gebhart/patrepeval huggingface dataset:
Frequency of Spontaneous Bacterial Peritonitis in Cirrhotic patients with ascites due to Hepatitis C Virus and Efficacy of Cirpfloxacin in its Treatment (2009)

Objective: The frequency of spontaneous bacterial peritonitis (SBP) in cirrhotic patients with ascites due to hepatitis “C” virus and efficacy of Ciprofloxacin in its treatment. Material and methods: This study was conducted in medical units of Khyber Teaching Hospital, Peshawar from July, 2008 to Jan, 2009. A total of 100 patients were studied. All those patients who had either already diagnosed or had symptoms and signs of chronic liver disease were included in the study. The main tool for the diagnosis of SBP was diagnostic peritoneal paracentesis which was then repeated after giving 200mg I.V ciprofloxacin for 5 days. Results: The overall frequency of Spontaneous Bacterial Peritonitis in cirrhotic patients with ascites due to HCV was 38 in 100 patients (38%). 52 males and 48 females were studied. Among 38 patients with SBP, 20 were males and 18 were females. All the patients with SBP were put on intravenous ciprofloxacin for 5 days and 79 % of them responded completely. Conclusion: Spontaneous bacterial peritonitis is a common complication of liver cirrhosis leading to significant morbidity and mortality. Although SBP responds excellently to Ciprofloxacin as shown in this study (79 %), even then the morbidity and mortality is high.
Recombinant chimeric OKT3 scFv IgM antibodies mediate immune suppression while reducing T cell activation in vitro (2001)

OKT3, a mouse anti-human CD3 monoclonal antibody (mAb), is a potent immunosuppressive agent used in clinical transplantation to treat allograft rejection. Two major drawbacks of this therapy are the systemic release of several cytokines due to cross-linking mediated by the mAb between T cells and FcγR-bearing cells and the human anti-mouse antibody (HAMA) response. To overcome these side effects, three chimeric OKT3 single chain variable fragment (scFv) IgM antibodies, scOKT3-γ ΔIgM wt, scOKT3-γ ΔIgM C575S and scOKT3-γ ΔIgM VAEVD, were generated. They consist of the light and heavy variable binding domains of OKT3 mAb as well as the CH3 and CH4 domains of different human IgM variants linked with a human IgG3 hinge region to provide more flexibility and stability. Like the native IgM, scOKT3-γ ΔIgM antibodies are able to form polymeric structures, which lead to an increase in binding affinity and immunosuppressive potential compared with the parental OKT3 mAb. However, independently of their polymerization, all scOKT3-γ ΔIgM constructs do not induce any significant T cell proliferation or cytokine release (IL-2, TNF-α and IFN-γ) in in vitro assays, while their CD3-modulating properties are retained. These results suggest that the use of scOKT3-γ ΔIgM antibodies may offer significant advantages over the OKT3 mAb in improving clinical immunosuppressive treatment.
Prognostic Impact of FoxP3+ Regulatory T Cells in Relation to CD8+ T Lymphocyte Density in Human Colon Carcinomas (2012)

The prognostic impact of FoxP3+ and CD8+ T cell density are inter-dependent, whereby FoxP3+ exerts a favorable influence on survival only in colon cancers with low CD8+ infiltration.
Construction and Characterization of Adenovirus Serotype 5 Packaged by Serotype 3 Hexon (2002)

Adenovirus serotype 5 (Ad5) has great potential for gene therapy applications. A major limitation, however, is the host immune response against Ad5 infection that often prevents the readministration of Ad5 vectors. In this regard, the most abundant capsid protein, hexon, has been implicated as the major target for neutralizing antibodies. In this study, we sought to escape the host neutralization response against Ad5 via hexon replacement. We constructed a chimeric adenovirus vector, Ad5/H3, by replacing the Ad5 hexon gene with the hexon gene of Ad3. The chimeric viruses were successfully rescued in 293 cells. Compared to that for the control Ad5/H5, the growth rate of Ad5/H3 was significantly slower and the final yield was about 1 log order less. These data indicate that the Ad3 hexon can encapsidate the Ad5 genome, but with less efficiency than the Ad5 hexon. The gene transfer efficacy of Ad5/H3 in HeLa cells was also lower than that of Ad5/H5. Furthermore, we tested the host neutralization responses against the two viruses by using C57BL/6 mice. The neutralizing antibodies against Ad5/H3 and Ad5/H5 generated by the immunized mice did not cross-neutralize each other in the context of in vitro infection of HeLa cells. Preimmunization of C57BL/6 mice with one of the two types of viruses also did not prevent subsequent infection of the other type. These data suggest that replacing the Ad5 hexon with the Ad3 hexon can circumvent the host neutralization response to Ad5. This strategy may therefore be used to achieve the repeated administration of Ad5 in gene therapy applications.
A new diamond search algorithm for fast block-matching motion estimation (2000)

Based on the study of motion vector distribution from several commonly used test image sequences, a new diamond search (DS) algorithm for fast block-matching motion estimation (BMME) is proposed in this paper. Simulation results demonstrate that the proposed DS algorithm greatly outperforms the well-known three-step search (TSS) algorithm. Compared with the new three-step search (NTSS) algorithm, the DS algorithm achieves close performance but requires less computation by up to 22% on average. Experimental results also show that the DS algorithm is better than the four-step search (4SS) and block-based gradient descent search (BBGDS), in terms of mean-square error performance and required number of search points.
Dihydropyrimidine angiotensin II receptor antagonists (1992)

The discovery of the nonpeptide angiotensin II (AII) receptor antagonist losartan, previously called DuP 753, has stimulated considerable interest in the synthesis of novel analogs of this compound. Our efforts in this area have resulted in the discovery of dihydropyrimidines as potent AII receptor antagonists. The chemistry leading to this novel class of AII antagonists and their biological properties are reported in this publication. Structure-activity studies showed that a variety of substituents are tolerated on the dihydropyrimidine ring, indicating that the AII receptor is permissive in accepting this region of the nonpeptide antagonists. As reported for imidazole-based AII antagonists, the tetrazolyl dihydropyrimidine analogs were found to be more potent than the corresponding carboxylic acids. Our studies show that dihydropyrimidine analogs 2-butyl-4-chloro-1,6-dihydro-6-methyl-1-[[2'-(1H-tetrazol-5-yl)[1, 1'-biphenyl]-4-yl]methyl]pyrimidine-5-carboxylic acid, ethyl ester (Ki = 8.3 nM), 2-butyl-4-chloro-1,6-dihydro-6-methyl-1- [[2'-(1H-tetrazol-5-yl)[1,1'-biphenyl]-4-yl]methyl]-5- pyrimidinecarboxylic acid (Ki = 1.0 nM), and 2-butyl-6-chloro-1,4-dihydro-4,4-dimethyl-1-[[2'-(1H-tetrazol-5-yl )[1,1'- biphenyl]-4-yl]methyl]-5-pyrimidinecarboxylic acid, ethyl ester (Ki = 1.1 nM), display affinities for the AII receptor which are comparable to or better than losartan (Ki = 9.0 nM). One of these derivatives, 2-butyl-4-chloro-1,6-dihydro-6-methyl-1-[[2'-(1H-tetrazol-5- yl)[1,1'-biphenyl]-4-yl]methyl]pyrimidine-5-carboxylic acid, ethyl ester, showed antihypertensive activity on oral administration to spontaneously hypertensive rats. These results demonstrate that the imidazole of losartan can be successfully replaced with a dihydropyrimidine ring.
Highly area efficient and cost effective double stacked S/sup 3/ (stacked single-crystal Si) peripheral CMOS SSTFT and SRAM cell technology for 512M bit density SRAM (2004)

For the first time, the highest density SRAM, such as 512M bit SRAM, is developed by implementing the smallest 25F/sup 2/S/sup 3/ SRAM cell technology, whose cell size is 0.16/spl mu/m/sup 2/, and area saving peripheral SSTFT (stacked single-crystal thin film transistor) technology. The SSTFT are used as the peripheral CMOS transistors as well as the cell transistors to save area to make the SRAM products comparative to the DRAM cell based products in the density and the cost. In the S/sup 3/ SRAM cell, the load PMOS and pass NMOS transistors are stacked over the planar pull-down NMOS transistors to drastically reduce the cell size. Also, in a periphery, the core logic transistors are stacked on the ILD to save the layout area for maximizing cell efficiency for the products.
Extracellular matrix of the central nervous system: from neglect to challenge (2008)

The basic concept, that specialized extracellular matrices rich in hyaluronan, chondroitin sulfate proteoglycans (aggrecan, versican, neurocan, brevican, phosphacan), link proteins and tenascins (Tn-R, Tn-C) can regulate cellular migration and axonal growth and thus, actively participate in the development and maturation of the nervous system, has in recent years gained rapidly expanding experimental support. The swift assembly and remodeling of these matrices have been associated with axonal guidance functions in the periphery and with the structural stabilization of myelinated fiber tracts and synaptic contacts in the maturating central nervous system. Particular interest has been focused on the putative role of chondroitin sulfate proteoglycans in suppressing central nervous system regeneration after lesions. The axon growth inhibitory properties of several of these chondroitin sulfate proteoglycans in vitro, and the partial recovery of structural plasticity in lesioned animals treated with chondroitin sulfate degrading enzymes in vivo have significantly contributed to the increased awareness of this long time neglected structure.
Peak-to-average power reduction in digital television transmitters (2002)

Orthogonal Frequency Division Multiplexing (OFDM) is one of the modulation techniques used in digital video broadcasting systems. A significant disadvantage of OFDM is that it has a high peak-to-average power ratio (PAPR). This means that the output amplifiers of digital television transmitters must be designed to handle signals that are far in excess of the mean levels. These amplifiers are expensive. One way to reduce the PAPR is to digitally limit the peak value before the signals reach the amplifier. Various clipping techniques have been described in the literature. This paper describes the application of the most effective of these techniques to the European digital video broadcasting system. It is shown that the PAPR can be reduced without significant increase in bit error rate. In practical systems, amplifier non-linearities cause unwanted out-of-band power which may interfere with adjacent television channels. Simulation results are presented for systems with and without clipping and for varying amplifier characteristics showing that clipping substantially reduces the level of out-of-band power. 1.
Dimer formation drives the activation of the cell death protease caspase 9 (2001)

A critical step in the induction of apoptosis is the activation of the apoptotic initiator caspase 9. We show that at its normal physiological concentration, caspase 9 is primarily an inactive monomer (zymogen), and that activity is associated with a dimeric species. At the high concentrations used for crystal formation, caspase 9 is dimeric, and the structure reveals two very different active-site conformations within each dimer. One site closely resembles the catalytically competent sites of other caspases, whereas in the second, expulsion of the "activation loop" disrupts the catalytic machinery. We propose that the inactive domain resembles monomeric caspase 9. Activation is induced by dimerization, with interactions at the dimer interface promoting reorientation of the activation loop. These observations support a model in which recruitment by Apaf-1 creates high local concentrations of caspase 9 to provide a pathway for dimer-induced activation.
High-affinity binding of the bactericidal/permeability-increasing protein and a recombinant amino-terminal fragment to the lipid A region of lipopolysaccharide (1992)

Bactericidal/permeability-increasing protein (BPI) is a 55-kDa cationic protein (nBPI55) elaborated by polymorphonuclear neutrophils (PMN). BPI has potent bactericidal activity against a wide variety of gram-negative organisms and neutralizes endotoxin activities. An N-terminal fragment of nBPI55 exhibits the bactericidal and antiendotoxin properties of the holoprotein. To further characterize the biological activities of the N-terminal fragment, a recombinant protein (rBPI23) corresponding to the first 199 amino acids of human BPI was produced and purified. rBPI23 had antibacterial activity equivalent to that of nBPI55 against Escherichia coli J5. Furthermore, both rBPI23 and nBPI55 bound identically to a broad range of R- and S-form lipopolysaccharides (LPS) and to natural and synthetic lipid A. Binding of radiolabeled nBPI55 to LPS was inhibited in an identical fashion by either nBPI55 or rBPI23. The binding of both proteins to immobilized E. coli J5 lipid A was inhibited in a comparable fashion by long- or short-chain LPS or lipid A. The binding of both rBPI23 and nBPI55 was specific, saturable, and of high affinity, with an apparent Kd of approximately 2 to 5 nM for all ligands tested. These results demonstrate that BPI recognizes the highly conserved lipid A region of bacterial LPS via residues contained within the amino-terminal portion of the BPI molecule.
High-throughput bioinformatics with the Cyrille2 pipeline system (2008)

The Cyrille2 system is an extensible, modular system, implementing the stated requirements. Cyrille2 enables easy creation and execution of high throughput, flexible bioinformatics pipelines.
An Antibody with a Variable‐Region Coiled‐Coil “Knob” Domain (2013)

The X-ray crystal structure of a bovine antibody (BLV1H12) revealed a unique structure in its ultralong heavy chain complementarity determining region 3 (CDR3H) that folds into a solvent-exposed β-strand "stalk" fused to a disulfide crosslinked "knob" domain. We have substituted an antiparallel heterodimeric coiled-coil motif for the β-strand stalk in this antibody. The resulting antibody (Ab-coil) expresses in mammalian cells and has a stability similar to that of the parent bovine antibody. MS analysis of H-D exchange supports the coiled-coil structure of the substituted peptides. Substitution of the knob-domain of Ab-coil with bovine granulocyte colony-stimulating factor (bGCSF) results in a stably expressed chimeric antibody, which proliferates mouse NFS-60 cells with a potency comparable to that of bGCSF. This work demonstrates the utility of this novel coiled-coil CDR3 motif as a means for generating stable, potent antibody fusion proteins with useful pharmacological properties.
Integral histogram: a fast way to extract histograms in Cartesian spaces (2005)

We present a novel method, which we refer as an integral histogram, to compute the histograms of all possible target regions in a Cartesian data space. Our method has three distinct advantages: 1) It is computationally superior to the conventional approach. The integral histogram method makes it possible to employ even an exhaustive search process in real-time, which was impractical before. 2) It can be extended to higher data dimensions, uniform and nonuniform bin formations, and multiple target scales without sacrificing its computational advantages. 3) It enables the description of higher level histogram features. We exploit the spatial arrangement of data points, and recursively propagate an aggregated histogram by starting from the origin and traversing through the remaining points along either a scan-line or a wave-front. At each step, we update a single bin using the values of integral histogram at the previously visited neighboring data points. After the integral histogram is propagated, histogram of any target region can be computed easily by using simple arithmetic operations.
Differential effects of wave reflections and peripheral resistance on aortic blood pressure: a model-based study (1994)

It has been generally accepted that arterial system wave reflections act to increase aortic blood pressure and the load placed on the left ventricle. Using a mathematical model of the coupled left ventricle-arterial system, we predict that this is not the case. With the model, two aspects of wave reflection, the global reflection coefficient [TG(omega)] and the pulse wave velocity (cph), were adjusted independently. In addition, TG(omega) and cph could be altered independently of the direct-current properties of the arterial system model. Reduction of TG(omega) yielded increases in stroke volume (SV) as well as in peak systolic (Ps), diastolic (Pd), and mean aortic (Pao) pressures and, hence, increased the load on the left ventricle. SV and Pao increased only in the range where strong reflection occurs. Reduced cph also yielded higher pressures, whereas increased cph resulted in reduced Pao and Pd but increased Ps. The changes in pressures and SV in response to altered TG(omega) and cph were relatively small compared with absolute levels. Simulated vasoconstriction and vasodilation further demonstrated the much greater importance of peripheral resistance on pressure and SV levels and lead to the prediction that pressure reduction in vasodilation occurs not because of, but in spite of, reduced wave reflections. We conclude that these results have not yet been observed experimentally, because reflection cannot yet be separated from the direct-current properties of the arterial system; therefore wave reflections themselves have not yet been adequately studied in the intact animal.
The Ras Antagonist, Farnesylthiosalicylic Acid (FTS), Decreases Fibrosis and Improves Muscle Strength in dy2J/dy2J Mouse Model of Muscular Dystrophy (2011)

The Ras superfamily of guanosine-triphosphate (GTP)-binding proteins regulates a diverse spectrum of intracellular processes involved in inflammation and fibrosis. Farnesythiosalicylic acid (FTS) is a unique and potent Ras inhibitor which decreased inflammation and fibrosis in experimentally induced liver cirrhosis and ameliorated inflammatory processes in systemic lupus erythematosus, neuritis and nephritis animal models. FTS effect on Ras expression and activity, muscle strength and fibrosis was evaluated in the dy(2J)/dy(2J) mouse model of merosin deficient congenital muscular dystrophy. The dy(2J)/dy(2J) mice had significantly increased RAS expression and activity compared with the wild type mice. FTS treatment significantly decreased RAS expression and activity. In addition, phosphorylation of ERK, a Ras downstream protein, was significantly decreased following FTS treatment in the dy(2J)/dy(2J) mice. Clinically, FTS treated mice showed significant improvement in hind limb muscle strength measured by electronic grip strength meter. Significant reduction of fibrosis was demonstrated in the treated group by quantitative Sirius Red staining and lower muscle collagen content. FTS effect was associated with significantly inhibition of both MMP-2 and MMP-9 activities. We conclude that active RAS inhibition by FTS was associated with attenuated fibrosis and improved muscle strength in the dy(2J)/dy(2J) mouse model of congenital muscular dystrophy.
ChemInform Abstract: Electrochemically Active Polymers for Rechargeable Batteries (1997)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 100 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a “Full Text” option. The original article is trackable via the “References” option.
Cerebral Microvascular Alterations in Aging, Leukoaraiosis, and Alzheimer's Diseasea (1997)

We have been using alkaline phosphatase (AP) histochemical staining, formerly a research tool for the study of cerebral cortical vascular morphology, to examine pathological changes in the cortex and deep cerebral structures. Deep structures stain similarly to the cortex. The AP stain is found in the afferent vessels (small arteries, arterioles, and capillaries), but not in venules and veins. The stain is also present in leaky vessels, such as those in the area postrema. The vascular supply to the cerebrum is not homogeneous. Supply to the deep white matter, for instance, derives from the leptomeningeal border zone, and then medullary arterioles must wind their way for up to 4 cm before arriving at their ultimate destination. Adding to the difficulties, tortuosities develop in some of these vessels with aging. According to some calculations, hypertensive levels of blood pressure would be required to maintain irrigation through some of these vessels. We have identified a venous alteration that attends aging: periventricular venous collagenosis (PVC) is a previously unrecognized, noninflammatory, mural disease of the periventricular veins. In severe cases, examples can be found of veins that are completely occluded by this process. PVC is found in 65% of subjects over 60 years old, and it strongly correlates with leukoaraiosis. In addition to previously mentioned aging-related changes, we have found extreme tortuosity, multiplications, and aneurysms of the smallest arterioles and lumpy-bumpy capillaries in the deep structures of patients with Alzheimer's disease.
Pharmacogenomics of Lung Cancer: With A View To Address EGFR-Targeted Therapies (2007)

Epidermal growth factor receptor (EGFR)-targeted therapies have demonstrated variable success in treating individuals with non-small-cell lung cancer. Understanding the molecular mechanisms of response and resistance to this class of treatment has led to patient selection strategies that may improve outcomes. The second generation of EGFR-targeted therapies is now under clinical evaluation and may prove to be successful at circumventing a portion of primary or acquired resistance to first-generation tyrosine kinase inhibitors. These principles are generally applicable to the field of targeted therapy and predictive pharmacogenomics.
A procedure for denoising dual-axis swallowing accelerometry signals (2009)

Dual-axis swallowing accelerometry is an emerging tool for the assessment of dysphagia (swallowing difficulties). These signals however can be very noisy as a result of physiological and motion artifacts. In this note, we propose a novel scheme for denoising those signals, i.e. a computationally efficient search for the optimal denoising threshold within a reduced wavelet subspace. To determine a viable subspace, the algorithm relies on the minimum value of the estimated upper bound for the reconstruction error. A numerical analysis of the proposed scheme using synthetic test signals demonstrated that the proposed scheme is computationally more efficient than minimum noiseless description length (MNDL)-based denoising. It also yields smaller reconstruction errors than MNDL, SURE and Donoho denoising methods. When applied to dual-axis swallowing accelerometry signals, the proposed scheme exhibits improved performance for dry, wet and wet chin tuck swallows. These results are important for the further development of medical devices based on dual-axis swallowing accelerometry signals.
Ultrastructure of the vitreoretinal interface following plasmin assisted vitrectomy (2001)

Plasmin induces a cleavage between the vitreous cortex and the ILM without morphological changes to the retina. In contrast with previous reports, plasmin produces a smooth retinal surface and additional surgery is not required in this experimental setting. The degree of vitreoretinal separation depends on the concentration and length of exposure to plasmin.