gebhart/patrepeval huggingface dataset:
Highly Methylated Genes in Colorectal Neoplasia: Implications for Screening (2007)

Discriminant markers are required for accurate cancer screening. We evaluated genes frequently methylated in colorectal neoplasia to identify the most discriminant ones. Four genes specifically methylated in colorectal cancer [bone morphogenetic protein 3 (BMP3), EYA2, aristaless-like homeobox-4 (ALX4), and vimentin] were selected from 41 candidate genes and evaluated on 74 cancers, 62 adenomas, and 70 normal epithelia. Methylation status was analyzed qualitatively and quantitatively and confirmed by bisulfite genomic sequencing. Effect of methylation on gene expression was evaluated in five colon cancer cell lines. K-ras and BRAF mutations were detected by sequencing. Methylation of BMP3, EYA2, ALX4, or vimentin was detected respectively in 66%, 66%, 68%, and 72% of cancers; 74%, 48%, 89%, and 84% of adenomas; and 7%, 5%, 11%, and 11% of normal epithelia (P < 0.01, cancer or adenoma versus normal). Based on area under the curve analyses, discrimination was not significantly improved by combining markers. Comethylation was frequent (two genes or more in 72% of cancers and 84% of adenomas), associated with proximal neoplasm site (P < 0.001), and linked with both BRAF and K-ras mutations (P < 0.01). Cell line experiments supported silencing of expression by methylation in all four study genes. This study shows BMP3, EYA2, ALX4, and vimentin genes are methylated in most colorectal neoplasms but rarely in normal epithelia. Comethylation of these genes is common, and pursuit of complementary markers for methylation-negative neoplasms is a rational strategy to optimize screening sensitivity.
A Nucleotide Binding Motif in Hepatitis C Virus (HCV) NS4B Mediates HCV RNA Replication (2004)

Hepatitis C virus (HCV) is a major cause of viral hepatitis. There is no effective therapy for most patients. We have identified a nucleotide binding motif (NBM) in one of the virus's nonstructural proteins, NS4B. This structural motif binds and hydrolyzes GTP and is conserved across HCV isolates. Genetically disrupting the NBM impairs GTP binding and hydrolysis and dramatically inhibits HCV RNA replication. These results have exciting implications for the HCV life cycle and novel antiviral strategies.
Simple Fluidic System for Purifying and Concentrating Diagnostic Biomarkers Using Stimuli-Responsive Antibody Conjugates and Membranes (2010)

We report a simple fluidic system that can purify and concentrate diagnostic biomarkers through the capture and triggered release of stimuli-responsive polymer-antibody conjugates at porous membranes that are grafted with the same stimuli-responsive polymer. This technique is applied here to the capture and detection of a model streptavidin antigen and subsequently to clinical ranges of the malaria antigen Plasmodium falciparum histidine-rich protein 2 (PfHRP2) from spiked human plasma. The carboxyl end-groups of semi-telechelic poly(N-isopropylacrylamide) (pNIPAAm) synthesized by reversible addition-fragmentation chain transfer (RAFT) polymerization were modified with tetrafluorophenol to yield amine-reactive ester groups for conjugation to amine groups of anti-streptavidin and anti-PfHRP2 antibodies. Stimuli-responsive membranes were constructed from 1.2 μm pore-size, hydroxylated, nylon-6,6 filters (Loprodyne, from Pall Corporation). The surface hydroxyl groups on the filters were conjugated to a 2-ethylsulfanylthiocarbonylsulfanyl-2-methyl propionic acid (EMP) RAFT chain transfer agent, and the surface-grafted pNIPAAm was obtained by subsequent polymerization. The number average molecular weight (Mn) and polydispersity indices (PDI) of the surface grafts were characterized, and membranes with either 4100 and 8400 dalton pNIPAAm grafts showed greater than 80% anti-streptavidin capture efficiency. The 8400 dalton-graft membrane showed the highest release efficiency, and it was demonstrated that at 0.2 nM starting concentration the streptavidin could be concentrated approximately 40-fold by releasing into a small 50 μL volume. This concentrator system was applied to the capture and concentration of the PfHRP2 antigen, and results showed that the PfHRP2 antigen could be processed and detected at clinically relevant concentrations of this malaria biomarker.
Single-Molecule Detection and Mismatch Discrimination of Unlabeled DNA Targets (2007)

We report on a single-molecule readout scheme on total internal reflection fluorescence microscopy (TIRFM) demonstrating a detection limit in the low fM regime for short (30-mer) unlabeled DNA strands. Detection of unlabeled DNA targets is accomplished by letting them mediate the binding of suspended fluorescently labeled DNA-modified small unilamellar vesicles (Ø approximately 100 nm) to a DNA-modified substrate. On top of rapid and sensitive detection, the technique is also shown capable of extracting kinetics data from statistics of the residence time of the binding reaction in equilibrium, that is, without following neither the rate of binding upon injection nor release upon rinsing. The potential of this feature is demonstrated by discriminating a single mismatch from a fully complementary sequence. The success of the method is critically dependent on a surface modification that provides sufficiently low background. This was achieved through self-assembly of a biotinylated copolymer, Poly(L-lysine)-g-poly(ethylene glycol) (PLL-g-PEG) on a silicon dioxide surface, followed by subsequent addition of streptavidin and biotinylated DNA. The proposed detection scheme is particularly appealing due to the simplicity of the sensor, which relies on self-assembly principles and conventional TIRFM. Therefore, we foresee a great potential of the concept to serve as an important component in future multiplexed sensing schemes. This holds in particular true in cases when information about binding kinetics is valuable, such as in single nucleotide polymorphism diagnostics.
Design of well and groove microchannel bioreactors for cell culture (2008)

Microfluidic bioreactors have been shown valuable for various cellular applications. The use of micro-wells/grooves bioreactors, in which micro-topographical features are used to protect sensitive cells from the detrimental effects of fluidic shear stress, is a promising approach to culture sensitive cells in these perfusion microsystems. However, such devices exhibit substantially different fluid dynamics and mass transport characteristics compared to conventional planar microchannel reactors. In order to properly design and optimize these systems, fluid and mass transport issues playing a key role in microscale bioreactors should be adequately addressed. The present work is a parametric study of micro-groove/micro-well microchannel bioreactors. Operation conditions and design parameters were theoretically examined via a numerical model. The complex flow pattern obtained at grooves of various depths was studied and the shear protection factor compared to planar microchannels was evaluated. 3D flow simulations were preformed in order to examine the shear protection factor in micro-wells, which were found to have similar attributes as the grooves. The oxygen mass transport problem, which is coupled to the fluid mechanics problem, was solved for various groove geometries and for several cell types, assuming a defined shear stress limitation. It is shown that by optimizing the groove depth, the groove bioreactor may be used to effectively maximize the number of cells cultured within it or to minimize the oxygen gradient existing in such devices. Moreover, for sensitive cells having a high oxygen demand (e.g., hepatocytes) or low endurance to shear (e.g., human embryonic stem cells), results show that the use of grooves is an enabling technology, since under the same physical conditions the cells cannot be cultured for long periods of time in a planar microchannel. In addition to the theoretical model findings, the culture of human foreskin fibroblasts in groove (30 microm depth) and well bioreactors (35 microm depth) was experimentally examined at various flow rates of medium perfusion and compared to cell culture in regular flat microchannels. It was shown that the wells and the grooves enable a one order of magnitude increase in the maximum perfusion rate compared to planar microchannels. Altogether, the study demonstrates that the proper design and use of microgroove/well bioreactors may be highly beneficial for cell culture assays.
Jump-oriented programming (2011)

10.1145/1966913.1966919
Gas Plasma Effects on Living Cells (2004)

This paper surveys the research activities at the Eindhoven University of Technology (The Netherlands) in the area of biomedical applications of gas discharge plasmas. A non-thermal atmospheric plasma source (the plasma needle) has been developed, and its interactions with living mammalian cells and bacteria are studied. It is concluded that plasma can efficiently kill bacteria without harming the cells, and also influence the cells without causing cell death (necrosis). In future it will lead to applications like skin (wound) and caries treatment.
Haemophilus pleuropneumoniae serotypes--cross protection experiments. (1984)

Pigs vaccinated with a killed 6-hour culture of Haemophilus pleuropneumoniae serotype 2 with Freund's incomplete adjuvant were not protected against challenge with serotypes 1, 5, 6 or 8. Equivalent results were obtained when pigs were vaccinated with serotypes 4 or 5 and challenged with serotype 2. In earlier studies of immunity induced by intranasal immunization with live H. pleuropneumoniae organisms, it was clearly shown that intranasal inoculation with one serotype of H. pleuropneumoniae would induce a strong immunity to both homologous and heterologous serotypes (Nielsen 1979). The present study has shown that cross immunity is not obtained with parenteral immunization. The results strongly suggest that the immune response of the pig to parenteral vaccination is different from the response seen after natural infection, and indicate that an important part of the defence mechanism against H. pleuropneumoniae infection is a local immune-barrier which is effective in preventing the bacterium from penetrating the mucosa. In earlier vaccination experiments 90 per cent of vaccinates were protected against homologous challenge (Nielsen 1976). In the present work a vaccine containing serotypes 1 through 6 was fully protective against serotypes 2 and 3 and also against serotype 8, which shares antigenic determinants with serotypes 3 and 6. These results indicate that the protection obtained by parenteral immunization is serotype-specific. Vaccines must therefore contain the serotypes existing in the swine population.
Antioxidant Activities of Rosemary and Sage Extracts and Vitamin E in a Model Meat System (1995)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTAntioxidant Activities of Rosemary and Sage Extracts and Vitamin E in a Model Meat SystemJon W. Wong, Kelly Hashimoto, and Takayuki ShibamotoCite this: J. Agric. Food Chem. 1995, 43, 10, 2707–2712Publication Date (Print):October 1, 1995Publication History Published online1 May 2002Published inissue 1 October 1995https://pubs.acs.org/doi/10.1021/jf00058a029https://doi.org/10.1021/jf00058a029research-articleACS PublicationsRequest reuse permissionsArticle Views767Altmetric-Citations88LEARN 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 Get e-Alerts
Immunopathogenesis of Respiratory Syncytial Virus Bronchiolitis (2007)

Background. The objective of this study was to elucidate the relation between respiratory syncytial virus (RSV) infection and cytokine/chemokine concentrations, as well as the impact that these factors have on the severity of bronchiolitis.
Flow rate analysis of a surface tension driven passive micropump (2007)

A microfluidic passive pumping method relying on surface tension properties is investigated and a physical model is developed. When a small inlet drop is placed on the entrance of a microfluidic channel it creates more pressure than a large output drop at the channel exit, causing fluid flow. The behavior of the input drop occurs in two characteristic phases. An analytical solution is proposed and verified by experimental results. We find that during the first phase the flow rate is stable and that this phase can be prolonged by refilling the inlet drop to produce continuous flow in the microchannel.
An OCR system to read two Indian language scripts: Bangla and Devnagari (Hindi) (2002)

An OCR system is proposed that can read two Indian language scripts: Bangla and Devnagari (Hindi), the most popular ones in the Indian subcontinent. These scripts, having the same origin in ancient Brahmi script, have many features in common and hence a single system can be modeled to recognize them. In the proposed model, document digitization, skew detection, text line segmentation and zone separation, word and character segmentation, character grouping into basic, modifier and compound character category are done for both scripts by the same set of algorithms. The feature sets and classification tree as well as the knowledge base required for error correction (such as lexicon) differ for Bangla and Devnagari. The system shows a good performance for single font scripts printed on clear documents.
A geometric approach to multi-view compressive imaging (2012)

In this paper, we consider multi-view imaging problems in which an ensemble of cameras collect images describing a common scene. To simplify the acquisition and encoding of these images, we study the effectiveness of non-collaborative compressive sensing encoding schemes wherein each sensor directly and independently compresses its image using randomized measurements. After these measurements and also perhaps the camera positions are transmitted to a central node, the key to an accurate reconstruction is to fully exploit the joint correlation among the signal ensemble. To capture such correlations, we propose a geometric modeling framework in which the image ensemble is treated as a sampling of points from a low-dimensional manifold in the ambient signal space. Building on results that guarantee stable embeddings of manifolds under random measurements, we propose a "manifold lifting" algorithm for recovering the ensemble that can operate even without knowledge of the camera positions. We divide our discussion into two scenarios, the near-field and far-field cases, and describe how the manifold lifting algorithm could be applied to these scenarios. At the end of this paper, we present an in-depth case study of a far-field imaging scenario, where the aim is to reconstruct an ensemble of satellite images taken from different positions with limited but overlapping fields of view. In this case study, we demonstrate the impressive power of random measurements to capture single- and multi-image structure without explicitly searching for it, as the randomized measurement encoding in conjunction with the proposed manifold lifting algorithm can even outperform image-by-image transform coding.
Generation of dendritic cells from human bone marrow mononuclear cells: Advantages for clinical application in comparison to peripheral blood monocyte derived cells (2002)

Dendritic cells (DCs) currently used for vaccination in clinical studies to induce immunity against malignant cells are normally generated from peripheral blood-derived monocytes. Here we studied conditions for the generation of DCs from unseparated human bone marrow (BM) mononuclear cells and compared them functionally with DCs from blood. The two types of DCs, from bone marrow (BM-DC) and peripheral blood (BL-DC), were generated in parallel from the same normal healthy donors by culturing in serum-free X-VIVO 20 medium containing GM-CSF and IL-4, and then the phenotypes and functions were compared. BM-DC generation occurred in 14 days and involved proliferative expansion from CD34 stem cells and differentiation while BL-DC generation occurred in 7 days from CD14 monocytes and involved only differentiation. A 7- to 25-fold higher number of DCs could be obtained from BM than from blood. BM-DC had similar phenotypes as BL-DC. The capacity to stimulate MLR reactivity in allogeneic T lymphocytes was higher with BM-DC than that with BL-DC. Also, the capacity to stimulate autologous memory T cell responses to tetanus toxoid (TT) or tuberculin (PPD) was higher with BM-DC than with BL-DC. These results suggest that BM-DC as produced here may be a very economic and useful source of professional antigen-presenting cells for anti-tumor immunotherapeutic protocols.
Enzyme-based CO2 capture for advanced life support. (2002)

Elevated CO2 levels in air can lead to impaired functioning and even death to humans. Control of CO2 is critical in confined spaces that have little physical or biological buffering capacity (e.g., spacecraft, submarines, or aircraft). A novel enzyme-based contained liquid membrane bioreactor was designed for CO2 capture and certain application cases are reported in this article. The results show that the liquid layer accounts for the major transport resistance. With addition of carbonic anhydrase, the transport resistance decreased by 71%. Volatile organic compounds of the type and concentration expected to be present in either the crew cabin or a plant growth chamber did not influence carbonic anhydrase activity or reactor operation during 1-day operation. Alternative sweep method studies, examined as a means of eliminating consumables, showed that the feed gas could be used successfully in a bypass mode when combined with medium vacuum pressure (-85 kPa) to achieve CO2 separation comparable to that with an inert sweep gas. The reactor exhibited a selectivity for CO2 versus N2 of 1400:1 and CO2 versus O2 is 866:1. The CO2 permeance was 1.44 x 10(-7) mol m-2 Pa-1 s-1 (4.3 x 10(-4) cm3 cm-2 s-1 cmHg-1) at a feed concentration of 0.1% CO2. These data show that the enzyme-based contained liquid membrane is a promising candidate technology that may be suitable for NASA applications to control CO2 in the crew or plant chambers.
T-Cell Targeted Immunofusion Proteins from Escherichia coli (1995)

Fusion proteins between cell-targeting domains and cytotoxic proteins may be particularly effective therapeutic reagents. We constructed a family of immunofusion proteins linking the humanized Fab, F(ab')2 or single-chain antibody forms of the H65 antibody (which recognizes the CD5 antigen on the surface of human T cells) with the plant ribosome-inactivating protein gelonin. We reasoned that an immunofusion could be identified that killed human target cells at least as efficiently as a chemical conjugate of H65 and gelonin. Each immunofusion protein was produced in E. coli as a secreted protein and was recovered directly from the bacterial culture supernatant in an active form. All of the immunofusion proteins were purified by a common process and each immunofusion protein was tested for cytotoxicity toward antigen-positive human cells. Interestingly, a wide range of cytotoxic activity was seen among the fusion family members, and several fusion proteins were identified which are approximately as active as the most effective chemical conjugates.
A novel therapeutic approach for thrombocytopenia by minibody agonist of the thrombopoietin receptor (2004)

Abstract Antibodies have brought valuable therapeutics in the clinical treatment of various diseases without serious adverse effects through their intrinsic features such as specific binding to the target antigen with high affinity, clinical safety as serum proteins, and long half-life. Agonist antibodies, furthermore, could be expected to maximize the value of therapeutic antibodies. Indeed, several IgG/IgM antibodies have been reported to induce cellular growth/differentiation and apoptosis. These agonist antibodies, however, should be further improved to exert more potent biologic activities and appropriate serum half-life depending upon the disease indications. Here, we report that IgG antibodies against the thrombopoietin receptor (Mpl), which have an absence or very weak agonist activity, can be engineered to be agonist minibodies, which include diabody or sc(Fv)2 as potent as natural ligand. Through this technological development, minibodies have been successfully constructed to bind and activate 2 types of dysfunctional mutant Mpls that cause congenital amegakaryocytic thrombocytopenia (CAMT). This drastic conversion of biologic activities by designing minibodies can be widely applicable to generate agonist minibodies for clinical application, which will constitute a new paradigm in antibody-based therapeutics.
Highly Regio-, Diastereo-, and Enantioselective C−H Insertions of Methyl Aryldiazoacetates into Cyclic N-Boc-Protected Amines. Asymmetric Synthesis of Novel C2-Symmetric Amines and threo-Methylphenidate (1999)

ADVERTISEMENT RETURN TO ISSUEPREVCommunicationNEXTHighly Regio-, Diastereo-, and Enantioselective C−H Insertions of Methyl Aryldiazoacetates into Cyclic N-Boc-Protected Amines. Asymmetric Synthesis of Novel C2-Symmetric Amines and threo-MethylphenidateHuw M. L. Davies, Tore Hansen, Darrin W. Hopper, and Stephen A. PanaroView Author Information Department of Chemistry State University of New York at Buffalo Buffalo, New York 14260-3000 Cite this: J. Am. Chem. Soc. 1999, 121, 27, 6509–6510Publication Date (Web):June 24, 1999Publication History Received5 April 1999Published online24 June 1999Published inissue 1 July 1999https://pubs.acs.org/doi/10.1021/ja9910715https://doi.org/10.1021/ja9910715rapid-communicationACS PublicationsCopyright © 1999 American Chemical SocietyRequest reuse permissionsArticle Views3548Altmetric-Citations163LEARN 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-AlertscloseSupporting Info (1)»Supporting Information Supporting Information SUBJECTS:Amines,Catalysts,Enantioselective synthesis,Molecular structure,Stereoselectivity Get e-Alerts