gebhart/patrepeval huggingface dataset:
Entry of Vaccinia Virus and Cell-Cell Fusion Require a Highly Conserved Cysteine-Rich Membrane Protein Encoded by the A16L Gene (2005)

The vaccinia virus A16L open reading frame encodes a 378-amino-acid protein with a predicted C-terminal transmembrane domain and 20 invariant cysteine residues that is conserved in all sequenced members of the poxvirus family. The A16 protein was expressed late in infection and incorporated into intracellular virus particles with the N-terminal segment of the protein exposed on the surface. The cysteine residues were disulfide bonded via the poxvirus cytoplasmic redox system. Unsuccessful attempts to isolate a mutant virus with the A16L gene deleted suggested that the protein is essential for replication. To study the role of the A16 protein, we made a recombinant vaccinia virus that has the Escherichia coli lac operator system regulating transcription of the A16L gene. In the absence of inducer, A16 synthesis was repressed and plaque size and virus yield were greatly reduced. Nevertheless, virus morphogenesis occurred and normal-looking intracellular and extracellular virus particles formed. Purified virions made in the presence and absence of inducer were indistinguishable, though the latter had 60- to 100-fold-lower specific infectivity. A16-deficient virions bound to cells, but their cores did not penetrate into the cytoplasm. Furthermore, A16-deficient virions were unable to induce low-pH-triggered syncytium formation. The phenotype of the inducible A16L mutant was similar to those of mutants in which synthesis of the A21, A28, H2, or L5 membrane protein was repressed, indicating that at least five conserved viral proteins are required for entry of poxviruses into cells as well as for cell-cell fusion.
Reversal of Experimental Allergic Encephalomyelitis with Monoclonal Antibody to a T-Cell Subset Marker (1985)

Administration of a monoclonal antibody (GK1.5) that recognizes the L3T4 marker present on helper T cells prevented the development of experimental allergic encephalomyelitis (EAE) in mice. Furthermore, treatment with GK1.5 reversed EAE when the antibody was given to paralyzed animals. In vivo injection of GK1.5 selectively reduced the number of L3T4+ cells in the spleen and the lymph nodes. These results suggest that manipulation of the human equivalent of the murine L3T4+ T-cell subset with monoclonal antibodies may provide effective therapy for certain autoimmune diseases.
Control of the three-dimensional growth pattern of mammary epithelium: role of genes of the Wnt and erbB families studied using reconstituted epithelium. (1998)

The mammary gland is possibly the best system in which to study the three-dimensional organization of tissues and how that organization is disrupted in tumour development. The principal approach used has been to express genes such as oncogenes and growth factor genes in mammary epithelium in vivo, by using mammary-specific promoters in germ-line transgenic mice; by injecting virus vectors into the lumen of the mammary gland; or by transplanting genetically manipulated mammary epithelial cells into a mammary fat pad from which the natural epithelium has been removed. This chapter focuses on the last approach. The Wnt genes are short-range signalling molecules related to Wnt-1, which was discovered as an oncogene in mouse mammary tumours. Several Wnt proteins are expressed in the mammary gland; notably, Wnt-4 is normally expressed in early pregnancy. Introducing Wnt-4 into the mammary epithelium of virgin mice induces a growth pattern very similar to that of mid-pregnancy. Wnt-4 may therefore be a local signal driving epithelial branching in pregnancy. ErbB/epidermal growth factor receptor and ErbB-2 are receptors that may be important in breast tumour development and normal mammary growth control. Overactive mutants of them, i.e. the genes v-erbB and neu, disturb the growth pattern of the mammary epithelium in quite distinct ways. Overactive ErbB-2 causes local development of alveoli, suggesting that it may be involved in normal alveolus development. The varied effects of these gene products show the complexity of the control of the three-dimensional growth pattern, and encourage the idea that we may be able to relate oncogenic effects to normal growth controls.
Immobilization of Histidine-Tagged Proteins on Nickel by Electrochemical Dip Pen Nanolithography (2003)

Dip-pen nanolithography (DPN) is becoming a popular technique to "write" molecules on a surface by using the tip of an atomic force microscope (AFM) coated with the desired molecular "ink". In this work, we demonstrate that poly-histidine-tagged peptides and proteins, and free-base porphyrins coated on AFM probes, can be chelated to ionized regions on a metallic nickel surface by applying an electric potential to the AFM tip in the DPN process. DPN has been accomplished in the Tapping Mode of AFM, which creates many possible applications of positioning and subsequently imaging biomolecules, especially on soft surfaces.
Influence of organic compounds and light limitation on the growth rate of estuarine benthic diatoms (1979)

Ten species of benthic diatoms from the Eems-Dollard estuary were grown in axenic cultures under various combinations of irradiance and supply of organic substrates.Six species were capable of growth in the dark on yeast extract, casamino acids, or glucose.Four of these species grew best in the presence of glucose, whereas the growth of the other two species was supported only by yeast extract and casamino acids.The light limited growth rate of only those species that were also capable of heterotrophic growth in the dark was increased by organic substrates.The rate of this "mixed" growth together with the absence of a lag-phase upon change from autotrophic to heterotrophic conditions indicates the nutritional versatility of these diatom species.A positive relation between the organic matter content of the natural habitat and the heterotrophic capacities of the diatom species is suggested.All species with heterotrophic capacities were isolated from muddy sediments, whereas two species isolated from a sandflat seem to be obligately autotrophic.Also two species from muddy sediments apparently had no heterotrophic capacities.The cells of the six species with heterotrophic capacities differed from those of the four species without such capacities in their higher surface to volume ratio.The present study was carried out as part of a series of experimental investigations on the relations between benthic diatoms from the Eems-Dollard estuary and their physico-chemical environment.Tbie microphytobenthos of the Eems-Dollard estuary, a part of the Dutch-German Wadden Sea, is dominated by diatoms that inhabit the large intertidal sand-and mudflats.The sediments of these flats have a rather high content of organic matter (up to 20 mg/g dry sediment, Schr6der et al., 1976), especially in the more sheltered inner part of the estuary.Large amounts of organic wastewater are discharged at a few places in the estuary, causing organic enrichment of certain areas, in which the diatoms are abundant (Fig. 1).Since the benthic diatoms live in intimate contact with these sediments, the organic carbon in the sediment may be of nutritive value for the diatoms.Moreover the surface of the sediments are flushed with very turbid tidal waters that considerably reduce the effective photoperiod for the benthic diatoms.In a previous paper (Admiraal, 1977a) it was shown that short daylengths strongly reduce the growth rate of benthic diatoms in culture.In the same paper it was suggested that the autotrophic growth rate of the diatoms on the intertidal flats is limited by the low daily irradiances reaching the sediment surface, especially in winter when daily photoperiods of only a few hours can occur.Furthermore a considerable part of the benthic diatom population is found
Isolation, by affinity chromatography, of mutant escherichia coli cells with novel regulation of lamB expression (1983)

Affinity chromatography was used as a positive genetic selection technique for the isolation of cells exhibiting high levels of surface receptor expression. Starting from a large population of Escherichia coli with no maltodextrin receptor due to a deletion of malT, the positive regulator gene required for receptor synthesis, cells were chromatographically enriched that could bind to starch-Sepharose, an immobilized ligand of the receptor. One such isolate showed over 25% of wild-type-induced levels of receptor in the absence of malT and levels higher than that of the wild type in a malT+ background. In contrast to wild-type cells, receptor expression in the isolate was insensitive to control by cAMP. The maltodextrin receptor synthesized by the mutant was identical to wild-type protein in terms of ligand affinity and electrophoretic mobility and was dependent on lamB, the structural gene for the receptor. The directed evolution of this novel form of lamB expression was dependent on at least two mutations in the isolate.
Assemblies of “Hinged” Iron−Porphyrins as Potential Oxygen Sensors (2000)

Sequential self-assembly of a two-component system on a solid support is described with respect to structure and function. Two ligands, which bind to the semiconductor surface through one end and axially ligate a heme analogue at the other end, are described. Monolayer assemblies of complexes formed by these ligands and iron-porphyrin perform reversible binding of molecular oxygen. In the monolayer, a metalloporphyrin (the sensing unit) is held by the intervening ligand that serves as a “hinge”, away from the solid surface. Sensing events based on porphyrin chemistry are communicated via the ligand to the solid support. The transduction manifests itself as a change in the solid's surface electronic properties. Synthesis of the ligands and analysis of its complex formation with FeIII-porphyrin are described. The anisotropic orientation of the porphyrin ring within the ligand cavity, due to restricted rotation around the FeIII−N imidazole bonds, was probed by 1H NMR measurements in solution. We show that the porphyrin substituents stand as barriers for the free rotation even at room temperature. Molecular modeling supports the NMR evidence and reveals the stable conformations for the porphyrin's orientation relative to the solid support. The complexes were assembled as films on the (0001) surface of etched n-CdSe single crystals, and the films were characterized using transmission Fourier transform infrared (FTIR) and X-ray photoelectron (XPS) spectroscopies. Contact potential difference (CPD) and steady-state photoluminescence (PL) measurements of the derivatized CdSe show that the intervening ligands yield better conjugation and stronger binding of the sensing unit to the semiconductor surface, relative to direct adsorption of metalloporphyrins. Furthermore, the PL changes in the CdSe can be used to follow the interaction of the surface-bound FeIII-porphyrin−ligand complexes with molecular oxygen. A model is proposed to explain the electronic changes resulting from binding of O2 to the monolayer.
Opportunities for Control of Meningococcal Disease in the United States (2004)

The United States currently has relatively low rates of meningococcal disease caused by Neisseria meningitidis. Serogroups Y, C, and B are most common. Although most cases are sporadic, a minority are associated with outbreaks. Pediatric populations have disproportionately higher rates of disease, but nearly two thirds of all cases occur in persons aged 15 years and older. The major challenge to control of domestic meningococcal disease is the absence of a vaccine to prevent sporadic cases spanning many age groups. The quadrivalent A/C/Y/W-135 meningococcal polysaccharide vaccine is licensed in the United States, but because of its limited efficacy in children under two years of age, it is recommended for high-risk groups and outbreak response rather than routine childhood immunization. New conjugate meningococcal vaccines have successfully reduced endemic disease in the United Kingdom, and similar vaccines promise to have a dramatic impact on the burden of meningococcal disease in the United States.
Quaternary Associations of Acetylcholinesterase (1997)

In transfected COS cells, we analyzed the formation of heteromeric associations between rat acetylcholinesterase of type T (AChET) and various constructions derived from the NH2-terminal region of the collagen tail of asymmetric forms, QN. Using a series of deletions and point mutations in QN, we showed that the binding of AChET to QN does not require the cysteines that normally establish intersubunit disulfide bonds with catalytic subunits and that it essentially relies on the presence of stretches of successive prolines, although adjacent residues also contribute to the interaction. We thus defined a proline-rich attachment domain or PRAD, which recruits AChET subunits to form heteromeric associations. Such molecules, consisting of one PRAD associated with a tetramer of AChET, are exported efficiently by the cells. Using the proportion of AChET subunits engaged in heteromeric tetramers, we ranked the interaction efficiency of various constructions. From these experiments we evaluated the contribution of different elements of the PRAD to the quaternary assembly of AChET subunits in the secretory pathway. The PRAD remained functional when reduced to six residues followed by a string of 10 prolines (Glu-Ser-Thr-Gly3-Pro10). We then showed that synthetic polyproline itself can associate with AChET subunits, producing well defined tetramers, when added to live transfected cells or even to cell extracts. This is the first example of an in vitro assembly of AChE tetramers from monomers and dimers. These results open the way to a chemical-physical exploration of the formation of these quaternary associations, both in the secretory pathway and in vitro.
Monte Carlo simulation studies of EEG and MEG localization accuracy (2002)

Both electroencephalography (EEG) and magnetoencephalography (MEG) are currently used to localize brain activity. The accuracy of source localization depends on numerous factors, including the specific inverse approach and source model, fundamental differences in EEG and MEG data, and the accuracy of the volume conductor model of the head (i.e., the forward model). Using Monte Carlo simulations, this study removes the effect of forward model errors and theoretically compares the use of EEG alone, MEG alone, and combined EEG/MEG data sets for source localization. Here, we use a linear estimation inverse approach with a distributed source model and a realistic forward head model. We evaluated its accuracy using the crosstalk and point spread metrics. The crosstalk metric for a specified location on the cortex describes the amount of activity incorrectly localized onto that location from other locations. The point spread metric provides the complementary measure: for that same location, the point spread describes the mis-localization of activity from that specified location to other locations in the brain. We also propose and examine the utility of a "noise sensitivity normalized" inverse operator. Given our particular forward and inverse models, our results show that 1) surprisingly, EEG localization is more accurate than MEG localization for the same number of sensors averaged over many source locations and orientations; 2) as expected, combining EEG with MEG produces the best accuracy for the same total number of sensors; 3) the noise sensitivity normalized inverse operator improves the spatial resolution relative to the standard linear estimation operator; and 4) use of an a priori fMRI constraint universally reduces both crosstalk and point spread.
Frustrated two-photon creation via interference (1994)

We demonstrate the suppression and enhancement of the spontaneous emission of entangled photon pairs in parametric down-conversion using suitably placed external mirrors. The mirrors permit interference between two possible ways of creating the photon pair. In principle these mirrors can be placed at an arbitrarily large distance from the crystal. The effect is of first order in the intensity of the down-conversion radiation.
Software Defect Identification Using Machine Learning Techniques (2006)

Software engineering is a tedious job that includes people, tight deadlines and limited budgets. Delivering what customer wants involves minimizing the defects in the programs. Hence, it is important to establish quality measures early on in the project life cycle. The main objective of this research is to analyze problems in software code and propose a model that will help catching those problems earlier in the project life cycle. Our proposed model uses machine learning methods. Principal Component Analysis is used for dimensionality reduction, and Decision Tree, Multi Layer Perceptron and Radial Basis Functions are used for defect prediction. The experiments in this research are carried out with different software metric datasets that are obtained from real-life projects of three big software companies in Turkey. We can say that, the improved method that we proposed brings out satisfactory results in terms of defect prediction.
Cutting Edge: Innate Immune System Discriminates between RNA Containing Bacterial versus Eukaryotic Structural Features That Prime for High-Level IL-12 Secretion by Dendritic Cells (2004)

RNA derived from bacterial but not eukaryotic sources, when transfected into human monocyte-derived dendritic cell precursors, induces high-level IL-12 secretion in conjunction with dendritic cell maturation stimuli. In vitro-transcribed mRNA that mimics the structure of bacterial mRNA in the lack of a long 3'-poly(A) tail likewise induces IL-12 secretion, but this property is lost upon efficient enzymatic 3'-polyadenylation. Among other tested RNAs, only polyuridylic acid induced IL-12 p70. This RNA response phenomenon appears biologically distinct from the classically defined response to dsRNA. RNA-transfected APC also polarize T cells in an IL-12-dependent manner toward the IFN-gamma(high)IL-5 (low) Th1 phenotype, suggesting a link between the detection of appropriately structured RNA and the skewing of immune responses toward those best suited for controlling intracellular microbes. RNA structured to emulate bacterial patterns constitutes a novel vaccine strategy to engender polarized Th1-type immune responses.
Phase I Study of Chimeric Human/Murine Anti–Ganglioside GD2Monoclonal Antibody (ch14.18) With Granulocyte-Macrophage Colony-Stimulating Factor in Children With Neuroblastoma Immediately After Hematopoietic Stem-Cell Transplantation: A Children’s Cancer Group Study (2000)

ch14.18 can be administered with GM-CSF after HSCT in patients with neuroblastoma with manageable toxicities. The MTD is 40 mg/m(2)/d for 4 days when given in this schedule with GM-CSF.
Gene Expression Profile Analysis in Human T Lymphocytes from Patients with Down Syndrome (2004)

Down Syndrome (DS) is caused by the presence of three copies of the whole human chromosome 21 (HC21) or of a HC21 restricted region; the phenotype is likely to have originated from the altered expression of genes in the HC21. We apply the cDNA microarray method to the study of gene expression in human T lymphocytes with trisomy 21 in comparison to normal cells. Two patients with DS were investigated, along with two normal subjects as a control, all being tested in independent, duplicated cell culture experiments. The most consistent finding was the overexpression of the superoxide dismutase gene (SOD1), located on 21q, and of MHC DR beta 3 (HLA-DRB3), GABA receptor A gamma 2 (GABRG2), acetyltransferase Coenzyme, A 2 (ACAT2) and ras suppressor protein 1 (RSU1) genes. When the data were clustered according to chromosome localization, the HC21 gene set showed, on average, the highest expression in DS cells in all the experiments. Moreover, separate clustering of patients and controls was obtained when analysis was restricted to HC21 gene expression values. These findings reinforce the specific gene dosage theory for the pathogenesis of the DS phenotype, and show a consistent overexpression of the SOD1 gene on 21q.
The role of the atmosphere and the hydrosphere in crustal evolution (1981)

Abstract The physical and chemical properties of the Earth’s crust have been shaped by the interaction of endogenic and exogenic processes during the course of history. The nature of this interaction between 4.6 and 3.8 Ga B.P. is still uncertain. Since then the nature of erosional processes, of transport, deposition, and the cycling of sea water through the ocean crust, has remained reasonably constant. However, variations in the nature and in the intensity of these processes due to changes in the endogenic cycle, due to biological evolution and probably due to variations in the input of solar energy have left easily discernible marks in the nature of the crust.
Deposition of Self-Assembled Monolayers in Mesoporous Silica from Supercritical Fluids (2001)

Deposition of silane-based self-assembled monolayers onto mesoporous ceramic substrates has been found to be substantially faster from supercritical fluids than from typical condensed phase solutions. In addition, the monolayers so prepared display higher silane population density (6.5 vs 4.6 silanes/nm2), fewer defects, and greater stability than those prepared via standard solution methods. A mechanistic rationale for the pressure-induced rate enhancement and reduced defect density is presented.
Concurrent Chemotherapy and Pelvic Radiation Therapy Compared With Pelvic Radiation Therapy Alone as Adjuvant Therapy After Radical Surgery in High-Risk Early-Stage Cancer of the Cervix (2000)

The addition of concurrent cisplatin-based CT to RT significantly improves progression-free and overall survival for high-risk, early-stage patients who undergo radical hysterectomy and pelvic lymphadenectomy for carcinoma of the cervix.
High-frequency digital controller IC for DC/DC converters (2003)

This paper describes a complete digital controller IC for high-frequency switching converters. Novel architecture and configurations of the key building blocks: A/D converter, compensator and digital pulse-width modulator, are introduced to meet the requirements of tight output voltage regulation, highspeed dynamic response, and programmability without external passive components. The implementation techniques are experimentally verified on a prototype chip that takes less than 1 mm/sup 2/ of silicon area in a standard 0.5 /spl mu/ digital CMOS process and operates at the switching frequency of 1 MHz.
Infection and Replication of HIV-1 in Purified Progenitor Cells of Normal Human Bone Marrow (1988)

Myeloid progenitor cells were highly purified from normal human bone marrow by positive immunoselection with high-affinity monoclonal antibodies linked to magnetic beads and were successfully infected in vitro with the human immunodeficiency virus type 1 (HIV-1). From 99 to 100 percent pure bone marrow cells expressing the CD34 phenotypic marker were obtained. These cells were devoid of mature myeloid or T cell surface and intracellular markers as analyzed by immunohistochemical staining and flow cytometry. HIV-1 particles were detected by supernatant reverse transcriptase activity and transmission electron microscopy 40 to 60 days after infection. Viral particles were predominantly observed assembling and accumulating from within intracellular membranes, while phenotypically the cells were observed to have differentiated into CD4+ monocytes. These studies have important implications in understanding the pathogenesis of HIV-1 as well as the possible cause of certain of the observed hematologic abnormalities in HIV-1 infection. They also indicate that the bone marrow may serve as a potentially important reservoir of HIV-1 in the body.