gebhart/patrepeval huggingface dataset:
Apurinic/apyrimidinic endonucleases in repair of pyrimidine dimers and other lesions in DNA. (1980)

The characteristics of the nicks (single-strand breaks) introduced into damaged DNA by Escherichia coli endonucleases III, IV, and VI and by phage T4 UV endonuclease have been investigated with E. coli DNA polymerase I (DNA nucleotidyltransferase). Nicks introduced into depurinated DNA by endonuclease IV or VI provide good primer termini for the polymerase, whereas nicks introduced into depurinated DNA by endonuclease III or into irradiated DNA by T4 UV endonuclease do not. This result suggests that endonuclease IV nicks depurinated DNA on the 5' side of the apurinic site, as does endonuclease VI, whereas endonuclease III has a different incision mechanism. T4 UV endonuclease also possesses apurinic endonuclease activity that generates nicks in depurinated DNA with low priming activity for the polymerase. The priming activity of DNA nicked with endonuclease III or T4 UV endonuclease can be enhanced by an additional incubation with endonuclease VI and, to a lesser extent, by incubation with endonuclease IV. These results indicate that endonuclease III and T4 UV endonuclease (acting upon depurinated and irradiated DNA, respectively) generate nicks containing apurinic/apyrimidinic sites at their 3' termini and that such sites are not rapidly excised by the 3' leads to 5' activity of DNA polymerase I. However, endonuclease IV or VI apparently can remove such terminal apurinic/apyrimidinic sites as well as cleave on the 5' side of the unnicked sites. These results suggest roles for endonucleases III, IV, and VI in the repair of apurinic/apyrimidinic sites as well as pyrimidine dimer sites in DNA. Our results with T4 UV endonuclease suggest that the incision of irradiated DNA by T4 UV endonuclease involves both cleavage of the glycosylic bond at the 5' half of the pyrimidine dimer and cleavage of the phosphodiester bond originally linking the two nucleotides of the dimer. They also imply that the glycosylic bond is cleaved before the phosphodiester bond.
Antibody Blockade of Semaphorin 4D Promotes Immune Infiltration into Tumor and Enhances Response to Other Immunomodulatory Therapies (2015)

Semaphorin 4D (SEMA4D, CD100) and its receptor plexin-B1 (PLXNB1) are broadly expressed in murine and human tumors, and their expression has been shown to correlate with invasive disease in several human tumors. SEMA4D normally functions to regulate the motility and differentiation of multiple cell types, including those of the immune, vascular, and nervous systems. In the setting of cancer, SEMA4D-PLXNB1 interactions have been reported to affect vascular stabilization and transactivation of ERBB2, but effects on immune-cell trafficking in the tumor microenvironment (TME) have not been investigated. We describe a novel immunomodulatory function of SEMA4D, whereby strong expression of SEMA4D at the invasive margins of actively growing tumors influences the infiltration and distribution of leukocytes in the TME. Antibody neutralization of SEMA4D disrupts this gradient of expression, enhances recruitment of activated monocytes and lymphocytes into the tumor, and shifts the balance of cells and cytokines toward a proinflammatory and antitumor milieu within the TME. This orchestrated change in the tumor architecture was associated with durable tumor rejection in murine Colon26 and ERBB2(+) mammary carcinoma models. The immunomodulatory activity of anti-SEMA4D antibody can be enhanced by combination with other immunotherapies, including immune checkpoint inhibition and chemotherapy. Strikingly, the combination of anti-SEMA4D antibody with antibody to CTLA-4 acts synergistically to promote complete tumor rejection and survival. Inhibition of SEMA4D represents a novel mechanism and therapeutic strategy to promote functional immune infiltration into the TME and inhibit tumor progression.
Carbon nanotube forests as top electrode in electroacoustic resonators (2015)

We grow carbon nanotube forests on piezoelectric AlN films and fabricate and characterize nanotube-based solidly mounted bulk acoustic wave resonators employing the forests as the top electrode material. The devices show values for quality factor at anti-resonance of ∼430, and at resonance of ∼100. The effective coupling coefficient is of ∼6%, and the resonant frequencies are up to ∼800 MHz above those observed with metallic top electrodes. AlN promotes a strong catalyst-support interaction, which reduces Fe catalyst mobility, and thus enforces the growth of forests by the base growth mechanism.
Centroid-based summarization of multiple documents: sentence extraction, utility-based evaluation, and user studies (2000)

We present a multi-document summarizer, called MEAD, which generates summaries using cluster centroids produced by a topic detection and tracking system. We also describe two new techniques, based on sentence utility and subsumption, which we have applied to the evaluation of both single and multiple document summaries. Finally, we describe two user studies that test our models of multi-document summarization.
Fatal meningococcal septicemia. (1977)

The morphologic and clinical findings in seven fatal cases of meningococcal septicemia are described and interpreted in light of recent experimental and clinical studies. We include evidence that suggests the disease has two distinct pathogenetic mechanisms. First, a shock-like terminal phase is associated with the development of widespread pulmonary microvascular thrombosis. These thrombi, composed largely of platelets and leukocytes, produce severe cor pulmonale that cannot be prevented with heparin sodium treatment. Meningococcal endotoxin also produces disseminated intravascular coagulation, which includes the rapid consumption of fibrinogen and the formation of fibrin thrombi in adrenal and renal glomerular capillaries, causing hemorrhagic infarction of the adrenal glands and renal cortical necrosis. This secondary phase of the disease can be modified with heparin therapy, but its control does not improve survival because the parenchymal lesions produced are not immediately life threatening.
Studies on the Constituents of Asclepiadaceae Plants. XXV. : On the Components of Cynanchun boerhavifolium H. et A. (1969)

The upper ground portion of Cynanchum boerhavifolium H. et A. (Asclepiadaceae), obtained by the scientific expedition to Patagonia by the Hokkaido University team in 1966, were proved to contain about 0.9% of glycoside mixture. Acid hydrolysis of this glycoside mixture gave β-amyrin, lineolon, isolineolon, isoramanone, benzoylisolineolon, and two unidentified crystals.
Prophylaxis and Treatment of Influenza (1990)

IT has been over 20 years since there has been a severe influenza pandemic. Nevertheless, influenza remains an important epidemic viral infection with the potential to return to its former magnitude.1 2 3 4 The Centers for Disease Control documented 10,000 or more excess deaths in the United States in each of 19 epidemics from 1957 to 1986, and more than 40,000 deaths in several of them.5 The major causes of death are pneumonia and the exacerbation of cardiopulmonary and other conditions,6 7 8 9 10 and 80 to 90 percent of those who die are 65 years of age or older. In addition, substantial morbidity occurs . . .
Linking entries in protein interaction database to structured text: The FEBS Letters experiment (2008)

The corpus of the scientific literature has reached such size that a lot of useful data, dispersed throughout millions different articles, are now hard to recover. For instance, many articles in the biological domain describe relationships between entities (gene, proteins, small molecules, etc.) yet this crucial information cannot be efficiently used because of the difficulties in retrieving it automatically from unstructured text. Databases are striving to capture this valuable information and to organize it in a structured format ready for automatic analysis. However, the current database model, based on manual curation, is not sustainable because the limited support is not compatible with complete and accurate coverage of published information. Several proposals have been put forward to increase the efficiency and accuracy of the curation process. Here we present an experiment, designed by the editorial board of FEBS Letters, aimed at integrating each manuscript with a structured summary precisely reporting, with database identifiers and predefined controlled vocabularies, the protein interactions reported in the manuscript. The authors play an important role in this process as they are requested to provide structured information to be appended, in the form of human-readable paragraphs, at the end of traditional summaries. It is envisaged that the structured text will become an integral part of Medline abstracts. In 6 months time the experience gained with this experiment will form the basis for a community discussion to propose a widely accepted strategy for information storage and retrieval.
Structural differences and the presence of unsubstituted amino groups in heparan sulphates from different tissues and species (1997)

This study presents a comparison of heparan sulphate chains isolated from various porcine and bovine tissues. 1H-NMR spectroscopy (500 MHz) was applied for structural and compositional studies on intact heparan sulphate chains. After enzymic digestion of heparan sulphate using heparin lyase I (EC 4.2.2.7) II and III (EC 4.2.2.8), the compositions of unsaturated disaccharides obtained were determined by analytical capillary electrophoresis. Correlations between the N-sulphated glucosamine residues and O-sulphation and between iduronic acid content and total sulphation were discovered using the data obtained by NMR and disaccharide analysis. Heparan sulphate chains could be classified into two groups based on the sulphation degree and the iduronic acid content. Heparan sulphate chains with a high degree of sulphation possessed also a significant number of iduronic acid residues and were isolated exclusively from porcine brain, liver and kidney medulla. The presence and amount of N-unsubstituted glucosamine residues (GlcNp) was established in all of the heparan sulphates examined. The structural context in which this residue occurs was demonstrated to be: high sulphation domain --> 4)-beta-D-GlcAp-(1 --> 4)-alpha-D-GlcNp-(1 --> 4)-beta-D-GlcAp-(1 --> low sulphation domain (where GlcNp is 2-amino-2-deoxyglucopyranose, and GlcAp is glucopyranosyluronic acid), based on the isolation and characterization of a novel, heparin lyase III-derived, GlcNp containing tetrasaccharide and hexasaccharide. The results presented suggest that structural differences may play a role in important biological events controlled by heparan sulphate in different tissues.
Array detection for speckle reduction in optical coherence microscopy (1997)

This paper introduces a spatial-diversity method for speckle suppression in optical coherence microscopy. The method is based on combining interference signals from an array of detectors placed in the back focal plane of the objective lens, such that elements receive light backscattered from the sample volume at different angles. Incoherently adding ('compounding') the signals increases the signal-to-noise ratio of the processed image compared to that attainable with a single detector. The speckle-reduction method was demonstrated with a benchtop microscope equipped with a quadrant photodiode. To evaluate its potential application in dermatology, images of living skin acquired with and without compounding were compared. The quality of the compounded images was found to be substantially better. A signal-to-noise gain close to a factor of two (the theoretical maximum attainable using four detectors) was achieved without a significant loss in resolution. The method can be applied to arrays with a larger number of elements, potentially enabling more advanced forms of spatial-diversity and adaptive-optics methods.
Standardization of an Experimental Murine Model of Invasive Pulmonary Aspergillosis (2006)

Evaluating new therapeutic agents for invasive aspergillosis requires animal models that are reproducible among different laboratories. We therefore evaluated a murine model of aerosol infection in two independent laboratories and found a high level of both intra- and interlaboratory reproducibility of survival, fungal burden over time, and the efficacy of liposomal amphotericin B.
Low-Dose Decitabine Versus Best Supportive Care in Elderly Patients With Intermediate- or High-Risk Myelodysplastic Syndrome (MDS) Ineligible for Intensive Chemotherapy: Final Results of the Randomized Phase III Study of the European Organisation for Research and Treatment of Cancer Leukemia Group and the German MDS Study Group (2011)

Decitabine administered in 6-week cycles is active in older patients with higher-risk MDS, resulting in improvements of OS and AMLFS (nonsignificant), of PFS and AML transformation (significant), and of QOL. Short MDS duration was an independent adverse prognosticator.
The Penumbra Stroke System: a technical review (2011)

Major ischemic strokes secondary to proximal artery occlusions are responsible for significant morbidity and mortality. Owing to extensive clot burden, these strokes are poorly responsive to intravenous tissue plasminogen activator. The introduction of endovascular therapy, particularly mechanical devices, has resulted in markedly improved recanalization rates of large vessel occlusions. With increasing experience with the Penumbra Stroke System and the 054 reperfusion catheter, there has been further improvement in TIMI 2 and 3 revascularization rates with faster times to vessel opening. The aim of this technical review is to convey various tips and tricks learnt from this experience.
Anhydrous Proton-Conducting Polymers (2003)

▪ Abstract Anhydrous proton-conducting polymers usually consist of a more or less inert polymer matrix that is swollen with an appropriate proton solvent (in most cases, phosphoric acid). An outline of the different materials is provided, with a focus on PBI/H 3 PO 4 blends that are currently most suitable for fuel cell applications. Also discussed are alternative concepts for fully polymeric materials, which establish proton conductivity as an intrinsic property using amphoteric heterocycles such as imidazole as a proton solvent. The development of some of the first polymers is described, and the fundamental relations between their material properties and conductivity are discussed. Closely related to this relatively new concept are mechanistic investigations focusing on intermolecular proton transfer and diffusion of (protonated) solvent molecules, the contributions of both transport processes to conductivity, and the dependence of these ratios on composition, charge carrier density, etc. Although the development of fully polymeric proton conductors is inseparably related to mechanistic considerations, relatively little attention has been paid to these concepts in the field of conventional membranes (hydrated ionomers, H 3 PO 4 -based materials). Consequently, their general relevance is emphasized, and according investigations are summarized to provide a more comprehensive picture of proton transport processes within proton exchange membranes.
Efficacy of mGlu2‐positive allosteric modulators alone and in combination with levetiracetam in the mouse 6 Hz model of psychomotor seizures (2017)

These studies suggest a potential positive pharmacodynamic effect of mGlu<sub>2</sub> -acting compounds in combination with LEV. If this effect is translated in a clinical setting, it can support a rational polypharmacy concept in treatment of epilepsy patients.
Use of Lactobacilli and their Pheromone-Based Regulatory Mechanism in Gene Expression and Drug Delivery (2009)

Lactobacilli are common microorganisms in diverse vegetables and meat products and several of these are also indigenous inhabitants in the gastro-intestinal (GI) tract of humans and animals where they are believed to have health promoting effects on the host. One of the highly appreciated probiotic effects is their ability to inhibit the growth of pathogens by producing antimicrobial peptides, so-called bacteriocins. Production of some bacteriocins has been shown to be strictly regulated through a quorum-sensing based mechanism mediated by a secreted peptide-pheromone (also called induction peptide; IP), a membrane-located sensor (histidine protein kinase; HPK) and a cytoplasmic response regulator (RR). The interaction between an IP and its sensor, which is highly specific, leads to activation of the cognate RR which in turn binds to regulated promoters and activates gene expression. The HPKs and RRs are built up by conserved modules, and the signalling between them within a network is efficient and directional, and can easily be activated by exogenously added synthetic IPs. Consequently, components from such regulatory networks have successfully been exploited in construction of a number of inducible gene expression systems. In this review, we discuss some well-characterised quorum sensing networks involved in bacteriocin production in lactobacilli, with special focus on the use of the regulatory components in gene expression and on lactobacilli as potential delivery vehicle for therapeutic and vaccine purposes.
Applying CDMA Technique to Network-on-Chip (2007)

The issues of applying the code-division multiple access (CDMA) technique to an on-chip packet switched communication network are discussed in this paper. A packet switched network-on-chip (NoC) that applies the CDMA technique is realized in register-transfer level (RTL) using VHDL. The realized CDMA NoC supports the globally-asynchronous locally-synchronous (GALS) communication scheme by applying both synchronous and asynchronous designs. In a packet switched NoC, which applies a point-to-point connection scheme, e.g., a ring topology NoC, data transfer latency varies largely if the packets are transferred to different destinations or to the same destination through different routes in the network. The CDMA NoC can eliminate the data transfer latency variations by sharing the data communication media among multiple users concurrently. A six-node GALS CDMA on-chip network is modeled and simulated. The characteristics of the CDMA NoC are examined by comparing them with the characteristics of an on-chip bidirectional ring topology network. The simulation results reveal that the data transfer latency in the CDMA NoC is a constant value for a certain length of packet and is equivalent to the best case data transfer latency in the bidirectional ring network when data path width is set to 32 bits.
Risk Factors for Hip Fracture in White Men: The NHANES I Epidemiologic Follow-up Study (1998)

This prospective population-based study assessed predictors of hip fracture risk in white men. Participants were members of the Epidemiologic Follow-up Study cohort of the First National Health and Nutrition Examination Survey, a nationally representative sample of noninstitutionalized civilians who were followed for a maximum of 22 years. A cohort of 2879 white men (2249 in the nutrition and weight-loss subsample, 1437 in the bone density subsample) aged 45-74 years at baseline (1971-1975) were observed through 1992. Ninety-four percent of the original cohort were successfully traced. Hospital records and death certificates were used to identify a total of 71 hip fracture cases (61 in the nutrition and weight-loss subsample, 26 in the bone-density subsample). Among the factors evaluated were age at baseline, previous fractures other than hip, body mass index, smoking status, alcohol consumption, nonrecreational physical activity, weight loss from maximum, calcium intake, number of calories, protein consumption, chronic disease prevalence, and phalangeal bone density. The risk adjusted relative risk (RR) of hip fracture was significantly associated with presence of one or more chronic conditions (RR = 1.91, 95% confidence interval [CI] = 1.19-3.06), weight loss from maximum > or = 10% (RR = 2.27, 95% CI 1.13-4.59), and 1 SD change in phalangeal bone density (RR = 1.73, 95% CI 1.11-2.68). No other variables were significantly related to hip fracture risk. Although based on a small number of cases, this is one of the first prospective studies to relate weight loss and bone density to hip fracture risk in men.
TGF-β1 Plays an Important Role in the Mechanism of CD4+CD25+ Regulatory T Cell Activity in Both Humans and Mice (2004)

In previous studies, we have shown that murine CD4+CD25+ regulatory T cells produce high levels of TGF-beta1 in a cell surface and/or secreted form, and blockade of such TGF-beta1 by anti-TGF-beta curtails the ability of these cells to suppress CD25- T cell proliferation and B cell Ig production in in vitro suppressor assays. In further support for the role of TGF-beta1 in suppression by CD4+CD25+ T cells, we show in this study that another TGF-beta1-blocking molecule, recombinant latency-associated peptide of TGF-beta1 (rLAP), also reverses suppression by mouse CD4+CD25+ T cells as well as their human counterparts, CD4+CD25(high) T cells. In addition, we show that CD25- T cells exposed to CD4+CD25+ T cells in vitro manifest activation of Smad-2 and induction of CD103, the latter a TGF-beta-inducible surface integrin. In further studies, we show that while CD4+CD25+ T cells from TGF-beta1-deficient mice can suppress CD25- T cell proliferation in vitro, these cells do not protect recipient mice from colitis in the SCID transfer model in vivo, and, in addition, CD4+LAP+, but not CD4+LAP- T cells from normal mice protect recipient mice from colitis in this model. Together, these studies demonstrate that TGF-beta1 produced by CD4+CD25+ T cells is involved in the suppressor activity of these cells, particularly in their ability to regulate intestinal inflammation.
Effects of anti-VLA-4 Monoclonal Antibody Treatment in Murine Model of Allergic Rhinitis (2000)

In order to study the role of VLA-4 in allergic rhinitis, the effects of anti-mouse VLA-4 monoclonal antibody (mAb) were evaluated in a murine model. BALB/c mice were sensitized first by i.p. injections (general sensitization) and then by daily nasal dripping of antigen (local sensitization) before performing a nasal antigen challenge. The mAb was applied either before the antigen challenge (BC group), before the local sensitization (BL group) or before the general sensitization (BS group). The effects were evaluated in terms of antigen-induced early-phase nasal symptoms (sneezing), late-phase nasal eosinophilia and the serum level of antigen-specific IgE. Antigen-induced nasal eosinophilia was significantly (p = 0.009) reduced in the BL group but not in the BC group (number of eosinophils = 114 +/- 15.1, 244 +/- 52.8 and 347 +/- 50.5 in the BL, BC and control groups, respectively). The serum level of the specific IgE was also significantly (p = 0.038) reduced in the BL group but not in the BC group (optical density = 1.18 +/- 0.07, 1.28 +/- 0.13 and 1.58 +/- 0.14 in the BL, BC and control groups, respectively). The suppressive effect on sneezing was not significant in either the BL or BC groups. In the BS group, suppressive effects on antigen-induced nasal responses and the specific IgE level were not statistically significant. These findings suggest that VLA-4 plays an important role in the topical booster or priming effects during repeated nasal antigen exposures in pre-sensitized animals.