Miracle-dz/UniFAR-FTUs huggingface dataset:
Transcriptome Profiles of Carcinoma-in-Situ and Invasive Non-Small Cell Lung Cancer as Revealed by SAGE

Background Non-small cell lung cancer (NSCLC) presents as a progressive disease spanning precancerous, preinvasive, locally invasive, and metastatic lesions. Identification of biological pathways reflective of these progressive stages, and aberrantly expressed genes associated with these pathways, would conceivably enhance therapeutic approaches to this devastating disease. Methodology/Principal Findings Through the construction and analysis of SAGE libraries, we have determined transcriptome profiles for preinvasive carcinoma-in-situ (CIS) and invasive squamous cell carcinoma (SCC) of the lung, and compared these with expression profiles generated from both bronchial epithelium, and precancerous metaplastic and dysplastic lesions using Ingenuity Pathway Analysis. Expression of genes associated with epidermal development, and loss of expression of genes associated with mucociliary biology, are predominant features of CIS, largely shared with precancerous lesions. Additionally, expression of genes associated with xenobiotic metabolism/detoxification is a notable feature of CIS, and is largely maintained in invasive cancer. Genes related to tissue fibrosis and acute phase immune response are characteristic of the invasive SCC phenotype. Moreover, the data presented here suggests that tissue remodeling/fibrosis is initiated at the early stages of CIS. Additionally, this study indicates that alteration in copy-number status represents a plausible mechanism for differential gene expression in CIS and invasive SCC. Conclusions/Significance This study is the first report of large-scale expression profiling of CIS of the lung. Unbiased expression profiling of these preinvasive and invasive lesions provides a platform for further investigations into the molecular genetic events relevant to early stages of squamous NSCLC development. Additionally, up-regulated genes detected at extreme differences between CIS and invasive cancer may have potential to serve as biomarkers for early detection.
Agouti Revisited: Transcript Quantification of the ASIP Gene in Bovine Tissues Related to Protein Expression and Localization

Beside its role in melanogenesis, the agouti signaling protein (ASIP) has been related to obesity. The potentially crucial role in adipocyte development makes it a tempting candidate for economic relevant, fat related traits in farm animals. The objective of our study was to characterize the mRNA expression of different ASIP transcripts and of putative targets in different bovine tissues, as well as to study consequences on protein abundance and localization. ASIP mRNA abundance was determined by RT-qPCR in adipose and further tissues of cattle representing different breeds and crosses. ASIP mRNA was up-regulated more than 9-fold in intramuscular fat of Japanese Black cattle compared to Holstein (p<0.001). Further analyses revealed that a transposon-derived transcript was solely responsible for the increased ASIP mRNA abundance. This transcript was observed in single individuals of different breeds indicating a wide spread occurrence of this insertion at the ASIP locus in cattle. The protein was detected in different adipose tissues, skin, lung and liver, but not in skeletal muscle by Western blot with a bovine-specific ASIP antibody. However, the protein abundance was not related to the observed ASIP mRNA over-expression. Immuno-histochemical analyses revealed a putative nuclear localization of ASIP additionally to the expected cytosolic signal in different cell types. The expression of melanocortin receptors (MCR) 1 to 5 as potential targets for ASIP was analyzed by RT-PCR in subcutaneous fat. Only MC1R and MC4R were detected indicating a similar receptor expression like in human adipose tissue. Our results provide evidence for a widespread expression of ASIP in bovine tissues at mRNA and, for the first time, at protein level. ASIP protein is detectable in adipocytes as well as in further cells of adipose tissue. We generated a basis for a more detailed investigation of ASIP function in peripheral tissues of various mammalian species.
The Role of Structural Information for Designing Navigational User Interfaces

Today, a variety of user interfaces exists for navigating information spaces, including, for example, tag clouds, breadcrumbs, subcategories and others. However, such navigational user interfaces are only useful to the extent that they expose the underlying topology---or network structure---of the information space. Yet, little is known about which topological clues should be integrated in navigational user interfaces. In detail, the aim of this paper is to identify what kind of and how much topological information needs to be included in user interfaces to facilitate efficient navigation. We model navigation as a variation of a decentralized search process with partial information and study its sensitivity to the quality and amount of the structural information used for navigation. We experiment with two strategies for node selection (quality of structural information provided to the user) and different amount of information (amount of structural information provided to the user). Our experiments on four datasets from different domains show that efficient navigation depends on the kind of structural information utilized. Additionally, node properties differ in their quality for augmenting navigation and intelligent pre-selection of which nodes to present in the interface to the user can improve navigational efficiency. This suggests that only a limited amount of high quality structural information needs to be exposed through the navigational user interface.
Determination of oleanolic acid and ursolic acid in Chinese medicinal plants using HPLC with PAH polymeric C18

Background: The RP-HPLC resolution of two triterpenic acid isomers was unstable. Objective: To separate the oleanolic acid (OA) and ursolic acid (UA) simply within RP-HPLC. Materials and Methods: The separation ability of five stationary phases was studied with the retention effect of their carbon loads. Also the resolution effects of mobile phase composition and different column temperatures were systematically investigated by using Drylab® (Rheodyne LLC.) after evaluating chromatograms automatically. Results: The best available resolution of two bioactive isomers was achieved (r = 3.4) via using PAH (polycyclic aromatic hydrocarbons) polymeric C18 bonded phase column. The chromatographic system was applied to the quantification in ten Chinese medicinal plants and the validation was carried out and the precision (RSD ≤1.34%), the linearity (r ≥ 0.9998) and the recovery (range from 92.1% to 102.6%) were acceptable. Conclusion: It is clear that the method was simple, rapid and reliable for the quantification of two compounds in new HPLC method within PAH polymeric C18.
Integrated classification of inflammatory myopathies

Inflammatory myopathies comprise a multitude of diverse diseases, most often occurring in complex clinical settings. To ensure accurate diagnosis, multidisciplinary expertise is required. Here, we propose a comprehensive myositis classification that incorporates clinical, morphological and molecular data as well as autoantibody profile. This review focuses on recent advances in myositis research, in particular, the correlation between autoantibodies and morphological or clinical phenotypes that can be used as the basis for an ‘integrated’ classification system.
Peginterferon α in the treatment of chronic hepatitis B

Introduction: Hepatitis B virus (HBV) infection is a global health problem. Peginterferon α (PEG-IFN), which includes PEG-IFN α-2a (Pegasys) and PEG-IFN α-2b (Peg-Intron), can be used to treat patients with chronic hepatitis B (CHB) infection. A finite duration of PEG-IFN therapy may lead to long-term viral suppression. Clinically, it is important to identify super-responders and null-responders to PEG-IFN due to its substantial side effects. Areas covered: From the literature review, it is known that PEG-IFN is more effective for hepatitis B e antigen (HBeAg)-positive patients who have high pre-treatment alanine aminotransferase level, lower HBV DNA level and genotype A (vs genotype D), as well as those with more favourable viral predictors, such as precore stop codon or basal core promoter mutants infections in Asian patients and wild-type virus in Caucasian patients. For HBeAg-positive patients and HBeAg-negative patients with genotype D infection, PEG-IFN therapy could be terminated early at week 12 or 24 in primary non-responders defined by the Hepatitis B surface antigen stopping rules. With regard to host factors, single nucleotide polymorphisms of IL28B do not seem to affect the treatment outcomes in Asian patients, but its role in Caucasian patients remains disputed. Expert opinion: Most of the known predictors need validation by large prospective trials. In addition, we need to identify more baseline predictors for super-responders in order to achieve personalised PEG-IFN treatment for CHB.
Physical and Electronic Properties of Nanoscale 2D Materials

OF DISSERTATION PHYSICAL AND ELECTRONIC PROPERTIES OF NANOSCALE 2D MATERIALS There is a great push towards reducing the size scale of both electronic components and machines. Two dimensional materials, such as graphene, are ideal candidates towards this push, as they are naturally atomically thin. In the case of nanoscale machines, the mechanical properties of the material surfaces become increasingly important. The use of laminar materials, such as graphene and MoS2, to modify the surface properties, yet maintain nanoscale topographical features, are very attractive. Towards this goal, we have investigated the surface properties of MoS2 at the nanoscale using Lateral Force Microscopy (LFM). In these investigations, we measure periodic frictional features with periodicity of ∼ 4 nm. Ultrashort devices that incorporate atomically thin components have the potential to be the smallest electronics. Such extremely scaled devices are expected to show ballistic nonlinear behavior that could make them tremendously useful for ultra fast electronic applications. We report nonlinear electron transport in ultrashort channel graphene devices. We observe this nonlinear response up to room temperature, with zero applied magnetic field, on a readily accessible oxide substrate. This makes the nanogap technology we utilize of great potential for achieving extremely scaled high-speed atomically thin devices.
GWAS Identifies Novel Susceptibility Loci on 6p21.32 and 21q21.3 for Hepatocellular Carcinoma in Chronic Hepatitis B Virus Carriers

Genome-wide association studies (GWAS) have recently identified KIF1B as susceptibility locus for hepatitis B virus (HBV)–related hepatocellular carcinoma (HCC). To further identify novel susceptibility loci associated with HBV–related HCC and replicate the previously reported association, we performed a large three-stage GWAS in the Han Chinese population. 523,663 autosomal SNPs in 1,538 HBV–positive HCC patients and 1,465 chronic HBV carriers were genotyped for the discovery stage. Top candidate SNPs were genotyped in the initial validation samples of 2,112 HBV–positive HCC cases and 2,208 HBV carriers and then in the second validation samples of 1,021 cases and 1,491 HBV carriers. We discovered two novel associations at rs9272105 (HLA-DQA1/DRB1) on 6p21.32 (OR = 1.30, P = 1.13×10−19) and rs455804 (GRIK1) on 21q21.3 (OR = 0.84, P = 1.86×10−8), which were further replicated in the fourth independent sample of 1,298 cases and 1,026 controls (rs9272105: OR = 1.25, P = 1.71×10−4; rs455804: OR = 0.84, P = 6.92×10−3). We also revealed the associations of HLA-DRB1*0405 and 0901*0602, which could partially account for the association at rs9272105. The association at rs455804 implicates GRIK1 as a novel susceptibility gene for HBV–related HCC, suggesting the involvement of glutamate signaling in the development of HBV–related HCC.
Arabidopsis thaliana as a model for the study of plant–virus co-evolution

Understanding plant–virus coevolution requires wild systems in which there is no human manipulation of either host or virus. To develop such a system, we analysed virus infection in six wild populations of Arabidopsis thaliana in Central Spain. The incidence of five virus species with different life-styles was monitored during four years, and this was analysed in relation to the demography of the host populations. Total virus incidence reached 70 per cent, which suggests a role of virus infection in the population structure and dynamics of the host, under the assumption of a host fitness cost caused by the infection. Maximum incidence occurred at early growth stages, and co-infection with different viruses was frequent, two factors often resulting in increased virulence. Experimental infections under controlled conditions with two isolates of the most prevalent viruses, cauliflower mosaic virus and cucumber mosaic virus, showed that there is genetic variation for virus accumulation, although this depended on the interaction between host and virus genotypes. Comparison of QST-based genetic differentiations between both host populations with FST genetic differentiation based on putatively neutral markers suggests different selection dynamics for resistance against different virus species or genotypes. Together, these results are compatible with a hypothesis of plant–virus coevolution.
Commitment-based and dialogue-game-based protocols: new trends in agent communication languages

This survey introduces existing approaches to Agent Communication Languages (ACLs) and particularly Conversation Policies (CPs) which can be viewed as general constraints on the sequence of semantically coherent messages leading to a goal. Then limitations of these CPs are discussed in detail, particularly limitations on flexibility and specification. Finally, ACLs are viewed from the dialectic point of view, and some approaches are introduced in this context: some focusing on commitment-based protocols and others on dialogue-game-based protocols.
The Modulation of Rifampin Action against Staphylococcus Epidermidis Biofilms by Drug Additives to Peritoneal Dialysis Solutions

Many drugs are added to peritoneal dialysis solutions In continuous ambulatory peritoneal dialysis (CAPD) patients, principally during episodes of peritonitis when antibiotics and nonantiblotic agents are often administered together. To evaluate the Influence of nonantiblotic drug additives on antibiotic action, we determined the effect of ten drug additives on the antimicrobial activity of rifampin against S. epidermiddis biofilms. None of the additives had any direct effect on biofilm bacteria. While five additives did not affect rifampin action, the other five strongly antagonized rifampin. Insulin and heparin were among these five antagonists. This antagonism suggests that a significant degree of Inhibition of antibiotic action may occur by the coadministration of agents In the treatment of peritonitis, particularty in diabetic patients.
Reduced Spontaneous Eye Blink Rates in Recreational Cocaine Users: Evidence for Dopaminergic Hypoactivity

Chronic use of cocaine is associated with a reduced density of dopaminergic D2 receptors in the striatum, with negative consequences for cognitive control processes. Increasing evidence suggests that cognitive control is also affected in recreational cocaine consumers. This study aimed at linking these observations to dopaminergic malfunction by studying the spontaneous eyeblink rate (EBR), a marker of striatal dopaminergic functioning, in adult recreational users and a cocaine-free sample that was matched on age, race, gender, and personality traits. Correlation analyses show that EBR is significantly reduced in recreational users compared to cocaine-free controls, suggesting that cocaine use induces hypoactivity in the subcortical dopamine system.
A comparison of genetic programming feature extraction languages for image classification

Visual pattern recognition and classification is a challenging computer vision problem. Genetic programming has been applied towards automatic visual pattern recognition. One of the main factors in evolving effective classifiers is the suitability of the GP language for defining expressions for feature extraction and classification. This research presents a comparative study of a variety of GP languages suitable for classification. Four different languages are examined, which use different selections of image processing operators. One of the languages does block classification, which means that an image is classified as a whole by examining many blocks of pixels within it. The other languages are pixel classifiers, which determine classification for a single pixel. Pixel classifiers are more common in the GP-vision literature. We tested the languages on different instances of Brodatz textures, as well as aerial and camera images. Our results show that the most effective languages are pixel-based ones with spatial operators. However, as is to be expected, the nature of the image will determine the effectiveness of the language used.
Industry learning environments and the heterogeneity of firm performance

This paper characterizes inter-industry heterogeneity in rates of learning-by-doing and examines how industry learning rates are connected with firm performance. Using data from the Census Bureau and Compustat, we measure the industry learning rate as the coefficient on cumulative output in a production function. We find that learning rates vary considerably among industries and are higher in industries with greater R&D, advertising, and capital intensity. More importantly, we find that higher rates of learning are associated with wider dispersion of Tobin’s q and profitability among firms in the industry. Together, these findings suggest that learning intensity represents an important characteristic of the industry environment.
PSFC / JA-10-18 Using mixed gases for massive gas injection disruption mitigation on Alcator C -

Mixed gases are used for massive gas injection disruption mitigation on Alcator C-Mod in order to optimize radiation efficiency, halo current reduction, and response time. Gas mixtures of helium and argon (argon fraction 0–50%) are investigated in detail, as well as mixtures of deuterium, argon, krypton, and helium. Experiments show that injecting He/Ar mixtures leads to faster thermal and current quenches than with pure helium or argon injection, thus improving the time response of the disruption mitigation system and reducing the halo current. Small fractions of argon (∼5–10%) in helium also lead to optimized radiation fractions with large electron density increases in the core plasma. These results are consistent with the expectation that small fractions of argon will be entrained with the faster helium in the early phases of gas flow. The gas mixing allows one to simultaneously exploit the fast particle delivery rate of light helium gas and the large radiation capability of argon. PACS numbers: 28.52. -s, 51.10. +y, 52.25. Vy, 52.25. Ya, 52.55. Fa Submitted to: Nuclear Fusion ‡ to whom correpondence should be addressed. § current address: Roswell Park Cancer Institute, Buffalo, New York, USA MGI with mixed gases on C-Mod 2
Prednisone response is the strongest predictor of treatment outcome in infant acute lymphoblastic leukemia.

To define prognostic factors in infant acute lymphoblastic leukemia (ALL), the outcome of 106 infants (age </=12 months) during 3 consecutive multicenter trials of the Berlin-Frankfurt-Münster group (ALL-BFM 83, 86, and 90) was retrospectively analyzed according to presenting features and early in vivo response to prednisone. The prednisone response was defined as the cytoreduction (number of blood blasts per microliter at day 8) to a 7-day prednisone prephase and 1 intrathecal dose of methotrexate on day 1. Prednisone good responder (PGR; <1,000 blasts/microL) received conventional therapy and prednisone poor responder (PPR; >/=1,000 blasts/microL) received intensified therapy. Infant ALL was characterized by a high incidence of a white blood cell count greater than 100 x 10(3)/microL (57%), central nervous system leukemia (24%), lack of CD10 expression (59%), 11q23 rearrangement (49%) including the translocation t(4;11) (29%), and a comparatively high proportion of PPR (26%), which were all significantly associated with inferior outcome by univariate analysis. The estimated probability for an event-free survival at 6 years (pEFS) was by far better for PGR compared with PPR, who had a dismal prognosis despite intensified treatment (pEFS, 53% +/- 6% v 15% +/- 7%, P =.0001). Infant PGR, who were less than 6 months of age (n = 40), lacked CD10 expression (n = 43), and/or had an 11q23 rearrangement (n = 17) fared significantly better compared with corresponding PPR, as indicated by a pEFS of 44% +/- 8%, 49% +/- 8%, and 41% +/- 12%, respectively. In multivariate analysis, PPR was the strongest adverse prognostic factor (relative risk, 3.3; 95% confidence interval, 1.9 to 5.8; P <.0001). Infants with PGR, comprising a major subgroup (74%) among infants, might successfully be treated with conventional therapy, whereas PPR require new therapeutic strategies, including early treatment intensification or bone marrow transplantation in first remission.
Biomechanical Properties of the Transverse Carpal Ligament

BIOMECHANICAL PROPERTIES OF THE TRANSVERSE CARPAL LIGAMENT Allan Walter Brett Advisors: University of Guelph, 2013 Dr. Michele Oliver Dr. Karen Gordon The mechanical properties of the transverse carpal ligament (TCL) have yet to be comprehensively measured. Failure strain, failure load, ultimate strength, stiffness and elastic modulus were reported from uniaxial tensile tests. On human cadaveric TCLs, failure strain was significantly higher in female specimens compared to males. Moreover, regional strain analysis showed the lateral end of the tissue to strain significantly more than the medial. Biaxial testing at three different tissue depths was also carried out. Mechanical properties were found to vary significantly by depth with the deeper layers displaying higher mechanical properties. A significant difference with respect to loading direction was also observed with the medial/lateral direction displaying higher mechanical properties than proximal/distal. These results provide mechanical properties which can be incorporated into finite element models or constitutive models of the TCL. Furthermore, this work provides a basis for recommendations for noninvasive treatment options for carpal tunnel syndrome.