gebhart/patrepeval huggingface dataset:
Dissection of the functions of antigen-presenting cells in the induction of T cell activation. (1985)

The functions of antigen-presenting cells (APC) in the initiation of T cell activation was examined by culturing antigen-bearing guinea pig macrophages (M phi) with T cells obtained from antigen-primed animals. Although such antigen-bearing M phi stimulated primed syngeneic T cell DNA synthesis, as assessed by tritiated thymidine incorporation, paraformaldehyde fixation (0.15% for 1 min at 37 degrees C) abolished this capacity. Analysis with acridine orange staining indicated that fixed antigen-bearing M phi could not trigger primed syngeneic T cells to progress from the G0 to the G1 phase of the cell cycle. The addition of control non-antigen-bearing syngeneic or allogeneic M phi but not interleukin 1 or 2 to cultures of T cells and fixed APC permitted a proliferative response. Although the interaction between fixed antigen-bearing M phi and responding T cells was genetically restricted, there was no similar restriction for the supplemental control M phi. In fact, completely Ia-negative endothelial cells (EC) and fibroblasts (FB) could restore antigen responsiveness to cultures of fixed antigen-bearing M phi and syngeneic responding T cells, although they could not directly present antigen. Moreover, metabolically intact accessory cells, including Ia-negative EC and FB, could take up and process antigen to an immunogenic moiety, which fixed Ia-positive M phi could present to primed T cells. These data indicate that recognition of the antigen-Ia complex on an APC is necessary but not sufficient to trigger proliferation of freshly obtained primed T cells. The results additionally support the conclusion that APC carry out at least two separate functions necessary for the initiation of antigen-induced T cell activation. Not only must the APC display the antigen-Ia complex, but it must also convey another required effect. This influence, which apparently involved the establishment of cell to cell contact, was neither Ia nor antigen dependent and could only be provided by a metabolically intact cell. By contrast, genetically restricted antigen presentation could be accomplished by a fixed Ia-positive cell. Only when both the antigen-Ia complex and the influence of an intact accessory cell were provided by the same or different accessory cell were T cells triggered to enter the cell cycle.
Solid tissues can be manipulated ex vivo and used as vehicles for gene therapy (2005)

The system can be used to study interactions between viruses and tissues both ex vivo and in vivo. Furthermore, the approach proposes a novel platform for ex vivo gene therapy. Such engineered structures could be used as autologous biological pumps for continuous secretion in vivo of gene products of clinical importance.
Reduced neuronal cell death after experimental brain injury in mice lacking a functional alternative pathway of complement activation (2006)

The alternative pathway of complement activation appears to play a more crucial role in the pathophysiology of TBI than previously appreciated. This notion is based on the findings of (a) the significant attenuation of overall complement activation in head-injured fB-/- mice, as determined by a reduction of serum C5a concentrations to constitutive levels in normal mice, and (b) by a dramatic reduction of TUNEL-positive neurons in conjunction with an upregulation of Bcl-2 and downregulation of the Fas receptor in head-injured fB-/- mice, compared to fB+/+ littermates. Pharmacological targeting of the alternative complement pathway during the "time-window of opportunity" after TBI may represent a promising new strategy to be pursued in future studies.
The androgen‐regulated type II serine protease TMPRSS2 is differentially expressed and mislocalized in prostate adenocarcinoma (2008)

Transmembrane serine protease 2 (TMPRSS2) is an androgen-regulated member of the type two transmembrane protease (TTSP) family. Two other members of the TTSP family, matriptase and hepsin, are over-expressed in prostate adenocarcinoma and mechanistically influence cancer cell invasion and metastasis. This study was performed to determine TMPRSS2 protein expression in primary and metastatic prostate cancers. We developed a monoclonal antibody capable of the sensitive and specific detection of TMPRSS2 protein. TMPRSS2 regulation by androgen and presence in seminal fluid was measured. TMPRSS2 localization and expression was evaluated in 415 cases of primary prostate cancer and 144 prostate cancer metastases by immunohistochemistry. We determined that TMPRSS2 protein expression is regulated by androgens and that TMPRSS2 is a component of the normal seminal fluid proteome. TMPRSS2 protein is abundantly expressed in the prostate, with low levels in the epithelia of the colon, stomach, epididymis and breast. Pancreatic acini, hepatic bile ducts, testicular Leydig cells and the kidney also express TMPRSS2. In the prostate, TMPRSS2 protein is specifically localized to the secretory epithelium, with enhanced expression in the plasma membrane orientated towards the ductal lumen. TMPRSS2 expression was significantly higher in both neoplastic prostate and in the epithelium of prostatic hyperplasia compared to normal epithelium (p < 0.01). TMPRSS2 expression was further elevated in higher Gleason grade cancers (patterns 4 and 5) compared to pattern 3 (p = 0.04). Furthermore, in most high-grade cancers, TMPRSS2 was mislocalized, being expressed in the cytoplasm as well as in the cell membrane. Prostate cancer metastases also generally expressed high levels of TMPRSS2. In summary, the TMPRSS2 protease is expressed highly in primary and metastatic prostate cancers and is associated with tumour cell differentiation. Based on studies with the related proteins matriptase and hepsin, TMPRSS2 should be investigated for causal roles in prostate carcinogenesis.
Radical Roles for RAGE in the Pathogenesis of Oxidative Stress in Cardiovascular Diseases and Beyond (2013)

Oxidative stress is a central mechanism by which the receptor for advanced glycation endproducts (RAGE) mediates its pathological effects. Multiple experimental inquiries in RAGE-expressing cultured cells have demonstrated that ligand-RAGE interaction mediates generation of reactive oxygen species (ROS) and consequent downstream signal transduction and regulation of gene expression. The primary mechanism by which RAGE generates oxidative stress is via activation of NADPH oxidase; amplification mechanisms in the mitochondria may further drive ROS production. Recent studies indicating that the cytoplasmic domain of RAGE binds to the formin mDia1 provide further support for the critical roles of this pathway in oxidative stress; mDia1 was required for activation of rac1 and NADPH oxidase in primary murine aortic smooth muscle cells treated with RAGE ligand S100B. In vivo, in multiple distinct disease models in animals, RAGE action generates oxidative stress and modulates cellular/tissue fate in range of disorders, such as in myocardial ischemia, atherosclerosis, and aneurysm formation. Blockade or genetic deletion of RAGE was shown to be protective in these settings. Indeed, beyond cardiovascular disease, evidence is accruing in human subjects linking levels of RAGE ligands and soluble RAGE to oxidative stress in disorders such as doxorubicin toxicity, acetaminophen toxicity, neurodegeneration, hyperlipidemia, diabetes, preeclampsia, rheumatoid arthritis and pulmonary fibrosis. Blockade of RAGE signal transduction may be a key strategy for the prevention of the deleterious consequences of oxidative stress, particularly in chronic disease.
Topographic imaging of mineral and collagen in the calcifying turkey tendon (1991)

Topographic imaging, a method of providing a direct view of ultrastructure in three dimensions, has been newly applied to a study of mineral crystals and collagen from calcifying turkey leg tendon. Individual crystals obtained from intact tendon were observed as thin platelets of irregular shape having a relatively smooth surface. Mineralized collagen fibrils isolated singly or examined in thin tissue sections were found to exhibit the characteristic 64-70 nm period and were associated with platelets and needle-like mineral. The crystals were disposed in numerous fashions, notably as small groups of platelets within individual collagen hole zones, as a number of needle-like densities arranged parallel to one another, or as a combination of platelets and needles over entire stretches of single collagen fibrils. The topographic observations of crystals and crystal-collagen interaction clearly demonstrate the plate-like habit of the mineral in calcifying turkey tendon and suggest that these crystals are located both within and on the surface of collagen fibrils. In certain sites such as the collagen hole zones, the crystals appear organized in a specific manner, possibly with a preferred c-axial orientation. Crystals of hydroxyapatite prepared in vitro and examined topographically are similar in habit and texture to the crystals from tendon. When interpretation of this method is corroborated by other independent microscopic techniques, topographic imaging has widespread potential application in many fields of study in which structural surface features of biological tissues or non-biological materials are of interest at the electron microscope level.
Colonization of Morus alba L. by the plant-growth-promoting and antagonistic bacterium Burkholderia cepacia strain Lu10-1 (2010)

Burkholderia cepacia strain Lu10-1 is an endophyte that can multiply and spread in mulberry seedlings rapidly and efficiently. The strain is antagonistic to C. dematium and acts as an efficient plant-growth-promoting agent on mulberry seedlings and is therefore a promising candidate as a biocontrol and growth-promoting agent.
Cell-penetrating peptides for the delivery of nucleic acids (2012)

CPPs have proved their potential as carriers for nucleic acids. However, similarly to other non-viral vectors, CPPs require further development, as efficient systemic delivery is still seldom achieved. To achieve this, CPPs should be modified with entities that would allow better endosomal escape, targeting of specific tissues and cells, and shielding agents that increase the half-life of the vehicles. Finally, to understand the clinical potential of CPPs, they require more thorough investigations in clinically relevant disease models and in pre-clinical and clinical studies.
Distortion model selecting and accuracy evaluation for CCD camera calibration (2002)

The precision of a CCD camera calibration depends on both the distortion models selected and the signal-to-noise. The former is called the intrinsic factor, and latter is the extrinsic factor. So far, none of the fixed criterion has been used for selecting the distortion model, and almost all are personal or experiential. None of the fixed criterion has been used for determining the degree of error with which we measure the 2D image coordinates, and the amount by which the calibration model can correctly compensate for the distortion in a fixed imagery system in current calibration methods. The paper presents notable and correlation coefficient checks in the statistics for selecting the distortion model, using the signal-to-noise ratio as the criterion to measure the compensation capability. A large number of simulation and practical experiments show: (1) various distortion models exist for imagery systems; (2) there is a high correlation among the distortion parameters or between the distortion parameters and the camera parameters; (3) the larger the signal-to-noise ratio, the larger the compensation capability, and the smaller signal-to-noise ratio, the smaller the compensation capability; and (4) the relation between the precision improvement and the signal-to-noise ratio is an exponential function.
Effects of Administration of Exogenous Growth Factors on Biomechanical Properties of the Elongation-type Anterior Cruciate Ligament Injury with Partial Laceration (2004)

Administration of certain growth factors is of value to be studied as one of the future therapeutic options for the overstretched anterior cruciate ligament injury.
New telechelic polymers and sequential copolymers by polyfunctional initiator‐transfer agents (inifers). III. Synthesis and characterization of poly(α‐methylstyrene‐b‐isobutylene‐b‐α‐methylstyrene) (1980)

Abstract The synthesis of a new glassy‐rubbery‐glassy triblock copolymer poly(α‐methylstyrene‐ b ‐isobutylene‐ b ‐α‐methylstyrene) has been demonstrated. The key to the synthesis was the preparation by inifer method of a perfectly bifunctional polyisobutylene which carries tert ‐chlorine end groups Cl‐PIB‐Cl. In conjunction with Et 2 AlCl coinitiator, the telechelic Cl‐PIB‐Cl molecule initiates the polymerization of α‐methylstyrene at both ends of the prepolymer. Triblock composition can be controlled by the judicious selection of synthesis conditions; that is, Cl‐PIB‐Cl molecular weight, α‐methylstyrene concentration, and solvent polarity. Theoretical triblock M n calculated from M n of Cl‐PIB‐Cl and triblock overall composition is in excellent agreement with experimental M n which indicates negligible homopolymer contamination. Extraction with a series of hydrocarbon solvents reveals broad composition distribution. The stress‐strain profile of a triblock is similar to that of a poly(styrene‐ b ‐butadiene‐ b ‐styrene) thermoplastic elastomer of similar composition.
Digital Light-in-Flight Recording by Holography by Use of a Femtosecond Pulsed Laser (2011)

We succeeded in digital light-in-flight recording by holography by use of a femtosecond pulsed laser. We recorded and reconstructed a moving picture of femtosecond light pulse propagation on a diffuser plate on which a test chart pattern was printed. A mode-locked Ti:sapphire laser was used as a femtosecond pulsed laser. The center wavelength and the duration of the light pulse were 800 nm and 96 fs, respectively. We conducted a numerical simulation in order to validate the proposed technique. We confirmed that the technique was capable of recording the moving picture of femtosecond light pulse propagation. In addition, we experimentally demonstrated the technique and successfully observed femtosecond light pulse propagation for 576 fs. The experimental results agreed well with the simulation results.
A Preliminary Investigation of Maximum Likelihood Logistic Regression versus Exact Logistic Regression (2002)

Logistic regression is used by practitioners and researchers in many fields, but is undoubtedly used most frequently in medical and biostatistical applications. Maximum likelihood is generally the estimation method of choice, but we show that maximum likelihood can produce very poor results under certain conditions. Specifically, the poor performance of maximum likelihood in the case of rare events is known and we review research on this topic. We primarily examine the performance of maximum likelihood in the presence of near separation, which has apparently not been studied. Exact logistic regression is the logical alternative to maximum likelihood. We offer a comparison of the two methods of estimation.
Evaluation of a Newly Developed Lateral Flow Immunoassay for the Diagnosis of Cryptococcosis (2011)

A high level of agreement was shown between LFA and EIA testing of serum. The LFA is a rapid, easy-to-perform assay that does not require refrigeration, demonstrating its potential usefulness as a point-of-care assay for diagnosis of cryptococcosis in resource-limited countries.
An exclusive human milk-based diet in extremely premature infants reduces the probability of remaining on total parenteral nutrition: a reanalysis of the data (2012)

This study was registered at http://www.clinicaltrials.gov reg. # NCT00506584.
Citrobacter rodentiumInfection in Mice Elicits a Mucosal Th1 Cytokine Response and Lesions Similar to Those in Murine Inflammatory Bowel Disease (1999)

Citrobacter rodentium is a classically noninvasive pathogen of mice that is similar to enteropathogenic Escherichia coli (EPEC) in man. Following oral infection of young mice, the organism colonizes the distal colon, and within 1 week the colonic mucosa doubles in thickness and there is massive epithelial cell hyperplasia. Since T-cell responses in mouse models of inflammatory bowel disease (IBD) also cause epithelial hyperplasia, we have investigated the possibility that C. rodentium promotes similar T-cell responses in the mucosa, thereby increasing epithelial shedding, transmission, and replication of the organism. Beginning 6 days after infection, bacteria were observed to be in close association with the epithelial surface and were also visible scattered throughout the lamina propria and in the submucosa. There was a CD3(+)-cell infiltrate into the colonic lamina propria and epithelium as well as mucosal thickening and crypt hyperplasia. The majority of CD3(+) cells were CD4(+) and were not gammadelta+. Reverse transcription-PCR analysis of cytokines also revealed a highly polarized Th1 response (interleukin-12, gamma interferon, and tumor necrosis factor alpha) in the mucosa and a large increase in the epithelial cell mitogen keratinocyte growth factor. None of the changes were seen in mice inoculated with bacteria lacking intimin (which is necessary for colonization), but they were seen in mice inoculated with C. rodentium complemented with intimin from EPEC. This is the first example of a classically noninvasive bacterial pathogen which elicits a strong mucosal Th1 response and which produces pathology similar to that seen in mouse models of IBD, which is also characterized by a strong Th1 response. These results also suggest that the colonic mucosa responds in a stereotypic way to Th1 responses.
Resveratrol-induced cyclooxygenase-2 facilitates p53-dependent apoptosis in human breast cancer cells (2006)

Cyclooxygenase-2 (COX-2) is antiapoptotic and is implicated in tumorigenesis. Recent reports, however, have also ascribed a proapoptotic action to inducible COX-2. We show here for the first time that a stilbene, resveratrol, induces nuclear accumulation of COX-2 protein in human breast cancer MCF-7 and MDA-MB-231 cell cultures. The induction of COX-2 accumulation by resveratrol is mitogen-activated protein kinase (MAPK; extracellular signal-regulated kinase 1/2)- and activator protein 1- dependent. Nuclear COX-2 in resveratrol-treated cells colocalizes with Ser(15)-phosphorylated p53 and with p300, a coactivator for p53-dependent gene expression. The interaction of COX-2, p53, and p300, as well as resveratrol-induced apoptosis, was inhibited by a MAPK activation inhibitor, PD98059. A specific inhibitor of COX-2, NS398, and small interfering RNA knockdown of COX-2 were associated with reduced p53 phosphorylation and consequent decrease in p53-dependent apoptosis in resveratrol-treated cells. We conclude that nuclear accumulation of COX-2 can be induced by resveratrol and that the COX has a novel intranuclear colocalization with Ser(15)-phosphorylated p53 and p300, which facilitates apoptosis in resveratrol-treated breast cancer cells.
Pharmacologic Disruption of Schlemm’s Canal Cells and Outflow Facility in Anterior Segments of Human Eyes (2004)

Pharmacologic disruption of Schlemm's canal cells appears possible. H-7 increased outflow facility, causing a partial loss of the endothelial lining of Schlemm's canal. A simple relationship between canal cells and outflow facility was not found; canal cells probably interact with the extracellular matrix in influencing outflow facility.
Peripheral blood leukocyte NO production and oxidative stress in multiple sclerosis (2007)

PBL nitrite levels and measures of oxidative stress are closely related in MS-patients as well as in healthy control persons. Increased serum NO levels in MS may be the result of a physiologic reaction to overall oxidative stress. The differences in the strength of correlation between different disease subtypes may reflect differences in leukocyte biology.
Focal loss of the glutamate transporter EAAT2 in a transgenic rat model of SOD1 mutant-mediated amyotrophic lateral sclerosis (ALS) (2002)

Transgenic overexpression of Cu(+2)/Zn(+2) superoxide dismutase 1 (SOD1) harboring an amyotrophic lateral sclerosis (ALS)-linked familial genetic mutation (SOD1(G93A)) in a Sprague-Dawley rat results in ALS-like motor neuron disease. Motor neuron disease in these rats depended on high levels of mutant SOD1 expression, increasing from 8-fold over endogenous SOD1 in the spinal cord of young presymptomatic rats to 16-fold in end-stage animals. Disease onset in these rats was early, approximately 115 days, and disease progression was very rapid thereafter with affected rats reaching end stage on average within 11 days. Pathological abnormalities included vacuoles initially in the lumbar spinal cord and subsequently in more cervical areas, along with inclusion bodies that stained for SOD1, Hsp70, neurofilaments, and ubiquitin. Vacuolization and gliosis were evident before clinical onset of disease and before motor neuron death in the spinal cord and brainstem. Focal loss of the EAAT2 glutamate transporter in the ventral horn of the spinal cord coincided with gliosis, but appeared before motor neuron/axon degeneration. At end-stage disease, gliosis increased and EAAT2 loss in the ventral horn exceeded 90%, suggesting a role for this protein in the events leading to cell death in ALS. These transgenic rats provide a valuable resource to pursue experimentation and therapeutic development, currently difficult or impossible to perform with existing ALS transgenic mice.
Structural features in TAR RNA of human and simian immunodeficiency viruses: a phylogenetic analysis (1992)

A comparative analysis of TAR RNA structures in human and simian immunodeficiency viruses reveals the conservation of certain structural features despite the divergence in sequence. Both the TAR elements of HIV-1 and SIV-chimpanzee can be folded into relatively simple one-stem hairpin structures. Chemical and RNAase probes were used to analyze the more complex structure of HIV-2 TAR RNA, which folds into a branched hairpin structure. A surprisingly similar RNA conformation can be proposed for SIV-mandrill, despite considerable divergence in nucleotide sequence. A third structural presentation of TAR sequences is seen for SIV-african green monkey. These results are generally consistent with the classification of HIV-SIV viruses in four subgroups based on sequence analyses (both nucleotide- and amino acid-sequences). However, some conserved TAR structures were detected for members of different virus subgroups. It is therefore proposed that RNA structure analysis might provide an additional tool for determining phylogenetic relationships among the HIV-SIV viruses.