gebhart/patrepeval huggingface dataset:
ATF6 Activated by Proteolysis Binds in the Presence of NF-Y (CBF) Directly to thecis-Acting Element Responsible for the Mammalian Unfolded Protein Response (2000)

Transcription of genes encoding molecular chaperones and folding enzymes in the endoplasmic reticulum (ER) is induced by accumulation of unfolded proteins in the ER. This intracellular signaling, known as the unfolded protein response (UPR), is mediated by the cis-acting ER stress response element (ERSE) in mammals. In addition to ER chaperones, the mammalian transcription factor CHOP (also called GADD153) is induced by ER stress. We report here that the transcription factor XBP-1 (also called TREB5) is also induced by ER stress and that induction of CHOP and XBP-1 is mediated by ERSE. The ERSE consensus sequence is CCAAT-N(9)-CCACG. As the general transcription factor NF-Y (also known as CBF) binds to CCAAT, CCACG is considered to provide specificity in the mammalian UPR. We recently found that the basic leucine zipper protein ATF6 isolated as a CCACG-binding protein is synthesized as a transmembrane protein in the ER, and ER stress-induced proteolysis produces a soluble form of ATF6 that translocates into the nucleus. We report here that overexpression of soluble ATF6 activates transcription of the CHOP and XBP-1 genes as well as of ER chaperone genes constitutively, whereas overexpression of a dominant negative mutant of ATF6 blocks the induction by ER stress. Furthermore, we demonstrated that soluble ATF6 binds directly to CCACG only when CCAAT exactly 9 bp upstream of CCACG is bound to NF-Y. Based on these and other findings, we concluded that specific and direct interactions between ATF6 and ERSE are critical for transcriptional induction not only of ER chaperones but also of CHOP and XBP-1.
Abstract 10076: Angiotensin II Downregulates Micro-RNA 22 to Promote CYR61-Mediated Vascular Smooth Muscle Cell Calcification (2011)

In this article, we primarily focus on the treatment approaches currently marketed and in advanced stages of development for Alzheimer's disease (AD). Amyloid plaques and neurofibrillary tangles remain the pathologic hallmarks of AD, and much progress has been made in unraveling the molecular biology of these changes. In addition, there is also intense research into inflammatory and oxidative mechanisms as well as vascular and neurochemical alterations in AD. Therapies targeted at these mechanisms are discussed.
New Gem- and Vic-Disubstituent Effects on Cyclizations (1999)

Several new gem-disubstituent effects on cyclizations - e.g., the gem-dialkoxy, -dicarboalkoxy, and -dithioalkoxy effects, have been discovered. In addition we have also observed a new vicinal disubstituent effect. A novel ring size effect of ketals on radical cyclizations has been investigated.
Follicle-Stimulating Isohormones: Characterization and Physiological Relevance (1995)

FOLLICLE-stimulating hormone (FSH), one of the major hormones produced by the anterior pituitary gland, is involved in the regulation and maintenance of essential reproductive processes, such as gametogenesis, follicular development, and ovulation (1–4). Like other glycoprotein hormones, FSH exists as a family of isohormones which have been identified within the anterior pituitary, serum, and urine of several mammalian species, including man (5–10) (Table 1). These isoforms differ in their oligosaccharide structures, including the degree of terminal sialylation and/or sulfation (5, 7, 9). The resulting acidic-basic charge differences provide the major basis for separation, with the number of isoforms identified often being a function of the resolution of the separation technique employed. Structural differences in these isoforms alter their MCRs and biological and immunological potency relationships (6–8). Consequently, target tissues within the gonads are exposed to a mixture of circulating FSH isoforms, the relative composition of which is dependent upon the physiological status of the animal (8–10, 39, 63, 67, 72).
R-253 Disrupts Microtubule Networks in Multiple Tumor Cell Lines (2006)

Both biochemical and cellular mechanistic studies indicate that R-253 could become a promising new tubulin-binding drug candidate for treating various malignancies.
AUA Guideline for the Diagnosis and Treatment of Interstitial Cystitis/Bladder Pain Syndrome (2011)

Interstitial cystitis/bladder pain syndrome is best identified and managed through use of a logical algorithm such as is presented in this Guideline. In the algorithm the panel identifies an overall management strategy for the interstitial cystitis/bladder pain syndrome patient. Diagnosis and treatment methodologies can be expected to change as the evidence base grows in the future.
ENTROPY AND SPECIFICITY IN A MATHEMATICAL THEORY OF EVIDENCE (1983)

Abstract We review Shafer's theory of evidence. We then introduce the concepts pf entropy and specificity in the framework of Shafer's theory. These become complementary aspects in the indication of the quality of evidence.
S-Adenosylmethionine attenuates the lipopolysaccharide-induced expression of the gene for tumour necrosis factor α (1999)

Intracellular deficiency of S-adenosylmethionine (AdoMet) and elevated serum concentrations of tumour necrosis factor alpha (TNF) are hallmarks of toxin-induced liver injury. In these models, the administration of either exogenous AdoMet or antibody/soluble receptor for TNF attenuates the injury. We have demonstrated previously that the administration of exogenous AdoMet to AdoMet-deficient rats attenuated lipopolysaccharide (LPS)-induced liver injury and serum TNF concentrations. Here we report that AdoMet lowered the amount of TNF secreted by LPS-stimulated murine macrophage cells (RAW 264.7) in a dose-dependent manner. The inhibition of TNF release was correlated with changes in the steady-state TNF mRNA concentrations. Changes in TNF mRNA were not due to its altered stability and might have been due to an attenuation of the transcription rate of the TNF gene. The inhibition of TNF release in RAW cells was not mediated by GSH because treatment with AdoMet did not increase intracellular GSH. In addition, N-acetylcysteine, whereas it did increase GSH concentration, had no effect on LPS-stimulated TNF release in these cells. Exogenous AdoMet also attenuated LPS-induced serum TNF levels in normal rats sensitized with lead. Thus AdoMet administration might exert its hepatoprotective effects at least in part by its inhibitory effect on expression of the gene for TNF.
Distinct contribution of IL-6, TNF-α, IL-1, and IL-10 to T cell–mediated spontaneous autoimmune arthritis in mice (2004)

Cytokines play key roles in spontaneous CD4(+) T cell–mediated chronic autoimmune arthritis in SKG mice, a new model of rheumatoid arthritis. Genetic deficiency in IL-6 completely suppressed the development of arthritis in SKG mice, irrespective of the persistence of circulating rheumatoid factor. Either IL-1 or TNF-α deficiency retarded the onset of arthritis and substantially reduced its incidence and severity. IL-10 deficiency, on the other hand, exacerbated disease, whereas IL-4 or IFN-γ deficiency did not alter the disease course. Synovial fluid of arthritic SKG mice contained high amounts of IL-6, TNF-α, and IL-1, in accord with active transcription of these cytokine genes in the afflicted joints. Notably, immunohistochemistry revealed that distinct subsets of synovial cells produced different cytokines in the inflamed synovium: the superficial synovial lining cells mainly produced IL-1 and TNF-α, whereas scattered subsynovial cells produced IL-6. Thus, IL-6, IL-1, TNF-α, and IL-10 play distinct roles in the development of SKG arthritis; arthritogenic CD4(+) T cells are not required to skew to either Th1 or Th2; and the appearance of rheumatoid factor is independent of joint inflammation. The results also indicate that targeting not only each cytokine but also each cell population secreting distinct cytokines could be an effective treatment of rheumatoid arthritis.
Therapeutic hypothermia after cardiac arrest: a survey of practice in intensive care units in the United Kingdom (2006)

A telephone survey was carried out on the use of hypothermia as part of the management of unconscious patients following cardiac arrest admitted to United Kingdom (UK) intensive care units (ICUs). All 256 UK ICUs listed in the Critical Care Services Manual 2004 were contacted to determine how many units have implemented therapeutic hypothermia for unconscious patients admitted following cardiac arrest, how it is implemented, and the reasons for non-implementation. Two hundred and forty-six (98.4%) ICUs agreed to participate. Sixty-seven (28.4%) ICUs have cooled patients after cardiac arrest, although the majority of these have treated fewer than 10 patients. The commonest reasons given for not using therapeutic hypothermia in this situation are logistical or resource issues, or the perceived lack of evidence or consensus within individual ICU teams.
Kinematic jump processes for monocular 3D human tracking (2003)

A major difficulty for 3D (three-dimensional) human body tracking from monocular image sequences is the near nonobservability of kinematic degrees of freedom that generate motion in depth. For known link (body segment) lengths, the strict nonobservabilities reduce to twofold 'forwards/backwards flipping' ambiguities for each link. These imply 2/sup # links/ formal inverse kinematics solutions for the full model, and hence linked groups of O(2/sup # links/) local minima in the model-image matching cost function. Choosing the wrong minimum leads to rapid mistracking, so for reliable tracking, rapid methods of investigating alternative minima within a group are needed. Previous approaches to this have used generic search methods that do not exploit the specific problem structure. Here, we complement these by using simple kinematic reasoning to enumerate the tree of possible forwards/backwards flips, thus greatly speeding the search within each linked group of minima. Our methods can be used either deterministically, or within stochastic 'jump-diffusion' style search processes. We give experimental results on some challenging monocular human tracking sequences, showing how the new kinematic-flipping based sampling method improves and complements existing ones.
Generation of functional antigen-specific T cells in defined genetic backgrounds by retrovirus-mediated expression of TCR cDNAs in hematopoietic precursor cells (2002)

We have developed an alternative to transgenesis for producing antigen-specific T cells in vivo. In this system, clonal naive T cells with defined antigen specificity are generated by retrovirus-mediated expression of T cell antigen receptor cDNAs in RAG1-deficient murine hematopoietic precursor cells. These T cells can be stimulated to proliferate and produce cytokines by exposure to antigen in vitro, and they become activated and expand in vivo after immunization. IL-2-deficient T cells generated by this technique show decreased proliferation and cytokine production, both of which can be rescued by exogenous addition of this growth factor. Thus, retrovirus-mediated expression of T cell antigen receptor cDNAs in hematopoietic precursor cells permits the rapid and efficient analysis of the life history of antigen-specific T cells in different genetic backgrounds and may allow for the long-term production of antigen-specific T cells with different functional properties for prophylactic and therapeutic purposes.
On view likelihood and stability (1997)

We define two measures on views: view likelihood and view stability. View likelihood measures the probability that a certain view of a given 3D object is observed; it may be used to identify typical, or "characteristic" views. View stability measures how little the-image changes as the viewpoint is slightly perturbed; it may be used to identify "generic" views. Both definitions are shown to be identical up to the prior probability of camera orientations, and determined by the 2D metric used to compare images. We analytically derive the stability and likelihood measures for two feature-based 2D metrics, where the most stable and most likely view is shown to be the flattest view of the 3D shape. Incorporating view likelihood or stability in 3D object recognition and 3D reconstruction increases the chance of robust performance. In particular, we propose to use these measures to enhance 3D object recognition and 3D reconstruction algorithms, by adding a second step where the most likely solution is selected among all feasible solutions. These applications are demonstrated using simulated and real images.
Localization of Functional Endothelin Receptor Signaling Complexes in Cardiac Transverse Tubules (2003)

Endothelin-1 (ET-1) is an autocrine factor in the mammalian heart important in enhancing cardiac performance, protecting against myocardial ischemia, and initiating the development of cardiac hypertrophy. The ETA receptor is a seven-transmembrane G-protein-coupled receptor whose precise subcellular localization in cardiac muscle is unknown. Here we used fluorescein ET-1 and 125I-ET-1 to provide evidence for ET-1 receptors in cardiac transverse tubules (T-tubules). Moreover, the ETA receptor and downstream effector phospholipase C-beta 1 were co-localized within T-tubules using standard immunofluorescence techniques, and protein kinase C (PKC)-epsilon-enhanced green fluorescent protein bound reversibly to T-tubules upon activation. Localized photorelease of diacylglycerol further suggested compartmentation of PKC signaling, with release at the myocyte "surface" mimicking the negative inotropic effects of bath-applied PKC activators and "deep" release mimicking the positive inotropic effect of ET-1. The functional significance of T-tubular ET-1 receptors was further tested by rendering the T-tubule lumen inaccessible to bath-applied ET-1. Such "detubulated" cardiac myocytes showed no positive inotropic response to 20 nM ET-1, despite retaining both a nearly normal twitch response to field stimulation and a robust positive inotropic response to 20 nm isoproterenol. We propose that ET-1 enhances myocyte contractility by activating ETA receptor-phospholipase C-beta 1-PKC-epsilon signaling complexes preferentially localized in cardiac T-tubules. Compartmentation of ET-1 signaling complexes may explain the discordant effects of ET-1 versus bath applied PKC activators and may contribute to both the specificity and diversity of the cardiac actions of ET-1.
On the Resolution of UWB Microwave Imaging of Tumors in Random Breast Tissue (2005)

Ultra-wideband (UWB) microwave imaging for early breast cancer detection can provide both the necessary imaging resolution and adequate penetration depth in the breast. It is shown that higher resolution can be achieved when the inhomogeneity increases, consequently, more clutter appears and the imaging contrast is reduced.
Inside Our Computable World, and the Mathematics of Universality (2016)

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Recovery of an erythropoietin inducing factor from the regenerating rat liver. (1981)

The perfusion of livers of partially hepatectomized (H mean) rats lends support to earlier findings that the regenerating rat liver is the source of an erythropoietin-inducing hepatic factor (Ep-IHF) which stimulates hepatic production of extrarenal erythropoietin (Ep). Blood plasma was collected from perfused livers of rats that were partially hepatectomized (H mean) 48 to 72 hrs prior to perfusion with whole blood from normal rats. This plasma, when injected into normal rats which were nephrectomized (N mean) and rendered hypoxic 18 hrs after injection, evoked a significant increase in Ep values when compared to blood plasma collected from perfused livers of normal rats. Ep values were significantly higher when regenerating livers were perfused with blood collected from nephrectomized (N mean) rats than when such livers were perfused with blood of normal rats. The highest Ep values resulting from the liver perfusions were obtained when the liver donor and blood donor rats were both H mean and N mean. The results demonstrate that the liver is the principal source of an Ep-inducing factor since perfusion of the liver eliminated other potential tissue sources of activity in the rat. This was achieved by perfusing the livers directly through the portal vein and collecting the perfusate from the hepatic vein, thereby eliminating potential contributions from organs draining into other parts of the systemic circulation. In addition, it was shown that the kidney inhibits the activity and/or production of the Ep-IHF which is evoked by H mean.
Boron Containing Oligonucleotides (1998)

Abstract Synthesis, physicochemical and biological properties of novel class of oligonucleotide analogues, bearing boron modifications are described.
Expression of endogenous tumor necrosis factor as a protective protein against the cytotoxicity of exogenous tumor necrosis factor. (1990)

Based on the finding that expression of endogenous tumor necrosis factor (TNF) which is not detected in TNF-susceptible cells was observed in TNF-resistant cells, the assumption was made that endogenous TNF may be a protective protein against the cytotoxic activity of TNF. In order to confirm this possibility, we investigated the relationship between expression of endogenous TNF and TNF susceptibility by using the gene transfection method. When L-M, TNF-highly sensitive murine fibrosarcoma cells were transfected with a human TNF gene, the stable transfectants expressed endogenous TNF and acquired resistance to TNF. Conversely, when endogenous TNF synthesis was inhibited by introducing an antisense TNF gene into HeLa, TNF-less sensitive human cervical cancer cells, the sensitivity was enhanced. These findings indicate that endogenous TNF is one of the protective factors against the cytotoxic activity of TNF.
Magnetite albumin suspension: a superparamagnetic oral MR contrast agent (1987)

Suspensions of magnetite albumin microspheres (MAM), a new biodegradable particulate iron superparamagnetic MR contrast material, were evaluated in vitro and in vivo as an oral contrast agent. MAM is stable over a broad range of pH and tolerates proteolytic enzyme exposure over 24 hr in vitro. MAM possesses a much larger magnetic moment than do paramagnetic contrast agents. The transverse relaxation rate (R2) of MAM can be as much as 40 times the longitudinal relaxation rate (R1). In vitro spectroscopy studies confirm the potency of MAM in promoting T2 relaxation at concentrations of 10-1000 mg/l. Preliminary studies in rabbits and dogs show that in contrast to oral gadolinium-DTPA, which causes increased signal in bowel, MAM causes marked signal loss in the stomach and small bowel on both T1- and T2-weighted pulse sequences. Radionuclide labeling studies of MAM suspension with 99mTc show no evidence of absorption of MAM suspension from the gastrointestinal tract in small animals. Superparamagnetic suspensions such as MAM that reduce bowel signal on T1- and T2-weighted pulse sequences offer the unique benefit of reducing motion artifacts throughout the gastrointestinal tract, which should allow for improved evaluation of intra- and retroperitoneal diseases, particularly with high-field strength and gradient-echo "fast-scan techniques." Unlike paramagnetic material, MAM appears effective as a small-bowel contrast material.
Some considerations on the use of peptides and mRNA for therapeutic vaccination against cancer (2006)

Active immunization against existing cancer is a field that is currently in development and is associated with a number of problems. The potential use of peptides as minimal essential T-cell antigens and of mRNA as a novel form of antigen with advantages is discussed, with special consideration of practical aspects.
Immunolocalization of Caspase‐3 in Pancreatic Islets of NOD Mice during Cyclophosphamide‐Accelerated Diabetes (2003)

Apoptosis may be a major mechanism of beta cell loss during insulin-dependent diabetes mellitus. Caspase-3 is a key enzyme involved in the terminal steps of this death process. Here, the intra-islet expression of caspase-3 in the NOD mouse was examined immunohistochemically following acceleration of the disease with cyclophosphamide. Female NOD mice were treated at day 95 with cyclophosphamide, and caspase-3 expression in pancreatic sections was studied at days 0, 4, 7, 11, and 14 and compared with age-matched control tissue. In the treated group at day 0, caspase-3 labeling was seen in several peri-islet macrophages and only extremely rarely in beta cells. At day 4, only a few beta cells weakly expressed the enzyme. From day 7, caspase-3 expression began to increase in intra-islet macrophages and reached a peak at days 11 and 14, when a small number of CD4 and CD8 T cells also showed positive labeling. Beta cell expression of caspase-3 at days 11 and 14 was rare. At this stage, several intra-islet immune cells with positive labeling for the enzyme coexpressed either Fas or interleukin-1beta. Only a small proportion of intra-islet caspase-3 cells showed apoptotic nuclei judged by terminal deoxynucleotidyl transferase-mediated dUTP nick end labeling (TUNEL). We conclude that, during cyclophosphamide-accelerated diabetes, the predominant caspase-3 immunolabeling in intra- and extra-islet macrophages suggests that apoptosis of macrophages may be an important mechanism for their elimination. The virtual absence of caspase-3 immunolabeling in most beta cells even during the height of beta cell loss supports the need for developing other markers of early beta cell apoptosis in the NOD mouse.
Expression of c-erbB receptors, MMPs and VEGF in squamous cell carcinoma of the head and neck (2004)

Head and neck squamous cell carcinomas (HNSCC) are characterized by a marked propensity for local invasion and cervical lymph node metastasis. The aim of this study was to investigate the expression of epidermal growth factor receptor (EGFR), c-erbB-2, vascular endothelial growth factor (VEGF) and matrix metalloproteinases (MMPs) in tumor samples of 91 HNSCC patients, and to study a possible correlation to various clinico-pathologic parameters. The expression of EGFR, c-erbB-2, VEGF, MMP-2, -3 and -9 was analyzed in the same paraffin embedded tissue by semi-quantitative immunohistochemical staining. High expression of EGFR, c-erbB-2, MMP-2 or -9 was associated with advanced clinical stages, nodal metastases and tumor-stages. However, high expression of VEGF or MMP-3 was not associated with any clinico-pathologic parameters except significant correlation between VEGF and the tumor site. There were significant correlations between EGFR, c-erbB-2, MMP-2 and -9 in HNSCC patients. Conversely, no correlation was found between VEGF or MMP-3 and the other markers. However, significant correlation was found between MMP-3 or -9 and VEGF. The results indicate that the expression of EGFR, c-erbB-2, VEGF or MMPs play an important role in tumor growth, invasion and metastasis in HNSCC. The authors conclude that EGFR, c-erbB-2, MMP-2 and -9 could be good independent prognostic markers, but not VEGF and MMP-3.
Cable and Phase Identification based on Power Line Communication (2015)

Phase and cable identification is a challenging issue. Power-line communication technology is applied to identify cable and phase of power distribution systems. Power cable circuits have only a limited ability to carry higher frequencies. Typically transformers prevent propagating the higher frequency carrier signal. The proposed method uses the limited propagation ability to identify the cable as well as the phase. A new cable and phase identification system is designed and implemented. The system consists of a transmitter and a receiver with power-line communication module. Some experiments are conducted to verify the theoretical concepts in a commercial building. Also some simulations are done to help and understand the concepts by using Simulink simulator. It can extend the application area of power-line communication.