gebhart/patrepeval huggingface dataset:
Experimental evaluation Celsior, a new heart preservation solution (1994)

An original heart preservation solution (Celsior) has been developed, the formulation of which has been designed to fulfil two major objectives: (1) to combine the general principles of hypothermic organ preservation with those specific for the myocardium, and (2) to offer the possibility of being used not only as a storage medium but also as a perfusion fluid during initial donor heart arrest, poststorage graft reimplantation and early reperfusion. The major principles addressed by the Celsior formulation include (1) prevention of cell swelling (by mannitol and lactobionate), (2) prevention of by the Celsior formulation include (1) prevention of cell swelling (by mannitol and lactobionate), (2) prevention of oxygen-derived free radical injury (by reduced glutathione, histidine and mannitol), and (3) prevention of contracture by enhancement of energy production (glutamate) and limitation of calcium overload (high magnesium content, slight degree of acidosis). Two experimental preparations were used: The isolated isovolumic buffer-perfused rat heart model and the heterotopic rabbit heart transplantation model. In isolated heart experiments, hearts were arrested with and stored in Celsior for 5 h at 4 degrees C and subsequently reperfused for 1 h. A similar protocol was used in the transplantation experiments except that the total ischemic time was approximately 1 1/2 h longer (corresponding to 6 h of storage followed by the 25 additional minutes of cold ischemia required for graft implantation.(ABSTRACT TRUNCATED AT 250 WORDS)
Strategy for the prevention and treatment of chronic lung disease of the premature infant (1999)

Based on the analyses of approximately 1,000 infants with CLD, this condition was classified into 7 types according to the preceding illnesses and the chest X-ray appearance. The profile of inflammatory enzymes, cytokines and chemical mediators supported the relevance of the classification. Since different insults to the lung with different onsets exhibit the different spectra of the disease, appropriate strategies adapted to each type of CLD should be pursued. For types I and II prophylactic administration of exogenous surfactant, early enough to prevent the oxygen toxicity and barotrauma, is important. RDS can be diagnosed by the stable microbubble rating on gastric aspirates within several minutes of birth. The application of milder modes of ventilation such as HFOV started at birth should also be remembered. The recommended strategies for type IV and V are the care of the very low birth weight infant in the fully humidified incubator with careful fluid administration to prevent symptomatic PDA, and early detection and treatment of infection by screening with sensitive methods such as the APR score. However, the most difficult problem is to identify the correct strategy for type III and III', because these types of CLD can only be prevented by the complete eradication of intrauterine infection.
The 25 -36 region of the Bacillus subtilis chromosome: determination of the sequence of a 146 kb segment and identification of 113 genes (1996)

We determined a 146 kb contiguous sequence at the 25 degrees-36 degrees region of the Bacillus subtilis chromosome containing the amyE-srfA segment. Among the 113 ORFs identified, 33 are already known. functions were assigned to 38 ORFs by a search of non-redundant protein sequence data banks and those of 16 ORFs were suggested through significant similarity with reported sequences. The amino acid sequences of 13 of the ORfs were similar to proteins of unknown function of Escherichia coli, Haemophilus influenzae and other species. We did not find similarities for 29 ORFs to any known proteins. The 146 kb region is rich in enzymes (35 ORFs) related to the metabolism of low molecular mass compounds and five genes for surfactin production occupy about 26 kb of the region.
The Effect of Eukaryotic Expression Vectors and Adjuvants on DNA Vaccines in Chickens Using an Avian Influenza Model (2000)

Vaccination of poultry with naked plasmid DNA has been successfully demonstrated with several different poultry pathogens, but the technology needs to be further developed before it can be practically implemented. Many different methods can conceivably enhance the efficacy of DNA vaccines, and this report examines the use of different eukaryotic expression vectors with different promoters and different adjuvants to express the influenza hemagglutinin protein. Four different promoters in five different plasmids were used to express the hemagglutinin protein of an H5 avian influenza virus, including two different immediate early cytomegaloviruses (CMVs), Rous sarcoma virus, chicken actin, and simian virus 40 promoters. All five constructs expressed detectable hemagglutinin protein in cell culture, but the pCI-neo HA plasmid with the CMV promoter provided the best response in chickens when vaccinated intramuscularly at 1 day of age on the basis of antibody titer and survivability after challenge with a highly pathogenic avian influenza virus at 6 wk postinoculation. A beneficial response was observed in birds boostered at 3 wk of age, in birds given larger amounts of DNA, and with the use of multiple injection sites to administer the vaccine. With the use of the pCI-neo construct, the effects of different adjuvants designed to increase the uptake of plasmid DNA, including 25% sucrose, diethylaminoethyl dextran, calcium phosphate, polybrene, and two different cationic liposomes, were examined. Both liposomes tested enhanced antibody titers as compared with the positive controls, but the other chemical adjuvants decreased the antibody response as compared with the control chickens that received just the plasmid alone. The results observed are promising for continued studies, but continued improvements in vaccine response and reduced costs are necessary before the technology can be commercially developed.
Methazolamide Calcium Phosphate Nanoparticles in an Ocular Delivery System (2010)

A new system for the local delivery of methazolamide to the eye has been developed based on calcium phosphate (CaP) nanoparticles. The methazolamide loaded CaP nanoparticles were prepared through the formation of an inorganic core of CaP and further adsorption of the methazolamide. The maximum loading of methazolamide studied using UV-vis spectrophotometry was about 0.2% (w/w). The drug-loaded particles had a negative surface charge at about -30 mV while their mean particle diameter was estimated to be 256.4 nm. In vitro release studies demonstrated diffusion-controlled release of methazolamide from the CaP nanoparticles over a period of 4 h. In vivo studies indicated that the intraocular pressure (IOP)-lowering effect of the inorganic nanoparticle eye drops lasted for 18 h, which was significantly better than the effect of 1% brinzolamide eye drops (6 h). Physical stability studies indicated that the preparation was stable for 6 months at 40 degrees C. These findings suggested that methazolamide bound to CaP nanoparticles might be useful in the local treatment of glaucoma.
Isolation of West Nile Virus from Mosquitoes, Crows, and a Cooper's Hawk in Connecticut (1999)

West Nile (WN) virus, a mosquito-transmitted virus native to Africa, Asia, and Europe, was isolated from two species of mosquitoes, Culex pipiens and Aedes vexans, and from brain tissues of 28 American crows, Corvus brachyrhynchos, and one Cooper's hawk, Accipiter cooperii, in Connecticut. A portion of the genome of virus isolates from four different hosts was sequenced and analyzed by comparative phylogenetic analysis. Our isolates from Connecticut were similar to one another and most closely related to two WN isolates from Romania (2.8 and 3.6 percent difference). If established in North America, WN virus will likely have severe effects on human health and on the health of populations of birds.
Mechanism of Action of Antisense RNA. Sometime Inhibition of Transcription, Processing, Transport, or Translationa (1992)

Anyone considering the use of AS RNA, generated endogenously, to inhibit gene expression should plan to generate several independent transfectants with nonoverlapping sequences; strategies that maximize both the transcription rate and the stability of the AS RNA are obviously desirable. Reasons why different results are obtained in different systems or with different constructs likely include the specific nucleotide sequence under investigation, the location of the AS gene in the nucleus relative to the endogenous gene, and the rate-limiting step in the expression of the target gene. Splicing may not be necessary, but an efficient polyadenylation signal likely is. Employment of a ribozyme-mediated strategy, discussed by various investigators in this volume, may be beneficial. There is no reason at present to conclude that any gene, however abundant its transcript might be, is inherently recalcitrant to AS-mediated down-regulation of expression.
Galectin-3 is an important mediator of VEGF- and bFGF-mediated angiogenic response (2010)

Recent studies have shown that a carbohydrate-binding protein, galectin-3, is a novel pro-angiogenic molecule. The mechanism by which galectin-3 promotes angiogenesis remains unknown. We demonstrate here that galectin-3 is a mediator of vascular endothelial growth factor (VEGF)- and basic fibroblast growth factor (bFGF)-mediated angiogenic response. Angiogenesis assays revealed that galectin-3 inhibitors, beta-lactose and dominant-negative galectin-3, reduce VEGF- and bFGF-mediated angiogenesis in vitro and that VEGF- and bFGF-mediated angiogenic response is reduced in galectin-3 knockdown cells and Gal3(-/-) animals. Integrin alphavbeta3 was identified as the major galectin-3-binding protein and anti-alphav, -beta3, and -alphavbeta3 integrin function-blocking antibodies significantly inhibited the galectin-3-induced angiogenesis. Furthermore, galectin-3 promoted the clustering of integrin alphavbeta3 and activated focal adhesion kinase. Knockdown of GnTV, an enzyme that synthesizes high-affinity glycan ligands for galectin-3, substantially reduced: (a) complex N-glycans on alphavbeta3 integrins and (b) VEGF- and bFGF-mediated angiogenesis. Collectively, these data suggest that galectin-3 modulates VEGF- and bFGF-mediated angiogenesis by binding via its carbohydrate recognition domain, to the GnTV synthesized N-glycans of integrin alphavbeta3, and subsequently activating the signaling pathways that promote the growth of new blood vessels. These findings have broad implications for developing novel, carbohydrate-based therapeutic agents for inhibition of angiogenesis.
An Ontology-Based Approach to Automate Tagging of Software Artifacts (2017)

Context: Software engineering repositories contain a wealth of textual information such as source code comments, developers' discussions, commit messages and bug reports. These free form text descriptions can contain both direct and implicit references to security concerns. Goal: Derive an approach to extract security concerns from textual information that can yield several benefits, such as bug management (e.g., prioritization), bug triage or capturing zero-day attack. Method: Propose a fully automated classification and tagging approach that can extract security tags from these texts without the need for manual training data. Results: We introduce an ontology based Software Security Tagger Framework that can automatically identify and classify cybersecurity-related entities, and concepts in text of software artifacts. Conclusion: Our preliminary results indicate that the framework can successfully extract and classify cybersecurity knowledge captured in unstructured text found in software artifacts.
Recovery of Fiber in the Corn Dry‐Grind Ethanol Process: A Feedstock for Valuable Coproducts (1999)

ABSTRACT A new process was developed to recover corn fiber from the mash before fermentation in dry‐grind ethanol production. In this process, corn is soaked in water (no chemicals) for a short period of time and then degermed using conventional degermination mills. In the remaining slurry, corn coarse fiber is floated by increasing the density of the slurry and then separated using density differences. The fiber recovered is called quick fiber to distinguish it from the conventional wet‐milled fiber. This study evaluated the percent of quick fiber recovery for a normal yellow dent and high oil corn hybrid. The quick fiber was analyzed for levels of corn fiber oil, levels of ferulate phytosterol esters (FPE) and other valuable phytosterol components in the oil and compared with conventional wet‐milled corn coarse and fine fiber samples. Fiber samples were also analyzed and compared for yields of potentially valuable corn fiber gum (CFG, hemicellulose B). Comparisons were made between the quick fiber samples obtained with and without chemicals in the soakwater. An average quick fiber yield of 6–7% was recovered from the two hybrids and represented 46–60% of the total fiber (fine and coarse) that could be recovered by wet‐milling these hybrids. Adding steep chemicals (SO 2 and lactic acid) to the soakwater increased the quick fiber yields, percent of FPE recoveries, and total percent of phytosterol components to levels either comparable to (for the dent corn hybrid) or higher than (for the high oil corn hybrid) those recovered from the total conventional wet‐milled fiber samples. CFG yields in the quick fiber samples were comparable to those from the wet‐milled fiber samples. CFG yields in the quick fiber samples were not significantly affected by the addition of chemicals (SO 2 and lactic acid) to the soakwater.
Sustained Elevation of Intracellular cGMP Causes Oxidative Stress Triggering Calpain-Mediated Apoptosis in Photoreceptor Degeneration (2007)

Sustained elevation in cGMP and a concomitant increase in intracellular Ca(2+) levels in the rd1 photoreceptors are followed by a rapid loss of photoreceptors. In a murine-derived photoreceptor cell line, 661W, treated with the phosphodiesterase inhibitor IBMX or the cyclic GMP-gated channel agonist 8-bromo-cGMP, it was previously found that the induced cell death was mediated by calpain and caspase-3. Because oxidative stress is a common product of ionic imbalance or elevated Ca(2+), we tested the role of oxidative stress in cGMP-induced photoreceptor cell death. In the rd1 mouse retina, oxidative stress was found to precede calpain and caspase-3 activation. In 661W cells, the increase in intracellular cGMP and Ca(2+) resulted in the generation of reactive oxygen species (ROS), the activation of oxidative stress enzymes, and the activation of calpain, followed by apoptosis mediated by the effector caspase-3. All these events, including calpain activation, were ameliorated by docosahexanoic acid (DHA). The cell-permeable inhibitor of calpain, SJA6017, while inhibiting cell death, had no effect on the generation of oxidative stress. These results establish a central role for oxidative stress in cGMP-induced cell death and suggest a ROS-mediated sequential activation of signal transduction events, which provide targets for future treatment strategies.
Autoimmune Destruction of Islets Transplanted Into RT6-Depleted Diabetes-Resistant BB/Wor Rats (1990)

We report a novel animal model of islet transplantation that distinguishes recurrence of autoimmunity from allograft rejection. In this study, diabetes-resistant (DR) BB rats, less than 1% of which develop spontaneous diabetes, were made hyperglycemic by either a single injection of streptozocin (STZ) or in vivo immune elimination of a regulatory T-lymphocyte subset that expresses the RT6 alloantigen. DR islet grafts were then transplanted into both groups. DR transplants into STZ-induced diabetic DR rats produced long-term normoglycemia. In contrast, DR transplants into DR rats that had been treated with anti-RT6 monoclonal antibody were all destroyed within an average of 4 days. Allogeneic islets transplanted into both STZ-induced and RT6-depleted diabetic DR rats were rejected within a mean of 3 days. We conclude that failure of DR islet grafts in RT6-depleted diabetic DR BB rats represents recurrent autoimmunity.
Microfabricated tools for nanoscience (1993)

Recent developments and advances in micro-electro-mechanical systems for nanometer-scale applications such as scanning force microscopy are presented. The microfabrication of tools so small that they enable access to the nanoworid, such as tips, flexible cantilevers, integrated deflection sensors and nanoactuators will be described. Bulk and surface micromachining of mono or polycrystalline silicon, extended by aligned-wafer-bonding, etch-back and sacrificial-iayer-etching steps are major fabrication steps used. Experiments on prototypes show that these devices are promising for use as ultra-sensitive stand-alone local probe micro-instruments.
Human Amnion-Derived Multipotent Progenitor Cell Treatment Alleviates Traumatic Brain Injury-Induced Axonal Degeneration (2009)

To identify a viable cell source with potential neuroprotective effects, we studied amnion-derived multipotent progenitor (AMP) cells in a rat model of penetrating ballistic-like brain injury (PBBI). AMP cells were labeled with fluorescent dye PKH26 and injected in rats immediately following right hemispheric PBBI or sham PBBI surgery by ipsilateral i.c.v. administration. At 2 weeks post-injury, severe necrosis developed along the PBBI tract and axonal degeneration was prominent along the corpus callosum (cc) and in the ipsilateral thalamus. Injected AMP cells first entered the subventricular zone (SVZ) in both sham and PBBI rats. Further AMP cell migration along the cc only occurred in PBBI animals. No significant difference in injury volume was observed across all treatment groups. In contrast, treatment with AMP cells significantly attenuated axonal degeneration in both the thalamus and the cc. Interestingly, PKH26-labeled AMP cells were detected only in the SVZ and the cc (in parallel with the axonal degeneration), but not in the thalamus. None of the labeled AMP cells appeared to express neural differentiation, as evidenced by the lack of double labeling with nestin, S-100, GFAP, and MAP-2 immunostaining. In conclusion, AMP cell migration was specifically induced by PBBI and requires SVZ homing, yet the neuroprotective effect of intracerebral ventrical treatment using AMP cells was not limited to the area where the cells were present. This suggests that the attenuation of the secondary brain injury following PBBI was likely to be mediated by mechanisms other than cell replacement, possibly through delivery or sustained secretion of neurotrophic factors.
Structure and mechanical properties of ultrahigh molecular weight polyethylene deformed near melting temperature (Technical report) (1991)

Abstract
Hematopoietic Progenitor Kinase 1 Associates Physically and Functionally with the Adaptor Proteins B Cell Linker Protein and SLP-76 in Lymphocytes (2001)

B cell linker protein (BLNK) is a SLP-76-related adaptor protein essential for signal transduction from the BCR. To identify components of BLNK-associated signaling pathways, we performed a phosphorylation-dependent yeast two-hybrid analysis using BLNK probes. Here we report that the serine/threonine kinase hematopoietic progenitor kinase 1 (HPK1), which is activated upon antigen-receptor stimulation and which has been implicated in the regulation of MAP kinase pathways, interacts physically and functionally with BLNK in B cells and with SLP-76 in T cells. This interaction requires Tyr(379) of HPK1 and the Src homology 2 (SH2) domain of BLNK/SLP-76. Via homology modeling, we defined a consensus binding site within ligands for SLP family SH2 domains. We further demonstrate that the SH2 domain of SLP-76 participates in the regulation of AP-1 and NFAT activation in response to T cell receptor (TCR) stimulation and that HPK1 inhibits AP-1 activation in a manner partially dependent on its interaction with SLP-76. Our data are consistent with a model in which full activation of HPK1 requires its own phosphorylation on tyrosine and subsequent interaction with adaptors of the SLP family, providing a mechanistic basis for the integration of this kinase into antigen receptor signaling cascades.
Transient isotachophoresis in on‐line solid phase extraction capillary electrophoresis time‐of‐flight‐mass spectrometry for peptide analysis in human plasma (2011)

In this study, we evaluated the combination of transient isotachophoresis with on-line solid-phase extraction capillary electrophoresis time-of-flight mass spectrometry (SPE-tITP-CE-TOF-MS) to improve sensitivity of peptide analysis, using several opioid peptides as model compounds. First, standard solutions were analyzed in order to establish the tITP-CE methodology using UV and TOF-MS detection. The volume and composition of the leading and terminating electrolytes (i.e. LE and TE) for an efficient tITP were investigated to obtain optimum detection sensitivity and electrophoretic separation. In the best cases, LODs in tITP-CE-TOF-MS were tenfold better than those obtained in CE-TOF-MS (i.e. 5 versus 50 ng/mL). Afterwards, the tITP-CE-TOF-MS methodology was adapted to perform SPE-tITP-CE-TOF-MS. Repeatability, linearity and LODs were investigated and compared to the values obtained by SPE-CE-TOF-MS. Furthermore, human plasma samples fortified with the opioid peptides were analyzed in order to show the potential of SPE-tITP-CE-TOF-MS for peptide analysis in biological fluids. The LODs attained in standard solutions and plasma samples for some of the studied peptides (i.e. 0.01 and 0.1 ng/mL, respectively) were tenfold better than those obtained in SPE-CE-TOF-MS, proving the enhanced sensitivity that could be achieved when both on-line preconcentration approaches were combined together.
Electron density, Kohn–Sham frontier orbitals, and Fukui functions (1984)

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Searching for the Memory Trace in a Mini-Brain, the Honeybee (2001)

To determine general or species-specific properties in neural systems, it is necessary to use comparative data in evaluating experimental findings. Presented here are data on associative learning and memory formation in honeybees, emphasizing a comparative approach. We focus on four aspects: (1) the role of an identified neuron, VUM(mx1), as a neural substrate of appetitive reinforcement; (2) the sequences of molecular events as they correlate with five forms of memory stages; (3) the localization of the memory traces following appetitive olfactory learning; and (4) the brief description of several forms of complex learning in bees (configuration in olfactory conditioning, categorization in visual feature learning, delayed matching-to-sample learning, and latent learning in navigation). VUM(mx1) activity following the conditioned stimulus odor is sufficient to replace the unconditioned stimulus, and VUM(mx1) changes its response properties during learning similarly to what is known from dopamine neurons in the basal ganglia of the mammalian brain. The transition from short- to mid- and long-term forms of memory can be related to specific activation of second messenger cascades (involving NOS, PKA, PKC, and PKM) resembling general features of neural plasticity at the cellular level. The particular time course of the various memory traces may be adapted to the behavioral context in which they are used; here, the foraging cycle of the bee. Memory traces for even such a simple form of learning as olfactory conditioning are multiple and distributed, involving first- and second-order sensory neuropils (antennal lobe and mushroom bodies), but with distinctly different properties. The wealth of complex forms of learning in the context of foraging indicates basic cognitive capacities based on rule extraction and context-dependent learning. It is believed that bees might be a useful model for studying cognitive faculties at a middle level of complexity.