gebhart/patrepeval huggingface dataset:
Potential Antiatherogenic Mechanisms of Ascorbate (Vitamin C) and α-Tocopherol (Vitamin E) (2000)

The premise that oxidative stress, among several other factors, plays an important role in atherogenesis implies that the development and progression of atherosclerosis can be inhibited by antioxidants. In this minireview we discuss several mechanisms by which the antioxidants ascorbate (vitamin C) and alpha-tocopherol (vitamin E) may protect against atherosclerosis. These mechanisms include inhibition of LDL oxidation and inhibition of leukocyte adhesion to the endothelium and vascular endothelial dysfunction. Overall, ascorbate appears to be more effective than alpha-tocopherol in mitigating these pathophysiological processes, most likely as a result of its abilities to effectively scavenge a wide range of reactive oxygen and nitrogen species and to regenerate alpha-tocopherol, and possibly tetrahydrobiopterin, from its radical species. In contrast, alpha-tocopherol can act either as an antioxidant or a pro-oxidant to inhibit or facilitate, respectively, lipid peroxidation in LDL. However, this pro-oxidant activity of alpha-tocopherol is prevented by ascorbate acting as a coantioxidant. Therefore, an optimum vitamin C intake or body status may help protect against atherosclerosis and its clinical sequelae, whereas vitamin E may only be effective in combination with vitamin C.
Molecular Cloning of Translocation t(1;14)(q21;q32) Defines a Novel Gene (BCL9) at Chromosome 1q21 (1998)

Abnormalities of chromosome 1q21 are common in B-cell malignancies and have been associated with a poor response to therapy. The nature of the involved gene(s) on chromosome 1q21 remains unknown. A cell line (CEMO-1) has recently been established from a patient with precursor-B-cell acute lymphoblastic leukemia (ALL), which exhibited a t(1;14)(q21;q32). To identify the gene involved in this translocation, we have cloned both rearranged IGHJ alleles using long-distance inverse polymerase chain reaction (LDI-PCR). Two IGHJ fragments were amplified from CEMO-1 DNA and sequenced. One allele showed novel sequences upstream of JH5 with no homology to either IGH or any other sequences on the databases. Using a single-copy Xho I fragment immediately 5' of JH5, PAC clones were isolated and mapped to chromosome 1q21 on normal metaphases by fluorescence in situ hybridization (FISH), confirming that this allele represented the t(1;14)(q21;q32) breakpoint. Sequence analysis of the 1q21 Xho I fragment showed identity with an expressed sequence tag (EST), and this probe was therefore used to probe Northern blots. Two transcripts of 6.3 kb and 4.2 kb expressed at low level in mRNA from all tissues were detected: a third transcript of 1.6 kb was expressed only in thymus, spleen, and small intestine. Full-length BCL9 cDNA clones were obtained from a normal human fetal brain cDNA library supplemented by 5' and 3' RACE. Sequence analysis predicted a protein of 1394 amino acids containing 18% proline, 11% glycine, 11% serine, and 6% methionine, but no recognizable protein motifs or significant homologies to any other known proteins. The CEMO-1 1q21 breakpoint fell within the 3' UTR of the BCL9 gene. Low-level expression of BCL9 was detected in Epstein-Barr virus-transformed normal B cells by Northern blot; in contrast, abundant BCL9 expression was observed in CEMO-1, indicating that deregulated expression of this gene was one pathological consequence of the translocation. Screening of a panel of 39 B-cell malignancies with 1q abnormalities by Southern blot showed one additional case with a breakpoint in the 3' UTR of BCL9, indicating that this was a recurrent breakpoint. FISH analysis using an 850-kb YAC spanning BCL9 identified a further case with t(1;22)(q21;q11) causing juxtaposition of BCL9 to the IGlambda locus. Other breakpoints were heterogeneous, falling both centromeric (10 cases) and telomeric (10 cases) of the BCL9 gene. These data suggest that BCL9 may be the target of translocation in some B-cell malignancies with abnormalities of 1q21 and that deregulated BCL9 expression may be important in their pathogenesis.
Eosinophils: ‘new’ roles for ‘old’ cells (2004)

Prominent blood and tissue eosinophilia is manifested in a number of inflammatory states, particularly in allergic diseases. Eosinophils are a source of numerous cytokines and growth factors, thus in principle they can display both pro-inflammatory and anti-inflammatory activities as well as immunoregulatory ones. In this review, we will discuss the cross-talk between eosinophils and other cell types that they come in contact with in the inflammatory milieu, such as mast cells, fibroblasts and endothelial cells. 'New' roles for eosinophils in cancer and novel activatory signals will also be described.
Antiviral Drugs for the Control of Pandemic Influenza Virus (2008)

In the advent of an influenza virus pandemic it is likely that the administration of antiviral drugs will be an important first line of defence against the virus. The drugs currently in use are effective against seasonal influenza virus infection, and some cases have been used in the treatment of patients infected with the avian H5N1 influenza virus. However, it is becoming clear that the emergence of drug-resistant viruses will potentially be a major problem in the future efforts to control influenza virus infection. In addition, during a new pandemic, sufficient quantities of these agents will need to be distributed to many different parts of the world, possibly at short notice. In this review we provide an overview of some of the drugs that are currently available for the treatment and prevention of influenza virus infection. In addition, basic research on influenza virus is providing a much better understanding of the biology of the virus, which is offering the possibility of new anti-influenza virus drugs. We therefore also review some new antiviral strategies that are being reported in the scientific literature, which may form the basis of the next generation of antiviral strategies during a future influenza virus pandemic.
PECAM-1 Ligation Negatively Regulates TLR4 Signaling in Macrophages (2007)

Uncontrolled TLR4 signaling may induce excessive production of proinflammatory cytokines and lead to harmful inflammation; therefore, negative regulation of TLR4 signaling attracts much attention now. PECAM-1, a member of Ig-ITIM family, can mediate inhibitory signals in T cells and B cells. However, the role and the mechanisms of PECAM-1 in the regulation of TLR4-mediated LPS response in macrophages remain unclear. In this study, we demonstrate that PECAM-1 ligation with CD38-Fc fusion protein negatively regulates LPS-induced proinflammatory cytokine TNF-alpha, IL-6, and IFN-beta production by inhibiting JNK, NF-kappaB, and IFN regulatory factor 3 activation in macrophages. In addition, PECAM-1 ligation-recruited Src homology region 2 domain-containing phosphatase 1 (SHP-1) and Src homology region 2 domain-containing phosphatase 2 (SHP-2) may be involved in the inhibitory effect of PECAM-1 on TLR4 signaling. Consistently, silencing of PECAM-1 enhances the macrophage response to LPS stimulation. Taken together with the data that PECAM-1 is constitutively expressed in macrophages and its expression is up-regulated by LPS stimulation, PECAM-1 might function as a feedback negative regulator of LPS inflammatory response in macrophages. This study may provide a potential target for intervention of inflammatory diseases.
Crystal Structure of PG16 and Chimeric Dissection with Somatically Related PG9: Structure-Function Analysis of Two Quaternary-Specific Antibodies That Effectively Neutralize HIV-1 (2010)

HIV-1 resists neutralization by most antibodies. Two somatically related human antibodies, PG9 and PG16, however, each neutralize 70 to 80% of circulating HIV-1 isolates. Here we present the structure of the antigen-binding fragment of PG16 in monoclinic and orthorhombic lattices at 2.4 and 4.0 A, respectively, and use a combination of structural analysis, paratope dissection, and neutralization assessment to determine the functional relevance of three unusual PG9/PG16 features: N-linked glycosylation, extensive affinity maturation, and a heavy chain-third complementarity-determining region (CDR H3) that is one of the longest observed in human antibodies. Glycosylation extended off the side of the light chain variable domain and was not required for neutralization. The CDR H3 formed an axe-shaped subdomain, which comprised 42% of the CDR surface, with the axe head looming approximately 20 A above the other combining loops. Comprehensive sets of chimeric swaps between PG9 and PG16 of light chain, heavy chain, and CDR H3 were employed to decipher structure-function relationships. Chimeric swaps generally complemented functionally, with differences in PG9/PG16 neutralization related primarily to residue differences in CDR H3. Meanwhile, chimeric reversions to genomic V genes showed isolate-dependent effects, with affinity maturation playing a significant role in augmenting neutralization breadth (P = 0.036) and potency (P < 0.0001). The structural and functional details of extraordinary CDR H3 and extensive affinity maturation provide insights into the neutralization mechanism of and the elicitation pathway for broadly neutralizing antibodies like PG9 and PG16.
Anisotropic epitaxial lateral growth in GaN selective area epitaxy (1997)

Epitaxial lateral mask overgrowth which occurs during GaN selective epitaxy has been studied using linear mask features. The lateral growth varies between its maximum and minimum over a 30° angular span and exhibits hexagonal symmetry. Vertical growth follows an opposite trend, with lateral growth maxima, and vertical growth minima occurring for lines parallel to the GaN 〈10•0〉. Large variations in the lateral growth are also obtained through variations in the growth temperature and NH3 flow. Under proper growth conditions, lateral to vertical growth rate ratios of up to 4.1 can be achieved, resulting in significant lateral mask overgrowth and coalescence of features without excessive growth times.
Air Stable, Sterically Hindered Ferrocenyl Dialkylphosphines for Palladium-Catalyzed C−C, C−N, and C−O Bond-Forming Cross-Couplings (2002)

Pentaphenylferrocenyl di-tert-butylphosphine has been prepared in high yield from a two-step synthetic procedure, and the scope of various cross-coupling processes catalyzed by complexes bearing this ligand has been investigated. This ligand creates a remarkably general palladium catalyst for aryl halide amination and for Suzuki coupling. Turnovers of roughly 1000 were observed for aminations with unactivated aryl bromides or chlorides. In addition, complexes of this ligand catalyzed the formation of selected aryl ethers under mild conditions. The reactions encompassed electron-rich and electron-poor aryl bromides and chlorides. In the presence of catalysts containing this ligand, these aryl halides coupled with acyclic or cyclic secondary alkyl- and arylamines, with primary alkyl- and arylamines, and with aryl- and primary alkylboronic acids. These last couplings provide the first general procedure for reaction of terminal alkylboronic acids with aryl halides without toxic or expensive bases. The ligand not only generates highly active palladium catalysts, but it is air stable in solution and in the solid state. Palladium(0) complexes of this ligand are also air stable as a solid and react only slowly with oxygen in solution.
Applications of spin dependent transport materials (1999)

Newly developed materials that exhibit large changes in effective resistance with applied fields are being put to practical use. Magnetic multilayers with giant magnetoresistance (GMR) and spin dependent tunnelling (SDT) structures are being used in magnetic field sensors. Spin valves are being sold in read heads for hard drives and galvanic isolators. Both spin valves and SDT structures are being used in non-volatile random access memory development. After a brief introduction to these materials, the development of their uses in sensors, read heads, isolators and non-volatile memory are summarized. GMR magnetic field sensors represent a small, but growing market. SDT sensors have the potential to sense very small fields (to 1 pT). Spin valve read heads have enabled very high aerial packing densities for hard drives, up to 24 Gbits per square inch. GMR isolators can be used to duplicate the function of opto-isolators, but at much higher speeds and packing densities. Application of these materials to non-volatile random access memory could result in speeds and densities of semiconductor memory with the non-volatility of hard disk drives. Future directions in this field indicate a merging of semiconductor and these new magnetic materials.
Recovery of Red Fluorescent Protein Chromophore Maturation Deficiency through Rational Design (2012)

Red fluorescent proteins (RFPs) derived from organisms in the class Anthozoa have found widespread application as imaging tools in biological research. For most imaging experiments, RFPs that mature quickly to the red chromophore and produce little or no green chromophore are most useful. In this study, we used rational design to convert a yellow fluorescent mPlum mutant to a red-emitting RFP without reverting any of the mutations causing the maturation deficiency and without altering the red chromophore's covalent structure. We also created an optimized mPlum mutant (mPlum-E16P) that matures almost exclusively to the red chromophore. Analysis of the structure/function relationships in these proteins revealed two structural characteristics that are important for efficient red chromophore maturation in DsRed-derived RFPs. The first is the presence of a lysine residue at position 70 that is able to interact directly with the chromophore. The second is an absence of non-bonding interactions limiting the conformational flexibility at the peptide backbone that is oxidized during red chromophore formation. Satisfying or improving these structural features in other maturation-deficient RFPs may result in RFPs with faster and more complete maturation to the red chromophore.
Infection studies on human cell lines with porcine circovirus type 1 and porcine circovirus type 2 (2004)

Although PCV gene expression and replication took place in human cells, the infection is non-productive. Alteration of protein localization suggests that protein targeting may be disturbed in human cells.
Error Control Systems for Digital Communication and Storage (1995)

1. Error Control Coding for Digital Communication Systems. 2. Galois Fields. 3. Polynomials over Galois Fields. 4. Linear Block Codes. 5. Cyclic Codes. 6. Hadamard, Quadratic Residue, and Golay Codes. 7. Reed-Muller Codes 8. BCH and Reed-Solomon Codes. 9. Decoding BCH and Reed-Solomon Codes. 10. The Analysis of the Performance of Block Codes. 11. Convolutional Codes. 12. The Viterbi Decoding Algorithm. 13. The Sequential Decoding Algorithms. 14. Trellis Coded Modulation. 15. Error Control for Channels with Feedback. 16. Applications. Appendices: A. Binary Primitive Polynomials. B. Add-on Tables and Vector Space Representations for GF(8) Through GF(1024). C. Cyclotronic Cosets Modulo 2m-1. D. Minimal Polynomials for Elements in GF (2m). E. Generator Polynomials of Binary BCH Codes of Lengths Through 511. Bibliography.
Antiangiogenic treatment with thrombospondin-1 enhances primary tumor radiation response and prevents growth of dormant pulmonary micrometastases after curative radiation therapy in human melanoma xenografts. (2003)

Thrombospondin-1 (TSP-1) is a potent antiangiogenic factor that has been shown to inhibit tumor growth by preventing endothelial cells from responding to a wide variety of angiogenic stimulators. We have demonstrated previously that D-12 primary tumors (human melanoma xenografts) suppress the growth of their spontaneous pulmonary micrometastases by secreting TSP-1 into the blood circulation. The same tumor model was used in the present work to study antitumor effects of combined radiation therapy and antiangiogenic treatment with TSP-1. Curative radiation treatment of D-12 primary tumors resulted in rapid growth of previously dormant micrometastases. Growth of dormant micrometastases could be prevented by treating the host mice with exogenous TSP-1 after the radiation treatment. Treatment with exogenous TSP-1 after subcurative radiation treatment reduced the growth rate of recurrent primary tumors in addition to suppressing metastatic growth. TSP-1 suppressed tumor growth at both primary and metastatic sites by inducing apoptosis in tumor-associated microvascular endothelial cells. Treatment with exogenous TSP-1 before radiation treatment enhanced the antitumor effect of the radiation treatment. The radiopotentiation by TSP-1 involved at least two distinctly different mechanisms, i.e., TSP-1 reduced the fraction of radiobiologically hypoxic parenchymal tumor cells and increased the radiation sensitivity of the tumor microvasculature by promoting radiation-induced endothelial cell apoptosis. In conclusion, the present preclinical study showed that TSP-1 has antiangiogenic, antimetastatic, and radiopotentiating properties that merit additional investigation in clinical studies.
Antiproliferative Effects of a Series of Cyclic Imides on Primary Endothelial Cells and a Leukemia Cell Line (2008)

The present study describes the cytotoxic properties of a series of 15 cyclic imides observed against different endothelial cells and K562 leukemic cells. Initially, eight structurally unrelated compounds were evaluated against cultured bone marrow endothelial cells (BMEC) and human umbilical vein endothelial cells (HUVEC). Only two imides showed cytotoxic activity at 10 microM. In continuation of our screening, eight compounds, structurally related to the compound with the higher cytotoxic activity, were assayed against endothelial cells and the K562 leukemic cell line. All of these new compounds except two exhibited cytotoxic and antiproliferative activities at concentrations below 10 microM against BMEC and HUVEC, respectively. The K562 leukemia cell line was only affected by concentrations of 100 microM. Preliminary SAR analysis indicated that the cytotoxic activity of these compounds was related to the presence of a planar imide ring directly bound to an aromatic ring.
Accuracy evaluation of a 3D ultrasound-based neuronavigation system (2002)

We have investigated the 3D navigation accuracy of a frameless ultrasound-based neuronavigation system (SonoWand) for surgical planning and intraoperative image guidance. In addition, we present a detailed description and review of the error sources associated with surgical neuronavigation based on preoperative MRI data and intraoperative ultrasound. A phantom with 27 precisely defined points was scanned with ultrasound by various translation and tilt movements of the ultrasound probe (180 3D scans in total), and the 27 image points in each volume were located using an automatic detection algorithm. These locations were compared to the physically measured locations of the same 27 points. The accuracy of the neuronavigation system and the effect of varying acquisition conditions were found through a thorough statistical analysis of the differences between the two point sets. The accuracy was found to be 1.40 +/- 0.45 mm (arithmetic mean) for the ultrasound-based neuronavigation system in our laboratory setting. Improper probe calibration was the major contributor to this figure. Based on our extensive data set and thorough evaluation, the accuracy found in the laboratory setting is expected to be close to the overall clinical accuracy for ultrasound-based neuronavigation. Our analysis indicates that the overall clinical accuracy may be as low as 2 mm when using intraoperative imaging to compensate for brain shift.
Spermatogenesis in birds. (1993)

It is concluded that in the birds which have been studied there is a well-defined, regular cycle of the seminiferous epithelium, and that spermatogenesis involves synchronization of the activities of germ cells within and between successive generations to produce cellular associations of the seminiferous epithelium which are essentially similar to those described in mammals. However, the area of a cellular association is smaller in birds than in most (and probably all) mammals so that numerous cellular associations are present in a cross-section of a seminiferous tubule. As in primates, in which a cellular association also covers a small area of seminiferous tubule, the wave of spermatogenesis in the Japanese quail follows a spiral path along and around a seminiferous tubule with consecutive stages of the cycle always occurring as adjacent stages along the tubule. The literature indicates that there are fewer mitotic divisions during spermatogonial proliferation in birds than has been reported for mammals and it is suggested that this difference explains the difference between birds and mammals in the area occupied by a cellular association. Work on the Japanese quail indicates that stem cell renewal and spermatogonial proliferation is simpler in the quail than has been described in some mammals. In the quail, both processes occur in the same compartment of the seminiferous epithelium and are synchronized with subsequent phases of spermatogenesis, and there does not seem to be a reserve pool of non-proliferating stem spermatogonia in the quail as has been reported for some mammals. Findings to date also indicate that spermatogenesis in birds is four times faster and produces four times the number of spermatozoa/g testis than in mammals, and that this difference is associated with a faster transit and poorer survival of spermatozoa in the male extragonadal ducts of birds than mammals. These differences between birds and mammals are interpreted as a response to selection pressure due to competition between males to inseminate partners frequently in order to provide the most viable spermatozoa at the site of fertilization when ova are ready for fertilization. In this respect, it is suggested that sperm production in birds and mammals have progressed along different lines of evolutionary development due to differences in ovulatory pattern and mating system. In particular, the high sperm production of birds is associated with the need to mate a (usually monogamous) partner numerous times a day over a period of days or weeks when a clutch of eggs is laid.(ABSTRACT TRUNCATED AT 400 WORDS)
Reconstitution of two isoforms of the human interleukin‐11 receptor and comparison of their functional properties (1997)

Long-term stable Ba/F3 transfectants (B13R alpha1 and B13R alpha2) expressing two isoforms of the human IL-IIR alpha receptor (alpha1 full length or alpha2 lacking the cytoplasmic domain) in combination with human gp130 were established. IL-11R alpha1 and IL-11R alpha2 were each expressed and detected as three bands upon Western blot analysis, with apparent molecular masses in agreement with those of the polypeptide backbone (47 and 44 kDa, respectively) with no, one or two N-linked sugars. B13R alpha1 and B13R alpha2 bound IL-11-thioredoxin with similar efficiencies and proliferated with superimposable dose-response curves to IL-11, demonstrating that the intracellular domain of IL-11R alpha has no significant contribution on ligand binding and signaling. Analysis of a set of anti-human gp130 mAbs confirmed the similar responsiveness of B13R alpha1 and B13R alpha2 transfectants.
In silico design, construction and cloning of Trastuzumab humanized monoclonal antibody: A possible biosimilar for Herceptin (2012)

This study was based on a recently developed technology for mAb expression in mammalian cells. The obtained constructs could be successfully used for biosimilar recombinant mAb production in CHO DG44 dihydrofolate reductase (DHFR) gene deficient cell line in the suspension culture medium.