gebhart/patrepeval huggingface dataset:
Inhibiting Sterilization-Induced Oxidation of Large Molecule Therapeutics Packaged in Plastic Parenteral Vials (2017)

For many years, glass has been the default material for parenteral packaging, but the development of advanced plastics such as cyclic olefin polymers and the rapidly increasing importance of biologic drugs have provided new choices, as well as more stringent performance requirements. In particular, many biologics must be stored at non-neutral pH, where glass is susceptible to hydrolysis, metal extraction, and delamination. Plastic containers are not susceptible to these problems, but suffer from higher gas permeability and a propensity for sterilization-induced radical generation, heightening the risk of oxidative damage to sensitive drugs. This study evaluates the properties of a hybrid material, SiOPlas™, in which an ultrathin multilayer coating is applied to the interior of cyclic olefin polymer containers via plasma-enhanced chemical vapor deposition. Our results show that the coating decreases oxygen permeation through the vial walls 33-fold compared to uncoated cyclic olefin polymers, which should allow for improved control of oxygen levels in sensitive formulations. We also measured degradation of two biologic drugs that are known to be sensitive to oxidation, teriparatide and erythropoietin, in gamma and electron beam sterilized SiOPlas™, glass, and uncoated cyclic olefin polymer vials. In both cases, solutions stored in SiOPlas™ vials did not show elevated susceptibility to oxidation compared to either glass or unsterilized controls. Taken together, these results suggest that hybrid materials such as SiOPlas™ are attractive choices for storing high-value biologic drugs.<i>LAY ABSTRACT:</i> One of the most important functions of parenteral drug containers is safeguarding their contents from damage, either chemical or physical. Glass has been the container material of choice for many years, but concerns over breakage and vulnerability to chemical attack at non-neutral pH have spurred the rise of advanced plastics as alternatives. Plastics solve many problems associated with glass but introduce several of their own, including increased gas permeation and generation of oxidizing radicals during sterilization. In this article, we evaluate SiOPlas™, a hybrid material consisting of plastic with a thin multilayer coating applied to the interior, for its ability to overcome these two problems. We find that SiOPlas™ is much less permeable to oxygen than uncoated plastic, and that two biologic drugs stored in gamma and electron beam sterilized SiOPlas™ vials do not display elevated levels of oxidation compared to either glass or unsterilized vials. This suggests that hybrid materials such as SiOPlas™ can exhibit the best qualities of both glass and plastic, making them attractive materials for storing high-value parenteral drugs.
Clinical Experience with a Helical Bipolar Stimulating Lead (1992)

Over 100 patients have been treated for partial epilepsy using a NeuroCybernetic Prosthesis System (NCP). The NCP System is comprised of an implantable pulse generator, an implantable bipolar stimulating lead, and an external communication system. The lead delivers electrical impulses from the NCP Generator to the vagus nerve, and includes a connector end that plugs into the generator, a silicone insulated lead body, and the helical electrode array that attaches to the nerve. The surgical implantation technique has a significant impact on lead reliability and performance. The lead electrode has performed well to date. Modifications to further improve reliability have been implemented. Clinical experience, case history examples, and voltage measurements are examined. The lead electrode is an important component of the overall system and plays a significant part in the success of vagus nerve stimulation therapy.
pcaExplorer: an R/Bioconductor package for interacting with RNA-seq principal components (2019)

pcaExplorer is distributed as an R package in the Bioconductor project ( http://bioconductor.org/packages/pcaExplorer/ ), and is designed to assist a broad range of researchers in the critical step of interactive data exploration.
Tumor epidermal growth factor receptor studies in patients with non-small-cell lung cancer or head and neck cancer treated with monoclonal antibody RG 83852. (1994)

RG 83852 causes no toxic effects at doses that result in high tumor EGFR saturation. Treatment with RG 83852 may enhance EGFR tyrosine kinase activity and/or EGFR expression. Because high EGFR expression by tumors has been associated with increased sensitivity to cytotoxic therapy, the suggestion of antibody-mediated upregulation of EGFR by agents such as RG 83852 may prove useful in enhancing chemotherapeutic efficacy.
p53 isoforms can regulate p53 transcriptional activity (2005)

The recently discovered p53-related genes, p73 and p63, express multiple splice variants and N-terminally truncated forms initiated from an alternative promoter in intron 3. To date, no alternative promoter and multiple splice variants have been described for the p53 gene. In this study, we show that p53 has a gene structure similar to the p73 and p63 genes. The human p53 gene contains an alternative promoter and transcribes multiple splice variants. We show that p53 variants are expressed in normal human tissue in a tissue-dependent manner. We determine that the alternative promoter is conserved through evolution from Drosophila to man, suggesting that the p53 family gene structure plays an essential role in the multiple activities of the p53 family members. Consistent with this hypothesis, p53 variants are differentially expressed in human breast tumors compared with normal breast tissue. We establish that p53beta can bind differentially to promoters and can enhance p53 target gene expression in a promoter-dependent manner, while Delta133p53 is dominant-negative toward full-length p53, inhibiting p53-mediated apoptosis. The differential expression of the p53 isoforms in human tumors may explain the difficulties in linking p53 status to the biological properties and drug sensitivity of human cancer.
Synthesis, Structure Determination, and Hydrogen Sorption Studies of New Metal−Organic Frameworks Using Triazole and Naphthalenedicarboxylic Acid (2007)

Two new metal−organic framework compounds were synthesized under solvothermal conditions using Zn2+ ion, 1,2,4-triazole (TRZ), and 1,4- and 2,6-naphthalenedicarboxylic acids (NDC): Zn4(TRZ)4(1,4-NDC)2·2DMF·2H2O (1) and Zn4(TRZ)4(2,6-NDC)2·2DMF·4H2O (2). Their crystal structures were characterized by single-crystal X-ray diffraction. Structure 1 crystallizes in the P21/n space group with a = 13.609(2) Å, b = 27.181(5) Å, c = 13.617(3) Å, β = 92.46(1) °, V = 5032.4(16) Å3, and Z = 4. Structure 2 crystallizes in orthorhombic Pna21 space group with a = 30.978(6) Å, b = 12.620(3) Å, c = 13.339(3) Å, V = 5215(2) Å3, and Z = 4. Both structures are analogues of the previously reported Zn4(TRZ)4(1,4-BDC)2·16H2O where the layers of Zn−triazole moieties are pillared by aromatic dicarboxylates to create 3-D open frameworks. Nitrogen sorption studies revealed that these structures have Brunaer−Emmett−Teller (BET) surface areas of 362.1−584.1 m2/g. Hydrogen sorption experiments showed they can store 0.84−1.09 wt % of H2 at 77 K and 1 atm. Although they do not contain large pores or surface areas, they possess the hydrogen sorption capacities comparable to those of highly porous metal−organic frameworks.
MicroRNAs in NF- B signaling (2011)

Nuclear factor κB (NF-κB) is a transcriptional factor that regulates a battery of genes that are critical to innate and adaptive immunity, cell proliferation, inflammation, and tumor development. MicroRNAs (miRNAs) are short RNA molecules of 20-25 nucleotides in length that negatively regulate gene expression in animals and plants primarily by targeting 3' untranslated regions of mRNAs. In this work, we review the convergence of miRNAs and NF-κB signaling and dysregulation of miRNAs and NF-κB activation in human diseases, particularly in cancer. The function of miR-146, miR-155, miR-181b, miR-21, and miR-301a in NF-κB activation and their impact on tumorigenesis are discussed. Given that over 1000 human miRNAs have been identified, rendering miRNAs one of the most abundant classes of regulatory molecules, deciphering their biological function and pathological contribution in NF-κB dysregulation is essential to appreciate the complexity of immune systems and to develop therapeutics against cancer.
RNA Computing in a Living Cell (2008)

A system based on RNA can perform simple logical computations within a living cell, marking a step toward programming cell behavior.
Developing adaptive systems to fit individual aptitudes (1993)

Article Free Access Share on Developing adaptive systems to fit individual aptitudes Authors: David Benyon Computing Department, Open University, U.K. Computing Department, Open University, U.K.View Profile , Dianne Murray Social and Computer Sciences Research Group, University of Surrey, U.K. Social and Computer Sciences Research Group, University of Surrey, U.K.View Profile Authors Info & Claims IUI '93: Proceedings of the 1st international conference on Intelligent user interfacesFebruary 1993 Pages 115–121https://doi.org/10.1145/169891.169925Published:01 February 1993Publication History 30citation1,012DownloadsMetricsTotal Citations30Total Downloads1,012Last 12 Months27Last 6 weeks5 Get Citation AlertsNew Citation Alert added!This alert has been successfully added and will be sent to:You will be notified whenever a record that you have chosen has been cited.To manage your alert preferences, click on the button below.Manage my AlertsNew Citation Alert!Please log in to your account Save to BinderSave to BinderCreate a New BinderNameCancelCreateExport CitationPublisher SiteeReaderPDF
The ubiquitin-proteasome system and endocytosis (1999)

Internalization of membrane proteins has been studied for more than three decades without solving all the underlying mechanisms. Our knowledge of clathrin-mediated endocytosis is certainly sufficient to understand the basic principles. However, more detailed insight is required to recognize why different proteins enter clathrin-coated pits with different rates and affinities. In addition to clathrin coat components, at least two adaptor systems and even more accessory proteins have been described to preselect membrane proteins before they can enter cells. Recent experimental data have identified the ubiquitin-proteasome system as a regulatory system for endocytosis. This system is well-known for its basic regulatory function in protein degradation, and controls a magnitude of key events. The ubiquitin-proteasome system is now identified as a regulator of the endocytosis of selected membrane proteins. In this review, we will discuss the complexity and implications of this mechanism for receptor-mediated endocytosis.
Advances in Secondary Spinal Cord Injury (2000)

The outcome of spinal cord injury depends on the extent of secondary damage produced by a series of cellular and molecular events initiated by the primary trauma. This article reviews the evidence that secondary spinal cord injury involves the apoptotic as well as necrotic death of neurons and glial cells. Also discussed are the major factors that can contribute to cell death, such as glutamatergic excitotoxicity, free radical damage, cytokines, and inflammation. The development of innovative therapeutic strategies to reduce secondary spinal cord injury depends on an increased understanding of secondary injury mechanisms at the molecular and biochemical level. Such therapeutic interventions may include the use of antiapoptotic drugs, free radical scavengers, and anti-inflammatory agents. These could be targeted to block key reactions on cellular and molecular injury cascades, thus reducing secondary tissue damage, minimizing side effects, and improving functional recovery.
Stable isotope breath tests for assessing gastric emptying: A comprehensive review (2010)

A stable isotope ([(13)C]) breath test is a promising method for assessing gastric emptying, but it has not been pervasive yet in Japan. We think that there are some barriers to its popularization, including the uncertainty concerning its theoretical backgrounds, the ambiguity of analyzing and interpreting the data, and the lack of standard protocols for breath sampling. The aim of the present review is to break through these barriers. We hope this article could make the [(13)C]-gastric breath test more maneuverable for and more accessible to researchers and clinicians.
Developments and Challenges for mAb-Based Therapeutics (2013)

The continuous increase in the number of approved monoclonal antibody (mAb)-based therapy suggests that mAbs, and their derivatives, will continue to be the focus of the biotherapeutics industry for years to come. Although vast improvements in our capability to manufacture, characterize, and stabilize mAbs have been achieved, there are still challenges to be overcome. These include analytical and stabilization approaches associated with the development of high concentration mAb formulations. In addition, several mAb-based modalities are under development, including antibody drug conjugates (ADCs), fusion proteins, and bispecific antibodies (bsAbs), all designed to overcome the limitations encountered with mAb therapy. The current status of their development, with emphasis on manufacturing challenges as well as preliminary clinical results, will be reviewed.
A mechanistic, predictive model of dose-response curves for cell cycle phase-specific and -nonspecific drugs. (2000)

In vitro dose-response curves for anticancer agents are useful for predicting the clinical response to chemotherapy, and models to capture the time-dependency of dose-response curves are necessary for potential clinical extrapolation. Usually, the modified Hill model is used (see Levasseur et al., Cancer Res., 58: 5749-5761, 1998), although this model is neither mechanistic nor predictive for understanding how drug and tumor cell characteristics affect the shape of the dose-response curve. A new exponential kill (EK) model is proposed to predict the shape of dose-response curves based on the cell cycle phase specificity of a drug, the cell cycle time, the duration and concentration of drug exposure at the site of action, and a scaling factor for the level of drug resistance. Explicit analytical equations are presented for predicting the ICx (the concentration required to reduce cell growth by x%), the maximum cell kill achievable at high doses after a given duration of drug exposure, and the slope of the survival fraction versus log (concentration) plot at the ICx. Numerical solutions illustrate that there may be an optimal, finite duration of drug exposure that maximizes cell kill for a given area under the concentration versus time curve, and an analytical equation is given to calculate when such an optimal, finite duration exists. The EK model generates sigmoidal dose-response curves, like those seen empirically and previously described by the Hill model, which eventually plateau with increasing drug concentration at levels that depend on the cell cycle specificity of the drug, the cell cycle time, and the duration of exposure to the drug. This study includes no original data. Instead, empirical results in the literature are used to test the model. Because data by Levasseur et al. (1998) was fit to the Hill model assuming the plateau in the effect versus concentration curve to be independent of exposure duration, a full test of the model is not possible using their published data. Some tests of the EK model were possible, however, showing that EK model predictions yield good fits to in vitro data published in that and in another study. In addition, combining the EK model with a pharmacokinetic model resulted in predictions that were consistent with results of clinical studies comparing etoposide given in different schedules. Further tests of the model are necessary.
Bend translation in multimode fiber imaging (2017)

Light propagation in multimode fibers is typically assumed to be extremely sensitive to changes in geometry. We study here a particular configuration where an S-shaped bend is translated between two sections of fiber. In this sliding bend configuration, we show that nearly constant propagation characteristics can be obtained in certain fibers. Several fibers were tested using a bend with a peak radius of curvature of 25 mm. We found large differences in bending behavior between fibers of varying core diameters and numerical apertures. Fibers with a large numerical aperture are found to be more stable. In several fibers, the bend can be translated over a distance of 25 mm with a limited impact on imaging performance. The experimental results are confirmed using simulations. Our findings shed a new light on bending sensitivity in multimode fibers, and open up more possibilities for their use as imaging devices.
Brain-to-Brain Synchrony Tracks Real-World Dynamic Group Interactions in the Classroom (2017)

The human brain has evolved for group living [1]. Yet we know so little about how it supports dynamic group interactions that the study of real-world social exchanges has been dubbed the "dark matter of social neuroscience" [2]. Recently, various studies have begun to approach this question by comparing brain responses of multiple individuals during a variety of (semi-naturalistic) tasks [3-15]. These experiments reveal how stimulus properties [13], individual differences [14], and contextual factors [15] may underpin similarities and differences in neural activity across people. However, most studies to date suffer from various limitations: they often lack direct face-to-face interaction between participants, are typically limited to dyads, do not investigate social dynamics across time, and, crucially, they rarely study social behavior under naturalistic circumstances. Here we extend such experimentation drastically, beyond dyads and beyond laboratory walls, to identify neural markers of group engagement during dynamic real-world group interactions. We used portable electroencephalogram (EEG) to simultaneously record brain activity from a class of 12 high school students over the course of a semester (11 classes) during regular classroom activities (Figures 1A-1C; Supplemental Experimental Procedures, section S1). A novel analysis technique to assess group-based neural coherence demonstrates that the extent to which brain activity is synchronized across students predicts both student class engagement and social dynamics. This suggests that brain-to-brain synchrony is a possible neural marker for dynamic social interactions, likely driven by shared attention mechanisms. This study validates a promising new method to investigate the neuroscience of group interactions in ecologically natural settings.
Bone Marrow Transplantation (1994)

Bone marrow transplantation is the intravenous infusion of hematopoietic progenitor cells to reestablish marrow function in a patient with damaged or defective bone marrow (Figure 1). Although some have traced the origin of this procedure to the end of the past century, when patients were given bone marrow orally as a treatment for hematologic disorders,1 a more realistic starting point is a 1939 report of a patient who received 18 ml of intravenous marrow from his brother as a treatment for aplastic anemia2. The beginning of modern bone marrow transplantation can be traced to work showing that rodents could . . .
Non-isotopic in situ hybridisation and immunophenotyping of infected cells in the investigation of human fetal parvovirus infection. (1992)

A relatively high proportion of cases of anatomically normal, non-immune hydrops are caused by B19 infection. Digoxigenin is a more reliable probe label than biotin for in situ hybridisation in archival fetal tissues. Double labelling for cellular antigens and viral nucleic acid is a powerful technique for investigating virus-host cell interactions, and provides evidence that cell types other than those of erythroid lineage may have a role in human fetal parvovirus infection.
Intumescent All‐Polymer Multilayer Nanocoating Capable of Extinguishing Flame on Fabric (2011)

An intumescent nanocoating composed of poly(allylamine) and poly(sodium phosphate) is deposited layer-by-layer on cotton fabric. Fire is extinguished right after ignition on the fabric during vertical flame testing. The individual fibers are conformally coated and bubbles form on the fiber surfaces during burning, which is due to an intumescent effect. Detailed facts of importance to specialist readers are published as ”Supporting Information”. Such documents are peer-reviewed, but not copy-edited or typeset. They are made available as submitted by the authors. 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.
Isolation and characterization of a complement-activating lipid extracted from human atherosclerotic lesions. (1990)

The major characteristics of human atherosclerotic lesions are similar to those of a chronic inflammatory reaction, namely fibrosis, mesenchymal cell proliferation, the presence of resident macrophages, and cell necrosis. Atherosclerosis exhibits in addition the feature of lipid (mainly cholesterol) accumulation. The results of the present report demonstrate that a specific cholesterol-containing lipid particle present in human atherosclerotic lesions activates the complement system to completion. Thus, lipid could represent a stimulatory factor for the inflammatory reaction, whose underlying mechanistic basis may be, at least in part, complement activation. The complement-activating lipid was purified from saline extracts of aortic atherosclerotic lesions by sucrose density gradient centrifugation followed by molecular sieve chromatography on Sepharose 2B. It contained little protein other than albumin, was 100-500 nm in size, exhibited an unesterified to total cholesterol ratio of 0.58 and an unesterified cholesterol to phospholipid ratio of 1.2. The lipid, termed lesion lipid complement (LCA), activated the alternative pathway of complement in a dose-dependent manner. Lesion-extracted low density lipoprotein (LDL) obtained during the purification procedure failed to activate complement. Specific generation of C3a desArg and C5b-9 by LCA indicated C3/C5 convertase formation with activation proceeding to completion. Biochemical and electron microscopic evaluations revealed that much of the C5b-9 present in atherosclerotic lesions is membraneous, rather than fluid phase SC5b-9. The observations reported herein establish a link between lipid insudation and inflammation in atherosclerotic lesions via the mechanism of complement activation.
Mapping the sugar dependency for rational generation of a DNA-RNA hybrid-guided Cas9 endonuclease (2017)

The CRISPR-Cas9 RNA-guided endonuclease system allows precise and efficient modification of complex genomes and is continuously developed to enhance specificity, alter targeting and add new functional moieties. However, one area yet to be explored is the base chemistry of the associated RNA molecules. Here we show the design and optimisation of hybrid DNA-RNA CRISPR and tracr molecules based on structure-guided approaches. Through careful mapping of the ribose requirements of Cas9, we develop hybrid versions possessing minimal RNA residues, which are sufficient to direct specific nuclease activity in vitro and in vivo with reduced off-target activity. We identify critical regions within these molecules that require ribose nucleotides and show a direct correlation between binding affinity/stability and cellular activity. This is the first demonstration of a non-RNA-guided Cas9 endonuclease and first step towards eliminating the ribose dependency of Cas9 to develop a XNA-programmable endonuclease.