gebhart/patrepeval huggingface dataset:
Antioxidant and oxidative stress changes during heart failure subsequent to myocardial infarction in rats. (1996)

Antioxidant enzyme activities and oxidative stress were evaluated in the myocardium in relation to hemodynamic function subsequent to myocardial infarction in rats. One week after the coronary ligation, the left ventricular peak systolic pressure, left ventricular end-diastolic pressure, and aortic pressures remained near control values and there were no differences in lung and liver wet/dry weight ratios between experimental and control animals. In the 4-, 8-, and 16-week experimental animals, there was a progressive drop in left ventricular peak systolic pressure and an increase in left ventricular end-diastolic pressure. Aortic systolic pressure was depressed at 8 and 16 weeks. In myocardial infarct rats, there was a significant increase in wet/dry weight ratio of lungs at 8 weeks and at 16 weeks; this ratio was increased for lungs as well as liver. Based on the hemodynamic data as well as other observations, animals in the 1-, 4-, 8-, and 16-week groups were arbitrarily categorized into nonfailure and mild, moderate, and severe failure stages, respectively. In the nonfailure stage, there was a marginal increase in superoxide dismutase, glutathione peroxidase, and catalase activities as well as vitamin E levels. The redox state in these hearts, assessed by the reduced/oxidized glutathione ratio, was significantly increased. Superoxide dismutase activity was unchanged in mild and moderate failure stages but significantly depressed at 16 weeks. Glutathione peroxidase and catalase activities showed progressive decreases through mild, moderate, and severe failure stages. Vitamin E levels were significantly depressed at moderate and severe failure stages. There was a progressive increase in lipid peroxidation at mild, moderate, and severe stages of heart failure and the redox ratio was significantly depressed in the severe failure stage. These data suggest that heart failure subsequent to myocardial infarction may be associated with an antioxidant deficit as well as increased myocardial oxidative stress.
Blood–spinal cord barrier breakdown and pericyte reductions in amyotrophic lateral sclerosis (2012)

The blood-brain barrier and blood-spinal cord barrier (BSCB) limit the entry of plasma components and erythrocytes into the central nervous system (CNS). Pericytes play a key role in maintaining blood-CNS barriers. The BSCB is damaged in patients with amyotrophic lateral sclerosis (ALS). Moreover, transgenic ALS rodents and pericyte-deficient mice develop BSCB disruption with erythrocyte extravasation preceding motor neuron dysfunction. Here, we studied whether BSCB disruption with erythrocyte extravasation and pericyte loss are present in human ALS. We show that 11 of 11 cervical cords from ALS patients, but 0 of 5 non-neurodegenerative disorders controls, possess perivascular deposits of erythrocyte-derived hemoglobin and hemosiderin typically 10-50 μm in diameter suggestive of erythrocyte extravasation. Immunostaining for CD235a, a specific marker for erythrocytes, confirmed sporadic erythrocyte extravasation in ALS, but not controls. Quantitative analysis revealed a 3.1-fold increase in perivascular hemoglobin deposits in ALS compared to controls showing hemoglobin confined within the vascular lumen, which correlated with 2.5-fold increase in hemosiderin deposits (r = 0.82, p < 0.01). Spinal cord parenchymal accumulation of plasma-derived immunoglobulin G, fibrin and thrombin was demonstrated in ALS, but not controls. Immunostaining for platelet-derived growth factor receptor-β, a specific marker for CNS pericytes, indicated a 54 % (p < 0.01) reduction in pericyte number in ALS patients compared to controls. Pericyte reduction correlated negatively with the magnitude of BSCB damage as determined by hemoglobin abundance (r = -0.75, p < 0.01). Thus, the BSCB disruption with erythrocyte extravasation and pericyte reductions is present in ALS. Whether similar findings occur in motor cortex and affected brainstem motor nuclei remain to be seen.
Reprogramming erythroid cells for lysosomal enzyme production leads to visceral and CNS cross-correction in mice with Hurler syndrome (2009)

Restricting transgene expression to maturing erythroid cells can reduce the risk for activating oncogenes in hematopoietic stem cells (HSCs) and their progeny, yet take advantage of their robust protein synthesis machinery for high-level protein production. This study sought to evaluate the feasibility and efficacy of reprogramming erythroid cells for production of a lysosomal enzyme, alpha-L-iduronidase (IDUA). An erythroid-specific hybrid promoter provided inducible IDUA expression and release during in vitro erythroid differentiation in murine erythroleukemia cells, resulting in phenotypical cross-correction in an enzyme-deficient lymphoblastoid cell line derived from patients with mucopolysaccharidosis type I (MPS I). Stable and higher than normal plasma IDUA levels were achieved in vivo in primary and secondary MPS I chimeras for at least 9 months after transplantation of HSCs transduced with the erythroid-specific IDUA-containing lentiviral vector (LV). Moreover, long-term metabolic correction was demonstrated by normalized urinary glycosaminoglycan accumulation in all treated MPS I mice. Complete normalization of tissue pathology was observed in heart, liver, and spleen. Notably, neurological function and brain pathology were significantly improved in MPS I mice by erythroid-derived, higher than normal peripheral IDUA protein. These data demonstrate that late-stage erythroid cells, transduced with a tissue-specific LV, can deliver a lysosomal enzyme continuously at supraphysiological levels to the bloodstream and can correct the disease phenotype in both viscera and CNS of MPS I mice. This approach provides a paradigm for the utilization of RBC precursors as a depot for efficient and potentially safer systemic delivery of nonsecreted proteins by ex vivo HSC gene transfer.
Peptide vaccination can lead to enhanced tumor growth through specific T-cell tolerance induction. (1996)

Vaccination with synthetic peptides representing cytotoxic T lymphocyte (CTL) epitopes can lead to a protective CTL-mediated immunity against tumors or viruses. We now report that vaccination with a CTL epitope derived from the human adenovirus type 5 E1A-region (Ad5E1A234-243), which can serve as a target for tumor-eradicating CTL, enhances rather than inhibits the growth of Ad5E1A-expressing tumors. This adverse effect of peptide vaccination was rapidly evoked, required low doses of peptide (10 micrograms), and was achieved by a mode of peptide delivery that induces protective T-cell-mediated immunity in other models. Ad5E1A-specific CTL activity could no longer be isolated from mice after injection of Ad5E1A-peptide, indicating that tolerization of Ad5E1A-specific CTL activity causes the enhanced tumor outgrowth. In contrast to peptide vaccination, immunization with adenovirus, expressing Ad5E1A, induced Ad5E1A-specific immunity and prevented the outgrowth of Ad5E1A-expressing tumors. These results show that immunization with synthetic peptides can lead to the elimination of anti-tumor CTL responses. These findings are important for the design of safe peptide-based vaccines against tumors, allogeneic organ transplants, and T-cell-mediated autoimmune diseases.
Multimedia Search and Retrieval (2000)

Multimedia search and retrieval has become an active research field thanks to the increasing demand that accompanies many new practical applications. The applications include largescale multimedia search engines on the Web, media asset management systems in corporations, audio-visual broadcast servers, and personal media servers for consumers. Diverse requirements derived from these applications impose great challenges and incentives for research in this field.
Ethanol production from starch by a coimmobilized mixed culture system of Aspergillus awamori and Zymomonas mobilis (1986)

The production of ethanol from starch by a coimmobilized mixed culture system of aerobic and anaerobic microorganisms in Ca-alginate gel beads was investigated. The mold Aspergillus awamori was used as an aerobic amylolytic microorganism and an anaerobic bacterium, Zymomonas mobilis, as an ethanol producer. By controlling the mixing ratio of the microorganisms in the inoculum size, a desirable coimmobilized mixed culture system, in which the aerobic mycelia grew on and near the oxygen-rich surface of the gel beads while the anaerobic bacterial cells mainly grew in the oxygen-deficient central part of the gel beads, was naturally established under the aerobic culture conditions, and ethanol could be directly produced from starch by the system. The ethanol productivity by the system in flask culture was particularly affected by the shear stress (dependent on the shaking speed) which controlled the mycelial growth on the surface of the gel beads. Under optimum culture conditions in the flask culture, the glucose produced was instantly consumed, and was not observed in the culture broth; the final concentration of ethanol produced from 100 g/L starch was 25 g/L and the yield coefficient for ethanol, Y(pls), was 0.38. The ethanol productivity by the coimmobilized mixed culture system was compared with those by other various culture systems and the advantages of the system were clarified.
The GOA database in 2009--an integrated Gene Ontology Annotation resource (2008)

The Gene Ontology Annotation (GOA) project at the EBI (http://www.ebi.ac.uk/goa) provides high-quality electronic and manual associations (annotations) of Gene Ontology (GO) terms to UniProt Knowledgebase (UniProtKB) entries. Annotations created by the project are collated with annotations from external databases to provide an extensive, publicly available GO annotation resource. Currently covering over 160 000 taxa, with greater than 32 million annotations, GOA remains the largest and most comprehensive open-source contributor to the GO Consortium (GOC) project. Over the last five years, the group has augmented the number and coverage of their electronic pipelines and a number of new manual annotation projects and collaborations now further enhance this resource. A range of files facilitate the download of annotations for particular species, and GO term information and associated annotations can also be viewed and downloaded from the newly developed GOA QuickGO tool (http://www.ebi.ac.uk/QuickGO), which allows users to precisely tailor their annotation set.
Primary antibody responses to a well-defined and unique hapten are not enhanced by preimmunization with carrier: analysis in a viral model. (1986)

We used a viral model to reexamine classical experiments showing that mice previously primed with a "carrier" molecule alone and then challenged with the carrier-hapten conjugate exhibited an enhanced antihapten antibody response. Mice were primed with live or UV-inactivated vesicular stomatitis virus (VSV) Indiana (Ind) serotype with or without complete Freund's adjuvant. After challenge with VSV New Jersey (NJ), these mice developed a secondary-type IgG response, measured by antibody binding in an ELISA, against both VSV-Ind and VSV-NJ. The same result was found for the reciprocal experiments where mice were primed with VSV-NJ. Similarly, when mice were primed with live VSV, UV-inactivated VSV, or purified VSV glycoprotein G of Ind or NJ serotype and later were challenged with dinitrophenyl (N2ph)-conjugated, UV-inactivated VSV or with N2ph-conjugated G protein of either serotype, they exhibited a secondary-type anti-N2ph antibody response as demonstrated by the binding of IgG to dinitrophenylated bovine serum albumin measured by ELISA. In contrast, when neutralizing antibody responses were monitored, VSV-Ind-primed mice challenged with VSV-NJ developed a strictly primary type of anti-VSV-NJ response and vice versa. We conclude that preexistent helper T cells specific for shared carrier determinants do not improve virgin B-cell responses specific for "new," unique determinants that are the target for the biologically relevant neutralizing antibodies. These findings suggest that priming of B cells rather than of helper T cells may be of importance to induce protective immunity mediated by antibodies.
Epitaxial Lateral Overgrowth of GaAs by LPE (1988)

Epitaxial lateral overgrowth (ELO) of GaAs on SiO 2 film was successfully performed by LPE. It was found that the lateral overgrowth on (111)B substrate was the slowest when the stripe opening in SiO 2 film oriented in the &lt;1̄10 &gt; and equivalent directions, while it was the fastest when the stripe oriented in the &lt;112̄ &gt; and equivalent directions. In the latter case, a large lateral to vertical growth velocity ratio (up to 50) of epitaxial GaAs was achieved. RC etching revealed that the etch pit density in the lateral epitaxial GaAs was found to be extremely low.
CD47-blocking immunotherapies stimulate macrophage-mediated destruction of small-cell lung cancer (2016)

Small-cell lung cancer (SCLC) is a highly aggressive subtype of lung cancer with limited treatment options. CD47 is a cell-surface molecule that promotes immune evasion by engaging signal-regulatory protein alpha (SIRPα), which serves as an inhibitory receptor on macrophages. Here, we found that CD47 is highly expressed on the surface of human SCLC cells; therefore, we investigated CD47-blocking immunotherapies as a potential approach for SCLC treatment. Disruption of the interaction of CD47 with SIRPα using anti-CD47 antibodies induced macrophage-mediated phagocytosis of human SCLC patient cells in culture. In a murine model, administration of CD47-blocking antibodies or targeted inactivation of the Cd47 gene markedly inhibited SCLC tumor growth. Furthermore, using comprehensive antibody arrays, we identified several possible therapeutic targets on the surface of SCLC cells. Antibodies to these targets, including CD56/neural cell adhesion molecule (NCAM), promoted phagocytosis in human SCLC cell lines that was enhanced when combined with CD47-blocking therapies. In light of recent clinical trials for CD47-blocking therapies in cancer treatment, these findings identify disruption of the CD47/SIRPα axis as a potential immunotherapeutic strategy for SCLC. This approach could enable personalized immunotherapeutic regimens in patients with SCLC and other cancers.
Transforming growth factor beta 1 suppresses acute and chronic arthritis in experimental animals. (1991)

Systemic administration of the cytokine, TGF beta 1, profoundly antagonized the development of polyarthritis in susceptible rats. TGF beta 1 administration (1 or 5 micrograms/animal), initiated one day before an arthritogenic dose of streptococcal cell wall (SCW) fragments, virtually eliminated the joint swelling and distortion typically observed during both the acute phase (articular index, AI = 2.5 vs. 11; P less than 0.025) and the chronic phase (AI = 0 vs. 12.5) of the disease. Moreover, TGF beta 1 suppressed the evolution of arthritis even when administration was begun after the acute phase of the disease. Histopathological examination of the joint revealed the systemic TGF beta 1 treatment greatly reduced inflammatory cell infiltration, pannus formation, and joint erosion. Consistent with the inhibition of inflammatory cell recruitment into the synovium, TGF beta 1 reversed the leukocytosis associated with the chronic phase of the arthritis. Control animals subjected to the same TGF beta 1 dosing regimen displayed no discernable immunosuppressive or toxic effects even after 4 wk of treatment. These observations not only provide insight into the immunoregulatory effects of TGF beta, but also implicate this cytokine as a potentially important therapeutic agent.
Emitter resistance of arsenic- and phosphorus-doped polysilicon emitter transistors (1985)

Measurements of emitter resistance have been made on arsenic- and phosphorus-doped polysilicon emitter bipolar transistors, fabricated with or without an interfacial oxide layer. It is found that the emitter resistance of phosphorus-doped transistors is considerably lower than that of arsenic-doped transistors. In addition the presence of a deliberately grown interfacial oxide layer leads to a significant increase in emitter resistance for both arsenic- and phosphorus-doped devices.
Robust design of Mars entry micro-probe with evidence theory and multi-fidelity strategies (2014)

Purpose A multi-disciplinary robust design optimization method for micro Mars entry probe (no more than 0.8 m in diameter) is proposed. The purpose of this paper is to design a Mars entry probe, not only the geometric configuration, but the trajectory and thermal protection system (TPS). In the design optimization, the uncertainties of atmospheric and aerodynamic parameters are taken into account. The probability distribution information of the uncertainties are supposed to be unknown in the design. To ensure accuracy levels, time-consuming numerical models are coupled in the optimization. Multi-fidelity approach is designed for model management to balance the computational cost and accuracy.
Ultrasound-Guided, Percutaneous Peripheral Nerve Stimulation (2010)

We describe a method of ultrasound-guided peripheral nerve stimulation that avoids the invasiveness of electrode placement via an open procedure while providing excellent pain relief. We further describe limitations of the percutaneous approach when navigating close to large blood vessels, a situation more appropriately managed with open peripheral nerve stimulator placement. Ultrasound-guided placement may be considered for patients receiving peripheral nerve stimulators placed within the deep tissues, and not easily placed in a blind fashion.
The lipocalin protein family: structure and function (1996)

The lipocalin protein family is a large group of small extracellular proteins. The family demonstrates great diversity at the sequence level; however, most lipocalins share three characteristic conserved sequence motifs, the kernel lipocalins, while a group of more divergent family members, the outlier lipocalins, share only one. Belying this sequence dissimilarity, lipocalin crystal structures are highly conserved and comprise a single eight-stranded continuously hydrogen-bonded antiparallel beta-barrel, which encloses an internal ligand-binding site. Together with two other families of ligand-binding proteins, the fatty-acid-binding proteins (FABPs) and the avidins, the lipocalins form part of an overall structural superfamily: the calycins. Members of the lipocalin family are characterized by several common molecular-recognition properties: the ability to bind a range of small hydrophobic molecules, binding to specific cell-surface receptors and the formation of complexes with soluble macromolecules. The varied biological functions of the lipocalins are mediated by one or more of these properties. In the past, the lipocalins have been classified as transport proteins; however, it is now clear that the lipocalins exhibit great functional diversity, with roles in retinol transport, invertebrate cryptic coloration, olfaction and pheromone transport, and prostaglandin synthesis. The lipocalins have also been implicated in the regulation of cell homoeostasis and the modulation of the immune response, and, as carrier proteins, to act in the general clearance of endogenous and exogenous compounds.
Vascular Active Contour for Vessel Tree Segmentation (2010)

In this paper, a novel active contour model is proposed for vessel tree segmentation. First, we introduce a region competition-based active contour model exploiting the gaussian mixture model, which mainly segments thick vessels. Second, we define a vascular vector field to evolve the active contour along its center line into the thin and weak vessels. The vector field is derived from the eigenanalysis of the Hessian matrix of the image intensity in a multiscale framework. Finally, a dual curvature strategy, which uses a vesselness measure-dependent function selecting between a minimal principal curvature and a mean curvature criterion, is added to smoothen the surface of the vessel without changing its shape. The developed model is used to extract the liver and lung vessel tree as well as the coronary artery from high-resolution volumetric computed tomography images. Comparisons are made with several classical active contour models and manual extraction. The experiments show that our model is more accurate and robust than these classical models and is, therefore, more suited for automatic vessel tree extraction.
An integrative approach for the identification of prognostic and predictive biomarkers in rectal cancer (2015)

Gene expression studies performed by: Agostini et al., Rimkus et al. and Kim et al. have been merged through a meta-analysis of the raw data. Gene expression data-sets have been processed using A-MADMAN. Common differentially expressed gene (DEG) were identified through SAM analysis. To further characterize the identified DEG we deeply investigated its biological role using an integrative computational biology approach.
Structural Basis for Recognition of CD20 by Therapeutic Antibody Rituximab (2007)

Rituximab is a widely used monoclonal antibody drug for treating certain lymphomas and autoimmune diseases. To understand the molecular mechanism of recognition of human CD20 by Rituximab, we determined the crystal structure of the Rituximab Fab in complex with a synthesized peptide comprising the CD20 epitope (residues 163-187) at 2.6-A resolution. The combining site of the Fab consists of four complementarity determining regions that form a large, deep pocket to accommodate the epitope peptide. The bound peptide assumes a unique cyclic conformation that is constrained by a disulfide bond and a rigid proline residue (Pro(172)). The (170)ANPS(173) motif of CD20 is deeply embedded into the pocket on the antibody surface and plays an essential role in the recognition and binding of Rituximab. The antigen-antibody interactions involve both hydrogen bonds and van der Waals contacts and display a high degree of structural and chemical complementarity. These results provide a molecular basis for the specific recognition of CD20 by Rituximab as well as valuable information for development of improved antibody drugs with better specificity and higher affinity.
The outer membrane protein, Antigen 43, mediates cell‐to‐cell interactions within Escherichia coli biofilms (2000)

Transcription of the agn43 locus, which specifies an outer membrane protein of Escherichia coli, is regulated in a phase-variable fashion by the OxyR-DNA binding protein and Dam methylase. Despite its well-characterized regulation, the function of Ag43 has remained elusive until now. Previous studies indicated that Ag43 mediates autoaggregation of certain strains of E. coli in liquid culture. Given this phenotype, we examined the role of Ag43 in biofilm formation. Here, we report that Ag43 contributes to E. coli biofilm formation in glucose-minimal medium, but not in Luria-Bertani broth. In addition, we show that flagellar-mediated motility is required for biofilm formation in both rich and minimal environments. Altogether, our results suggest that E. coli uses both common and specific gene sets for the development of biofilms under various growth conditions.