gebhart/patrepeval huggingface dataset:
Butyryl-CoA dehydrogenase from Megasphaera elsdenii. Specificity of the catalytic reaction (1984)

The absorption coefficient of butyryl-CoA dehydrogenase from Megasphaera elsdenii at 450 nm is determined as 14.4 mM-1 X cm-1 in the CoA-free form and 14.2 mM-1 X cm-1 in the CoA-liganded form (both yellow). The latter value is considerably higher than the earlier published estimate. Phenazine ethosulphate offers great advantages over phenazine methosulphate as a coupling dye in the catalytic assay despite giving lower Vmax. values (506 min-1 as compared with 1250 min-1 under the conditions used). The phenazine ethosulphate assay is used to establish a pH optimum of 8.05 for oxidation of 100 microM-butyryl-CoA. The rates of oxidation of a range of straight-chain, branched-chain and alicyclic acyl thioesters are used to provide the following information. Only straight-chain acyl groups containing 4-6 carbon atoms are easily accommodated by the postulated hydrophobic pocket of the enzyme. C-3-substituted acyl-CoA thioesters are not oxidized at a significant rate, suggesting that the C-3 pro-S-hydrogen atom of straight-chain substrates is partially exposed to the solvent. Acyl-CoA thioesters with substitutions at C-2 are oxidized, though at a lower rate than their straight-chain counterparts. This implies that the C-2 pro-S-hydrogen atom of straight-chain substrates is partially exposed to the solvent. Saturated alicyclic carboxylic acyl-CoA thioesters with 4-7 carbon atoms in the ring are oxidized, with maximal activity for the cyclohexane derivative. This implies that optimal oxidation requires a true trans orientation of the two departing hydrogen atoms. The strain imposed by bound unsaturated alicyclic acyl thioesters strikingly perturbs the flavin visible-absorption spectrum, with the exception of the cyclohex-2-ene derivative, which forms a complex with similar spectral properties to those of the crotonyl-CoA complex. In the thiol moiety of thioester substrates the amide bond of N-acetylcysteamine is essential for both binding and catalysis. The adenosine structure contributes substantially to strong binding, but is less important in determining the catalytic rate.
Relationship between vitamin D status, parathyroid hormone levels and bone mineral density in patients with chronic kidney disease stages 3 and 4 (2007)

Vitamin D insufficiency and deficiency are very common in CKD stages 3 and 4 population and may indirectly affect, via effects on iPTH, the BMD of these patients.
P2X1 Purinoceptor in Human Platelets (1998)

ADP is an important physiological platelet agonist. The molecular identity of the ADP receptor(s) in human platelets, however, is still unclear. Although P2T purinoceptor was believed to be the ligand-gated cation channel for ADP in human platelets, recent patch clamp studies now suggest it is P2X1 type. In the present study, we have cloned a cDNA encoding a P2X1 purinoceptor from human platelets using degenerate reverse transcription and polymerase chain reaction. Northern blotting with a P2X1-specific probe revealed a band of 1.8 kilobases in human platelets as well as in several megakaryoblastic cell lines. 1321N1 human astrocytoma cells expressing the cloned P2X1 cDNA exhibited both ATP- and ADP-stimulated Ca2+ influx that could be blocked by the purinoceptor antagonist pyridoxalphosphate-6-azophenyl-2',4'-disulfonic acid and suramin. Additionally, a polyclonal antibody raised against glutathione-S-transferase-P2X1 fusion peptide reacted with a 70-kDa band on Western blot of human platelets. It is therefore concluded that functional P2X1 purinoceptors are present in human platelets.
Fundamentals of Wireless Communication (2005)

The past decade has seen many advances in physical layer wireless communication theory and their implementation in wireless systems. This textbook takes a unified view of the fundamentals of wireless communication and explains the web of concepts underpinning these advances at a level accessible to an audience with a basic background in probability and digital communication. Topics covered include MIMO (multi-input, multi-output) communication, space-time coding, opportunistic communication, OFDM and CDMA. The concepts are illustrated using many examples from real wireless systems such as GSM, IS-95 (CDMA), IS-856 (1 x EV-DO), Flash OFDM and UWB (ultra-wideband). Particular emphasis is placed on the interplay between concepts and their implementation in real systems. An abundant supply of exercises and figures reinforce the material in the text. This book is intended for use on graduate courses in electrical and computer engineering and will also be of great interest to practising engineers
Suppression of Radixin and Moesin Alters Growth Cone Morphology, Motility, and Process Formation In Primary Cultured Neurons (1998)

In this study we have examined the cellular functions of ERM proteins in developing neurons. The results obtained indicate that there is a high degree of spatial and temporal correlation between the expression and subcellular localization of radixin and moesin with the morphological development of neuritic growth cones. More importantly, we show that double suppression of radixin and moesin, but not of ezrin-radixin or ezrin-moesin, results in reduction of growth cone size, disappearance of radial striations, retraction of the growth cone lamellipodial veil, and disorganization of actin filaments that invade the central region of growth cones where they colocalize with microtubules. Neuritic tips from radixin-moesin suppressed neurons displayed high filopodial protrusive activity; however, its rate of advance is 8-10 times slower than the one of growth cones from control neurons. Radixin-moesin suppressed neurons have short neurites and failed to develop an axon-like neurite, a phenomenon that appears to be directly linked with the alterations in growth cone structure and motility. Taken collectively, our data suggest that by regulating key aspects of growth cone development and maintenance, radixin and moesin modulate neurite formation and the development of neuronal polarity.
Studies of the cell surface of mouse dendritic cells and other leukocytes (1981)

The surface of dendritic cells (DC) has been analyzed by means of monoclonal antibodies (Ab) and lactoperoxidase (LPO)-mediated radioiodination. Antigens and other exteriorily disposed polypeptides of purified spleen DC were compared with those of tissue macrophages (Mphi), monocytes, and other bone marrow-derived elements. Quantitative binding studies and autoradiography with (125)I-Ab established that DC expressed high levels of I-A and H-2D, 2 x 10(5) and 1 x 10(5) Ab binding sites per cell, respectively. DC from conventional, germ-free, and specific pathogen-free mice were all rich in Ia. Expression of Ia on B cells was 5-10 percent of that on DC and increased fivefold during lipopolysaccharide mitogenesis. More than 70-90 percent of purified Mphi and monocytes from specific pathogen-free mice were Ia negative, but increased levels of Ia were noted on cells from mice reared under conventional conditions. Thus large amounts of Ia on DC is a constitutive trait, whereas the expression of Ia by other cell types may be governed by the environmental and immunological status of the host. The 2.4G2 Fc receptor Ag was not detected on DC. Peritoneal and spleen Mphi had 10(5) 2.4G2 binding sites/cell, whereas monocytes and lymphocytes were less reactive (1 x 10(4)-3 x 10(4) binding sites/cell). Four other Mphi-related antigens were evaluated. Each had a distinctive tissue distribution and none bound exclusively to Mphi and monocytes. Neither 1.21J (Mac-1) nor F4/80 reacted with DC. Immunoprecipitation studies of externally ((125)I) and biosynthetically ([(35)S]methionine)dabeled cells confirmed the binding data. Sensitive binding assays with (125)I-Ab confirmed previous observations that DC lack Ig and Thy-1. Lyt-1 was also not found on DC, but 5-12 percent of the cells in purified DC preparations expressed both Lyt-2 and Ia. All DC expressed the leukocyte common antigens at levels similar to other leukocytes. The spectrum of surface polypeptides labeled by LPO-mediated iodination was different on Mphi, DC, and lymphocytes. Polypeptides migrating at molecular weights of 155,000, 85,000, and 62,000 appeared to be restricted to DC. These observations establish that the cell surface of DC differs considerably from other leukocytes, including the blood monocyte, and suggest that the DC is part of a unique Ia-rich leukocyte differentiation pathway.
Prognostic factors and response to therapy in breast cancer. (1993)

For the integration of new cell biological prognostic factors in daily clinical practice, we need to know not only their prognostic power with respect to prediction of relapse free and overall survival, but also their possible relation to response to endocrine therapy or chemotherapy in order to select adequate treatment for each patient. A large number of cell biological parameters are currently available to predict the prognosis of patients with breast cancer, but it is still difficult to predict the response to treatment accurately. A valuable prognostic factor can be a worthless predictive factor for endocrine therapy or chemotherapy, and vice versa. High tumour levels of ER, PGR, AR and PS2 protein predict a relatively good response to endocrine therapy, whereas EGFR positivity, HER2/neu positivity, aneuploidy, high proliferation indices and possibly high u-PA levels indicate a good chance of a poor response to endocrine therapy in metastatic breast cancer. With respect to chemotherapy, a high proliferation rate and HER2/neu amplification predict a good response to therapy in metastatic disease, whereas MDR gene expression and possibly c-myc amplification are related to a worse response. In conclusion, the newer cell biological parameters can be used to select high and low risk patients and type of systemic treatment and can be used as targets for new treatment modalities.
Complement sensitivity of erythrocytes in a patient with inherited complete deficiency of CD59 or with the Inab phenotype (1999)

We investigated the complement sensitivity of erythrocytes from three patients, one with inherited complete deficiency of CD59, one with the Inab phenotype, and one with paroxysmal nocturnal haemoglobinuria (PNH). The complement lysis sensitivity units on the erythrocytes were 11.7, 4.6, and 47.6 for inherited CD59 deficiency, Inab phenotype, and PNH, respectively. Two-colour flow cytometric analysis showed that the erythrocytes from the three patients consisted of a single population negative for CD59, negative for decay accelerating factor (DAF), and negative for both proteins, respectively. In addition, only the Inab phenotype patient had no haemolysis in vivo. These facts suggest that CD59 deficiency plays a more important role than DAF deficiency in complement-mediated haemolysis in vitro and in vivo, and that deficiency of both proteins, but not CD59 or DAF alone, causes complement sensitivity corresponding to that of PNH III erythrocytes in vitro.
HIV-1 tat gene induces tumor necrosis factor-beta (lymphotoxin) in a human B-lymphoblastoid cell line (1990)

The tat protein from human immunodeficiency virus type 1 (HIV-1) activates viral gene expression and is essential for HIV replication in vitro. It has also been shown that the tat gene product specifically inhibits antigen-induced proliferation of human peripheral blood lymphocytes. In order to understand the growth and immunomodulatory roles of HIV-1 tat, we have examined the effect of the tat gene on the expression of tumor necrosis factors in a human B-lymphoblastoid cell line (Raji). We report here that the HIV-1 tat gene introduced into Raji cells by retroviral-mediated transformation induces production of tumor necrosis factor-beta (TNF-beta). The tat-mediated induction of TNF-beta seems to be both at the transcriptional and post-transcriptional levels because, concurrent with a 30-fold increase in the levels of TNF-beta protein, an approximate 8-fold increase in mRNA was observed in tat-transformed Raji cells. It is recently reported that tat protein of HIV-1 stimulates growth of cells derived from Kaposi's sarcoma lesions of AIDS patients (Ensoli, B., Barillari, G., Salahuddin, S.Z., Gallo, R.C., and Wong-Staal, F. (1990) Nature 345, 84-86). Since TNF has been shown to function as a growth factor for several cell types, our results showing induction of TNF-beta by tat indicate the possibility that a growth-stimulatory role of HIV-1 tat on Kaposi's sarcoma cells is mediated through TNF-beta.
Computer Graphics, C Version (1996)

(NOTE: Each chapter concludes with a Summary, References and Exercises.) 1. A Survey of Computer Graphics. 2. Overview of Graphics Systems. 3. Output Primitives. 4. Attributes of Output Primitives. 5. Two-Dimensional Geometric Transformations. 6. Two-Dimensional Viewing. 7. Structures and Hierarchical Modeling. 8. Graphical User Interfaces and Interactive Input Methods. 9. Three-Dimensional Concepts. 10. Three-Dimensional Object Representations. 11. Three-Dimensional Geometric and Modeling Transformations. 12. Three-Dimensional Viewing. 13. Visible-Surface Detection Methods. 14. Illumination Models and Surface-Rendering Methods. 15. Color Models and Color Applications. 16. Computer Animation. Appendix A: Mathematics for Computer Graphics. Bibliography. Index.
Cloning and Chromosomal Mapping of Bovine Interleukin-2 Receptor Gamma Gene (1996)

Interleukin-2 receptor (IL-2R) gamma chain, a member of the cytokine receptor superfamily, forms a high-affinity receptor with IL-2R alpha and beta chains that plays an important role in interleukin-2 (IL-2) signal transduction. We have cloned and characterized the bovine IL-2Rgamma gene and corresponding cDNA. Bovine IL-2Rgamma is a single-copy gene that contains 8 exons and spans approximately 3.8 kb. The promoter region lacks conventional TATA and CCAAT consensus sites, but contains several regulatory elements that are recognition sites for the GATA binding proteins, AP-1 and AP-2. Physical assignment by fluorescence in situ hybridization (FISH) placed the bovine IL-2Rgamma gene on chromosome Xq23.
A survey of factor prophylaxis in the Canadian haemophilia A population (2004)

High-dose factor prophylaxis, defined as the infusion of 25-40 factor (F) VIII International Units (IU) kg bodyweight (bw)(-1)> or = x 3 per week, started at age 1-2 years of life in boys with severe haemophilia A prevents the development of significant bleed-related arthropathy. However, programmes of prophylaxis are very expensive and venous access is a challenge. To ascertain patterns of prophylaxis in Canada during the period of a global shortage of recombinant FVIII concentrate a survey was conducted in 2001. The response rate was 83% and the survey identified 247 inhibitor-negative haemophilia A cases receiving prophylaxis, defined as the regular administration of FVIII at least once weekly, from 14 Canadian haemophilia treatment centres. The median age of the group identified was 13 years (range: 1-65) and 95% of cases had severe haemophilia A defined by a circulating factor level of <1%. The median FVIII infusion dose was 26 (range: 16-33) IU kg(-1); infusions were administered > or = x 3 per week in 67% of cases. High-dose factor prophylaxis was used most frequently in boys <5 years of age (23 of 28 cases, 82%) as compared with 56% (56 of 100), 66% (40 of 61) and 62% (36 of 58) of males ages 5-12, 13-18 and >18 years. Prophylaxis accounted for 50% of the annual Canadian FVIII consumption and was a major driving force in the 10% increase (=19.3 million FVIII IU) in the FVIII consumption in Canada in the 4-year period 1999-2003. Given the economic implications of increased use of prophylaxis prospective studies are warranted to better define optimal prophylaxis regimens in the haemophilia A population.
Highly Sensitive Skin‐Mountable Strain Gauges Based Entirely on Elastomers (2012)

Abstract Quantifying naturally occurring strains in soft materials, such as those of the human body, requires strain gauges with equal or greater mechanical compliance. This manuscript reports materials and mechanics approaches are reported for an all‐elastomer strain measurement device with gauge factor as high as 29 and with Young's modulus that approaches that of the human epidermis. These systems use thin carbon‐black‐doped poly(dimethylsiloxane) (CB‐PDMS) for the strain gauges due to its high resistivity and strong dependence on strain, and thick carbon‐nanotube‐doped PDMS (CNT‐PDMS) for the interconnects due to its comparatively low resistivity and weak dependence on strain. Devices composed of molded, straight resistors of CB‐PDMS joined by serpentine‐shaped interconnects of CNT‐PDMS, both in a matrix substrate of PDMS, have electrical responses that depend almost entirely on the strain in the CB‐PDMS. Integrated structures of this type have Young's moduli of 244 kPa, which lies within the range of values for the human epidermis. Such sheets can be readily laminated on and form conformal contact to the human skin, with only modest mechanical constraints on natural motions. Strains measured in this mode on the wrist are between 11.2% and 22.6%.
Endocytic trafficking of megalin/RAP complexes: dissociation of the complexes in late endosomes. (1997)

Megalin (gp330) is a member of the low-density lipoprotein receptor gene family. Like other members of the family, it is an endocytic receptor that binds a number of specific ligands. Megalin also binds the receptor-associated protein (RAP) that serves as an exocytic traffic chaperone and inhibits ligand binding to the receptor. To investigate the fate of megalin/RAP complexes, we bound RAP glutathione-S-transferase fusion protein (RAP-GST) to megalin at the surface of L2 yolk sac carcinoma cells and followed the trafficking of the complexes by immunofluorescence and immunogold labeling and by their distribution on Percoll gradients. We show that megalin/RAP-GST complexes, which are internalized via clathrin-coated pits, are delivered to early endosomes where they accumulate during an 18 degrees C temperature block and colocalize with transferrin and transferrin receptor. Upon release from the temperature block, the complexes travel to late endosomes where they colocalize with rab7 and can be coprecipitated with anti-RAP-GST antibodies. Dissociation of the complex occurs in late endosomes and is most likely triggered by the low pH (approximately 5.5) of this compartment. RAP is then rapidly delivered to lysosomes and degraded whereas megalin is recycled to the cell surface. When the ligand, lipoprotein lipase, was bound to megalin, the receptor was found to recycle through early endosomes. We conclude that in contrast to receptor/ligand complexes, megalin/RAP complexes traffic through late endosomes, which is a novelty for members of the low-density lipoprotein receptor gene family.
Luminance-model-based DCT quantization for color image compression (1992)

A model is developed to approximate visibility thresholds for discrete cosine transform (DCT) coefficient quantization error based on the peak-to-peak luminance of the error image. Experimentally measured visibility thresholds for R, G, and B DCT basis functions can be predicted by a simple luminance-based detection model. This model allows DCT coefficient quantization matrices to be designed for display conditions other than those of the experimental measurements: other display luminances, other veiling luminances, and other spatial frequencies (different pixel spacings, viewing distances, and aspect ratios).
Behavior of Naphthoyloxyl and Methoxynaphthoyloxyl Radicals Generated from the Photocleavage of Dinaphthoyl Peroxides and 1-(Naphthoyloxy)-2-pyridones (2003)

Abstract 1-Naphthoyloxyl and 2-naphthoyloxyl radicals were generated from photocleavage of dinaphthoyl peroxides and 1-(naphthoyloxy)-2-pyridones in acetonitrile. The difference in product distribution between the precursors is ascribed to the contribution of the two-bond cleavage in the peroxide decomposition in the singlet state. A series of methoxynaphthoyloxyl radicals were also generated from the corresponding (methoxynaphthoyloxy)pyridones and their behavior was compared with that of unsubstituted naphthoyloxyl radicals. The introduction of a methoxy group in the naphthalene ring stabilizes the naphthoyloxyl radicals to prevent their decarboxylation completely and reduces remarkably their reactivities in the addition to olefins and hydrogen-atom abstraction. The structure of the naphthoyloxyl radicals was discussed on the basis of their absorption spectra and MO calculations.
Real value prediction of solvent accessibility from amino acid sequence (2003)

The solvent accessibility of amino acid residues has been predicted in the past by classifying them into exposure states with varying thresholds. This classification provides a wide range of values for the accessible surface area (ASA) within which a residue may fall. Thus far, no attempt has been made to predict real values of ASA from the sequence information without a priori classification into exposure states. Here, we present a new method with which to predict real value ASAs for residues, based on neighborhood information. Our real value prediction neural network could estimate the ASA for four different nonhomologous, nonredundant data sets of varying size, with 18.0-19.5% mean absolute error, defined as per residue absolute difference between the predicted and experimental values of relative ASA. Correlation between the predicted and experimental values ranged from 0.47 to 0.50. It was observed that the ASA of a residue could be predicted within a 23.7% mean absolute error, even when no information about its neighbors is included. Prediction of real values answers the issue of arbitrary choice of ASA state thresholds, and carries more information than category prediction. Prediction error for each residue type strongly correlates with the variability in its experimental ASA values.
XIST RNA paints the inactive X chromosome at interphase: evidence for a novel RNA involved in nuclear/chromosome structure. (1996)

The XIST gene is implicated in X chromosome inactivation, yet the RNA contains no apparent open reading frame. An accumulation of XIST RNA is observed near its site of transcription, the inactive X chromosome (Xi). A series of molecular cytogenetic studies comparing properties of XIST RNA to other protein coding RNAs, support a critical distinction for XIST RNA; XIST does not concentrate at Xi simply because it is transcribed and processed there. Most notably, morphometric and 3-D analysis reveals that XIST RNA and Xi are coincident in 2- and 3-D space; hence, the XIST RNA essentially paints Xi. Several results indicate that the XIST RNA accumulation has two components, a minor one associated with transcription and processing, and a spliced major component, which stably associates with Xi. Upon transcriptional inhibition the major spliced component remains in the nucleus and often encircles the extra-prominent heterochromatic Barr body. The continually transcribed XIST gene and its polyadenylated RNA consistently localize to a nuclear region devoid of splicing factor/poly A RNA rich domains. XIST RNA remains with the nuclear matrix fraction after removal of chromosomal DNA. XIST RNA is released from its association with Xi during mitosis, but shows a unique highly particulate distribution. Collective results indicate that XIST RNA may be an architectural element of the interphase chromosome territory, possibly a component of nonchromatin nuclear structure that specifically associates with Xi. XIST RNA is a novel nuclear RNA which potentially provides a specific precedent for RNA involvement in nuclear structure and cis-limited gene regulation via higher-order chromatin packaging.