gebhart/patrepeval huggingface dataset:
c-FLIP downregulation contributes to apoptosis induction by the novel synthetic triterpenoid methyl-2-cyano-3, 12-dioxooleana-1, 9-dien-28-oate (CDDO-Me) in human lung cancer cells (2007)

The novel synthetic triterpenoid methyl-2-cyano-3, 12-dioxooleana-1, 9-dien-28-oate (CDDO-Me) induces apoptosis of cancer cells, enhances tumor necrosis factor-related apoptosis-inducing ligand (TRAIL)-induced apoptosis, and exhibits potent anticancer activity in animal models with a favorable pharmacokinetic profile. Thus, CDDO-Me is being tested in Phase I clinical trials. In an effort to understand the mechanism by which CDDO-Me induces apoptosis, particularly in human lung cancer cells, we previously demonstrated that CDDO-Me induces apoptosis involving c-Jun N-terminal kinase (JNK)-dependent upregulation of death receptor 5 (DR5) expression. In the current work, we determined the modulatory effects of CDDO-Me on the levels of c-FLIP, a major inhibitor of death receptor-mediated caspase-8 activation, and its impact on CDDO-Me-induced apoptosis and enhancement of TRAIL-induced apoptosis in human lung cancer cells. CDDO-Me rapidly and potently decreased c-FLIP levels including both long (FLIP(L)) and short (FLIP(S)) forms of c-FLIP in multiple human lung cancer cell lines. The presence of the proteasome inhibitor MG132, but not the JNK inhibitor SP600125, prevented CDDO-Me-induced c-FLIP reduction. Moreover, CDDO-Me increased ubiquitination of c-FLIP. Thus, CDDO-Me induces ubiquitin/proteasome-dependent c-FLIP degradation independently of JNK activation. Importantly, overexpression of c-FLIP (e.g., FLIP(L)) protected cells not only from CDDO-Me-induced apoptosis, but also from induction of apoptosis by the combination of CDDO-Me and TRAIL. Accordingly, silencing of c-FLIP with c-FLIP siRNA sensitized cancer cells to CDDO-Me. Collectively, these results indicate that c-FLIP downregulation contributes to CDDO-Me-initiated apoptosis and also to enhancement of TRAIL-induced apoptosis by CDDO-Me.
Second Structural Motif for Recognition of DNA by Oligonucleotide-Directed Triple-Helix Formation (1991)

Relative orientations of the DNA strands within a purine.purine.pyrimidine triple helix have been determined by affinity cleaving. A purine-rich oligonucleotide bound in the major groove of double-helical DNA antiparallel to the Watson-Crick purine strand. Binding depended upon the concentration of multivalent cations such as spermine or Mg2+, and appeared to be relatively independent of pH. Two models with specific hydrogen-bonding patterns for base triplets (G.GC, A.AT, and T.AT) are proposed to explain the sequence specificity of binding. The two models differ in the conformation about the glycosyl bond (syn or anti) and the location of the phosphate-deoxyribose backbone in the major groove of DNA. This motif broadens the structural frameworks available as a basis for the design of sequence-specific DNA binding molecules.
Cytotoxic T lymphocyte antigen 4 expression in human breast cancer: implications for prognosis (2015)

To examine the relationship between cytotoxic T lymphocyte antigen 4 (CTLA-4) expression and breast cancer prognosis, CTLA-4 expression was immunohistochemically detected in paraffin-embedded specimens of primary tumors from 130 patients with breast cancer who had a mean follow-up period of 112 months. CTLA-4 expressed in cytoplasm of breast cancer cells and in cytoplasm and cell membranes of interstitial lymphocytes. Univariate analysis (log-rank) associated higher density of interstitial CTLA-4(+) lymphocytes with longer DFS and OS, but higher tumor CTLA-4 expression with shorter OS. After controlling for age, clinical stage, Scarff-Bloom-Richardson grade, tumor thrombus, ER, PR, HER2 and Ki-67, multivariate analysis (Cox) showed that density of interstitial CTLA-4(+) lymphocytes independently predicted longer DFS (HR 0.315, P = 0.002) and OS (HR 0.313, P = 0.005), whereas tumor CTLA-4 expression independently predicted shorter DFS (HR 2.176, P = 0.029) and OS (HR 2.820, P = 0.007), i.e., patients with high CTLA-4(+) lymphocyte density and CTLA-4(low) tumor cells had the best prognoses. These results indicated that CTLA-4 expression in lymphocytes was associated with better prognosis, but that in tumor cells was associated with worse prognosis. Patients' CTLA-4 profiles might thus be used to predict the benefits and toxicity of CTLA-4 blockade.
Development of a Traffic Information System using Ad-hoc Control and DSRC based V2V Communication (2013)

Since 1971, a number of articles have been published regarding the complications encountered with laser surgery of the larynx. Most investigations focus on complications such as accidental burns caused by the reflection of the laser beam, endotracheal explosion, special anesthesiologic problems, edema of the mucosa leading to airway obstruction, and abnormal scar formation with functional problems. Secondary hemorrhage has played a subordinate role, and in the few articles that have focused on it, cases requiring postoperative treatment have been reported only sporadically. All of these cases occurred within the first postoperative week, and no case resulting in the death of a patient was reported. We describe a patient in whom a lethal secondary hemorrhage occurred 10 days after a laser supraglottic laryngectomy. Because of the increase of laser applications in the treatment of laryngeal carcinoma, similar complications may be encountered. We comment on possible pathophysiological mechanisms and consequences.
PET and MRI of Metastatic Peritoneal and Pulmonary Colorectal Cancer in Mice with Human Epidermal Growth Factor Receptor 1–Targeted 89Zr-Labeled Panitumumab (2012)

The potential utility of (89)Zr-panitumumab in assessing HER1 status in distant metastases and understanding the variations in antibody uptake at different lesion sites is demonstrated in this study. (89)Zr-panitumumab can play a vital role in patient stratification and immunotherapy and therefore warrants further investigation for clinical translation.
Clustering user queries of a search engine (2001)

Article Share on Clustering user queries of a search engine Authors: Ji-Rong Wen Microsoft Research, China, 5F, Beijing Sigma Center, No.49, Zhichun Road Haidian District, Beijing, P.R.China Microsoft Research, China, 5F, Beijing Sigma Center, No.49, Zhichun Road Haidian District, Beijing, P.R.ChinaView Profile , Jian-Yun Nie Dept. Informatique et Recherche, opérationnelle, University of Montreal, CP 6128, succursale Centre-ville, Montreal, H3C 3J7 Canada Dept. Informatique et Recherche, opérationnelle, University of Montreal, CP 6128, succursale Centre-ville, Montreal, H3C 3J7 CanadaView Profile , Hong-Jiang Zhang Microsoft Research, China, 5F, Beijing Sigma Center, No.49, Zhichun Road Haidian District, Beijing, P.R.China Microsoft Research, China, 5F, Beijing Sigma Center, No.49, Zhichun Road Haidian District, Beijing, P.R.ChinaView Profile Authors Info & Claims WWW '01: Proceedings of the 10th international conference on World Wide WebMay 2001 Pages 162–168https://doi.org/10.1145/371920.371974Online:01 April 2001Publication History 276citation2,916DownloadsMetricsTotal Citations276Total Downloads2,916Last 12 Months62Last 6 weeks2 Get Citation AlertsNew Citation Alert added!This alert has been successfully added and will be sent to:You will be notified whenever a record that you have chosen has been cited.To manage your alert preferences, click on the button below.Manage my Alerts New Citation Alert!Please log in to your account Save to BinderSave to BinderCreate a New BinderNameCancelCreateExport CitationPublisher SiteGet Access
The arginine-rich domain of hepatitis B virus precore and core proteins contains a signal for nuclear transport (1990)

Precore and core proteins are two related co-carboxy-terminal proteins of hepatitis B virus. Precore protein contains the entire sequence of core protein plus an amino-terminal extension of 29 amino acid residues. Both proteins can display a common antigenic determinant known as core antigen (HBcAg). Clinically, HBcAg is detected in the nucleus, cytoplasm, or both of hepatitis B virus-infected hepatocytes. In order to understand the mechanism that regulates nuclear transport of HBcAg, various portions of precore and core proteins were linked to a reporter protein, human alpha-globin, and expressed in mammalian cells. Our results indicate that the precore protein-specific sequence, although important for nuclear transport, does not contain a nuclear localization signal. Instead, a signal for nuclear transport is located near the carboxy termini of precore and core proteins in the arginine-rich domain. This signal is made up of a set of two direct PRRRRSQS repeats and is highly conserved among mammalian hepadnaviruses.
Milliwatt power deep ultraviolet light-emitting diodes over sapphire with emission at 278 nm (2002)

We report on AlGaN multiple-quantum-well (MQW)-based deep ultraviolet light-emitting diodes over sapphire with peak emission at 278 nm. A new buffer layer growth process was used to reduce the number of defects and hence the nonradiative recombination. The improved material quality and carrier confinement resulted in pulsed powers as high as 3 mW at 278 nm and a significantly reduced deep-level-assisted long-wavelength emission.
A short history of ionic liquids—from molten salts to neoteric solvents (2002)

Ionic liquids, defined here as salts with melting temperatures below 100 °C, evolved from traditional high temperature molten salts. Some materials we would now recognize as ionic liquids were observed as far back as the mid 19th century. The quest for useful molten salts with lower melting temperatures led to inorganic chloroaluminates, to organic chloroaluminates, then to the water and air stable salts now being developed for green chemistry applications.
IL‐1, IL‐18, and IL‐33 families of cytokines (2008)

The interleukin-1 (IL-1), IL-18, and IL-33 families of cytokines are related by mechanism of origin, receptor structure, and signal transduction pathways utilized. All three cytokines are synthesized as precursor molecules and cleaved by the enzyme caspase-1 before or during release from the cell. The NALP-3 inflammasome is of crucial importance in generating active caspase-1. The IL-1 family contains two agonists, IL-1alpha and IL-1beta, a specific inhibitor, IL-1 receptor antagonist (IL-1Ra), and two receptors, the biologically active type IL-1R and inactive type II IL-1R. Both IL-1RI and IL-33R utilize the same interacting accessory protein (IL-1RAcP). The balance between IL-1 and IL-1Ra is important in preventing disease in various organs, and excess production of IL-1 has been implicated in many human diseases. The IL-18 family also contains a specific inhibitor, the IL-18-binding protein (IL-18BP), which binds IL-18 in the fluid phase. The IL-18 receptor is similar to the IL-1 receptor complex, including a single ligand-binding chain and a different interacting accessory protein. IL-18 provides an important link between the innate and adaptive immune responses. Newly described IL-33 binds to the orphan IL-1 family receptor T1/ST2 and stimulates T-helper 2 responses as well as mast cells.
The RD1 virulence locus of Mycobacterium tuberculosis regulates DNA transfer in Mycobacterium smegmatis (2004)

Conjugal DNA transfer occurs by an atypical mechanism in Mycobacterium smegmatis. The transfer system is chromosomally encoded and requires recipient recombination functions for both chromosome and plasmid transfer. Cis-acting sequences have been identified that confer mobility on nontransferable plasmids, but these are larger and have different properties to canonical oriT sites found in bacterial plasmids. To identify trans-acting factors required for mediating DNA transfer, a library of transposon insertion mutants was generated in the donor strain, and individual mutants were screened for their effect on transfer. From this screen, a collection of insertion mutants was isolated that increased conjugation frequencies relative to wild type. Remarkably, the mutations map to a 25-kb region of the M. smegmatis chromosome that is syntenous with the RD1 region of Mycobacterium tuberculosis, which is considered to be the primary attenuating deletion in the related vaccine strain Mycobacterium bovis bacillus Calmette-Guérin. The genes of the RD1 region encode a secretory apparatus responsible for exporting Cfp10- and Esat-6, both potent antigens and virulence factors. In crosses using two M. smegmatis donors, we show that wild-type cells can suppress the elevated transfer phenotype of mutant donors, which is consistent with the secretion of a factor that suppresses conjugation. Most importantly, the RD1 region of M. tuberculosis complements the conjugation phenotype of the RD1 mutants in M. smegmatis. Our results indicate that the M. tuberculosis and M. smegmatis RD1 regions are functionally equivalent and provide a unique perspective on the role of this critical secretion apparatus.
Identification of novel targeting peptides for human ovarian cancer cells using “one-bead one-compound” combinatorial libraries (2005)

Using "one-bead one-compound" combinatorial chemistry technology, we generated random peptide libraries containing millions of 90 mum TentaGel beads, each with its own unique amino acid sequence. A cyclic random 8-mer library was screened with CAOV-3 (a human ovarian adenocarcinoma cell line) and beads with a unique ligand that bind to the cell surface receptors were coated by one or more layers of cells. These positive beads were isolated, stripped, and microsequenced. Several peptide motifs were identified from these screenings, some of which were novel and unique, e.g., cDGX(4)GX(6)X(7)c. Structure-activity relationship studies of this peptide revealed that the l-aspartate residue at position 2, the two glycines at positions 3 and 5, and the two d-cysteines at the amino and COOH terminus are critical for activity. In addition, a hydrophobic residue was preferred at position X(4), whereas amino acids at positions X(6) and X(7) were more variable. Binding of this peptide to a number of different cancer cell lines and normal cells was also determined and we observed that peptides with this motif bound preferentially to three other human ovarian cancer cell lines (ES-2, SKOV-3, and OVCAR-3) as well as a human glioblastoma cancer cell line (A172). Structural analysis of the peptides using high-resolution nuclear magnetic resonance spectroscopy revealed strong conformational similarity among all peptides with cX(1)GX(4)GX(6)X(7)c motif. Blocking study with a panel of anti-integrin antibodies strongly suggests alpha3 integrin present on these ovarian adenocarcinoma cells is the target receptor for this peptide.
Fluorescence Ratio Imaging Microscopy Shows Decreased Access of Vancomycin to Cell Wall Synthetic Sites in Vancomycin-Resistant Staphylococcus aureus (2007)

A new method of fluorescence ratio imaging microscopy was used to compare the in vivo binding capacity and the access of a fluorescent derivative of vancomycin to the cell wall synthetic sites in isogenic pairs of vancomycin-susceptible and -resistant laboratory mutants and vancomycin-intermediate and -susceptible clinical isolates of Staphylococcus aureus. Live cells of resistant strains were found to bind approximately 1.5 times more antibiotic, but there was no correlation between the increased binding capacity and the MICs of the strains. In both susceptible and resistant bacteria, the subcellular sites of wall synthesis were localized to the division septa, but the rate of diffusion of drug molecules to these sites was reduced in resistant cells. The findings allow a reinterpretation of the mechanism of vancomycin resistance in which the path of vancomycin to its lethal target (lipid II) is considered to be through the division septum and therefore is dependent on the stage of the staphylococcal cell cycle.
Transcriptional organization, regulation and role of the Porphyromonas gingivalis W83 hmu haemin-uptake locus (2006)

Porphyromonas gingivalis, an oral bacterium associated with periodontal disease, requires haemin for growth. Although several multigenic clusters encoding haemin-uptake systems are present on the genome of P. gingivalis, little is known regarding their transcriptional organization and expression. This study identified a 23 kDa iron-regulated haemin-binding protein encoded by a larger than previously reported variant of hmuY. It was shown that the hmu locus is larger than previously reported and is composed of six genes, hmuYRSTUV, encoding a novel hybrid haemin-uptake system. The locus has an operonic organization and the transcriptional start site is located 292 bp upstream of hmuY. The data indicate that the regulation of the operon is iron-dependent. Interestingly, differential regulation within the operon was demonstrated, resulting in excess of the hmuYR message encoding the outer-membrane proteins when compared to the full-length transcript. In addition, the hmuY transcript is more prevalent than the hmuR transcript. Secondary structure analysis of the hmuYRSTUV mRNA predicted the formation of several potential stem-loops in the 5' ends of hmuR- and hmuS-specific mRNAs, consistent with the differential regulation observed. Finally, it was demonstrated that haemin binding and uptake are elevated in iron-depleted conditions and are reduced 45 % and 70 %, respectively, in an hmu-deficient strain when compared to the parental strain, indicating that the hmu locus plays a major role in haemin acquisition in P. gingivalis. Since homologues of the hmu locus were also found in Bacteroides fragilis, Bacteroides thetaiotaomicron and Prevotella intermedia, these findings may have implications for a better understanding of haemin acquisition in those organisms as well.
Minicircle‐DNA production by site specific recombination and protein–DNA interaction chromatography (2008)

The results obtained in the present study demonstrate that the described technology facilitates the production of highly pure minicircle-DNA for direct application in gene therapy and vaccination. The process described is efficient, stable and suitable for further scale-up in industrial large-scale manufacturing.
International patterns of tuberculosis and the prevalence of symptoms of asthma, rhinitis, and eczema (2000)

These findings are consistent with recent experimental evidence which suggests that exposure to Mycobacterium tuberculosis may reduce the risk of developing asthma.
Ultrawideband Propagation Channels-Theory, Measurement, and Modeling (2005)

This paper presents an overview of ultrawideband (UWB) propagation channels. It first demonstrates how the frequency selectivity of propagation processes causes fundamental differences between UWB channels and "conventional" (narrowband) channels. The concept of pathloss has to be modified, and the well-known WSSUS model is not applicable anymore. The paper also describes deterministic and stochastic models for UWB channels, identifies the key parameters for the description of delay dispersion, attenuation, and directional characterization, and surveys the typical parameter values that have been measured. Measurement techniques and methods for extracting model parameters are also different in UWB channels; for example, the concepts of narrowband channel parameter estimation (e.g., maximum-likelihood estimation) have to be modified. Finally, channel models also have an important impact on the performance evaluation of various UWB systems.
PHOTOACOUSTIC TOMOGRAPHY: PRINCIPLES AND ADVANCES (Invited Review) (2014)

Photoacoustic tomography (PAT) is an emerging imaging modality that shows great potential for preclinical research and clinical practice. As a hybrid technique, PAT is based on the acoustic detection of optical absorption from either endogenous chromophores, such as oxy-hemoglobin and deoxy-hemoglobin, or exogenous contrast agents, such as organic dyes and nanoparticles. Because ultrasound scatters much less than light in tissue, PAT generates high-resolution images in both the optical ballistic and diffusive regimes. Over the past decade, the photoacoustic technique has been evolving rapidly, leading to a variety of exciting discoveries and applications. This review covers the basic principles of PAT and its different implementations. Strengths of PAT are highlighted, along with the most recent imaging results.
Measurement of Cardiac Troponins (2001)

The cardiac troponins form part of the regulatory mechanism for muscle contraction. Specific cardiac isoforms of cardiac troponin T and cardiac troponin I exist and commercially available immunoassay systems have been developed for their measurement. A large number of clinical and analytical studies have been performed and the measurement of cardiac troponins is now considered the 'gold standard' biochemical test for diagnosis of myocardial damage. There have been advances in understanding the development and structure of troponins and their degradation following myocardial cell necrosis. This has contributed to the understanding of the problems with current assays. Greater clinical use has also highlighted areas of analytical and clinical confusion. The assays are reviewed based on manufacturers' information, current published material as well as the authors' in-house experience.
Reactive nitrogen species regulate autophagy through ATM-AMPK-TSC2–mediated suppression of mTORC1 (2013)

Reactive intermediates such as reactive nitrogen species play essential roles in the cell as signaling molecules but, in excess, constitute a major source of cellular damage. We found that nitrosative stress induced by steady-state nitric oxide (NO) caused rapid activation of an ATM damage-response pathway leading to downstream signaling by this stress kinase to LKB1 and AMPK kinases, and activation of the TSC tumor suppressor. As a result, in an ATM-, LKB1-, TSC-dependent fashion, mTORC1 was repressed, as evidenced by decreased phosphorylation of S6K, 4E-BP1, and ULK1, direct targets of the mTORC1 kinase. Decreased ULK1 phosphorylation by mTORC1 at S757 and activation of AMPK to phosphorylate ULK1 at S317 in response to nitrosative stress resulted in increased autophagy: the LC3-II/LC3-I ratio increased as did GFP-LC3 puncta and acidic vesicles; p62 levels decreased in a lysosome-dependent manner, confirming an NO-induced increase in autophagic flux. Induction of autophagy by NO correlated with loss of cell viability, suggesting that, in this setting, autophagy was functioning primarily as a cytotoxic response to excess nitrosative stress. These data identify a nitrosative-stress signaling pathway that engages ATM and the LKB1 and TSC2 tumor suppressors to repress mTORC1 and regulate autophagy. As cancer cells are particularly sensitive to nitrosative stress, these data open another path for therapies capitalizing on the ability of reactive nitrogen species to induce autophagy-mediated cell death.