gebhart/patrepeval huggingface dataset:
Exploring Recurrent Neural Networks to Detect Named Entities from Biomedical Text (2015)

Biomedical named entity recognition (bio-NER) is a crucial and basic step in many biomedical information extraction tasks. However, traditional NER systems are mainly based on complex hand-designed features which are derived from various linguistic analyses and maybe only adapted to specified area. In this paper, we construct Recurrent Neural Network to identify entity names with word embeddings input rather than hand-designed features. Our contributions mainly include three aspects: (1) we adapt a deep learning architecture Recurrent Neural Network (RNN) to entity names recognition; (2) based on the original RNNs such as Elman-type and Jordan-type model, an improved RNN model is proposed; (3) considering that both past and future dependencies are important information, we combine bidirectional recurrent neural networks based on information entropy at the top layer. The experiments conducted on the BioCreative II GM data set demonstrate RNN models outperform CRF and deep neural networks (DNN), furthermore, the improved RNN model performs better than two original RNN models and the combined method is effective.
Melanocyte Destruction after Antigen-Specific Immunotherapy of Melanoma (2000)

Current strategies for the immunotherapy of melanoma include augmentation of the immune response to tumor antigens represented by melanosomal proteins such as tyrosinase, gp100, and MART-1. The possibility that intentional targeting of tumor antigens representing normal proteins can result in autoimmune toxicity has been postulated but never demonstrated previously in humans. In this study, we describe a patient with metastatic melanoma who developed inflammatory lesions circumscribing pigmented areas of skin after an infusion of MART-1-specific CD8(+) T cell clones. Analysis of the infiltrating lymphocytes in skin and tumor biopsies using T cell-specific peptide-major histocompatibility complex tetramers demonstrated a localized predominance of MART-1-specific CD8(+) T cells (>28% of all CD8 T cells) that was identical to the infused clones (as confirmed by sequencing of the complementarity-determining region 3). In contrast to skin biopsies obtained from the patient before T cell infusion, postinfusion biopsies demonstrated loss of MART-1 expression, evidence of melanocyte damage, and the complete absence of melanocytes in affected regions of the skin. This study provides, for the first time, direct evidence in humans that antigen-specific immunotherapy can target not only antigen-positive tumor cells in vivo but also normal tissues expressing the shared tumor antigen.
Endogenous formation of N-nitrosoproline in cigarette smokers. (1983)

It was the goal of this study to assay the potential of inhaled cigarette smoke for endogenous N-nitrosation of amines in smokers by means of measuring urinary excretion of N-nitrosoproline (NPRO). For 12 days, nonsmoking and smoking men were placed on a controlled diet which was relatively low in proline and in ascorbic acid. On Days 1 through 3, the volunteers received the controlled diet alone (Group 1); on Days 4 through 6, the diet was supplemented by a single daily dose of 300 mg of proline (Group 2); on Days 7 through 9, the diet was supplemented by a single daily dose of 1 g of ascorbic acid followed by 300 mg of proline (Group 3); and for the last 3 days, a single daily dose of 1 g ascorbic acid was given (Group 4). Collections of 24-hr urine were made on Days 3, 6, 9, and 12 of the study. The urine was analyzed for NPRO and creatinine and for cotinine, the major metabolite of nicotine. The mean 24-hr NPRO excretion for 13 nonsmokers in Group 1 was 3.6 micrograms. The NPRO excretion in 13 smokers in Group 1 was found to be 5.9 micrograms/24 hr, which is significantly higher than that of the nonsmokers (p less than 0.05). Urinary NPRO in 14 nonsmokers of Group 2 was significantly lower than that of the 14 smoking volunteers (p less than 0.05). Data for Group 3 indicated that those smokers who had shown elevated NPRO excretion in Group 2 had reduced urinary levels of NPRO as a consequence of ascorbic acid intake. Differences in NPRO excretion by smokers and nonsmokers on controlled diet with ascorbic acid but without proline supplements (Group 4) were also insignificant. These findings suggest that the documented endogenous N-nitrosation of proline which occurs as a result of cigarette smoke inhalation may also apply to other N-nitrosatable amines including nicotine and thus lead to in vivo formation of carcinogenic N-nitrosamines.
Vibrational Behavior and Structure of Disulfide Dioxides (Thiolsulfonates) (1966)

Infrared and Raman spectra of disulfide dioxides were examined to determine whether they possess the thiolsulfonate or disulfoxide structure. Strong absorptions identified with the SO 2 group support the thiolsulfonate structure. A comparison of infrared spectra of a butyl series of sulfide, sulfoxide, sulfone, sulfinate, sulfonate, disulfide, thiolsulfinate, disulfide dioxide (thiolsulfonate), and α-disulfone confirms the evidence for the thiolsulfonate structure for both the symmetrical and unsymmetrical compounds. With isomeric pairs of mixed disulfide dioxides, the spectra are different in all cases. Where R is CH 3 , there are strong absorptions at 10.4–10.5 and 20.7–20.8 μ only when the methyl is attached to the sulfur atom presumed by synthesis to be in the oxidized SO 2 form. In the reverse isomers, these strong bands, which are associated with CH 3 SO 2 − , are absent.
Interactions with tenascin and differential effects on cell adhesion of neurocan and phosphacan, two major chondroitin sulfate proteoglycans of nervous tissue. (1994)

We have studied interactions of tenascin with two chondroitin sulfate proteoglycans, neurocan and phosphacan. Neurocan is a multi-domain proteoglycan with a 136-kDa core protein that is synthesized by neurons and binds to hyaluronic acid, whereas the 173-kDa core protein of phosphacan, which is synthesized by glia, represents an extracellular variant of the receptor-type protein tyrosine phosphatase RPTP zeta/beta. Keratan sulfate-containing glycoforms of phosphacan (designated phosphacan-KS) are also present in brain. Immunocytochemical studies of early postnatal rat cerebellum demonstrated that the localization of neurocan, phosphacan, and phosphacan-KS all overlap extensively with that of tenascin, an extracellular matrix protein that modulates cell adhesion and migration. Binding studies using purified proteins covalently attached to fluorescent microbeads demonstrated that proteoglycan-coated beads co-aggregated with differently fluorescing beads coated with tenascin. The co-aggregation was specifically inhibited by Fab' fragments of antibodies against tenascin or the proteoglycans and by soluble neurocan, phosphacan, and tenascin. A solid phase radioligand binding assay confirmed that neurocan, phosphacan, and phosphacan-KS bind to tenascin but not to laminin and fibronectin. Chondroitinase treatment of the proteoglycans or addition of free chondroitin sulfate had no significant effect, indicating that the binding activity is mediated largely via the core glycoproteins. Scatchard analysis demonstrated high affinity binding of 125I-phosphacan, phosphacan-KS, and neurocan to a single site in tenascin, and neurocan and various glycoforms of phosphacan all inhibited binding of 125I-phosphacan to tenascin. In studies of cell adhesion to proteins adsorbed to Petri dishes, phosphacan inhibited adhesion of C6 glioma cells to tenascin whereas neurocan had no effect. Our results suggest that tenascin binds phosphacan and neurocan in vivo and that interactions between chondroitin sulfate proteoglycans and tenascin may play important roles in nervous tissue histogenesis, possibly by modulating signal transduction across the plasma membrane.
A video‐based patient contour acquisition system for the design of radiotherapy compensators (1989)

Recent advances in computer and video technology have enabled significant advances in the field of surface topography measurement. This paper will describe a digital video patient contour acquisition system for the design of radiotherapy beam compensators. The system is mounted on a tray which slides into the collimator of a radiotherapy simulator. The tray holds a source which projects a 1-mm wide fan beam of light along the simulator beam axis onto the patient. The tray also holds a small solid state video camera which views the projected line of light on the patient surface. Video images are digitized and processed on an 80386 based IBM PC-compatible computer. Transverse contours are obtained from one digitized video image or, in case of opposed fields, from two or more image frames taken at different gantry angles. Entire surfaces are measured by scanning the bed longitudinally and acquiring a number of transverse contours. Posterior surfaces are obtained by scanning a mold. A printer produces a template for making the compensator from sheet lead.
Solid‐Supported Synthesis and Biological Evaluation of the Lantibiotic Peptide Bis(desmethyl) Lacticin 3147 A2 (2008)

Lan-tastic! A lanthionine analogue of lacticin 3147 A2 (Lan-A2, 2) containing multiple thioether bridges (see picture) has been successfully synthesized by a combination of solid- and solution-phase peptide synthesis. Chemically synthesized Lan-A2 (2) exhibits synergistic biological activity similar to natural lacticin A2 (1) in the presence of natural lacticin A1 against Gram-positive bacteria.
Interleukin 1 receptor antagonist (IL-1ra) levels in patients with burns (1994)

Endo, S.1; Inada, K.2; Baba, N.1; Kasai, T.1; Yamada, Y.1; Kondo, M.1; Kikuchi, M.1; Suzuki, T.1; Taniguchi, S.1; Yoshida, M.2,3 Author Information
Clinical Characteristics and Serum Essential Fatty Acid Levels in Hyperactive Children (1987)

This study compared 48 hyperactive children with 49 age-and-sex-matched controls. Significantly more hyperactive children had auditory, visual, language, reading, and learning difficulties, and the birth weight of hyperactive children was significantly lower than that of controls (3,058 and 3,410 g, respectively; p less than 0.01). In addition, significantly more hyperactive children had frequent coughs and colds, polydypsia, polyuria, and a serious illness or accident in the past year than controls, but there was no increase in asthma, eczema, or other allergies. Serum essential fatty acid (EFA) levels were measured in 44 hyperactive subjects and 45 controls. The levels of docasahexaenoic, dihomogammalinolenic, and arachidonic acids were significantly lower in hyperactive children than controls (docosahexaenoic: 41.6 and 49.5 micrograms/ml serum respectively, p = 0.045; dihomogammolinolenic: 34.9 and 41.3 micrograms/ml serum, p = 0.007; arachidonic: 127.1 and 147.0 micrograms/ml serum, p = 0.027). These findings have possible therapeutic and diagnostic implications, but further research is needed to attempt to replicate these differences.
A236 parallel DSP chip provides real-time video processing economically and efficiently (2002)

Oxford Computer's A236 parallel digital signal processor chip is flexible, fully programmable and designed to compactly and inexpensively provide live video capture, processing and display. The use of single-chip, parallel processing with integrated data and instruction caches, and an inexpensive, high performance memory system, provide high performance at low cost. An extended, single-instruction multiple-data (SIMD) architecture with one, 24-bit scalar processor and four, 16-bit vector processors, is used. Five instructions are issued each clock cycle with a 40 MHz clock, providing up to 200 MIPS. Two, 16-bit, bi-directional, double-buffered, DMA ports support simultaneous video acquisition and display, and interface directly to common video decoder and encoder chips with no glue logic. A minimum system that provides all input and output frame buffering contains only three chips, an A236 Chip, a 32-bit wide, synchronous DRAM, and a serial I/sup 2/C EEPROM, plus analog video interface chips. A full set of software development tools that runs under MS Windows is available free, including an enhanced C-compiler that provides a simple method for representing parallel operations on data structures. An evaluation kit containing the software tools and the A236 Video Processing System I is also available.
Learning From the Placenta (2010)

Preeclampsia is a common and potentially lethal pregnancy complication for women and offspring. Women who develop preeclampsia also run a long-term augmented risk of cardiovascular disease and premature death, and two theories are discussed. Women developing preeclampsia and persons developing cardiovascular disease may have common risk factors, which are unmasked by the "stress" of pregnancy. Alternatively, a new risk factor might occur de novo during the preeclamptic pregnancy. In preeclampsia, lipid deposition in walls of the maternal uterine arteries leading to the placenta, named spiral arteries, regularly occurs. These vascular lesions resemble early stages of atherosclerosis and are named "acute atherosis" and is thought to regress after delivery. The mechanisms that contribute to acute atherosis in preeclampsia are largely unknown, but are related to the impaired vascular remodeling of the spiral arteries in the first half of pregnancy. One striking feature is that the development of these "atherosclerosis-like" lesions requires a few months in pregnancy and may be partly linked to invasion of trophoblasts (specialized fetally derived placenta cells). We summarize normal and pathological vessel remodeling in pregnancy and discuss similarities and differences between preeclampsia and arteriosclerosis. The transient appearance of acute atherosis of uterine wall spiral arteries seen in pregnancy complications and the molecular interaction between trophoblast, smooth muscle and vascular cells could add important elements to explain arteriosclerosis and stenosis in cardiovascular disease. Further understanding of the process underlying spiral artery atherosis in the months of pregnancy may cast light on development of cardiovascular disease later in life.
Application of dynamic capillary isoelectric focusing to the analysis of human hemoglobin variants (1994)

Capillary isoelectric focusing (CIEF) with electro-osmotic zone displacement of normal and pathological hemoglobins (Hb) is reported. CIEF is performed in untreated, open-tubular, fused-silica capillaries of 75 microns internal diameter using methylcellulose for dynamic column conditioning. After direct injection of hemolysates mixed with carrier ampholytes, high resolution separation of Hb variants, including Hb A1c, A, F, D, S, E and A2, is obtained, this permitting unambiguous characterization of Hb patterns of normal adults, newborns, patients with diabetes, different hemoglobinopathies and thalassemia syndromes. Qualitatively, the CIEF data compare well with those obtained by gel isoelectric focusing and high-performance liquid chromatography. CIEF is demonstrated to be a simple, rapid and fully instrumental approach to Hb analysis. Run times of less than 20 min make CIEF an attractive method for routine Hb investigations and screening programs.
Blockade of A2a Adenosine Receptors Positively Modulates Turning Behaviour and c‐Fos Expression Induced by D1 Agonists in Dopamine‐denervated Rats (1996)

In rats with unilateral 6-hydroxydopamine lesions of the dopaminergic nigrostriatal pathway, administration of the A2a adenosine antagonist SCH 58261 alone did not induce any motor asymmetry but strongly potentiated the contralateral turning behaviour induced by the dopamine D1 agonist SKF 38393. SCH 58261 also increased the number of Fos-like positive nuclei induced by SKF 38393 in the 6-hydroxydopamine-lesioned striatum. Intense potentiation of D1-dependent turning behaviour and c-Fos expression was also observed after administration of the A2a/A1 antagonist CGS 15943. Administration of the A1 adenosine receptor antagonist DPCPX induced a small potentiation of D1-mediated contralateral turning while c-Fos expression induced by SKF 38393 was not modified. The results suggest that endogenous adenosine acting on A2a receptors can exert an inhibitory influence on the functional expression of D1-mediated responses in dopamine-denervated rats, and propose new possible therapeutic approaches in the treatment of Parkinson's disease.
Mapping and ranking of potential cytotoxic T epitopes in the p53 protein: effect of mutations and polymorphism on peptide binding to purified and refolded HLA molecules (1995)

In many cancer cells, the p53 gene displays point mutations that result in stabilization and accumulation of the p53 protein. Therefore, p53 peptides could be presented to the immune system by tumor cells; thus, p53 might be a suitable target antigen for developing an immunotherapy against tumors using cytotoxic T lymphocytes (CTL). To map candidate CTL epitopes, we synthesized 150 peptides of 8-11 residues that contained putative anchor motifs required for binding to common HLA class I molecules. They were tested for their capacity to promote the assembly of purified and refolded HLA-A1, A2, B7 and B8 molecules. The following wild-type p53 peptides were found to be reactive with the HLA molecules tested: 196-205 and 226-234 bound moderately to HLA-A1; 25-35, 65-73, 129-137, 187-197, 263-272 and 264-272 bound strongly, and 187-195 and 256-264 moderately to HLA-A2; 26-35, 63-73, 189-197, 249-257 and 321-330 bound strongly to HLA-B7; and 135-143, 210-218 and 375-383 bound weakly to HLA-B8. We also analyzed the effects of p53 mutations occurring naturally in tumors on peptide/HLA assembly. We found substitutions that enhanced, diminished or had no effect on the peptide binding to HLA molecules. Polymorphism at position 72 mainly affected peptide/HLA-B7 binding, the proline allele P72 giving a less-reactive peptide (63-73) than the arginine allele R72. We have ranked potential p53 epitopes according to their reactivity for purified HLA molecules, allowing the selection of appropriate peptides and HLA molecules to attempt CTL induction in vitro.
Os genes ERCC1 e RRM1 no carcinoma broncopulmonar (2009)

In lung cancer, expressive survival has not yet been achieved in non surgical stages. Non-small cell lung cancer (NSCLC) patients are treated with platinum and other drugs. To choose these agents we can actual ly define predictive biomarkers to preview therapeutic response. A literature revision was done in order to define the role of ERCC1 e RRM1 genes in the response to chemotherapy based in platinum and gemcitabine respectively. The expression of these genes is faced as a predictive marker to the chemotherapy response in patients with adenocarcinomas and squamous cell carcinomas, providing a personalized therapy. Published data supports this behaviour and is useful to individualize therapy accordingly to individual levels of ERCC1 which are modified by genetic mutations. Polymorphisms in codons 118 C/T and C8092A, seem to influence the carcinogenesis, cytostatic resistance, survival and even the prognosis. Clinical and laboratorial trials showed that high expression of RRM1 gene in NSCLC has impact in the tumoral phenotype. Patients having done surgical resection and presenting high expression of RRM1 have better survival than those with lower expression. However, patients with advanced NSCLC and treated with chemotherapy with gemcitabine and cisplatin appear to have a poor outcome if the tumor express elevated levels of RRM1 gene.
Rapamycin reduces disease activity and normalizes T cell activation–induced calcium fluxing in patients with systemic lupus erythematosus (2006)

Rapamycin appears to be a safe and effective therapy for SLE that has been refractory to traditional medications. Mitochondrial dysfunction and Ca2+ fluxing could serve as biomarkers to guide decisions regarding future therapeutic interventions in SLE.
Optical and Conductive Characteristics of Metallic Single-Wall Carbon Nanotubes with Three Basic Colors; Cyan, Magenta, and Yellow (2008)

We present protocols to prepare high-purity metallic single-wall carbon nanotubes (SWCNTs) with three basic colors, cyan, magenta, and yellow, through density gradient centrifugations. Addition of deoxycholate sodium salts as a co-surfactant could improve separation capability for metallic SWCNTs in centrifugations. We applied the improved separation protocols to the SWCNTs with different average diameters (1.34, 1.0, and 0.84 nm), and obtained the metallic SWCNTs with cyan, magenta, and yellow colors. Their optical/conductive characteristics were revealed, and conductive color films were formed from the metallic SWCNTs.
Improvements in 2.4 kbps high-quality speech coding (1992)

An algorithm for 2.4 kb/s speech coding is described. The main problem addressed is the coding of voiced speech. A way of coding the pitch structure is introduced. Compared with traditional coding schemes, it results in a better compromise between bit allocation for short-term quantization and residual coding. The coder uses vector quantization of the short-term parameters (line spectrum frequencies). The residual is lowpass filtered to obtain the baseband signal. Unvoiced frames are coded by means of a method based on repetition and interpolation of pitch pulses. The method exploits the high correlation between pitch pulses. Harmonic postfiltering is applied to obtain an improved high-frequency regeneration.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Biosynthesis of lactate‐containing polyesters by metabolically engineered bacteria (2011)

Due to increasing concerns about environmental problems, climate change and limited fossil resources, bio-based production of chemicals and polymers is gaining attention as one of the solutions to these problems. Polyhydroxyalkanoates (PHAs) are polyesters that can be produced by microbial fermentation. PHAs are synthesized using monomer precursors provided from diverse metabolic pathways and are accumulated as distinct granules inside the cells. On the other hand, most so-called bio-based polymers including polybutylene succinate, polytrimethylene terephthalate, and polylactic acid (PLA) are synthesized by a chemical process using monomers produced by fermentation. PLA, an attractive biomass-derived plastic, is currently synthesized by heavy metal-catalyzed ring opening polymerization of L-lactide that is made from fermentation-derived L-lactic acid. Recently, a complete biological process for the production of PLA and PLA copolymers from renewable resources has been developed by direct fermentation of recombinant bacteria employing PHA biosynthetic pathways coupled with a novel metabolic pathway. This could be accomplished by establishing a pathway for generating lactyl-CoA and engineering PHA synthase to accept lactyl-CoA as a substrate combined with systems metabolic engineering. In this article, we review recent advances in the production of lactate-containing homo- and co-polyesters. Challenges remaining to efficiently produce PLA and its copolymers and strategies to overcome these challenges through metabolic engineering combined with enzyme engineering are discussed.