gebhart/patrepeval huggingface dataset:
The Role of Pore Geometry in Single Nanoparticle Detection (2012)

We observe single nanoparticle translocation events via resistive pulse sensing using silicon nitride pores described by a range of lengths and diameters. Pores are prepared by focused ion beam milling in 50 nm-, 100 nm-, and 500 nm-thick silicon nitride membranes with diameters fabricated to accommodate spherical silica nanoparticles with sizes chosen to mimic that of virus particles. In this manner, we are able to characterize the role of pore geometry in three key components of the detection scheme, namely, event magnitude, event duration, and event frequency. We find that the electric field created by the applied voltage and the pore's geometry is a critical factor. We develop approximations to describe this field, which are verified with computer simulations, and interactions between particles and this field. In so doing, we formulate what we believe to be the first approximation for the magnitude of ionic current blockage that explicitly addresses the invariance of access resistance of solid-state pores during particle translocation. These approximations also provide a suitable foundation for estimating the zeta potential of the particles and/or pore surface when studied in conjunction with event durations. We also verify that translocation achieved by electro-osmostic transport is an effective means of slowing translocation velocities of highly charged particles without compromising particle capture rate as compared to more traditional approaches based on electrophoretic transport.
Cloning of neurotrimin defines a new subfamily of differentially expressed neural cell adhesion molecules (1995)

Previous studies in the laboratory indicated that glycosylphosphatidylinositol (GPI)-anchored proteins may generate diversity of the cell surface of different neuronal populations (Rosen et al., 1992). In this study, we have extended these findings and surveyed the expression of GPI-anchored proteins in the developing rat CNS. In addition to several well characterized GPI-anchored cell adhesion molecules (CAMs), we detected an unidentified broad band of 65 kDa that is the earliest and most abundantly expressed GPI-anchored species in the rat CNS. Purification of this protein band revealed that it is comprised of several related proteins that define a novel subfamily of immunoglobulin-like (Ig) CAMs. One of these proteins is the opiate binding-cell adhesion molecule (OBCAM). We have isolated a cDNA encoding a second member of this family, that we have termed neurotrimin, and present evidence for the existence of additional family members. Like OBCAM, with which it shares extensive sequence identity, neurotrimin contains three immunoglobulin-like domains. Both proteins are encoded by distinct genes that may be clustered on the proximal end of mouse chromosome 9. Characterization of the expression of neurotrimin and OBCAM in the developing CNS by in situ hybridization reveals that these proteins are differentially expressed during development. Neurotrimin is expressed at high levels in several developing projection systems: in neurons of the thalamus, subplate, and lower cortical laminae in the forebrain and in the pontine nucleus, cerebellar granule cells, and Purkinje cells in the hindbrain. Neurotrimin is also expressed at high levels in the olfactory bulb, neural retina, dorsal root ganglia, spinal cord, and in a graded distribution in the basal ganglia and hippocampus. OBCAM has a much more restricted distribution, being expressed at high levels principally in the cortical plate and hippocampus. These results suggest that these proteins, together with other members of this family, provide diversity to the surfaces of different neuronal populations that could be important in the specification of neuronal connectivity.
Effect of Photodynamic Therapy on Tumor Necrosis Factor Production by Murine Macrophages (1990)

Photodynamic therapy (PDT) involves the treatment of tumors in the presence of sensitizer, light, and oxygen, causing energy-dependent cytotoxicity. A vascular effect that causes hemorrhagic tumor necrosis has been described with PDT, but its basis remains undefined. To investigate the possible role of tumor necrosis factor (TNF) production in the generation of such a vascular effect and/or a direct tumor effect, we treated thioglycollate-elicited murine macrophages with PDT, and we measured the possible production of TNF using the L929 assay. An energy-dependent production of TNF by macrophage treated with PDT, stimulated or unstimulated with endotoxin, was demonstrated, and TNF production was inhibited at the highest treatment energy levels. These data represent the first description of cytokine production by PDT-treated macrophages, and may serve as another mechanism of PDT cytotoxicity in vivo, either directly by TNF-mediated tumor necrosis, or indirectly by vascular effects on tumor vessels.
Nephelometric determination of phosphorus in soybean and corn oil processing (1986)

Abstract A procedure to measure phosphorus content of soybean and corn oil samples has been developed using nephelometry (turbidity). The method uses the relationship between phosphorus level due to phosphatides in vegetable oil and turbidity formed in phosphatide mixtures. The rapid 10‐min determination of phosphorus in process samples is 30 times faster than colorimetric methods. Phosphorus vs turbidity data formed nearly linear relationships for crude, degummed, once‐refined, bleached and deodorized soybean and corn oil process samples.
3D-Printed Optics for Wafer-Scale Probing (2018)

Mass production of photonic integrated circuits requires high-throughput wafer-level testing. We demonstrate that optical probes equipped with 3D-printed elements allow for efficient coupling of light to etched facets of nanophotonic waveguides. The technique is widely applicable to different integration platforms.
Comparative sequence analysis of rotavirus genomic segment 6--the gene specifying viral subgroups 1 and 2 (1984)

Cloned DNA copies of rotavirus genomic segment 6 from simian 11 (subgroup 1) and human strain Wa (subgroup 2) rotaviruses have been used to determine the nucleotide sequences of the gene that determines viral subgroup specificity. Both genomic segments are 1,356 nucleotides in length and possess 5'- and 3'-terminal untranslated regions of 23 and 142 nucleotides, respectively. The inferred amino acid sequence reveals VP6 to be a polypeptide of 397 amino acids in which more than 90% of the amino acid sequence is conserved between the two viruses. There are 34 amino acid changes between the subgroup 1 and 2 polypeptides, most clustered in three regions of the molecule at residues 39 through 62, 80 through 122, and 281 through 315.
Immunological studies in patients with isolated growth hormone deficiency. (1983)

The proportion of total T cells, OKT4+ (helper/inducer phenotype) T cells and activated T cells (Tac+) in four growth hormone deficient children were compared to simultaneously studied age and sex matched healthy controls. Proportions of OKT8+ T cells (suppressor/cytotoxic phenotype), and B lymphocytes (surface immunoglobulin positive) were increased when compared to healthy controls. Increased proportion of OKT8+ T cells resulted in abnormally low ratios of OKT4+/OKT8+ cells. Proliferative response to PHA and in the AMLR were comparable to the control group. In allogeneic MLR, T cells from three of four patients responded poorly and three of four patients non-T cells stimulated poorly in MLR. Con A activated suppressor cell activity was comparable to healthy control group. This study supports the role of growth hormone in certain immune response.
OVERINVESTMENT IN TEAM SPORTS LEAGUES: A CONTEST THEORY MODEL (2008)

ABSTRACT This paper applies contest theory to provide an integrated framework of a team sports league and analyzes the competitive interaction between clubs. We show that dissipation of the league revenue arises from ‘overinvestment’ in playing talent as a direct consequence of the ruinous competitive interaction between clubs. This overinvestment problem increases if the discriminatory power of the contest function increases, revenue‐sharing decreases, and the size of an additional exogenous prize increases. We further show that clubs invest more when they play in an open league compared with a closed league. Moreover, the overinvestment problem within open leagues increases with the revenue differential between leagues.
130nm Single Event Upset Performance Evaluation: Commercial vs. Hardened by Design Architectures (2011)

Two test chips have been built and SEE data has been collected to validate the radiation hardness of both commercial and Hardened-by-Design elements on a 130nm RadHard-by-Design ASIC Library.
Peptide Transport through the Blood-Brain Barrier (1989)

Most neuropeptides are incapable of entering brain from blood owing to the presence of unique anatomical structures in the brain capillary wall, which makes up the blood-brain barrier (BBB). Such neuropeptides could be introduced into the bloodstream by intranasal insufflation and , thus, could have powerful medicinal properties (e.g., beta B-endorphin for the treatment of pain, vasopressin analogues for treatment of memory, ACTH analogues for treatment of post-traumatic epilepsy), should these peptides be capable of traversing the BBB. One such strategy for peptide delivery through the BBB is the development of chimeric peptides, which is the basis of the present contract. The production of chimeric peptides involves the covalent coupling of an nontransportable peptide (e.g., B-endorphin, vasopressin) to a transportable vector peptide (e.g., insulin, transferrin, cationized albumin, histone). The transportable peptide is capable of penetrating the BBB via receptor-mediated or absorptive-mediated transcytosis. Therefore, the introduction of chimeric peptides allows the nontransportable peptide to traverse the BBB via physiologic mechanisms by piggy back on the transportable Vector. Keywords: Peptide transport, Chimeric peptides, Hybrid peptides.
SF3B1 and Other Novel Cancer Genes in Chronic Lymphocytic Leukemia (2011)

Our study defines the landscape of somatic mutations in chronic lymphocytic leukemia and highlights pre-mRNA splicing as a critical cellular process contributing to chronic lymphocytic leukemia.
Authentication In Multi-Hop Wireless Mesh Networks (2008)

Wireless Mesh Networks (WMNs) are an emerging technology for last-mile broadband access. In WMNs, similar to ad hoc networks, each user node operates not only as a host but also as a router. User packets are forwarded to and from an Internet-connected gateway in multi-hop fashion. The WMNs can be integrated with other networking technologies i.e. ad hoc networks, to implement a smooth network extension. The meshed topology provides good reliability and scalability, as well as low upfront investments. Despite the recent start-up surge in WMNs, much research remains to be done in standardizing the functional parameters of WMNs to fully exploit their full potential. An edifice of the security concerns of these networks is authentication of a new client joining an integrated ad hoc network and such a scenario will require execution of a multihop authentication technique. Our endeavor in this paper is to introduce a secure authentication technique, with light over-heads that can be conveniently implemented for the ad-hoc nodes forming clients of an integrated WMN, thus facilitating their inter-operability.
Stimulation of human platelet guanylate cyclase by fatty acids. (1977)

Guanylate cyclase from human platelets was over 90% soluble, even when assayed in the presence of Triton X-100. A time-dependent increase in activity occurred when the enzyme was incubated at 37 degrees and this spontaneous activation was prevented by dithiothreitol. Arachidonic acid stimulated the soluble enzyme activity approximately 2- to 3-fold. Linear double reciprocal plots of guanylate cyclase activation as a function of arachidonic acid concentration were obtained with a Ka value of 2.1 muM. A Hill coefficient of 0.98 was obtained indicating that one fatty acid binding site is present for each catalytic site. Concentrations of arachidonic acid in excess of 10 muM caused less than maximal stimulation. Dihomo-gamma-linolenic acid and two polyunsaturated 22 carbon fatty acids stimulated the activity of guanylate cyclase to the same degree as did arachidonic acid. The methyl ester of arachidonic acid was much less effective. Diene, monoene, and saturated fatty acids of various carbon chain lengths as well as prostaglandins E1, E2, and F2alpha, had little or no effect. These data indicate that the structural determined required for stimulation by fatty acids of soluble platelet guanylate cyclase is a 1,4,7-octatriene group with its first double bond in the omega6 position. This structural group is similar to the substrate specificity determinants of fatty acid cyclooxygenase, the first enzyme of the prostaglandin synthetase complex. However, conversion of arachidonic acid to a metabolite of the cyclooxygenase pathway did not appear to be required for activation of the cyclase since activation occurred in the 105,000 X g supernatant fraction and pretreatment of this fraction with aspirin did not alter the ability of arachidonic acid to activate guanylate cyclase. Kinetic studies showed that the stimulation of guanylate cyclase by arachidonic acid is primarily an effect on maximal velocity. Arachidonic acid did not alter the concentration of free Mn2+ required for optimal activity. It is concluded that the activity of the soluble form of guanylate cyclase in cell-free preparations of human platelets can be increased by a lipid-protein interaction involving specific polyunsaturated fatty acids.
Effects of Ventilation with Different Positive End-expiratory Pressures on Cytokine Expression in the Preterm Lamb Lung (2001)

Ventilator-induced lung injury increases proinflammatory cytokines in the adult lung. We asked if positive end-expiratory pressure (PEEP) affects proinflammatory cytokine mRNA expression in the preterm lung. Preterm lambs at 129 +/- 3 d gestation were treated with 100 mg/kg recombinant human surfactant protein-C surfactant and ventilated for 2 or 7 h with 0, 4, or 7 cm H(2)O of PEEP. Unventilated fetal lambs were used as controls. Within 2 h of ventilation, alveolar total protein and activated neutrophils were increased and expression of mRNAs for the proinflammatory cytokines interleukin (IL)-1beta, IL-6, IL-8, and tumor necrosis factor-alpha (TNF-alpha) was increased in lung tissue of all ventilated animals relative to unventilated controls. Alveolar protein and neutrophils were higher for 0 and 7 PEEP animals than 4 PEEP animals. IL-1beta, IL-6, and IL-8 mRNAs were significantly elevated in animals ventilated with 0 PEEP compared with 4 PEEP. The percentage fractional area of collapsed alveoli was significantly higher for 0 PEEP compared with 4 and 7 PEEP groups. Mechanical ventilation increased the expression of proinflammatory mediators in surfactant-treated preterm lungs and the use of 4 PEEP minimized this response.
Volume management in SAN environment (2002)

Logical volume managers have long been key components of a storage system. Their key features are creation of logical or virtual views of physical storage devices and support for various software RAID levels. These make it possible to overcome the limits to capacity, availability and performance of a physical storage device. Most logical volume managers are operated in a single system environment. They are not adequate for SAN (storage area network) environments where several hosts share and access a logical volume at the same time. Some recent logical volume managers are run in a multi-host environment. However, they cannot support the enterprise computing environments in which the system must support 24/spl times/7/spl times/365 uptime operations such as online resizing and online backup. We propose a logical volume manager called 'SANtopia Volume Manager' that supports multihost environments and provides various volume management features to support enterprise computing. Also it is a cluster enabled logical volume manager that maximizes the parallelism for high performance, and provides high scalability and high availability.
CEREBRAL PROTECTIVE EFFECT OF LOW GRADE HYPOTHERMIA (1980)

Department of Anesthesia, University of Lund, S-221 85 Lund, SwedenDepartment of Anesthesia, University of Pennsylvania Hospital, Philadelphia, PA 19104Department of Anesthesia, Temple University Hospital, Philadelphia, PA 19140
RetargetingClostridium difficileToxin B to Neuronal Cells as a Potential Vehicle for Cytosolic Delivery of Therapeutic Biomolecules to Treat Botulism (2011)

Botulinum neurotoxins (BoNTs) deliver a protease to neurons which can cause a flaccid paralysis called botulism. Development of botulism antidotes will require neuronal delivery of agents that inhibit or destroy the BoNT protease. Here, we investigated the potential of engineering Clostridium difficile toxin B (TcdB) as a neuronal delivery vehicle by testing two recombinant TcdB chimeras. For AGT-TcdB chimera, an alkyltransferase (AGT) was appended to the N-terminal glucosyltransferase (GT) of TcdB. Recombinant AGT-TcdB had alkyltransferase activity, and the chimera was nearly as toxic to Vero cells as wild-type TcdB, suggesting efficient cytosolic delivery of the AGT/GT fusion. For AGT-TcdB-BoNT/A-Hc, the receptor-binding domain (RBD) of TcdB was replaced by the equivalent RBD from BoNT/A (BoNT/A-Hc). AGT-TcdB-BoNT/A-Hc was >25-fold more toxic to neuronal cells and >25-fold less toxic to Vero cells than AGT-TcdB. Thus, TcdB can be engineered for cytosolic delivery of biomolecules and improved targeting of neuronal cells.
Transcription Factors Stat3 and Stat5b Are Present in Rat Liver Nuclei Late in an Acute Phase Response and Bind Interleukin-6 Response Elements (1995)

Proteins binding at the interleukin-6 response element of the rat α2 macroglobulin gene were purified by a combination of chromatographic procedures including binding site-specific DNA-affinity chromatography as the principal step. Three polypeptides of 92, 91, and 86 kDa were enriched approximately 6,300-fold from nuclei of rat livers excised 12 h after the induction of an experimental acute phase response. Amino acid sequence analysis identified the 86- and 91-kDa species as two forms of the transcription factor Stat3 and the 92-kDa species as the factor Stat5b. This identification was confirmed by gel mobility shift-supershift experiments using specific antisera for Stat3 and Stat5. Unexpectedly, activated Stat5 was also detected in the nuclei of untreated control rats. cDNA clones representing Stat3 and two isoforms of Stat5b were isolated from a cDNA library prepared with mRNA from rat livers excised at the peak of an experimental acute phase response. Full-length Stat5b, predicted from cDNA, consisted of 786 amino acids, while the variant Stat5bΔ40C lacked 41 amino acids at the COOH terminus. The amino acid sequence of rat Stat5b showed 26.7% overall identity with rat Stat3, 87.3% with sheep Stat5a, 92.5% with murine Stat5a, and 98.7% with murine Stat5b. Proteins binding at the interleukin-6 response element of the rat α2 macroglobulin gene were purified by a combination of chromatographic procedures including binding site-specific DNA-affinity chromatography as the principal step. Three polypeptides of 92, 91, and 86 kDa were enriched approximately 6,300-fold from nuclei of rat livers excised 12 h after the induction of an experimental acute phase response. Amino acid sequence analysis identified the 86- and 91-kDa species as two forms of the transcription factor Stat3 and the 92-kDa species as the factor Stat5b. This identification was confirmed by gel mobility shift-supershift experiments using specific antisera for Stat3 and Stat5. Unexpectedly, activated Stat5 was also detected in the nuclei of untreated control rats. cDNA clones representing Stat3 and two isoforms of Stat5b were isolated from a cDNA library prepared with mRNA from rat livers excised at the peak of an experimental acute phase response. Full-length Stat5b, predicted from cDNA, consisted of 786 amino acids, while the variant Stat5bΔ40C lacked 41 amino acids at the COOH terminus. The amino acid sequence of rat Stat5b showed 26.7% overall identity with rat Stat3, 87.3% with sheep Stat5a, 92.5% with murine Stat5a, and 98.7% with murine Stat5b.
Phosphorylation-dependent Interactions between ADAM15 Cytoplasmic Domain and Src Family Protein-tyrosine Kinases (2002)

The adamalysins (ADAMs) are transmembrane glycoproteins involved in cell adhesion and proteolytic ectodomain processing of cytokines and adhesion molecules. Many ADAM cytoplasmic domains are proline-rich and have potential phosphorylation sites. We show here that the cytoplasmic domain of ADAM15, metargidin, can interact specifically with Src family protein-tyrosine kinases (PTKs) and the adaptor protein Grb2 in hematopoietic cells (Jurkat, THP-1, U937, and K562 cell lines). Src homology 3 domains from several Src family PTKs including Lck, Fyn, Abl, and Src associate with ADAM15 in vitro. Dephosphorylation of cell extracts resulted in decreased association of ADAM15 with Src family PTK SH3 domains, indicating that phosphorylation influences ADAM15 interactions with its binding partners. This was confirmed in vitro for Hck, Lck, and Grb2, which showed enhanced association with tyrosine-phosphorylated glutathione S-transferase-ADAM15 cytoplasmic domain compared with unphosphorylated protein. In contrast, binding of MAD2 to ADAM15 was slightly reduced by phosphorylation of the ADAM. Immunoprecipitation of ADAM15 from Jurkat cells confirmed the association with Lck in vivo, and upon PMA stimulation, the phosphorylation level of ADAM15 was increased. Cotransfection of ADAM15 and Hck showed Hck-dependent phosphorylation of ADAM15 in vivo. Hck, and to a lesser extent Lck, phosphorylated the ADAM15 cytoplasmic domain in vitro in immune complex kinase assays. Binding of ADAM15 cytoplasmic domain to Hck and Lck was also shown by Far Western analysis. In contrast to Hck, Lck activity was not required for binding to ADAM15, as shown by treatment of cells with PP1. Deletion and point mutation analysis of the ADAM15 cytoplasmic domain confirmed the importance of the proline-rich motifs for Grb2 and Lck binding and indicated the regulatory nature of Tyr(715) and Tyr(735). These data demonstrate selective, phosphorylation-dependent interactions of ADAM15 with Src family PTKs and Grb2, which highlight the potential for integration of ADAM functions and cellular signaling.
Functional genes for cellobiose utilization in natural isolates of Escherichia coli (1987)

The genes for utilization of cellobiose are normally cryptic in both laboratory strains and natural isolates of Escherichia coli. A survey of natural isolates of E. coli reveals that functional genes for cellobiose utilization, while rare, are present. The fraction of E. coli that utilized cellobiose ranged from less than 0.01% in human fecal samples to 7% in fecal samples obtained from horses. Samples obtained from sheep, cows, dogs, and pigs contained 0.1 to 0.5% cellobiose-positive E. coli. Neither the previously identified cel genes nor the bgl genes from E. coli K-12 were expressed during growth on cellobiose by any of the 14 naturally occurring Cel+ isolates that were tested. All of the naturally occurring Cel+ isolates possessed a cel operon, but all were deleted for the major portion of the bgl operon. The functional cel+ genes from these natural isolates differed from the mutationally activated cel+ genes obtained in earlier studies in that (i) the mutationally activated cel+ genes were temperature sensitive, while the functional genes were not, and (ii) transport of cellobiose was inducible in the strains carrying functional cel+ genes, while it was expressed constitutively in strains carrying mutationally activated genes.