Miracle-dz/UniFAR-FTUs huggingface dataset:
TNF Receptor-Associated Factor 5 Is Required for Optimal T Cell Expansion and Survival in Response to Infection1

Receptors belonging to the TNF-receptor (TNF-R) superfamily include important costimulatory molecules, many of which specifically affect T cell activation. TNF receptor-associated factors (TRAFs) are recruited to many TNF-R superfamily members and are important modulators of the proximal signaling events that occur at the time of receptor engagement and activation. TRAF5 has been shown to be a positive regulator of a number of these receptors that are involved in T cell costimulation. However, the potential importance of TRAF5 in cellular immune responses to infection or in T cell expansion and memory have not been studied. We report in this study that TRAF5 was required for optimal CD8+ T cell responses following infection with Listeria monocytogenes expressing OVA (LM-OVA). TRAF5 was necessary for optimal T cell expansion following primary infection with LM-OVA, and its absence resulted in fewer memory CD8+ T cells following LM-OVA infection, together with higher bacterial loads in the liver. The effect of TRAF5 on CD8+ T cell expansion was T cell intrinsic and not due to effects of TRAF5 deficiency on APCs. Although their proliferative ability remained intact, CD8+ T cells from TRAF5−/− mice were more sensitive to apoptosis and were unresponsive to the prosurvival effects of the TNF-R superfamily costimulator CD27. Collectively, these studies identify TRAF5 as an important positive signaling element that enhances T cell expansion and pathogen containment by providing a survival advantage to responding Ag-specific CD8+ T cells during infection.
Impact of Sample Heterogeneity on Methylation Analysis

The recent emergence of high-throughput arrays for methylation analysis has made the influence of tumor content on the interpretation of methylation levels increasingly pertinent. However, to what degree does tumor content have an influence, and what degree of tumor content makes a specimen acceptable for accurate analysis remains unclear. Taking a systematic approach, we analyzed 98 unselected formalin-fixed and paraffin-embedded gastric tumors and matched normal tissue samples using the Illumina GoldenGate methylation assay. Unsupervised hierarchical clustering showed 2 separate clusters with a significant difference in average tumor content levels. The probes identified to be significantly differentially methylated between the tumors and normals also differed according to the tumor content of the samples included, with the sensitivity of identifying the “top” candidate probes significantly reduced when including samples below 70% tumor content. We also tested whether the removal of the probes featuring single nucleotide polymorphisms and/or DNA repetitive elements, reportedly present in GoldenGate arrays, would significantly affect the study's findings, and found little change in the results with their omission. Our findings suggest that tumor content significantly influences the interpretation of methylation levels and candidate gene identification, and that 70% tumor content may be a suitable threshold for selecting samples for methylation studies.
A MorphoSyntactic Approach to Language Typology 2 . 1

Various linguistic phenomena may serve a basis for the classification of languages and nominal forms make part of the criteria for the classification. In this study, two major approaches are closely compared for language typology based on nominal forms. Chierchia (1998a, b) assumes that morpho-syntactic features should be crucial in determining the denotations and grammatical categories of NPs. He suggests three classificatory categories with the notion of nominal mapping parameters. Contrastingly, the OT analysis of de Swart & Zwarts (2009, 2010) do not assume that morpho-syntactic features should be collapsed with countability and plurality. They propose several general constraints governing nominal forms and argue that different ordering of the constraints in optimality accounts for different nominal forms crosslinguistically. I have shown that the OT
Use of Immunodampening To Overcome Diversity in the Malarial Vaccine Candidate Apical Membrane Antigen 1

ABSTRACT Apical membrane antigen 1 (AMA1) is a leading malarial vaccine candidate; however, its polymorphic nature may limit its success in the field. This study aimed to circumvent AMA1 diversity by dampening the antibody response to the highly polymorphic loop Id, previously identified as a major target of strain-specific, invasion-inhibitory antibodies. To achieve this, five polymorphic residues within this loop were mutated to alanine, glycine, or serine in AMA1 of the 3D7 and FVO Plasmodium falciparum strains. Initially, the corresponding antigens were displayed on the surface of bacteriophage, where the alanine and serine but not glycine mutants folded correctly. The alanine and serine AMA1 mutants were expressed in Escherichia coli, refolded in vitro, and used to immunize rabbits. Serological analyses indicated that immunization with a single mutated form of 3D7 AMA1 was sufficient to increase the cross-reactive antibody response. Targeting the corresponding residues in an FVO backbone did not achieve this outcome. The inclusion of at least one engineered form of AMA1 in a biallelic formulation resulted in an antibody response with broader reactivity against different AMA1 alleles than combining the wild-type forms of 3D7 and FVO AMA1 alleles. For one combination, this extended to an enhanced relative growth inhibition of a heterologous parasite line, although this was at the cost of reduced overall inhibitory activity. These results suggest that targeted mutagenesis of AMA1 is a promising strategy for overcoming antigenic diversity in AMA1 and reducing the number of variants required to induce an antibody response that protects against a broad range of Plasmodium falciparum AMA1 genotypes. However, optimization of the immunization regime and mutation strategy will be required for this potential to be realized.
INFLUENCES OF WATERSHED URBANIZATION AND INSTREAM HABITAT ON MACROINVERTEBRATES IN COLD WATER STREAMS 1

ABSTRACT: We analyzed data from riffle and snag habitats for 39 small cold water streams with different levels of watershed urbanization in Wisconsin and Minnesota to evaluate the influences of urban land use and instream habitat on macroinvertebrate communities. Multivariate analysis indicated that stream temperature and amount of urban land use in the watersheds were the most influential factors determining macroinvertebrate assemblages. The amount of watershed urbanization was nonlinearly and negatively correlated with percentages of Ephemeroptera‐Plecoptera‐Trichoptera (EPT) abundance, EPT taxa, filterers, and scrapers and positively correlated with Hilsenhoff biotic index. High quality macroinvertebrate index values were possible if effective imperviousness was less than 7 percent of the watershed area. Beyond this level of imperviousness, index values tended to be consistently poor. Land uses in the riparian area were equal or more influential relative to land use elsewhere in the watershed, although riparian area consisted of only a small portion of the entire watershed area. Our study implies that it is extremely important to restrict watershed impervious land use and protect stream riparian areas for reducing human degradation on stream quality in low level urbanizing watersheds. Stream temperature may be one of the major factors through which human activities degrade cold‐water streams, and management efforts that can maintain a natural thermal regime will help preserve stream quality.
SIMILITUDE MODEL EXPERIMENTS TO DETECT MINE CAVITIES 1 F .

A resistivity technique for cavity location has been developed. This technique is a combination of the Bristow arrangement and line electrode method. In this technique three line electrodes are used so that the sinkhole electrode is placed far from the other two electrodes. When one of the two electrodes and the sinkhole electrode are activated, several resistivity profiles parallel arid perpendicular to the line electrode are measured for different electrode activated. Subsurface cavities cause resistivity anomalies if they are crossed by the resistivity profiles. The anomalies are interpreted and used to locate the sources of the anomalies (cavities). A tank model and a similitude model are developed to verify the effectiveness of this method for cavity detection in the saline medium and in the actual materials. The results of the experiment indicate that the location and the dimensions of the. , cavities can be estimated successfully. Additional
Influenza virus hemagglutinin containing an altered hydrophobic carboxy terminus accumulates intracellularly

The influenza virus hemagglutinin (HA) glycoprotein synthesized from cloned DNA in a simian virus 40 vector is expressed on the surface of infected primate cells. Previously, it has been demonstrated that mutant HAs lacking the hydrophobic carboxy terminus fail to anchor on the cell surface and therefore are secreted extracellularly. During analysis of additional HA deletion mutants derived from an HA-simian virus 40 recombinant, we found a mutant with an altered hydrophobic carboxy terminus that exhibited another phenotype. This deletion mutant, dl-12, produced HA that was neither secreted nor expressed on the infected cell surface. The mutant HA was similar to the wild-type HA in apparent molecular weight and extent of glycosylation as assayed by endoglycosidase H sensitivity. The mutant HA localized near the perinuclear region of infected cells as indicated by an indirect immunofluorescence assay. Sequence analysis showed that a 5-base-pair deletion had occurred before the region encoding the hydrophobic carboxy terminus. Nevertheless, the physicochemical properties of the wild-type HA carboxy terminus were maintained in that the truncated HA carboxy terminus consisted of predominantly hydrophobic amino acids followed by several charged amino acids residues. This similarity in the carboxy terminus between the wild-type and mutant HAs may be responsible for the functional similarities observed. In spite of these similarities, the mutant HA failed to mature at the surface. These results suggest that the maturation of the mutant HA is blocked during a late stage in the transit to the cell surface.
The Efficacy of Gadobenate Dimeglumine (Gd-BOPTA) at 3 Tesla in Brain Magnetic Resonance Imaging: Comparison to 1.5 Tesla and a Standard Gadolinium Chelate Using a Rat Brain Tumor Model

Objectives:The objectives of this study were to analyze the differences in contrast enhancement using gadobenate dimeglumine (Gd-BOPTA or MultiHance) at 3 T versus 1.5 T and to compare Gd-BOPTA with a standard gadolinium chelate, gadopentetate dimeglumine (Gd-DTPA or Magnevist), at 3 T in a rat glioma model. Materials and Methods:Twelve rats with surgically implanted gliomas were randomized to either comparing Gd-BOPTA at 1.5 T versus 3 T (n = 7) or comparing Gd-BOPTA and Gd-DTPA at 3 T (n = 5). Matched T1-weighted spin-echo techniques were used for both comparisons and the order of examinations was randomized. Signal-to-noise ratio (SNR), contrast-to-noise ratio (CNR), and lesion enhancement (LE) were evaluated using a region-of-interest analysis. A veterinary histopathologist evaluated all brain specimens. Results:In the evaluation of Gd-BOPTA at 3 T and 1.5 T, there were significant increases in SNR, LE, and CNR at 3 T. Average increases in brain and tumor SNR were 93% (P < 0.0001) and 92% (P < 0.0001), respectively. CNR increased by 121% (P < 0.0001). Comparison of Gd-BOPTA and Gd-DTPA at 3 T demonstrated significantly higher CNR and LE with Gd-BOPTA. CNR increased by 35% (P = 0.002). LE increased by 44% (P = 0.03). Conclusions:Gd-BOPTA provides significantly higher CNR at 3 T compared with 1.5 T and also demonstrates significantly higher CNR when compared with a standard Gd-chelate at 3 T. As a result of transient protein binding, Gd-BOPTA may be superior to standard gadolinium chelates in neurologic imaging at 3 T.
FAILURE ANALYSIS OF COMPOSITE LAMINATES WITH AN OPEN HOLE UNDER BIAXIAL COMPRESSION-TENSION LOADING

An approximate solution for the normal stress distribution adjacent to a circular hole in an orthotropic laminate is employed with a recently developed fracture mechanics model to predict its failure strength under compressiontensionl loading. Using the independently measured laminate parameters of unnotched strength and in-plane fracture toughness, the model successfully predicts the damage initiation, growth and final fracture of notched multidirectional laminates under various biaxiality ratios. British Crown Copyright  2000 Published by ICAS.
Anti-TNF-&agr; Agents Are Less Effective for the Treatment of Rheumatoid Arthritis in Current Smokers

Objectives:To assess if smoking status at the time of commencing an anti-TNF-&agr; agent for rheumatoid arthritis (RA) reduces the likelihood of achieving at least a moderate response on the European League Against Rheumatism (EULAR) response criteria at 3-month assessment. Methods:All patients with RA treated with their first anti-TNF-&agr; agent at the Department of Rheumatology, Derby Hospital NHS Trust between April 2001 and October 2008 were included in this retrospective case control study. Information about age, gender, disease duration, body mass index, smoking status (current smoker, ex-smoker, and nonsmoker), comorbidities, oral prednisolone use, and 28 joint 4 variables disease activity score (DAS28) at the time of commencing an anti-TNF-&agr; agent was recorded. Details of rheumatoid factor (RF) and past and present disease modifying antirheumatic drugs were recorded. A case control study was carried out to examine possible baseline predictors of treatment effects at the 3-month assessment. Results:Results were available for 395 patients at 3-month assessment. According to the EULAR response criteria 42 patients failed to show at least a moderate response. After adjusting for confounders using multivariate analysis, current smoking at the time of commencing an anti-TNF-&agr; agent reduced the chance of achieving at least a moderate response on the EULAR response criteria when compared with nonsmokers (aOR [95% CI] 0.20 [0.05–0.83], P = 0.03). Conclusions:RA patients who smoke are less likely to respond to an anti-TNF-&agr; agent.
The use of the objective structured clinical examination (OSCE) in dental education

Aim of this study is to elucidate which standard setting method is the optimal instrument to prevent that incompetent students pass and competent students fail a dental OSCE. Material and methods: An OSCE with 14 test-stations was used to assess the performance of 119 dental 3 rd year students in a training group practice. Three standard setting methods were applied: the Angoff I method, the modified Angoff II with reality check and the Borderline Regression (BR) method to establish the pass/fail standard per station. For the final decision about passing or failing the complete OSCE, the 3 methods were compared in a Total Compensatory (TC), a Partial Compensatory (PC) within clusters of competence, and a Non-Compensatory (NC) model. The reliability of the pass/fail standard of the 3 methods was indicated by the Root Mean Square Error (RMSE). As a criterion measure, a sample of the students (n=89) was rated in the clinic by their instructors and accordingly these students were divided into two groups: competent and incompetent students. The students’ clinical rating (considered for this study as “true qualification”) was compared with the pass-fail classification resulting from the OSCE. Undeserved passing of an incompetent student was considered as more damaging than failing of a competent student. Results: The BR method showed more acceptable results than the two Angoff methods. In terms of pass rate the BR method showed the highest pass rates: for the TC model the Angoff method I and II and the BR showed the pass rates: 86.6%, 86.6%, and 97.5 % respectively. For the PC model the pass rates were 30.3%, 34.5%, and 61.3%, and for the NC model the pass rates were 0.8%, 1.7% and 7.6%. The BR method showed lower RMSEs (higher reliability): for the TC model the RMSEs were 1.3%, 1.0% and 0.3% for the Angoff I , Angoff II and BR method respectively, and for the PC model, the RMSE of the clusters of competence ranged for Angoffs I: 2.0%-3.7%; for Angoff II: 1.8%-2.2
Larvae of the coral eating crown‐of‐thorns starfish, Acanthaster planci in a warmer‐high CO2 ocean

Outbreaks of crown‐of‐thorns starfish (COTS), Acanthaster planci, contribute to major declines of coral reef ecosystems throughout the Indo‐Pacific. As the oceans warm and decrease in pH due to increased anthropogenic CO2 production, coral reefs are also susceptible to bleaching, disease and reduced calcification. The impacts of ocean acidification and warming may be exacerbated by COTS predation, but it is not known how this major predator will fare in a changing ocean. Because larval success is a key driver of population outbreaks, we investigated the sensitivities of larval A. planci to increased temperature (2–4 °C above ambient) and acidification (0.3–0.5 pH units below ambient) in flow‐through cross‐factorial experiments (3 temperature × 3 pH/pCO2 levels). There was no effect of increased temperature or acidification on fertilization or very early development. Larvae reared in the optimal temperature (28 °C) were the largest across all pH treatments. Development to advanced larva was negatively affected by the high temperature treatment (30 °C) and by both experimental pH levels (pH 7.6, 7.8). Thus, planktonic life stages of A. planci may be negatively impacted by near‐future global change. Increased temperature and reduced pH had an additive negative effect on reducing larval size. The 30 °C treatment exceeded larval tolerance regardless of pH. As 30 °C sea surface temperatures may become the norm in low latitude tropical regions, poleward migration of A. planci may be expected as they follow optimal isotherms. In the absence of acclimation or adaptation, declines in low latitude populations may occur. Poleward migration will be facilitated by strong western boundary currents, with possible negative flow‐on effects on high latitude coral reefs. The contrasting responses of the larvae of A. planci and those of its coral prey to ocean acidification and warming are considered in context with potential future change in tropical reef ecosystems.
Tethered Epidermal Growth Factor Provides a Survival Advantage to Mesenchymal Stem Cells

MSC can act as a pluripotent source of reparative cells during injury and therefore have great potential in regenerative medicine and tissue engineering. However, the response of MSC to many growth factors and cytokines is unknown. Many envisioned applications of MSC, such as treating large defects in bone, involve in vivo implantation of MSC attached to a scaffold, a process that creates an acute inflammatory environment that may be hostile to MSC survival. Here, we investigated cellular responses of MSC on a biomaterial surface covalently modified with epidermal growth factor (EGF). We found that surface‐tethered EGF promotes both cell spreading and survival more strongly than saturating concentrations of soluble EGF. By sustaining mitogen‐activated protein kinase kinase‐extracellular‐regulated kinase signaling, tethered EGF increases the contact of MSC with an otherwise moderately adhesive synthetic polymer and confers resistance to cell death induced by the proinflammatory cytokine, Fas ligand. We concluded that tethered EGF may offer a protective advantage to MSC in vivo during acute inflammatory reactions to tissue engineering scaffolds. The tethered EGF‐modified polymers described here could be used together with structural materials to construct MSC scaffolds for the treatment of hard‐tissue lesions, such as large bony defects.
A review on vision-based pedestrian detection

This paper describes the state-of-the-art in vision-based pedestrian detection, including pedestrian detection methods, training of classifiers and commonly used pedestrian databases. In this paper, we classify the pedestrian detection algorithms into static pedestrian detection and dynamic pedestrian detection, according to the application of motion information. The former is further divided into model-based methods and feature-classifier-based methods, and we mainly focus on the latter ones. Unlike other surveys in pedestrian detection, we also introduce the newest techniques of training classifiers and some general databases of pedestrian detection. Finally, we compare and conclude various pedestrian detection algorithms. Challenges and future trends are also discussed in that section.
The Yin Yang 1 Transcription Factor Associates with Ribonucleoprotein (mRNP) Complexes in the Cytoplasm of Xenopus Oocytes*

Yin Yang 1 (YY1) is a multifunctional transcription factor that activates, represses, or initiates transcription of a diverse assortment of genes. Previous studies suggest a role for YY1 in cellular growth and differentiation, but its biological function during development of the vertebrate oocyte or embryo remains to be determined. We recently showed that YY1 is abundantly expressed throughout oogenesis and early embryonic stages ofXenopus, but it is sequestered in the cytoplasm and does not function directly in transcriptional regulation. In the present study we used a series of biochemical analyses to explore the potential function of YY1 in the oocyte cytoplasm. YY1 was isolated from oocyte lysates by oligo(dT)-cellulose chromatography, suggesting that it associates with maternally expressed mRNA in vivo. RNA mobility shift assays demonstrate that endogenous YY1 binds to labeled histone mRNA. Size exclusion chromatography of oocyte lysates revealed that YY1 exists in high molecular mass complexes in the range of 480 kDa. Destruction of endogenous RNA by RNase treatment of lysates, abolished the binding of YY1 to oligo(dT)-cellulose and resulted in redistribution from 480-kDa complexes to the monomeric form. Microinjection of RNase directly into the cytoplasm released YY1 from 480-kDa complexes and unmasked its DNA-binding activity, but did not promote translocation to the nucleus. These results provide evidence that YY1 is a component of ribonucleoprotein (mRNP) complexes in the Xenopus oocyte, indicating a novel function for YY1 in the storage or metabolism of maternal transcripts.