gebhart/patrepeval huggingface dataset:
Synthesis of pseudo-α-L-fucopyranose from toluene (1995)

H. A. J. Carless and S. S. Malik, J. Chem. Soc., Chem. Commun., 1995, 2447 DOI: 10.1039/C39950002447
Neoepitopes of Cancers: Looking Back, Looking Ahead (2015)

The search for specificity in cancers has been a holy grail in cancer immunology. Cancer geneticists have long known that cancers harbor transforming and other mutations. Immunologists have long known that inbred mice can be immunized against syngeneic cancers, indicating the existence of cancer-specific antigens. With the technological advances in high-throughput DNA sequencing and bioinformatics, the genetic and immunologic lines of inquiry are now converging to provide definitive evidence that human cancers are vastly different from normal tissues at the genetic level, and that some of these differences are recognized by the immune system. The very vastness of genetic changes in cancers now raises different question. Which of the many cancer-specific genetic (genomic) changes are actually recognized by the immune system, and why? New observations are now beginning to probe these vital issues with unprecedented resolution and are informing a new generation of studies in human cancer immunotherapy.
Effects of hypoxia on iron absorption and mobilization in the rat (1964)

Rats exposed to an atmosphere of 10% oxygen increase their absorption of a test dose of iron after 6 8 hr. Release of tissue storage iron begins within 2 hr of the start of hypoxia and continues for at least 8 hr. An oral iron load does not prevent the release of tissue iron in response to hypoxia. Iron-loaded rats also release iron from storage depots and increase their minimal absorption in response to hypoxia. Iron-deficient rats apparently have a diminished tissue release and also increase absorption above their elevated base-line levels. Xanthine loading had no effect on the release of tissue iron or changes in absorption with hypoxia, and there was no evidence that changes in xanthine oxidase activity in the liver or bowel were directly associated with tissue release or absorption of iron.
Granzymes A and B are targeted to the lytic granules of lymphocytes by the mannose-6-phosphate receptor. (1993)

To investigate the question of whether lytic granules share a common biogenesis with lysosomes, cloned cytolytic T cell lines were derived from a patient with I-cell disease. The targeting of two soluble lytic granule components, granzymes A and B, was studied in these cells which lack a functional mannose-6-phosphate (Man-6-P) receptor-mediated pathway to lysosomes. Using antibodies and enzymatic substrates to detect the lytic proteins, I-cells were found to constitutively secrete granzymes A and B in contrast to normal cells in which these proteins were stored for regulated secretion. These results suggest that granzymes A and B are normally targeted to the lytic granules of activated lymphocytes by the Man-6-P receptor. In normal cells, the granzymes bear Man-6-P residues, since the oligosaccharide side chains of granzymes A and B, as well as radioactive phosphate on granzyme A from labeled cells, were removed by endoglycosidase H (Endo H). However, in I-cells, granzymes cannot bear Man-6-P and granzyme B acquires complex glycans, becoming Endo H resistant. Although the levels of granzymes A and B in cytolytic I-cell lymphocytes are < 30% of the normal levels, immunolocalization and cell fractionation of granzyme A demonstrated that this reduced amount is correctly localized in the lytic granules. Therefore, a Man-6-P receptor-independent pathway to the lytic granules must also exist. Cathepsin B colocalizes with granzyme A in both normal and I-cells indicating that lysosomal proteins can also use the Man-6-P receptor-independent pathway in these cells. The complete overlap of these lysosomal and lytic markers implies that the lytic granules perform both lysosomal and secretory roles in cytolytic lymphocytes. The secretory role of lytic granules formed by the Man-6-P receptor-independent pathway is intact as assessed by the ability of I-cell lymphocytes to lyse target cells by regulated secretion.
E-cadherin Is Critical for Collective Sheet Migration and Is Regulated by the Chemokine CXCL12 Protein During Restitution (2012)

Chemokines and other immune mediators enhance epithelial barrier repair. The intestinal barrier is established by highly regulated cell-cell contacts between epithelial cells. The goal of these studies was to define the role for the chemokine CXCL12 in regulating E-cadherin during collective sheet migration during epithelial restitution. Mechanisms regulating E-cadherin were investigated using Caco2(BBE) and IEC-6 model epithelia. Genetic knockdown confirmed a critical role for E-cadherin in in vitro restitution and in vivo wound repair. During restitution, both CXCL12 and TGF-β1 tightened the monolayer by decreasing the paracellular space between migrating epithelial cells. However, CXCL12 differed from TGF-β1 by stimulating the significant increase in E-cadherin membrane localization during restitution. Chemokine-stimulated relocalization of E-cadherin was paralleled by an increase in barrier integrity of polarized epithelium during restitution. CXCL12 activation of its cognate receptor CXCR4 stimulated E-cadherin localization and monolayer tightening through Rho-associated protein kinase activation and F-actin reorganization. These data demonstrate a key role for E-cadherin in intestinal epithelial restitution.
Identification of Cross‐Reactive Antibodies with Low Opsonophagocytic Activity forStreptococcus pneumoniae (1997)

Opsonophagocytic capacity and concentrations of antibodies to the capsular polysaccharide (PS) of Streptococcus pneumoniae serotypes 6A, 6B, 19F, and 19A were determined for sera from adults immunized with 14- and 23-valent S. pneumoniae capsular PS vaccines. The concentration of anticapsular PS antibodies strongly correlated (r = .72 to r = .91) with the opsonophagocytic activities. However, 10%-20% of serum samples display strikingly less opsonophagocytic activity for the cross-reactive serotypes than expected on the basis of their antibody concentrations to the cross-reactive serotypes. From 1 poorly opsonic serum sample, kappa and lambda fractions of anti-6B antibodies were purified by affinity chromatography. Kappa (but not lambda) type antibody was found to have less opsonophagocytic capacity than expected. Thus, ELISA measurements of antibody responses to pneumococcal capsular PSs may not be reflective of opsonophagocytic function of the antibody.
The hallmarks of cancer (2012)

With the advent of next generation sequencing methods and progress in transcriptome analysis, it became obvious that the human genome contains much more than just protein-coding genes. In fact, up to 70% of our genome is transcribed into RNA that does not serve as templates for proteins. In this review, we focus on the emerging roles of these long non-coding RNAs (lncRNAs) in the field of tumor biology. Long ncRNAs were found to be deregulated in several human cancers and show tissue-specific expression. Functional studies revealed a broad spectrum of mechanisms applied by lncRNAs such as HOTAIR, MALAT1, ANRIL or lincRNA-p21 to fulfill their functions. Here, we link the cellular processes influenced by long ncRNAs to the hallmarks of cancer and therefore provide an ncRNA point-of-view on tumor biology. This should stimulate new research directions and therapeutic options considering long ncRNAs as novel prognostic markers and therapeutic targets.
MICROMINIATURE FLUIDIC AMPLIFIER (1986)

A microminiature fluidic amplifier with vertical-walled features 6 m wide and 35 m deep has been fabricated in silicon using dry anisotropic etch ing. Operation was demonstrated using nitrogen as the working fluid. DC gains greater than unity were seen over a supply pressure range of 10 to 80 psi. The amplifi er is intended to be used as a circuit element in integrated fluidic circuits or, together with on-board electronics, as part of a transducer system. Dry etch ing techniques similar to those used here offer new op portunities for the micromachining of integrated sen sors and actuators.
Event Detection in Twitter (2021)

Twitter, as a form of social media, is fast emerging in recent years. Users are using Twitter to report real-life events. This paper focuses on detecting those events by analyzing the text stream in Twitter. Although event detection has long been a research topic, the characteristics of Twitter make it a non-trivial task. Tweets reporting such events are usually overwhelmed by high flood of meaningless “babbles”. Moreover, event detection algorithm needs to be scalable given the sheer amount of tweets. This paper attempts to tackle these challenges with EDCoW (Event Detection with Clustering of Wavelet-based Signals). EDCoW builds signals for individual words by applying wavelet analysis on the frequencybased raw signals of the words. It then filters away the trivial words by looking at their corresponding signal autocorrelations. The remaining words are then clustered to form events with a modularity-based graph partitioning technique. Experimental results show promising result of EDCoW.
Peeling Process in Living Cell Movement Under Shear Flow (2002)

We present a direct optical observation of the behavior of the contact area between a living cell (Dictyostelium discoideum) and a solid substrate under shear flow. It is shown that the membrane is peeled off the substrate. The relationship between the peeling velocity and the applied force is obtained experimentally and explained from the behavior of individual adhesion bridges. The dissipation occurring during the peeling process is explicitly calculated in terms of out-of-equilibrium thermodynamics.
Oxyhemoglobin Is a Quantifiable Measure of Experimentally Induced Chronic Tretinoin Inflammation and Accommodation in Photodamaged Skin (1997)

Chronic exposure to a weak irritant leads to inflammatory changes which may be followed by pigmentary changes and accommodation. The inflammatory responses to acute exposure to an irritant have been extensively studied. This study investigated quantitatively the inflammatory reactions produced in photodamaged skin with chronic application of a weak chemical irritant (tretinoin cream 0.025%) over a period of 9 months (36 weeks). Forty-eight subjects with moderately to severely photodamaged skin were enrolled in a 36-week, double-blind placebo-controlled study. Tretinoin cream was applied nightly on the distal two thirds of one dorsal forearm and placebo on the other. The proximal third of each dorsal forearm received no treatment and served as control. Clinical assessments and diffuse reflectance measurements were made at 7 time points during treatment. Apparent concentrations of oxyhemoglobin (HbO2), deoxyhemoglobin (Hb) and melanin were estimated by analysis of the diffuse reflectance spectra. No changes were observed in the apparent HbO2 or the Hb concentration of the placebo-treated or control sites, thus establishing a reliable baseline. The apparent HbO2 concentration of the tretinoin-treated sites increased significantly from baseline to a maximum at 12-18 weeks of treatment, then returned to baseline with continued applications. The changes in HbO2 concentration agreed closely with clinical assessments of erythema. The apparent melanin concentration, corresponding to diffuse hyperpigmentation, showed a large seasonal decrease in both the control and the treated sites, with an additional decrease in the treated sites between 12 and 18 weeks. Erythema appeared after repeated applications and eventually resolved under continuous treatment. The maximum decrease in hyperpigmentation occurred simultaneously with the maximum increase in erythema.
Protein-Sulfenic Acids:  Diverse Roles for an Unlikely Player in Enzyme Catalysis and Redox Regulation (1999)

While it has been known for more than 20 years that unusually stable cysteine-sulfenic acid (Cys-SOH) derivatives can be introduced in selected proteins by mild oxidation, only recently have chemical and crystallographic evidence for functional Cys-SOH been presented with native proteins such as NADH peroxidase and NADH oxidase, nitrile hydratase, and the hORF6 and AhpC peroxiredoxins. In addition, Cys-SOH forms of protein tyrosine phosphatases and glutathione reductase have been suggested to play key roles in the reversible inhibition of these enzymes during tyrosine phosphorylation-dependent signal transduction events and nitrosative stress, respectively. Substantial chemical data have also been presented which implicate Cys-SOH in redox regulation of transcription factors such as Fos and Jun (activator protein-1) and bovine papillomavirus-1 E2 protein. Functionally, the Cys-SOHs in NADH peroxidase, NADH oxidase, and the peroxiredoxins serve as either catalytically essential redox centers or transient intermediates during peroxide reduction. In nitrile hydratase, the active-site Cys-SOH functions in both iron coordination and NO binding but does not play any catalytic redox role. In Fos and Jun and the E2 protein, on the other hand, a key Cys-SH serves as a sensor for intracellular redox status; reversible oxidation to Cys-SOH as proposed inhibits the corresponding DNA binding activity. These functional Cys-SOHs have roles in diverse cellular processes, including signal transduction, oxygen metabolism and the oxidative stress response, and transcriptional regulation, as well as in the industrial production of acrylamide, and their detailed analyses are beginning to provide the chemical foundation necessary for understanding protein-SOH stabilization and function.
Metallopeptide Design:  Tuning the Metal Cation Affinities with Unnatural Amino Acids and Peptide Secondary Structure (1996)

The ability to tune the metal binding affinity of small peptides through the incorporation of unnatural multidentate α-amino acids and the preorganization of peptide structure is illustrated. Herein, we describe the exploitation of a family of α-amino acids that incorporate powerful bidentate ligands (bipyridyl and phenanthrolyl groups) as integral constituents of the residues' side chains. The residues involved are the 6-, 5-, and 4-substituted (S)-2-amino-3-(2,2‘-bipyridyl)propanoic acids (1, 6Bpa; 2, 5Bpa; 3, 4Bpa), (S)-2-amino-3-(1,10-phenanthrol-2-yl)propanoic acid (4, Fen), and a novel neocuproine-containing α-amino acid, (S)-2-amino-3-(9-methyl-1,10-phenanthrol-2-yl)propanoic acid (5, Neo). Within this family of amino acids, variations in metal binding due to the nature of the ring system (2,2‘-bipyridyl or 1,10-phenanthrolyl) and the point of attachment to the amino acid β-carbon are observed. Additionally, the underlying peptide architecture significantly influences binding for peptides that include multiple metal-ligating residues. These differences in affinity arise from the interplay of ligand type and structural preorganization afforded by the peptide sequence, resulting in dissociation constants ranging from 10-3 to <10-6 M for ZnII. These studies illustrate that significant control of metal cation binding affinity, preference, and stoichiometry may be achieved through the use of a wide variety of native and unnatural metal-coordinating amino acids incorporated into a polypeptide architecture.
Measuring the cost-effectiveness of various disaster risk management (DRM) measures (2012)

The Japanese experience shows that if done right- preventive investments pay. The Japanese government invested about 7 to 8 percent of the total budget for disaster risk management (DRM) in the 1960s, a move that most probably decreased disaster deaths. Cost-effectiveness analysis (CEA) and cost-benefit analysis (CBA) of DRM projects have been widely implemented both at national and local levels in Japan. Different procedures for such analysis have been followed according to the type of project, the funds, and the governing entity responsible. The Japanese experience shows that CBA is applicable to DRM-related projects and is a useful tool in choosing among different options and understanding the effectiveness of a project. This report gives introduction; findings; lessons; and recommendations for developing countries.
The virtual museum: Interactive 3D navigation of a multimedia database (1992)

Abstract The Virtual Museum is an interactive, electronic museum where users can move from room to room, and select any exhibit in a room for more detailed examination. The exhibits in the museum are educational, encompassing topics such as medicine, plant growth, the environment, and space. To facilitate interaction with the museum, a new method for navigating through a prerendered 3D space, and interacting with objects in that space has been developed, called ‘virtual navigation’. Virtual navigation employs real‐time video decompression for the display of, and interaction with, high‐quality computer animation. In addition, a representation for 3D objects in animated sequences is used which permits pixel‐accurate, frame‐accurate object picking, so that a viewer can select any 3D object to trigger movement within the 3D space, to examine an exhibit in animated form, or to play a digital movie or soundtrack. The use of precomputed video permits 3D navigation in a realistic‐looking space, without requiring special‐purpose graphics hardware.
Detrimental Thixotropic Thinning of Filter Cake of SiO2–Al2O3 Composite Coated TiO2 Particles and Its Control (2011)

A SiO2–Al2O3 double layer coating process is widely used for TiO2 particle to reduce its photocatalytic activity. The conventional coating process needs a long time and uses large amounts of acid and alkali solutions. We recently developed a new SiO2–Al2O3 composite coating process that needs less time and does not use acid and alkali solutions. This process produced coated TiO2 particles with excellent weather durability, but it had the problem that the filter cakes composed of these particles were thixotropically thin and were easily broken up by shear or disturbance on a conveyor belt; that is, the cakes thinned into slurries very quickly. A slurry is not a suitable physical form for the subsequent drying process in industrial production. To understand this problem better, the rheology of the filter cakes was measured. Experiments to investigate the mechanism of the thixotropic thinning behavior indicated that the Si–O–H groups on the surface of the coated particles formed, by hydrogen bonding, a network structure of the particles that entrapped water within the structure. This structure was easily destroyed by an applied shear or disturbance, leading to the release of the occluded water, and the presence of water caused the cake to become a slurry and its viscosity to decrease sharply. This thixotropic thinning behavior of the filter cake was eliminated by coating the particle surface with a thin film of aluminum oxide.
High hepatotoxic dose of paracetamol produces generalized convulsions and brain damage in rats. A counteraction with the stable gastric pentadecapeptide BPC 157 (PL 14736). (2010)

We focused on stable gastric pentadecapeptide BPC 157 (GEPPPGKPADDAGLV, MW 1419, an anti-ulcer peptide efficient in inflammatory bowel disease trials (PL 14736), no toxicity reported) because of its hepatoprotective effects. We investigate a particular aspect of the sudden onset of encephalopathy with extreme paracetamol overdose (5 g/kg intraperitoneally) so far not reported: rapidly induced progressive hepatic encephalopathy with generalized convulsions in rats. BPC 157 therapy (10 microg, 10 ng, 10 pg/kg, intraperitoneally or intragastrically) was effective (microg-ng range) against paracetamol toxicity, given in early (BPC 157 immediately after paracetamol, prophylactically) or advanced stage (BPC 157 at 3 hours after paracetamol, therapeutically). At 25 min post-paracetamol increased ALT, AST and ammonium serum values precede liver lesion while in several brain areas, significant damage became apparent, accompanied by generalized convulsions. Through the next 5 hour seizure period and thereafter, the brain damage, liver damage enzyme values and hyperammonemia increased, particularly throughout the 3-24 h post-paracetamol period. BPC 157 demonstrated clinical (no convulsions (prophylactic application) or convulsions rapidly disappeared (therapeutic effect within 25 min)), microscopical (markedly less liver and brain lesions) and biochemical (enzyme and ammonium serum levels decreased) counteraction. Both, the prophylactic and therapeutic benefits (intraperitoneally and intragastrically) clearly imply BPC 157 (microg-ng range) as a highly effective paracetamol antidote even against highly advanced damaging processes induced by an extreme paracetamol over-dose.
Evaluation of the viscometric constants for chitosan (1988)

Abstract Viscosity‐average relative molecular masses have been determined for a series of chitosans having the same relative molecular mass and relative molecular mass distribution but differing extents of N‐acetylation. The results obtained show that the same viscometric constants in the Mark‐Houwink equation [η] = K m ·M a are applicable to chitosans over the range between 0 and 40% N ‐acetylation Comparison of literature values for number‐ and weight‐avepge rela‐tive molecular masses M n , and M w , with the viscosity‐average relative molecular mass M, values calculated using the related viscosity data and each of the three sets of viscometric constants that have been proposed for chitosan, confirms that the most accurate values currently available are k m = 1,81 · cm −3 · 10 −1 and a = 0,93, using 0,l M acetic acid/0,2M NaCl as solvent.
Involvement of IL‐31 on scratching behavior in NC/Nga mice with atopic‐like dermatitis (2006)

Pruritus is an important symptom in atopic dermatitis (AD), but the major pruritogen has not been identified. NC/Nga mice, spontaneously develop an eczematous AD-like skin lesion when kept under conventional conditions, but not under specific pathogen-free (SPF) conditions, have been thought to be an animal model for AD. In this study, to determine whether newly identified cytokine, IL-31, may be involved in pruritus of AD, we examined the IL-31 expression in spontaneous dermatitis model which showed itch-associated long-lasting (over 1.5 s duration) scratching behavior and compared with that of hapten-induced contact dermatitis model without itch-associated long-lasting scratching behavior, using NC/Nga mice. In NC/Nga mice cohabited with NC/Nga mice which developed severe dermatitis for 2 weeks (conventional NC/Nga mice), the numbers of long-lasting scratching counts were significantly increased. Yet in 2,4,6-trinitrochlorobenzene (TNCB)-sensitized and challenged mice (TNCB-applied NC/Nga mice), no significant increase in long-lasting scratching counts was observed. In conventional NC/Nga mice with long-lasting scratching behavior, expression of IL-31 mRNA was increased, while in TNCB-applied NC/Nga mice without long-lasting scratching behavior, the expression of IL-31 mRNA were unchanged. There was a good correlation between the scratching counts and expression of IL-31 mRNA in conventional NC/Nga mice, but not so in TNCB-applied NC/Nga mice. These results suggest that IL-31 causes the itch-associated scratching behavior in conventional NC/Nga mice, an experimental animal model for AD.