gebhart/patrepeval huggingface dataset:
A Viral Discovery Methodology for Clinical Biopsy Samples Utilising Massively Parallel Next Generation Sequencing (2011)

Here we describe a virus discovery protocol for a range of different virus genera, that can be applied to biopsy-sized tissue samples. Our viral enrichment procedure, validated using canine and human liver samples, significantly improves viral read copy number and increases the length of viral contigs that can be generated by de novo assembly. This in turn enables the Illumina next generation sequencing (NGS) platform to be used as an effective tool for viral discovery from tissue samples.
Mattress double anchor footprint repair: A novel, arthroscopic rotator cuff repair technique (2004)

In an effort to increase the immediate strength of a rotator cuff repair and to simulate the standard open reconstruction with its effective suture fixation, we have developed a novel technique for suture anchor reconstruction of the rotator cuff. The technique, termed mattress double anchor (MDA), is simple and adaptable. It makes use of 2 suture anchors that are placed independently and then connected by a suture loop. The technique produces a repair construct that distributes the stress across 2 anchors. The method also restores a large surface area for healing between the rotator cuff and the tuberosity.
Life, Liberty, or Your Children: California Parents’ Fifth Amendment Quandary between Self- Incrimination and Family Preservation (2008)

domestic violence against a spouse or part-
Site‐specific linkage of methotrexate to monoclonal antibodies using an intermediate carrier (1988)

Abstract The site‐specific conjugation of methotrexate, 4‐amino‐N 10 ‐methylpteroylglutamic acid, to a monoclonal anti‐carcinoembryonic antigen (CEA) antibody, using an intermediate aminodextran carrier system, resulted in a ratio of 30‐50 molecules of MTX per molecule of immunoglobulin. The immunoreactivity of the conjugate was analyzed using flow cytometry or a competitive binding assay, which showed that the conjugate has significant retention of the antigen‐binding activity. The pharmacokinetic behavior of the immunoconjugate in BALB/c mice and tumor localization in hamsters indicated that the conjugate remained in the circulation with higher concentration than free antibody, and could recognize the tumor as efficiently as the unconjugated antibody. The high degree of drug incorporation with retained immunoreactivity makes this method preferable to direct antibody conjugation.
Failure of Elastin or Collagen as Possible Critical Connective Tissue Alterations Underlying Aneurysmal Dilatation (1994)

Previous studies in the authors' laboratory have demonstrated that degradation of arterial elastin produces vessel dilatation, decreased vessel distensibility, and vessel elongation which can cause tortuosity. By contrast, degradation of collagen produces increased vessel distensibility and rupture. However, neither degradation of elastin nor of collagen produced the true gross enlargement characteristic of human aneurysms. The present study was performed to identify the connective tissue critical to aneurysm formation. Vessel dimensions were measured repeatedly in human arteries during progressive enzymatic degradation. Experiments were performed on six intact human common, external and internal iliac arteries, and two aneurysmal human common iliac arteries. The vessels were mounted in vitro and subjected to pressure steps up to 200 mmHg while diameters were measured. Repeated pressure-diameter curves were obtained for up to 18 h during treatment with elastase or collagenase. Degradation of elastin produced moderate dilatation (6-10% at 100 mmHg) with decreased vessel distensibility; this occurred as the load was shifted to remaining collagen. Degradation of collagen produced greater dilatation (10-23% at 100 mmHg), increased distensibility, and vessel rupture. These findings suggest that the critical element in both the gross enlargement and rupture of aneurysms resides in collagen. They also suggest that, in vessels obtained from patients with a family history of aneurysms, defects should be sought in: (i) the structure of collagen; (ii) increased susceptibility of collagen to degradation by endogenous mechanisms; (iii) increased endogenous collagenolytic activity; or (iv) decreased inhibition of endogenous collagenolytic activities.
Remyelination is extensive in a subset of multiple sclerosis patients (2006)

Although spontaneous remyelination does occur in multiple sclerosis lesions, its extent within the global population with this disease is presently unknown. We have systematically analysed the incidence and distribution of completely remyelinated lesions (so-called shadow plaques) or partially remyelinated lesions (shadow plaque areas) in 51 autopsies of patients with different clinical courses and disease durations. The extent of remyelination was variable between cases. In 20% of the patients, the extent of remyelination was extensive with 60-96% of the global lesion area remyelinated. Extensive remyelination was found not only in patients with relapsing multiple sclerosis, but also in a subset of patients with progressive disease. Older age at death and longer disease duration were associated with significantly more remyelinated lesions or lesion areas. No correlation was found between the extent of remyelination and either gender or age at disease onset. These results suggest that the variable and patient-dependent extent of remyelination must be considered in the design of future clinical trials aimed at promoting CNS repair.
The Time-Dependent Mechanical Properties of the Human Heel Pad in the Context of Locomotion (1996)

Previous measurements of the mechanical properties of the heel pad, especially of the energy loss during a cycle of compressive loading and unloading, have given contrasting values according to whether the investigators used isolated single impacts (e.g. pendulum tests; energy loss approximately 48%) or continuous oscillations (energy loss approximately 30%). To investigate this discrepancy, rest periods were inserted between single compressive cycles, giving intermittent loading as in locomotion. The energy loss, measured as the percentage area of the hysteresis loop, was found to change linearly with the logarithm of the rest time. It was approximately 33% when the rest time was 1 s. Each 10-fold increase in the rest time added approximately 3.7% to the energy loss. Thus, with rest times appropriate to locomotion, the pad is far from fully relaxed. The springy heel pad may help to reposition the foot during the transfer of load from the heel to the forefoot. Information is also included on the load-deformation curves for the heel pad and the way in which these change with rest time. This is presented as equations which may be useful in future models relating the mechanical properties of the heel to either its structure or its function.
Ursodiol for Hepatobiliary Disorders (1994)

Ursodiol is a safe and effective therapy for the treatment of patients with cholesterol gallstones. Although treatment with ursodiol leads to improvement in biochemical markers for cholestatic liver diseases, whether it alters the natural history of these disorders is the subject of ongoing trials.
Animal models in myositis (2008)

Several new animal models of myositis have emerged over the last few years that have revealed new insights regarding the pathophysiology of idiopathic inflammatory myopathy and that should set the foundation for development of new, more effective therapies against this often intractable disease.
The role of cyclic nucleotide phosphodiesterases in the regulation of adipocyte lipolysis (2004)

This study assessed the effects of selective inhibitors of 3',5'-cyclic nucleotide phosphodiesterases (PDEs) on adipocyte lipolysis. IC224, a selective inhibitor of type 1 phosphodiesterase (PDE1), suppressed lipolysis in murine 3T3-L1 adipocytes (69.6 +/- 5.4% of vehicle control) but had no effect in human adipocytes. IC933, a selective inhibitor of PDE2, had no effect on lipolysis in either cultured murine 3T3-L1 adipocytes or human adipocytes. Inhibition of PDE3 with cilostamide moderately stimulated lipolysis in murine 3T3-L1 and rat adipocytes (397 +/- 25% and 235 +/- 26% of control, respectively) and markedly stimulated lipolysis in human adipocytes (932 +/- 7.6% of control). Inhibition of PDE4 with rolipram moderately stimulated lipolysis in murine 3T3-L1 adipocytes (291 +/- 13% of control) and weakly stimulated lipolysis in rat adipocytes (149 +/- 7.0% of control) but had no effect on lipolysis in human adipocytes. Cultured adipocytes also responded differently to a combination of PDE3 and PDE4 inhibitors. Simultaneous exposure to cilostamide and rolipram had a synergistic effect on lipolysis in murine 3T3-L1 and rat adipocytes but not in human adipocytes. Hence, the relative importance of PDE3 and PDE4 in regulating lipolysis differed in cultured murine, rat, and human adipocytes.
Proteasomal Degradation of Runx2 Shortens Parathyroid Hormone-induced Anti-apoptotic Signaling in Osteoblasts (2003)

It is unknown why sustained elevation of parathyroid hormone (PTH) stimulates bone resorption, whereas intermittent administration stimulates bone formation. We show in mice that daily injections of PTH attenuate osteoblast apoptosis, thereby increasing osteoblast number, bone formation rate, and bone mass, but do not affect osteoclast number. In contrast, sustained elevation of PTH, achieved either by infusion or by raising endogenous hormone secretion with a calcium-deficient diet, does not affect osteoblast apoptosis but increases osteoclast number. Attenuation of apoptosis by PTH in cultured osteoblastic cells requires protein kinase A-mediated phosphorylation and inactivation of the pro-apoptotic protein Bad as well as transcription of survival genes, like Bcl-2, mediated by CREB (cAMP response element-binding protein) and Runx2. But, PTH also increases proteasomal proteolysis of Runx2. Moreover, the anti-apoptotic effect of PTH is prolonged by inhibition of proteasomal activity, by overexpressing a dominant negative form of the E3 ligase (ubiquitin-protein isopeptide ligase) that targets Runx2 for degradation (Smurf1), or by overexpressing Runx2 itself. The duration of the anti-apoptotic effect of PTH, thus, depends on the level of Runx2, which in turn is decreased by PTH via Smurf1-mediated proteasomal proteolysis. The self-limiting nature of PTH-induced survival signaling might explain why intermittent administration of the hormone is required for bone anabolism.
Arithmetic co-transformations in the real and complex logarithmic number systems (2002)

The real logarithmic number system, which represents a value with a sign bit and a quantized logarithm, can be generalized to create the complex logarithmic number system, which replaces the sign bit with a quantized angle in a log/polar coordinate system. Although multiplication and related operations are easy in both real and complex systems, addition and subtraction are hard, especially when interpolation is used to implement the system. Both real and complex logarithmic arithmetic benefit from the use of co-transformation, which converts an addition or subtraction from a region where interpolation is expensive to a region where it is easier. Two co-transformations that accomplish this goal are introduced. The first is an approximation based on real analysis of the subtraction logarithm. The second is based on simple algebra that applies for both real and complex values and that works for both addition and subtraction.
Human single-chain Fv immunoconjugates targeted to a melanoma-associated chondroitin sulfate proteoglycan mediate specific lysis of human melanoma cells by natural killer cells and complement (1999)

Two antimelanoma immunoconjugates containing a human single-chain Fv (scFv) targeting domain conjugated to the Fc effector domain of human IgG1 were synthesized as secreted two-chain molecules in Chinese hamster ovary and Drosophila S2 cells, and purified by affinity chromatography on protein A. The scFv targeting domains originally were isolated as melanoma-specific clones from a scFv fusion-phage library, derived from the antibody repertoire of a vaccinated melanoma patient. The purified immunoconjugates showed similar binding specificity as did the fusion-phage clones. Binding occurred to human melanoma cells but not to human melanocytes or to several other types of normal cells and tumor cells. A 250-kDa melanoma protein was immunoprecipitated by the immunoconjugates and analyzed by mass spectrometry, using two independent procedures. A screen of protein sequence databases showed an exact match of several peptide masses between the immunoprecipitated protein and the core protein of a chondroitin sulfate proteoglycan, which is expressed on the surface of most human melanoma cells. The Fc effector domain of the immunoconjugates binds natural killer (NK) cells and also the C1q protein that initiates the complement cascade; both NK cells and complement can activate powerful cytolytic responses against the targeted tumor cells. An in vitro cytolysis assay was used to test for an immunoconjugate-dependent specific cytolytic response against cultured human melanoma cells by NK cells and complement. The melanoma cells, but not the human fibroblast cells used as the control, were efficiently lysed by both NK cells and complement in the presence of the immunoconjugates. The in vitro results suggest that the immunoconjugates also could activate a specific cytolytic immune response against melanoma tumors in vivo.
Effect of FK506 and Anti-CD4 Therapy on Fetal Pig Pancreas Xenografts and Host Lymphoid Cells in NOD/Lt, CBA, and BALB/c Mice (1994)

Varying doses of FK506, and a cell-depleting anti-CD4 monoclonal antibody, GK1.5, were tested as either monotherapy or in combination for their effect on the survival of renal subcapsular xenografts of organ-cultured fetal pig pancreas in three strains of mice. Subcutaneous injections of FK506 at 4.0 mg/kg/day for 28 d prevented graft rejection to day 35 posttransplantation (i.e., 7 days after cessation of treatment in NOD/Lt, and CBA mice) while BALB/c mice had intact grafts at 28 days. Lower doses were less effective and immunosuppression was less effective in NOD mice than in the other strains. Even 2.0 mg/kg/day of FK506 prevented rejection in CBA mice until day 35, but not in NOD/Lt mice. GK1.5 alone did not prevent rejection in NOD/Lt mice but when a low dose of FK506 (2.0 mg/day) was added, the grafts were present, essentially intact, at 35 days. There were no obvious toxic effects of FK506 in NOD/Lt and CBA mice. With FK506 treatment there was no significant difference in absolute numbers of total leucocytes or lymphocytes in peripheral blood and spleen, but there was a decrease in thymus cellularity. Flow cytometric analysis of lymphocyte subsets in blood and spleen also showed no significant differences, but in the thymus the percentage of immature CD4/CD8 "double positive" cells increased while the more mature CD3"high", and CD4 or CD8 "single-positive" cells decreased. Thus, prolonged discordant xenograft survival in mice is possible and the use of two agents that act on different parts of the immune system allows a reduction in the dose of FK506 to safe levels.
Polarization maintaining fiber based ultra-high resolution spectral domain polarization sensitive optical coherence tomography (2009)

We present a new ultra high resolution spectral domain polarization sensitive optical coherence tomography (PS-OCT) system based on polarization maintaining (PM) fibers. The method transfers the principles of our previous bulk optic PS-OCT systems to a fiberized setup. The phase shift between the orthogonal polarization states travelling in the two orthogonal modes of the PM fiber is compensated by software in post processing. Thereby, the main advantage of our bulk optics setups, i.e. the use of only a single input polarization state to simultaneously acquire reflectivity, retardation, optic axis orientation, and Stokes vector, is maintained. The use of a broadband light source of 110 nm bandwidth provides improved depth resolution and smaller speckle size. The latter is important for improved resolution of depolarization imaging. We demonstrate our instrument for high-resolution PS-OCT imaging of the healthy human retina.
MITOCHONDRIAL KATP CHANNEL OPENER PREVENTS ISCHEMIA-REPERFUSION INJURY IN RAT LIVER (2004)

P73 Aims: Ischemia-reperfusion injury is responsible for the morbidity associated with liver surgery under total vascular exclusion or after liver transplantation. To reduce the injury, ischemic preconditioning has been shown to protect some organs such as heart, kidney, and liver against a more prolonged ischemic insult. Recently, mitochondrial KATP (mito KATP) channel rather than surface KATP channels, has emerged as likely mediators of preconditioning in the heart. Therefore, it has been reported that KATP channel opener has an effect on myocardial protection via an effort to inquire into the pharmacological preconditioning action. However, the final effecter molecules of the action remain unclear. It is unclear even whether KATP channel openers can reduce ischemia-reperfusion injury in the liver. The aim of this study is to determine the effect of mito KATP channel opener, nicorandil (SG-75), on ischemia-reperfusion injury in rat liver. Methods: Male Wistar rats were used and anesthetized with urethane. The blood supply to right and middle lobe of the liver was interrupted to 73% ischemia for 45 min, followed by 120 min of reperfusion. SG-75 (3 mg/kg) was orally administered 60 min before hepatic ischemia. Rats were sacrificed at 120 min after reperfusion (IR group) and after reperfusion with SG-75 administration (SG+IR group). Samples of blood and liver tissues were collected at the indicated times. Plasma levels of ALT and LDH were measured for examination of the liver function. Apoptosis was determined by TUNEL staining. The expression of cytochrome c, Bax, Bcl-2 and caspase-3 were analyzed by western blotting. TNF-α levels of plasma and liver were quantified using ELISA. Results: Plasma levels of ALT and LDH in IR group markedly increased to 5588 ± 646 and 28270 ± 3325 (IU / L), respectively. SG-75 significantly decreased their levels by about 60% (p<0.05). TUNEL-positive hepatocytes remarkably increased in about 30% of total hepatocytes in IR group. In SG-75 group, the increase of TUNEL-positive hepatocytes was inhibited to about 10%. Levels of cytochrome c in the corresponding mitochondrial fraction of the liver did not differ between the two groups. Cytochrome c and activated caspase-3 levels in the cytosol increased in IR group and SG-75 inhibited the release of cytochrome c and activation of caspase-3. The expression of Bax and Bcl-2 significantly increased in IR group and was slightly inhibited by administration of SG-75. Hepatic TNF-α levels slightly increased after reperfusion in both groups. Conclusions: These results suggested that its protective effect of SG-75 against hepatic ischemia-reperfusion injury was correlated with the inhibition of mitochondrial cytochrome c release and caspase-3 activation. These findings demonstrate that SG-75 may also become a therapeutic drug for IR-related hepatocellular damage.
Placental Hofbauer cells assemble and sequester HIV‐1 in tetraspanin‐positive compartments that are accessible to broadly neutralizing antibodies (2015)

These findings suggest that placental HCs possess intrinsic adaptations facilitating unique sequestration of HIV-1, and may serve as a protective viral reservoir to permit viral neutralization and/or antiretroviral drug entry in utero.
Improvement of Rinsing Efficiency after Sulfuric Acid Hydrogen Peroxide Mixture (H2SO4/H2O2) by HF Addition (1996)

We report on the improvement in efficiency of deionized water rinsing after using a H 2 SO 4 /H 2 O 2 /HF mixture which produces hydrophobic Si surfaces by means of fluorine passivation, providing better sulfur removal and shorter rinsing time than the conventional H 2 SO 4 /H 2 O 2 mixture. After removing this passivation agent by rinsing in deionized water, the surfaces are still covered with chemical oxide, which protects them from organic contamination. Furthermore this treatment does not induce surface roughening.
Cloning and Molecular Analysis of the Poly(3-hydroxybutyrate) and Poly(3-hydroxybutyrate-co-3-hydroxyalkanoate) Biosynthesis Genes inPseudomonassp. Strain 61-3 (1998)

Two types of polyhydroxyalkanoate (PHA) biosynthesis gene loci (phb and pha) of Pseudomonas sp. strain 61-3, which produces a blend of poly(3-hydroxybutyrate) [P(3HB)] homopolymer and a random copolymer (poly(3-hydroxybutyrate-co-3-hydroxyalkanoate) [P(3HB-co-3HA]) consisting of 3HA units of 4 to 12 carbon atoms, were cloned and analyzed at the molecular level. In the phb locus, three open reading frames encoding polyhydroxybutyrate (PHB) synthase (PhbCPs), beta-ketothiolase (PhbAPs), and NADPH-dependent acetoacetyl coenzyme A reductase (PhbBPs) were found. The genetic organization showed a putative promoter region, followed by phbBPs-phbAPs-phbCPs. Upstream from phbBPs was found the phbRPs gene, which exhibits significant similarity to members of the AraC/XylS family of transcriptional activators. The phbRPs gene was found to be transcribed in the opposite direction from the three structural genes. Cloning of phbRPs in a relatively high-copy vector in Pseudomonas sp. strain 61-3 elevated the levels of beta-galactosidase activity from a transcriptional phb promoter-lacZ fusion and also enhanced the 3HB fraction in the polyesters synthesized by this strain, suggesting that PhbRPs is a positive regulatory protein controlling the transcription of phbBACPs in this bacterium. In the pha locus, two genes encoding PHA synthases (PhaC1Ps and PhaC2Ps) were flanked by a PHA depolymerase gene (phaZPs), and two adjacent open reading frames (ORF1 and phaDPs), and the gene order was ORF1, phaC1Ps, phaZPs, phaC2Ps, and phaDPs. Heterologous expression of the cloned fragments in PHA-negative mutants of Pseudomonas putida and Ralstonia eutropha revealed that PHB synthase and two PHA synthases of Pseudomonas sp. strain 61-3 were specific for short chain length and both short and medium chain length 3HA units, respectively.
Synaptic Rewiring in Neuromorphic VLSI for Topographic Map Formation (2009)

A generalised model of biological topographic map development is presented which combines both weight plasticity and the formation and elimination of synapses (synaptic rewiring) as well as both activity-dependent and -independent processes. The question of whether an activity-dependent process can refine a mapping created by an activity-independent process is investigated using a statistical approach to analysingmapping quality. The model is then implemented in custom mixed-signal VLSI. Novel aspects of this implementation include: (1) a distributed and locally reprogrammable address-event receiver, with which large axonal fan-out does not reduce channel capacity; (2) an analogue current-mode circuit for Euclidean distance calculation which is suitable for operation across multiple chips; (3) slow probabilistic synaptic rewiring driven by (pseudo-)random noise; (4) the application of a very-low-current design technique to improving the stability of weights stored on capacitors; (5) exploiting transistor non-ideality to implement partially weightdependent spike-timing-dependent plasticity; (6) the use of the non-linear capacitance of MOSCAP devices to compensate for other non-linearities. The performance of the chip is characterised and it is shown that the fabricated chips are capable of implementing the model, resulting in biologically relevant behaviours such as activity-dependent reduction of the spatial variance of receptive fields. Complementing a fast synaptic weight change mechanism with a slow synapse rewiring mechanism is suggested as a method of increasing the stability of learned patterns.