gebhart/patrepeval huggingface dataset:
Noncognate Interaction with MHC Class II Molecules Is Essential for Maintenance of T Cell Metabolism to Establish Optimal Memory CD4 T Cell Function (2007)

CD4 memory T cells surviving in the absence of MHC class II contact lose their characteristic memory function. To investigate the mechanisms underlying the impaired function of memory T cells in the absence of MHC class II molecules, we analyzed gene expression profiles of resting memory T cells isolated from MHC class II-competent or -deficient hosts. The analysis focused on five transcripts related to T cell activation, metabolism, and survival that are underexpressed in resting memory T cells from MHC class II-deficient hosts compared with MHC class II-competent hosts. CD4 memory cells isolated from MHC class II-deficient hosts display alterations in their degree of differentiation as well as metabolic activity, and these changes are already manifest in the effector phase despite the presence of Ag-expressing dendritic cells. Our data suggest that the absence of interactions with noncognate MHC class II molecules compromises the progressive accumulation of signals that ensure optimal survival and fitness to sustain the metabolic activity of activated T cells and shape the functional capacity of the future memory compartment. Signals via AKT coordinate survival and metabolic pathways and may be one of the crucial events linking interaction with MHC class II molecules to the successful generation of a long-lived functional memory CD4 T cell population.
Carpal tunnel syndrome: surgical treatment using the Paine retinaculatome (1991)

The operative technique for the relief of carpal tunnel syndrome has remained controversial. This report presents the results of 445 patients or 577 hands operated on using a transverse technique that varies little from that described by Paine and Polyzoidis. The patients were followed for 9 months to 3 years. In addition to the data received from follow-up visits, a questionnaire was sent to each patient for evaluation of their results. All surgery was performed under local anesthesia, sometimes with intravenous supplement. Of the 445 patients, 313 had unilateral operations and 132 had bilateral operations at one sitting. Postoperatively, normal hand function was achieved in 59.4% of patients in 1 week or less. Of the 577 hands operated on, 535 (92.7%) exhibited satisfactory results from surgery. No patient required postoperative physical therapy or splinting. There were no injuries to the median nerve or any of its branches.
Immunogenicity of premalignant lesions is the primary cause of general cytotoxic T lymphocyte unresponsiveness (2008)

Cancer is sporadic in nature, characterized by an initial clonal oncogenic event and usually a long latency. When and how it subverts the immune system is unknown. We show, in a model of sporadic immunogenic cancer, that tumor-specific tolerance closely coincides with the first tumor antigen recognition by B cells. During the subsequent latency period until tumors progress, the mice acquire general cytotoxic T lymphocyte (CTL) unresponsiveness, which is associated with high transforming growth factor (TGF) beta1 levels and expansion of immature myeloid cells (iMCs). In mice with large nonimmunogenic tumors, iMCs expand but TGF-beta1 serum levels are normal, and unrelated CTL responses are undiminished. We conclude that (a) tolerance to the tumor antigen occurs at the premalignant stage, (b) tumor latency is unlikely caused by CTL control, and (c) a persistent immunogenic tumor antigen causes general CTL unresponsiveness but tumor burden and iMCs per se do not.
Diversity of the Human Intestinal Microbial Flora (2005)

The human endogenous intestinal microflora is an essential "organ" in providing nourishment, regulating epithelial development, and instructing innate immunity; yet, surprisingly, basic features remain poorly described. We examined 13,355 prokaryotic ribosomal RNA gene sequences from multiple colonic mucosal sites and feces of healthy subjects to improve our understanding of gut microbial diversity. A majority of the bacterial sequences corresponded to uncultivated species and novel microorganisms. We discovered significant intersubject variability and differences between stool and mucosa community composition. Characterization of this immensely diverse ecosystem is the first step in elucidating its role in health and disease.
Oxygen radicals and asbestos-mediated disease. (1994)

Asbestos fibers are potent elaborators of active oxygen species whether by reactions involving iron on the surface of the fiber, or by attempted phagocytosis of fibers by cell types resident in the lung. The link between production of active oxygen species and the pathogenesis of asbestos-mediated disease has been highlighted by studies outlined here exploring the use of antioxidant scavengers which inhibit the cytotoxic effects of asbestos both in vitro and in vivo. The use of antioxidant enzymes ameliorates the induction of certain genes necessary for cell proliferation, such as ornithine decarboxylase, implicating oxidants as causative factors in some abnormal cell replicative events. Based on these observations, antioxidant enzymes likely represent an important lung defense mechanism in response to oxidative stress. In addition, their gene expression in lung or in cells from bronchoalveolar lavage might be a valuable biomarker of chronic inflammation and pulmonary disease after inhalation of oxidants.
Mitochondrial Biogenesis and Remodeling during Adipogenesis and in Response to the Insulin Sensitizer Rosiglitazone (2003)

White adipose tissue is an important endocrine organ involved in the control of whole-body metabolism, insulin sensitivity, and food intake. To better understand these functions, 3T3-L1 cell differentiation was studied by using combined proteomic and genomic strategies. The proteomics approach developed here exploits velocity gradient centrifugation as an alternative to isoelectric focusing for protein separation in the first dimension. A 20- to 30-fold increase in the concentration of numerous mitochondrial proteins was observed during adipogenesis, as determined by mass spectrometry and database correlation analysis. Light and electron microscopy confirmed a large increase in the number of mitochondrion profiles with differentiation. Furthermore, mRNA profiles obtained by using Affymetrix GeneChips revealed statistically significant increases in the expression of many nucleus-encoded mitochondrial genes during adipogenesis. Qualitative changes in mitochondrial composition also occur during adipose differentiation, as exemplified by increases in expression of proteins involved in fatty acid metabolism and of mitochondrial chaperones. Furthermore, the insulin sensitizer rosiglitazone caused striking changes in mitochondrial shape and expression of selective mitochondrial proteins. Thus, although mitochondrial biogenesis has classically been associated with brown adipocyte differentiation and thermogenesis, our results reveal that mitochondrial biogenesis and remodeling are inherent to adipose differentiation per se and are influenced by the actions of insulin sensitizers.
PSMA expression in the neovasculature of colorectal cancers (2007)

A146 Background  >Prostate Specific Membrane Antigen (PSMA), a type II transmembrane metallo-peptidase highly overexpressed in prostate cancer cells has been studied as a targeting molecule in prostate cancer. Recently, it has been found to be also expressed in the neo-vasculature of multiple non-prostatic solid tumors. Because of its unique expression pattern limited to tumor-associated endothelial cells, PSMA may be an interesting molecule for vascular targeting. Here we investigated the protein expression and cellular distribution of PSMA in a large number of cases of colorectal cancer (CRC) and liver metastasis.  >Methods  >130 formalin-fixed paraffin-embedded tissue sections of patients with colorectal cancer and 18 samples of metastatic liver lesions of were immunostained with antibodies directed against PSMA and the pan-endothelial marker CD31. Immunoreactivity was scored semiquantitatively based on staining intensity and distribution. Using whole coding region spanning primers, mRNA expression of PSMA was further determined in colorectal cancer and normal mucosa biopsy material. To test the tumor-specificity of PSMA expression, inflammatory bowel disease (IBD), psoriasis and granulation tissue, all know to be associated with neo-angiogenesis as well as normal colon mucosa were evaluated for PSMA expression. Confocal-immuno-fluorescence microscopy was used to determine the expression pattern of CD31 and PSMA in tumor associated vessels.  >Results  >High endothelial PSMA expression was observed in tumor-associated neo-vasculature of 94 of 130 CRC samples (72 %). 15 of 18 liver metastasis (83%) were positive for PSMA. Interestingly, tumor adjacent vasculature, normal colorectal mucosa as well as inflammatory bowel disease and psoriasis showed no PSMA expression. Confocal-immuno-fluorescence microscopy revealed co-expression of CD31 and PSMA in the majority of tumor-associated endothelial cells. A subpopulation of PSMA positive vessel-lining-cells however, did not show CD31 staining. In addition, 15 (12%) colorectal cancer samples showed strong epithelial PSMA expression.  >There was a trend for high grade tumors to higher PSMA expression (Spearman r = 0.18, P = 0.046) and men generally had higher PSMA level than women (Spearman r = 0.23, P = 0.009). No statistically significant association between PSMA expression and overall survival was observed (P = 0.375).  >Conclusion  >This study gives new insights in PSMA expression pattern in colorectal cancer. Because of its highly tumorspecific expression and its accessibility to antibody based therapies, PSMA represents an excellent target for anti-angiogenic therapy in colorectal cancers. The potential of an anti-PSMA directed therapy warrants testing in clinical trials.
New-Concept Chemotherapy by Nanoparticles of Biodegradable Polymers: Where Are We Now? (2006)

Among several promising new drug-delivery systems, liposomes represent an advanced technology to deliver active molecules to the site of action, and at present several formulations are in clinical use. Research on liposome technology has progressed from conventional vesicles ("first-generation liposomes") to "second-generation liposomes", in which long-circulating liposomes are obtained by modulating the lipid composition, size, and charge of the vesicle. Liposomes with modified surfaces have also been developed using several molecules, such as glycolipids or sialic acid. A significant step in the development of long-circulating liposomes came with inclusion of the synthetic polymer poly-(ethylene glycol) (PEG) in liposome composition. The presence of PEG on the surface of the liposomal carrier has been shown to extend blood-circulation time while reducing mononuclear phagocyte system uptake (stealth liposomes). This technology has resulted in a large number of liposome formulations encapsulating active molecules, with high target efficiency and activity. Further, by synthetic modification of the terminal PEG molecule, stealth liposomes can be actively targeted with monoclonal antibodies or ligands. This review focuses on stealth technology and summarizes pre-clinical and clinical data relating to the principal liposome formulations; it also discusses emerging trends of this promising technology.
Rigid Pore Structure from Highly Swollen Polymer Gels (2002)

3325-3327
Distinct expression and ligand‐binding profiles of two constitutively active GPR17 splice variants (2010)

We present the first isoform-specific characterization of GPR17 and show that differences exist between the isoforms, in both expression pattern and pharmacological profile. In turn, our results indicate that the two human isoforms might serve tissue-specific functions.
Translating short-term environmental effects on leaf growth rate into differences in whole-plant profiles of maize leaf area: Impact of temperature, evaporative demand and soil water status. (2007)

The model was calibrated with data performed in field, growth chamber and greenhouse experiments (first row). It combines (i) the estimation of key developmental stages (Fig. 2A) that fixes the period during which leaves grow, and (ii) environmental responses of leaf elongation rate (Fig. 2B-D) that are applied to every leaf (Fig. 2E). Each leaf thus expands during a fixed period at a rate determinate by the environmental factors (Fig. 2G). This model of leaf growth and development was interfaced with the crop model APSIM for simulation of the leaf environmental variables (inputs of the leaf model) and for simulation at canopy level. 1 Context
Simple range cameras based on focal error (1994)

We describe research on two imaging range sensors that use defocus to estimate range. One technique is completely passive and provides dense range measurements in textured areas with an rms error of 2.5%. This method can be useful when stereo is unreliable because of correspondence errors or when imaging geometry prevents the use of multiple viewpoints (e.g., microscopy). The second technique uses structured light and provides dense range measurements with an rms error of 0.5%. This method can be useful when imaging geometry prevents the use of multiple viewpoints and for acquiring range imagery of rapidly moving objects, as the structured light can be delivered in a single stroboscopic flash.
AUTOALERT: AUTOMATED ACOUSTIC DETECTION OF INCIDENTS (1995)

This Innovations Deserving Exploratory Analysis (IDEA) project included the design and preliminary evaluation, as well as feasibility demonstration, of AutoAlert, an acoustic traffic sensor system that applies new signal processing algorithms to passive acoustic data to advance the state of practical acoustic incident detection techniques. These techniques, originally developed for national defense applications, will perform reliable, automatic, nearly instantaneous, all-weather incident detection under highly variable traffic conditions. Effective operation of urban high-capacity Intelligent Transportation Systems (ITS) requires speedy detection of incidents at chokepoints, such as tunnels, bridges and other aerial structures, and dense urban arterials. AutoAlert overcomes shortcomings of loop and video detectors, such as their inability to distinguish between incidents and congestion, and the need for a human-in-the-loop for video detection. The AutoAlert processor hears an incident before congestion builds, and can be used either as an independent detector, or its outputs can be combined (data fusion) with other detector outputs for joint improved decisions and incident verification. AutoAlert algorithms will provide a new level of incident detection timeliness and reliability (low false alarms) by applying sophisticated statistical models: Hidden Markov Models and Canonical Variates Analysis. These are used to analyze both short-term and time-varying signals that characterize incidents.
Cerebral Blood Flow Autoregulation and Edema Formation During Pregnancy in Anesthetized Rats (2007)

Eclampsia is considered a form of hypertensive encephalopathy in which an acute elevation in blood pressure causes autoregulatory breakthrough, blood-brain barrier disruption, and edema formation. We hypothesized that pregnancy predisposes the brain to eclampsia by lowering the pressure of autoregulatory breakthrough and enhancing cerebral edema formation. Because NO production is increased in pregnancy, we also investigated the role of NO in modulating autoregulation. Cerebral blood flow autoregulation was determined by phenylephrine infusion and laser Doppler flowmetry. Four groups were studied: untreated nonpregnant (n=7) and late-pregnant (days 19 to 21; n=8) Sprague-Dawley rats and nonpregnant (n=8) and late-pregnant (n=8) animals treated with an NO synthase inhibitor (N(G)-nitro-l-arginine methyl ester; 0.5 to 0.7 g/L). Brain water content and blood-brain barrier permeability to sodium fluorescein were determined after breakthrough. Pregnancy caused no change in autoregulation or the pressure of breakthrough. However, treatment with the NO synthase inhibitor significantly increased the pressure of autoregulatory breakthrough (nonpregnant: 183.6+/-3.0 mm Hg versus 212.0+/-2.8 mm Hg, P<0.05; late-pregnant: 180.8+/-3.2 mm Hg versus 209.3+/-4.7 mm Hg, P<0.05). After autoregulatory breakthrough, only late-pregnant animals showed a significant increase in cerebral edema formation, which was attenuated by NO synthase inhibition. There was no difference in blood-brain barrier permeability between nonpregnant and late-pregnant animals in response to acute hypertension, suggesting that pregnancy may predispose the brain to eclampsia by increasing cerebral edema through increased hydraulic conductivity.
Molecular cloning and characterization of human endothelial nitric oxide synthase (1992)

The constitutive calcium/calmodulin-dependent nitric oxide (NO) synthase expressed in vascular endothelium shares common biochemical and pharmacologic properties with neuronal NO synthase. However, recent cloning and molecular characterization of NO synthase from bovine endothelial cells indicated the existence of a family of constitutive NO synthases. Accordingly, we undertook molecular cloning and sequence analysis of human endothelial NO synthase. Complementary DNA clones predict a protein of 1,203 amino acids sharing 94% identity with the bovine endothelial protein, but only 60% identity with the rat brain NO synthase isoform. Northern blot analysis with an endothelial-derived cDNA identified a 4.6-4.8 kb mRNA transcript in HUVEC and in situ hybridization localized transcripts to vascular endothelium but not neuronal tissue.
Hormone-like (endocrine) Fgfs: their evolutionary history and roles in development, metabolism, and disease (2010)

Fibroblast growth factors (Fgfs) are proteins with diverse functions in development, repair, and metabolism. The human Fgf gene family with 22 members can be classified into three groups, canonical, intracellular, and hormone-like Fgf genes. In contrast to canonical and intracellular Fgfs identified in invertebrates and vertebrates, hormone-like Fgfs, Fgf15/19, Fgf21, and Fgf23, are vertebrate-specific. The ancestral gene of hormone-like Fgfs was generated from the ancestral gene of canonical Fgfs by gene duplication early in vertebrate evolution. Later, Fgf15/19, Fgf21, and Fgf23 were generated from the ancestral gene by genome duplication events. Canonical Fgfs act as autocrine/paracrine factors in an Fgf receptor (Fgfr)-dependent manner. In contrast, hormone-like Fgfs act as endocrine factors in an Fgfr-dependent manner. Canonical Fgfs have a heparin-binding site necessary for the stable binding of Fgfrs and local signaling. In contrast, hormone-like Fgfs acquired endocrine functions by reducing their heparin-binding affinity during their evolution. Fgf15/19 and Fgf23 require βKlotho and αKlotho as cofactors, respectively. However, Fgf21 might physiologically require neither. Hormone-like Fgfs play roles in metabolism at postnatal stages, although they also play roles in development at embryonic stages. Fgf15/19 regulates bile acid metabolism in the liver. Fgf21 regulates lipid metabolism in the white adipose tissue. Fgf23 regulates serum phosphate and active vitamin D levels. Fgf23 signaling disorders caused by hereditary diseases or tumors result in metabolic disorders. In addition, serum Fgf19 or Fgf21 levels are significantly increased by metabolic disorders. Hormone-like Fgfs are newly emerging and quite unique in their evolution and function.
A shading language on graphics hardware (1998)

Over the years, there have been two main branches of computer graphics image-synthesis research; one focused on interactivity, the other on image quality. Procedural shading is a powerful tool, commonly used for creating high-quality images and production animation. A key aspect of most procedural shading is the use of a shading language, which allows a high-level description of the color and shading of each surface. However, shading languages have been beyond the capabilities of the interactive graphics hardware community. We have created a parallel graphics multicomputer, PixelFlow, that can render images at 30 frames per second using a shading language. This is the first system to be able to support a shading language in real-time. In this paper, we describe some of the techniques that make this possible.
Tuning the response of magnetic suspensions (2003)

Electrochemical template synthesis of multilayer nanowires consisting of alternating ferromagnetic and nonmagnetic layers provides an approach to control the properties of magnetic particles in suspension. Copper/nickel multilayer nanowires were fabricated by electrochemical deposition from a solution containing both nickel and copper ions. We demonstrate that the magnetic shape anisotropy and dipolar interactions between magnetic layers can be exploited to tailor the magnetic response in ferromagnetic/nonmagnetic multilayer nanowires in a suspension.
The contribution of morphology to our understanding of the pathogenesis of experimentally produced corneal vascularization. (1977)

Guinea pig bone marrow cells were separated by buoyant density utilizing linear gradients of bovine serum albumin (BSA). It has finally become possible to characterize the cells present in the density fractions in terms of classical morphology. The development of the Cell Type computer program which calculates the percentages of the individual types of cells present in the fractions and their buoyant density distributions and plots the data has greatly facilitated and improved the accuracy of these studies. Approximately 40 cell types were observed in guinea pig bone marrow. Cells with definitive morphologies such as erythrocytes, the neutrophilic series, the binucleate blast megakaryocyte precursor and cells in mitosis band as virtually single peaks. Cells which are parts of continua or can easily be wrongly classified are found in multiple peaks. The small lymphocytes which are known to be polydisperse are found as five peaks. Because of the very strong benzidine staining by the glutaraldehyde-fixed hemoglobin, some of the erythroblasts were wrongly staged, resulting in a multimodal distribution. The presence of macrocytes further complicated these distributions. The rule that the younger cells are always less dense than the mature cells was adhered to in those cases where the cells could be definitively characterized, such as the neutrophilic series and the blasts. These results indicate that morphology is a good first approximation of reality.
Bacterial Expression and Characterization of the Mitochondrial Outer Membrane Channel (1998)

Several forms of the voltage-dependent anion-selective channel (VDAC) have been expressed at high yield in Escherichia coli. Full-length constructs of the proteins of Neurospora crassa and Saccharomyces cerevisiae (ncVDAC and scVDAC) have been made with 20-residue-long, thrombin-cleavable, His6-containing N-terminal extensions. ncVDAC purified from bacteria or mitochondria displays a far-UV CD spectrum (in 1% lauryl dimethylamine oxide at pH 6-8) similar to that of bacterial porins, indicating extensive beta-sheet structure. Under the same conditions, the CD spectrum of bacterially expressed scVDAC indicates lower beta-sheet content, albeit higher than that of mitochondrial scVDAC under the same conditions. In phospholipid bilayers, the bacterially expressed proteins (with or without N-terminal extensions) form typical VDAC-like channels with stable, large conductance open states (4-4.5 nanosiemens in 1 M KCl) and voltage-dependent transitions to a predominant substate (about 2 nanosiemens). A variant of scVDAC missing the first eight residues and having no N-terminal extension also has been expressed in E. coli. The truncated protein has a CD spectrum similar to that of mitochondrial scVDAC, but its channel activity is abnormal, exhibiting an unstable open state and rapid transitions between multiple subconductance levels.