gebhart/patrepeval huggingface dataset:
Dendritic Cells and the Promise of Therapeutic Vaccines for Human Immunodeficiency Virus (HIV)-1 (2003)

Treatment of human immunodeficiency virus (HIV)-1 infection with potent antiretroviral medications has provided considerable clinical benefit. However because of the limitations of current therapy, innovative approaches are needed to better control HIV-1 infection. Several studies have suggested that robust CD4+ T helper and CD8+ T cell responses may contribute to the immunologic control of HIV-1 infection in certain individuals. Most chronically infected patients, however, cannot control the infection and may benefit from stimulation of cellular immunity with immunotherapy. Dendritic cells (DCs) are potent professional antigen-presenting cells (APCs) and have a central role in directing the adaptive immune response to pathogens. The ability of DCs to stimulate naive T cells has long been thought to be crucial in initiating an effective immune response. As DCs are uniquely situated at the interface between the innate and adaptive immune systems, they are currently under intense scrutiny as potential adjuvants for vaccines in many clinical settings. Studies in healthy volunteers and patients with cancer have shown that antigen-pulsed DCs can boost both CD8+ and CD4+ T cell responses in vivo. Based on these promising findings, ex vivo antigen-pulsed DCs are being actively investigated in studies aimed at developing a therapeutic vaccine for individuals with HIV-1 infection.
A simple physical model for binding energy hot spots in protein–protein complexes (2002)

Protein-protein recognition plays a central role in most biological processes. Although the structures of many protein-protein complexes have been solved in molecular detail, general rules describing affinity and selectivity of protein-protein interactions do not accurately account for the extremely diverse nature of the interfaces. We investigate the extent to which a simple physical model can account for the wide range of experimentally measured free energy changes brought about by alanine mutation at protein-protein interfaces. The model successfully predicts the results of alanine scanning experiments on globular proteins (743 mutations) and 19 protein-protein interfaces (233 mutations) with average unsigned errors of 0.81 kcal/mol and 1.06 kcal/mol, respectively. The results test our understanding of the dominant contributions to the free energy of protein-protein interactions, can guide experiments aimed at the design of protein interaction inhibitors, and provide a stepping-stone to important applications such as interface redesign.
M-net: A Convolutional Neural Network for deep brain structure segmentation (2017)

In this paper, we propose an end-to-end trainable Convolutional Neural Network (CNN) architecture called the M-net, for segmenting deep (human) brain structures from Magnetic Resonance Images (MRI). A novel scheme is used to learn to combine and represent 3D context information of a given slice in a 2D slice. Consequently, the M-net utilizes only 2D convolution though it operates on 3D data, which makes M-net memory efficient. The segmentation method is evaluated on two publicly available datasets and is compared against publicly available model based segmentation algorithms as well as other classification based algorithms such as Random Forrest and 2D CNN based approaches. Experiment results show that the M-net outperforms all these methods in terms of dice coefficient and is at least 3 times faster than other methods in segmenting a new volume which is attractive for clinical use.
Laser Treated Carbon Nanotube Yarn Microelectrodes for Rapid and Sensitive Detection of Dopamine in Vivo (2016)

Carbon nanotube yarn microelectrodes (CNTYMEs) exhibit rapid and selective detection of dopamine with fast-scan cyclic voltammetry (FSCV); however, the sensitivity limits their application <i>in vivo</i>. In this study, we introduce laser treatment as a simple, reliable, and efficient approach to improve the sensitivity of CNTYMEs by three fold while maintaining high temporal resolution. The effect of laser treatment on the microelectrode surface was characterized by scanning electron microscopy, Raman spectroscopy, energy dispersion spectroscopy, and laser confocal microscopy. Laser treatment increases the surface area and oxygen containing functional groups on the surface, which provides more adsorption sites for dopamine than at unmodified CNTYMEs. Moreover, similar to unmodified CNTYMEs, the dopamine signal at laser treated CNTYMEs is not dependent on scan repetition frequency, unlike the current at carbon fiber microelectrodes (CFMEs) which decreases with increasing scan repetition frequency. This frequency independence is caused by the significantly larger surface roughness which would trap dopamine-o-quinone and amplify the dopamine signal. CNTYMEs were applied as an <i>in vivo</i> sensor with FSCV for the first time and laser treated CNTYMEs maintained high dopamine sensitivity compared to CFMEs with an increased scan repetition frequency of 50 Hz, which is five-fold faster than the conventional frequency. CNTYMEs with laser treatment are advantageous because of their easy fabrication, high reproducibility, fast electron transfer kinetics, high sensitivity, and rapid <i>in vivo</i> measurement of dopamine and could be a potential alternative to CFMEs in the future.
BGC 945, a Novel Tumor-Selective Thymidylate Synthase Inhibitor Targeted to α-Folate Receptor–Overexpressing Tumors (2005)

BGC 945 is a cyclopenta[g]quinazoline-based, thymidylate synthase inhibitor specifically transported into alpha-folate receptor (alpha-FR)-overexpressing tumors. Affinity of BGC 945 for the alpha-FR is 70% of the high-affinity ligand folic acid. In contrast to conventional antifolates, BGC 945 has low affinity for the widely expressed reduced-folate carrier (RFC). The K(i) for isolated thymidylate synthase is 1.2 nmol/L and the IC(50) for inhibition of the growth of alpha-FR-negative mouse L1210 or human A431 cells is approximately 7 micromol/L. In contrast, BGC 945 is highly potent in a range of alpha-FR-overexpressing human tumor cell lines (IC(50) approximately 1-300 nmol/L). Pharmacokinetic variables measured following i.v. injection of 100 mg/kg BGC 945 to KB tumor-bearing mice showed rapid plasma clearance (0.021 L/h) and tissue distribution. The terminal half-lives in plasma, liver, kidney, spleen, and tumor were 2, 0.6, 5, 21, and 28 hours, respectively. Tumor BGC 945 concentration at 24 hours was approximately 1 nmol/g tissue, at least 10-fold higher than that in plasma or normal tissues. Inhibition of thymidylate synthase in tissues leads to increased incorporation of 5-[(125)I]-iodo-2'-deoxyuridine ([(125)I]dUrd) into DNA. Forty-eight hours after injection of 100 mg/kg 6RS-BGC 945 ([(125)I]dUrd injected at 24 hours), tumor was the only tissue with incorporation above control level (6-fold). The RFC-mediated thymidylate synthase inhibitor plevitrexed also increased uptake of [(125)I]dUrd in tumor (10-fold) but, in contrast, also caused increased incorporation in other normal tissues such as spleen and small bowel (4.5- and 4.6-fold, respectively). These data suggest that BGC 945 selectively inhibits thymidylate synthase in alpha-FR-overexpressing tumors and should cause minimal toxicity to humans at therapeutic doses.
Generalized Fluorocarbon‐Surfactant‐Mediated Synthesis of Nanoparticles with Various Mesoporous Structures (2004)

Tunable mesostructures and ultrafine particle sizes were achieved by means of triblock-copolymer and fluorocarbon surfactants, respectively, in the hydrothermal synthesis of mesoporous silica nanoparticles. The TEM image shows one such nanoparticle with a diameter of approximately 300 nm. Supporting information for this article is available on the WWW under http://www.wiley-vch.de/contents/jc_2002/2005/z460892_s.pdf or from the author. Please note: The publisher is not responsible for the content or functionality of any supporting information supplied by the authors. Any queries (other than missing content) should be directed to the corresponding author for the article.
Fusion regulation proteins on the cell surface: isolation and characterization of monoclonal antibodies which enhance giant polykaryocyte formation in Newcastle disease virus-infected cell lines of human origin (1992)

Newcastle disease virus (NDV)-infected HeLa and FL cells showed small polykaryocytes at about 24 h postinfection, while the addition of anti-FL-cell rabbit, rat, or mouse serum to the NDV-infected cells gave rise to giant polykaryocytes at 15 h postinfection. We isolated three monoclonal antibodies (MAbs) (4-5-1, 6-1-13, and 7-2-1) capable of enhancing giant polykaryocyte formation in NDV-infected HeLa cells. These MAbs immunoprecipitated gp80 or gp135, which were detected mainly on the surface of HeLa cells. A functionally intact F protein was essential for antibody-enhanced cell fusion, and hemagglutinating (receptor-binding) activity of HN protein was involved in the fusion at an early stage; that is, the MAbs enhanced NDV-mediated syncytium formation. These molecules were considered to have the ability to regulate NDV-mediated cell fusion and thus were designated fusion regulation protein (FRP)-1 (gp80) and FRP-2 (gp135). Anti-FRP MAbs enhanced the susceptibility of cells to fusion activity of NDV. Anti-FRP-1 MAbs reacted with a molecule on the surface of every cell derived from humans and monkeys but showed no cross-reactivity with mouse or hamster cells. FRP-2 could be detected in limited cell lines of human origin.
Roles of Water for Chemical Reactions in High-Temperature Water (2002)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTRoles of Water for Chemical Reactions in High-Temperature WaterNaoko Akiya and Phillip E. SavageView Author Information Department of Chemical Engineering, University of Michigan, Ann Arbor, Michigan 48109-2136 Cite this: Chem. Rev. 2002, 102, 8, 2725–2750Publication Date (Web):June 21, 2002Publication History Received11 June 2001Published online21 June 2002Published inissue 1 August 2002https://pubs.acs.org/doi/10.1021/cr000668whttps://doi.org/10.1021/cr000668wresearch-articleACS PublicationsCopyright © 2002 American Chemical SocietyRequest reuse permissionsArticle Views11728Altmetric-Citations1300LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InRedditEmail Other access optionsGet e-Alertsclose SUBJECTS:Hydrolysis,Kinetic parameters,Solvation,Solvents,Water Get e-Alerts
The Difficult Airway (2013)

This resource provides practical guidelines for improving the success rates of airway managers of all specialties who use modern airway devices and techniques, and addresses various clinical scenarios that mimic the approach clinicians encounter at educational workshops. Sections address airway devices and techniques, awake intubation, algorithms of difficult airway management, pharmacologic adjuncts useful in airway management, equipment, preoxygenation, and patient positioning strategies to ensure effective airway management.
Composition, recruitment and regulation of the PRC2 complex (2011)

The PRC2 histone methyltransferase complex is an important regulator of gene expression programs in metazoans. Gene expression regulation by the PRC2 complex is critical for development and cell differentiation. Several recent studies have begun to shed light on the molecular basis for the physiological function of the PRC2 complex. Here, we discuss some of these results and how they provide new insights into the composition, recruitment and regulation of the PRC2 complex.
Association of AR-V7 on Circulating Tumor Cells as a Treatment-Specific Biomarker With Outcomes and Survival in Castration-Resistant Prostate Cancer (2016)

The results validate CTC nuclear expression of AR-V7 protein in men with mCRPC as a treatment-specific biomarker that is associated with superior survival on taxane therapy over ARS-directed therapy in a clinical practice setting. Continued examination of this biomarker in prospective studies will further aid clinical utility.
Physically touching virtual objects using tactile augmentation enhances the realism of virtual environments (2002)

The study explored the impact of physically touching a virtual object on how realistic the VE seems to the user. Subjects in a "no touch" group picked up a 3D virtual image of a kitchen plate in a VE, using a traditional 3D wand. "See and touch" subjects physically picked up a virtual plate possessing solidity and weight, using a mixed-reality force feedback technique. Afterwards, subjects made predictions about the properties of other virtual objects they saw but did not interact with in the VE. "See and touch" subjects predicted these objects would be more solid, heavier, and more likely to obey gravity than the "no touch" group. Results provide converging evidence for the value of adding physical qualities to virtual objects. The study first empirically demonstrates the effectiveness of mixed reality as a simple, safe, inexpensive technique for adding physical texture and force feedback cues to virtual objects with large freedom of motion. Examples of practical applications are discussed.
Compact Forward Error Correction (FEC) Schemes (2004)

This document introduces some Forward Error Correction (FEC) schemes that supplement the FEC schemes described in RFC 3452. The primary benefits of these additional FEC schemes are that they are designed for reliable bulk delivery of large objects using a more compact FEC Payload ID, and they can be used to sequentially deliver blocks of an object of indeterminate length. Thus, they more flexibly support different delivery models with less packet header overhead.
Morphology and Function of the Parietal Cells after Proximal Selective Vagotomy in Duodenal Ulcer Patients (1984)

The effects of proximal selective vagotomy (PSV) on parietal cell morphology and the degree of gastric inflammation were investigated and correlated with changes in gastric acid secretion and serum gastrin concentrations in 17 duodenal ulcer patients. Endoscopy, acid secretion tests, and blood sampling were performed preoperatively and 2 months, 1 year, and 3 years postoperatively. The mucosal biopsy specimens obtained at endoscopy were analyzed both light- and electron-microscopically. Five healthy persons also underwent gastroscopy and biopsy for comparison. Preoperatively, the duodenal ulcer patients differed significantly from this control group, 33% of whose parietal cells appeared 'secretory'; the corresponding figure for the duodenal ulcer patients was 47%. Two months after the operation the number of secretory parietal cells had fallen to 30%, after which the percentage increased slightly again to 35% 3 years after PSV. A similar phenomenon was observed in the acid secretion capacities, which were maximally depressed 2 months postoperatively and recovered slightly but significantly during the 3-year follow-up period. There was a significant increase in the degree of gastric inflammation after the operation.
Treatment of rats with glucagon or mannoheptulose increases mitochondrial 3-hydroxy-3-methylglutaryl-CoA synthase activity and decreases succinyl-CoA content in liver (1989)

1. The activity of 3-hydroxy-3-methylglutaryl-CoA (HMG-CoA) synthase (EC 4.1.3.5) in extracts of rapidly frozen rat livers was doubled in animals treated in various ways to increase ketogenic flux. 2. Some 90% of the activity measured was mitochondrial, and changes in mitochondrial activity dominated changes in total enzyme activity. 3. The elevated HMG-CoA synthase activities persisted throughout the isolation of liver mitochondria. 4. Intramitochondrial succinyl-CoA content was lower in whole liver homogenates and in mitochondria isolated from animals treated with glucagon or mannoheptulose. 5. HMG-CoA synthase activity in mitochondria from both ox and rat liver was negatively correlated with intramitochondrial succinyl-CoA levels when these were manipulated artificially. Under these conditions, the differences between mitochondria from control and hormone-treated rats were abolished. 6. These findings show that glucagon can decrease intramitochondrial succinyl-CoA concentration, and that this in turn can regulate mitochondrial HMG-CoA synthase. They support the hypothesis that the formation of ketone bodies from acetyl-CoA may be regulated by the extent of succinylation of mitochondrial HMG-CoA synthase.
Fabrication and surface modification of macroporous poly(L‐lactic acid) and poly(L‐lactic‐co‐glycolic acid) (70/30) cell scaffolds for human skin fibroblast cell culture (2002)

The fabrication and surface modification of a porous cell scaffold are very important in tissue engineering. Of most concern are high-density cell seeding, nutrient and oxygen supply, and cell affinity. In the present study, poly(L-lactic acid) and poly(L-lactic-co-glycolic acid) (70/30) cell scaffolds with different pore structures were fabricated. An improved method based on Archimedes' Principle for measuring the porosity of scaffolds, using a density bottle, was developed. Anhydrous ammonia plasma treatment was used to modify surface properties to improve the cell affinity of the scaffolds. The results show that hydrophilicity and surface energy were improved. The polar N-containing groups and positive charged groups also were incorporated into the sample surface. A low-temperature treatment was used to maintain the plasma-modified surface properties effectively. It would do help to the further application of plasma treatment technique. Cell culture results showed that pores smaller than 160 microm are suitable for human skin fibroblast cell growth. Cell seeding efficiency was maintained at above 99%, which is better than the efficiency achieved with the common method of prewetting by ethanol. The plasma-treatment method also helped to resolve the problem of cell loss during cell seeding, and the negative effects of the ethanol trace on cell culture were avoided. The results suggest that anhydrous ammonia plasma treatment enhances the cell affinity of porous scaffolds. Mass transport issues also have been considered.
An overview on dry reforming of methane: strategies to reduce carbonaceous deactivation of catalysts (2016)

Catalytic reforming of methane (CH<sub>4</sub>) with carbon dioxide (CO<sub>2</sub>), known as dry reforming of methane (DRM), produces synthesis gas, which is a mixture of hydrogen (H<sub>2</sub>) and carbon monoxide (CO).
Repair Response of the Inner and Outer Regions of the Porcine Meniscus in Vitro (2007)

These findings support the hypothesis that the regional differences in meniscal repair observed clinically are owed to the additional vascular supply of the outer meniscus rather than intrinsic differences between the extracellular matrix and cells from these 2 areas.
Carbon dioxide instantly sensitizes female yellow fever mosquitoes to human skin odours (2005)

Female mosquitoes are noted for their ability to use odours to locate a host for a blood meal. Two sensory organs contribute to their sense of smell: the maxillary palps, which measure the level of CO2, and the antennae, which detect other host-released odours. To establish the relative importance and interactions of CO2 and other body emissions in freely flying mosquitoes, we presented female yellow fever mosquitoes Aedes aegypti L. with broad plumes of human skin odour and CO2 at natural concentrations and dilutions thereof in a wind tunnel. 3-D video-recorded flight tracks were reconstructed. Activation, flight velocity, upwind turning and source finding waned quickly as skin odours were diluted, whereas in the presence of CO2 these parameters remained unchanged over more than a 100-fold dilution from exhaled concentrations. Although mosquitoes were behaviourally less sensitive to skin odours than to CO2, their sensitivity to skin odours increased transiently by at least fivefold immediately following a brief encounter with a filament of CO2. This sensitization was reflected in flight velocity, track angle, turning rate upon entering and exiting the broad odour plume and, ultimately, in the source-finding rate. In Ae. aegypti, CO2 thus functions as a ;releaser' for a higher sensitivity and responsiveness to skin odours. The initially low responsiveness of mosquitoes to skin odours, their high sensitivity to CO2, and the sensitization of the olfactory circuitry by CO2 are ecologically relevant, because rapidly fluctuating CO2 levels reliably signal a potential host. Possible mechanisms of the instantaneous sensitization are considered.
BIOCHEMISTRY OF PEROXISOMES (1992)

The Hippo pathway was initially discovered in Drosophila melanogaster as a key regulator of tissue growth. It is an evolutionarily conserved signaling cascade regulating numerous biological processes, including cell growth and fate decision, organ size ...Read More
Polymer Microfluidic Chips with Integrated Waveguides for Reading Microarrays (2007)

A microfluidic chip with an integrated planar waveguide was fabricated in poly(methyl methacrylate), PMMA, using a single-step, double-sided hot-embossing approach. The waveguide was embedded in air on three sides, the solution being interrogated on the fourth. DNA probes were covalently attached to the waveguide surface by plasma activating the PMMA and the use of carbodiimide coupling chemistry. Successful hybridization events were read using evanescent excitation monitored by an imaging microscope, which offered high spatial resolution (2 microm) and a large field-of-view (20 mm diameter field-of-view), providing imaging of the entire array without scanning. The application of the microfluidic/waveguide assembly was demonstrated by detecting low abundant point mutations; insertion C mutations in BRCA1 genes associated with breast cancer were analyzed using a universal array coupled to an allele-specific ligation assay. DNA probes consisting of amine-terminated oligonucleotides were printed inside the microfluidic channel using a noncontact microspotter. Mutant and wild-type genomic DNAs of BRCA1 were PCR (polymerase chain reaction) amplified, with the amplicons subjected to ligation detection reactions (LDRs). LDR solutions were allowed to flow over the microarray positioned on the polymer waveguide with successful ligation events discerned through fluorescence signatures present at certain locations of the array. The microfluidic/waveguide assembly could detect polymorphisms present at <1% of the total DNA content.