0.33 to 0.67. Density estimates ranged from 8.49 (SE = 0.22) individuals per 100 km2 in 2003 to 4.45 (SE = 0.16) in 2004. We believe the density disparity between years is attributable to different trap density and placement rather than to an actual decline in population size. Our results suggest that photographic capture–mark–recapture sampling may be a useful tool for monitoring demographic patterns. However, we believe a larger sample size would be necessary for generating a statistically robust estimate of population density and abundance based on CMR models.