gebhart/patrepeval huggingface dataset:
Unintended Harm and Benefit of the Implantable Defibrillator in an Unfortunate 19-Year-Old Male: Featuring a Sequence of Rare Life-threatening Complications of Cardiac Procedures (2013)

All procedures have inherent risk. Our patient endured a sequence of rare life-threatening complications from commonly preformed procedures. The sequence of these complications was; large pericardial effusion post implantable cardioverter-defibrillator (ICD) implantation with echocardiographic signs of tamponade, left main narrowing post radiofrequency ablation, and late stent thrombosis post coronary intervention with a bare metal stent. All these occurred to one unfortunate young man. Furthermore, our patient demonstrated an unintended benefit of ICD which saved his life.
Contrast sensitivity after implantation of toric iris-claw lenses in phakic eyes (2004)

Implantation of the Verisyse toric iris-claw lens in phakic eyes to correct high or moderate myopia with astigmatism has the potential to improve contrast vision. The mean contrast sensitivity increased considerably at all spatial frequencies compared with preoperative levels.
D³ Data-Driven Documents (2011)

Data-Driven Documents (D3) is a novel representation-transparent approach to visualization for the web. Rather than hide the underlying scenegraph within a toolkit-specific abstraction, D3 enables direct inspection and manipulation of a native representation: the standard document object model (DOM). With D3, designers selectively bind input data to arbitrary document elements, applying dynamic transforms to both generate and modify content. We show how representational transparency improves expressiveness and better integrates with developer tools than prior approaches, while offering comparable notational efficiency and retaining powerful declarative components. Immediate evaluation of operators further simplifies debugging and allows iterative development. Additionally, we demonstrate how D3 transforms naturally enable animation and interaction with dramatic performance improvements over intermediate representations.
Quantitative oestrogen and progesterone receptor values in primary breast cancer and predictability of response to endocrine therapy. (1983)

The concentrations of oestrogen receptors (ER) and progesterone receptors (PgR) were measured in the tumours from 47 patients with advanced primary carcinoma of the breast who were immediately treated by endocrine therapy after confirmatory histology. All patients were followed-up for at least 3 months and 27 patients for 18 months. The ER and PgR content in their primary tumour was correlated with the response to treatment, the duration of remission and the survival rate. The actual concentrations of ER and PgR were found to be better indicators of endocrine responsiveness than the mere presence of these receptors, particularly in the postmenopausal group. The remission rate improved with increasing concentrations of ER but not with increasing concentrations of PgR in the primary tumour. The predictability was enhanced when ER and PgR concentrations were considered together. Patients with ER concentrations above 150 fmol/mg cytosol protein and PgR concentrations above 100 fmol/mg cytosol protein in the same tumour were in remission after 18 months of treatment. At this time, only two of the 14 patients with ER and PgR concentrations below these levels were in remission and six had died of the disease.
Walk 'n scroll (2005)

In this paper, we present a field study comparing software-based navigation techniques (scrollbars, tap-and-drag, and touch-n-go) on mobile devices. In particular, we were interested in exploring the efficiency and user preference of these navigation techniques for different levels of mobility (sitting, walking, and standing) in a naturalistic environment. Results show that while there was no significant difference in performance between tap-and-drag and touch-n-go, both techniques significantly outperformed scrollbars for simple, multi-directional navigation tasks. In addition, the users preferred the touch-n-go technique over the other two methods. The results also revealed that users' interactions and preferences differed between the levels of mobility.
Polymerase Chain Reaction on Microchips (2006)

The polymerase chain reaction (PCR) provides an in vitro method for rapid enzymatic amplification of fragments of DNA. Microchip-based PCR devices (with reaction volumes from picoliters to microliters) have been realized using various combinations of silicon, glass, and/or plastic materials. Passivation of exposed surfaces in the microreactor is critical for successful PCR. Silicon and plastic surfaces can be passivated by silanization. With surface passivation, PCR can be performed efficiently and economically in chip-based microreactors. The reduced thermal mass of microchips allows for extremely fast temperature ramping. PCR protocols established for benchtop reactors may need to be adjusted accordingly when transferred to microchips. Here, we provide detailed protocols for microchip PCR including procedures for surface passivation and bonding of glass to silicon with ultraviolet curable glue, because both procedures have a major influence on the success or failure of the PCR.
Transmembrane proteins in the Protein Data Bank: identification and classification (2004)

Here, we present a new geometrical approach to distinguish between transmembrane and globular proteins using structural information only and to locate the most likely position of the lipid bilayer. An automated algorithm (TMDET) is given to determine the membrane planes relative to the position of atomic coordinates, together with a discrimination function which is able to separate transmembrane and globular proteins even in cases of low resolution or incomplete structures such as fragments or parts of large multi chain complexes. This method can be used for the proper annotation of protein structures containing transmembrane segments and paves the way to an up-to-date database containing the structure of all known transmembrane proteins and fragments (PDB_TM) which can be automatically updated. The algorithm is equally important for the purpose of constructing databases purely of globular proteins.
Efficacy of Melatonin Treatment in Jet Lag, Shift Work, and Blindness (1997)

Melatonin has chronobiotic properties in humans. It is able to phase shift strongly endogenous rhythms, such as core temperature and its own endogenous rhythm, together with the sleep-wake cycle. Its ability to synchronize free-running rhythms has not been fully investigated in humans. There is evidence for synchronization of the sleep-wake cycle, but the available data suggest that it is less effective with regard to endogenous melatonin and core temperature rhythms. When suitably timed, most studies indicate that fast release preparations are able to hasten adaptation to phase shift in both field and simulation studies of jet lag and shift work. Both subjective and objective measures support this statement. However, not all studies have been successful. Careful evaluation of the effects on work-related performance is required. When used to alleviate the non-24-h sleep-wake disorder in blind subjects, again most studies report a successful outcome using behavioral measures, albeit in a small number of individuals. The present data suggest, however, that although sleep-wake can be stabilized to 24 h, entrainment of other rhythms is exceptionally rare.
Characterization of the murine 5T4 oncofoetal antigen: a target for immunotherapy in cancer (2002)

Human 5T4 oncofoetal antigen defined by the murine 5T4 monoclonal antibody is a highly glycosylated protein expressed by trophoblast and a few specialized adult epithelia. Up-regulation of 5T4 expression in some cancers is associated with poor clinical outcome; overexpression of human 5T4 cDNA in epithelial cells can alter their morphology and motility, supporting a role for such functions in cancer and development. A murine model to study 5T4 biology and tumour immunology would be useful. The production of m5T4-specific antibodies, their use in establishing transfected cells and documenting their biological properties in vitro are described. A rat monoclonal antibody specific for mouse 5T4 molecules by ELISA, flow cytometry, immunohistochemistry and immunoprecipitation was isolated and epitope mapped. Similar to its human counterpart, murine 5T4 antigen is a 72 kDa glycoprotein (immunoprecipitation and Western blot analysis) and exhibits punctate cell surface expression, dependent upon the integrity of the actin cytoskeleton. Likewise, overexpression of autologous murine 5T4 by B16 F10 melanoma cells and A9 L fibroblasts accentuates the 5T4 phenotype, which is characterized by a spindle-like morphology, increased motility, and reduced adhesion and proliferation rate. Immunohistochemical analysis of adult mouse tissues shows a restricted pattern of expression similar to that of human 5T4 antigen. The murine 5T4 antigen-expressing cell lines and antibody reagents are now being used to explore novel immunotherapies in pre-clinical models and the biology of 5T4 in development.
Detection of Apoptosis and Drug Resistance of Human Breast Cancer Cells to Taxane Treatments Using Quartz Crystal Microbalance Biosensor Technology (2005)

Taxanes are used for the treatment of many human cancers, as first- and second-line chemotherapeutics. In the course of treatment many patients develop resistance or hypersensitivity to one form of taxane and require a different taxane to rescue the therapeutic benefit of the drug. There is currently no method to reliably predict tumor responses to taxanes prior to therapy or when resistance or hypersensitivity develops. We adapted the quartz crystal microbalance (QCM) biosensor technique to study responses of human mammary epithelial tumor cells to taxanes. Studies indicate that stable frequency and resistance levels are reached at 24 h. Cells in the QCM can then be treated with taxanes and responses monitored in real time via frequency and resistance changes reflecting alterations of cell mass distribution and viscoelastic properties. Distinct shifts in frequency and resistance accurately predicted apoptosis or resistance to treatment, as determined in parallel convention assays. QCM analysis accurately predicted docetaxel was more effective than paclitaxel and MCF-7 cells were more resistant to taxanes compared to MDA-MB-231 cells. These studies suggest "signature" patterns for taxane responsivity could be compared to those of patient biopsy samples to predict therapy outcome prior to treatment for initial therapy or to rescue therapy efficacy.
Advanced Sensors and Controls for Building Applications: Market Assessment and Potential R&amp;D Pathways (2005)

This document provides a market assessment of existing building sensors and controls and presents a range of technology pathways (R&D options) for pursuing advanced sensors and building control strategies.
Combinatorial Library of Peptide Isosters Based on Diels−Alder Reactions:  Identification of Novel Inhibitors against a Recombinant Cysteine Protease fromLeishmania mexicana (2001)

A combinatorial split-and-mix library of peptide isosters based on a Diels-Alder reaction was synthesized as a "one-bead-two-compounds" library and encoded by ladder synthesis for facile analysis by matrix-assisted laser desorption ionization time-of-flight (MALDI-TOF) mass spectrometry. In the "one-bead-two-compounds" library approach, each bead contains a library member as a putative protease inhibitor along with a fluorescence-quenched substrate for the protease. When the library was screened with CPB2.8 DeltaCTE, a recombinant cysteine protease from L. mexicana, several beads containing compounds with inhibitory activity could be selected from the library and analyzed by MALDI-TOF MS for structure elucidation. Two types of inhibitors were revealed. One novel class of inhibitors had the bicyclic Diels-Alder product isosteric element incorporated internally in a peptide, while the other type was an N-terminal alpha,beta-unsaturated ketone Michael acceptor used as starting material for the Diels-Alder reaction. Selected hit sequences and constructed consensus sequences based on the observed frequencies of amino acids in different subsites were resynthesized and assayed in solution for inhibitor activity and were shown to have IC(50) values in the high nanomolar to low micromolar range.
Synthesis of Oligonucleotides Containing 2′‐Deoxyisoguanosine and 2′‐Deoxy‐5‐methylisocytidine Using Phosphoramidite Chemistry (1998)

Abstract The synthesis of oligonucleotides containing 2′‐deoxy‐5‐methylisocytidine and 2′‐deoxyisoguanosine using phosphoramidite chemistry in solid‐phase oligonucleotide synthesis is described. Supporting previous observations, the N , N ‐diisobutylformamidine moiety was found to be a far superior protecting group than N ‐benzoyl for 2′‐deoxy‐5‐methylisocytidine. 2′‐Deoxy‐ N 2 ‐[(diisobutylamino)methylidene]‐5′‐(4,4′‐dimethoxytityl)‐5‐methylisocytidine 3′‐(2‐cyanoethyl diisopropylphosphoramidite) ( 1c ) incorporated multiple consecutive residues during a standard automated synthesis protocol with a coupling efficiency &gt; 99% according to dimethoxytrityl release. Extending coupling times of the standard protocol to ≥ 600s using 2′‐deoxy‐ N 6 ‐[(diisobutylamino)methylidene]‐5′‐ O ‐(dimethoxytrityl)‐ O 2 ‐(diphenylcarbamoyl)isoguanosine, 3′‐(2‐cyanoethyl diisopropylphosphoramidite) ( 7e ) led to successful incorporation of multiple consecutive 2′‐deoxyisoguanosine bases with a coupling efficiency &gt; 97% according to dimethoxytrityl release.
Fyn and PTP-PEST–mediated Regulation of Wiskott-Aldrich Syndrome Protein (WASp) Tyrosine Phosphorylation Is Required for Coupling T Cell Antigen Receptor Engagement to WASp Effector Function and T Cell Activation (2004)

Involvement of the Wiskott-Aldrich syndrome protein (WASp) in promoting cell activation requires its release from autoinhibitory structural constraints and has been attributed to WASp association with activated cdc42. Here, however, we show that T cell development and T cell receptor (TCR)-induced proliferation and actin polymerization proceed normally in WASp-/- mice expressing a WASp transgene lacking the cdc42 binding domain. By contrast, mutation of tyrosine residue Y291, identified here as the major site of TCR-induced WASp tyrosine phosphorylation, abrogated induction of WASp tyrosine phosphorylation and its effector activities, including nuclear factor of activated T cell transcriptional activity, actin polymerization, and immunological synapse formation. TCR-induced WASp tyrosine phosphorylation was also disrupted in T cells lacking Fyn, a kinase shown here to bind, colocalize with, and phosphorylate WASp. By contrast, WASp was tyrosine dephosphorylated by protein tyrosine phosphatase (PTP)-PEST, a tyrosine phosphatase shown here to interact with WASp via proline, serine, threonine phosphatase interacting protein (PSTPIP)1 binding. Although Fyn enhanced WASp-mediated Arp2/3 activation and was required for synapse formation, PTP-PEST combined with PSTPIP1 inhibited WASp-driven actin polymerization and synapse formation. These observations identify key roles for Fyn and PTP-PEST in regulating WASp and imply that inducible WASp tyrosine phosphorylation can occur independently of cdc42 binding, but unlike the cdc42 interaction, is absolutely required for WASp contributions to T cell activation.
Firefly luciferase is targeted to peroxisomes in mammalian cells. (1987)

Although several enzymes known to reside in peroxisomes have been studied extensively, no cis-acting amino acid sequences involved in the transport of these proteins to peroxisomes have been described. As a first step towards the determination of a putative peroxisomal targeting sequence, we have expressed the cDNA encoding the firefly luciferase [Photinus-luciferin:oxygen 4-oxidoreductase (decarboxylating, ATP-hydrolyzing), EC 1.13.12.7] in monkey kidney cells and found that the product of the gene is transported to peroxisomes. Luciferase is derived from the firefly (Photinus pyralis) and is synthesized and stored in the cells of the firefly's lantern organ, where it is also found in peroxisomes. The fact that this protein is similarly targeted in cells from such different organisms suggests that the process of protein transport to peroxisomes has been highly conserved through evolution.
The Influence of Chromosomal Location on the Expression of Two Transgenes in Mice (1999)

We have generated mice having a single copy of the human haptoglobin gene (Hp2), driven by its natural promoter, and a neomycin resistance gene (Neo), driven by a herpes simplex thymidine kinase promoter with polyoma enhancers, inserted into two defined chromosomal locations, the Hprt locus on the X-chromosome and the apolipoprotein (apo) AI-CIII gene cluster on chromosome 9. The haptoglobin promoter is highly specialized in its tissue of action; the viral promoter has few restrictions. The apoAI-CIII gene is naturally active in only two tissues, whereas the Hprt gene region is ubiquitously active. Expression of both transgenes at substantial levels was achieved only (a) when the transgenes were inserted into the genome close to a known tissue-specific enhancer/locus control region in the apoAI-CIII gene cluster, and (b) when known conditions for function of their promoters were met. The specificities of the two chromosomal regions and of the two promoters are preserved, but their interactions are not specific. We conclude that transgenes are affected by locus-related enhancers in the same manner as nearby endogenous genes. Our experiments reinforce the usefulness of using gene targeting to direct single-copy transgenes to appropriate chromosomal locations.
In vitro alterations in dental enamel exposed to acidic medicines (2010)

Dimetapp(®) (lowest pH and viscosity) and deionized water (control) showed the most pronounced erosive patterns. Klaricid(®) (highest pH and viscosity) presented an in vitro protective effect against acid attacks perhaps due to its mineral content and viscosity.
Human Monoclonal Antibodies to Pandemic 1957 H2N2 and Pandemic 1968 H3N2 Influenza Viruses (2012)

Investigation of the human antibody response to the 1957 pandemic H2N2 influenza A virus has been largely limited to serologic studies. We generated five influenza virus hemagglutinin (HA)-reactive human monoclonal antibodies (MAbs) by hybridoma technology from the peripheral blood of healthy donors who were born between 1950 and 1968. Two MAbs reacted with the pandemic H2N2 virus, two recognized the pandemic H3N2 virus, and remarkably, one reacted with both the pandemic H2N2 and H3N2 viruses. Each of these five naturally occurring MAbs displayed hemagglutination inhibition activity, suggesting specificity for the globular head domain of influenza virus HA. When incubated with virus, MAbs 8F8, 8M2, and 2G1 each elicited H2N2 escape mutations immediately adjacent to the receptor-binding domain on the HA globular head in embryonated chicken eggs. All H2N2-specific MAbs were able to inhibit a 2006 swine H2N3 influenza virus. MAbs 8M2 and 2G1 shared the V(H)1-69 germ line gene, but these antibodies were otherwise not genetically related. Each antibody was able to protect mice in a lethal H2N2 virus challenge. Thus, even 43 years after circulation of H2N2 viruses, these subjects possessed peripheral blood B cells encoding potent inhibiting antibodies specific for a conserved region on the globular head of the pandemic H2 HA.
Cathepsins D, B, and L in malignant human lung tissue. (1996)

The levels of cathepsins in malignant and surrounding nonmalignant lung tissue were determined in 17 non-small cell lung cancer specimens. Cathepsin (Cat) D activity was assayed using hemoglobin, whereas Cat B and Cat L activities were assayed using fluorimetric substrates, benzoylcarbonyl-Ala-Arg-Arg-7-amino-4-methylcoumarine and benzoylcarbonyl-Phe-Arg-7-amino-4-methylcoumarine, respectively. Cat protein concentrations were determined using ELISAs. In malignant tissues, the activities of Cat B and Cat L were significantly higher than the activities in nonmalignant tissues (P < 0.0012 and P < 0.0003, respectively), whereas Cat D concentration was not. There was also a 5.6-fold increase in median Cat B protein (P < 0.054) and a 2.2-fold increase in Cat L protein (P < 0.069). By contrast, the aspartic proteinase, Cat D protein, was not significantly increased in tumors versus control lung tissues. Moderate but significant correlation (r = 0.5, P < 0.045) between Cat B and Cat L expression was observed, but neither correlated with Cat D. The relative increase in median Cat L activity (P < 0.037) and protein (P < 0.0005) was greater in poorly differentiated tumors than in moderate ones. Cat L activity (P < 0.003) and protein (P < 0. 005) increases were higher in adenocarcinoma than in squamous cell carcinoma. We conclude that in lung cancers the three lysosomal enzymes are regulated in a noncoordinate manner and that there is specific induction of cysteine cathepsins. Whether Cat B and/or Cat L would be of diagnostic and/or prognostic value requires further study in a larger patient population.
Frame retransmissions considered harmful (2012)

Retransmissions reduce the efficiency of data communication in wireless networks because of: (i) per-retransmission packet headers, (ii) contention overhead on every retransmission, and (iii) redundant bits in every retransmission. In fact, every retransmission nearly doubles the time to successfully deliver the packet. To improve spectrum efficiency in a lossy environment, we propose a new in-frame retransmission scheme using uACKs. Instead of waiting for the entire transmission to end before sending the ACK, the receiver sends smaller uACKs for every few symbols, on a separate narrow feedback channel. Based on these uACKs, the sender only retransmits the lost symbols after the last data symbol in the frame, thereby adaptively changing the frame size to ensure it is successfully delivered. We have implemented uACK on the Sora platform. Experiments with our prototype validate the feasibility of symbol-level uACK . By significantly reducing the retransmistion overhead, the sender is able to aggressively use higher data rate for a lossy link. Both improve the overall network efficiency. Our experimental results from a controlled environment and an 9-node software radio testbed show that uACK can have up to 140% throughput gain over 802.11g and up to 60% gain over the best known retransmission scheme.
Cooperative Spectrum Sensing in Cognitive RadioNetworks Using Multidimensional Correlations (2014)

In this paper, a multidimensional-correlation-based sensing scheduling algorithm, (CORN)2, is developed for cognitive radio networks to minimize energy consumption. A sensing quality metric is defined as a measure of the correctness of spectral availability information based on the fact that spectrum sensing information at a given space and time can represent spectrum information at a different point in space and time. The scheduling algorithm is shown to achieve a cost of sensing (e.g., energy consumption, sensing duration) arbitrarily close to the possible minimum, while meeting the sensing quality requirements. To this end, (CORN)2 utilizes a novel sensing deficiency virtual queue concept and exploits the correlation between spectrum measurements of a particular secondary user and its collaborating neighbors. The proposed algorithm is proved to achieve a distributed and arbitrarily close to optimal solution under certain, easily satisfied assumptions. Furthermore, a distributed Selective-(CORN)2 (S-(CORN)2) is introduced by extending the distributed algorithm to allow secondary users to select collaboration neighbors in densely populated cognitive radio networks. In addition to the theoretically proved performance guarantees, the algorithms are evaluated through simulations.