gebhart/patrepeval huggingface dataset:
Relating structure to function in the hepatitis delta virus antigen (1993)

Hepatitis delta virus expresses two forms of a single protein, the small (delta Ag-S) and large (delta Ag-L) antigens, which are identical except for an additional 19 residues present at the C terminus of delta Ag-L. While delta Ag-S is required to promote genome replication, delta Ag-L potently inhibits this process and also facilitates packaging of the viral genome by envelope proteins of the helper virus (hepatitis B virus). Regions within the antigens responsible for nuclear localization, RNA binding, and dimerization have been identified, yet it is not clear how these particular activities contribute to the ultimate replication and packaging phenotypes. Here we report the following findings. (i) Although the removal of the nuclear localization signal from either antigen resulted in significant cytoplasmic accumulation, both proteins still had access to the nucleus. As a consequence, no functional defect was observed with either mutant. (ii) The RNA-binding domain, although necessary for delta Ag-S function, could be deleted from delta Ag-L without compromising its ability to either inhibit replication or promote packaging. (iii) In contrast, the coiled-coil dimerization domain was required for both the activation of replication by delta Ag-S and the inhibition of replication by delta Ag-L. This region, with an additional 20 amino acids C-terminal to it, was necessary and sufficient to potently inhibit replication by interacting with the small antigen. (iv) The packaging property of delta Ag-L required a C-terminal Pro/Gly-rich region which is hypothesized to interact with the hepatitis B virus envelope proteins during the assembly process.
Advanced thermal imaging of composites (1996)

Composite materials were studied by Scanning Thermal Conductivity Microscope (STCM) and high speed thermography. The STCM is a qualitative technique which is used to study thermal conductivity variations on a sub-micrometer scale. High speed thermography is a quantitative technique for measuring thermal diffusivity with a variable spatial resolution from centimeters down to less than 25 gm. A relative thermal conductivity contrast map was obtained from a SiC/Si3N4 continuous fiber ceramic composite using the STCM. Temperature changes of a carbon/carbon composite after a heat pulse were captured by an IR camera to generate a thermal diffusivity map of the specimen. Line profiles of the temperature distribution showed significant variations as a result of fiber orientation.
Adaptive Coding and Modulation for the DVB-S2 Standard Interactive Applications: Capacity Assessment and Key System Issues (2007)

Point-to-point multibeam satellite systems based on the DVB-S standard are currently designed for link closure in the worst-case propagation and location conditions. The DVB-S standard, conceived for broadcasting applications, considers a fixed coding rate and modulation format that are selected according to the assumed coverage and availability requirements. This approach implies the occurrence of high margins in the majority of the cases, when interference and propagation conditions allow for higher signal-to-noise-plus-interference ratio. The adaptive coding and modulation (ACM) introduction in the new DVB-S2 standard for the interactive service profile opens up a number of appealing opportunities for the design and development of satellite broadband networks. In this article we show how the ACM introduction in the satellite downlink enables greatly enhanced system performance but also has a profound impact on the way the system and some of the key system components are designed.
Transforming Growth Factor-β and the Immune Response: Implications for Anticancer Therapy (2007)

Immune homeostasis is a delicate balance between the immune defense against foreign pathogens and suppression of the immune system to maintain self-tolerance and prevent autoimmune disease. Maintenance of this balance involves several crucial networks of cytokines and various cell types. Among these regulators, transforming growth factor-beta (TGF-beta) is a potent cytokine with diverse effects on hematopoietic cells. Its pivotal function within the immune system is to maintain tolerance via the regulation of lymphocyte proliferation, differentiation, and survival. In addition, TGF-beta controls the initiation and resolution of inflammatory responses through the regulation of chemotaxis and activation of leukocytes in the periphery, including lymphocytes, natural killer cells, dendritic cells, macrophages, mast cells, and granulocytes. Through its pleiotropic effects on these immune cells, TGF-beta prevents the development of autoimmune diseases without compromising immune responses to pathogens. However, overactivation of this pathway can lead to several immunopathologies under physiologic conditions including cancer progression, making it an attractive target for antitumor therapies. This review discusses the biological functions of TGF-beta and its effects on the immune system and addresses how immunosuppression by this cytokine can promote tumorigenesis, providing the rationale for evaluating the immune-enhancing and antitumor effects of inhibiting TGF-beta in cancer patients.
Highly specific protein sequence motifs for genome analysis (1998)

We present a method for discovering conserved sequence motifs from families of aligned protein sequences. The method has been implemented as a computer program called EMOTIF (http://motif. stanford.edu/emotif). Given an aligned set of protein sequences, EMOTIF generates a set of motifs with a wide range of specificities and sensitivities. EMOTIF also can generate motifs that describe possible subfamilies of a protein superfamily. A disjunction of such motifs often can represent the entire superfamily with high specificity and sensitivity. We have used EMOTIF to generate sets of motifs from all 7,000 protein alignments in the BLOCKS and PRINTS databases. The resulting database, called IDENTIFY (http://motif. stanford.edu/identify), contains more than 50,000 motifs. For each alignment, the database contains several motifs having a probability of matching a false positive that range from 10(-10) to 10(-5). Highly specific motifs are well suited for searching entire proteomes, while generating very few false predictions. IDENTIFY assigns biological functions to 25-30% of all proteins encoded by the Saccharomyces cerevisiae genome and by several bacterial genomes. In particular, IDENTIFY assigned functions to 172 of proteins of unknown function in the yeast genome.
From Batch to Continuous Manufacturing of Microbiomedical Devices (2000)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTFrom Batch to Continuous Manufacturing of Microbiomedical DevicesMarc Madou and John FlorkeyView Author Information Center for Industrial Sensors & Measurements, The Ohio State University, 291 Watts Hall, 2041 College Road, Columbus, Ohio 43210 Cite this: Chem. Rev. 2000, 100, 7, 2679–2692Publication Date (Web):June 20, 2000Publication History Received2 August 1999Published online20 June 2000Published inissue 1 July 2000https://pubs.acs.org/doi/10.1021/cr980098ohttps://doi.org/10.1021/cr980098oresearch-articleACS PublicationsCopyright © 2000 American Chemical SocietyRequest reuse permissionsArticle Views930Altmetric-Citations37LEARN 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:Biotechnology,Manufacturing,Plastics,Sensors,Silicon Get e-Alerts
Preoperative Evaluation of Pancreatic Masses with Positron Emission Tomography Using 18F‐fluorodeoxyglucose: Diagnostic Limitations (2000)

Identification of pancreatic cancer in patients presenting with an enlarged pancreatic mass is a major diagnostic problem. Positron emission tomography (PET) using the radiolabeled glucose analogue 18F-fluorodeoxyglucose (FDG) has been suggested to provide excellent accuracy for noninvasive determination of suspicious pancreatic masses. We conducted a prospective study to verify these results. Forty-two patients admitted for pancreatic surgery underwent PET scanning. Image analysis was based on visual film evaluation and quantification of regional tracer uptake. PET imaging was visually analyzed by three observers blinded for the results of other diagnostic tests; they qualitatively graded the scans using a five-point scale (I = low to V = high) for the presence and intensity of focal FDG uptake. Diagnosis was proven by histology (n = 38) or follow-up (n = 4). Furthermore, the results of PET were compared with helical computed tomography (CT) and conventional ultrasonography (US), done during the routine diagnostic workup before pancreatic cancer surgery. Regarding only the results with scores of IV and V as positive for representing definite malignancy yielded a sensitivity of 71% and a specificity of 64% for film reading. Quantification of regional tracer uptake contributed no significant diagnostic advantage for differentiation between benign and malignant tumors. Helical CT revealed a sensitivity of 74% and a specificity of 45.5% and abdominal US 56% and 50%, respectively. We concluded that PET imaging provides only fair diagnostic accuracy (69%) for characterizing enlarged pancreatic masses. PET does not allow exclusion of malignant tumors. In doubtful cases, the method must be combined with other imaging modalities, such as helical CT. The results indicate that the number of invasive procedures is not significantly reduced by PET imaging.
Electrochemical Desorption of Self-Assembled Monolayers Noninvasively Releases Patterned Cells from Geometrical Confinements (2003)

This report describes a method to pattern mammalian cells using self-assembled monolayers (SAMs), and then to use electrochemical desorption of these monolayers to release cells from their patterns. This method uses an oligo(ethyleneglycol)-terminated SAM to prevent,-and a methyl-terminated SAM to allow-adsorption of proteins and attachment of bovine capillary endothelial cells. Electrochemical removal of the oligo(ethyleneglycol)-terminated SAM allowed proteins to adsorb onto areas that had been previously inert and enabled cells to migrate into these areas. This straightforward technique is useful in bioassays for drug screening and for fundamental studies in cell biology.
Developmental hierarchy of immunoglobulin gene rearrangements in human leukemic pre-B-cells. (1981)

We have used a special class of human acute lymphocytic leukemias, the common "non-T/non-B" cell type, to define a hierarchy of genetic rearrangements that occur during the earliest stages of B-cell maturation. This has allowed us to identify intermediate cells predicted by a hierarchial model in which immunoglobulin heavy chain variable region gene formation precedes that of light chain and in which kappa light chain gene formation precedes that of lambda. The model emphasizes the flexible nature of immunoglobulin gene recombination that not infrequently produces aberrant or null genes that are phenotypically excluded from expression. Remaining alleles or isotypic genes can then be utilized as "spares" undergoing recombination until a valid gene is formed. Significantly, the excluded allele or isotype is frequently deleted from the genome. In addition to defining a pathway of genetic maturation, this analysis provides a powerful means to further classify cases of non-T/non-B-cell acute lymphocytic leukemia, most of which seem to reside at early stages along the B-cell pathway of differentiation.
Activation of Group I Metabotropic Glutamate Receptors Produces a Direct Excitation and Disinhibition of GABAergic Projection Neurons in the Substantia Nigra Pars Reticulata (2001)

A pathological increase in excitatory glutamatergic input to substantia nigra pars reticulata (SNr) from the subthalamic nucleus (STN) is believed to play a key role in the pathophysiology of Parkinson's disease. We present an analysis of the physiological roles that group I metabotropic glutamate receptors (mGluRs) play in regulating SNr functions. Immunocytochemical analysis at the light and electron microscopic levels reveal that both mGuR1a and mGluR5 are localized postsynaptically in the SNr. Consistent with this, activation of group I mGluRs depolarizes SNr GABAergic neurons. Interestingly, although both group I mGluRs (mGluR1 and mGluR5) are expressed in these neurons, the effect is mediated solely by mGluR1. Light presynaptic staining for mGluR1a and mGluR5 was also observed in some terminals forming symmetric synapses and in small unmyelinated axons. Consistent with this, activation of presynaptic mGluR1a and mGluR5 decreases inhibitory transmission in the SNr. The combination of direct excitatory effects and disinhibition induced by activation of group I mGluRs could lead to a large excitation of SNr projection neurons. This suggests that group I mGluRs are likely to play an important role in the powerful excitatory control that the STN exerts on basal ganglia output neurons.
Immunological Mechanisms Underneath the Efficacy of Cancer Therapy (2016)

Accumulating preclinical and clinical evidence indicates that the success of several anticancer agents-including some conventional chemotherapeutics, targeted anticancer agents as well as specific forms of radiotherapy-depends (at least in part) on their ability to stimulate anticancer immune responses. Such immunostimulatory effects can be "on-target," i.e., they originate within cancer cells, or "off-target," i.e., they develop from a heretofore unsuspected interaction between cancer therapy and the immune system. Here, we briefly discuss the immunologic mechanisms that underlie the efficacy of some forms of cancer therapy, as we highlight the rationale for combining these treatment modalities with immunotherapy to achieve superior therapeutic effects. Cancer Immunol Res; 4(11); 895-902. ©2016 AACR.
Semi-automatic wrapper generation for Internet information sources (2002)

To simplify the task of obtaining information from the vast number of information sources that are available on the World Wide Web (WWW), the authors are building information mediators for extracting and integrating data from multiple Web sources. In a mediator based approach, wrappers are built around individual information sources to translate between the mediator query language and the individual sources. They present an approach for semi-automatically generating wrappers for structured Internet sources. The key idea is to exploit formatting information in Web pages to hypothesize the underlying structure of a page. From this structure the system generates a wrapper that facilitates querying of a source and possibly integrating it with other sources. They demonstrate the ease with which they are able to build wrappers for a number of Web sources using their implemented wrapper generation toolkit.
Covalent Capture and Stabilization of Cylindricalβ-Sheet Peptide Assemblies (1999)

Covalent capture of supramolecular peptide assemblies such as A leads to kinetically stable cylindrical β-sheet structures B. The covalent bond-forming processes employed must be mild enough to tolerate peptide backbone groups as well as intersubunit hydrogen bonding. On the basis of these criteria, olefin metathesis using a selective RuII catalyst developed by Grubbs et al. as well as cysteine disulfide formation were investigated. This general strategy involving the marriage of noncovalent and covalent chemistry may prove useful in preparation of functional molecular constructs.
Characterization of purified recombinant fibrinogen: partial phosphorylation of fibrinopeptide A (1993)

Human fibrinogen has been expressed in Chinese hamster ovary (CHO) cells using a novel two-step procedure which permits efficient synthesis of engineered variant fibrinogens. CHO cells secreting recombinant fibrinogen were grown in roller bottles and maintained in serum-free media for several months. Recombinant protein was purified from media containing 2-4 micrograms/mL fibrinogen using protamine-Sepharose chromatography. Recombinant fibrinogen was identical to plasma fibrinogen when examined on Coomassie-stained SDS gels run under reducing conditions, and on SDS gels when run under nonreducing conditions after partial or complete plasmin degradation, indicating normal chain assembly, disulfide bond formation, and overall protein conformation. Thrombin digestion of purified fibrinogen led to clot formation with release of normal fibrinopeptides, as identified by HPLC. Fibrinopeptide A released from recombinant fibrinogen was partially phosphorylated (22%), similar to the degree of phosphorylation found for human plasma fibrinogen (20-25%), indicating that partial phosphorylation in inherent in fibrinogen synthesis.
Implant Electrical Characteristics Predict Response to Cardiac Resynchronization Therapy (2014)

Background: The optimal site for left ventricular (LV) lead placement in cardiac resynchronization therapy (CRT) remains uncertain. Intra-procedural measures for predicting response to CRT have shown mixed results. Hypothesis: This study analyzed intracardiac electrogram (IEGM) characteristics at implant and assessed patients’ response rates (RR) to CRT. Methods: Forty-one consecutive patients undergoing CRT were enrolled. Medically optimized patients in sinus rhythm, with ejection fraction (EF) 34 were included. Right ventricular (RV) leads were positioned mid-septum. LV leads were targeted to the latest mechanical activation on echocardiography. IEGMs were measured, assessing intrinsic RV-to-LV delay (int RV-LV), RV-paced delay (RVp-LV), and LV-paced delay (LVp-RV). The difference between LVp-RV and RVp-LV was recorded as delta-LV. Response was defined as improvement of EF > 10%, reduction in LVEDD > 15% and improvement of ≥1 NYHA class. Results: Overall RR was 79%. LV leads were placed in the target location in 91%. Int RV-LV was 101 ± 14 ms in responders; 78 ± 11 ms in non-responders (p 100 had a RR of 87%; int RV-LV 40 ms had a RR of 56%; delta-LV < 40 ms had a RR of 85%. There was no significant correlation between lead position, DI, QRS duration or EF and IEGM measurements. Conclusions: IEGM measures at implant are easily obtained. Significant intrinsic electrical delay and shorter delta-LV both predict response, even when LV leads are implanted in the targeted mechanically-delayed segment. These assessments of electrical dyssynchrony may be used to determine optimal lead positions and response to CRT.
Energy Harvesting for Marine-Wildlife Monitoring (2014)

Bio-logging devices are systems mounted to an animal that measure parameters associated with the animal or its environment. These devices date back to the 1930’s in their simplest form, while modern devices use suites of digital sensors, microcontrollers, and wireless data communication. Despite these advances, there has always been a fundamental relationship between power consumption and the amount of science that can be conducted. There are now a number of commercially available devices that use solar cells to supplement their daily energy budget, but supplemental solar power is not useful for species that are nocturnal, subterranean, aquatic, or spend significant time beneath dense forest canopies. As such, there have been calls from the marine biology community for devices that could harvest power from their environments. For these marine species, alternative energy harvesting techniques are required. Here we explore a new application for energy harvesting as a power source for marine wildlife bio-logging tags. Marine animals cover wide swaths of the ocean, making tracking and data collection challenging. Tagging these animals with devices that track their location and/or collect data about the animal or its surroundings require large batteries and have limited life spans due to high power requirements for satellite data relays. With limited solar irradiance at depth making solar power less attractive, we review and explore other forms of energy that could be harvested, such as energy from fluid flow and hydrostatic pressure cycles. We investigate the energy potential from a number of sources and compare these values with the requirements of current bio-logging systems to assess required transduction efficiencies. The application of energy harvesting on animal tags could result in nearly indefinite life systems allowing for data collection from a single animal over the course of many years.
Nanoporous Elements in Microfluidics for Multiscale Manipulation of Bioparticles (2011)

Solid materials, such as silicon, glass, and polymers, dominate as structural elements in microsystems including microfluidics. Porous elements have been limited to membranes sandwiched between microchannel layers or polymer monoliths. This paper reports the use of micropatterned carbon-nanotube forests confined inside microfluidic channels for mechanically and/or chemically capturing particles ranging over three orders of magnitude in size. Nanoparticles below the internanotube spacing (80 nm) of the forest can penetrate inside the forest and interact with the large surface area created by individual nanotubes. For larger particles (>80 nm), the ultrahigh porosity of the nanotube elements reduces the fluid boundary layer and enhances particle-structure interactions on the outer surface of the patterned nanoporous elements. Specific biomolecular recognition is demonstrated using cells (≈10 μm), bacteria (≈1 μm), and viral-sized particles (≈40 nm) using both effects. This technology can provide unprecedented control of bioseparation processes to access bioparticles of interest, opening new pathways for both research and point-of-care diagnostics.