gebhart/patrepeval huggingface dataset:
Effectiveness of shunting in patients with normal pressure hydrocephalus predicted by temporary, controlled-resistance, continuous lumbar drainage: a pilot study. (1994)

From 1984 to 1992 15 consecutive cases of normal pressure hydrocephalus were included in this pilot study. A series of tests included CT of the brain, grading of the cognitive mental state with the mini-mental state examination; urodynamic studies, and gait evaluation. These tests were carried out on admission, and repeated on day 1, day 3, and day 5 after controlled-resistance, continuous lumbar drainage (CRCLD). During this period, eight patients showed significant improvements of cognitive mental state, urodynamic studies, or gait and were regarded as CRCLD responders; the remaining seven patients were regarded as CRCLD non-responders. The CRCLD was routinely removed on day 6 after the drainage procedure and a ventriculoperitoneal (VP) or a lumboperitoneal (LP) shunt was randomly selected for each patient. The tests were repeated one week after shunting and a year later. All the CRCLD responders continued to benefit from shunting at one week and one year after the procedure irrespective of the type of shunting they received. By comparison, none of the CRCLD non-responders showed any improvement a year after the shunting. In conclusion, CRCLD proved to be a safe and effective way to predict the effectiveness of shunting in patients with normal pressure hydrocephalus.
Staging of hepatocellular carcinoma: assessment of the CLIP, Okuda, and Child-Pugh staging systems in a cohort of 257 patients in Toronto (2002)

The CLIP classification for HCC is easy to implement and more accurate than the Okuda classification. Our cohort was different from the CLIP cohort (more hepatitis B) but the results were still consistent.
Autophagy Activation by Transcription Factor EB (TFEB) in Striatum of HDQ175/Q7 Mice (2016)

These results suggest that TFEB expression in the striatum of HDQ175/Q7 mice stimulates autophagy and lysosome activity, and lowers mHTT, but may also increase a neuronal stress response.
Interactions of recombinant human pulmonary surfactant protein D and SP-D multimers with influenza A (1996)

To further study the structure and function of surfactant protein D (SP-D), recombinant human SP-D (rhSP-D) was isolated from the culture medium of Chinese hamster ovary (CHO)-K1 cells stably transfected with a full-length hSP-D cDNA. Although a significant fraction of the secreted rhSP-D was recovered as dodecamers similar to recombinant rat SP-D (rrSP-D), a major fraction accumulated as multimers of dodecamers indistinguishable from human proteinosis SP-D. As previously shown for the rat protein, rhSP-D agglutinated specific strains of influenza A virus (IAV), inhibited viral hemagglutinin activity, and protected neutrophils (PMN) from deactivation by IAV. However, the potency of rhSP-D multimers was severalfold greater than for purified dodecamers, comparable to natural, proteinosis hSP-D. Although rhSP-D multimers were also more potent than the serum collectins in mediating viral aggregation and protection of PMN, they were less potent than conglutinin in inhibiting infectivity in vitro. These studies establish that the propensity of hSP-D to form multimers of dodecamers is determined by its primary structure and demonstrate carbohydrate recognition domain valency-dependent interactions of SP-D with IAV.
Calorimetric Analysis of the Binding of Lectins with Overlapping Carbohydrate-Binding Ligand Specificities (1995)

The thermodynamics of binding of a system of plant lectins specific for the oligosaccharide methyl 3,6-di-O-(alpha-D-mannopyranosyl)-alpha-D-mannopyranoside have been studied calorimetrically. This system of lectins consists of concanavalin A, the lectin isolated from Dioclea grandiflora, and the lectin from Galanthus nivalis. The group thus contains lectins with similar structures and similar binding properties as well as lectins with different structures but similar binding properties. Concanavalin A and the lectin from Dioclea are highly homologous, while the lectin from Galanthus nivalis shares no sequence homology with either of the legume lectins, although it also binds the mannose trisaccharide tightly. Calorimetric data for oligosaccharide binding to both of the legume lectins suggests that the total binding site comprises a single high-affinity site and an additional extended site. The pattern of binding for the lectin from Galanthus is significantly different. Binding studies with the same saccharides indicate that the lectin has binding sites designed specifically for the 1-->3 and 1-->6 arms of the mannose trisaccharide that are unable to accommodate other saccharides. Enthalpy--entropy compensation was observed for several saccharides as a function of lectin structure. Contributions of solvation effects to the enthalpy of binding and the configurational entropies were determined experimentally. For those systems studied here, solute-solute attractive interactions and configurational entropies were the greatest contributors to enthalpy-entropy compensation. Our studies clearly demonstrate that, despite their common affinity for the mannose trisaccharide, the three lectins bind oligosaccharides very differently.
DP-SLAM 2.0 (2004)

Probabilistic approaches have proved very successful at addressing the basic problems of robot localization and mapping and they have shown great promise on the combined problem of simultaneous localization and mapping (SLAM). One approach to SLAM assumes relatively sparse, relatively unambiguous landmarks and builds a Kalman filter over landmark positions. Other approaches assume dense sensor data which individually are not very distinctive, such as those available from a laser range finder. In earlier work, we presented an algorithm called DP-SLAM, which provided a very accurate solution to the latter case by efficiently maintaining a joint distribution over robot maps and poses. The approach assumed an extremely accurate laser range finder and a deterministic environment. In this work we demonstrate an improved map representation and laser penetration model, an improvement in the asymptotic efficiency of the algorithm, and empirical results of loop closing on a high resolution map of a very challenging domain.
Tumor-associated macrophages suffocate NKT cells: a novel tumor escape mechanism and a target for therapy (48.7) (2011)

Abstract Vα24-invariant Natural Killer T cells (NKTs) are important for antitumor immunity and immunotherapy. We have demonstrated that NKTs inhibit tumor growth indirectly via targeting tumor-associated monocytes/macrophages (TAMs) in neuroblastoma (NB), suggesting that tumor progression requires an escape from NKTs via yet unknown mechanism. Here, we demonstrate that NB cells via membrane-bound TNFα induce CCL20 production in monocytes and this effect is amplified in hypoxia. Anti-CCL20 neutralizing mAb strongly inhibited NKT-cell in vitro migration towards tumor-conditioned hypoxic monocytes and in vivo localization in NB/TAM xenografts in NOD/SCID mice. The immunofluorescent staining of primary NB tumors revealed selective CCL20 accumulation in TAMs. We also found that hypoxia impairs NKT-cell function, suggesting that NKT-cell trafficking toward CCL20-producing TAMs may serve as a hypoxic trap for tumor-infiltrating NKTs and other T cells. IL-15 protected NKTs from hypoxia in vitro and IL-15-transduced NKTs more efficiently inhibited tumor growth in metastatic NB model in humanized NOD/SCID/IL2rgamma(null) mice compared with parental NKTs. Thus, CCL20 production in hypoxic TAMs and consequent inhibition of NKTs reveals what we believe to be a novel mechanism of immune escape that can be reversed by adoptive immunotherapy with IL-15-transduced NKTs.
Stem cells in the periodontal ligament (2006)

The ability to identify and manipulate stem cells has been a significant advancement in regenerative medicine and has contributed to the development of tissue engineering-based clinical therapies. Difficulties associated with achieving predictable periodontal regeneration, means that novel techniques such as tissue engineering need to be developed in order to regenerate the extensive soft and hard tissue destruction that results from periodontitis. One of the critical requirements for a tissue engineering approach is the delivery of ex vivo expanded progenitor populations or the mobilization of endogenous progenitor cells capable of proliferating and differentiating into the required tissues. By definition, stem cells fulfill these requirements and the recent identification of stem cells within the periodontal ligament represents a significant development in the progress toward predictable periodontal regeneration. In order to explore the importance of stem cells in periodontal wound healing and regeneration, this review will examine contemporary concepts in stem cell biology, the role of periodontal ligament progenitor cells in the regenerative process, recent developments in identifying periodontal stem cells and the clinical implications of these findings.
Orientational Coupling Amplification in Ferroelectric Nematic Colloids (2006)

We investigated the physical properties of low concentration ferroelectric nematic colloids, using calorimetry, optical methods, infrared spectroscopy, and capacitance studies. The resulting homogeneous colloids possess a significantly amplified nematic orientational coupling. We find that the nematic orientation coupling increases by approximately 10% for particle concentrations of 0.2%. A manifestation of the increased orientational order is that the clearing temperature of a nematic colloid increases by up to 40 degrees C compared to the pure liquid crystal host. A theoretical model is proposed in which the ferroelectric particles induce local dipoles whose effective interaction is proportional to the square of the orientational order parameter.
De Novo Peptide Sequencing Based on a Divide-and-Conquer Algorithm and Peptide Tandem Spectrum Simulation (2004)

Mass spectrometry-based de novo peptide sequencing is generally more reliable on high-resolution instruments owing to their high resolution and mass accuracy. On a lower resolution instrument such as the more widely used quadrupole ion traps, de novo peptide sequencing is not so reliable or requires more MS(3) experiments. However, the peptide CID spectrum has been demonstrated to be quite reproducible on an ion trap instrument and can be predicted with good accuracy. A new de novo peptide sequencing technique, DACSIM, combining a divide-and-conquer algorithm for deriving sequence candidates and spectrum simulation for sequence refinement, is developed for spectra acquired on an ion trap instrument. When DACSIM was used to sequence peptides 500-1900 u in mass generated from proteolytic digests of hemoglobin and myoglobin, the success rate was 70% with a false positive rate of only 6%, when isoleucine and leucine residues were not distinguished.
Epidemiology of functional dyspepsia: A global perspective (2006)

Dyspepsia refers to group of upper gastrointestinal symptoms that occur commonly in adults. Dyspepsia is known to result from organic causes, but the majority of patients suffer from non-ulcer or functional dyspepsia. Epidemiological data from population-based studies of various geographical locations have been reviewed, as they provide more realistic information. Population-based studies on true functional dyspepsia (FD) are few, due to the logistic difficulties of excluding structural disease in large numbers of people. Globally, the prevalence of uninvestigated dyspepsia (UD) varies between 7%-45%, depending on definition used and geographical location, whilst the prevalence of FD has been noted to vary between 11%-29.2%. Risk factors for FD have been shown to include females and underlying psychological disturbances, whilst environmental/ lifestyle habits such as poor socio-economic status, smoking, increased caffeine intake and ingestion of non-steroidal anti-inflammatory drugs appear to be more relevant to UD. It is clear that dyspepsia and FD in particular are common conditions globally, affecting most populations, regardless of location.
Fluorescence‐based continuous assay for the aspartyl protease of human immunodeficiency virus‐1 (1990)

5-Dimethylaminoaphthalene-1-sulfonyl-Ser-Gln-Asn-Tyr-Pro-Ile-Val-T rp (Dns-SQNYPIVW) is a fluorescent substrate for the aspartyl protease of human immunodeficiency virus-1. In intact substrate, fluorescence of Trp (lambda ex 290 nm, lambda em 360 nm) was 60% quenched by energy transfer to the dansyl group. Protease-catalyzed cleavage at the Tyr-Pro bond abolished the energy transfer, and the consequent increase in Trp fluorescence was used to follow the enzymatic reaction. At substrate concentrations less than 60 microM, initial reaction velocity increased as a linear function of substrate concentration, with kcat/KM = 9700 M-1 s-1. Limited solubility and internal fluorescence quenching precluded a determination of KM for Dns-SQNYPIVW, but this was clearly greater than 100 microM.
Immunogenicity of granulocyte-macrophage colony-stimulating factor (GM-CSF) products in patients undergoing combination therapy with GM-CSF. (1999)

In this study, we have assessed the development of neutralizing and nonneutralizing granulocyte-macrophage colony-stimulating factor (GM-CSF) antibodies in two groups of patients with metastatic colorectal carcinoma receiving two different GM-CSF products. Three clinical trials were carried out, and a combination of GM-CSF and a colon carcinoma-reactive antibody was used in the absence of any concomitant chemotherapy. Two different GM-CSF products, both rDNA-derived and produced in Escherichia coli, were used. Patients in Trial 1 received product X, and those in Trials 2 and 3 received product Y. Patients in Trial 2 also received interleukin 2 in an attempt to potentiate immune responses. After the first cycle of treatment, no GM-CSF antibodies were detected, but on subsequent therapy, 28 of the 38 patients tested receiving product Y (Trials 2 and 3) developed antibodies that bound to the GM-CSF product used for therapy. However, none of the patients developed antibodies that neutralized the biological activity of GM-CSF, as assessed using an in vitro bioassay. Furthermore, there was no in vivo impairment in GM-CSF-induced expansion of leukocytes, neutrophils, and eosinophils in the patients. In contrast, 19 of the 20 patients given product X (Trial 1) developed GM-CSF binding antibodies, and 9 of these patients were shown to develop antibodies that neutralized the biological activity of GM-CSF. The presence of the latter was associated with a significant reduction in GM-CSF-induced expansion of leukocytes, neutrophils, and eosinophils in patients. Therefore, product X appears to be more immunogenic than product Y. Immunochemical characterization confirmed that the specificity of the antibody responses varied depending on the product used for therapy. Whereas sera from Trial 1 patients treated with product X showed the presence of antibodies with strong recognition of GM-CSF proteins, sera from patients treated with product Y showed varied recognition of GM-CSF ranging from fairly strong to very weak but bound predominantly to two E. coli-derived, non-GM-CSF-related proteins of Mr approximately 20,000 and Mr approximately 30,000. Therefore, in sera from patients receiving product Y, the antibody specificity appeared to be directed not only against GM-CSF but also against non-product-related host cell contaminants. This study shows that GM-CSF products used for therapy are potentially immunogenic and generate antibodies to GM-CSF and/or other non-product-related contaminants. However, only antibodies that neutralize the biological activity of GM-CSF compromise therapeutic efficacy of the cytokine.
Trefoil factor 3 overexpression in prostatic carcinoma: Prognostic importance using tissue microarrays (2004)

These studies validate that TFF3 is overexpressed at the protein level in a subset of primary and metastatic prostate cancers, show the first use of the TMAJ database, and demonstrate the ability to semi-automatically scan and score immunohistochemically stained tissue microarray slides.
A MAP Kinase-Signaling Pathway Mediates Neurite Outgrowth on L1 and Requires Src-Dependent Endocytosis (2000)

The neural cell adhesion molecule L1 mediates the axon outgrowth, adhesion, and fasciculation necessary for proper development of synaptic connections. Mutations of human L1 cause an X-linked mental retardation syndrome termed CRASH (corpus callosum hypoplasia, retardation, aphasia, spastic paraplegia, and hydrocephalus), and L1 knock-out mice display defects in neuronal process extension resembling the CRASH phenotype. Little is known about the biochemical or cellular mechanism by which L1 performs neuronal functions. Here it is demonstrated that clustering of L1 with antibodies or L1 protein in rodent B35 neuroblastoma and cerebellar neuron cultures induced the phosphorylation/activation of the mitogen-activated protein kinases (MAPKs) and extracellular signal-regulated kinases 1 and 2. MAPK activation was essential for L1-dependent neurite outgrowth, because chemical inhibitors [2-(2'-amino-3'-methoxyphenyl)-oxanaphthalen-4-one and 1,4-diamino-2, 3-dicyano-1,4-bis(2-aminophenylthio)butadiene] of the MAPK kinase MEK strongly suppressed neurite outgrowth by cerebellar neurons on L1. The nonreceptor tyrosine kinase pp60(c-src) was required for L1-triggered MAPK phosphorylation, as shown in src-minus cerebellar neurons and by expression of the kinase-inactive mutant Src(K295M) in B35 neuroblastoma cells. Phosphatidylinositol 3-kinase (PI3-kinase) and the small GTPase p21(rac) were identified as signaling intermediates to MAPK by phosphoinositide and Rac-GTP assays and expression of inhibitory mutants. Antibody-induced endocytosis of L1, visualized by immunofluorescence staining and confocal microscopy of B35 cells, was blocked by expression of kinase-inactive Src(K295M) and dominant-negative dynamin(K44A) but not by inhibitors of MEK or PI3-kinase. Dynamin(K44A) also inhibited L1 antibody-triggered MAPK phosphorylation. This study supports a model in which pp60(c-src) regulates dynamin-mediated endocytosis of L1 as an essential step in MAPK-dependent neurite outgrowth on an L1 substrate.
On‐line real‐time physics‐based predictive motion control with balance recovery (2014)

Abstract In this paper, we present an on‐line real‐time physics‐based approach to motion control with contact repositioning based on a low‐dimensional dynamics model using example motion data. Our approach first generates a reference motion in run time according to an on‐line user request by transforming an example motion extracted from a motion library. Guided by the reference motion, it repeatedly generates an optimal control policy for a small time window one at a time for a sequence of partially overlapping windows, each covering a couple of footsteps of the reference motion, which supports an on‐line performance. On top of this, our system dynamics and problem formulation allow to derive closed‐form derivative functions by exploiting the low‐dimensional dynamics model together with example motion data. These derivative functions and their sparse structures facilitate a real‐time performance. Our approach also allows contact foot repositioning so as to robustly respond to an external perturbation or an environmental change as well as to perform locomotion tasks such as stepping on stones effectively.
A Comparison of Linkage Disequilibrium Measures for Fine-Scale Mapping (1995)

Linkage mapping generally localizes disease genes to 1- to 2-cM regions of chromosomes. In theory, further refinement of location can be achieved by population-based studies of linkage disequilibrium between disease locus alleles and alleles at adjacent markers. One approach to localization, dubbed simple disequilibrium mapping, is to determine the relative location of the disease locus by plotting disequilibrium values against marker locations. We investigate the simple mapping properties of five disequilibrium measures, the correlation coefficient delta, Lewontin's D', the robust formulation of the population attributable risk delta, Yule's Q, and Kaplan and Weir's proportional difference d under the assumption of initial complete disequilibrium between disease and marker loci. The studies indicate that delta is a superior measure for fine mapping because it is directly related to the recombination fraction between the disease and the marker loci, and it is invariant when disease haplotypes are sampled at a rate higher than their population frequencies, as in a case-control study. D' yields results comparable to those of delta in many realistic settings. Of the remaining three measures, Q, delta, and d, Q yields the best results. From simulations of short-term evolution, all measures show some sensitivity to marker allele frequencies; however, as predicted by analytic results, Q, delta, and d exhibit the greatest sensitivity to variation in marker allele frequencies across loci.
Gonadotropin-releasing hormone receptor mRNA expression by human pituitary tumors in vitro. (1994)

An important question in the pathogenesis and regulation of human gonadotroph adenomas is whether heterogeneous gonadotropin responses to gonadotropin-releasing hormone (GnRH) are due to dysregulation of GnRH receptor biosynthesis and/or cell-signaling pathways. We investigated gonadotropin responsiveness to pulsatile GnRH in 13 gonadotroph adenomas. All tumors had evidence of follicle-stimulating hormone (FSH) beta and alpha subunit biosynthesis using reverse transcriptase/polymerase chain reaction (RTPCR) techniques. Four tumors significantly increased gonadotropin and/or free subunit secretion during pulsatile 10(-8) M GnRH administration. The GnRH antagonist Antide (10(-6) to 10(-8) M) blocked secretory increases in all GnRH-responsive tumors. Gonadotropin and/or free subunit secretion increased after 60 mM KCl, confirming that GnRH nonresponsiveness was not due to intracellular gonadotropin depletion. We hypothesized that GnRH nonresponsiveness in these tumors may be due to GnRH receptor (GnRH-Rc) biosynthetic defects. RTPCR analyses detected GnRH-Rc transcripts only in responsive tumors and normal human pituitary. This is the first demonstration of a cell-surface receptor biosynthetic defect in human pituitary tumors. We conclude (a) one third of gonadotroph tumors respond to pulsatile GnRH in vitro, (b) GnRH-Rc mRNA is detected in human gonadotroph adenomas and predicts GnRH responsiveness, and (c) GnRH-Rc biosynthetic defects may underlie GnRH nonresponsiveness in gonadotroph tumors.