gebhart/patrepeval huggingface dataset:
Naloxone treatment in opioid addiction: the risks and benefits (2007)

Naloxone is a non-selective, short-acting opioid receptor antagonist that has a long clinical history of successful use and is presently considered a safe drug over a wide dose range (up to 10 mg). In opioid-dependent patients, naloxone is used in the treatment of opioid-overdose-induced respiratory depression, in (ultra)rapid detoxification and in combination with buprenorphine for maintenance therapy (to prevent intravenous abuse). Risks related to naloxone use in opioid-dependent patients are: i) the induction of an acute withdrawal syndrome (the occurrence of vomiting and aspiration is potentially life threatening); ii) the effect of naloxone may wear off prematurely when used for treatment of opioid-induced respiratory depression; and iii) in patients treated for severe pain with an opioid, high-dose naloxone and/or rapidly infused naloxone may cause catecholamine release and consequently pulmonary edema and cardiac arrhythmias. These risks warrant the cautious use of naloxone and adequate monitoring of the cardiorespiratory status of the patient after naloxone administration where indicated.
Image editing in the contour domain (2001)

We propose a novel method for image editing in which the primitive working unit is not a pixel but an edge. The feasibility of this proposal is suggested by the recent work of Elder et al. (1998) showing that a gray-scale image can be accurately represented by its edge map if a suitable edge model and scale selection method are employed. In particular, an efficient algorithm has been reported by Elder et al. (1996) and Elder (1999) to invert such an edge representation to yield a high-fidelity reconstruction of the original image. We combined these algorithms together with an efficient method for contour grouping and an intuitive user interface to allow users to perform image editing operations directly in the contour domain. Experimental results suggest that this novel combination of vision algorithms may increase the efficiency of certain classes of image editing operations.
Two distinct proteolytic processes in the generation of a major histocompatibility complex class I-presented peptide (1997)

Although cellular proteins degraded by proteasomes are the source of most antigenic peptides presented on major histocompatibility complex class I molecules, it is unknown whether the eight- to nine-residue peptides that fit in the binding groove of class I molecules are directly produced by proteasomes alone in vivo. If the eight-residue peptide SIINFEKL from chicken ovalbumin is extended by one or several residues at its C terminus and microinjected into cells or expressed from a minigene, it is processed and presented on major histocompatibility complex class I. However, processing and presentation are inhibited by proteasome inhibitors, such as lactacystin. In contrast, when SIINFEKL is extended by 2 to 25 residues at its N terminus, its presentation is not blocked by proteasome inhibitors. N-terminal processing also can occur when the extended peptide is cotranslationally inserted into the endoplasmic reticulum. Thus, two different proteolytic steps in the generation of an chicken ovalbumin-presented peptide can be distinguished. Cleavage by the proteasome defines the proper C terminus, whereas distinct peptidase(s) in the cytosol or endoplasmic reticulum may generate the appropriate N terminus from extended peptides.
XSQ: Streaming XPath Queries (2002)

We describe the design and implementation of XSQ, a system for evaluating XPath 1.0 queries on streaming XML data. Each XML element in the input data is presented to the system only once in a serial order determined by the data source. It is not possible to seek forward or backward in the data stream, and data cannot be recalled unless explicitly buffered by the system. Processing XPath queries correctly and efficiently in this environment is a challenging task and, to the best of our knowledge, XSQ is the first system that efficiently implements XPath queries with features such as closures and multiple predicates. XSQ is efficient in both time and space. Stream query processing typically adds only 25% to the time required for parsing the stream (and discarding results). XSQ's space usage is optimal in the sense that it buffers only data that must be buffered by all streaming query processors. We describe the formal framework of hierarchical pushdown transducers that forms the basis of the XSQ system and highlight experimental results on real and synthetic data. (Also UMIACS-TR-2002-81)
Isolation & cryo-preservation of human foetal articular chondrocytes. (1993)

An attempt to determine the ideal temperature and duration of storage of human foetal chondrocytes yielded highly cellular preparations with no alteration in morphology or loss of viability. Initial digestion with activated papain was followed by incubation in 0.5 per cent collagenase. Trypan blue exclusion test revealed a viability count of 95-99 per cent and radioactive thymidine uptake a corresponding labelling index. On TEM no subcellular damage was evident. The isolated viable chondrocytes were further banked at varying temperatures of +4 degrees, -4 degrees, -30 degrees, -79 degrees and -196 degrees C, in Eagles MEM with 10 per cent dimethyl sulfoxide. Post storage morphology and viability of these cells, thawed after durations of 20 h, 1 wk, 1, 2, 3, 4 and 6 months, were compared with prestorage readings in an attempt to define the ideal temperature for banking. Storage in liquid nitrogen at -196 degrees C demonstrated excellent preservation even at the end of six months with minimal subcellular change. Electron microscopy and labelling index were found to be superior to Trypan blue exclusion test in assessing the stored chondrocytes for retention of their functions.
Structure changes caused by strain annealing of nylon 6 fibers (1978)

Abstract Abstract Experiments are described in which nylon 6 fibers are annealed while subjected to a constant stretch (or slack). Subsequent mechanical and structural measurements are described and analyzed. A paracrystalline structure model is proposed in which folded chains, fully extended chains, partially folded, and partially extended chains coexist in the highly drawn high strength fiber. An explanation of structural changes occurring during the thermal-mechanical treatment is that the folded and partially folded chains are arranged randomly in staggered fashion in small units throughout the structure. During slack annealing, the chains become more folded and shrinkage occurs. Some of the chain refolding will be permanent and may act as new defect sites thereby reducing fracture stress. During annealing in the presence of comparatively high tensile stresses the folded chains are unfolded to some extent, but not completely, and the load-carrying chains in the structure are more uniformly loaded. At the higher applied strains during annealing, chains are broken and may snap back into folds. The tension annealing increases the overall chain orientation, the strained segment uniformity, and the number of load-bearing chains. These factors may contribute to an increased fracture stress.
Blockade of neuronal nitric oxide synthase protects against excitotoxicity in vivo (1995)

Nitric oxide may be a key mediator of excitotoxic neuronal injury in the central nervous system. We examined the effects of the neuronal nitric oxide synthase inhibitor 7-nitroindazole (7-NI) on excitotoxic striatal lesions. 7-NI significantly attenuated lesions produced by intrastriatal injections of NMDA, but not kainic acid or alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid (AMPA) 7-NI attenuated secondary striatal excitotoxic lesions produced by the succinate dehydrogenase inhibitor malonate, and the protection was reversed by L-arginine but not by D-arginine, 7-NI produced nearly complete protection against striatal lesions produced by systemic administration of 3-nitropropionic acid (3-NP), another succinate dehydrogenase inhibitor, 7-NI protected against malonate induced decreases in ATP, and increases in lactate, as assessed by 1H magnetic resonance spectroscopy. 7-NI had no effects on spontaneous electrophysiologic activity in the striatum in vivo, suggesting that its effects were not mediated by an interaction with excitatory amino acid receptors. 7-NI attenuated increases in hydroxyl radical, 8-hydroxy-2-deoxyguanosine and 3-nitrotyrosine generation in vivo, which may be a consequence of peroxynitrite formation. The present results implicate neuronal nitric oxide generation in the pathogenesis of both direct and secondary excitotoxic neuronal injury in vivo. As such they suggest that neuronal nitric oxide synthase inhibitors may be useful in the treatment of neurologic diseases in which excitotoxic mechanisms play a role.
Methanogen Homoaconitase Catalyzes Both Hydrolyase Reactions in Coenzyme B Biosynthesis (2008)

Homoaconitase enzymes catalyze hydrolyase reactions in the alpha-aminoadipate pathway for lysine biosynthesis or the 2-oxosuberate pathway for methanogenic coenzyme B biosynthesis. Despite the homology of this iron-sulfur protein to aconitase, previously studied homoaconitases catalyze only the hydration of cis-homoaconitate to form homoisocitrate rather than the complete isomerization of homocitrate to homoisocitrate. The MJ1003 and MJ1271 proteins from the methanogen Methanocaldococcus jannaschii formed the first homoaconitase shown to catalyze both the dehydration of (R)-homocitrate to form cis-homoaconitate, and its hydration is shown to produce homoisocitrate. This heterotetrameric enzyme also used the analogous longer chain substrates cis-(homo)(2)aconitate, cis-(homo)(3)aconitate, and cis-(homo)(4)aconitate, all with similar specificities. A combination of the homoaconitase with the M. jannaschii homoisocitrate dehydrogenase catalyzed all of the isomerization and oxidative decarboxylation reactions required to form 2-oxoadipate, 2-oxopimelate, and 2-oxosuberate, completing three iterations of the 2-oxoacid elongation pathway. Methanogenic archaeal homoaconitases and fungal homoaconitases evolved in parallel in the aconitase superfamily. The archaeal homoaconitases share a common ancestor with isopropylmalate isomerases, and both enzymes catalyzed the hydration of the minimal substrate maleate to form d-malate. The variation in substrate specificity among these enzymes correlated with the amino acid sequences of a flexible loop in the small subunits.
CXCL12 (SDF-1)/CXCR4 Pathway in Cancer (2010)

Chemokines, small proinflammatory chemoattractant cytokines that bind to specific G-protein-coupled seven-span transmembrane receptors, are major regulators of cell trafficking and adhesion. The chemokine CXCL12 [stromal cell-derived factor-1 (SDF-1)] binds primarily to CXC receptor 4 (CXCR4; CD184). The binding of CXCL12 to CXCR4 induces intracellular signaling through several divergent pathways initiating signals related to chemotaxis, cell survival and/or proliferation, increase in intracellular calcium, and gene transcription. CXCR4 is expressed on multiple cell types including lymphocytes, hematopoietic stem cells, endothelial and epithelial cells, and cancer cells. The CXCL12/CXCR4 axis is involved in tumor progression, angiogenesis, metastasis, and survival. This pathway is a target for therapeutics that can block the CXCL12/CXCR4 interaction or inhibit downstream intracellular signaling.
Phosphorolysis of Aminoacyl‐tRNA by Polynucleotide Phosphorylase from Escherichia coli (1970)

Valyl‐transfer ribonucleic acid was degraded by polynucleotide phosphorylase from Escherichia coli in the presence of phosphate or arsenate. A compound that was identified as 2′(3′)‐ O ‐valyladenosine 5′‐pyrophosphate was isolated from the phosphorolytic digest of valyl‐tRNA while 2′(3′)‐ O ‐valyladenosine 5′‐monophosphate was isolated from the arsenolytic digest. It was concluded that valyl‐tRNA can be phosphorolyzed by polynucleotide phosphorylase. The rate of phosphorolysis of aminoacylated tRNA was lower than that of uncharged tRNA. N‐blocked derivatives of valyl‐tRNA and phenylalanyl‐tRNA were also phosphorolyzed by polynucleotide phosphorylase. Some possible uses of nucleoside diphosphates substituted in their sugar moiety are suggested.
Novel Conjugated Ladder-Structured Oligomer Anode with High Lithium Storage and Long Cycling Capability (2016)

Herein we report the development of nanostructured poly(1,4-dihydro-11H-pyrazino[2′,3′:3,4]cyclopenta[1,2-b]quinoxalin-11-one) (PPCQ), a novel conjugated ladderlike oligomer with the presence of a rich amount of heteroatoms, as the anode material. Beyond its remarkable lithium storage of 972 mAh g–1 after 120 cycles, the superior cycle life and stable capacity performance of 489 mAh g–1 revealed by ultralong testing of 1000 cycles (with an average Coulombic efficiency 99.8%) at a high current density of 2.5 A g–1 indicate its excellent electrochemical stability to be promisingly applied for high-performance lithium-ion batteries (LIBs).
Specific oncolytic effect of a new hypoxia-inducible factor-dependent replicative adenovirus on von Hippel-Lindau-defective renal cell carcinomas. (2003)

Mutations in the von Hippel-Lindau (VHL) tumor suppressor gene are responsible for a hereditary cancer syndrome characterized by high susceptibility to hemangioblastomas of the retina and central nervous system, pheochromocytomas, and renal cell carcinomas. In agreement with its role as a tumor suppressor, the vast majority of spontaneous clear cell carcinomas of the kidney present loss of heterozygosity at the VHL locus. Recently, it has been shown that VHL works as the substrate recognition component of an E3 ubiquitination complex that targets the hypoxia-inducible factor (HIF) for proteosomal degradation. Under normal oxygen tension, the half-life of HIF transcription factors is extremely short because of its high degradation rate by the proteasome, resulting in undetectable HIF activity in normal cells. However, in VHL-deficient tumor cells, the HIF transcriptional pathway is constitutively activated because of impaired ubiquitination of this transcription factor. To target VHL-deficient tumors, we have exploited this feature to develop a conditionally replicative adenovirus (Ad9xHRE1A), the replication of which is HIF dependent. In this new oncolytic adenovirus, the expression of the E1A gene is controlled by an optimized minimal promoter containing HIF recognition elements. Here, we show that the induction of the E1A gene, as well as the viral replication and cytolytic effect of Ad9xHRE1A, are dependent on HIF activity. As a consequence, this virus efficiently kills VHL-deficient cells both in vitro and in vivo, as well as cells growing under hypoxic conditions. These data suggest that Ad9xHRE1A could be used as a highly specific therapy for VHL-deficient cancers and probably many other tumors that show extensive hypoxic areas or increased HIF activity by genetic alterations other than VHL loss.
Correlates of Immune Protection Induced by Live, Attenuated, Cold‐Adapted, Trivalent, Intranasal Influenza Virus Vaccine (2000)

The authors conducted a 2-year, multicenter, double-blind, placebo-controlled efficacy field trial of live, attenuated, cold-adapted, trivalent influenza vaccine administered by nasal spray to children 15-71 months old. Overall, vaccine was 92% efficacious at preventing culture-confirmed infection by influenza A/H3N2 and influenza B. Because influenza A/H1N1 did not cause disease during the years in which this study was conducted, the authors sought to determine vaccine efficacy and correlates of immune protection against experimental challenge with 107 TCID50 of attenuated H1N1 (vaccine strain) by intranasal spray. Prechallenge assessments included serum hemaglutination-inhibiting (HAI) antibody and nasal wash IgA antibody to H1N1. Vaccine was 83% efficacious (95% confidence interval, 60%-93%) at preventing shedding of H1N1 virus after challenge. Any serum HAI antibody or any nasal wash IgA antibody was correlated with significant protection from H1N1 infection as indicated by vaccine-virus shedding, and high efficacy against H1N1 challenge was demonstrated.
DiamondTouch (2001)

A technique for creating a touch-sensitive input device is proposed which allows multiple, simultaneous users to interact in an intuitive fashion. Touch location information is determined independently for each user, allowing each touch on a common surface to be associated with a particular user. The surface generates location dependent, modulated electric fields which are capacitively coupled through the users to receivers installed in the work environment. We describe the design of these systems and their applications. Finally, we present results we have obtained with a small prototype device.
Correction by Dexamethasone Treatment of the Altered Lipolytic Cascade Induced by Adrenalectomy in Rat Adipocytes (1990)

The ability of glucocorticoid-treatment to reverse the metabolic alterations caused by adrenalectomy in rat adipocytes was studied. Correction of the enhanced adenosine antilipolytic effect and of the defect in lipolysis, cyclic AMP and adenylate cyclase responsiveness to guanine nucleotides were all achieved after a 24 h dexamethasone treatment, whereas correction of the defect in beta-adrenoceptor-density required a 48 h treatment. The latter treatment, however, failed to reverse the defect in both the adenylate cyclase catalytic activity and protein content per fat cell. These different kinetics of restoration indicate that correction by dexamethasone of the defective cyclic AMP and lipolytic responses on one hand and of the guanine nucleotide control of adenylate cyclase on the other one are two related phenomenoms.
Plume formation and resonant bifurcations in porous-media convection (1994)

The classical boundary-layer scaling laws proposed by Howard for Rayleigh–Bénard convection at high Rayleigh number extend to the analogous case of convection in saturated porous media. We computationally study two-dimensional porous-media convection near the onset of this scaling behaviour. The main result of the paper is the observation and study of instabilities that lead to deviations from the scaling relations. At Rayleigh numbers below the scaling regime, boundary-layer fluctuations born at a Hopf bifurcation strengthen and eventually develop into thermal plumes. The appearance of plumes corresponds to the onset of the boundary-layer scaling behaviour of the oscillation frequency and mean Nusselt number, in agreement with the classical theory. As the Rayleigh number increases further, the flow undergoes instabilities that lead to ‘bubbles’ in parameter space of quasi-periodic flow, and eventually to weakly chaotic flow. The instabilities disturb the plume formation process, effectively leading to a phase modulation of the process and to deviations from the scaling laws. We argue that these instabilities correspond to parametric resonances between the timescale for plume formation and the characteristic convection timescale of the flow.
Multiclass Total Variation Clustering (2014)

Ideas from the image processing literature have recently motivated a new set of clustering algorithms that rely on the concept of total variation. While these algorithms perform well for bi-partitioning tasks, their recursive extensions yield unimpressive results for multiclass clustering tasks. This paper presents a general framework for multiclass total variation clustering that does not rely on recursion. The results greatly outperform previous total variation algorithms and compare well with state-of-the-art NMF approaches.
Genetically modified pigs produced with a nonviral episomal vector (2006)

Genetic modification of cells and animals is an invaluable tool for biotechnology and biomedicine. Currently, integrating vectors are used for this purpose. These vectors, however, may lead to insertional mutagenesis and variable transgene expression and can undergo silencing. Scaffold/matrix attachment region-based vectors are nonviral expression systems that replicate autonomously in mammalian cells, thereby making possible safe and reliable genetic modification of higher eukaryotic cells and organisms. In this study, genetically modified pig fetuses were produced with the scaffold/matrix attachment region-based vector pEPI, delivered to embryos by the sperm-mediated gene transfer method. The pEPI vector was detected in 12 of 18 fetuses in the different tissues analyzed and was shown to be retained as an episome. The reporter gene encoded by the pEPI vector was expressed in 9 of 12 genetically modified fetuses. In positive animals, all tissues analyzed expressed the reporter gene; moreover in these tissues, the positive cells were on the average 79%. The high percentage of EGFP-expressing cells and the absence of mosaicism have important implications for biotechnological and biomedical applications. These results are an important step forward in animal transgenesis and can provide the basis for the future development of germ-line gene therapy.
Structural organization of the human gene encoding nuclear lamin A and nuclear lamin C (1993)

We have determined the structural organization of the human gene that encodes nuclear lamins A and C, intermediate filament proteins of the nuclear lamina. Sequencing and restriction mapping show that the coding region spans approximately 24 kilobases. The 5'-proximal promoter region contains several GC-rich stretches, a CCAAT box, and a TATA-like element of sequence TATTA. The lamin A/C gene contains 12 exons. Alternative splicing within exon 10 gives rise to two different mRNAs that code for pre-lamin A and lamin C. Consequently, two proteins are generated, only one of which, pre-lamin A, can be modified by isoprenylation. The intron positions in the human lamin A/C gene are generally conserved in the previously characterized genes for Xenopus lamin LIII and mouse lamin B2, but different from those in a Drosophila lamin gene. In the regions coding for the central rod domains, the intron positions are also conserved when compared with the intron positions in the genes for most cytoplasmic intermediate filament proteins except those for nestin and neurofilaments. Analysis of the intron positions in these genes supports the hypothesis that the nuclear lamins and other intermediate filament proteins arose from a common ancestor.
Fiber Crossing in Human Brain Depicted with Diffusion Tensor MR Imaging (2000)

Human white matter fiber crossings were investigated with use of the full eigenstructure of the magnetic resonance diffusion tensor. Intravoxel fiber dispersions were characterized by the plane spanned by the major and medium eigenvectors and depicted with three-dimensional graphics. This method improves the analysis of fiber orientations, beyond the principal fiber directions, to a broader range of complex fiber architectures.