gebhart/patrepeval huggingface dataset:
IVIg inhibits reticuloendothelial system function and ameliorates murine passive‐immune thrombocytopenia independent of anti‐idiotype reactivity (2001)

Although the mechanism of action of intravenous immunoglobulin (IVIg) in treating antibody-dependent thrombocytopenia remains unclear, most studies have suggested that IVIg blocks the function of Fc receptors in the reticuloendothelial system (RES) and/or the protective effect may be due to the presence of variable region-reactive (anti-idiotype) antibodies within IVIg. We evaluated the effect of IVIg on platelet counts in a murine model of passively induced immune thrombocytopenia (PIT). Although IVIg was unable to neutralize the binding of two platelet-specific monoclonal antibodies to their target antigens either in vivo or in vitro, it was able to prevent PIT as well as ameliorate pre-established PIT mediated by these antibodies. IVIg adsorbed against the antibody used to induce thrombocytopenia or endogenous murine immunoglobulin also protected against PIT, indicating that antibodies with anti-idiotype activity present in IVIg are not necessary for its effective treatment of PIT. IVIg significantly blocked the ability of the RES to clear antibody-sensitized red blood cells. F(ab')2 fragments of IVIg, which are unable to block the RES but retain the idiotypic regions, were ineffective at protecting mice from PIT. Our data suggest that IVIg exerts its rapid effect by inhibiting RES function and that anti-idiotype interactions are not required.
The tetratricopeptide repeat: a structural motif mediating protein-protein interactions (1999)

The tetratricopeptide repeat (TPR) motif is a protein-protein interaction module found in multiple copies in a number of functionally different proteins that facilitates specific interactions with a partner protein(s). Three-dimensional structural data have shown that a TPR motif contains two antiparallel alpha-helices such that tandem arrays of TPR motifs generate a right-handed helical structure with an amphipathic channel that might accommodate the complementary region of a target protein. Most TPR-containing proteins are associated with multiprotein complexes, and there is extensive evidence indicating that TPR motifs are important to the functioning of chaperone, cell-cycle, transcription, and protein transport complexes. The TPR motif may represent an ancient protein-protein interaction module that has been recruited by different proteins and adapted for specific functions. BioEssays 1999;21:932-939.
Routes to improving the reliability of low level DNA analysis using real-time PCR (2006)

Abstract Background Accurate quantification of DNA using quantitative real-time PCR at low levels is increasingly important for clinical, environmental and forensic applications. At low concentration levels (here referring to under 100 target copies) DNA quantification is sensitive to losses during preparation, and suffers from appreciable valid non-detection rates for sampling reasons. This paper reports studies on a real-time quantitative PCR assay targeting a region of the human SRY gene over a concentration range of 0.5 to 1000 target copies. The effects of different sample preparation and calibration methods on quantitative accuracy were investigated. Results At very low target concentrations of 0.5–10 genome equivalents (g.e.) eliminating any replicates within each DNA standard concentration with no measurable signal (non-detects) compromised calibration. Improved calibration could be achieved by eliminating all calibration replicates for any calibration standard concentration with non-detects ('elimination by sample'). Test samples also showed positive bias if non-detects were removed prior to averaging; less biased results were obtained by converting to concentration, including non-detects as zero concentration, and averaging all values. Tube plastic proved to have a strongly significant effect on DNA quantitation at low levels ( p = 1.8 × 10 -4 ). At low concentrations (under 10 g.e.), results for assays prepared in standard plastic were reduced by about 50% compared to the low-retention plastic. Preparation solution (carrier DNA or stabiliser) was not found to have a significant effect in this study. Detection probabilities were calculated using logistic regression. Logistic regression over large concentration ranges proved sensitive to non-detected replicate reactions due to amplification failure at high concentrations; the effect could be reduced by regression against log (concentration) or, better, by eliminating invalid responses. Conclusion Use of low-retention plastic tubes is advised for quantification of DNA solutions at levels below 100 g.e. For low-level calibration using linear least squares, it is better to eliminate the entire replicate group for any standard that shows non-detects reasonably attributable to sampling effects than to either eliminate non-detects or to assign arbitrary high Ct values. In calculating concentrations for low-level test samples with non-detects, concentrations should be calculated for each replicate, zero concentration assigned to non-detects, and all resulting concentration values averaged. Logistic regression is a useful method of estimating detection probability at low DNA concentrations.
Quantum transport through one-dimensional aluminum wires (2002)

Quantum conductance in narrow channels has been well understood by using the two-dimensional electron gas, a model system which has been realized in semiconductor heterojunctions. An essential property of this electron gas is its ability to support a constriction of width comparable to the Fermi wavelength, a property not shared by even thin metal films. The advent of scanning tunneling microscope has made possible the fabrication of metallic wires of atomic widths. We investigate one-dimensional wires consisting of aluminum atoms, to be specific. Using the first-principles density functional calculations, we obtain the optimal structures and report the bonding as deduced from the charge density analysis. With the calculated electronic structure in hand, we discussed the quantum ballistic transport using channel capacity arguments motivated by the Heisenberg’s uncertainty principle. By comparing our results with the detailed pioneering calculations by Lang, we inferred an average value for channel transmitivity and touched upon material specific contact resistance. Finally, the validity of the Wiedemann–Franz law in the quantum domain is established by studying thermal conductance in nanowires.
HuMax-CD4 (2003)

Treatment with HuMax-CD4 led to a moderate, not statistically significant reduction in PASI. The efficacy results obtained after only 4 weeks of treatment suggest that longer treatment would lead to even further reduction of PASI.
Origin of Different Cell Types in the Bovine Corpus Luteum as Characterized by Specific Monoclonal Antibodies1 (1984)

Specific monoclonal antibodies to granulosa and thecal cell surface antigens were produced and used to determine the contributions of theca and granulosa cells to the bovine corpus luteum (CL). Binding of each antibody was examined on collagenase-dispersed luteal cells from 18 cycling and 14 pregnant heifers by indirect immunofluorescence. The percent binding of the large luteal cells to granulosa antibody (GrAb) declined (P less than 0.01) as the age of the CL advanced: 77 +/- 6, 47.5 +/- 3, and 30 +/- 2 for Days 4-6, 10-12 and 16-18, respectively. Further reduction in binding of GrAb to large cells occurred between 50 and 100 days of pregnancy and no labeling was seen thereafter. Fourteen percent of the small luteal cells were bound by GrAb on Days 4-6 of the cycle, and none were labeled during subsequent stages. In contrast, when thecal antibody (TAb) was used, the proportions of large cells that were labeled increased (P less than 0.01) between Days 4-6 (10 +/- 1.3%) and 10-12 (46 +/- 3%). The percentage of large cells bound by TAb then remained unchanged until midpregnancy, declined as pregnancy advanced, and disappeared during late gestation. A majority of small luteal cells were bound by TAb throughout the estrous cycle: 70 +/- 4%, 69 +/- 3% and 58 +/- 6% at Days 4-6, 10-12, 16-18, respectively. Labeling of small cells by TAb occurred throughout pregnancy but declined (P less than 0.05) as gestation advanced. These studies suggest that the large cells of the early cyclic CL are derived from granulosa cells, while most of the small cells are of thecal origin. Small cells develop into large cells as the age of the CL increases. Granulosa-derived cells disappear during early pregnancy, while cells of thecal origin persist throughout pregnancy.
Minireview: Not Picking Pockets: Nuclear Receptor Alternate-Site Modulators (NRAMs) (2009)

Because of their central importance in gene regulation and mediating the actions of many hormones, the nuclear receptors (NRs) have long been recognized as very important biological and pharmaceutical targets. Of all the surfaces available on a given NR, the singular site for regulation of receptor activity has almost invariably been the ligand-binding pocket of the receptor, the site where agonists, antagonists, and selective NR modulators interact. With our increasing understanding of the multiple molecular components involved in NR action, researchers have recently begun to look to additional interaction sites on NRs for regulating their activities by novel mechanisms. The alternate NR-associated interaction sites that have been targeted include the coactivator-binding groove and allosteric sites in the ligand-binding domain, the zinc fingers of the DNA-binding domain, and the NR response element in DNA. The studies thus far have been performed with the estrogen receptors, the androgen receptor (AR), the thyroid hormone receptors, and the pregnane X receptor. Phenotypic and conformation-based screens have also identified small molecule modulators that are believed to function through the NRs but have, as yet, unknown sites and mechanisms of action. The rewards from investigation of these NR alternate-site modulators should be the discovery of new therapeutic approaches and novel agents for regulating the activities of these important NR proteins.
Oligo- and poly-nucleotides: 50 years of chemical synthesis (2005)

It is fifty years since the first chemical synthesis of a dinucleoside phosphate and a dinucleotide with natural 3'-->5'-internucleotide linkages was reported. The main developments in the methodology of oligo- and poly-nucleotide synthesis that have taken place since are described.
Radioprotection of rat subependymal plate with 4-OH sodium butyrate. (1988)

The central nervous system is a radiation-dose-limiting structure, and cellularity of the rat subependymal plate (a location of neuroglial stem cells) has been used as a model of radiation damage. In the present work, an attempt has been made to improve its radiation tolerance using 4-OH sodium butyrate (gamma OH). Adult rats received 10-Gy 250-kV (peak) x-rays or 3.5-Gy 15-MeV deuterons plus Be neutrons. Cell counts were obtained by histological examination of the subependymal plate. Photon and neutron irradiation alone resulted in a mean cell depletion of 62% and 58%, respectively, compared with sham-irradiated controls, which was not statistically significant; the relative biologic effectiveness was 2.9. In the absence of radiation, gamma OH did not significantly alter the cellularity of the subependymal plate, compared with that in controls treated with chloral hydrate. At doses greater than or equal to 1 g/kg, gamma OH was associated with a statistically significant reduction of subependymal plate cell depletion in animals treated with photon or neutron radiation, and the magnitude of the effect was similar. Arterial blood gas analysis failed to show a significant difference in arterial oxygen tension between control and test animals.
Comprehensive Mapping of Long-Range Interactions Reveals Folding Principles of the Human Genome (2009)

We describe Hi-C, a method that probes the three-dimensional architecture of whole genomes by coupling proximity-based ligation with massively parallel sequencing. We constructed spatial proximity maps of the human genome with Hi-C at a resolution of 1 megabase. These maps confirm the presence of chromosome territories and the spatial proximity of small, gene-rich chromosomes. We identified an additional level of genome organization that is characterized by the spatial segregation of open and closed chromatin to form two genome-wide compartments. At the megabase scale, the chromatin conformation is consistent with a fractal globule, a knot-free, polymer conformation that enables maximally dense packing while preserving the ability to easily fold and unfold any genomic locus. The fractal globule is distinct from the more commonly used globular equilibrium model. Our results demonstrate the power of Hi-C to map the dynamic conformations of whole genomes.
Differentiation-associated expression of prostaglandin H and thromboxane A synthases in monocytoid leukemia cell lines (1991)

To elucidate the differentiation-associated expression of enzymes catalyzing arachidonic acid metabolism, we measured arachidonate metabolites by reverse-phase high pressure liquid chromatography in monocytoid leukemia (ML-1, THP-1, and U937) and myeloid leukemia (KG-1) cell lines. Undifferentiated ML-1 or THP-1 cells produced trace amounts of eicosanoids via the cyclooxygenase (COX) and lipoxygenase (LOX) pathways. Upon differentiation induced by phorbol ester (phorbol 12- myristate 13-acetate [PMA]), metabolites via the COX pathway were increased by 100-fold in ML-1 and THP-1 cells, while the LOX products remained barely detectable. All the COX metabolites were elevated, but thromboxane A2 (TXA2) formation was threefold higher in ML-1 cells than in THP-1 cells. Similar time-related increases in COX metabolites were observed in THP-1 cells induced to differentiate with retinoic acid. Undifferentiated U937 cells were capable of generating a much higher quantity of COX products than ML-1 or THP-1 cells, but, upon PMA- induced differentiation, COX products were increased by only two-fold to threefold over the undifferentiated cells and the total COX products in differentiated U937 cells were only one-seventh of those produced by differentiated ML-1 or THP-1 cells. KG-1 cells had an entirely different metabolic profile. They produced a large quantity of a metabolite coeluted with prostaglandin D2, and PMA had no effect on inducing changes in arachidonic acid (AA) metabolism. Increased COX metabolite formation in differentiated THP-1 and ML-1 cells was due to an enhanced level of prostaglandin H synthase enzyme mass, as measured by Western blot analysis. The TXA synthase activity was also increased by approximately 100-fold in PMA-induced ML-1 cells and 10-fold in THP- 1 cells. These findings indicate that increased expression of prostaglandin H and TXA synthase enzymes is a feature of differentiated monocytoid leukemia cell lines.
Pneumococcal resistance to antibiotics (1990)

The geographic distribution of pneumococci resistant to one or more of the antibiotics penicillin, erythromycin, trimethoprim-sulfamethoxazole, and tetracycline appears to be expanding, and there exist foci of resistance to chloramphenicol and rifampin. Multiply resistant pneumococci are being encountered more commonly and are more often community acquired. Factors associated with infection caused by resistant pneumococci include young age, duration of hospitalization, infection with a pneumococcus of serogroup 6, 19, or 23 or serotype 14, and exposure to antibiotics to which the strain is resistant. At present, the most useful drugs for the management of resistant pneumococcal infections are cefotaxime, ceftriaxone, vancomycin, and rifampin. If the strains are susceptible, chloramphenicol may be useful as an alternative, less expensive agent. Appropriate interventions for the control of resistant pneumococcal outbreaks include investigation of the prevalence of resistant strains, isolation of patients, possible treatment of carriers, and reduction of usage of antibiotics to which the strain is resistant. The molecular mechanisms of penicillin resistance are related to the structure and function of penicillin-binding proteins, and the mechanisms of resistance to other agents involved in multiple resistance are being elucidated. Recognition is increasing of the standard screening procedure for penicillin resistance, using a 1-microgram oxacillin disk.
Silicon nanowhiskers grown on 〈111〉Si substrates by molecular-beam epitaxy (2004)

Silicon nanowhiskers in the diameter range of 70 to 200 nm were grown on 〈111〉-oriented silicon substrates by molecular-beam epitaxy. Assuming the so-called “vapor–liquid–solid” (VLS) growth process to operate, we initiated the growth by using small clusters of gold at the silicon interface as seeds. The in situ generation of the Au clusters as well as the growth parameters of the whiskers are discussed. The experimentally observed radius dependence of the growth velocity of the nanowhiskers is opposite to what is known for VLS growth based on chemical vapor deposition and can be explained by an ad-atom diffusion on the surface of the whiskers.
Involvement of CED-3/ICE Proteases in the Apoptosis of B-Chronic Lymphocytic Leukemia Cells (1997)

B-chronic lymphocytic leukemia (B-CLL) is characterized by the accumulation of long-lived B lymphocytes that express high levels of Bcl-2. We examined the involvement of CED-3/ICE-like proteases in the apoptosis of B-CLL cells. One of the substrates of these proteases is poly(ADP [adenosine 5'-diphosphate]-ribose) polymerase (PARP). The effect of different factors that induce the apoptosis of B-CLL cells on the proteolytic cleavage of PARP has been studied. Treatment of B-CLL cells with different concentrations of dexamethasone (1 to 1,000 micromol/L) induced in a dose-dependent manner the cleavage of PARP. Dexamethasone induced PARP cleavage after 12 hours of incubation, which was almost complete at 48 hours. PARP cleavage during apoptosis of B-CLL cells was studied in cells from eight patients and a correlation was found between cell viability and the degree of PARP cleavage. Incubation in vitro of B-CLL cells with fludarabine for 48 hours induced PARP cleavage in all the cases studied. Protein kinase C (PKC) activation with 100 nmol/L TPA (12-O-tetradecanoylphorbol 13-acetate) or incubation with interleukin-4 (10 ng/mL) prevented either dexamethasone- or fludarabine-induced proteolysis of PARP. Incubation of B-CLL cells with the CED-3/ICE-like protease inhibitor Z-VAD.fmk inhibited spontaneous and dexamethasone-induced PARP cleavage and DNA fragmentation in a dose-dependent manner. Furthermore, Z-VAD.fmk prevented the cytotoxic effect of dexamethasone. These results indicate that CED-3/ICE-like proteases play an important role in the apoptosis of B-CLL cells.
Delayed Systemic Nogo-66 Receptor Antagonist Promotes Recovery from Spinal Cord Injury (2003)

Traumatized axons possess an extremely limited ability to regenerate within the adult mammalian CNS. The myelin-derived axon outgrowth inhibitors Nogo, oligodendrocyte-myelin glycoprotein, and myelin-associated glycoprotein, all bind to an axonal Nogo-66 receptor (NgR) and at least partially account for this lack of CNS repair. Although the intrathecal application of an NgR competitive antagonist at the time of spinal cord hemisection induces significant regeneration of corticospinal axons, such immediate local therapy may not be as clinically feasible for cases of spinal cord injury. Here, we consider whether this approach can be adapted to systemic therapy in a postinjury therapeutic time window. Subcutaneous treatment with the NgR antagonist peptide NEP1-40 (Nogo extracellular peptide, residues 1-40) results in extensive growth of corticospinal axons, sprouting of serotonergic fibers, upregulation of axonal growth protein SPRR1A (small proline-rich repeat protein 1A), and synapse re-formation. Locomotor recovery after thoracic spinal cord injury is enhanced. Furthermore, delaying the initiation of systemic NEP1-40 administration for up to 1 week after cord lesions does not limit the degree of axon sprouting and functional recovery. This indicates that the regenerative capacity of transected corticospinal tract axons persists for weeks after injury. Systemic Nogo-66 receptor antagonists have therapeutic potential for subacute CNS axonal injuries such as spinal cord trauma.
A small-molecule antagonist of CXCR4 inhibits intracranial growth of primary brain tumors (2003)

The vast majority of brain tumors in adults exhibit glial characteristics. Brain tumors in children are diverse: Many have neuronal characteristics, whereas others have glial features. Here we show that activation of the Gi protein-coupled receptor CXCR4 is critical for the growth of both malignant neuronal and glial tumors. Systemic administration of CXCR4 antagonist AMD 3100 inhibits growth of intracranial glioblastoma and medulloblastoma xenografts by increasing apoptosis and decreasing the proliferation of tumor cells. This reflects the ability of AMD 3100 to reduce the activation of extracellular signal-regulated kinases 1 and 2 and Akt, all of which are pathways downstream of CXCR4 that promote survival, proliferation, and migration. These studies (i) demonstrate that CXCR4 is critical to the progression of diverse brain malignances and (ii) provide a scientific rationale for clinical evaluation of AMD 3100 in treating both adults and children with malignant brain tumors.
Cloning, sequencing, and overexpression of a [2Fe-2S] ferredoxin gene from Escherichia coli. (1992)

Escherichia coli contains a soluble, [2Fe-2S] ferredoxin of unknown function (Knoell, H.-E., and Knappe, J. (1974) Eur. J. Biochem. 50, 245-252). Using antiserum to the purified protein to screen E. coli genomic expression libraries, we have cloned a gene (designated fdx) encoding this protein. The DNA sequence of the gene predicts a polypeptide of 110 residues after removal of the initiator methionine (polypeptide M(r) = 12,186, holoprotein M(r) = 12,358). The deduced amino acid sequence is strikingly similar to those of the ferredoxins found in animal mitochondria which function with cytochrome P450 enzymes and to the ferredoxin from Pseudomonas putida which functions with P450cam. The overall sequence identity is approximately 36% when compared with human mitochondrial and P. putida ferredoxins, and the identities include 4 cysteine residues proposed to coordinate the iron cluster. The protein was overproduced approximately 500-fold using an expression plasmid, and the holoprotein was assembled and accumulated in amounts exceeding 30% of the total cell protein. The overexpressed ferredoxin exhibits absorption, circular dichroism, and electron paramagnetic resonance spectra closely resembling those of the animal ferredoxins and P. putida ferredoxin.
A Genomic View of the Human- Bacteroides thetaiotaomicron Symbiosis (2003)

The human gut is colonized with a vast community of indigenous microorganisms that help shape our biology. Here, we present the complete genome sequence of the Gram-negative anaerobe Bacteroides thetaiotaomicron , a dominant member of our normal distal intestinal microbiota. Its 4779-member proteome includes an elaborate apparatus for acquiring and hydrolyzing otherwise indigestible dietary polysaccharides and an associated environment-sensing system consisting of a large repertoire of extracytoplasmic function sigma factors and one- and two-component signal transduction systems. These and other expanded paralogous groups shed light on the molecular mechanisms underlying symbiotic host-bacterial relationships in our intestine.