gebhart/patrepeval huggingface dataset:
Intimal fibromuscular hyperplasia at the venous anastomosis of PTFE grafts in hemodialysis patients. Clinical, immunocytochemical, light and electron microscopic assessment. (1989)

Failure of arteriovenous communications used for chronic hemodialysis was studied during sequential 5-year periods after placement of either endogenous Brescia-Cimino (B-C) fistulas (50 patients) or polytetrafluoroethylene (PTFE, Gore-Tex) grafts (66 patients). Venous stenosis near the anastomosis was the reason for failure in 45% of PTFE grafts compared with 16% of B-C fistulas (p less than 0.001). Failure occurred, on average, 16 months after PTFE graft placement compared with 22 for B-C fistulas (p = NS). Proximal vein segments removed from five failed and two functioning PTFE graft communications were studied using light and electron microscopy and immunocytochemical techniques. All venous segments removed during surgical shunt repair exhibited a marked intimal hyperplasia. The intimal cellular component was almost exclusively smooth muscle. Accumulation of intracellular lipid droplets was not seen. Foam cells as well as extracellular lipid deposits were absent; macrophages and lymphocytes were absent from the zone of proliferation. Ultrastructural examination revealed a large proportion of extracellular matrix surrounding smooth muscle cells in the neointima. Collagen and elastin were present in the extracellular matrix, in greatest concentration deeper in the intima. Closer to the lumen, most of the extracellular volume consisted of proteoglycan. Hemosiderin was absent from the lesions as were consistent signs of luminal and intimal fibrin. Uniform intimal gradients of actin, collagen, and proteoglycan suggest that this is a steadily progressive, rather than episodic, proliferative response. These clinical and histologic observations and an analysis of hemodynamic stresses support the postulate that upstream release of platelet-derived growth factor, and possibly, shear-induced intimal injury stimulate this response. This myointimal proliferative process provides a readily accessible model of fibromuscular hyperplasia in humans; its understanding may lead to effective methods for its prevention and may provide clues to the pathogenesis of arteriosclerosis.
Activation of natural regulatory T cells by IgG Fc–derived peptide “Tregitopes” (2008)

We have identified at least 2 highly promiscuous major histocompatibility complex class II T-cell epitopes in the Fc fragment of IgG that are capable of specifically activating CD4(+)CD25(Hi)FoxP3(+) natural regulatory T cells (nT(Regs)). Coincubation of these regulatory T-cell epitopes or "Tregitopes" and antigens with peripheral blood mononuclear cells led to a suppression of effector cytokine secretion, reduced proliferation of effector T cells, and caused an increase in cell surface markers associated with T(Regs) such as FoxP3. In vivo administration of the murine homologue of the Fc region Tregitope resulted in suppression of immune response to a known immunogen. These data suggest that one mechanism for the immunosuppressive activity of IgG, such as with IVIG, may be related to the activity of regulatory T cells. In this model, regulatory T-cell epitopes in IgG activate a subset of nT(Regs) that tips the resulting immune response toward tolerance rather than immunogenicity.
Modulation of radiation response after epidermal growth factor receptor blockade in squamous cell carcinomas: inhibition of damage repair, cell cycle kinetics, and tumor angiogenesis. (2000)

We have recently demonstrated that molecular blockade of the epidermal growth factor receptor with the anti-epidermal growth factor receptor (EGFR) monoclonal antibody C225 enhances the in vitro radiosensitivity of human squamous cell carcinomas (SCCs) derived from the head and neck. In the present study, we further investigated the capacity of C225 to modulate the in vitro and in vivo radiation response of human SCC tumor cells and xenografts, and we examined several potential mechanisms that may contribute to the enhanced radiation response induced by C225. Tumor xenograft studies demonstrated complete regression of both newly established (20 mm3) and well-established (100 mm3) SCC tumors over a 55-100 day follow-up period in athymic mice treated with the combination of C225 (i.p. injection) and radiation. Cell cycle analysis via flow cytometry confirmed that combined treatment with C225 and radiation induced an accumulation of cells in the more radiosensitive cell cycle phases (G1, G2-M) with concurrent reduction in the proportion of cells in the more radioresistant S phase. Results from sublethal damage repair and potentially lethal damage repair analyses in cultured SCC cells demonstrated a strong inhibitory effect of C225 on postradiation damage repair. Further, exposure of SCC cells to C225 induced a redistribution of DNA-dependent protein kinase from the nucleus to the cytosol, suggesting one potential mechanism whereby C225 may influence the cellular response to radiation. Immunohistochemical analysis of SCC tumor xenografts after systemic administration of C225 demonstrated inhibition of the in vivo expression of tumor angiogenesis markers, including vascular endothelial growth factor and Factor VIII. Taken together, the collective data suggest that the profound in vivo antitumor activity identified in the xenograft setting when C225 is combined with radiation derives from more than simply the antiproliferative and cell cycle effects of EGFR system inhibition. In addition to antiproliferative growth inhibition, EGFR blockade with C225 appears to influence the capacity of human SCCs to effect DNA repair after exposure to radiation, and to express classic markers of tumor angiogenesis.
Adult Neurogenesis and Neuronal Regeneration in the Central Nervous System of Teleost Fish (2001)

In contrast to mammals, teleost fish exhibit an enormous potential to produce new neurons in the adult central nervous system and to replace damaged neurons by newly generated ones. In the gymnotiform fish Apteronotus leptorhynchus, on average, 100,000 cells, corresponding to roughly 0.2% of the total population of cells in the adult brain, are in S-phase within any 2-h period. As in all other teleosts examined thus far, many of these cells are produced in specific proliferation zones located at or near the surface of ventricular, paraventricular, and cisternal systems, or in areas that are likely derived from proliferation zones located at ventricular surfaces during embryonic development. The majority of cells born in such proliferation zones migrate within the first few weeks following their generation to specific target areas. In the cerebellum, where approximately 75% of all brain cells are born during adulthood, cells originate from the molecular layers of the corpus cerebelli and the valvula cerebelli partes lateralis and medialis, as well as from the eminentia granularis pars medialis. From these proliferation zones, the young cells migrate to the associated granule cell layers or to the eminentia granularis pars posterior, respectively. In the course of their migration, the young cells appear to be guided by radial glial fibers. Upon arrival at their target region, approximately 50% of the young cerebellar cells undergo apoptosis. The remaining cells survive for the rest of the fish's life, thus contributing to permanent brain growth. At least some cells differentiate into granule cell neurons. The potential to produce new neurons, together with the ability to guide the young cells to their target areas by radial glial fibers and to eliminate damaged cells through apoptosis, also forms the basis for the enormous regenerative capability of the central nervous system of Apteronotus, as demonstrated in the cerebellum and spinal cord. A factor involved in the cerebellar regeneration appears to be somatostatin, as the expression of this neuropeptide is up-regulated in a specific spatio-temporal fashion following mechanical lesions. Besides its involvement in neuronal regeneration adult neurogenesis in Apteronotus, and possibly teleost fish in general, appears to play a role in providing central neurons to match the growing number of sensory and motor elements in the periphery, and to establish the neural substrate to accommodate behavioral plasticity.
Dissociation of a glucan fraction (CO-1) from protein-bound polysaccharide of Cordyceps ophioglossoides and analysis of its antitumor effect. (1988)

A glucan moiety (CO-1) was dissociated from the antitumor protein-bound polysaccharide (SN-C) obtained from the culture of Cordyceps ophioglossoides by ultrasonication and heat treatment.CO-1 exhibited antitumor activity against murine sarcoma 180 when given by oral administration.CO-1 was also effective against syngeneic MM46 mammary carcinoma (solid form), but did not show any effect on ascitic tumors such as P388 leukemia.On intraperitoneal administration to normal mice, CO-1 increased the number of peritoneal exudate cells and strongly enhanced the chemiluminescence response of these exudate cells.The activity of CO-1 was higher than that of zymosan-A.
Sampling Moments and Reconstructing Signals of Finite Rate of Innovation: Shannon Meets Strang–Fix (2007)

Consider the problem of sampling signals which are not bandlimited, but still have a finite number of degrees of freedom per unit of time, such as, for example, nonuniform splines or piecewise polynomials, and call the number of degrees of freedom per unit of time the rate of innovation. Classical sampling theory does not enable a perfect reconstruction of such signals since they are not bandlimited. Recently, it was shown that, by using an adequate sampling kernel and a sampling rate greater or equal to the rate of innovation, it is possible to reconstruct such signals uniquely . These sampling schemes, however, use kernels with infinite support, and this leads to complex and potentially unstable reconstruction algorithms. In this paper, we show that many signals with a finite rate of innovation can be sampled and perfectly reconstructed using physically realizable kernels of compact support and a local reconstruction algorithm. The class of kernels that we can use is very rich and includes functions satisfying Strang-Fix conditions, exponential splines and functions with rational Fourier transform. This last class of kernels is quite general and includes, for instance, any linear electric circuit. We, thus, show with an example how to estimate a signal of finite rate of innovation at the output of an RC circuit. The case of noisy measurements is also analyzed, and we present a novel algorithm that reduces the effect of noise by oversampling
Proton-pump inhibitors are associated with a reduced risk for bleeding and perforated gastroduodenal ulcers attributable to non-steroidal anti-inflammatory drugs: a nested case-control study (2007)

Treatment with non-steroidal anti-inflammatory drugs (NSAIDs) is hampered by gastrointestinal ulcer complications, such as ulcer bleeding and perforation. The efficacy of proton-pump inhibitors in the primary prevention of ulcer complications arising from the use of NSAIDs remains unproven. Selective cyclooxygenase-2 (COX-2) inhibitors reduce the risk for ulcer complications, but not completely in high-risk patients. This study determines which patients are especially at risk for NSAID ulcer complications and investigates the effectiveness of different preventive strategies in daily clinical practice. With the use of a nested case-control design, a large cohort of NSAID users was followed for 26 months. Cases were patients with NSAID ulcer complications necessitating hospitalisation; matched controls were selected from the remaining cohort of NSAID users who did not have NSAID ulcer complications. During the observational period, 104 incident cases were identified from a cohort of 51,903 NSAID users with 10,402 patient years of NSAID exposure (incidence 1% per year of NSAID use, age at diagnosis 70.4 +/- 16.7 years (mean +/- SD), 55.8% women), and 284 matched controls. Cases were characterised by serious, especially cardiovascular, co-morbidity. In-hospital mortality associated with NSAID ulcer complications was 10.6% (incidence 21.2 per 100,000 NSAID users). Concomitant proton-pump inhibitors (but not selective COX-2 inhibitors) were associated with a reduced risk for NSAID ulcer complications (the adjusted odds ratio 0.33; 95% confidence interval 0.17 to 0.67; p = 0.002). Especially at risk for NSAID ulcer complications are elderly patients with cardiovascular co-morbidity. Proton-pump inhibitors are associated with a reduced risk for NSAID ulcer complications.
Measurements of Single-Molecule Electromechanical Properties (2003)

The electromechanical properties of a single molecule covalently attached to two gold electrodes are studied by simultaneously measuring the conductance and the force during the stretching of the molecule. The conductance, the spring constant of the molecular junction, and the dependence of the conductance on the stretching force are determined. Like the conductance, the spring constant of a molecule depends also on the molecule-electrode contacts. The forces required to break the molecule-gold contacts are 1.5 nN for alkanedithiols and 0.8 nN for 4,4' bipyridine, indicating that the breakdowns take place at the Au-Au bond and at the N-Au bond, respectively.
The interaction dynamics of a negative feedback loop regulates flagellar number in Salmonella enterica serovar Typhimurium (2010)

Each Salmonella enterica serovar Typhimurium cell produces a discrete number of complete flagella. Flagellar assembly responds to changes in growth rates through FlhD(4) C(2) activity. FlhD(4) C(2) activity is negatively regulated by the type 3 secretion chaperone FliT. FliT is known to interact with the flagellar filament cap protein FliD as well as components of the flagellar type 3 secretion apparatus. FliD is proposed to act as an anti-regulator, in a manner similar to FlgM inhibition of σ(28) activity. We have found that efficient growth-dependent regulation of FlhD(4) C(2) requires FliT regulation. In turn, FliD regulation of FliT modulates the response. We also show that, unlike other flagellar-specific regulatory circuits, deletion of fliT or fliD did not lead to an all-or-nothing response in FlhD(4) C(2) activity. To investigate why, we characterized the biochemical interactions in the FliT : FliD : FlhD(4) C(2) circuit. When FlhD(4) C(2) was not bound to DNA, FliT disrupted the FlhD(4) C(2) complex. Interestingly, when FlhD(4) C(2) was bound to DNA it was insensitive to FliT regulation. This suggests that the FliT circuit regulates FlhD(4) C(2) activity by preventing the formation of the FlhD(4) C(2) :DNA complex. Our data would suggest that this level of endogenous regulation of FlhD(4) C(2) activity allows the flagellar system to efficiently respond to external signals.
Automating crowd-supervised learning for spoken language systems (2012)

Spoken language systems often rely on static speech recognizers. When the underlying models are improved on-the-fly, training is usually performed using unsupervised methods. In this work, we explore an alternative approach that uses human computation to provide crowd-supervised training of a deployed system. Although the framework we describe is applicable to any stochastic model for which the training data can be generated by non-experts, we demonstrate its utility on the lexicon and language model of a speech recognizer in a cinema voicesearch domain. We show how an initially shaky system can achieve over a 10% absolute improvement in word error rate (WER) – entirely without expert intervention. We then analyze how these gains were made.
Transduction of Growth or Mitogenic Signals into Translational Activation of TOP mRNAs Is Fully Reliant on the Phosphatidylinositol 3-Kinase-Mediated Pathway but Requires neither S6K1 nor rpS6 Phosphorylation (2002)

Translation of terminal oligopyrimidine tract (TOP) mRNAs, which encode multiple components of the protein synthesis machinery, is known to be controlled by mitogenic stimuli. We now show that the ability of cells to progress through the cell cycle is not a prerequisite for this mode of regulation. TOP mRNAs can be translationally activated when PC12 or embryonic stem (ES) cells are induced to grow (increase their size) by nerve growth factor and retinoic acid, respectively, while remaining mitotically arrested. However, both growth and mitogenic signals converge via the phosphatidylinositol 3-kinase (PI3-kinase)-mediated pathway and are transduced to efficiently translate TOP mRNAs. Translational activation of TOP mRNAs can be abolished by LY294002, a PI3-kinase inhibitor, or by overexpression of PTEN as well as by dominant-negative mutants of PI3-kinase or its effectors, PDK1 and protein kinase Balpha (PKBalpha). Likewise, overexpression of constitutively active PI3-kinase or PKBalpha can relieve the translational repression of TOP mRNAs in quiescent cells. Both mitogenic and growth signals lead to phosphorylation of ribosomal protein S6 (rpS6), which precedes the translational activation of TOP mRNAs. Nevertheless, neither rpS6 phosphorylation nor its kinase, S6K1, is essential for the translational response of these mRNAs. Thus, TOP mRNAs can be translationally activated by growth or mitogenic stimuli of ES cells, whose rpS6 is constitutively unphosphorylated due to the disruption of both alleles of S6K1. Similarly, complete inhibition of mammalian target of rapamycin (mTOR) and its effector S6K by rapamycin in various cell lines has only a mild repressive effect on the translation of TOP mRNAs. It therefore appears that translation of TOP mRNAs is primarily regulated by growth and mitogenic cues through the PI3-kinase pathway, with a minor role, if any, for the mTOR pathway.
Hormonal control of alpha-fetoprotein secretion in human hepatoma cell lines proliferating in chemically defined medium. (1985)

The regulation of alpha-fetoprotein (AFP) secretion and growth rate by various hormones in established human hepatoma (HuH-7, PLC/PRF/5, huH-1, huH-4, and KIM-1/c-4) and hepatoblastoma (HUH-6 Clone 5) cell lines was studied. These 6 cell lines replicated continuously in a chemically defined medium and secreted 84 ng (HuH-7) to 23 pg (huH-4) AFP per 24 h per 1 X 10(4) cells into the culture medium. The addition of insulin increased the growth rate of all examined cell lines and partially inhibited the AFP secretion in those cell lines except KIM-1/c-4, while the addition of dexamethasone inhibited the growth and stimulated the AFP secretion in all of the cell lines. The addition of 3,3',5-triiodothyronine inhibited the growth of all cell lines; however, different effects on the AFP secretion were observed depending on the cell lines used. Obviously, the AFP secretion was unrelated to the change in growth rate. When dexamethasone and N6-O2-dibutyryl cyclic AMP were added together, the AFP secretion was further stimulated. On the other hand, when dexamethasone and insulin were added simultaneously, the dexamethasone-mediated stimulation of AFP secretions was diminished. The data indicated that the regulatory mechanisms of AFP secretion by the hormones in the established human hepatoma and hepatoblastoma cell lines cannot be deduced according to the results of one cell line.
Vaginal clindamycin and oral metronidazole for bacterial vaginosis: a randomized trial (2000)

A 3-day regimen of clindamycin, given as intravaginal ovules, was as effective as and better tolerated than a 7-day regimen of oral metronidazole 500 mg, given twice daily, for treatment of bacterial vaginosis.
NONPARAMETRIC TESTS FOR ORDERED DIVERSITY IN A GENOMIC SEQUENCE (2005)

summary In genomics (SNP and RNA amino acid studies), typically, we encounter enormously large dimensional qualitative categorical data models without an ordering of the categories, thus preempting the use of conventional measures of dispersion (variation or diversity) as well as other measures which assume some latent trait variable(s). The Gini-Simpson diversity measure, often advocated for diversity analysis in one-dimensional models, has been adapted to formulate measures of diversity and co-diversity based on the Hamming distance in the multidimensional setup. Based on certain (molecular) biologically interpretable monotone diversity perspectives, an ordering of the Gini-Simpson measures across the genome (positions) is formulated in a meaningful way. Motivated by this feature, nonparametric inference for such ordered measures is considered here, and their applications stressed.
Human major histocompatibility complex class II-restricted T cell responses in transgenic mice. (1994)

Transgenic mice expressing human major histocompatibility complex (MHC) class II molecules would provide a valuable model system for studying human immunology. However, attempts to obtain human class II-restricted T cell responses in such transgenic mice have had only limited success, possibly due to an inability of mouse CD4 to interact efficiently with human MHC class II molecules. To circumvent this problem, we constructed recombinant MHC class II genes in which the peptide-binding domain was derived from human DR sequences whereas the CD4-binding domain was derived from mouse I-E sequences. Purified chimeric human/mouse MHC class II molecules were capable of specifically binding DR-restricted peptides. Human B cell transformants that expressed these chimeric MHC class II molecules could present peptide antigens to human T cell clones. Expression of these chimeric class II molecules in transgenic mice led to the intrathymic deletion of T cells expressing superantigen-reactive V beta gene segments, indicating that the chimeric class II molecules could influence the selection of the mouse T cell repertoire. These transgenic mice were fully capable of mounting human DR-restricted immune responses after challenge with peptide or whole protein antigens. Thus, the chimeric class II molecules can serve as functional antigen presentation molecules in vivo. In addition, transgenic mice expressing chimeric class II molecules could be used to generate antigen-specific mouse T cell hybridomas that were capable of interacting with human antigen-presenting cells.
WebWatcher: Machine Learning and Hypertext (1995)

Abstract : This paper describes the first implementation of WebWatcher, a Learning Apprentice for the World Wide Web. We also explore the possibility of extracting information from the structure of hypertext. We introduce an algorithm which identifies pages that are related to a given page using only hypertext structure. We motivate the algorithm by using the Minimum Description Length principle.