gebhart/patrepeval huggingface dataset:
Long-Lasting Rescue of Age-Associated Deficits in Cognition and the CNS Cholinergic Phenotype by a Partial Agonist Peptidomimetic Ligand of TrkA (2004)

Previously, we developed a proteolytically stable small molecule peptidomimetic termed D3 as a selective ligand of the extracellular domain of the TrkA receptor for the NGF. Ex vivo D3 was defined as a selective, partial TrkA agonist. Here, the in vivo efficacy of D3 as a potential therapeutic for cholinergic neurons was tested in cognitively impaired aged rats, and we compared the consequence of partial TrkA activation (D3) versus full TrkA/p75 activation (NGF). We show that in vivo D3 binds to TrkA receptors and affords a significant and long-lived phenotypic rescue of the cholinergic phenotype both in the cortex and in the nucleus basalis. The cholinergic rescue was selective and correlates with a significant improvement of memory/learning in cognitively impaired aged rats. The effects of the synthetic ligand D3 and the natural ligand NGF were comparable. Small, proteolytically stable ligands with selective agonistic activity at a growth factor receptor may have therapeutic potential for neurodegenerative disorders.
Semantic grasping: Planning robotic grasps functionally suitable for an object manipulation task (2012)

We design an example based planning framework to generate semantic grasps, stable grasps that are functionally suitable for specific object manipulation tasks. We propose to use partial object geometry, tactile contacts, and hand kinematic data as proxies to encode semantic constraints, which are task-related constraints. We introduce a semantic affordance map, which relates local geometry to a set of predefined semantic grasps that are appropriate to different tasks. Using this map, the pose of a robotic hand can be estimated so that the hand is adjusted to achieve the ideal approach direction required by a particular task. A grasp planner is then used to generate a set of final grasps which have appropriate stability, tactile contacts, and hand kinematics along this approach direction. We show experiments planning semantic grasps on everyday objects and executing these grasps with a physical robot.
The right way to write a good tale (2000)

Writing your own play means you really can tailor it to your needs. It can, however, be a bit daunting. Margaret Cornell has some advice for beginners.
Cloning, partial sequence, expression, and antigenic analysis of the filamentous hemagglutinin gene of Bordetella pertussis (1990)

The gene coding for the filamentous hemagglutinin (FHA), one of the main factors involved in mediating adherence of Bordetella pertussis to ciliated host cells, was cloned in Escherichia coli, and the 3,500-base-pair nucleotide sequence encoding the amino-terminal region was determined. Molecular cloning, together with the characterization of recombinant FHA-related proteins produced in E. coli, revealed that the primary translation product is a protein of about 370 kilodaltons (kDa). The mature 220-kDa FHA polypeptide secreted by B. pertussis is most probably generated by proteolytic processing that eliminates a carboxy-terminal portion of about 150 kDa. The 1,087 amino-terminal residues of the predicted FHA sequence showed a number of remarkable features. Extensive homology to the Serratia marcescens and Proteus mirabilis hemolysin proteins was found between amino acids 91 and 205 of the FHA sequence, suggesting involvement of this FHA domain in host cell binding or secretion of FHA from B. pertussis. In addition, two regions containing repetitive amino acid sequences were identified. One region, extending from residues 382 to 664, was formed by six repeats, and a second, extending from residues 701 to 912, contained three repeats. The reactivities of several recombinant FHA-derived proteins with a panel of monoclonal antibodies identified at least four epitopes composing an immunoreactive domain present in the carboxy-terminal moiety of the mature FHA.
Genetic Toggling of Alkaline Phosphatase Folding Reveals Signal Peptides for All Major Modes of Transport across the Inner Membrane of Bacteria (2008)

Prediction of export pathway specificity in prokaryotes is a challenging endeavor due to the similar overall architecture of N-terminal signal peptides for the Sec-, SRP- (signal recognition particle), and Tat (twin arginine translocation)-dependent pathways. Thus, we sought to create a facile experimental strategy for unbiased discovery of pathway specificity conferred by N-terminal signals. Using a limited collection of Escherichia coli strains that allow protein oxidation in the cytoplasm or, conversely, disable protein oxidation in the periplasm, we were able to discriminate the specific mode of export for PhoA (alkaline phosphatase) fusions to signal peptides for all of the major modes of transport across the inner membrane (Sec, SRP, or Tat). Based on these findings, we developed a mini-Tn5 phoA approach to isolate pathway-specific export signals from libraries of random fusions between exported proteins and the phoA gene. Interestingly, we observed that reduced PhoA was exported in a Tat-independent manner when targeted for Tat export in the absence of the essential translocon component TatC. This suggests that initial docking to TatC serves as a key specificity determinant for Tat-specific routing of PhoA, and in its absence, substrates can be rerouted to the Sec pathway, provided they remain compatible with the Sec export mechanism. Finally, the utility of our approach was demonstrated by experimental verification that four secreted proteins from Mycobacterium tuberculosis carrying putative Tat signals are bona fide Tat substrates and thus represent potential Tat-dependent virulence factors in this important human pathogen.
Flow cytometric immunophenotyping of feline bone marrow cells and haematopoietic progenitor cells using anti-human antibodies (2013)

There is a paucity of species-specific antibodies available for feline haematopoietic conditions. The purpose of this study was to broaden the panel of antibodies available for use in the immunophenotypic characterisation of feline haematopoietic cells by testing clones of anti-human monoclonal antibodies (mAbs) on normal, neoplastic and cultured feline haematopoietic progenitors to determine cross-reactivity to feline counterparts. In this study, 24 clones of anti-human mAbs were tested on normal or neoplastic feline bone marrow and peripheral blood cells. Six of these mAbs, including anti-cluster of differentiation (CD)61, anti-CD18, anti-CD14, anti-CD235a, anti-CD41 and anti-CD29, cross-reacted with normal feline bone marrow cells, whereas anti-CD33 and anti-CD117 cross-reacted with the blast cells in the bone marrow of two cats with myelodysplastic syndrome, and anti-CD71, anti-235a, anti-41 and anti-42 cross-reacted with immature erythroid cells in a cat with erythroleukaemia. In a feline immunodeficiency virus-positive cat, bone marrow cells were labelled with anti-CD33, anti-14 and anti-45. Anti-CD18, anti-CD14, anti-CD41 and anti-CD61 also reacted with the peripheral blood cells of the healthy cats. The feline haematopoietic progenitors formed colonies in the methylcellulose-based semisolid medium with significant enrichment of colony-forming unit-granulocyte, monocyte and burst-forming unit-erythroid. A panel of six anti-feline mAbs (anti-CD21-like, anti-T lymphocytes, anti-CD172a, anti-granulocyte, anti-CD45-like and anti-CD18) and eight anti-human antibodies (anti-CD71, anti-CD33, anti-CD235a, anti-CD41, anti-CD61, anti-CD117, anti-CD38 and anti-CD34) were used for the immunophenotypic characterisation of the feline bone marrow progenitors. CD45, CD33, CD235a and CD18 were expressed by the feline haematopoietic progenitor cells, with the highest expression level for CD45.
Dilute barium as a contrast agent for abdominal CT (1980)

Dilute barium as a contrast agent for abdominal CTAJ Megibow and MA BosniakAudio Available | Share
Targeting of liposomes surface-modified with glycyrrhizin to the liver. I. Preparation and biological disoposition. (1991)

We consider glycyrrhizin to be a new ligand for liposomes to the liver because it is known that about 80% of glycyrrhizin is excreted into the bile after intravenous administration in rats. In order to modify the liposomal surface with glycyrrhizin, 30-stearyl glycyrrhizin (GLOSt), one of the lipophilic glycyrrhizin derivatives, was synthesized. The structure of this new compound was identified by nuclear magnetic resonance (NMR), infrared (IR) and mass spectra (MS). Sonicated liposomes were prepared from hydrogenated egg phosphatidylcholine-cholesterol-GLOSt or dicetyl phosphate (DCP) (4:4:1) and were labelled with [3H]inulin as an aqueous marker. It was confirmed by measuring the encapsulation efficiencies and the mean diameters that GLOSt-containing sonicated liposomes (GLOSt-SUV) were SUV-type as well as DCP-containing control liposomes (control-SUV). Four hours after intravenous injection into rats at a dose of 90 mumol as total lipid per kg of rat body weight, GLOSt-SUV showed 4-fold more accumulation (42.4%) in the liver than control-SUV. Therefore, glycyrrhizin is considered to be a useful new ligand on liposomes for targeting to the liver.
Molecular cloning of a peroxisomal Ca 2+ -dependent member of the mitochondrial carrier superfamily (1997)

A cDNA from a novel Ca2+-dependent member of the mitochondrial solute carrier superfamily was isolated from a rabbit small intestinal cDNA library. The full-length cDNA clone was 3,298 nt long and coded for a protein of 475 amino acids, with four elongation factor-hand motifs located in the N-terminal half of the molecule. The 25-kDa N-terminal polypeptide was expressed in Escherichia coli, and it was demonstrated that it bound Ca2+, undergoing a reversible and specific conformational change as a result. The conformation of the polypeptide was sensitive to Ca2+ which was bound with high affinity (Kd approximately 0.37 microM), the apparent Hill coefficient for Ca2+-induced changes being about 2.0. The deduced amino acid sequence of the C-terminal half of the molecule revealed 78% homology to Grave disease carrier protein and 67% homology to human ADP/ATP translocase; this sequence homology identified the protein as a new member of the mitochondrial transporter superfamily. Northern blot analysis revealed the presence of a single transcript of about 3,500 bases, and low expression of the transporter could be detected in the kidney but none in the liver. The main site of expression was the colon with smaller amounts found in the small intestine proximal to the ileum. Immunoelectron microscopy localized the transporter in the peroxisome, although a minor fraction was found in the mitochondria. The Ca2+ binding N-terminal half of the transporter faces the cytosol.
<title>Comparative analysis of SNR for image sensors with enhanced dynamic range</title> (1999)

Dynamic range is a critical figure of merit for image sensors. Often a sensor with higher dynamic range is regarded as higher quality than one with lower dynamic range. For CCD and CMOS sensors operating in the integration mode the sensor SNR monotonically increases with the signal. Therefore, a sensor with higher dynamic range, generally, produces higher quality images than one with lower dynamic range. This, however, is not necessarily the case when dynamic range enhancement schemes are used. For example, suing the well capacity adjusting scheme dynamic range is enhanced but at the expense of substantial degradation in SNR. On the other hand, using multiple sampling dynamic range can be enhanced without degrading SNR. Therefore, even if both schemes achieve the same dynamic range the latter can produce higher image quality than the former. The paper provides a quantitative framework for comparing SNR for image sensors with enhanced dynamic range. We introduce a simple model to describe the sensor output response as a function of the photogenerate signal, dark signal, and noise for sensors operation in integration mode with and without dynamic range enhancement schemes. We use the model to quantify and compare dynamic range and SNR for three sensor operation modes, integration with shuttering, using the well capacity adjusting scheme, and using multiple sampling.
Differential and Special Properties of the Major Human UGT1-encoded Gastrointestinal UDP-glucuronosyltransferases Enhance Potential to Control Chemical Uptake (2004)

UDP-glucuronosyltransferase (UGT) isozymes detoxify metabolites, drugs, toxins, and environmental chemicals via conjugation to glucuronic acid. Based on the extended UGT1 locus combined with Northern blot analysis and in situ hybridization, we determined the distribution of UGT1A1 and UGT1A7 through UGT1A10 mRNAs and found them for the first time segmentally distributed in the mucosal epithelia layer of the gastrointestinal tract. Biochemically, recombinant isozymes exhibited pH optima of 5.5, 6.4, 7.6, 8.5, and/or a broad pH range, and activities were found to be unaffected or progressively inhibited by increasing substrate concentrations after attaining Vmax for certain chemicals. Under different optimal conditions, all exhibited wide substrate selections for dietary and environmentally associated chemicals. Evidence also suggests tandem effects of isozymes in the time for completion of reactions when comparing short- and long-term incubations. Moreover, treatment of colon cells with certain diet-associated constituents, curcumin and nordihydroguaiaretic acid, reversibly targets UGTs causing inhibition without affecting protein levels; there is no direct inhibition of control UGT using curcumin as substrate in the in vitro assay. In summary, we demonstrate that UGTs are located in gastrointestinal mucosa, have vast overlapping activities under differential optimal conditions, and exhibit marked sensitivity to certain dietary substrates/constituents, representing a first comprehensive study of critical properties concerning glucuronidating isozymes in alimentary tissues. Additionally, the highly dynamic, complex, and variable properties necessarily impact absorption of ingested chemicals and therapeutic drugs.
The Contact Phase of Blood Coagulation in Diabetes Mellitus and in Patients with Vasculopathy (1984)

The contact phase has been studied in diabetics and patients with macroangiopathy. Factor XII and high molecular weight kininogen (HMWK) are normal. C1-inhibitor and also alpha 2-macroglobulin are significantly elevated in diabetics with complications, for alpha 2-macroglobulin especially in patients with nephropathy, 137.5% +/- 36.0 (p less than 0.001). C1-inhibitor is also increased in vasculopathy without diabetes 113.2 +/- 22.1 (p less than 0.01). Prekallikrein (PK) is increased in all patients' groups (Table 2) as compared to normals. PK is particularly high (134% +/- 32) in 5 diabetics without macroangiopathy but with sensomotor neuropathy. This difference is remarkable because of the older age of diabetics and the negative correlation of PK with age in normals.
Therapeutic Potential of Neurotrophic Factors and Neural Stem Cells Against Ischemic Brain Injury (2000)

Development of neuronal and glial cells and their maintenance are under control of neurotrophic factors (NTFs). An exogenous administration of NTFs protects extremely sensitive brain tissue from ischemic damage. On the other hand, it is now known that neural stem cells are present in normal adult brain, and have a potential to compensate and recover neural functions that were lost due to ischemic stroke. These stem cells are also under control of NTFs to differentiate into a certain species of neural cells. Thus, the purpose of this review is to summarize the present understanding of the role of NTFs in normal and ischemic brain and the therapeutic potential of NTF protein itself or gene therapy, and then to summarize the role of NTFs in stem cell differentiation and a possible therapeutic potential with the neural stem cells against ischemic brain injury.
Role of lysozyme in the microbicidal activity of rat alveolar macrophages (1977)

Lysozyme release from alveolar macrophages is stimulated by exposure to particles, such as latex and zymosan, and to bacteria. Rat alveolar marcophages contain 10-fold-greater intracellualr concentrations of lysozyme and release more lysozyme after stimulation than rat blood neutrophils. During 30 min of incubation in vitro, alveolar macrophages kill more than 99% of Micrococcus lysodeikticus in the incubation mixture, whereas neutrophils kill approximately 50% of the bacteria. The bactericidal capacity of alveolar macrophages for M. lysodeikticus exceeds that of neutrophils at all bacteria-to-cell ratios tested. This bacterial killing by alveolar macrophages is inhibited when specific rabbit antirat lysozyme serum is added to the incubation mixture. Electron microscopy studies indicate that bacterial killing occurs extracellularly. Initial degradation of bacteria occurs within 5 min, and lysis is complete by 25 to 30 min. Phagocytosis of lysed bacteria is maximum after 25 to 30 min. The greater quantities of lysozyme, both intracellularly and released into the extracellular environment by alveolar macrophages, suggest that this factor may be a mechanism by which alveolar macrophages contribute to pulmonary defense.
Substrate specificity of mitochondrial 2'-deoxyguanosine kinase. Efficient phosphorylation of 2-chlorodeoxyadenosine. (1993)

Mitochondrial deoxyguanosine kinase (dGK) (EC 2.7.1.113) was purified to apparent homogeneity from bovine brain. The molecular mass of the native protein was 56 kDa, as judged by gel filtration, and one single band of 28 kDa was seen in sodium dodecyl sulfate-gel electrophoresis. 2'-Deoxyguanosine (dGuo) (Km, 7.6 microM), 2'-deoxyinosine, and 2'-deoxyadenosine (Km, 60 microM) were substrates for the enzyme as well as several dGuo analogs containing a lipophilic substituent at C-2'. Carbocyclic dGuo, 9-beta-D-arabinofuranosylguanine, 9-beta-D-arabinofuranosylhypoxanthine, and 9-beta-D-arabinofuranosyladenine were substrates for the enzyme, whereas no 3'-modified dGuo analogs were effective. Interestingly, 2-chloro-2'-deoxyadenosine (CdA) was found to be an efficient substrate for dGK (Km, 85 microM). Subcellular fractionation of human CEM lymphoblasts showed that extracts of mitochondria contain significant CdA phosphorylating activity (71.5 pmol/mg/min) that is not inhibited by excess of 2'-deoxycytidine (dCyd). This contrasts with the CdA phosphorylating activity found in cytosolic extracts, which is carried out by dCyd kinase and strongly inhibited by excess of dCyd. The efficient CdA phosphorylation by mitochondrial dGK is a novel finding that may have far reaching implications for the clinical use of this potent cytostatic drug.
Role of Tumor Endothelium in CD4+CD25+ Regulatory T Cell Infiltration of Human Pancreatic Carcinoma (2007)

Tumor-induced expression of addressins on the surface of endothelial cells allows a selective transmigration of Treg cells from peripheral blood to tumor tissues.
Masquerade Detection Using a Taxonomy-Based Multinomial Modeling Approach in UNIX Systems (2008)

This paper presents one-class Hellinger distance-based and one-class SVM modeling techniques that use a set of features to reveal user intent. The specific objective is to model user command profiles and detect deviations indicating a masquerade attack. The approach aims to model user intent, rather than only modeling sequences of user issued commands. We hypothesize that each individual user will search in a targeted and limited fashion in order to find information germane to their current task. Masqueraders, on the other hand, will likely not know the file system and layout of another user's desktop, and would likely search more extensively and broadly. Hence, modeling a user search behavior to detect deviations may more accurately detect masqueraders. To that end, we extend prior research that uses UNIX command sequences issued by users as the audit source by relying upon an abstraction of commands. We devised a taxonomy of UNIX commands that is used to abstract command sequences. The experimental results show that the approach does not lose information and performs comparably to or slightly better than the modeling approach based on simple UNIX command frequencies.
HEB, a helix-loop-helix protein related to E2A and ITF2 that can modulate the DNA-binding ability of myogenic regulatory factors. (1992)

Proteins containing the basic-helix-loop-helix (B-HLH) domain have been shown to be important in regulating cellular differentiation. We have isolated a cDNA for a human B-HLH factor, denoted HEB, that shares nearly complete identity in the B-HLH domain with the immunoglobulin enhancer binding proteins encoded by the E2A and ITF2 genes (E proteins). Functional characterization of the protein expressed from this cDNA indicates that HEB is a third member of the E-protein class of B-HLH factors. HEB mRNA was found to be expressed in several tissues and cell types, including skeletal muscle, thymus, and a B-cell line. HEB, ITF2, and the E12 product of the E2A gene all bound to a similar spectrum of E-box sequences as homo-oligomers. All three factors also formed hetero-oligomers with myogenin, and the DNA-binding specificity and binding off-rates (dissociation rates) were modulated after hetero-oligomerization. Both homo- and hetero-oligomers of these proteins were able to distinguish between very closely related E-box sequences. In addition, HEB was shown to form hetero-oligomers with the E12 and ITF2 proteins. Finally, HEB was able to activate gene expression. These data demonstrate that HEB shares characteristics with other E proteins and show that HEB can interact with members of both the myogenic regulatory class and the E-protein class of B-HLH factors. HEB is therefore likely to play an important role in regulating lineage-specific gene expression.
Perivenous expression of the mRNA of the three hypoxia-inducible factor α-subunits, HIF1α, HIF2α and HIF3α, in rat liver (2001)

The cDNAs of three hypoxia-inducible factor (HIF) α-subunits were cloned from RNA of primary rat hepatocytes by reverse transcriptase PCR. All three cDNAs encoded functionally active proteins, of 825, 874 and 662 amino acids. After transfection they were able to activate luciferase activity of a luciferase gene construct containing three HIF-responsive elements. The mRNAs of the rat HIF α-subunits were expressed predominantly in the perivenous zone of rat liver tissue; the nuclear HIFα proteins, however, did not appear to be zonated. The sequence data reported here have been deposited in the EMBL Nucleotide Sequence Database under the following accession numbers: rHIF1α, Y09507; rHIF2α, AJ277828; rHIF3α, AJ277827.
An adenovirus vector system used to express polyoma virus tumor antigens. (1985)

We have used a generalized adenovirus vector system to express the three polyoma tumor (T) antigen proteins under the control of the adenovirus major late promoter. One hybrid virus, Ad-PySVR498, expresses high levels of polyoma middle and small T antigens. A second hybrid virus, Ad-LTSVR545, which contains a cDNA copy of the polyoma A gene, overproduces large T antigen. The T antigens produced are indistinguishable from their authentic polyoma counterparts as determined by immunoprecipitation and partial cleavage by V8 protease. Analysis of polyoma mRNAs encoded by the recombinant viruses showed that they initiate from the adenovirus major late promoter and contain the tripartite leader at their 5' ends. Large T antigen isolated from Ad-LTSVR545-infected cells by immunoaffinity was shown to bind selectively to polyoma DNA sequences that contain the origin of viral DNA replication as well as the sites for transcription initiation.