gebhart/patrepeval huggingface dataset:
α-Phenyl- N - tert -Butylnitrone Provides Protection from Dextran Sulfate Sodium-Induced Colitis in Mice (2002)

Nuclear factor-kappaB (NF-kappaB)-dependent up-regulation of inflammatory cytokines and inducible nitric oxide (iNOS) occurs in inflammatory bowel disease. We investigated the effect of alpha-phenylN-tert-butylnitrone (PBN), a spin-trapping agent that inhibits NF-kappaB activity, on dextran sulfate sodium (DSS)-induced colonic mucosal injury and inflammation in mice. Acute colitis was induced with DSS in female BALB/c mice receiving 0, 0.3, 3, and 30 mg/kg i.p. PBN daily. Colonic mucosal inflammation was evaluated biochemically and histologically. Nitric oxide was evaluated as luminal nitrite/nitrite concentration by the Griess reaction and as immunoreactive nitrotyrosine in mucosal cells. Mucosal tumor necrosis factor-alpha (TNF-alpha) and interferon-gamma (IFN-gamma) were determined by immunoassay. Colonic mRNA expression for iNOS, TNF-alpha, and IFN-gamma was measured by reverse transcription-polymerase chain reaction, and NF-kappaB activation was evaluated by electrophoretic mobility shift assay. After DSS administration, mice showed increased luminal nitrite/nitrate, mucosal TNF-alpha and IFN-gamma, and mRNA for iNOS and these cytokines, in addition to decreased colonic length and increased inflammatory score, luminal hemoglobin, and colonic myeloperoxidase activity. PBN inhibited increases in luminal nitric oxide production, nitrotyrosine immunoreactivity, and mucosal TNF-alpha and IFN-gamma. Colonic iNOS, TNF-alpha, and IFN-gamma mRNA were suppressed by PBN, as was a DSS-induced increase in colonic NF-kappaB DNA-binding activity. NF-kappaB is essential to DSS-induced colitis, suggesting molecular approach targeting of NF-kappaB for treatment of inflammatory bowel disease.
Parkin , a gene implicated in autosomal recessive juvenile parkinsonism, is a candidate tumor suppressor gene on chromosome 6q25–q27 (2003)

In an effort to identify tumor suppressor gene(s) associated with the frequent loss of heterozygosity observed on chromosome 6q25-q27, we constructed a contig derived from the sequences of bacterial artificial chromosomeP1 bacteriophage artificial chromosome clones defined by the genetic interval D6S1581-D6S1579-D6S305-D6S1599-D6S1008. Sequence analysis of this contig found it to contain eight known genes, including the complete genomic structure of the Parkin gene. Loss of heterozygosity (LOH) analysis of 40 malignant breast and ovarian tumors identified a common minimal region of loss, including the markers D6S305 (50%) and D6S1599 (32%). Both loci exhibited the highest frequencies of LOH in this study and are each located within the Parkin genomic structure. Whereas mutation analysis revealed no missense substitutions, expression of the Parkin gene appeared to be down-regulated or absent in the tumor biopsies and tumor cell lines examined. In addition, the identification of two truncating deletions in 3 of 20 ovarian tumor samples, as well as homozygous deletion of exon 2 in the lung adenocarcinoma cell lines Calu-3 and H-1573, supports the hypothesis that hemizygous or homozygous deletions are responsible for the abnormal expression of Parkin in these samples. These data suggest that the LOH observed at chromosome 6q25-q26 may contribute to the initiation andor progression of cancer by inactivating or reducing the expression of the Parkin gene. Because Parkin maps to FRA6E, one of the most active common fragile sites in the human genome, it represents another example of a large tumor suppressor gene, like FHIT and WWOX, located at a common fragile site.
Photovoltaic yield from exciton dissociation in organic dye layers (1999)

Researchers working on organic photovoltaic cells are confronted with the problem of finding the optimal thickness of the organic layers. Obviously, there is a competition between the absorption length of the incident light and the exciton diffusion length, leading to optimal film thicknesses lying somewhere between these two mean path lengths (D. Wöhrle, L. Kreienhoop and D. Schlettwein, PhthalocyaninesandRelatedMacrocyclesinOrganicPhotovoltaicJunctions, ed. C. C. Leznoff and A. B. P. Lever, VCH, New York, 1996). In this paper we investigate the general conditions for optimization of the thickness of the organic layer for a maximum photovoltaic yield. At normal absorption, the optimal layer thickness is typically 1.5 times the exciton diffusion length. As an application we consider the zinc phthalocyanine layer in an organic p–n cell, for which an exciton diffusion length of 30±10 nm is determined from simulations. Using this value, a good correlation between simulations and experiments is found with respect to the thickness-dependent photocurrent yield of the solar cells.
Self-Assembled One-Dimensional Nanostructure Arrays (2006)

A range of proposed devices relies on the electronic, optical or magnetic properties of one-dimensional (1D) chains of nanoparticles. Here, well-controlled 1D arrays have been formed by templating a spherical-morphology block copolymer within a narrow groove. Significantly, the domains are distorted into ellipses with aspect ratio and major axis orientation controlled by the groove width. This technique gives unprecedented control over the period, particle size, aspect ratio, and orientation of nanoparticles in 1D arrays, making it valuable for creating self-assembled masks for the fabrication of novel devices.
A Case-Control Analysis of Nonsteroidal Anti-Inflammatory Drugs and Alzheimer’s Disease: Are They Protective? (2002)

In many studies of nonsteroidal anti-inflammatory drugs (NSAIDs) and Alzheimer's disease (AD), the exposure to NSAIDs was concurrent with AD or based on self (or surrogate) report. We conducted a case-control analysis of the Québec participants in the Canadian Study of Health and Aging who received a diagnosis of AD (cases) or were found to be cognitively unimpaired on screening (controls). Information on drug use was obtained from the Québec Provincial Pharmaceutical Services Database. There was no significant difference in the proportion of cases and controls who had received any NSAID prescriptions in the 3 years prior to the onset of symptoms of dementia; amongst NSAID users, there was no difference in mean dose or duration. Our findings, using a measure of drug use prior to symptom onset and not subject to recall bias, do not support a protective effect for NSAIDs.
Lexical chains for topic tracking (2003)

Describes research into the use of lexical chains to build effective topic tracking systems. Lexical chaining is a method of grouping lexically related terms into so called lexical chains, using simple natural language processing techniques. Topic tracking involves tracking a given news event in a stream of news stories i.e. finding all subsequent storks in the news stream that discuss the given event. It has grown out of the Topic Detection and Tracking (TDT) initiative sponsored by DARPA. The paper describes the results of a topic tracking system, LexTrack, based on lexical chaining and compares it to a tracking system designed using traditional IR techniques.
Phase 2 study of alemtuzumab (anti-CD52 monoclonal antibody) in patients with advanced mycosis fungoides/Sezary syndrome (2003)

This phase 2 study evaluated the safety and efficacy of alemtuzumab in 22 patients with advanced mycosis fungoides/Sézary syndrome (MF/SS). Most patients had stage III or IV disease, reduced performance status, and severe itching. The overall response (OR) rate was 55%, with 32% of patients in complete remission (CR) and 23% in partial remission (PR). Sézary cells were cleared from the blood in 6 of 7 (86%) patients, and CR in lymph nodes was observed in 6 of 11 (55%) patients. The effect was better on erythroderma (OR, 69%) than on plaque or skin tumors (OR, 40%) and in patients who had received 1 to 2 previous regimens (OR, 80%) than in those who had received 3 or more prior regimens (OR, 33%). Itching, self-assessed on a 0 to 10 visual analog scale, was reduced from a median of 8 before treatment to 2 at end of therapy. Median time to treatment failure was 12 months (range, 5-32+ months). Cytomegalovirus (CMV) reactivation (causing fever without pneumonitis and responding to ganciclovir) occurred in 4 (18%) patients. Six additional patients had suspect or manifest infection (fever of unknown origin, 3; generalized herpes simplex, 1; fatal aspergillosis, 1). One patient had fatal Mycobacterium pneumonia at 10+ months. All serious infectious adverse events (except CMV) occurred in patients who had received 3 or more prior regimens. Progression of squamous cell skin carcinoma was noted in 1 patient. Alemtuzumab shows promising clinical activity and an acceptable safety profile in patients with advanced MF/SS, particularly in patients with erythroderma and severe itching and those who were not heavily pretreated.
Recovery of Replication-Competent HIV Despite Prolonged Suppression of Plasma Viremia (1997)

In evaluating current combination drug regimens for treatment of human immunodeficiency virus (HIV) disease, it is important to determine the existence of viral reservoirs. After depletion of CD8 cells from the peripheral blood mononuclear cells (PBMCs) of both patients and normal donors, activation of patient CD4 lymphocytes with immobilized antibodies to CD3 and CD28 enabled the isolation of virus from PBMCs of six patients despite the suppression of their plasma HIV RNA to fewer than 50 copies per milliliter for up to 2 years. Partial sequencing of HIV pol revealed no new drug resistance mutations or discernible evolution, providing evidence for viral latency rather than drug failure.
Galvanic coupling of flux qubits: simple theory and tunability (2006)

Galvanic coupling of small-area (three-junction) flux qubits, using shared large Josephson junctions, has been shown to yield appreciable interaction strengths in a flexible design, which does not compromise the junctions' intrinsic good coherence properties. For an introduction, I recapitulate an elementary derivation of the coupling strength, which is subsequently generalized to the case of tunable coupling for a current-biased shared junction. While the ability to vary coupling constants by, say, 20% would be useful in experiments, sign-tunability (implying switchability) is highly preferable for several quantum-computing paradigms. This note sketches two ideas: a "crossbar" design with competing ferro- and antiferromagnetic current-biased tunable couplings, and a "mediated" one involving an extra loop between the qubits. The latter is a variation on proposals for tunable capacitive coupling of charge qubits, and tunable inductive coupling of large-area flux qubits.
Skin Lipids: Their Biochemical Uniqueness (1974)

Two key words characterize the uniqueness of skin lipids: complexity and perversity. Each suggests a function. Complexity manifests itself in the large number and variety of both saturated and unsaturated fatty chains synthesized by human skin. Functionally, this allows each individual to have a distinct odor or chemical fingerprint. Perversity manifests itself when one compares the lipids synthesized by skin with those synthesized by internal tissues. For example, skin makes odd instead of only even chains, branched instead of only straight chains, free instead of only esterified acids, places double bonds in unusual positions in the fatty chains, extends chains to extreme lengths, and accumulates intermediates in the synthesis of a biologically valuable compound such as cholesterol. Functionally, these products may pose metabolic problems to potential pathogens and thus contribute to the survival of only compatible microorganisms.
Mammalian G1 and G2 phase checkpoints. (1997)

This present review explores the mechanisms for DNA damage induced G1 and G2 arrest in mammalian cells. The complexity of the TP53 pathway is attested to by the variety of genes regulated by TP53, many of which require further investigation to bring their importance into focus. One gene intensely studied, p21, has been linked to the G1 arrest mechanism and may, like TP53, be involved in some aspect of DNA repair. The outcome of TP53 activation for cell survival is equally complex and relies much upon cellular context and the type of DNA damaging agent employed. Although TP53 may participate in sensing DNA damage, additional components are likely to be required. Much of the focus on defining the mechanism of G2 arrest in mammalian cells has concentrated on the cyclin B1/CDC2 kinase. Activation of this kinase is suppressed by DNA damage, and this may result from the imposition of inhibitory phosphorylations on the CDC2 kinase as well as downregulation of cyclin B1 levels. The logical point where the G2 checkpoint interacts with the CDC2-CDC25C autocatalytic loop to prevent CDC2 activation remains to be defined and could involve inhibition of CDC25C-CDC2 interaction. It is hoped that moving upstream of CDC2 towards the point where DNA damage is sensed by the cell will uncover homologues of yeast components implicated in G2 checkpoint control. The finding that certain G2 checkpoint abrogators preferentially synergize with DNA damaging agents in cells with defective TP53 provides a potential pharmacological route through which TP53 defective cells might be targeted for destruction. Further exploration of this vulnerability might prove useful for future anti-cancer drug discovery efforts.
A simple method for simultaneous R- or G-banding and fluorescence in situ hybridization of small single-copy genes (1992)

A significant improvement in fluorescence in situ hybridization, enabling the detection of single-copy genes as small as 500 bp directly on banded chromosomes, is presented. The induction of chromosome banding, which does not require additional handling or any system of amplification, is obtained simply by using an alkaline (pH 11) p-phenylenediamine anti-fade solution. As the banding produced is related to the timing of 5-bromodeoxyuridine incorporation, either R- or G-banding, constitutive heterochromatin staining, or chromosome asymmetry can be observed simultaneously with the fluorescent hybridized spots. Results of hybridization of small cDNA probes for the human genes for motilin, thymidylate synthetase, and lymphocyte activation-3 are provided as examples of the high-resolution mapping obtainable with this technique.
The effect of surface roughness on surface enhanced Raman scattering (1980)

A molecule adsorbed on the surface of a conducting prolate ellipsoid will Raman scAtter with an enhanced cross section. The relevance of this fact to the phenomenon of surface enhanced Raman scattering (SERS) is discussed. (AIP)
Intercellular mRNA trafficking via membrane nanotube-like extensions in mammalian cells (2017)

RNAs have been shown to undergo transfer between mammalian cells, although the mechanism behind this phenomenon and its overall importance to cell physiology is not well understood. Numerous publications have suggested that RNAs (microRNAs and incomplete mRNAs) undergo transfer via extracellular vesicles (e.g., exosomes). However, in contrast to a diffusion-based transfer mechanism, we find that full-length mRNAs undergo direct cell-cell transfer via cytoplasmic extensions characteristic of membrane nanotubes (mNTs), which connect donor and acceptor cells. By employing a simple coculture experimental model and using single-molecule imaging, we provide quantitative data showing that mRNAs are transferred between cells in contact. Examples of mRNAs that undergo transfer include those encoding GFP, mouse β-actin, and human Cyclin D1, BRCA1, MT2A, and HER2. We show that intercellular mRNA transfer occurs in all coculture models tested (e.g., between primary cells, immortalized cells, and in cocultures of immortalized human and murine cells). Rapid mRNA transfer is dependent upon actin but is independent of de novo protein synthesis and is modulated by stress conditions and gene-expression levels. Hence, this work supports the hypothesis that full-length mRNAs undergo transfer between cells through a refined structural connection. Importantly, unlike the transfer of miRNA or RNA fragments, this process of communication transfers genetic information that could potentially alter the acceptor cell proteome. This phenomenon may prove important for the proper development and functioning of tissues as well as for host-parasite or symbiotic interactions.
PCR detection of 9 polymorphisms in the WT1 gene (1993)

Journal Article PCR detection of 9 polymorphisms in the WT1 gene Get access Keiko Tadokoro, Keiko Tadokoro 1National Children's Medical Research Center, 3–35–31Taishdo, Setagaya, Tokyo Search for other works by this author on: Oxford Academic PubMed Google Scholar Noriko Oki, Noriko Oki 1National Children's Medical Research Center, 3–35–31Taishdo, Setagaya, Tokyo2Laboratory of Nucleic Acid Science, College of Agriculture and Veterinary Medicine, Nihon UniversityFujisawa, Kanagawa 252, Japan Search for other works by this author on: Oxford Academic PubMed Google Scholar Akira Sakai, Akira Sakai 1National Children's Medical Research Center, 3–35–31Taishdo, Setagaya, Tokyo Search for other works by this author on: Oxford Academic PubMed Google Scholar Hanako Fujii, Hanako Fujii 1National Children's Medical Research Center, 3–35–31Taishdo, Setagaya, Tokyo2Laboratory of Nucleic Acid Science, College of Agriculture and Veterinary Medicine, Nihon UniversityFujisawa, Kanagawa 252, Japan Search for other works by this author on: Oxford Academic PubMed Google Scholar Akira Ohshima, Akira Ohshima 1National Children's Medical Research Center, 3–35–31Taishdo, Setagaya, Tokyo2Laboratory of Nucleic Acid Science, College of Agriculture and Veterinary Medicine, Nihon UniversityFujisawa, Kanagawa 252, Japan Search for other works by this author on: Oxford Academic PubMed Google Scholar Shigeo Nagafuchi, Shigeo Nagafuchi 1National Children's Medical Research Center, 3–35–31Taishdo, Setagaya, Tokyo Search for other works by this author on: Oxford Academic PubMed Google Scholar Tadashi Inoue, Tadashi Inoue 2Laboratory of Nucleic Acid Science, College of Agriculture and Veterinary Medicine, Nihon UniversityFujisawa, Kanagawa 252, Japan Search for other works by this author on: Oxford Academic PubMed Google Scholar Masao Yamada Masao Yamada * 1National Children's Medical Research Center, 3–35–31Taishdo, Setagaya, Tokyo *To whom correspondence should be addressed Search for other works by this author on: Oxford Academic PubMed Google Scholar Human Molecular Genetics, Volume 2, Issue 12, December 1993, Pages 2205–2206, https://doi.org/10.1093/hmg/2.12.2205 Published: 01 December 1993
Egg Nutrition and Biotechnology (1999)

Food fats and health yolk fat and egg nutrition the egg as a life-supporting chemical store ovo-technology and nutraceuticals shell egg management technologies.
Analytical approximation to the accessible surface area of proteins (1980)

We propose an analytical substitute to the geometrical construction that is commonly used in calculating the protein surface area that is accessible to the solvent. A statistical approach leads to an expression of accessible surface areas as a function of distances between pairs of atoms or of residues in the protein structure, assuming only that these atoms or residues are randomly distributed in space but not penetrating each other. This function gives good estimates of the accessible surface area and of the area buried in subunit contacts for a number of proteins. Its evaluation is very fast, and the function can be differentiated, which opens the way to new applications of accessibility measurements in the study of proteins. As an example, we show that the presence of domains is easily detected by an automatic procedure based on surface areas only.
The Human Immune Response to Streptococcal Extracellular Antigens: Clinical, Diagnostic, and Potential Pathogenetic Implications (2010)

Single time-point cultures and single antibody titers are often misleading. Sequential samples more accurately define infection, allowing correlation of titer increases with temporal confirmation of GAS acquisition. Understanding kinetics of the immune response(s) to GAS infection is necessary in formulating accurate clinical diagnostic conclusions, to appropriate design of clinical and epidemiological studies examining the association of GAS with subsequent sequelae, and to providing insight into pathogenetic mechanisms associated with this important human pathogen.
Phase 1b of anticancer stem cell antibody OMP-59R5 (anti-Notch2/3) in combination with etoposide and cisplatin (EP) in patients (pts) with untreated extensive-stage small-cell lung cancer (ED-SCLC). (2014)

7601 Background: The Notch pathway plays a central role in embryonic development, the regulation of stem and progenitor cells, and is implicated centrally in many human cancers, including SCLC. OMP-59R5, a fully human IgG2 antibody, inhibits signaling of Notch2 and 3 receptors. Anti-tumor activity was noted in 7 of 8 pt-derived SCLC xenografts expressing Notch 2 and 3 with OMP-59R5 treatment. The maximum tolerated dose (MTD) of single agent OMP-59R5 was 7.5mg/kg IV every 3 weeks (Smith, EORTC 2012); the main dose-limiting toxicity (DLT) was Grade 3 diarrhea. This study is to determine the MTD, pharmacokinetics (PK), pharmacodynamics (PD), and preliminary efficacy of OMP-59R5 in combination with EP in ED-SCLC. Methods: Cohorts of 3 to 6 pts were treated at each dose level of OMP-59R5. OMP-59R5 was given IV on Day 1 of each 21 day cycle along with etoposide 100 mg/m2 on Days 1, 2, and 3 and cisplatin 80 mg/m2 on Day 1. After 6 cycles, pts continued OMP-59R5 alone every 21 days in the absence of disease progression or unacceptable toxicities. Results: By Jan 17, 2014, 8 pts were treated. No DLTs have occurred. Frequently reported (>25%) adverse events (all grades, G) regardless of relationship were: fatigue(62.5%), nausea(62.5%), anemia(50%), diarrhea(50%), peripheral edema(50%), alopecia(37.5%), blood creatinine increase(37.5%), decreased appetite(37.5%), neutropenia(37.5%), and weight loss(37.5%); Of these, fatigue(50%), anemia(37.5%), diarrhea(37.5%), nausea(37.5%), alopecia(25%), decreased appetite(25%), and weight loss(25%) were considered related to OMP-59R5-treatment. The events were mostly G 1 or 2, and managed with supportive care. Additional data are below (see Table). Conclusions: OMP-59R5 with EP is well tolerated. The MTD has not been reached. Encouraging anti-tumor activity is observed. Updated Safety, PK/PD, and efficacy data will be presented. Clinical trial information: NCT01859741. OMP-59R5 Dose (mg/kg) 5 (n=3) 7.5 (n=3) 10 (n=2) Etoposide (mg/m2) 100 Cisplatin (mg/m2) 80 DLT evaluable 3 3 2 incidence - - - RECIST 1.1 evaluable 3 3 -- Best response PR 3 - 2 SD - 3 - PD - - - mPFS (days) 175 - - Pts still on treatment 1 3 2