gebhart/patrepeval huggingface dataset:
Characterization of Cry34/Cry35 Binary Insecticidal Proteins from Diverse Bacillus thuringiensis Strain Collections (2005)

Bacillus thuringiensis crystal proteins of the Cry34 and Cry35 classes function as binary toxins showing activity on the western corn rootworm, Diabrotica virgifera virgifera LeConte. We surveyed 6,499 B. thuringiensis isolates by hybridization for sequences related to cry35A genes, identifying 78 strains. Proteins of the appropriate molecular mass (ca. 44 kDa) for Cry35 were observed in 42 of the strains. Full-length, or nearly full-length, sequences of 34 cry34 genes and 16 cry35 genes were also obtained from cloning, PCR analysis, and DNA sequencing. These included representatives of all known Cry34A, Cry34B, Cry35A, and Cry35B classes, as well as a novel Cry34A/Cry35A-like pair. Bioassay analysis indicated that cry35-hybridizing strains not producing a ca. 14-kDa protein, indicative of Cry34, were not active on corn rootworms, and that the previously identified Cry34A/Cry35A pairs were more active than the Cry34B/Cry35B pairs. The cry35-hybridizing B. thuringiensis strains were found in locales and materials typical for other B. thuringiensis strains. Comparison of the sequences with the geographic origins of the strains showed that identical, or nearly identical, sequences were found in strains from both Australasia and the Americas. Sequence similarity searches revealed that Cry34 proteins are similar to predicted proteins in Photorhabdus luminescens and Dictyostelium discoidium, and that Cry35Ab1 contains a segment similar to beta-trefoil domains that may be a binding motif. The binary Cry34/Cry35 B. thuringiensis crystal proteins thus appear closely related to each other, are environmentally ubiquitous, and share sequence similarities consistent with activity through membrane disruption in target organisms.
Acetaminophen Hepatotoxicity and Targeted Rescue: A Model for Specific Chemotherapy of Hepatocellular Carcinoma (1985)

We have taken advantage of the presence of hepatic receptors for galactose-terminal (asialo-)glycoproteins to achieve targeted rescue of differentiated hepatocytes from acetaminophen-induced toxicity in vitro. To accomplish this, a conjugate was formed by covalent coupling of N-acetylcysteine (an acetaminophen antagonist) to galactose-terminal (asialo-)fetuin. We used two human hepatocyte-derived cell lines to test our targeted-rescue method: Hep G2 cells are capable of receptor-mediated endocytosis of galactose-terminal glycoproteins and PLC/PRF/5 cells are not. In the presence of acetaminophen alone, both cell lines demonstrated a similar concentration-dependent sensitivity. Growth rates of both cell lines became normal when N-acetylcysteine was administered in equimolar quantities with acetaminophen indicating that both cell lines had the potential of responding to the antagonist. When asialofetuin-N-acetylcysteine conjugate was given to both cell lines in the presence of acetaminophen, PLC/PRF/5, receptor (-) cells failed to respond. However, Hep G2, receptor (+) cells treated with asialofetuin-N-acetylcysteine conjugate under identical conditions, increased their populations and eventually reached confluence. Control conjugate fetuin-N-acetylcysteine as well as asialofetuin alone had no effect on either cell line.
The formation of skeletal muscle: from somite to limb (2003)

During embryogenesis, skeletal muscle forms in the vertebrate limb from progenitor cells originating in the somites. These cells delaminate from the hypaxial edge of the dorsal part of the somite, the dermomyotome, and migrate into the limb bud, where they proliferate, express myogenic determination factors and subsequently differentiate into skeletal muscle. A number of regulatory factors involved in these different steps have been identified. These include Pax3 with its target c-met, Lbx1 and Mox2 as well as the myogenic determination factors Myf5 and MyoD and factors required for differentiation such as Myogenin, Mrf4 and Mef2 isoforms. Mutants for genes such as Lbx1 and Mox2, expressed uniformly in limb muscle progenitors, reveal unexpected differences between fore and hind limb muscles, also indicated by the differential expression of Tbx genes. As development proceeds, a secondary wave of myogenesis takes place, and, postnatally, satellite cells become located under the basal lamina of adult muscle fibres. Satellite cells are thought to be the progenitor cells for adult muscle regeneration, during which similar genes to those which regulate myogenesis in the embryo also play a role. In particular, Pax3 as well as its orthologue Pax7 are important. The origin of secondary/fetal myoblasts and of adult satellite cells is unclear, as is the relation of the latter to so-called SP or stem cell populations, or indeed to potential mesangioblast progenitors, present in blood vessels. The oligoclonal origin of postnatal muscles points to a small number of founder cells, whether or not these have additional origins to the progenitor cells of the somite which form the first skeletal muscles, as discussed here for the embryonic limb.
Practical Synthesis of (Z)-Civetone Utilizing Ti-Dieckmann Condensation (2002)

An efficient, practical, and stereocontrolled synthesis of (Z)-civetone (1), a representative musk perfume, has been performed utilizing a Ti-Dieckmann (intramolecular Ti-Claisen) condensation of dimethyl (Z)-9-octadecenedioate (3) as the key step. This cyclization reaction has some advantages compared with the traditional basic Dieckmann condensation such as higher concentration (100–300 mM), lower reaction temperature (0–5 °C), shorter reaction time (1–3 h), use of environmentally benign (low toxicity and safe) reagents (TiCl4 and Et3N or Bu3N), and economical reagents and solvents. 15-, 17-, and 19-membered saturated β-ketoesters (6–8) were also prepared by the present method.
Radio Frequency (RF) Interface Management Information Base for MCNS/DOCSIS compliant RF interfaces (1999)

This memo defines a portion of the Management Information Base (MIB) for use with network management protocols in the Internet community.In particular, it defines a basic set of managed objects for SNMPbased management of MCNS/DOCSIS compliant Radio Frequency (RF) interfaces.This memo specifies a MIB module in a manner that is compliant to the SNMP SMIv2 [5][6][7].The set of objects are consistent with the SNMP framework and existing SNMP standards.
Use of commercial enzyme immunoassays and immunomagnetic separation systems for detecting Escherichia coli O157 in bovine fecal samples (1997)

A commercial enzyme immunoassay (EIA) (E. coli O157 Visual Immunoassay; Tecra Diagnostics) performed on enrichment cultures in modified Escherichia coli broth (mECn) was compared with immunomagnetic separation (IMS) (Dynabeads anti-E. coli O157; Dynal) performed on enrichment cultures in modified buffered peptone water (BPW-VCC) for the detection of E. coli O157 in bovine fecal samples. Tests on fecal suspensions inoculated with each of 12 different strains of E. coli O157 showed that both the EIA and IMS methods were 10- to 100-fold more sensitive than direct culture or enrichment subculture methods for detection of the organism. EIA and IMS were then compared for detection of E. coli O157 in bovine rectal swabs. For confirmation of positive EIA tests, a commercial system (Immunocapture System [ICS]; Tecra Diagnostics) was compared with IMS; both were performed on mECn enrichment cultures. Of 200 rectal swabs examined, 17 gave positive results in the EIA which were confirmed by both confirmation systems, 2 gave positive results in the EIA which were confirmed by IMS but not by ICS, and 1 gave a positive result in the EIA which was confirmed by ICS but not by IMS. Of these 20, 15 were also positive by the BPW-VCC-IMS culture system; a further 3 samples were positive by this culture system but gave a negative result in the EIA. Eight samples were negative by the BPW-VCC-IMS culture system but gave a positive result in the EIA which could not be confirmed by either confirmation system. Further examination of the eight unconfirmed EIA-positive samples yielded sorbitol-fermenting E. coli O157 from three samples. Of the remaining five cultures, four were positive in an EIA for verocytotoxins (VT) and two were positive in a cell culture assay for VT1. The remaining 170 samples were negative by both EIA and BPW-VCC-IMS. The Tecra EIA and IMS are both technically simple and sensitive methods for detecting E. coli O157 in bovine fecal samples. There was no statistically significant difference between the numbers of positives detected by the different assays (P = 0.29).
Estimating Harrell's Optimism on Predictive Indices Using Bootstrap Samples (2013)

In aging research, it is important to develop and validate accurate prognostic models whose predictive accuracy will not degrade when applied in external data sources. While the most common method of validation is split sample, alternative methods such as cross-validation and bootstrapping have some significant advantages. The macro that we present calculates Harrell’s optimism for logistic and Cox regression models based on either the c-statistic (for logistic) or Harrell’s c (for Cox). It allows for both stepwise and best subset variable selection methods (and can handle class variables for both methods), and uses both traditional and .632 bootstrapping methods. In addition, we present and discuss the advantages of using Best Subsets regression for model selection instead of stepwise procedures. The uses of Best Subsets regression and our Harrell_Optimism macro are demonstrated using data on post-hospitalization mortality.
Functional involvement of P-glycoprotein in blood-brain barrier. (1992)

P-glycoprotein, an active efflux pump of antitumor agents in multidrug-resistant tumor cells, exists in various normal tissues, including brain capillaries. To study the physiological function of P-glycoprotein expressed in brain capillary endothelium, we established nine mouse brain capillary endothelial cell (MBEC) lines and examined the transport of antitumor agents across the monolayer of MBEC epithelia. In the MBECs, the activities of alkaline phosphatase and gamma-glutamyl transpeptidase, specific markers for brain capillary endothelial cells, were about three times higher than those in other cells including human umbilical vein endothelial cells. By immunoblot analysis, P-glycoprotein was detected in all of the nine MBEC clones. The P-glycoprotein expressed in MBECs specifically bound [125I]iodoaryl azidoprazosin as that in multidrug-resistant cells, and efflux of vincristine was observed in the MBECs. When MBECs were grown on a porous filter membrane, they formed a monolayer of epithelium. By immunoelectron microscopic analysis, P-glycoprotein in MBEC epithelia was shown to be localized to the apical surface of the cells. Moreover, the unidirectional transepithelial transport of vincristine from basal side to apical side was demonstrated in vitro. These observations indicate that P-glycoprotein in brain capillary endothelium prevents vincristine from entering the central nervous system and thus may be one of the functional components of the blood-brain barrier.
Enzyme Reaction in Organic Solvent. III. (1989)

Lipase catalyzed transestrification of tributyrin (1) with 1-octanol (2) in (1) was studied so as to determine how it is affected by water content and four different kinds of lipase (P.f. : Pseudomonas fluorescens, P.s. : Pseudomonas sp., C.c. : Candida cylindracea, and P.p. : Porcine pancreas) at various concentrations. In all cases, an optimum water content that would give a maximum transesterification rate increased with the concentrations of (2) and enzyme. The effect of the initial concentration of (2) on the reaction rate was also studied. The inhibitory effect of (2) was observed above 0.2M of (2), and P.s. and P.f. lipases were inhibited greater than the others.
Detection of mitochondrial DNA alterations in the serum of hepatocellular carcinoma patients. (2002)

mtDNA mutation may be a novel tumor marker of HCC and may prove effective for detection of tumor DNA in the serum.
Acoustic Detection of Pathogens using Rupture Event Scanning (REVS) (2002)

A team of Cambridge scientists have invented a new method that could revolutionise the way scientists detect bacteria, viruses, proteins and DNA. Particles are 'vibrated' on a quartz crystal oscillator and then the sound the particles emit as they break away from the surface is detected by the crystal acting as a very sensitive microphone. Diagnosis of bacterial and viral infections is of paramount importance for disease prognosis and rapid administration of appropriate therapy. It is also important to accurately monitor bacterial and viral load to determine the efficacy of drug treatment. Traditional methods of diagnosis involve direct culture techniques that are time consuming, prone to problems of contamination, and may take days or weeks to give a result. Immunoassays such as antibody ELISA are more rapid, but have limited sensitivity and generally are used only to detect the antibodies produced following infection, rather than the infectious agent itself. Oligonucleotide-based assays, which detect pathogenic DNA or RNA, are very sensitive, but are expensive and require considerable experimental skill, as the genetic material must be isolated before PCR amplification. These methods can provide valuable early results in some situations, but in many cases local facilities are not available and specimens are often transported to central reference laboratories for testing. Hence, there is a real need for methods that rapidly detect and identify pathogens, especially those organisms that cause life-threatening infections such as meningitis and septicaemia.
Protein composition of lung fluids in acute alloxan edema in dogs (1976)

In 11 anesthetized dogs with acute alloxan-induced pulmonary edema, we measured the protein composition of 1-mul samples of plasma, free interstitial fluid, alveolar fluid, and airway fluid. We obtained plasma and airway fluid at regular intervals as edema developed. We sampled alveolar fluid by pleural micropuncture in the unfrozen, excised lung and free interstitial fluid from perivascular cuffs in the frozen, excised lung. The average (+/- 1 SD) total protein concentration of plasma was 4.9 +/- 0.6, airway fluid 4.4 +/- 0.7, free interstitial fluid 4.9 +/- 0.7, and alveolar fluid 5.2 +/- 0.8 g/100 ml. The average fractions of albumin were 0.42 +/- 0.05, 0.50 +/- 0.05, 0.49 +/- 0.06, and 0.49 +/- 0.07, respectively. By paired analysis, the protein concentration of interstitial fluid was not significantly different from alveolar fluid. The protein concentration of airway fluid was significantly less than that in interstitial and alveolar fluid. The albumin fraction of the three lung fluids was identical but significantly different from plasma. We conclude that in alloxan-induced pulmonary edema the lung fluids contain high concentrations of protein and the alveolar epithelial membrane becomes freely permeable to protein molecules.
Sampling signals with finite rate of innovation (2002)

The authors consider classes of signals that have a finite number of degrees of freedom per unit of time and call this number the rate of innovation. Examples of signals with a finite rate of innovation include streams of Diracs (e.g., the Poisson process), nonuniform splines, and piecewise polynomials. Even though these signals are not bandlimited, we show that they can be sampled uniformly at (or above) the rate of innovation using an appropriate kernel and then be perfectly reconstructed. Thus, we prove sampling theorems for classes of signals and kernels that generalize the classic "bandlimited and sinc kernel" case. In particular, we show how to sample and reconstruct periodic and finite-length streams of Diracs, nonuniform splines, and piecewise polynomials using sinc and Gaussian kernels. For infinite-length signals with finite local rate of innovation, we show local sampling and reconstruction based on spline kernels. The key in all constructions is to identify the innovative part of a signal (e.g., time instants and weights of Diracs) using an annihilating or locator filter: a device well known in spectral analysis and error-correction coding. This leads to standard computational procedures for solving the sampling problem, which we show through experimental results. Applications of these new sampling results can be found in signal processing, communications systems, and biological systems.
Tensegrity:  Construction of Rigid DNA Triangles with Flexible Four-Arm DNA Junctions (2004)

A tensegrity strategy has been explored to construct a rigid geometrical structure (triangles) from flexible DNA four-arm junctions. The resulting DNA triangles could self-assemble into 1D and 2D arrays. This tensegrity strategy is expected to play an important role in the design of biomimetic nanomaterials.
Biology and Plasticity of CD133+ Hematopoietic Stem Cells (2003)

AC133 (CD133) is a highly conserved antigen expressed on hematopoietic stem cells with unknown function. In order to further characterize CD133(+) progenitor cells, we purified CD133(+) stem cells using the method of magnetic activated cell sorting (MACS) from healthy adult volunteers mobilized with granulocyte colony-stimulating growth factor (G-CSF) to a mean purity of 94%. The purified CD133(+) cells highly engrafted NOD/SCID mice. In addition, unseparated mononuclear cells or CD133(+) stem cells isolated from the bone marrow of transplanted NOD/SCID mice gave rise to engraftment of secondary recipients. Upon ex vivo culture of purified CD133(+) cells with FLT3/Flk2 ligand (FL) and interleukin-6 (IL-6), a plastic-adherent cell population could be observed after 6 weeks in culture. These adherent cells did not express CD34 or CD133 antigens on their surface, nor did they express markers for endothelial, mesenchymal, or dendritic cells. After incubation of these adherent cells with stem cell factor (SCF), non-adherent cells were observed which partially co-expressed CD133, but were negative for CD34. These nonadherent CD34(-) cells showed a high engraftment capacity in NOD/SCID mice. From our results, we conclude that CD133 might be a marker of early progenitors with a high NOD/SCID engraftment potential. The fact that CD133(+) hematopoietic progenitors can give rise to an adherent population which is CD133(-) and CD34(-) and that these cells can again give rise to a CD133(+)CD34(-) stem cell population with high NOD/SCID engraftment potential indicates the plasticity of hematopoietic precursors. CD133(+) stem cells might be useful for research and for clinical application.
N‐ and O‐linked carbohydrates and glycosylation site occupancy in recombinant human granulocyte‐macrophage colony‐stimulating factor secreted by a Chinese hamster ovary cell line (2004)

GM-CSF is one of several naturally occurring glycoproteins that regulate leukocyte production, migration and function. It has been produced in different cell types, with different properties that depend on the production process used. The purpose of this work was to characterize the recombinant human GM-CSF from an engineered Chinese hamster ovary cell line grown in suspension and as adherent culture for the identification of the glycosylation sites and the definition of the glycosidic moiety, including the degree of site occupancy. Both preparations exhibited size heterogeneity in SDS/PAGE with multiple bands containing glycoprotein forms with either two or one N-glycosylation sites occupied. Minor low molecular mass forms completely lacked N-linked oligosaccharides but contained 1-3 O-linked glycans. Twelve differently charged isoforms were detected in isoelectric focusing gels. At least 16 glycoforms, differing in the number of Hex-HexNAc units (Deltam 365 Da), were detected in MALDI-TOF MS spectra of the desialylated GM-CSFs. MALDI-TOF MS and HPAEC-PAD analysis indicated the presence of predominantly tri- and tetraantennary N-linked oligosaccharide chains with and without N-acetyllactosamine repeat units and some 10% of biantennary oligosaccharides, all containing more than 90% proximal alpha1-6-linked fucose. The oligosaccharide patterns of both GM-CSF preparations were found to be very similar. More than 90% of terminal galactose residues of the N-glycans were found alpha2-3 sialylated with NeuNAc (93%) or NeuNGc (7%). Site specific glycosylation was analysed by electrospray ionization MS and it was found that in the mono glycosylated GM-CSF form more than 90% of the Asn37 were occupied by N-glycans. O-glycosylation at the N-terminus of the polypeptide was detected at Ser7 and Ser9 or Thr10, in the predominantly doubly O-glycosylated glycoprotein form. In the triply modified GM-CSF molecules, Ser5 was additionally O-glycosylated. The major difference between both preparations was found in the MALDI spectra of the desialylated glycoproteins, revealing a higher proportion of forms with a single N-glycosylation site occupied in the preparation derived from suspension culture. ESI-MS and MALDI-MS analysis of endoproteolytically cleaved peptides as well as MALDI-TOF MS of the intact glycoprotein demonstrated the N- and C-termini integrity of the GM-CSF preparations.
Dissection of the human acetylcholinesterase active center determinants of substrate specificity. Identification of residues constituting the anionic site, the hydrophobic site, and the acyl pocket (1993)

Substrate specificity determinants of human acetylcholinesterase (HuAChE) were identified by combination of molecular modeling and kinetic studies with enzymes mutated in residues Trp-86, Trp-286, Phe-295, Phe-297, Tyr-337, and Phe-338. The substitution of Trp-86 by alanine resulted in a 660-fold decrease in affinity for acetythiocholine but had no effect on affinity for the isosteric uncharged substrate (3,3-dimethylbutylthioacetate). The results demonstrate that residue Trp-86 is the anionic site which binds, through cation-pi interactions, the quaternary ammonium of choline, and that of active center inhibitors such as edrophonium. The results also suggest that in the non-covalent complex, charged and uncharged substrates with a common acyl moiety (acetyl) bind to different molecular environments. The hydrophobic site for the alcoholic portion of the covalent adduct (tetrahedral intermediate) includes residues Trp-86, Tyr-337, and Phe-338, which operate through nonpolar and/or stacking interactions, depending on the substrate. Substrates containing choline but differing in the acyl moiety (acetyl, propyl, and butyryl) revealed that residues Phe-295 and Phe-297 determine substrate specificity of the acyl pocket for the covalent adducts. Phe-295 also determines substrate specificity in the non-covalent enzyme substrate complex and thus, the HuAChE F295A mutant exhibits over 130-fold increase in the apparent bimolecular rate constant for butyrylthiocholine compared with wild type enzyme. Reactivity toward specific butyrylcholinesterase inhibitors is similarly dependent on the nature of residues at positions 295 and 297. Amino acid Trp-286 at the rim of the active site "gorge" and Trp-86, in the active center, are essential elements in the mechanism of inhibition by propidium, a peripheral anionic site ligand. Molecular modeling and kinetic data suggest that a cross-talk between Trp-286 and Trp-86 can result in reorientation of Trp-86 which may then interfere with stabilization of substrate enzyme complexes. It is proposed that the conformational flexibility of aromatic residues generates a plasticity in the active center that contributes to the high efficiency of AChE and its ability to respond to external stimuli.