gebhart/patrepeval huggingface dataset:
Acute rejection in non‐compliant renal allograft recipients: a distinct morphology (2007)

Non-compliance for immunosuppressive medication is frequent in renal transplant recipients, and associated with late acute rejection and graft loss. Although numerous studies were published on risk factors and outcome, no data are available on the histopathology of the 'non-compliant' allograft. As non-compliant patients swing between subtherapeutic and toxic doses of immunosuppression, trough levels show large variation. We questioned whether the histology of acute rejection in non-compliers (i) differs from the 'classical' acute rejection; (ii) shows more concomitant calcineurin-inhibitor toxicity; (iii) is associated with C4d and plasma cell (PC)-rich infiltrates. Based on validated interview methods/self reporting, 145 adult renal allograft recipients, transplanted for greater than one yr, on cyclosporine A and corticosteroids, were categorized as either compliant or non-compliant. Non-compliance was defined in 32 patients (22.1%). All late (greater than one yr) allograft biopsies were reviewed (Banff) and immuno-stained for C4d. Computerized morphometry was performed on late biopsies with features of acute cellular rejection. Sixty-two patients had > or =1 late biopsy [41 (36.2%) compliant/21 (65.6%) non-compliant; p = 0.0043], comprising a pool of 90 biopsies (61 compliant/29 non-compliant; p = 0.0303). 'Non-compliant' biopsies had higher scores of C4d (p = 0.0092), acute tubular damage (p = 0.0058), and peritubular capillaritis (p = 0.0070). 'Non-compliant' biopsies with acute cellular rejection showed less interstitial edema (p = 0.0165), more interstitial infiltrate (p = 0.0100), more interstitial fibrosis (p = 0.0277), and more tubular atrophy (p = 0.0197). PC-rich infiltrates correlated with C4d (p = 0.0080). Detection of non-compliance is mandatory as it represents an important cause of graft loss. This study describes histologic features of renal allograft biopsies in non-compliant patients that could help identifying this patient profile.
BNP Consensus Panel 2004: A Clinical Approach for the Diagnostic, Prognostic, Screening, Treatment Monitoring, and Therapeutic Roles of Natriuretic Peptides in Cardiovascular Diseases (2004)

Among the most exciting developments in the field of heart failure in recent times has been the rediscovery of the natriuretic peptide system and its pleuripotent effects on cardiac structure and function. This is particularly true of its natriuretic and hemodynamic effects. There has been an explosion of the knowledge base seeking to understand the wide range of homeostatic, regulatory, and counter-regulatory functions in which the natriuretic peptide system participates. Additional interest has been stimulated by advances in technology such as point-of-care and core laboratory BNP assays and the use of the recombinant B-type natriuretic peptide nesiritide as a treatment option. Despite this recent interest, the available literature lacks a comprehensive expert review of the current science and roles of natriuretic peptides for diagnostic, prognostic, screening, treatment monitoring, and therapeutic purposes. More importantly, a summary updating and guiding the clinician on most of these advances was lacking. An expert Consensus Panel with basic, methodological, and clinical expertise was convened to summarize current knowledge in these areas and the findings and consensus statements are contained herein.
Comparative study on the insertion behavior of cerebral microprobes (2007)

A series of experiments has been conducted with probes made from silicon, glass, tungsten and polyimide within a developed brain phantom, and the insertion behavior, forces and dimpling are compared to in vitro and in vivo models. This allows the choice of proper insertion parameters and probe structure to reach a compromise between needle stability and tissue trauma as a result of insertion. According to the performed experiments, the reduced interfacial area between the needle tip and the brain will result in reduced insertion force. High insertion speed (100 mm/min) reduces the dimpling but not the penetration force necessarily. In vivo insertion and retraction of the fragile probes made from silicon is possible without pia and/or dura removal.
Particle size of solid food after human mastication andin vitrosimulation of oral breakdown (2000)

Mastication, the first step in food digestion, results in the breakdown of solid food and its lubrication with saliva. Although the rate and extent of starch digestion are closely dependent on the way food is chewed, this factor has not been adequately considered in the preparation of food for in vitro digestion experiments. The purpose of this study was to determine the size distribution of starchy food particles before swallowing and to use an in vitro mincing procedure to simulate how food is divided up during chewing. Foods differing in texture and size (bread, spaghetti and tortiglioni) were chewed by 12 healthy subjects and spat out before swallowing. Chewing time and saliva impregnation were measured for each mouthful. The particle sizes resulting from experiments with chewed and minced bread and pasta were analysed respectively by light laser diffraction and image analysis. Chewing time was longer for bread than pasta, resulting in higher saliva impregnation. Chewed bread showed a bimodal distribution of particle size (30 microns, 500 microns), whereas both kinds of pasta produced particles of similar size (0.5 to 30 mm2) after mastication. Mincing reproduced the division of bread and pasta as achieved by chewing in an acceptable way. From our results it seems that the size of particles resulting from mastication depends on food texture. We succeeded by wetting and mincing food to prepare food in a similar bolus-like form before swallowing. Mincing provides a simple means of simulating the reduction of food into particles for in vitro digestion studies.
Extracting Places and Activities from GPS Traces Using Hierarchical Conditional Random Fields (2007)

Learning patterns of human behavior from sensor data is extremely important for high-level activity inference. This paper describes how to extract a person’s activities and significant places from traces of GPS data. The system uses hierarchically structured conditional random fields to generate a consistent model of a person’s activities and places. In contrast to existing techniques, this approach takes the high-level context into account in order to detect the significant places of a person. Experiments show significant improvements over existing techniques. Furthermore, they indicate that the proposed system is able to robustly estimate a person’s activities using a model that is trained from data collected by other persons.
Erythrocyte structure and dynamics quantified by Hilbert phase microscopy (2005)

We present a new quantitative method for investigating red blood cell morphology and dynamics. The instrument integrates quantitative phase microscopy with an inverted microscope, which makes it particularly suitable for the noninvasive assessment of live erythrocytes. In particular, we demonstrate the ability of this approach to quantify noninvasively cell volume and dynamic morphology. The subnanometer path-length sensitivity at the millisecond time scales is exemplified by measuring the hemoglobin flow out of the cell during hemolysis.
Numerical investigation of mixing in microchannels with patterned grooves (2003)

Mixing in microchannels with patterned grooves was studied numerically by CFD simulations and particle tracking technique. Point location, velocity interpolation and a fourth-order adaptive Runge–Kutta integration scheme were applied in the particle tracking algorithms. Using these algorithms, Poincaré maps were calculated from the 3D velocity field exported from a CFD package for microfluidics (MemCFD™). For small aspect ratio (α = 0.05) grooves, the results showed that there was no significant irregularity in the Poincaré map, and indicated little chaotic effect. For high aspect ratio (α = 0.30) grooves, the flow pattern became more jumbled, but there was no apparent evidence that indicated the flow was chaotic, for Reynolds numbers up to five. However, Poincaré maps could still be used to evaluate the performance of this type of micro-mixer. The particle trajectories recorded in the Poincaré maps were circular-like patterns. By counting the number of dots to form one circle in the Poincaré maps, the length of the channel to enable one recirculation could be calculated. The results indicated that this length had an exponential relation to the aspect ratio of grooves, and it was independent of the flow velocity. The CFD simulation showed that the transverse motion could fold and stretch fluids to increase their interfacial area. The results showed that micro-mixers with patterned grooves caused rotation of the fluid streams. This rotation can reorient the folding in the depth direction, and can enhance passive mixing in microfluidic devices with shallow channels.
Clinical Use of Marrow Osteoprogenitor Cells to Stimulate Osteogenesis (1998)

This review of 15 years research into various methods and techniques of using marrow osteoprogenitor cells shows that marrow grafts can be useful for numerous skeletal healing problems, but not all. The method offers considerable improvement over standard open iliac crest grafting and provides an attractive and advantageous method of stimulating osteogenesis in the management and prevention of nonunion.
A promising p-type transparent conducting material: Layered oxysulfide [Cu2S2][Sr3Sc2O5] (2007)

Sr 3 Cu 2 Sc 2 O 5 S 2 , a layered oxysulfide, composed of anti-PbO-like [Cu2S2] slabs alternating with perovskitelike [Sr3Sc2O5] slabs, was systematically studied as a p-type transparent conducting material. The material has a wide energy gap of 3.1eV and a p-type electrical conductivity of 2.8Scm−1 at room temperature. The hole mobility of +150cm2V−1S−1 at room temperature, which is much higher than the typical value of ∼10−1–10cm2V−1S−1 found in other copper compounds. The performances of bulk undoped Sr3Cu2Sc2O5S2 show the promise of copper oxysulfides as a class of p-type transparent conductive materials that is essential for optoelectronic applications.
HITTM cells?high-efficiency crystalline Si cells with novel structure (2000)

Our unique, high-efficiency c-Si solar cell, named the HIT cell, has shown considerable potential to improve junction properties and surface passivation since it was first developed. The improved properties in efficiency and temperature dependence compared to conventional p – n diffused c-Si solar cells are featured in HIT power 21TM solar cell modules and other applications which are now on the market. In the area of research, further improvement in the junction properties of the a-Si/c-Si heterojunction has been examined, and the highest efficiency to date of 20.1% has recently been achieved for a cell size of 101 cm2. The high open circuit voltage exceeding 700 mV, due to the excellent surface passivation of the HIT structure, is responsible for this efficiency. In this paper, recent progress in HIT cells by Sanyo will be introduced. Copyright © 2000 John Wiley & Sons, Ltd.
Research Article Identification of Two Novel HLA-A ∗ 0201-Restricted CTL Epitopes Derived from MAGE-A4 (2010)

Copyright © 2010 Zheng-Cai Jia et al. This is an open access article distributed under the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. MAGE-A antigens belong to cancer/testis (CT) antigens that are expressed in tumors but not in normal tissues except testis and placenta. MAGE-A antigens and their epitope peptides have been used in tumor immunotherapy trials. MAGE-A4 antigen is extensively expressed in various histological types of tumors, so it represents an attractive target for tumor immunotherapy. In this study, we predicted HLA-A ∗ 0201-restricted cytotoxic T lymphocyte (CTL) epitopes of MAGE-A4, followed by peptide/HLA-A ∗ 0201 affinity and complex stability assays. Of selected four peptides (designated P1, P2, P3, and P4), P1 (MAGE-A4286−294, KVLEHVVRV) and P3 (MAGE-A4272−280, FLWGPRALA) could elicit peptide-specific CTLs both in vitro from HLA-A ∗ 0201positive PBMCs and in HLA-A ∗ 0201/K b transgenic mice. And the induced CTLs could lyse target cells in an HLA-A ∗ 0201restricted fashion, demonstrating that the two peptides are HLA-A ∗ 0201-restricted CTL epitopes and could serve as targets for therapeutic antitumoral vaccination. 1.
Effect of temperature, pH, dissolved oxygen, and hydrolysate on the formation of triple light chain antibodies in cell culture (2010)

THIOMABs are recombinant antibodies with reactive cysteine residues used for forming THIOMAB-drug conjugates (TDCs). We recently reported a new impurity associated with THIOMABs: one of the engineered cysteines forms a disulfide bond with an extra light chain (LC) to generate a triple light chain antibody (3LC). In our previous investigations, increased LC expression increased 3LC levels, whereas increased glutathione (GSH) production decreased 3LC levels. In this work, on three stably transfected CHO cell lines, we investigated the effects of temperature, pH, dissolved oxygen (DO), and hydrolysate on 3LC formation during THIOMAB fed-batch cell culture production. Although pH between 6.8 and 7.0 had no significant impact on 3LC formation, temperature at 35°C instead of 33 or 31°C generated the lowest 3LC values for two cell lines. The decreased 3LC level correlated with increased GSH production. We implemented a 35°C temperature process for large-scale (2,000 L) production of a THIOMAB. This process reduced 3LC levels by ∼50% compared with a 33°C temperature process. By contrast, DO and hydrolysate had modest effect on 3LC levels for the model cell line studied. Overall, we did not find significant changes in LC expression under the conditions tested, whereas changes in GSH production were more evident. By investigating the impact of bioreactor process and medium conditions on 3LC levels, we identified strategies that reduced 3LC levels.
Phosphorylation sites at the C-terminus of the platelet-derived growth factor receptor bind phospholipase C gamma 1. (1993)

We have identified two tyrosine phosphorylation sites, Tyr 1009 and Tyr 1021, in the C-terminal noncatalytic region of the human platelet-derived growth factor (PDGF) receptor beta subunit. Mutant receptors with phenylalanine substitutions at either or both of these tyrosines were expressed in dog epithelial cells. Mutation of Tyr 1021 markedly reduced the PDGF-stimulated binding of phospholipase C (PLC) gamma 1 but had no effect on binding of the GTPase activator protein of Ras or of phosphatidylinositol 3 kinase. Mutation of Tyr 1009 reduced binding of PLC gamma 1 less severely. Mutation of Tyr 1021, or both Tyr 1009 and Tyr 1021, also reduced the PDGF-dependent binding of a transiently expressed fusion protein containing the two Src-homology 2 domains from PLC gamma 1. Mutation of Tyr 1021, or both Tyr 1009 and Tyr 1021, greatly reduced PDGF-stimulated tyrosine phosphorylation of PLC gamma 1 but did not prevent the tyrosine phosphorylation of other cell proteins, including mitogen-activated protein kinase. We conclude that Tyr 1021, and possibly Tyr 1009, is a binding site for PLC gamma 1.
Abstracting application-level web security (2002)

Application-level web security refers to vulnerabilities inherent in the code of a web-application itself (irrespective of the technologies in which it is implemented or the security of the web-server/back-end database on which it is built). In the last few months application-level vulnerabilities have been exploited with serious consequences: hackers have tricked e-commerce sites into shipping goods for no charge, user-names and passwords have been harvested and condential information (such as addresses and credit-card numbers) has been leaked.In this paper we investigate new tools and techniques which address the problem of application-level web security. We (i) describe a scalable structuring mechanism facilitating the abstraction of security policies from large web-applications developed in heterogenous multi-platform environments; (ii) present a tool which assists programmers develop secure applications which are resilient to a wide range of common attacks; and (iii) report results and experience arising from our implementation of these techniques.
Piezoelectric Nanoparticle–Polymer Composite Foams (2014)

Piezoelectric polymer composite foams are synthesized using different sugar-templating strategies. By incorporating sugar grains directly into polydimethylsiloxane mixtures containing barium titanate nanoparticles and carbon nanotubes, followed by removal of the sugar after polymer curing, highly compliant materials with excellent piezoelectric properties can be fabricated. Porosities and elasticity are tuned by simply adjusting the sugar/polymer mass ratio which gave an upper bound on the porosity of 73% and a lower bound on the elastic coefficient of 32 kPa. The electrical performance of the foams showed a direct relationship between porosity and the piezoelectric outputs, giving piezoelectric coefficient values of ∼112 pC/N and a power output of ∼18 mW/cm3 under a load of 10 N for the highest porosity samples. These novel materials should find exciting use in a variety of applications including energy scavenging platforms, biosensors, and acoustic actuators.
Phenotypic characterization of individuals with 30-40 CAG repeats in the Huntington disease (HD) gene reveals HD cases with 36 repeats and apparently normal elderly individuals with 36-39 repeats. (1996)

Abnormal CAG expansions in the IT-15 gene are associated with Huntington disease (HD). In the diagnostic setting it is necessary to define the limits of the CAG size ranges on normal and HD-associated chromosomes. Most large analyses that defined the limits of the normal and pathological size ranges employed PCR assays, which included the CAG repeats and a CCG repeat tract that was thought to be invariant. Many of these experiments found an overlap between the normal and disease size ranges. Subsequent findings that the CCG repeats vary by 8 trinucleotide lengths suggested that the limits of the normal and disease size ranges should be reevaluated with assays that exclude the CCG polymorphism. Since patients with between 30 and 40 repeats are rare, a consortium was assembled to collect such individuals. All 178 samples were reanalyzed in Cambridge by using assays specific for the CAG repeats. We have optimized methods for reliable sizing of CAG repeats and show cases that demonstrate the dangers of using PCR assays that include both the CAG and CCG polymorphisms. Seven HD patients had 36 repeats, which confirms that this allele is associated with disease. Individuals without apparent symptoms or signs of HD were found at 36 repeats (aged 74, 78, 79, and 87 years), 37 repeats (aged 69 years), 38 repeats (aged 69 and 90 years), and 39 repeats (aged 67, 90, and 95 years). The detailed case histories of an exceptional case from this series will be presented: a 95-year-old man with 39 repeats who did not have classical features of HD. The apparently healthy survival into old age of some individuals with 36-39 repeats suggests that the HD mutation may not always be fully penetrant.
gp49B1 and Its Related Family of Counterregulatory Receptors of the Immunoglobulin Superfamily (1999)

Cross-linking of FcepsilonRI on mast cells elicits positive signal transduction cascades that lead to the release of a variety of proinflammatory mediators. Mouse mast cells also express gp49B1 on their surface, an immunoglobulin superfamily member that bears two immunoreceptor tyrosine-based inhibitory motifs in its cytoplasmic domain and inhibits FcepsilonRI-induced release of secretory granule mediators and the cysteinyl leukotriene, LTC4. gp49B1 belongs to a growing family of inhibitory receptors expressed in mouse and man. Thus, FcepsilonRI-induced mast cell activation is counterregulated by several receptors belonging to the same superfamily as FcepsilonRI itself.
Synergistic effect of recombinant interferon-gamma and interleukin-3 on the growth of immature human hematopoietic progenitors (1991)

Purified peripheral blood hematopoietic progenitors from children in early remission from cancer respond to recombinant human interleukin-3 (IL-3), but not to granulocyte colony-stimulating factor (G-CSF). With these purified cells as a target, we studied the effect of recombinant human interferon-gamma (IFN-gamma) on progenitor growth, using both liquid-suspension limiting dilution assay (LDA) and regular methylcellulose culture of progenitors. We found that in LDA with IL-3, IFN-gamma directly stimulated the growth of blood progenitors in a dose-dependent manner with single-hit kinetics, whereas IFN-gamma suppressed the growth of G-CSF-supported progenitors obtained from bone marrow. The stimulatory effect was also observed in methylcellulose culture, but the addition of antibodies for G-CSF, granulocyte-macrophage CSF, IL-1 alpha, IL-1 beta, IL-6, or tumor necrosis factor did not result in a decrease of the colony number, supporting further the possible direct effect of IFN-gamma on progenitor growth. These results suggest that the inhibitory effect of IFN-gamma on hematopoietic progenitors is limited to those in an advanced stage of maturation. IFN-gamma may be one of the essential lymphokines upregulating the growth of human hematopoietic progenitor cells.
Enzymatic synthesis of nucleoside antibiotics. Part V. Properties of nucleoside phosphorylase from Enterobacter aerogenes. (1985)

The properties of uridine phosphorylase (UPase) and purine nucleoside phosphorylase (PNPase) at high temperature were investigated. Both enzymes were found to be distributed in a wide range of bacteria and were partially purified from Enterobacter aerogenes AJ 11125 by heat treatment, ammonium sulfate fractionation and column chromatographies onDEAE-cellulose and Sephadex G-150. The UPase Was purified 109-fold, and it showed an optimum pH of 8.5 and optimum temperature of 65°C, and activity toward uridine, 2'-deoxyuridine, thymidine and uracil arabinoside but not cytidine. The Km values of UPase for uridine were 0.7 mm at 40°C and 1.8mM at 60°C. The PNPase was purified 83-fold, and it showed an optimum pH of 6.8 and optimum temperature of 60°C, and significant activity toward purine arabinosides as well as purine ribosides. The Km values of PNPase for inosine were 0.8 mM at 40°C and 2.2 mM at 60°C.
Directed Colloidal Assembly of 3D Periodic Structures (2002)

Colloidal inks, comprised of silica microspheres with tailored attractive interactions between them, have been directly assembled via a robotically controlled deposition technique. 3D periodic lattices, whose periodicity far exceeds the dimensions of the colloidal building blocks (see Figure for a cross-sectional image), were created through layer- by-layer patterning of parallel rods.
Spectral imaging and its applications in live cell microscopy (2003)

In biological microscopy, the ever expanding range of applications requires quantitative approaches that analyze several distinct fluorescent molecules at the same time in the same sample. However, the spectral properties of the fluorescent proteins and dyes presently available set an upper limit to the number of molecules that can be detected simultaneously with common microscopy methods. Spectral imaging and linear unmixing extends the possibilities to discriminate distinct fluorophores with highly overlapping emission spectra and thus the possibilities of multicolor imaging. This method also offers advantages for fast multicolor time-lapse microscopy and fluorescence resonance energy transfer measurements in living samples. Here we discuss recent progress on the technical implementation of the method, its limitations and applications to the imaging of biological samples.