gebhart/patrepeval huggingface dataset:
Phosphorylation of eIF2 Facilitates Ribosomal Bypass of an Inhibitory Upstream ORF to Enhance CHOP Translation (2011)

In response to different environmental stresses, phosphorylation of eukaryotic initiation factor-2 (eIF2) rapidly reduces protein synthesis, which lowers energy expenditure and facilitates reprogramming of gene expression to remediate stress damage. Central to the changes in gene expression, eIF2 phosphorylation also enhances translation of ATF4, a transcriptional activator of genes subject to the integrated stress response (ISR). The ISR increases the expression of genes important for alleviating stress or alternatively triggering apoptosis. One ISR target gene encodes the transcriptional regulator CHOP whose accumulation is critical for stress-induced apoptosis. In this study, we show that eIF2 phosphorylation induces preferential translation of CHOP by a mechanism involving a single upstream ORF (uORF) located in the 5'-leader of the CHOP mRNA. In the absence of stress and low eIF2 phosphorylation, translation of the uORF serves as a barrier that prevents translation of the downstream CHOP coding region. Enhanced eIF2 phosphorylation during stress facilitates ribosome bypass of the uORF due to its poor start site context, and instead it allows scanning ribosomes to translate CHOP. This new mechanism of translational control explains how expression of CHOP and the fate of cells are tightly linked to the levels of phosphorylated eIF2 and stress damage.
Thrombocytopenia associated with ranitidine. (1985)

underlines the importance of considering inflammatory bowel disease.We thank the many doctors who referred these patients to us and the other physicians at the Hospital for Tropical Diseases for allowing us to abstract case records of patients admitted under their care.1 Cook GC.Tropicalgastroenterology.
Distance metric learning and feature combination for shape-based 3D model retrieval (2010)

This paper proposes a 3D model retrieval algorithm that employs an unsupervised distance metric learning with a combination of appearance-based features; two sets of local visual features and a set of global features. These visual features are extracted from range images rendered from multiple viewpoints about the 3D model to be compared. The local visual features are bag-of-features histograms of a set of Scale Invariant Feature Transform (SIFT) features by Lowe [7] sampled at either salient or dense and random points. The global visual feature is also a SIFT feature sampled at an image center. The proposed method then uses an unsupervised distance metric learning based on the Manifold Ranking (MR) [15] to compute distances between these features. However, the original MR may not be effective when applied to a set of features having certain distance distribution. We propose an empirical method to adjust the distance profile so that the MR becomes effective. Experiments showed that the retrieval algorithm using a linear combination of distances computed from the proposed set of features by using the modified MR performed well across multiple benchmarks having different characteristics.
Towards an ISO Standard for Dialogue Act Annotation (2010)

HAL is a multi-disciplinary open access archive for the deposit and dissemination of sci-entific research documents, whether they are pub-lished or not. The documents may come from teaching and research institutions in France or abroad, or from public or private research centers. L’archive ouverte pluridisciplinaire HAL, est destinée au dépôt et a ̀ la diffusion de documents scientifiques de niveau recherche, publiés ou non, émanant des établissements d’enseignement et de recherche français ou étrangers, des laboratoires publics ou privés. Towards an ISO standard for dialogue act annotation
Recommendations for the Standardization and Interpretation of the Electrocardiogram (2007)

This statement examines the relation of the resting ECG to its technology. Its purpose is to foster understanding of how the modern ECG is derived and displayed and to establish standards that will improve the accuracy and usefulness of the ECG in practice. Derivation of representative waveforms and measurements based on global intervals are described. Special emphasis is placed on digital signal acquisition and computer-based signal processing, which provide automated measurements that lead to computer-generated diagnostic statements. Lead placement, recording methods, and waveform presentation are reviewed. Throughout the statement, recommendations for ECG standards are placed in context of the clinical implications of evolving ECG technology.
Vernalization: Winter and the Timing of Flowering in Plants (2009)

Plants have evolved many systems to sense their environment and to modify their growth and development accordingly. One example is vernalization, the process by which flowering is promoted as plants sense exposure to the cold temperatures of winter. A requirement for vernalization is an adaptive trait that helps prevent flowering before winter and permits flowering in the favorable conditions of spring. In Arabidopsis and cereals, vernalization results in the suppression of genes that repress flowering. We describe recent progress in understanding the molecular basis of this suppression. In Arabidopsis, vernalization involves the recruitment of chromatin-modifying complexes to a clade of flowering repressors that are silenced epigenetically via histone modifications. We also discuss the similarities and differences in vernalization between Arabidopsis and cereals.
Inferring grammar from lexis: machine-readable dictionaries as sources of wholesale syntactic and semantic information (1993)

The main idea behind research into machine-readable dictionaries (MRDs) is that the re-use of such resources enables the NLP community to build up large-scale lexicons with a realistic level of coverage instead of the customary purpose-built 'toy' lexicons containing just a few sample items. Most of the earlier work in this area was concerned with the systematic extraction of easily identifiable types of information: pronunciation etc. More recently the focus has shifted to less tractable aspects: subcategorization, semantic typing, taxonomic-thesauric relations etc. The research performed by the author's group at Amsterdam University reflects this. The ASCOT project was restricted to the extraction of syntactic information from the MRD version of the Longman Dictionary of Contemporary English (LDOCE-P. Procter, 1978). In the LINKS project attention was turned to the semantic interconnections in the same dictionary, and in ACQUILEX this line of approach has been extended, on the basis of both LDOCE and two Van Dale dictionaries (P.J.G. van Sterkenburg & W.J.J. Pijnenburg, 1984; and W. Martin & G.A.J. Tops, 1986) to the construction of semantic taxonomies and lexical knowledge bases.
Purine metabolism of human glioblastoma in vivo. (1990)

The aim of this study was to identify targets for rational chemotherapy of glioblastoma. In order to elucidate differences in the biochemistry of tumor and normal human brain, in vivo pool sizes of purine nucleotides, nucleosides, and nucleobases and of purine metabolizing enzymes in biopsy material from 14 grade IV astrocytomas and 4 normal temporal lobe samples were analyzed. Specimens were collected during surgery using the freeze-clamp sampling technique and analyzed by high pressure liquid chromatography. Total purine nucleotides, adenylates, and guanylates in the tumors were 2186, 1865, and 310 nmol/g (wet weight), respectively, which corresponds to 61, 60, and 71% of normal brain tissue concentrations. Relative to normal brain the tumors had significantly lower ATP and GTP levels, essentially normal pool sizes of purine nucleosides and bases, unchanged activities of the salvage enzymes hypoxanthine-guanine phosphoribosyltransferase, adenine phosphoribosyltransferase, and adenosine kinase (659, 456, and 98 nmol/h/mg protein, respectively) and 4-fold higher activities of IMP dehydrogenase (11.6 nmol/h/mg protein); the latter is the rate limiting enzyme for guanylate de novo synthesis. IMP pools in the tumors were 64% of values in normal brain. Modulation of the guanylate pathway in glioblastoma by inhibition of IMP dehydrogenase with tumor specific agents such as tiazofurin (2-beta-D-ribofuranosylthiazole-4-carboxamide) appears to be a rational therapeutic approach. Preliminary in vitro experiments with normal and malignant tissue specimens from 2 additional patients revealed that significant amounts of the active metabolite thiazole-4-carboxamide adenine dinucleotide are formed from tiazofurin. At a concentration of 200 microM this drug was able to deplete guanylate pools in the tumors to a median of 54% of phosphate buffered saline treated controls. Flux studies with [14C]formate showed that tiazofurin strongly inhibited de novo synthesis of guanylates in glioblastoma to an average of 10% of controls. This effect was more pronounced in the tumors as compared to normal brain. No inhibition of salvage of [14C]guanine by tiazofurin could be observed in normal and malignant tissues. Supportive measures have to be considered to inhibit the highly active salvage enzyme hypoxanthine-guanine phosphoribosyltransferase that can partly antagonize a tiazofurin induced decrease in guanine nucleotides.
Pertussis Toxin Inhibits Induction of Tissue-Specific Autoimmune Disease by Disrupting G Protein-Coupled Signals (2001)

Pertussis toxin (PTX) has been used for many years as an adjuvant that promotes development of tissue-specific experimental autoimmune diseases such as experimental autoimmune encephalomyelitis, experimental autoimmune uveitis (EAU), and others. Enhancement of vascular permeability and of Th1 responses have been implicated in this effect. Here we report a surprising observation that, in a primed system, PTX can completely block the development of EAU. Disease was induced in B10.RIII mice by adoptive transfer of uveitogenic T cells, or by immunization with a uveitogenic peptide. A single injection of PTX concurrently with infusion of the uveitogenic T cells, or two injections 7 and 10 days after active immunization, completely blocked development of EAU. EAU also was prevented by a 1-h incubation in vitro of the uveitogenic T cells with PTX before infusing them into recipients. Uveitogenic T cells treated with PTX in vitro and lymphoid cells from mice treated with PTX in vivo failed to migrate to chemokines in a standard chemotaxis assay. Neither the isolated B-oligomer subunit of PTX that lacks ADP ribosyltransferase activity nor the related cholera toxin that ADP-ribosylates G(s) (but not G(i)) proteins blocked EAU induction or migration to chemokines. We conclude that PTX present at the time of cell migration to the target organ prevents EAU, and propose that it does so at least in part by disrupting signaling through G(i) protein-coupled receptors. Thus, the net effect of PTX on autoimmune disease would represent an integration of enhancing and inhibitory effects.
Mitotic inhibition and chromosome displacement induced by estradiol in chinese hamster cells (1987)

We tested diethylstilbestrol (DES) and 17 beta-estradiol as mitotic arrestants to determine their effects on chromosome distribution, spindle microtubules, and the cytoplasmic microtubule complex (CMTC) in the Chinese hamster strain Don. Cytological experiments assessed micronuclei induction, chromosome displacement, and anaphase recovery. Indirect immunofluorescence microscopy with antibody to tubulin and electron microscopy were used to illustrate effects on microtubules. Both DES and estradiol were potent inhibitors of mitosis when applied to cells in vitro. Estradiol induced micronuclei at a greater frequency than did DES. Estradiol-arrested metaphases often contained misaligned chromosomes despite the presence of a bipolar spindle and an equatorial plate. Equatorial plates were not observed in DES-arrested cells. Cells recovered quickly from estradiol exposure upon removal of the steroid. The frequency of abnormal metaphases and abnormal anaphases declined as the recovery period increased. Microtubule experiments showed that DES inhibited spindle assembly and disassembled the CMTC, whereas estradiol, at similar concentrations, arrested mitosis in a manner that allowed spindle assembly. A definite effect on the CMTC by estradiol could not be determined. However, changes in cell morphology were observed. In the presence of estradiol, centrosomes organized microtubules that joined with kinetochores of chromosomes at the equatorial plate as well as with those of misaligned chromosomes. Misaligned chromosomes appeared predominantly at polar regions of mitotic cells. Following drug removal, the pole-oriented chromosomes reoriented at the equatorial plate. The unique arresting properties of estradiol may prove useful in studies of chromosome migration and segregation during mitosis.
Null mutation of the prolactin receptor gene produces multiple reproductive defects in the mouse. (1997)

Mice carrying a germ-line null mutation of the prolactin receptor gene have been produced by gene targeting in embryonic stem cells. Heterozygous females showed almost complete failure of lactation attributable to greatly reduced mammary gland development after their first, but not subsequent, pregnancies. Homozygous females were sterile owing to a complete failure of embryonic implantation. Moreover, they presented multiple reproductive abnormalities, including irregular cycles, reduced fertilization rates, defective preimplantation embryonic development, and lack of pseudopregnancy. Half of the homozygous males were infertile or showed reduced fertility. This work establishes the prolactin receptor as a key regulator of mammalian reproduction, and provides the first total ablation model to further study the role of the prolactin receptor and its ligands.
Fast and Slow Deposition of Silver Nanorods on Planar Surfaces:  Application to Metal-Enhanced Fluorescence (2005)

Two methods have been considered for the deposition of silver nanorods onto conventional glass substrates. In the first method, silver nanorods were deposited onto 3-(aminopropyl)triethoxysilane-coated glass substrates simply by immersing the substrates into the silver nanorod solution. In the second method, spherical silver seeds that were chemically attached to the surface were subsequently converted and grown into silver nanorods in the presence of a cationic surfactant and silver ions. The size of the silver nanorods was controlled by sequential immersion of silver seed-coated glass substrates into a growth solution and by the duration of immersion, ranging from tens of nanometers to a few micrometers. Atomic force microscopy and optical density measurements were used to characterize the silver nanorods deposited onto the surface of the glass substrates. The application of these new surfaces is for metal-enhanced fluorescence (MEF), whereby the close proximity of silver nanostructures can alter the radiative decay rate of fluorophores, producing enhanced signal intensities and an increased fluorophore photostability. In this paper, it is indeed shown that irregularly shaped silver nanorod-coated surfaces are much better MEF surfaces as compared to traditional silver island or colloid films. Subsequently, these new silver nanorod preparation procedures are likely to find a common place in MEF, as they are a quicker and much cheaper alternative as compared to surfaces fabricated by traditional nanolithographic techniques.
TNF suppresses acute intestinal inflammation by inducing local glucocorticoid synthesis (2010)

Although tumor necrosis factor (alpha) (TNF) exerts proinflammatory activities in a variety of diseases, including inflammatory bowel disease, there is increasing evidence for antiinflammatory actions of TNF. In contrast, glucocorticoids (GCs) are steroid hormones that suppress inflammation, at least in part by regulating the expression and action of TNF. We report that TNF induces extraadrenal production of immunoregulatory GCs in the intestinal mucosa during acute intestinal inflammation. The absence of TNF results in a lack of colonic GC synthesis and exacerbation of dextran sodium sulfate-induced colitis. TNF seems to promote local steroidogenesis by directly inducing steroidogenic enzymes in intestinal epithelial cells. Therapeutic administration of TNF induces GC synthesis in oxazolone-induced colitis and ameliorates intestinal inflammation, whereas inhibition of intestinal GC synthesis abrogates the therapeutic effect of TNF. These data show that TNF suppresses the pathogenesis of acute intestinal inflammation by promoting local steroidogenesis.
Physical and biologic impermeability of intestinal sutures in the first twenty-four hours after operations on the gastrointestinal tract. (1992)

The author has substantiated a concept that in the general notion of the impermeability of intestinal sutures, it is necessary to distinguish between physical impermeability (imperviousness of sutures to liquids and gases) and biologic impermeability (imperviousness of sutures to microbes and toxins). It was established in experiments on 165 dogs that infection that invaded peritoneum during operation disappeared from the peritoneal cavity within an hour of small-bowel and stomach surgery and within 1 1/2 hours of colon surgery. Then a period of sterility of peritoneum was observed, which lasted for 8 to 9 hours after operations on the stomach and the small bowel (p = 0.01) and for 4 to 7 hours after operations on the colon (p = 0.01). In the following hours the peritoneal cavity was infected through physically hermetic intestinal sutures. At the end of 24 hours the peritoneum of operated organs showed the presence of 10(4) to 10(6) intestinal microbes. Greater omentum, bowel loops, and their mesentery adhered to the suture in response to the infection through the suture. Complete covering of the suture with adjacent viscera prevented infection of the peritoneal cavity through the suture. The author suggests a well-grounded concept of the leading role of infection through a physically hermetic intestinal suture in the development of postoperative peritonitis and peritoneal adhesions.
Levenshtein error-correcting barcodes for multiplexed DNA sequencing (2013)

We present an adaptation of Levenshtein codes to DNA contexts capable of correction of a pre-defined number of insertion, deletion, and substitution mutations. Our improved method is additionally capable of recovering the new length of the corrupted codeword and of correcting on average more random mutations than traditional Levenshtein or Hamming codes.As part of this work we prepared software for the flexible generation of DNA codes based on our new approach. To adapt codes to specific experimental conditions, the user can customize sequence filtering, the number of correctable mutations and barcode length for highest performance.
High-speed bidirectional four-channel optical FDM-NCFSK transmission using an Er/sup 3+/-doped fiber amplifier (1993)

A four-channel optical frequency division multiplexed-noncoherent frequency-shift keying (FDM-NCFSK) bidirectional transmission experiment using an Er/sup 3+/ doped fiber amplifier at 1.7 Gb/s for 100 km fiber length is demonstrated. Using commercial distributed feedback (DFB) laser diodes (LDs), a received power of -35 dBm at 10/sup -9/ BER is obtained, and the dispersion degradation over 100-km bidirectional transmission is negligible. With channel spacing of about 30 GHz, the differential power penalty is about 0.1 dB.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Cholesterol crystals cause mechanical damage to biological membranes: A proposed mechanism of plaque rupture and erosion leading to arterial thrombosis (2005)

These observations suggest that crystallization of supersaturated cholesterol in atherosclerotic plaques can induce cap rupture and/or erosion. This novel insight may help in the development of therapeutic strategies that can alter cholesterol crystallization and prevent acute cardiovascular events.
Cell Size Checkpoint Control by the Retinoblastoma Tumor Suppressor Pathway (2006)

Size control is essential for all proliferating cells, and is thought to be regulated by checkpoints that couple cell size to cell cycle progression. The aberrant cell-size phenotypes caused by mutations in the retinoblastoma (RB) tumor suppressor pathway are consistent with a role in size checkpoint control, but indirect effects on size caused by altered cell cycle kinetics are difficult to rule out. The multiple fission cell cycle of the unicellular alga Chlamydomonas reinhardtii uncouples growth from division, allowing direct assessment of the relationship between size phenotypes and checkpoint function. Mutations in the C. reinhardtii RB homolog encoded by MAT3 cause supernumerous cell divisions and small cells, suggesting a role for MAT3 in size control. We identified suppressors of an mat3 null allele that had recessive mutations in DP1 or dominant mutations in E2F1, loci encoding homologs of a heterodimeric transcription factor that is targeted by RB-related proteins. Significantly, we determined that the dp1 and e2f1 phenotypes were caused by defects in size checkpoint control and were not due to a lengthened cell cycle. Despite their cell division defects, mat3, dp1, and e2f1 mutants showed almost no changes in periodic transcription of genes induced during S phase and mitosis, many of which are conserved targets of the RB pathway. Conversely, we found that regulation of cell size was unaffected when S phase and mitotic transcription were inhibited. Our data provide direct evidence that the RB pathway mediates cell size checkpoint control and suggest that such control is not directly coupled to the magnitude of periodic cell cycle transcription.
Low molecular weight PLA: a suitable polymer for pulmonary administered microparticles? (1993)

Beclomethasonedipropionate (BDP)-containing microparticles were prepared by the solvent evaporation/extraction method. Different preparation parameters were optimized before investigations. Polylactic acid (PLA) and polylactic/glycolic acid (PLGA) with molecular weights of 2000 and 15,000 were used as matrix polymers. In all experiments the mean diameter of the microparticles was 1-5 microns with a drug content > or = 23 per cent. Microparticles of PLA, MW 2000, showed a prolonged and complete release over 8 h, whereas those of PLGA liberated only 20 per cent of the encapsulated drug within 8 h. BDP was determined by a validated reversed-phase HPLC method with a detection limit of 20 ng/ml. The encapsulated steroid seemed to be dissolved within the polymer, as differential scanning calorimetry suggested. Considering mean particle size, drug load, release characteristics and the status of the drug inside the matrix, the dosage form showed very good characteristics for inhalatory application. Surface characteristics of the microparticles were visualized by scanning electron microscopy (SEM). Although in vitro studies with human bronchial fluid resulted in a strong deterioration of microparticles, main structures were still visible by SEM after an incubation of 36 h in diluted bronchial fluid ex vivo. Degradation in phosphate buffered saline, protein solution and even in port liver esterase suspension resulted in minor effects on the particle surface.