gebhart/patrepeval huggingface dataset:
Human immunodeficiency virus types 1 and 2 and simian immunodeficiency virus env proteins possess a functionally conserved assembly domain (1990)

The envelope (env) glycoproteins of human immunodeficiency viruses type 1 (HIV-1) and type 2 (HIV-2) form dimers shortly after synthesis. Analysis of the simian immunodeficiency virus (SIV) env protein expressed by a recombinant vaccinia virus revealed that it, too, forms stable homodimers. When the HIV-1 and SIV env proteins or the HIV-1 and HIV-2 env proteins were coexpressed in the same cells, heterodimers were formed. Thus, the env proteins of HIV-1, HIV-2, and SIV possess a functionally conserved domain involved in subunit-subunit recognition and assembly that likely involves the ectodomain of gp41.
Monoclonal antibody JSB‐1 detects a highly conserved epitope on the P‐glycoprotein associated with multi‐drug‐resistance (1988)

Resistance to multiple chemotherapeutic agents is a common clinical problem in the treatment of cancer. This resistance may occur before primary therapy or be acquired during treatment. We have generated a monoclonal antibody (MAb) (JSB-I), specific for a conserved epitope on the plasma membrane 170- to 180-kDa glycoprotein, the expression of which is strongly correlated with the degree of multi-drug resistance (MDR). JSB-I strongly binds to both Chinese-hamster-derived MDR cell lines and human MDR cell lines, including cell lines derived from lung and ovary. A drug-sensitive revertant line, and the corresponding drug-sensitive parent lines, showed only weak reactivity or none at all. JSB-I reacts strongly to air-dried or acetone-fixed cells and therefore has potential value for diagnostic detection of MDR cells in human tumor samples.
X-ray Analysis of the Structure of Harman, C12H10N2. (1958)

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Genomic patterns resembling BRCA1- and BRCA2-mutated breast cancers predict benefit of intensified carboplatin-based chemotherapy (2014)

Distinct aCGH patterns differentiated between HER2-negative patients with a markedly improved outcome after adjuvant treatment with an intensified DNA-DSB-inducing regimen (BRCA-likeCGH patients) and those without benefit (non-BRCA-likeCGH patients).
Millisecond Kinetics on a Microfluidic Chip Using Nanoliters of Reagents (2003)

This paper describes a microfluidic chip for performing kinetic measurements with better than millisecond resolution. Rapid kinetic measurements in microfluidic systems are complicated by two problems: mixing is slow and dispersion is large. These problems also complicate biochemical assays performed in microfluidic chips. We have recently shown (Song, H.; Tice, J. D.; Ismagilov, R. F. Angew. Chem., Int. Ed. 2003, 42, 768-772) how multiphase fluid flow in microchannels can be used to address both problems by transporting the reagents inside aqueous droplets (plugs) surrounded by an immiscible fluid. Here, this droplet-based microfluidic system was used to extract kinetic parameters of an enzymatic reaction. Rapid single-turnover kinetics of ribonuclease A (RNase A) was measured with better than millisecond resolution using sub-microliter volumes of solutions. To obtain the single-turnover rate constant (k = 1100 +/- 250 s(-1)), four new features for this microfluidics platform were demonstrated: (i) rapid on-chip dilution, (ii) multiple time range access, (iii) biocompatibility with RNase A, and (iv) explicit treatment of mixing for improving time resolution of the system. These features are discussed using kinetics of RNase A. From fluorescent images integrated for 2-4 s, each kinetic profile can be obtained using less than 150 nL of solutions of reagents because this system relies on chaotic advection inside moving droplets rather than on turbulence to achieve rapid mixing. Fabrication of these devices in PDMS is straightforward and no specialized equipment, except for a standard microscope with a CCD camera, is needed to run the experiments. This microfluidic platform could serve as an inexpensive and economical complement to stopped-flow methods for a broad range of time-resolved experiments and assays in chemistry and biochemistry.
Degradation Kinetics of Dihydroxyacetone and Glyceraldehyde in Subcritical and Supercritical Water (1997)

The degradation kinetics of dihydroxyacetone and glyceraldehyde were studied at temperature ranges of 573−673 K, pressures of 25−40 MPa, and residence times from 0.06 to 1.7 s. The reactions of glyceraldehyde gave both dihydroxyacetone and pyruvaldehyde, and yields of dihydroxyacetone were always higher than those of pyruvaldehyde. The reactions of dihydroxyacetone gave glyceraldehyde and pyruvaldehyde, while the yields of pyruvaldehyde were always higher than those of dihydroxyacetone. This pathway involves the reversible isomerization between glyceraldehyde and dihydroxyacetone and their subsequent dehydration to pyruvaldehyde. A model was formulated on the basis of this pathway, and the kinetic rate constants involved were calculated using the experimental results. As the conditions change from subcritical to supercritical, the Arrhenius relationship becomes discontinuous near the critical point of water. At a constant temperature of 673 K, the kinetics constants showed a general increase with an increase in pressure.
Cross-correlation-based image acquisition technique for manually-scanned optical coherence tomography (2009)

We present a novel image acquisition technique for Optical Coherence Tomography (OCT) that enables manual lateral scanning. The technique compensates for the variability in lateral scan velocity based on feedback obtained from correlation between consecutive A-scans. Results obtained from phantom samples and biological tissues demonstrate successful assembly of OCT images from manually-scanned datasets despite non-uniform scan velocity and abrupt stops encountered during data acquisition. This technique could enable the acquisition of images during manual OCT needle-guided biopsy or catheter-based imaging, and for assembly of large field-of-view images with hand-held probes during intraoperative in vivo OCT imaging.
Antibiotic-DNA interactions: intermolecular nuclear Overhauser effects in the netropsin-d(C-G-C-G-A-A-T-T-C-G-C-G) complex in solution. (1982)

The proton markers located in the minor groove of the d(C-G-C-G-A-A-T-T-C-G-C-G) duplex and its netropsin complex have been assigned from measurements of intramolecular nuclear Overhauser effects (NOEs) between exchangeable imino protons and nonexchangeable base protons on the same and adjacent base pairs. Several points of contact between the concave face of the antibiotic and the minor groove d(A-A-T-T) tetranucleotide segment of the dodecanucleotide duplex have been established based on intermolecular NOE effects between the pyrrole ring and side-chain methylene protons of netropsin and the adenosine H-2 protons of dA X dT base pairs in the center of the duplex. These NOE measurements provide a powerful method for differentiating between minor and major groove contacts in ligand-DNA complexes in solution. A model for netropsin interaction at dA X dT sites on duplex DNA is proposed.
Group 4 metal dicarbollide chemistry. Synthesis, structures, and reactivity of electrophilic alkyl complexes (Cp*)(C2B9H11)M(R), M = Hf, Zr (1991)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTGroup 4 metal dicarbollide chemistry. Synthesis, structures, and reactivity of electrophilic alkyl complexes (Cp*)(C2B9H11)M(R), M = Hf, ZrDonna J. Crowther, Norman C. Baenziger, and Richard F. JordanCite this: J. Am. Chem. Soc. 1991, 113, 4, 1455–1457Publication Date (Print):February 1, 1991Publication History Published online1 May 2002Published inissue 1 February 1991https://pubs.acs.org/doi/10.1021/ja00004a080https://doi.org/10.1021/ja00004a080research-articleACS PublicationsRequest reuse permissionsArticle Views461Altmetric-Citations121LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InRedditEmail Other access optionsGet e-AlertscloseSupporting Info (1)»Supporting Information Supporting Information Get e-Alerts
VALMAP2.0: contour maps using the bond-valence-sum method (1999)

VALMAP 2.0 is a Microsoft-Windows-based program designed to assist material scientists in accurate structural investigations. The aim of VALMAP is to calculate the sum of bond valences that a particular atom would have if it were placed at any arbitrary point in the crystal. By movement of this atom through all possible points, its valence-sum contour map can be displayed. Parameters of the bond-valence model are available and may be modified. The program was tested in a number of cases and two examples of applications are reported: (i) finding probable atom sites in crystal structures; (ii) displacive and order–disorder phase transition mechanisms, analysing steric effects.
Laser-generated focused ultrasound for arbitrary waveforms (2016)

Transducers for laser generated focused ultrasound can achieve photoacoustic waves with several hundred bars positive pressure in water. Previous designs employed concave glass substrates decorated with catalytically grown carbon nanotubes. Here, we show that arbitrarily shaped surfaces made of polymers and printed with 3d printers allow the generation of waveforms with complex temporal and spatial shape. We first present three different polymer materials together with a simplified deposition technique. This is achieved by painting layers of carbon-nanotube powder and polydimethylsiloxane. Together with a clear resin (Formlabs Photopolymer Clear Resin), pressure amplitudes of 300 bar peak positive were obtained. With the flexibility of polymer substrates, complex waveforms can be generated. This is demonstrated with a stepped surface which launches two waves separated by 0.8 μs. Detailed pressure measurements are supported with shadowgraphy images and simulations of the wave.
Effects of threshold choice on biological conclusions reached during analysis of gene expression by DNA microarrays (2005)

Global analysis of gene expression by using DNA microarrays is employed increasingly to search for differences in biological properties between normal and diseased tissue. In such studies, expression that deviates from defined thresholds commonly is used for creating genetic signatures that characterize disease vs. normality. Although it is axiomatic that the threshold parameters applied to microarray analysis will alter the contents of such genetic signatures, the extent to which threshold choice can affect the fundamental conclusions made from microarray-based studies has not been elucidated. We used GABRIEL (Genetic Analysis By Rules Incorporating Expert Logic), a platform of knowledge-based algorithms for the global analysis of gene expression, together with conventional statistical approaches, to examine the sensitivity of conclusions to threshold choice in recently published microarray-based studies. An analysis of the effects of threshold decisions in one of these studies [Ramaswamy, S., Ross, K. N., Lander, E. S. & Golub, T. R. (2003) Nat. Genet. 33, 49-54], which arrived at the important conclusion that the metastatic potential of primary tumors is encoded by the bulk of cells in the tumor, is the focus of this article. We discovered that support for this conclusion highly depends on the threshold used to create gene expression signatures. We also found that threshold choice dramatically affected the gene function categories represented nonrandomly in signatures. Our results suggest that the robustness of biological conclusions made by using microarray analysis should be routinely assessed by examining the validity of the conclusions by using a range of threshold parameters.
Monoclonal antibody therapeutics with up to five specificities: Functional enhancement through fusion of target-specific peptides (2013)

The recognition that few human diseases are thoroughly addressed by mono-specific, monoclonal antibodies (mAbs) continues to drive the development of antibody therapeutics with additional specificities and enhanced activity. Historically, efforts to engineer additional antigen recognition into molecules have relied predominantly on the reformatting of immunoglobulin domains. In this report we describe a series of fully functional mAbs to which additional specificities have been imparted through the recombinant fusion of relatively short polypeptides sequences. The sequences are selected for binding to a particular target from combinatorial libraries that express linear, disulfide-constrained, or domain-based structures. The potential for fusion of peptides to the N- and C- termini of both the heavy and light chains affords the bivalent expression of up to four different peptides. The resulting molecules, called zybodies, can gain up to four additional specificities, while retaining the original functionality and specificity of the scaffold antibody. We explore the use of two clinically significant oncology antibodies, trastuzumab and cetuximab, as zybody scaffolds and demonstrate functional enhancements in each case. The affect of fusion position on both peptide and scaffold function is explored, and penta-specific zybodies are demonstrated to simultaneously engage five targets (ErbB2, EGFR, IGF-1R, Ang2 and integrin αvβ3). Bispecific, trastuzumab-based zybodies targeting ErbB2 and Ang2 are shown to exhibit superior efficacy to trastuzumab in an angiogenesis-dependent xenograft tumor model. A cetuximab-based bispecific zybody that targeting EGFR and ErbB3 simultaneously disrupted multiple intracellular signaling pathways; inhibited tumor cell proliferation; and showed efficacy superior to that of cetuximab in a xenograft tumor model.
Development and Application of a High-Throughput Formulation Screening Strategy for Oral Administration in Drug Discovery (2010)

For small-molecule drugs the oral route of administration remains the most popular means of delivery for many indications. Optimizing oral bioavailability is, therefore, of critical importance in both drug discovery and development. However, while formulation development is routinely evaluated in clinical development, limited attention appears to be focused on improving exposure following oral delivery in early preclinical testing. The reasons for this appear to be limited compound availability and the requirement for a very rapid turnaround time. While some effort has been made to address solubility for intravenous formulation development, there is limited information available regarding formulation screening for oral delivery in drug discovery and preclinical development. In this brief article, we provide some details on our high-throughput, low compound requirement screen for oral formulation development. This screen has direct application in lead identification and development. The assay has been validated across multiple chemical series targeting different therapeutic areas, and is routinely applied with significant success in improving oral bioavailability.
Frequency of inhibitor development in severe haemophilia A children treated with cryoprecipitate and low‐dose immune tolerance induction (2000)

The frequency of factor VIII inhibitor development was evaluated in a hundred severe haemophilia A patients < 18 years of age (mean 10.4 +/- 5.1 years); 25 were previously untreated patients (PUPs), with a mean age of 11.2 +/- 2.9 months. All were followed up for 3 years from December 1996. Immune tolerance (IT) was induced with low-dose factor VIII (FVIII); 25-50 IU kg(-1) every other day for the 10 haemophiliacs who developed persistent inhibitors. The incidence of inhibitors for PUPs was 3/25 (12%; 95% confidence interval [CI], 0. 7-24.7%) and were detected after 4, 15 and 20 exposure days (mean 13 +/- 8.2 days; 95% CI, 3.7-22.2%). Children with maximum inhibitor levels of > 40 Bethesda units (BU) per mL (n=4) received IT therapy as 25 U kg(-1) FVIII in the form of cryoprecipitate every other day for 1-4 months (mean 2.4 +/- 1.6 months; 95% CI, 0.8-3.9%), which was successful in all of them. FVIII (50 U kg(-1)) was given every other day for six patients with maximum inhibitor level > 40 BU mL(-1) for 3-9 months (mean 5.4 +/- 3.2 months; 95% CI, 2.9 -7.9%) with success in 4/6 (66.6%; 95% CI, 28.8-104.3%). Patients who showed a good IT response had an inhibitor level < or = 30 BU mL(-1), were < or = 9 years of age at inhibitor development with few exposure days to FVIII and had an early immune tolerance. In conclusion, inhibitor development in severe haemophilia A children exclusively treated with cryoprecipitate is low. Early low-dose IT induction for high responders may be achieved successfully if inhibitor level is < or = 50 BU mL(-1).
Cholesterol movement from plasma membrane to rough endoplasmic reticulum. Inhibition by progesterone. (1994)

The effect of progesterone on the movement of sterols from the cell surface to the rough endoplasmic reticulum (ER) was examined in rat hepatoma cells. Plasma membranes were labeled exogenously with [3H]cholesterol or [3H]zymosterol. Translocation of the labeled sterols to the rough ER was inferred from their conversion to [3H]cholesteryl esters and [3H]cholesterol, respectively. Progesterone inhibited both of these reactions by more than 90%. The concentration for half-maximal inhibition was 0.7 microgram/ml. Progesterone did not inhibit acyl-CoA:cholesterol acyltransferase activity itself, since the steroid had no effect on the esterification of [3H]cholesterol synthesized in vitro in the rough ER from [3H]zymosterol. Moreover, the small amount of [3H]cholesterol synthesized from plasma membrane [3H]zymosterol in progesterone-treated intact cells was esterified at the same fractional rate as cholesterol in control cells. Subcellular fractionation of cells pulse-labeled with [3H]cholesterol and treated with progesterone suggested that the block in plasma membrane cholesterol transfer to the rough ER occurred at the level of the plasma membrane.
Properties of crosslinked casein/waterborne polyurethane composites (2003)

Abstract Waterborne polyurethane (WPU) and casein (1 : 1 by weight) were blended at 90°C for 30 min, and then were crosslinked by adding 1–10 wt % ethanedial to prepare a series of sheets. Their structure and properties were characterized by using infrared spectroscopy, scanning electron microscopy, thermogravimetric analysis, dynamic mechanical analysis, and tensile testing. The results indicated that crosslinked blend sheets exhibited a certain degree of miscibility, and exhibited much higher tensile strength and water resistivity than did the WPU, casein, and the uncrosslinked blend from WPU and casein. When the ethanedial content was 2 wt %, the tensile strength and elongation at break of crosslinked sheets achieved 19.5 MPa and 148% in the dry state, and 5.0 MPa and 175% in the wet state, respectively. A 2 wt % content of ethanedial plays an important role in the enhancement of mechanical properties, thermal stability, and water resistivity of the blends of WPU and casein as a result of intermolecular crosslinking. This work provided a new protein plastic with good water resistivity. © 2003 Wiley Periodicals, Inc. J Appl Polym Sci 91: 332–338, 2004
Sympathetic Activation in Chronic Renal Failure (2008)

The potential involvement of sympathetic overactivity has been neglected in this population despite accumulating experimental and clinical evidence suggesting a crucial role of sympathetic activation for both progression of renal failure and the high rate of cardiovascular events in patients with chronic kidney disease. The contribution of sympathetic neural mechanisms to the occurrence of cardiac arrhythmias, the development of hypertension, and the progression of heart failure are well established; however, the exact mechanisms contributing to heightened sympathetic tone in patients with chronic kidney disease are unclear. This review analyses potential mechanisms underlying sympathetic activation in chronic kidney disease, the range of adverse consequences associated with this activation, and potential therapeutic implications resulting from this relationship.
Recombinant immunotoxins for the treatment of haematological malignancies (2004)

Recombinant immunotoxins are fusion proteins which contain a ligand derived from the immune system fused to a toxin. The protein toxin is truncated to delete its binding domain, allowing selective ligand-directed binding. Growth factor fusion toxins are often considered immunotoxins. One of these molecules, containing the truncated diphtheria toxin and human IL-2 (Ontak), Ligand Pharmaceuticals), has been approved for the treatment of cutaneous T-cell lymphoma. Recombinant immunotoxins have also been produced containing the variable domains (Fv fragment) of monoclonal antibodies fused to toxins. These agents are relatively versatile with respect to the range of antigens possible. Several of these recombinant immunotoxins have showed clinical effectiveness in Phase I testing against haematological malignancies. One of these molecules, BL22, targets CD22 on hairy-cell leukaemia and has enabled patients to achieve complete remissions despite previous treatment and resistance to chemotherapy.
The heterodimer of the Ca2+‐binding proteins MRP8 and MRP14 binds arachidonic acid (1997)

The S100 proteins MRP8 and MRP14 have been shown to be expressed by myeloid cells during inflammatory reactions. Since the majority of S100 proteins exhibit their biological activity when associated as complex it was investigated whether murine MRP8 and MRP14 form heterodimers and whether this complex may bind lipids of the cell membrane. This is of particular importance since their anchoring into the plasma membrane is unclear although upon calcium binding the proteins translocate from the cytoplasma to the cytoskeleton and the plasma membrane. Using recombinant proteins we could show that not the monomers but only the heterodimers specifically bind arachidonic acid. This finding opens new perspectives for the role of MRP8 and MRP14 in acute and chronic inflammatory processes.
Figs at the Arboretum (1985)

(Uploaded by Plazi from the Biodiversity Heritage Library) No abstract provided.