gebhart/patrepeval huggingface dataset:
Calcium/calmodulin dependent kinase II contributes to persistent central neuropathic pain following spinal cord injury (2012)

Chronic central neuropathic pain after central nervous system injuries remains refractory to therapeutic interventions. A novel approach would be to target key intracellular signaling proteins that are known to contribute to continued activation by phosphorylation of kinases, transcription factors, and/or receptors that contribute to changes in membrane excitability. We demonstrate that one signaling kinase, calcium/calmodulin-dependent kinase II (CaMKII), is critical in maintaining aberrant dorsal horn neuron hyperexcitability in the neuropathic pain condition after spinal cord injury (SCI). After contusion SCI at spinal level T10, activated CaMKII (phosphorylated, pCaMKII) expression is significantly upregulated in the T7/8 spinal dorsal horn in neurons, but not glial cells, and in oligodendrocytes in the dorsal column in the same rats that displayed at-level mechanical allodynia. Furthermore, identified spinothalamic neurons demonstrated significant increases of pCaMKII after SCI compared to sham-treated control animals. However, neither astrocytes nor microglia showed pCaMKII expression in either sham-treated or SCI rats. To demonstrate causality, treatment of SCI rats with KN-93, which prevents CaMKII activation, significantly attenuated at-level mechanical allodynia and aberrant wide dynamic range neuronal activity evoked by brush, pressure, and pinch stimuli and a graded series of von Frey stimuli, respectively. Persistent CaMKII activation contributes to chronic central neuropathic pain by mechanisms that involve maintained hyperexcitability of wide dynamic range dorsal horn neurons. Furthermore, targeting key signaling proteins is a novel, useful therapeutic strategy for treating chronic central neuropathic pain.
Computer program (SEQPEP) to aid in the interpretation of high-energy collision tandem mass spectra of peptides (1989)

An algorithm (SEQPEP) that aids in the interpretation of high-energy (greater than 1 kV) collision-induced dissociation mass spectra of peptide ions generated by fast atom bombardment (FAB) ionization is described. The only required input is a list of product ion masses and relative abundances generated by the mass spectrometer data system, the mass of the precursor [M + H]+ ion, and the mass of any C-terminal modification, if present (e.g., amide). Possible N-terminal modifications and amino acid compositions are not required as input. In the output, sequences are ranked according to the fraction of total product ion current that can be accounted for as either sequence-specific or non-sequence-specific fragment ions. These are listed by ion type. One of the major advantages of this program over algorithms described earlier is the incorporation of ion types more recently discovered. Also, this program is much faster, requiring less than 5 min of central processing unit time for an input of as many as 100 product ions. The results obtained from 50 peptides, including some generated when sequencing a protein of previously unknown structure, are discussed.
Antibacterial effect of autologous platelet gel enriched with growth factors and other active substances (2007)

Platelet-rich plasma is a new inductive therapy which is being increasingly used for the treatment of the complications of bone healing, such as infection and nonunion. The activator for platelet-rich plasma is a mixture of thrombin and calcium chloride which produces a platelet-rich gel. We analysed the antibacterial effect of platelet-rich gel in vitro by using the platelet-rich plasma samples of 20 volunteers. In vitro laboratory susceptibility to platelet-rich gel was determined by the Kirby-Bauer disc-diffusion method. Baseline antimicrobial activity was assessed by measuring the zones of inhibition on agar plates coated with selected bacterial strains. Zones of inhibition produced by platelet-rich gel ranged between 6 mm and 24 mm (mean 9.83 mm) in diameter. Platelet-rich gel inhibited the growth of Staphylococcus aureus and was also active against Escherichia coli. There was no activity against Klebsiella pneumoniae, Enterococcus faecalis, and Pseudomonas aeruginosa. Moreover, platelet-rich gel seemed to induce the in vitro growth of Ps. aeruginosa, suggesting that it may cause an exacerbation of infections with this organism. We believe that a combination of the inductive and antimicrobial properties of platelet-rich gel can improve the treatment of infected delayed healing and nonunion.
Use of electroporation to introduce biologically active foreign genes into primary rat hepatocytes. (1986)

A method is described for introducing and expressing cloned genes in isolated hepatocytes. Primary rat hepatocytes isolated by collagenase perfusion were transfected in suspension with plasmid pSV2CAT by electroporation. Forty-eight hours later, soluble extracts from transfected hepatocytes showed chloramphenicol acetyltransferase activity comparable to that obtained in rat hepatoma cell line H4AzC2 by calcium phosphate or DEAE-dextran transfection. The latter two methods could not be used successfully for primary hepatocytes because of cytotoxicity of these reagents. This indicates that electroporation is a useful method to obtain transient expression of foreign genes in primary epithelial cells, such as rat hepatocytes, which are difficult to maintain in cell culture.
Staphylococcal Protein A and Human IgG Subclasses and Allotypes (1982)

Staphylococcal protein A binds molecules belonging to the IgG1, IgG2, and IgG4 subclasses. IgG3 proteins generally do not bind, except for those coded by the two gamma 3 alleles, which are G3m(u-): G3m(b0,b3,b5,s,v). G3m(u) is located in the CH2 domain. The difference between G3m(u-) and G3m(u+) IgG3 proteins correlates with the sequence at position 339 in the CH2 domain--Ala and Thr respectively. There is another structural difference in the CH3 domain which correlates with protein A binding and non-binding: all IgG proteins that bind protein A have His at position 435, whereas those that do not, have Arg at that position.
Inertial Focusing for Tumor Antigen–Dependent and –Independent Sorting of Rare Circulating Tumor Cells (2013)

Circulating tumor cells (CTCs) are shed into the bloodstream from primary and metastatic tumor deposits. Their isolation and analysis hold great promise for the early detection of invasive cancer and the management of advanced disease, but technological hurdles have limited their broad clinical utility. We describe an inertial focusing-enhanced microfluidic CTC capture platform, termed "CTC-iChip," that is capable of sorting rare CTCs from whole blood at 10(7) cells/s. Most importantly, the iChip is capable of isolating CTCs using strategies that are either dependent or independent of tumor membrane epitopes, and thus applicable to virtually all cancers. We specifically demonstrate the use of the iChip in an expanded set of both epithelial and nonepithelial cancers including lung, prostate, pancreas, breast, and melanoma. The sorting of CTCs as unfixed cells in solution allows for the application of high-quality clinically standardized morphological and immunohistochemical analyses, as well as RNA-based single-cell molecular characterization. The combination of an unbiased, broadly applicable, high-throughput, and automatable rare cell sorting technology with generally accepted molecular assays and cytology standards will enable the integration of CTC-based diagnostics into the clinical management of cancer.
Small intestinal bacterial overgrowth syndrome (2010)

Human intestinal microbiota create a complex polymicrobial ecology. This is characterised by its high population density, wide diversity and complexity of interaction. Any dysbalance of this complex intestinal microbiome, both qualitative and quantitative, might have serious health consequence for a macro-organism, including small intestinal bacterial overgrowth syndrome (SIBO). SIBO is defined as an increase in the number and/or alteration in the type of bacteria in the upper gastrointestinal tract. There are several endogenous defence mechanisms for preventing bacterial overgrowth: gastric acid secretion, intestinal motility, intact ileo-caecal valve, immunoglobulins within intestinal secretion and bacteriostatic properties of pancreatic and biliary secretion. Aetiology of SIBO is usually complex, associated with disorders of protective antibacterial mechanisms (e.g. achlorhydria, pancreatic exocrine insufficiency, immunodeficiency syndromes), anatomical abnormalities (e.g. small intestinal obstruction, diverticula, fistulae, surgical blind loop, previous ileo-caecal resections) and/or motility disorders (e.g. scleroderma, autonomic neuropathy in diabetes mellitus, post-radiation enteropathy, small intestinal pseudo-obstruction). In some patients more than one factor may be involved. Symptoms related to SIBO are bloating, diarrhoea, malabsorption, weight loss and malnutrition. The gold standard for diagnosing SIBO is still microbial investigation of jejunal aspirates. Non-invasive hydrogen and methane breath tests are most commonly used for the diagnosis of SIBO using glucose or lactulose. Therapy for SIBO must be complex, addressing all causes, symptoms and complications, and fully individualised. It should include treatment of the underlying disease, nutritional support and cyclical gastro-intestinal selective antibiotics. Prognosis is usually serious, determined mostly by the underlying disease that led to SIBO.
Rapid noninvasive detection of experimental atherosclerotic lesions with novel 99m Tc-labeled diadenosine tetraphosphates (1998)

The development of a noninvasive imaging procedure for identifying atherosclerotic lesions is extremely important for the clinical management of patients with coronary artery and peripheral vascular disease. Although numerous radiopharmaceuticals have been proposed for this purpose, none has demonstrated the diagnostic accuracy required to replace invasive angiography. In this report, we used the radiolabeled purine analog, 99mTc diadenosine tetraphosphate (Ap4A; AppppA, P1,P4-di(adenosine-5')-tetraphosphate) and its analogue 99mTc AppCHClppA for imaging experimental atherosclerotic lesions in New Zealand White rabbits. Serial gamma camera images were obtained after intravenous injection of the radiolabeled dinucleotides. After acquiring the final images, the animals were sacrificed, ex vivo images of the aortas were recorded, and biodistribution was measured. 99mTc-Ap4A and 99mTc AppCHClppA accumulated rapidly in atherosclerotic abdominal aorta, and lesions were clearly visible within 30 min after injection in all animals that were studied. Both radiopharmaceuticals were retained in the lesions for 3 hr, and the peak lesion to normal vessel ratio was 7.4 to 1. Neither of the purine analogs showed significant accumulation in the abdominal aorta of normal (control) rabbits. The excised aortas showed lesion patterns that were highly correlated with the in vivo and ex vivo imaging results. The present study demonstrates that purine receptors are up-regulated in experimental atherosclerotic lesions and 99mTc-labeled purine analogs have potential for rapid noninvasive detection of plaque formation.
Simultaneously Monitoring Gene Expression Kinetics and Genetic Noise in Single Cells by Optical Well Arrays (2004)

An optical fiber based well array platform was used for simultaneous, dynamic gene expression monitoring from hundreds of individual live Escherichia coli cells carrying promoter-fluorescent reporter gene fusions. High information content about gene expression kinetics and cell-to-cell gene expression variability can be collected from a single experiment. These data are invaluable for investigating gene regulation and gene networks as well as for systems biology applications.
Novel diagnostic assays for heparin-induced thrombocytopenia (2013)

Laboratory testing for heparin-induced thrombocytopenia (HIT) has important shortcomings. Immunoassays fail to discriminate platelet-activating from nonpathogenic antibodies. Specific functional assays are impracticable due to the need for platelets and radioisotope. We describe 2 assays that may overcome these limitations. The KKO-inhibition test (KKO-I) measures the effect of plasma on binding of the HIT-like monoclonal antibody KKO to platelet factor 4 (PF4)/heparin. DT40-luciferase (DT40-luc) is a functional test comprised of a B-cell line expressing FcγRIIa coupled to a luciferase reporter. We compared these assays to polyspecific and immunoglobulin (Ig)G-specific PF4/heparin enzyme-linked immunosorbent assays (ELISAs) in samples from 58 patients with suspected HIT and circulating anti-PF4/heparin antibodies. HIT was defined as a 4Ts score ≥ 4 and positive (14)C-serotonin release assay. HIT-positive plasma demonstrated greater mean inhibition of KKO binding than HIT-negative plasma (78.9% vs 26.0%; P < .0001) and induced greater luciferase activity (3.14-fold basal vs 0.96-fold basal; P < .0001). The area under the receiver-operating characteristic curve was greater for KKO-I (0.93) than for the polyspecific (0.82; P = .020) and IgG-specific ELISA (0.76; P = .0044) and for DT40-luc (0.89) than for the IgG-specific ELISA (P = .046). KKO-I and DT40-luc showed better discrimination than 2 commercially available immunoassays, are simple to perform, and hold promise for improving the specificity and feasibility of HIT laboratory testing.
Adjuvant Effect of Cholera Enterotoxin on the Immune Response of the Mouse to Sheep Red Blood Cells (1972)

Intensive efforts are currently being made to develop a cholera toxoid for use in immunization against cholera. Recent reports have demonstrated that a toxoid prepared by inactivation of cholera toxin with formalin was highly immunogenic but reverted in part to toxin [1, 2]. The possibility that some of the immunogenicity of this toxoid was related to the reactivated toxin acting as an adjuvant is suggested by these preliminary studies of the immune response of mice to sheep red blood cells (SRBC) in the presence of cholera toxin. Threeto four-week-old male Balb/c mice were given an iv injection of 10s washed SRBC and cholera enterotoxin. Controls received only SRBC. Five days later, the animals were sacrificed, and the spleens were individually assayed for direct plaque-forming cells (PFC) against SRBC by a modification [3] of the Jerne technique [4]. The cholera enterotoxin used was a highly purified preparation (choleragen) supplied by Dr. Richard A. Finkelstein [5]. Since endotoxin, a known adjuvant, might be present as a contaminant in the preparation, the enterotoxin was assayed for pyrogenicity in rabbits at a dose of 45 sg per rabbit [6]. No pyrogenicity was observed. Only the enterotoxin component was present when the material was tested in immunodiffusion in agar against a multispecific antiserum. The combined data from five separate experiments are presented in table 1. Mice were given SRBC with doses of cholera enterotoxin ranging
Development of an infrared thermopile detector with a thin self-supporting SU-8 membrane (2007)

In this paper we present the development and characterization of thermopile detector on a 4 mum thin self-supporting membrane made of the epoxy based photoresist SU-8. The membrane is realized using silicon bulk micromachining techniques. In many existing thermopile detectors, a temperature difference over the thermocouple junctions is achieved by connecting a thin membrane of either Si or Si <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">3</sub> N <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">4</sub> to a silicon bulk. These materials suffer from relatively high thermal conductivity, which lowers the sensitivity of the detector. A material such as SU-8 has much lower thermal conductivity and is applied using standard photolithographic processing steps. Simulation results are presented which verifies SU-8 as a better choice than Si and Si <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">3</sub> N <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">4</sub> when used as thermal insulating membrane in a thermopile detector. A thermopile consisting of 196 series coupled Ti/Ni thermocouples has been fabricated. Results from measurements are presented, showing a sensitivity of 5.6 V/W and a noise equivalent power (NEP) of 9.9 nW/radicHz.
The influence of material and mesh characteristics on transmission mode desorption electrospray ionization (2008)

Adaptation of desorption electrospray ionization to a transmission mode (TM-DESI) entails passing an electrospray plume through a sample that has been deposited onto a mesh substrate. A combination of mass spectrometry and fluorescence microscopy studies is used to illustrate the critical role material composition, mesh open space, and mesh fiber diameter play on the transmission, desorption, and ionization process. Substrates with open spaces less than 150 microm and accompanying minimal strand diameters produce less scattering of the plume and therefore favor transmission. Larger strand diameters typically encompass larger open spaces, but the increase in the surface area of the strand increases plume scattering as well as solvent and analyte spreading on the mesh. Polypropylene (PP), ethylene tetrafluoroethylene (ETFE), and polyetheretherketone (PEEK) materials afford much better desorption than similarly sized polyethylene terephthalate (PETE) or nylon-6,6 (PA66) substrates. Ultimately, the manner in which the electrospray plume interacts with the mesh as it is transmitted through the substrate is shown to be critical to performing and optimizing TM-DESI analyses. In addition, evidence is presented for analyte dependent variations in the desorption mechanisms of dry and solvated samples.
Visual Adaptation in the Retina of the Skate (1970)

The electroretinogram (ERG) and single-unit ganglion cell activity were recorded from the eyecup of the skate (Raja erinacea and R. oscellata), and the adaptation properties of both types of response compared with in situ rhodopsin measurements obtained by fundus reflectometry. Under all conditions tested, the b-wave of the ERG and the ganglion cell discharge showed identical adaptation properties. For example, after flash adaptation that bleached 80% of the rhodopsin, neither ganglion cell nor b-wave activity could be elicited for 10-15 min. Following this unresponsive period, thresholds fell rapidly; by 20 min after the flash, sensitivity was within 3 log units of the dark-adapted level. Further recovery of threshold was slow, requiring an additional 70-90 min to reach absolute threshold. Measurements of rhodopsin levels showed a close correlation with the slow recovery of threshold that occurred between 20 and 120 min of dark adaptation; there is a linear relation between rhodopsin concentration and log threshold. Other experiments dealt with the initial unresponsive period induced by light adaptation. The duration of this unresponsive period depended on the brightness of the adapting field; with bright backgrounds, suppression of retinal activity lasted 20-25 min, but sensitivity subsequently returned and thresholds fell to a steady-state value. At all background levels tested, increment thresholds were linearly related to background luminance.
Identification and authentication of integrated circuits (2004)

Abstract This paper describes a technique to reliably and securely identify individual integrated circuits (ICs) based on the precise measurement of circuit delays and a simple challenge–response protocol. This technique could be used to produce key‐cards that are more difficult to clone than ones involving digital keys on the IC. We consider potential venues of attack against our system, and present candidate implementations. Experiments on Field Programmable Gate Arrays show that the technique is viable, but that our current implementations could require some strengthening before it can be considered as secure. Copyright © 2004 John Wiley &amp; Sons, Ltd.
Characterization and mapping of a nonessential pseudorabies virus glycoprotein (1986)

Antigenic variants of pseudorabies virus (PRV) containing mutations in a viral glycoprotein with a molecular weight of 82,000 (gIII) were isolated by selecting for resistance to a complement-dependent neutralizing monoclonal antibody (MCA82-2) directed against gIII. These mutants were completely resistant to neutralization with MCA82-2 in the presence of complement. Two mutants selected for further studies either did not express gIII or expressed an improperly processed form of the glycoprotein. The mutations were also associated with an altered plaque morphology (syncytium formation). The gIII gene was mapped by marker rescue of a gIII- mutant with cloned restriction enzyme fragments to the long unique region of the PRV genome between 0.376 and 0.383 map units. This corresponds to the map location of a glycoprotein described by Robbins et al. (J. Mol. Appl. Gen. 2:485-496, 1984). Since gIII is nonessential for viral replication in cell culture and has several other characteristics in common with the herpes simplex virus glycoprotein gC, gIII may represent the PRV equivalent to herpes simplex virus gC.
High multiplexity PCR basedon PCR suppression (2004)

We present a protocol for effi cient amplifi cation of a large number of DNA targets using a single-tube polymerase chain reaction (PCR) based on PCR suppression. This method allows amplifi cation of each DNA target with only one target-specifi c primer whereas the other primer is common for all targets. Thus, this approach requires n+1 primers for n targets instead of 2n in conventional PCR and substantially reduces the cost and complexity of the assay. The method has been successfully applied for amplifi cation of 30 SNP-related DNA targets from human genomic DNA and for genotyping complex (plant) genomes.
Control of the Electro-Optic Bistability of Some Ferroelectric Liquid Crystals Useful for Binary Phase Optical Modulators (2000)

Abstract We report measurements on the bistability of the electrooptic response of a commercially available material (CS2005) and an experimental liquid crystal material (CDRR8) based on an organosiloxane structure. Both materials have a first order transition to the SmC* phase. CS2005 gave the normal monostable behaviour with layers tilted with respect to the rubbing direction. However, the second material, CDRR8, exhibited true bistability and at the same time its smectic layers were found to lie perpendicularly to the rubbing direction. We were able to control the bistable behaviour of the CDRR8 material by means of layer rotation using asymmetrical triangular pulses. As expected the sample shows a monostable response each time the layers are rotated so that one of the two switched states approaches the rubbing direction.
Impedance pneumography: Noise as signal in impedance cardiography (1999)

Thoracic impedance is modulated by events within the respiratory cycle, which represents a source of "noise" in impedance cardiography. Respiration itself, however, is a physiological rhythm of interest to psychophysiologists. We report here methods and validation for deriving impedance pneumographic measures of respiration from impedance cardiography signals, based on standard tetrapolar band electrodes. We recorded the change in impedance (delta Z), the first derivative of the change in impedance (dZ/dt), output from a strain-gauge respirometer, and criterion spirometry from eight healthy adults during rest, paced breathing, abdominal breathing, thoracic breathing, and a mental arithmetic task. Transfer function analyses revealed that a delta Zd signal (derived by integration of the dZ/dt signal) provided the best estimate of the criterion spirometric measure for all parameters (coherence, phase, and gain), accounting for almost 90% of the variance in respiratory waveform morphology. The results document the potential utility of impedance pneumography, as derived from standard impedance cardiography signals.