gebhart/patrepeval huggingface dataset:
Keyword extraction for social snippets (2010)

Today, a huge amount of text is being generated for social purposes on social networking services on the Web. Unlike traditional documents, such text is usually extremely short and tends to be informal. Analysis of such text benefit many applications such as advertising, search, and content filtering. In this work, we study one traditional text mining task on such new form of text, that is extraction of meaningful keywords. We propose several intuitive yet useful features and experiment with various classification models. Evaluation is conducted on Facebook data. Performances of various features and models are reported and compared.
Structure−Activity Relationship Analysis of Peptides Targeting the EphA2 Receptor (2010)

The EphA2 receptor tyrosine kinase has emerged as a promising new therapeutic target in cancer because of its high level of expression in tumors. EphA2-specific antibodies have been used to deliver drugs and toxins to tumor cells, leading to inhibition of tumor growth and metastatic dissemination. We previously identified two related peptides, YSA and SWL, that selectively bind to the ligand-binding domain of EphA2 but not other Eph receptors and could therefore be useful as selective targeting agents. Here we characterize the two peptides and a series of derivatives. On the basis of systematic amino acid replacements, only five YSA residues appear to be critical for high-affinity receptor binding. Furthermore, a peptide comprising only the first five residues of YSA retains selectivity for EphA2. Similar to ephrin-A1, the physiological ligand for EphA2, both YSA and SWL activate EphA2 and inhibit downstream oncogenic signaling pathways in PC3 cancer cells. The two peptides and derivatives are quite stable in conditioned cell culture medium and show promise for delivering drugs and imaging agents to EphA2-expressing tumors.
Motilin induces gall bladder emptying and antral contractions in the fasted state in humans (1998)

Exogenous motilin reducted fasting gall bladder volume and increased antral contractions. After reaching maximal reduction, the gall bladder volume did not decrease further during continuous motilin infusion at higher doses and stayed at the same reduced volume. The degree of gall bladder volume reduction during motilin infusion mimicked gall bladder emptying preceding antral phase III activity of the migrating motor complex in humans. This study indicates that motilin may play a physiological role in the regulation of gall bladder emptying in the fasted state.
Immune memory redefined: characterizing the longevity of natural killer cells (2010)

Natural killer (NK) cells respond rapidly to transformed, stressed, or virally infected cells and provide a first-line immune defense against pathogen invasion and cancer. Thought to involve short-lived effector cells that are armed for battle, NK cells were not previously known to contribute in recall responses to pathogen re-encounter. Here, we highlight recent discoveries demonstrating that NK cells are not limited to driving primary immune responses to foreign antigen but can mount secondary responses contributing to immune memory. We also further characterize the phenotype and function of long-lived memory NK cells generated during viral infection.
Extended Target Sequence Specificity of PNA–Minor‐Groove Binder Conjugates (2004)

Conjugal bliss. We show that a peptide nucleic acid–Hoechst conjugate (see scheme) kinetically and sequence preferentially guides the PNA moiety to target a binding site proximal to an A–T region that has an affinity for the minor-groove binder. These results demonstrate a new strategy for constructing DNA recognition ligands composed of a sequence-guiding domain that increases the target specificity and a DNA-modification domain that determines the biological activity of the conjugate.
CD39: A complementary target to immune checkpoints to counteract tumor-mediated immunosuppression (2015)

We report that CD39-expressing-melanoma cells inhibited both T-cell proliferation and the generation of cytotoxic effectors in an adenosine-dependent manner, and that treatment with a CD39-blocking antibody alleviated tumor-mediated immunosuppression. Thus, blocking CD39 ectonucleotidase may represent a novel immunotherapeutic strategy to restore antitumor immunity.
Improved Protocol for the Preparation of Tetraselmis suecica Axenic Culture and Adaptation to Heterotrophic Cultivation (2010)

The effectiveness of various physical and chemical methods for the removal of contaminants from the microal-gae, Tetraselmis suecica, culture was investigated. The information obtained was used as the basis for the development of improved protocol for the preparation of axenic culture to be adapted to heterotrophic cultivation. Repeated centrifugation and rinsing effectively removed the free bacterial contaminants from the microalgae culture while sonication helped to loosen up the tightly attached bacterial contaminants on the microalgae cells. Removal of bacterial spores was accom- plished using a mixture of two antibiotics, 5 mg/mL vancomycine and 10 mg/mL neomycine. Walne medium formulation with natural seawater was preferred for the enhancement of growth of T. suecica. Adaptation of growth from photoautot- rophic to heterotrophic conditions was achieved by the repeated cultivation of photoautotrophic culture with sequential reduction in illumination time, and finally the culture was inoculated into the medium containing 10 g/L glucose, incu- bated in total darkness to obtain heterotrophic cells. Changes in the morphology and composition of T. suecica cells dur- ing the adaptation from photoautotrophic to heterotrophic condition, as examined under Transmission Electron Micro- scope, were also reported.
Nanoliter scale PCR with TaqMan detection (1997)

We monitored PCR in volumes of the order of 10 nl in glass microcapillaries using a fluorescence energy transfer assay in which fluorescence increases if product is made due to template-dependent nucleolytic degradation of an internally quenched probe (TaqMan assay). This assay detected single starting template molecules in dilutions of genomic DNA. The results suggest that it may be feasible to determine the number of template molecules in a sample by counting the number of positive PCRs in a set of replicate reactions using terminally diluted sample. Since the assay system is closed and potentially automatable, it has promise for clinical applications.
P2Y receptor signaling regulates phenotype and IFN-α secretion of human plasmacytoid dendritic cells (2007)

Plasmacytoid dendritic cells (PDCs) play powerful regulatory roles in innate and adaptive immune responses and are a major source of type I interferon (IFN) following viral infection. During inflammation and mechanical stress, cells release nucleotides into the extracellular space where they act as signaling molecules via G protein-coupled P2Y receptors. We have previously reported on the regulation of myeloid dendritic cell (DC) function by nucleotides. Here, we report that human PDCs express several subtypes of P2Y receptors and mobilize intracellular calcium in response to nucleotide exposure. As a functional consequence, PDCs acquire a mature phenotype that is further enhanced in the context of CD40 ligation. Strikingly, nucleotides strongly inhibit IFN-alpha secretion induced by influenza virus or CpG-A. This effect is most pronounced for the uridine nucleotides UDP and UTP and the sugar nucleotide UDP-glucose, ligands of P2Y(6), P2Y(4), and P2Y(14), respectively. Nucleotide-induced inhibition of IFN-alpha production is blocked by suramin, a P2Y receptor antagonist. Pharmacological data point toward a role of protein kinase C in the negative regulation of type I IFN. Manipulating PDC function with P2Y receptor agonists may offer novel therapeutic strategies for autoimmune diseases or cancer.
Major histocompatibility complex class II-associated peptides control the presentation of bacterial superantigens to T cells. (1996)

Recent studies have shown that only a subset of major histocompatibility complex (MHC) class II molecules are able to present bacterial superantigens to T cells, leading to the suggestion that class-II associated peptides may influence superantigen presentation. Here, we have assessed the potential role of peptides on superantigen presentation by (a) analyzing the ability of superantigens to block peptide-specific T cell responses and (b) analyzing the ability of individual peptides to promote superantigen presentation on I-Ab-expressing T2 cells that have a quantitative defect in antigen processing. A series of peptides is described that specifically promote either toxic shock syndrome toxin (TSST) 1 or staphylococcal enterotoxin A (SEA) presentation. Whereas some peptides promoted the presentation of TSST-1 (almost 5,000-fold in the case of one peptide), other peptides promoted the presentation of SEA. These data demonstrate that MHC class II-associated peptides differentially influence the presentation of bacterial superantigens to T cells.
Comb Capacitor Structures for On-Chip Physical Uncloneable Function (2009)

Planar inter-digitated comb capacitor structures are an excellent tool for on-chip capacitance measurement and evaluation of properties of coating layers with varying composition. These comb structures are easily fabricated in a single step in the last metallization layer of a standard IC process. Capacitive coupling of these structures with a coating layer is modelled based on the electric field distribution to have a detailed understanding of contributing capacitance components. The coating composition is optimized to provide maximum spread in capacitance values of comb capacitor structures. This spread in measured capacitance values can be used to implement a physical uncloneable function (PUF). A PUF is a random function which can be evaluated only with the help of a physical system. We present an on-chip capacitive PUF for chip security and data storage in which the unlock key algorithm is generated from capacitors which are physically linked to the chip in an inseparable way. The strength of this key increases with the spread in capacitance values and measurement accuracy.
Primary structure and properties of the Na+/glucose symporter (Sg1S) of Vibrio parahaemolyticus (1997)

Previously, we cloned and sequenced a DNA fragment from Vibrio parahaemolyticus and found four open reading frames (ORFs). Here, we clearly demonstrate that one of the ORFs, ORF1, is the gene (sglS) encoding a Na+/glucose symporter (SglS). We characterize the Na+/glucose symporter produced in Escherichia coli mutant (JM1100) cells which lack original glucose transport activity and galactose transport activity. We also show that phlorizin, a potent inhibitor of the SGLT1 Na+/glucose symporter of animal cells, inhibited glucose transport, but not galactose transport, via the SglS system.
Differential expression of carcinoembryonic antigen in early gastric adenocarcinomas versus benign gastric lesions defined by monoclonal antibodies reactive with restricted antigen epitopes. (1987)

Murine monoclonal antibodies (MAbs) reactive with distinct epitopes on carcinoembryonic antigen (CEA) have been analyzed systematically by radioimmunoassays, Western blotting, and immunohistochemical assays to define CEA expression in adenocarcinomas, benign lesions, and normal tissues of the stomach. Each of four COL-MAbs (COL-1, COL-4, COL-6, and COL-12) reacted preferentially with cell extracts of adenocarcinomas versus those of normal mucosae in solid-phase radioimmunoassays. Using Western blotting analyses MAbs COL-1, COL-4, COL-6, and COL-12 detected only the Mr 180,000 molecule characteristic of CEA in adenocarcinoma of the stomach; no reactivity was observed in an extract of normal gastric mucosa. Antibody competition radioimmunoassays were then carried out to define relations among COL-MAbs using 125I-radiolabeled MAbs, and nonradiolabeled MAbs as competitors. A spectrum of formalin-fixed, paraffin-embedded normal, benign, and malignant tissue sections of the stomach were examined for immunoreactivities with COL-MAbs using immunohistochemical assays to define whether the COL-MAbs were able to detect CEA expression in early foci of gastric carcinomas. All of the COL-MAbs generally demonstrated selective reactivities to adenocarcinomas (n = 40) versus benign lesions (n = 15) and normal mucosae (n = 6) of the stomach. From 72 to 100% of adenocarcinomas at early stage (n = 18) were reactive with the COL-MAbs, suggesting that these MAbs might serve as immunohistochemical diagnostic tools to detect early foci of gastric carcinoma. The data reported here indicate that the COL-MAbs can potentially be utilized as radioimmunological and immunohistochemical adjuncts to differentiate early adenocarcinomas from normal mucosae or benign lesions of the stomach on the basis of differential CEA expression.
Association between TAFI antigen and Ala147Thr polymorphism of the TAFI gene and the angina pectoris incidence (2003)

Summary Thrombin activatable fibrinolysis inhibitor (TAFI), a recently described inhibitor of fibrinolysis, has been hypothesized as playing a role in atherothrombosis. However, the evidence from retrospective studies, which have evaluated the role of TAFI in vascular risk, is conflicting. In a prospective cohort (the PRIME Study) of nearly 10 000 apparently healthy men recruited in France (Lille, Strasbourg, Toulouse) and Northern Ireland (Belfast), we measured baseline plasma concentration of TAFI antigen among 143 participants (81 from France and 62 from Ireland) who subsequently developed angina pectoris and among 286 age-matched participants who remained free of disease during the 5 years of follow-up. Genotyping of the Ala147Thr polymorphism located in the TAFI gene was performed using an allele specific PCR. In France, mean levels of TAFI were significantly higher at baseline among men who subsequently developed angina pectoris compared with their control subjects (119 versus 107 %; p = 0.02). The risk of future angina pectoris increased with increasing tertiles of TAFI (p = 0.02), such that men in the highest tertile at study entry had a 5-fold higher relative risk than those in the lowest tertile (95% confidence interval, 1.38 to 18.58) after controlling for the conventional cardiovascular risk factors. No such difference was observed in Northern Ireland. In France, Thr/Thr carriers of the Ala147Thr polymorphism were significantly more frequent in cases than in controls (p = 0.01) leading to a relative risk of angina pectoris of 2.7 (95%CI 1.2-5.8). Increase in plasma TAFI antigen levels is a risk factor for angina pectoris in France. Genotyping for the Ala147Thr polymorphism seems to be a reliable tool to assess the risk mediated by TAFI.
Endoscopic optical coherence tomography and laser-induced fluorescence spectroscopy in a murine colon cancer model (2006)

These preliminary data indicate endoscopic OCT-LIF has the potential to identify colorectal adenomas in murine models.
Canola Quality Indian Mustard Oil (Brassica juncea) is More Stable to Oxidation than Conventional Canola Oil (Brassica napus) (2008)

Abstract Canola‐quality Indian mustard ( Brassica juncea ) is being developed as a complimentary oilseed crop to canola ( Brassica napus ) for cultivation in hot and low‐rainfall areas, where canola does not perform well. In Australia, several B. juncea breeding lines have been developed for commercial cultivation and for eventual processing as canola oil. However, there still are significant species‐based differences in the fatty acid composition with B. juncea containing lower levels of linoleic acid and higher levels of oleic and linolenic acids compared with B. napus . This has raised concern about possible oxidative stability differences between the oils. Oils (unrefined) extracted from different breeding lines of each species were subjected to accelerated autoxidation, and development of oxidative rancidity was assessed by four separate techniques: depletion of polyunsaturated fatty acids, depletion of tocopherol, development of primary oxidation products, and development of secondary oxidation products (propanal and hexanal). All the tests showed that the newly developed B. juncea oils are more stable to autoxidation than conventional canola ( B. napus ) oil, despite containing marginally higher linolenic levels. Oxidative stability does not appear to be a barrier to using oils from these emerging lines of B. juncea for partial or full replacement of conventional canola oil.
Visualization of Dystrophic Muscle Fibers in Mdx Mouse by Vital Staining with Evans Blue: Evidence of Apoptosis in Dystrophin-Deficient Muscle (1995)

Degenerating muscle fibers in the skeletal muscle of mdx mice were visualized by vital staining with Evans blue. Evans blue injected intravenously stained only degenerating muscle fibers which were visible as blue fibers macroscopically and could also be seen as red fluorescent fibers microscopically. Evans blue-stained muscle fibers were either hypercontracted or degrading. Intact or regenerating muscle fibers in mdx mice and muscle fibers in B10 control mice were not stained with the dye. DNA isolated from Evans blue-stained fibers exhibited fragmentation to approximately 180 base pairs on agarose gel electrophoresis. Such DNA fragmentation was not found in DNA from unstained muscle fibers in mdx or B10 mice. Terminal deoxynucleotidyl transferase (TdT)-mediated dUTP nick end-labeling (TUNEL)-positive myonuclei were also found in Evans blue-stained muscle fibers but not in unstained ones. These results indicate that degenerating muscle fibers in the mdx mouse show an increase in membrane permeability and undergo apoptosis. Vital staining with Evans blue is useful not only for distinguishing degenerating muscle fibers, but also for studying the degeneration process biochemically in dystrophin-deficient muscle. This method may also be useful for evaluating the therapeutic effects of drug administration, gene transfer, and myoblast transfer in the mdx mouse.
YAC transgenic mice carrying pathological alleles of the MJD1 locus exhibit a mild and slowly progressive cerebellar deficit (2002)

Machado-Joseph disease (MJD; MIM 109150) is a late-onset neurodegenerative disorder caused by the expansion of a polyglutamine tract within the MJD1 gene. We have previously reported the generation of human yeast artificial chromosome (YAC) constructs encompassing the MJD1 locus into which expanded (CAG)(76) and (CAG)(84) repeat motifs have been introduced by homologous recombination. Transgenic mice containing pathological alleles with polyglutamine tract lengths of 64, 67, 72, 76 and 84 repeats, as well as the wild type with 15 repeats, have now been generated using these YAC constructs. The mice with expanded alleles demonstrate a mild and slowly progressive cerebellar deficit, manifesting as early as 4 weeks of age. As the disease progresses, pelvic elevation becomes markedly flattened, accompanied by hypotonia, and motor and sensory loss. Neuronal intranuclear inclusion (NII) formation and cell loss is prominent in the pontine and dentate nuclei, with variable cell loss in other regions of the cerebellum from 4 weeks of age. Interestingly, peripheral nerve demyelination and axonal loss is detected in symptomatic mice from 26 weeks of age. In contrast, transgenic mice carrying the wild-type (CAG)(15) allele of the MJD1 locus appear completely normal at 20 months. Disease severity increases with the level of expression of the expanded protein and the size of the repeat. These mice are representative of MJD and will be a valuable resource for the detailed analysis of the roles of repeat length, tissue specificity and level of expression in the neurodegenerative processes underlying MJD pathogenesis.
Thermoelectric mems generators as a power supply for a body area network (2005)

Miniaturized and cost-effective thermoelectric generators (TEG) scavenging energy from environment could potentially provide power autonomy to consumer electronic products operating at low power. For example, TEG mounted in a wristwatch have been used to generate electricity from human heat. The key point of IMEC's research in this field is the realization of a body area network, consisting of a set of wireless sensors/actuators, able to provide health, sports, comfort, and safety monitoring functions to the user. The development of miniature energy scavengers built on MEMS technology is a primary goal of the ongoing research, as this will make the network truly power autonomous. In this paper, the modeling and a novel design of MEMS TEG especially conceived for human body applications are described. The design is built on the basis of a thermal model of the device, which includes the human body as one of its important elements. For this purpose, the research on human body thermal features is performed. The TEG prototype made with commercial thermopiles is tested with power conditioning electronics and a wireless module mounted on a watchstrap.
Merge Coding of Atoms for Wavelet/Matching Pursuits Image Compression (2007)

Improved coding of atoms in image compression by matching pursuits (MP) after a wavelet decomposition is achieved. The positions of atoms in the wavelet sub-bands are communicated by run length coding. The MERGE coding scheme replaces individual coding of any alphabet of symbols by dividing the symbols into groups and run length coding their positions. It is shown theoretically that the use of MERGE with an efficient run length coder approaches the theoretical entropy of an alphabet of symbols. The embedded nature of MERGE makes it a near-ideal coding scheme for the amplitudes of atoms. An additional layer of MERGE coding for the basis indices of atoms approaches the theoretical optimum and is superior to either separable or combined Huffman coding.