gebhart/patrepeval huggingface dataset:
Clinical decision support with IM-agents and ERMA multi-agents (2004)

IM-Agents (intelligent monitoring agents) provides a system infrastructure and proof of concept applications demonstrating meaningful diagnosis and intervention advice for healthcare personnel. The problem domain is extremely complex, with uncertainties and interdependencies. The monitored environment for a patient is comprised of a number of influences from numerous sources involving asynchronous, dynamic changes. Agents act as a collaborative team of specialists. Data is dynamically collected, filtered and integrated. Dynamic inference is accomplished within agents through a hybrid approach of fuzzy logic, causal Bayesian networks, trend analysis and qualitative logic. Emergency medical assistant (ERMA) components demonstrate the system for the trauma environment with particular emphasis on types of shock and stabilization of arterial blood gases. This approach for clinical decision support systems shows promise for a number of critical care scenarios.
The many faces of sequence alignment (2005)

Starting with the sequencing of the mouse genome in 2002, we have entered a period where the main focus of genomics will be to compare multiple genomes in order to learn about human biology and evolution at the DNA level. Alignment methods are the main computational component of this endeavour. This short review aims to summarise the current status of research in alignments, emphasising large-scale genomic comparisons and suggesting possible directions that will be explored in the near future.
RAG Mutations in Human B Cell-Negative SCID (1996)

Patients with human severe combined immunodeficiency (SCID) can be divided into those with B lymphocytes (B+ SCID) and those without (B- SCID). Although several genetic causes are known for B+ SCID, the etiology of B- SCID has not been defined. Six of 14 B- SCID patients tested were found to carry a mutation of the recombinase activating gene 1 (RAG-1), RAG-2, or both. This mutation resulted in a functional inability to form antigen receptors through genetic recombination and links a defect in one of the site-specific recombination systems to a human disease.
Hydrocarbon molar water solubility predicts NMDA vs. GABAA receptor modulation (2014)

Hydrocarbon modulation of NMDA receptor function exhibits a molar water solubility cut-off. Differences between unrelated receptor cut-off values suggest that the number, affinity, or efficacy of protein-hydrocarbon interactions at these sites likely differ.
Increased levels of deleted in malignant brain tumours 1 (DMBT1) in active bacteria‐related appendicitis (2012)

Our data demonstrate that bacteria-related active inflammation results in a sharp increase of DMBT1 levels in enterocytes. These findings substantiate the view that DMBT1 is of functional relevance for host defence and modulation of the course of intestinal bacteria-related inflammatory responses.
Laser-capture microdissection of plasma cells from subacute sclerosing panencephalitis brain reveals intrathecal disease-relevant antibodies (2005)

Increased IgG and oligoclonal bands are found in cerebrospinal fluid of humans with chronic infectious CNS disease. Studies have shown that these oligoclonal bands are antibodies directed against the agent that causes disease. Laser-capture microdissection was used to isolate individual CD38+ plasma cells from the brain of a patient with subacute sclerosing panencephalitis, and single-cell RT-PCR was used to analyze individual IgG heavy and light chains expressed by each cell. Based on overrepresented IgG sequences, we constructed functional recombinant antibodies (recombinant IgGs) and determined their specificities. Five of eight recombinant IgGs recognized measles virus, the cause of subacute sclerosing panencephalitis. These results demonstrate that overrepresented IgG sequences in postmortem brains can be used to produce functional recombinant antibodies that recognize their target antigens. This strategy can be used to identify disease-relevant antigens in CNS inflammatory diseases of unknown etiology.
A single base change in the Shine-Dalgarno region of 16S rRNA of Escherichia coli affects translation of many proteins. (1987)

A single base mutation was constructed at position 1538 of Escherichia coli 16S rRNA, changing a cytidine to a uridine. This position is in the Shine-Dalgarno region, thought to be involved in base-pairing to mRNA during initiation of protein synthesis. The mutation was constructed by using a synthetic oligodeoxynucleotide that differs in sequence by one base from the wild-type sequence of 16S rRNA. This oligonucleotide was used as a primer on single-stranded DNA of phage M13, into which was cloned a specific region of DNA encoding 16S rRNA. The mutation is lethal when expressed from the normal promoters of rRNA operons, P1 and P2, in a high-copy-number plasmid. Expression can be repressed by a temperature-sensitive repressor, cI857, in combination with the bacteriophage lambda PL promoter. Induction of transcription by temperature shift yields mutant 16S rRNA that is processed and assembled into functional ribosomal subunits. The presence of mutant ribosomes retards cell growth and dramatically alters incorporation of [35S]methionine into a large proportion of the cellular proteins. The change in level of synthesis of individual proteins correlates with the change in base-pairing between mutant rRNA and the Shine-Dalgarno region of the mRNA.
Client-server synchronization and buffering for variable rate multimedia retrievals (1996)

We consider the use of large buffers and feedback as a mechanism to maintain loosely coupled synchronization between a multimedia server and a client. The multimedia stream is modeled as a fluid flow through rate controlled valves and buffers with multiple thresholds. These thresholds are used to control the rates upstream. The quality of service for the multimedia connection is characterized in terms of the jitter in the received media stream due to buffer underflow and overflow. This quality of service is used to exercise rate and admission control in the presence of congestion. The feedback mechanism is, implemented in GRAMS (gopher-style real time ATM multimedia system), an adaptive multimedia client-server system. Experimental statistics are gathered for the purpose of traffic engineering. We employ a fluid flow and first passage time analysis to understand the traffic process through the pipelines and the buffers and to estimate the amount of signaling required by the feedback mechanism.
Neurological abnormalities in a knock-in mouse model of Huntington's disease (2001)

Mice representing precise genetic replicas of Huntington's disease (HD) were made using gene targeting to replace the short CAG repeat of the mouse Huntington's disease gene homolog (HDH:) with CAG repeats within the length range found to cause HD in humans. Mice with alleles of approximately 150 units in length exhibit late-onset behavioral and neuroanatomic abnormalities consistent with HD. These symptoms include a motor task deficit, gait abnormalities, reactive gliosis and the formation of neuronal intranuclear inclusions predominating in the striatum. This model differs from previously described HDH: knock-ins by its method of construction, longer repeat length and more severe phenotype. To our knowledge, this is the first knock-in mouse model of HD to show increased glial fibrillary acidic protein immunoreactivity in the striatum, suggesting that these mice have neuronal injury similar to that found early in the course of HD. These mice will serve as useful reagents in experiments designed to reveal the molecular nature of neuronal dysfunction underlying HD.
Evidence That NiNi Acetyl-CoA Synthase Is Active and That the CuNi Enzyme Is Not (2004)

The bifunctional CO dehydrogenase/acetyl-CoA synthase (CODH/ACS) plays a central role in the Wood-Ljungdahl pathway of autotrophic CO(2) fixation. One structure of the Moorella thermoacetica enzyme revealed that the active site of ACS (the A-cluster) consists of a [4Fe-4S] cluster bridged to a binuclear CuNi center with Cu at the proximal metal site (M(p)) and Ni at the distal metal site (M(d)). In another structure of the same enzyme, Ni or Zn was present at M(p). On the basis of a positive correlation between ACS activity and Cu content, we had proposed that the Cu-containing enzyme is active [Seravalli, J., et al. (2003) Proc. Natl. Acad. Sci. U.S.A. 100, 3689-3694]. Here we have reexamined this proposal. Enzyme preparations with a wider range of Ni (1.6-2.8) and Cu (0.2-1.1) stoichiometries per dimer were studied to reexamine the correlation, if any, between the Ni and Cu content and ACS activity. In addition, the effects of o-phenanthroline (which removes Ni but not Cu) and neocuproine (which removes Cu but not Ni) on ACS activity were determined. EXAFS results indicate that these chelators selectively remove M(p). Multifrequency EPR spectra (3-130 GHz) of the paramagnetic NiFeC state of the A-cluster were examined to investigate the electronic state of this proposed intermediate in the ACS reaction mechanism. The combined results strongly indicate that the CuNi enzyme is inactive, that the NiNi enzyme is active, and that the NiNi enzyme is responsible for the NiFeC EPR signal. The results also support an electronic structure of the NiFeC-eliciting species as a [4Fe-4S](2+) (net S = 0) cluster bridged to a Ni(1+) (S = (1)/(2)) at M(p) that is bridged to planar four-coordinate Ni(2+) (S = 0) at M(d), with the spin predominantly on the Ni(1+). Furthermore, these studies suggest that M(p) is inserted during cell growth. The apparent vulnerability of the proximal metal site in the A-cluster to substitution with different metals appears to underlie the heterogeneity observed in samples that has confounded studies of CODH/ACS for many years. On the basis of this principle, a protocol to generate nearly homogeneous preparations of the active NiNi form of ACS was achieved with NiFeC signals of approximately 0.8 spin/mol.
Anthrax Biosensor, Protective Antigen Ion Channel Asymmetric Blockade (2005)

The significant threat posed by biological agents (e.g. anthrax, tetanus, botulinum, and diphtheria toxins) (Inglesby, T. V., O'Toole, T., Henderson, D. A., Bartlett, J. G., Ascher, M. S., Eitzen, E., Friedlander, A. M., Gerberding, J., Hauer, J., Hughes, J., McDade, J., Osterholm, M. T., Parker, G., Perl, T. M., Russell, P. K., and Tonat, K. (2002) J. Am. Med. Assoc. 287, 2236-2252) requires innovative technologies and approaches to understand the mechanisms of toxin action and to develop better therapies. Anthrax toxins are formed from three proteins secreted by fully virulent Bacillus anthracis, protective antigen (PA, 83 kDa), lethal factor (LF, 90 kDa), and edema factor (EF, 89 kDa). Here we present electrophysiological measurements demonstrating that full-length LF and EF convert the current-voltage relationship of the heptameric PA63 ion channel from slightly nonlinear to highly rectifying and diode-like at pH 6.6. This effect provides a novel method for characterizing functional toxin interactions. The method confirms that a previously well characterized PA63 monoclonal antibody, which neutralizes anthrax lethal toxin in animals in vivo and in vitro, prevents the binding of LF to the PA63 pore. The technique can also detect the presence of anthrax lethal toxin complex from plasma of infected animals. The latter two results suggest the potential application of PA63 nanopore-based biosensors in anthrax therapeutics and diagnostics.
Inhibition of Acinetobacter baumannii, Staphylococcus aureus and Pseudomonas aeruginosa biofilm formation with a class of TAGE-triazole conjugates (2009)

A chemically diverse library of TAGE-triazole conjugates was synthesized utilizing click chemistry on the TAGE scaffold. This library of small molecules was screened for anti-biofilm activity and found to possess the ability of inhibiting biofilm formation against Acinetobacter baumannii, Staphylococcus aureus and Pseudomonas aeruginosa. One such compound in this library demonstrated the most potent inhibitory effect against Staphylococcus aureus biofilm formation that has been displayed by any 2-aminoimidazole derivative.
MicroRNA enrichment among short 'ultraconserved' sequences in insects (2006)

MicroRNAs are short (approximately 22 nt) regulatory RNA molecules that play key roles in metazoan development and have been implicated in human disease. First discovered in Caenorhabditis elegans, over 2500 microRNAs have been isolated in metazoans and plants; it has been estimated that there may be more than a thousand microRNA genes in the human genome alone. Motivated by the experimental observation of strong conservation of the microRNA let-7 among nearly all metazoans, we developed a novel methodology to characterize the class of such strongly conserved sequences: we identified a non-redundant set of all sequences 20 to 29 bases in length that are shared among three insects: fly, bee and mosquito. Among the few hundred sequences greater than 20 bases in length are close to 40% of the 78 confirmed fly microRNAs, along with other non-coding RNAs and coding sequence.
Non-stationary noise characteristics for SPECT images (2002)

A theoretical formulation for characterization of SPECT (single photon emission computed tomography) image noise for a filtered-backprojection reconstructed image was derived. The formulation takes into account all segments of the reconstruction process including the effects of discrete filtering and backprojection as well as nonstationarity in both the projection data and the reconstructed image. It allows calculations of the local noise properties of a reconstructed image in the spatial and frequency domains. This facilitates studies of nonstationary image noise. The formulation was validated by comparing the local autocovariance matrix and noise power spectrum calculated using the theoretical formulation with these quantities calculated from an ensemble of 12000 reconstructed images. The assumption of stationarity for SPECT reconstructed images is examined. The results show that SPECT image noise is nonstationary over large uniform regions, except near the center of the uniform region and over small regions of interest near image edges.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Quantum dots in suspended single-wall carbon nanotubes (2001)

We present a simple technique which uses a self-aligned oxide etch to suspend individual single-wall carbon nanotubes between metallic electrodes. This enables one to compare the properties of a particular nanotube before and after suspension, as well as to study transport in suspended tubes. As an example of the utility of the technique, we study quantum dots in suspended tubes, finding that their capacitances are reduced owing to the removal of the dielectric substrate.
Conditional MHC class I ligands and peptide exchange technology for the human MHC gene products HLA-A1, -A3, -A11, and -B7 (2008)

Major histocompatibility complex (MHC) class I multimer technology has become an indispensable immunological assay system to dissect antigen-specific cytotoxic CD8(+) T cell responses by flow cytometry. However, the development of high-throughput assay systems, in which T cell responses against a multitude of epitopes are analyzed, has been precluded by the fact that for each T cell epitope, a separate in vitro MHC refolding reaction is required. We have recently demonstrated that conditional ligands that disintegrate upon exposure to long-wavelength UV light can be designed for the human MHC molecule HLA-A2. To determine whether this peptide-exchange technology can be developed into a generally applicable approach for high throughput MHC based applications we set out to design conditional ligands for the human MHC gene products HLA-A1, -A3, -A11, and -B7. Here, we describe the development and characterization of conditional ligands for this set of human MHC molecules and apply the peptide-exchange technology to identify melanoma-associated peptides that bind to HLA-A3 with high affinity. The conditional ligand technology developed here will allow high-throughput MHC-based analysis of cytotoxic T cell immunity in the vast majority of Western European individuals.
Electrical breakdown of gases (1953)

A collection of individual works on electrical discharges is presented. Topics covered include: fundamental processes in the electrical breakdown of gases; vacuum breakdown; spark breakdown in uniform fields; corona discharge; spark breakdown in non-uniform fields; breakdown voltage characteristics; irradiation and time lags; high-frequency breakdown of gases; laser-induced electrical breakdown of gases; spark channels; and electrode phenomena. (GHT)
Parallel analysis of tissue-type plasminogen activator and type 1 plasminogen activator inhibitor in plasma and endothelial cells derived from patients with chronic pulmonary thromboemboli. (1994)

The data suggest that an inherent EC-mediated fibrinolytic imbalance is not a generalized phenomenon observed in pulmonary arteries of patients with chronic pulmonary thromboemboli.
Optimization of an implantable volume conduction antenna (2005)

As implantable devices become increasingly sophisticated, there is a strong need for developing a wireless data communication channel between these devices and external computers. This important problem has been studied and an antenna is being designed based on the volume conduction of biological tissues. Closed-form equation and finite element analyses were performed for the case of brain implantation using a spherical volume conduction model of the head. Finite element proofs of concept in 2D and 3D demonstrated the influence of epoxy and a volume conductor reflector on volume currents, exhibiting changes in the far field as controlled by the near field. A 3D finite element analysis showed an increased signal transduction of 35% as compared to the 3D analytical analysis, which was not able to simulate the epoxy. The optimum angle of inclination is shallower than what was intuitively thought, indicating that the antenna elements destructively interfere with the generated surface voltages, requiring the antenna elements to be rotated away from each other.
PbSnSeTe–PbSeTe Lattice-Matched Double-Heterostructure Lasers (1982)

The first successful growth of PbSnSeTe–PbSeTe double heterostructure layers lattice-matched to Pb 0.8 Sn 0.2 Te substrate by liquid phase epitaxy is reported. PbSnSeTe–PbSeTe lattice-matched double heterostructure layers have also been grown on PbTe substrate by employing step-graded PbSeTe layers with solid compositions intermediate between the PbTe substrates and the double heterostructure layers. The lasing characteristics of the resulting laser diodes suggest that nonradiative interface recombination at PbSnSeTe–PbSeTe lattice-matched heterojunctions is negligibly small and that the temperature dependence of the laser threshold current at low temperatures is mainly determined by the doping in the active region. The lowest threshold current density for lasers with 11 cm emission wavelength has been found to be as low as 90 A/cm 2 at 4.2 K. Laser oscillation has been observed at temperatures as high as 165 K.
Human Dendritic Cells Are Activated by Dengue Virus Infection: Enhancement by Gamma Interferon and Implications for Disease Pathogenesis (2001)

The ability of dendritic cells (DCs) to shape the adaptive immune response to viral infection is mediated largely by their maturation and activation state as determined by the surface expression of HLA molecules, costimulatory molecules, and cytokine production. Dengue is an emerging arboviral disease where the severity of illness is influenced by the adaptive immune response to the virus. In this report, we have demonstrated that dengue virus infects and replicates in immature human myeloid DCs. Exposure to live dengue virus led to maturation and activation of both the infected and surrounding, uninfected DCs and stimulated production of tumor necrosis factor alpha (TNF-alpha) and alpha interferon (IFN-alpha). Activation of the dengue virus-infected DCs was blunted compared to the surrounding, uninfected DCs, and dengue virus infection induced low-level release of interleukin-12 p70 (IL-12 p70), a key cytokine in the development of cell-mediated immunity (CMI). Upon the addition of IFN-gamma, there was enhanced activation of dengue virus-infected DCs and enhanced dengue virus-induced IL-12 p70 release. The data suggest a model whereby DCs are the early, primary target of dengue virus in natural infection and the vigor of CMI is modulated by the relative presence or absence of IFN-gamma in the microenvironment surrounding the virus-infected DCs. These findings are relevant to understanding the pathogenesis of dengue hemorrhagic fever and the design of new vaccination and therapeutic strategies.
Noncarbon Support Materials for Polymer Electrolyte Membrane Fuel Cell Electrocatalysts (2011)

The developments in the field of several important kinds of noncarbon supporting materials in recent years are reviewed. The challenges for developing noncarbon supporting materials are analyzed, and the possible future research directions, in particular the material preparation methods, are also proposed. To address the issue of carbon oxidation, effort has been placed on developing alternative noncarbon materials for catalyst supports. As compared to carbon-based supports, some noncarbon materials and their supported Pt-based catalysts have shown unique structures, suitable physical and chemical properties, and high catalytic activity toward fuel cell reactions such as the oxygen reduction reaction and small alcohol electrooxidation. To make noncarbon-supported Pt-based catalysts practically feasible in PEM fuel cells, material improvements in electronic conductivity, solubility, chemical/electrochemical and thermal stability, and surface area are required.
Inhibition of Glucocorticoid-induced Apoptosis in 697 Pre-B Lymphocytes by the Mineralocorticoid Receptor N-terminal Domain (2002)

The glucocorticoid and mineralocorticoid receptors (GR and MR) share considerable structural and functional homology and bind as homodimers to hormone-response elements. We have shown previously that MR and GR can form heterodimers that inhibit transcription from a glucocorticoid (GC)-responsive gene and that this inhibition was mediated by the N-terminal domain (NTD) of MR. In this report, we examined the effect of NTD-MR on GC-induced apoptosis in the GC-sensitive pre-B lymphoma cell line, 697. In GC-treated 697 cells, we demonstrated that stable expression of NTD-MR blocks apoptosis and inhibits proteolytic processing of pro-caspases-3, -8, and -9 and poly(ADP-ribose) polymerase. Importantly, gel shift and immunoprecipitation analyses revealed a direct association between the GR and amino acids 203-603 of NTD-MR. We observed down-regulation of c-Myc and of the anti-apoptotic proteins Bcl-2 and Bfl-1 as well as high levels of the pro-apoptotic proteins Bax and Bid. Conversely, cells stably expressing NTD-MR exhibited increased expression of Bcl-2 and Bfl-1 and diminished levels of Bid and Bax. These data provide a potential mechanism for the observed inhibition of cytochrome c and Smac release from the mitochondria of NTD-MR cells and resultant resistance to GC-induced apoptosis. Thus, NTD-MR may mediate GC effects through heterodimerization with GR and ensuing inhibition of GC-regulated gene transcription.