gebhart/patrepeval huggingface dataset:
VIPS: a Vision-based Page Segmentation Algorithm (2003)

A new web content structure analysis based on visual representation is proposed in this paper. Many web applications such as information retrieval, information extraction and automatic page adaptation can benefit from this structure. This paper presents an automatic top-down, tag-tree independent approach to detect web content structure. It simulates how a user understands web layout structure based on his visual perception. Comparing to other existing techniques, our approach is independent to underlying documentation representation such as HTML and works well even when the HTML structure is far different from layout structure. Experiments show satisfactory results. 1
Cardiac effects of electrically induced intrathoracic autonomic reflexes (1988)

Electrical stimulation of the afferent components in one cardiopulmonary nerve (the left vagosympathetic complex at a level immediately caudal to the origin of the left recurrent laryngeal nerve) in acutely decentralized thoracic autonomic ganglionic preparations altered cardiac chronotropism and inotropism in 17 of 44 dogs. Since these neural preparations were acutely decentralized, the effects were mediated presumably via intrathoracic autonomic reflexes. The lack of consistency of these reflexly generated cardiac responses presumably were due in part to anatomical variation of afferent axons in the afferent nerve stimulated. As stimulation of the afferent components in the same neural structure caudal to the heart (where cardiopulmonary afferent axons are not present) failed to elicit cardiac responses in any dog, it is presumed that when cardiac responses were elicited by the more cranially located stimulations, these were due to activation of afferent axons arising from the heart and (or) lungs. When cardiac responses were elicited, intramyocardial pressures in the right ventricular conus as well as the ventral and lateral walls of the left ventricle were augmented. Either bradycardia or tachycardia was elicited. Following hexamethonium administration no responses were produced, demonstrating that nicotonic cholinergic synaptic mechanisms were involved in these intrathoracic cardiopulmonary-cardiac reflexes. In six of the animals, when atropine was administered before hexamethonium, reflexly generated responses were attenuated. The same thing occurred when morphine was administered in four animals. In contrast, in four animals following administration of phentolamine, the reflexly generated changes were enhanced.(ABSTRACT TRUNCATED AT 250 WORDS)
The Possible Diagnostic and Prognostic Use of Systemic Chemokine Profiles in Clinical Medicine—The Experience in Acute Myeloid Leukemia from Disease Development and Diagnosis via Conventional Chemotherapy to Allogeneic Stem Cell Transplantation (2013)

Chemokines are important regulators of many different biological processes, including (i) inflammation with activation and local recruitment of immunocompetent cells; (ii) angiogenesis as a part of inflammation or carcinogenesis; and (iii) as a bridge between the coagulation system and inflammation/immune activation. The systemic levels of various chemokines may therefore reflect local disease processes, and such variations may thereby be used in the routine clinical handling of patients. The experience from patients with myeloproliferative diseases, and especially patients with acute myeloid leukemia (AML), suggests that systemic plasma/serum cytokine profiles can be useful, both as a diagnostic tool and for prognostication of patients. However, cytokines/chemokines are released by a wide range of cells and are involved in a wide range of biological processes; the altered levels may therefore mainly reflect the strength and nature of the biological processes, and the optimal clinical use of chemokine/cytokine analyses may therefore require combination with organ-specific biomarkers. Chemokine levels are also altered by clinical procedures, therapeutic interventions and the general status of the patients. A careful standardization of sample collection is therefore important, and the interpretation of the observations will require that the overall clinical context is considered. Despite these limitations, we conclude that analysis of systemic chemokine/cytokine profiles can reflect important clinical characteristics and, therefore, is an important scientific tool that can be used as a part of future clinical studies to identify clinically relevant biomarkers.
[Differential gene expression profiles of gastric cancer]. (2012)

To explore the different gene expressions of normal versus tumor tissues of gastric cancer at molecular levels.Gene chip technology was used to determine the differentially expressed genes between gastric cancer (n = 12) and normal tissues (n = 12) from December 2009 to June 2010 of Xinhua Hospital of Shanghai Jiaotong University School of Medicine. And reverse transcriptase (RT)-PCR was performed to validate the results of gene chip analysis.Sixty-nine up-regulated genes and 80 down-regulated genes were identified by significance analysis of microarrays (SAM). And these genes were correlated with cell adhesion, angiogenesis, cell proliferation and apoptosis, et al. They were also closely correlated with the signaling pathways of Wnt (1/151, 0.66%) and vascular endothelial growth factor (VEGF) (2/76, 2.63%). The differential expressions of ATP4A, CLDN10, OLFM4, SAA1 and PROK2 were confirmed by RT-PCR (0.94 ± 0.19 vs 4.33 ± 0.39, 1.00 ± 0.14 vs 3.04 ± 0.26, 5.37 ± 0.30 vs 1.02 ± 0.14, 4.37 ± 0.30 vs 0.95 ± 0.29, 2.62 ± 0.54 vs 1.35 ± 0.35, all P < 0.05).The classifier genes identified in this study may be closely correlated with the carcinogenesis of gastric cancer.
Confocal microscopy: principles and applications to the field of reproductive biology. (2001)

Confocal microscopy allows analysis of fluorescent labeled thick specimens without physical sectioning. Optical sections are generated by eliminating out-of-focus fluorescence and displayed as digitalized images. It allows 3-dimensional reconstruction (XYZ) and time-analysis (XYT), thus providing unique chance to link morphology with cell function. Since images are obtained by scanning, excess illumination of the specimen and quick decrease of the fluorescent signal are avoided. Resolution obtained with a Laser Scanning Confocal Microscopy (LSCM) is theoretically better than that of a conventional microscope. The preparation of the specimen may be based on standard techniques, such as immunocytochemistry applied to fixed cells, or on staining of living cells, following the use of different fluorescent probes at the same time (colocalization). In our laboratory, we use the LSCM system Fluoview version 2.1 (Olympus) to study reproductive biology of animals and humans. We work on stainings of oocytes and blastocysts (mouse, bovine, human), and human ovarian tissues. We study mitochondrial distribution, cortical granule migration, calcium oscillations and spindle quality to link culture conditions and oocyte quality. Staining of F-actin is used to check transzonal projections (in zona pellucida) or to detect abnormalities following experimental treatment. Blastocyst quality is analyzed in sequential optical sections for microfilament organization and counting of total cell number (staining with phalloidin (actin) and picogreen (DNA). Trophectoderm and inner cell mass distribution (differential staining), apoptotic cells (TUNEL method) and viable cells (live/dead test) are also evaluated. Confocal imaging can be helpful for rapid determination of follicle density (staining with AM Calcein) and follicle morphology (picogreen) in ovarian cortical biopsies. The current review describes the principles of confocal microscopy and illustrates its applications to the field of reproductive biology by a large collection of pictures.
Adalimumab Induction Therapy for Crohn Disease Previously Treated with Infliximab (2007)

Adalimumab induces remissions more frequently than placebo in adult patients with Crohn disease who cannot tolerate infliximab or have symptoms despite receiving infliximab therapy. For more information on adalimumab in Crohn disease, click here. ClinicalTrials.gov registration number: NCT00105300.
HER2-positive gastric cancer (2013)

Human epidermal growth factor receptor 2 (HER2) is involved in the pathogenesis and poor outcomes of several types of cancer, including advanced gastric and gastroesophageal junction cancer. Molecular-targeted drugs, such as trastuzumab, which prolong overall survival and progression-free survival in HER2-positive breast cancer, may also be beneficial in patients with HER2-positive gastric cancer. Several studies have examined this possibility, such as the Trastuzumab for Gastric Cancer trial. In this context, the first part of this review provides an update on our knowledge of HER2 in breast and gastric cancer, including the detection and prognostic relevance of HER2 in gastric cancer. The second part of the review discusses the results of pivotal clinical trials that examined the potential for using trastuzumab to treat this disease. This section also summarizes the trials that have been conducted or that are underway to determine the optimal uses of trastuzumab in gastric cancer, including its use as monotherapy and continuation beyond disease progression. The final section discusses the future prospects of other anti-HER2 drugs, including lapatinib, trastuzumab emtansine, and pertuzumab, for the treatment of HER2-positive gastric cancer. The introduction of trastuzumab led to the establishment of a new disease entity, "HER2-positive gastric cancer," similar to HER2-positive breast cancer. It is expected that more anti-HER2 drugs will be developed and introduced into clinical practice to treat HER2-positive cancers, including gastric cancer.
Unexpected role for MHC II–peptide complexes in shaping CD8 T-cell expansion and differentiation in vivo (2012)

Here we report a unique role for MHC II-peptide complexes in controlling immune responses of naïve CD8 T cells. Compared with CD8 T cells from WT mice, CD8 T cells isolated from MHC II(-/-) mice hyperproliferated under lymphopenic conditions, differentiated into effector cells producing proinflammatory cytokines, and mediated more severe tissue inflammation. The elevated responses of MHC II(-/-) CD8 T cells were due to the absence of MHC II, but not CD4, T cells. The hyperreactivity appeared to be a feature of mature T cells, given its absence in CD8 single positive thymocytes derived from MHC II(-/-) mice. Expression of the MHC II ligand LAG3 was markedly enhanced during in vivo activation of MHC II(-/-) CD8 T cells, and blockade of MHC II-LAG3 interactions further enhanced T-cell expansion. Importantly, CD8 T cells isolated from H-2M(-/-) mice expressing WT levels of MHC II also displayed hyperresponsiveness similar to that of MHC II(-/-) CD8 T cells, suggesting that peptides presented on MHC II are involved in the control of CD8 T-cell responses. Our results uncover a previously undefined MHC II-dependent regulation that tunes CD8 T-cell reactivity and may have implications for an improved understanding of CD8 T-cell homeostasis and functions.
Protein Splicing of the Saccharomyces cerevisiae VMA Intein without the Endonuclease Motifs (1997)

The protein splicing element (intein) of the vacuolar ATPase subunit (VMA) of Saccharomyces cerevisiae catalyzes both protein splicing and site-specific DNA cleavage. It has been demonstrated that the conserved splice junction residues are directly involved in protein splicing and the central dodecapeptide motifs are required for DNA cleavage. To examine whether the splicing activity of the intein can be structurally separated from the endonuclease motifs, we made large in-frame deletions at the central region of the intein. We demonstrate for the first time that protein splicing can proceed efficiently after the removal of the central region of the intein including the endonuclease motifs. Our results suggest that the N- and C-terminal regions of the Sce VMA intein may form a separate domain that is not only catalytically sufficient for protein splicing but also structurally independent from the endonuclease domain.
The Interleukin 2 Receptor (1989)

Cells organize many of their biochemical reactions in non-membrane compartments. Recent evidence has shown that many of these compartments are liquids that form by phase separation from the cytoplasm. Here we discuss the basic physical concepts necessary ...Read More
A Group of "Characters" (1934)

The character is a literary form usually presenting a type, and most highly developed during the 17th century.
LAPS - localisation using appearance of prior structure: 6-DoF monocular camera localisation using prior pointclouds (2012)

This paper is about pose estimation using monocular cameras with a 3D laser pointcloud as a workspace prior. We have in mind autonomous transport systems in which low cost vehicles equipped with monocular cameras are furnished with preprocessed 3D lidar workspaces surveys. Our inherently cross-modal approach offers robustness to changes in scene lighting and is computationally cheap. At the heart of our approach lies inference of camera motion by minimisation of the Normalised Information Distance (NID) between the appearance of 3D lidar data reprojected into overlapping images. Results are presented which demonstrate the applicability of this approach to the localisation of a camera against a lidar pointcloud using data gathered from a road vehicle.
Wine Yeasts Strain Idenification (1989)

Commercially produced strains of wine yeast are being widely accepted in the wine industry, and many new strains are finding their way into the market. However, most of the strains belong to the <i>Saccharomyces cerevisiae</i> group and cannot be readily distinguished and identified by classical biochemical methods. We have, therefore, developed a series of tests to identify and characterize yeast strains including rapid biochemical methods, killer profile, protein electrophoresis profile, volatile fatty acids profile, chromosome electrophoresis, and DNA fingerprinting. We applied these techniques to several commercially available wine yeast strains (Prise de Mousse) used for the production of sparkling wines and found them to be different. Therefore, they have the potential to impart different characters to wines.
IL-21 Influences the Frequency, Phenotype, and Affinity of the Antigen-Specific CD8 T Cell Response (2005)

IL-21, a newly described cytokine belonging to the IL-2 gamma-chain receptor cytokine family (that includes IL-2, IL-7, and IL-15), has been described as an important regulator of the cellular immune response. In this study, the role of IL-21 in the generation of a human Ag-specific CD8+ T cell response is characterized by tracking a rare, but measurable population of self-Ag-specific T cells in vitro. Autologous dendritic cells pulsed with the melanoma antigen recognized T cells 1 self-peptide were used to stimulate CD8+ T cells from HLA-A2+ healthy donors and melanoma patients. We demonstrate that exposure to IL-21 increased the total number of MART-1-specific CD8+ T cells that could be elicited by >20-fold and, at the clonal level, enriched for a population of high-affinity CD8+ T cells with a peptide dose requirement more than 1 log(10)-fold less than their untreated counterparts. Phenotypic analysis of T cells from IL-21-treated cultures revealed a unique population of CD45RO+ CD28(high) CD8+ T cells, a phenotype that was stable for at least 4 wk after IL-21 exposure. These CD28(high) CD8+ T cells produced IL-2 upon Ag stimulation and represent potential helper-independent CTLs. Our studies demonstrate a significant role for IL-21 in the primary Ag-specific human CTL response and support the use of IL-21 in the ex vivo generation of potent Ag-specific CTLs for adoptive therapy or as an adjuvant cytokine during in vivo immunization against tumor Ags.
Antiulcer Activity of the Root Bark ofOroxylum indicum. Against Experimental Gastric Ulcers (2006)

The current study was undertaken to investigate the effect of the root bark of Oroxylum indicum. Vent. (Bignoniaceae) against experimental gastric ulcers. The 50% alcohol extract of root bark of Oroxylum indicum. and its different fractions, viz., petroleum ether, chloroform, ethyl acetate and n.-butanol, were studied (p.o.) against ethanol-induced gastric mucosal damage. The alcohol extract (300 mg/kg) and its different fractions (100 and 300 mg/kg) showed significant reduction in gastric ulceration. Out of all these fractions, the petroleum ether (96%) and n.-butanol (99%) fractions showed maximum inhibition of gastric lesions against ethanol-induced gastric mucosal damage. The results were comparable with omeprazole (reference standard). In the ethanol-induced gastric ulcer model, treatment with both the active fractions and omeprazole showed significant antioxidant activity as evident from the reduction in the extent of lipid peroxidation that was measured in terms of malondialdehyde (MDA), along with significant rise in the superoxide dismutase (SOD), catalase (CAT), and reduced glutathione levels (GSH), when compared with the control group. In 6-h pylorus-ligated animals, active fractions of drug at 100 mg/kg showed significant reduction in the ulcer index. Furthermore, in the pylorus-ligation model, significant reduction (p < 0.05) was observed in total acidity, total acid output, pepsin activity, and pepsin output, along with a significant rise in the total carbohydrate to protein ratio (reflecting mucin activity) when compared with the control group. TLC studies revealed the presence of baicalein in the petroleum ether and hydrosylate in n.-butanol fraction. Fingerprinting of both the active fractions was developed by performing HPLC analysis. Baicalein was found to be a major flavonoid present both in petroleum ether and n.-butanol hydrosylate. The mechanism of its antiulcer activity could be attributed to a decrease in gastric acid secretory and antioxidant activities leading to gastric cytoprotection. This activity could be linked to the presence of baicalein in the root bark of the plant.
Insulin-like growth factor I overexpression in human pancreatic cancer: evidence for autocrine and paracrine roles. (1995)

We assessed the potential roles of insulin-like growth factor-I (IGF-I) and the IGF-I receptor (IGF-IR) in human pancreatic cancer. IGF-I enhanced the growth of ASPC-1 and COLO-357 human pancreatic cancer cells, and this effect was significantly inhibited by a highly specific monoclonal anti-IGF-IR antibody (alpha IR3). Both cell lines expressed mRNA transcripts for IGF-IR, and basal cell growth was significantly reduced by an IGF-IR antisense oligodeoxynucleotide. IGF-I mRNA transcripts were not detected in either cell line or in two additional pancreatic cancer cell lines. In contrast, analysis of 12 pancreatic cancers revealed a 32-fold increase (P < 0.01) in IGF-I mRNA levels by comparison with the low levels observed in the normal pancreas. By in situ hybridization, IGF-I mRNA grains were present in both the cancer cells and in the surrounding connective tissue. Six of the cancers exhibited a 4.4-fold increase in IGF-IR mRNA levels. These findings suggest that IGF-I may participate in aberrant autocrine and paracrine activation of IGF-IR in pancreatic cancer in vivo.
Fluid and Air-Stable Lipopolymer Membranes for Biosensor Applications (2005)

The behavior of poly(ethylene glycol) (PEG) conjugated lipids was investigated in planar supported egg phosphatidylcholine bilayers as a function of lipopolymer density, chain length of the PEG moiety, and type of alkyl chains on the PEG lipid. Fluorescence recovery after photobleaching measurements verified that dye-labeled lipids in the membrane as well as the lipopolymer itself maintained a substantial degree of fluidity under most conditions that were investigated. PEG densities exceeding the onset of the mushroom-to-brush phase transition were found to confer air stability to the supported membrane. On the other hand, substantial damage or complete delamination of the lipid bilayer was observed at lower polymer densities. The presence of PEG in the membrane did not substantially hinder the binding of streptavidin to biotinylated lipids present in the bilayer. Furthermore, above the onset of the transition into the brush phase, the protein binding properties of these membranes were found to be very resilient upon removal of the system from water, rigorous drying, and rehydration. These results indicate that supported phospholipid bilayers containing lipopolymers show promise as rugged sensor platforms for ligand-receptor binding.
Enantioselective Total Synthesis of (−)-Acetylaranotin, a Dihydrooxepine Epidithiodiketopiperazine (2011)

The first total synthesis of the dihydrooxepine-containing epidithiodiketopiperazine (ETP) (-)-acetylaranotin (1) is reported. The key steps of the synthesis include an enantioselective azomethine ylide (1,3)-dipolar cycloaddition reaction to set the absolute and relative stereochemistry, a rhodium-catalyzed cycloisomerization/chloride elimination sequence to generate the dihydrooxepine moiety, and a stereoretentive diketopiperazine sulfenylation to install the epidisulfide. This synthesis provides access to (-)-1 in 18 steps from inexpensive, commercially available starting materials. We anticipate that the approach described herein will serve as a general strategy for the synthesis of additional members of the dihydrooxepine ETP family.
Activation of vanilloid receptor 1 by resiniferatoxin mobilizes calcium from inositol 1,4,5‐trisphosphate‐sensitive stores (2003)

1 Capsaicin and resiniferatoxin (RTX) stimulate Ca2+ influx by activating vanilloid receptor 1 (VR1), a ligand-gated Ca2+ channel on sensory neurones. We investigated whether VR1 activation could also trigger Ca2+ mobilization from intracellular Ca2+ stores. 2 Human VR1-transfected HEK293 cells (hVR1-HEK293) were loaded with Fluo-3 or a mixture of Fluo-4 and Fura Red and imaged on a fluorometric imaging plate reader (FLIPR) and confocal microscope respectively. 3 In Ca2+ -free media, RTX caused a transient elevation in intracellular free Ca2+ concentration in hVR1-HEK293 cells (pEC(50) 6.45+/-0.05) but not in wild type cells. Capsaicin (100 microM) did not cause Ca2+ mobilization under these conditions. 4 RTX-mediated Ca2+ mobilization was inhibited by the VR1 receptor antagonist capsazepine (pIC(50) 5.84+/-0.04), the Ca2+ pump inhibitor thapsigargin (pIC(50) 7.77+/-0.04), the phospholipase C inhibitor U-73122 (pIC(50) 5.35+/-0.05) and by depletion of inositol 1,4,5-trisphosphate-sensitive Ca2+ stores by pretreatment with the acetylcholine-receptor agonist carbachol (20 microM, 2 min). These data suggest that RTX causes Ca2+ mobilization from inositol 1,4,5-trisphosphate-sensitive Ca2+ stores in hVR1-HEK293 cells. 5 In the presence of extracellular Ca2+, both capsaicin-mediated and RTX-mediated Ca2+ rises were attenuated by U-73122 (10 microM, 30 min) and thapsigargin (1 microM, 30 min). We conclude that VR1 is able to couple to Ca2+ mobilization by a Ca2+ dependent mechanism, mediated by capsaicin and RTX, and a Ca2+ independent mechanism mediated by RTX alone.
Exploring underwater target detection by imaging polarimetry and correlation techniques (2013)

Underwater target detection is investigated by combining active polarization imaging and optical correlation-based approaches. Experiments were conducted in a glass tank filled with tap water with diluted milk or seawater and containing targets of arbitrary polarimetric responses. We found that target estimation obtained by imaging with two orthogonal polarization states always improves detection performances when correlation is used as detection criterion. This experimental study illustrates the potential of polarization imaging for underwater target detection and opens interesting perspectives for the development of underwater imaging systems.