gebhart/patrepeval huggingface dataset:
Interaction of CArG Elements and a GC-rich Repressor Element in Transcriptional Regulation of the Smooth Muscle Myosin Heavy Chain Gene in Vascular Smooth Muscle Cells (1997)

We have previously shown that maximal expression of the rat smooth muscle myosin heavy chain (SM-MHC) gene in cultured rat aortic smooth muscle cells (SMCs) required the presence of a highly conserved domain (nucleotides -1321 and -1095) that contained two positive-acting serum response factor (SRF) binding elements (CArG boxes 1 and 2) and a negative-acting GC-rich element that was recognized by Sp1 (Madsen, C. S., Hershey, J. C., Hautmann, M. B., White, S. L., and Owens, G. K. (1997) J. Biol. Chem. 272, 6332-6340). In this study, to better understand the functional role of these three cis elements, we created a series of SM-MHC reporter-gene constructs in which each element was mutated either alone or in combination with each other and tested them for activity in transient transfection assays using primary cultured rat aortic SMCs. Results demonstrated that the most proximal SRF binding element (CArG-box1) was active in the absence of CArG-box2, but only upon removal of the GC-rich repressor. In contrast, regardless of sequence context, CArG-box2 was active only when CArG-box1 was present. We further demonstrated using electrophoretic mobility shift assays that Sp1 binding to the GC-rich repressor element did not prevent SRF binding to the adjacent CArG-box2. Thus, unlike other proteins reported to inhibit SRF activity, the repressor activity associated with the GC-rich element does not appear to function through direct inhibition of SRF binding. As a first step toward understanding the importance of these elements in vivo, we performed in vivo footprinting on the intact rat aorta. We demonstrated that both CArG boxes and the GC-rich element were bound by protein within the animal. Additionally, using the rat carotid injury model we showed that Sp1 protein was significantly increased in SMCs located within the myointimal lesion, suggesting that increased expression of this putative repressor factor may contribute to the decreased SM MHC expression within SMCs found in myointimal lesions.
A pH Study on the Chiral Ketone Catalyzed Asymmetric Epoxidation of Hydroxyalkenes (1998)

A detailed study shows that the chiral ketone catalyzed asymmetric epoxidations of hydroxyalkenes are highly pH dependent. The lower enantioselectivity obtained at low pH is attributed to the substantial contribution of the direct epoxidation by Oxone. At high pH the epoxidation mediated by chiral ketone out-competes the racemic epoxidation, leading to higher enantioselectivity. The effective substrates include allylic alcohol, homoallylic alcohol, and bishomoallylic alcohol. In most cases, over 90% ee was obtained.
Rapid Detection of Hepatitis B Virus Surface Antigen by an Agglutination Assay Mediated by a Bispecific Diabody against Both Human Erythrocytes and Hepatitis B Virus Surface Antigen (2007)

Bispecific antibodies have immense potential for use in clinical applications. In the present study, a bispecific diabody against human red blood cells (RBCs) and hepatitis B virus surface antigen (HBsAg) was used to detect HBsAg in blood specimens. The bispecific diabody was constructed by crossing over the variable region of the heavy chains and the light chains of anti-RBC and anti-HBsAg antibodies with a short linker, SRGGGS. In enzyme-linked immunosorbent assays, this bispecific diabody showed specific binding to both RBCs and HBsAg. When this bispecific diabody was mixed with human blood specimens in the presence of HBsAg, the dual binding sites of the diabody caused agglutination of human RBCs. This diabody-mediated agglutination assay was then used to test 712 clinical blood specimens and showed 97.7% sensitivity and 100% specificity when the results were compared with those of the conventional immunoassay, which was used as a reference. This autologous RBC agglutination assay provides a simple approach for rapid screening for HBsAg in blood specimens.
Illustrated Principles of Exercise Physiology (2000)

1. Bioenergetics. 2. Metabolism. 3. Energy Systems. 4. Skeletal Muscle. 5. Cardiovascular System. 6. Respiratory System. 7. Endocrine System. 8. Temperature Regulation. 9. Training for Strength and Endurance. 10. Nutrition. 11. Body Composition and Weight Control.
Increased expression and plasma levels of myeloperoxidase are closely related to the presence of angiographically-detected complex lesion morphology in unstable angina (2010)

This study shows that increased expression and plasma MPO levels are closely related to the presence of angiographically-detected complex lesion morphology in patients with UAP.
NOD2 Signaling Contributes to the Innate Immune Response Against Helper-Dependent Adenovirus Vectors Independently of MyD88 In Vivo (2011)

We previously demonstrated that Toll-like receptor/myeloid differentiation primary response gene 88 (MyD88) signaling is required for maximal innate and acquired [T helper cell type 1 (Th1)] immune responses following systemic administration of helper-dependent adenoviral vectors (HDAds). However, MyD88-deficient mice injected with HDAdLacZ exhibited only partial reduction of innate immune cytokine expression compared with wild-type mice, suggesting MyD88-independent pathways also respond to HDAds. We now show that NOD2, a nucleotide-binding and oligomerization domain (NOD)-like receptor known to detect muramyl dipeptides in bacterial peptidoglycans, also contributes to innate responses to HDAds, but not to humoral or Th1 immune responses. We established NOD2/MyD88 double-deficient mice that, when challenged with HDAds, showed a significant reduction of the innate response compared with mice deficient for either gene singly, suggesting that NOD2 signaling contributes to the innate response independently of MyD88 signaling following systemic administration of HDAds. In addition, NOD2-deficient mice exhibited significantly higher transgene expression than did wild-type mice at an early time point (before development of an acquired response), but not at a later time point (after development of an acquired response). These results indicate that the intracellular sensor NOD2 is required for innate responses to HDAds and can limit transgene expression during early phases of infection.
Phenotypic Characterization of Mononuclear Cells Following Anorganic Bovine Bone Implantation in Rats (1994)

The purpose of this study was to measure inflammatory changes associated with implantation of anorganic bovine bone and bovine bone/collagen composite grafts, and to compare the response to that obtained following grafting with hydroxyapatite. Anorganic bovine bone, either with or without bovine collagen, as well as granular and block forms of synthetic hydroxyapatite, were implanted subcutaneously in Wistar rats. Saline and turpentine oil were used as controls. Biopsies were obtained after 3 days and at 1, 2, 4, 6, and 8 weeks. A panel of 6 monoclonal antibodies was used to detect monocytes, several distinct macrophage subsets, Ia-antigen expression, and T- and B-lymphocytes. Cells identified by each antibody were counted after immunocytochemical staining, and sera obtained 6 weeks after grafting were used in immunoblotting assays to detect antibodies to bovine serum proteins and collagen. Anorganic bovine bone, bovine bone/collagen, and hydroxyapatite all produced a transient macrophage infiltrate that was maximum 3 days after implantation, but resolved to normal levels within 6 to 8 weeks. Lymphocyte infiltration was not elicited by any bovine graft material, and antibodies to bovine serum proteins or type I collagen were not detected in any of the animals examined. These data indicate that a systemic or local immune response does not develop following implantation with anorganic bovine bone or with anorganic bovine bone/collagen materials. It appears appropriate to explore further the merits of these materials for periodontal regenerative procedures.
Metabolic engineering of Lactococcus lactis: influence of the overproduction of alpha-acetolactate synthase in strains deficient in lactate dehydrogenase as a function of culture conditions (1995)

The als gene for alpha-acetolactate synthase of Lactococcus lactis MG1363 was cloned on a multicopy plasmid under the control of the inducible L. lactis lacA promoter. More than a hundredfold overproduction of alpha-acetolactate synthase was obtained in L. lactis under inducing conditions as compared with that of the host strain, which contained a single chromosomal copy of the als gene. The effect of alpha-acetolactate synthase overproduction on the formation of end products in various L. lactis strains was studied under different fermentation conditions. Under aerobic conditions and with an initial pH of 6.0, overexpression of the als gene resulted in significant acetoin production that amounted to more than one-third of the pyruvate converted. However, the effect of the alpha-acetolactate synthase overproduction was even more pronounced in the lactate dehydrogenase-deficient strain L. lactis NZ2700. Anaerobic cultivation of this strain resulted in a doubling of the butanediol formation of up to 40% of the converted pyruvate. When cultivated aerobically at an initial pH of 6.8, overexpression of the als gene in L. lactis NZ2700 resulted in the conversion of more than 60% of the pyruvate into acetoin, while no butanediol was formed. Moreover, at an initial pH of 6.0, similar amounts of acetoin were obtained, but in addition approximately 20% of the pyruvate was converted into butanediol. These metabolic engineering studies indicate that more than 80% of the lactose can be converted via the activity of the overproduced alpha-acetolactate synthase in L. lactis.
DNA MISMATCH REPAIR AND GENETIC INSTABILITY (2000)

Mismatch repair (MMR) systems play a central role in promoting genetic stability by repairing DNA replication errors, inhibiting recombination between non-identical DNA sequences and participating in responses to DNA damage. The discovery of a link between human cancer and MMR defects has led to an explosion of research on eukaryotic MMR. The key proteins in MMR are highly conserved from bacteria to mammals, and this conservation has been critical for defining the components of eukaryotic MMR systems. In eukaryotes, there are multiple homologs of the key bacterial MutS and MutL MMR proteins, and these homologs form heterodimers that have discrete roles in MMR-related processes. This review describes the genetic and biochemical approaches used to study MMR, and summarizes the diverse roles that MMR proteins play in maintaining genetic stability.
Autologous fibroblasts to treat deep and complicated leg ulcers in diabetic patients (2007)

Large complicated leg ulcers, not responsive to standard therapy, after surgical debridement and under parenteral specific antibiosis, must be occlusively covered to improve wound healing. In 10 diabetic patients with deep (Wagner degree 3), large, and Staphylococcus aureus (n=7) or Pseudomonas aeruginosa (n=5)-infected leg (n=1), or foot (n=9) ulcers, we have applied, as a coverage, meshes of in vitro expanded autologous fibroblasts. Complete ulcer healing was observed in seven patients after 8, 12, 12, 14, 16, 18, and 20 weeks from the first graft application (Figures 2 and 3). Two patients had >70% wound healing at 20 and 28 weeks after the first treatment. One patient, previously submitted to a bypass vascular procedure, died of acute myocardial infarction 16 weeks after the first fibroblast autograft application and with a healing wound evenly filled with granulation tissue. In our opinion, the application of autologous in vitro expanded fibroblasts is a satisfactory therapeutic option to treat large leg ulcers and is particularly indicated in patients with chronic diseases such as diabetes or autoimmune diseases on steroid treatment.
A Hall Sensor Analog Front End for Current Measurement With Continuous Gain Calibration (2007)

This paper presents a new technique for continuously calibrating the sensitivity of a current measurement microsystem based on a Hall magnetic field sensor. An integrated reference coil generates a magnetic field for calibration. Using a variant of the chopper modulation, the spinning current technique, combined with a second modulation of the reference signal, the sensitivity of the complete system is continuously measured without interrupting normal operation. Modulation and demodulation schemes allowing the joint processing of both external and reference magnetic fields are proposed. Additional techniques for extracting the very low reference signal are presented. The implementation of the microsystem is then discussed. Finally, measurements validate the calibration principle. A thermal drift lower than 50 ppm/degC is achieved. This is 6-10 times less than in state-of-the-art implementations. Furthermore, the calibration technique also compensates drifts due to mechanical stresses and ageing
Association of Alleles for High Stearic Acid with Agronomic Characters of Soybean1 (1987)

Alleles that control four to sevenfold increases in the content of stearic acid in soybean [ Glycine max (L.) Merr.] oil have been obtained by artificial mutagenesis. The objective of this study was to evaluate the association of three alleles for high stearic acid with agronomic and chemical characters of soybean. Three mutant lines, A6 with 282 g kg −1 stearic acid, A9 with 163 g kg −1 stearic acid, and A10 with 146 g kg −1 stearic acid, each with a different allele at a single locus controlling stearic acid content in the seed oil, were crossed to one of three high‐yielding genotypes with stearic acid content of about 40 g kg −1 . The F 1 plants of each mating were backcrossed without selection to the high‐yielding parent. Pairs of highand low‐stearic‐acid lines were selected from BC 1 F 2 ‐derived lines segregating for a high‐stearic‐acid allele. The pairs of lines were evaluated in a replicated test at three Iowa locations. There were no significant differences in the average yield of the high‐ and the low‐stearic‐acid lines from the A9 and A10 crosses. In the A6 cross, the low‐stearic‐acid lines had significantly greater seed yield than high‐stearic‐acid lines by an average of 7.7%. For the other characters measured, the maximum differences between the mean performance of high‐ and low‐stearic‐acid lines for any of the three crosses were 2.9 days for time of maturity, 4 cm for plant height, 0.3 units for lodging score, 8 mg seed −1 for seed weight, 13 g kg −1 for seed protein, and 1 g kg −1 for seed oil. The stearic acid contents of the BC 1 F 3 ‐derived lines generally were less than those of their donor parent, which indicated that modifying genes may influence this character.
Arabidopsis LEAFY COTYLEDON2 induces maturation traits and auxin activity: Implications for somatic embryogenesis (2008)

LEAFY COTYLEDON2 (LEC2) is a central regulator of embryogenesis sufficient to induce somatic cells to form embryos when expressed ectopically. Here, we analyze the cellular processes induced by LEC2, a B3 domain transcription factor, that may underlie its ability to promote somatic embryogenesis. We show auxin-responsive genes are induced after LEC2 activation in seedlings. Genes encoding enzymes involved in auxin biosynthesis, YUC2 and YUC4, are activated within 1 h after induction of LEC2 activity, and YUC4 appears to be a direct transcriptional target of LEC2. We also show ectopic LEC2 expression induces accumulation of seed storage protein and oil bodies in vegetative and reproductive organs, events that normally occur during the maturation phase of embryogenesis. Furthermore, LEC2 activates seed protein genes before an increase in RNAs encoding LEC1 or FUS3 is observed. Thus, LEC2 causes rapid changes in auxin responses and induces cellular differentiation characteristic of the maturation phase. The relevance of these changes to the ability of LEC2 to promote somatic embryogenesis is discussed.
In vitro trans-differentiation of adult hepatic stem cells into pancreatic endocrine hormone-producing cells (2002)

Although organ-specific stem cells possess plasticity that permit differentiation along new lineages, production of endocrine pancreas and insulin-secreting beta cells from adult nonpancreatic stem cells has not been demonstrated. We present evidence that highly purified adult rat hepatic oval "stem" cells, which are capable of differentiation to hepatocytes and bile duct epithelium, can trans-differentiate into pancreatic endocrine hormone-producing cells when cultured in a high-glucose environment. These differentiated cells can self-assemble to form three-dimensional islet cell-like clusters that express pancreatic islet cell differentiation-related transcripts detectable by reverse transcription-PCR/nested PCR (e.g., PDX-1, PAX-4, PAX-6, Nkx2.2 and Nkx6.1, insulin I, insulin II, glucose transporter 2, and glucagon) and islet-specific hormones detectable by immunocytochemistry (e.g., insulin, glucagon, and pancreatic polypeptide). In addition, these cells concomitantly lose expression of the hepatocyte protein Hep-par. When stimulated with glucose, these cells synthesize and secrete insulin, a response enhanced by nicotinamide. In a pilot study, the oval cell-derived islet cell-like clusters displayed the ability to reverse hyperglycemia in a diabetic NOD-scid mouse. These results indicate that primary adult liver stem cells can differentiate in a nonlineage-restricted manner. Trans-differentiation into endocrine pancreas could have significant implications for future therapies of diabetes.
Sugar Sensing and Signaling in Plants (2002)

In addition to their essential roles as substrates in carbon and energy metabolism and in polymer biosynthesis, sugars have important hormone-like functions as primary messengers in signal transduction. The pivotal role of sugars as signaling molecules is well illustrated by the variety of sugar
Latest views of the sparse Radon transform (2003)

Abstract The Radon transform (RT) suffers from the typical problems of loss of resolution and aliasing that arise as a consequence of incomplete information, including limited aperture and discretization. Sparseness in the Radon domain is a valid and useful criterion for supplying this missing information, equivalent somehow to assuming smooth amplitude variation in the transition between known and unknown (missing) data. Applying this constraint while honoring the data can become a serious challenge for routine seismic processing because of the very limited processing time available, in general, per common midpoint. To develop methods that are robust, easy to use and flexible to adapt to different problems we have to pay attention to a variety of algorithms, operator design, and estimation of the hyperparameters that are responsible for the regularization of the solution. In this paper, we discuss fast implementations for several varieties of RT in the time and frequency domains. An iterative conjugate gradient algorithm with fast Fourier transform multiplication is used in all cases. To preserve the important property of iterative subspace methods of regularizing the solution by the number of iterations, the model weights are incorporated into the operators. This turns out to be of particular importance, and it can be understood in terms of the singular vectors of the weighted transform. The iterative algorithm is stopped according to a general cross validation criterion for subspaces. We apply this idea to several known implementations and compare results in order to better understand differences between, and merits of, these algorithms.
Identification of Interleukin 1 Receptor-associated Kinase as a Conserved Component in the p75-Neurotrophin Receptor Activation of Nuclear Factor-κB (2002)

The neurotrophin nerve growth factor (NGF) supports neuronal survival by activating the transcription factor nuclear factor-kappaB (NF-kappaB). We report here, for the first time, the identification of p75-associated kinase that mediates NGF-driven NF-kappaB activation. Using co-immunoprecipitation, we demonstrate an NGF-dependent association of interleukin 1 receptor-associated kinase (IRAK) with the p75 neurotrophin receptor in PC12 cells. Our results reveal that IRAK is recruited to the p75-NGF receptor leading to formation of a complex between IRAK, atypical protein kinase C interacting protein, p62, and TRAF6. Activation of NF-kappaB occurs predominantly through the p75 receptor, and TrkA activity suppresses NF-kappaB activation and retards IkappaBbeta degradation. In addition, we observe a requirement for the kinase activity of IRAK in mediating NGF-induced NF-kappaB activation, recruitment of the adapter protein p62 to the p75 receptor, and cell survival. Moreover, p75-IRAK-mediated kappaB activation and the recruitment of IKKbeta, but not IKKalpha, to the receptor require p62. Altogether, our data provide novel information regarding the proximal components involved in p75 receptor signaling and underscore the importance of the atypical PKC interacting protein p62 in this process.
Determining service dependencies in distributed systems (2002)

We describe an architecture and its implementation for retrieving and handling dependency information from various managed resources in a Web-based environment. The core of our architecture is a dependency query facility that allows the application of queries and filters to dependency models; its output is a consolidated dependency graph that can then be used as input for event correlators and various management applications to display service topologies or to perform additional problem determination tasks. The definition of an XML-based notation for specifying dependencies facilitates the sharing of information between the various components involved in the process.
Role of ADP-Ribosyltransferase Activity of Pertussis Toxin in Toxin-Adhesin Redundancy with Filamentous Hemagglutinin duringBordetella pertussisInfection (2001)

Pertussis toxin (PT) and filamentous hemagglutinin (FHA) are two major virulence factors of Bordetella pertussis. FHA is the main adhesin, whereas PT is a toxin with an A-B structure, in which the A protomer expresses ADP-ribosyltransferase activity and the B moiety is responsible for binding to the target cells. Here, we show redundancy of FHA and PT during infection. Whereas PT-deficient and FHA-deficient mutants colonized the mouse respiratory tract nearly as efficiently as did the isogenic parent strain, a mutant deficient for both factors colonized substantially less well. This was not due to redundant functions of PT and FHA as adhesins, since in vitro studies of epithelial cells and macrophages indicated that FHA, but not PT, acts as an adhesin. An FHA-deficient B. pertussis strain producing enzymatically inactive PT colonized as poorly as did the FHA-deficient, PT-deficient strain, indicating that the ADP-ribosyltransferase activity of PT is required for redundancy with FHA. Only strains producing active PT induced a local transient release of tumor necrosis factor alpha (TNF-alpha), suggesting that the pharmacological effects of PT are the basis of the redundancy with FHA, through the release of TNF-alpha. This may lead to damage of the pulmonary epithelium, allowing the bacteria to colonize even in the absence of FHA.