gebhart/patrepeval huggingface dataset:
High‐Performance, Layered, 3D‐LiCoO<sub>2</sub> Cathodes with a Nanoscale Co<sub>3</sub>O<sub>4</sub> Coating via Chemical Etching (2011)

Chemical etching concurrently modifies pristine to layer-by-layer 3D-LiCoO2 with a Co3O4 coating. Not only can the layered morphology affect the high electrochemical performance, but also the coating effect reduces the structure instability of the LiCoO2 during cycling. This process can be applied to design other compounds to enhance their performance in Li-ion batteries. 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.
Evolutionary principles and synthetic biology: avoiding a molecular tragedy of the commons with an engineered phage (2012)

These results challenge efforts to engineer phages with exoenzymes that degrade biofilm polymers. If biofilms do not facilitate spatially structured phage growth, the transgenic enzymes may be rapidly eliminated from the phage population after release in the environment, even if the transgene benefits overall phage growth on the biofilm.
72.4L: <i>Late‐News Paper</i> : Maradin's Micro‐Mirror ‐ System Level Synchronization Notes (2012)

Abstract Maradin's novel MEMS‐based micro‐mirror is designed to operate as part of laser beam steering projection systems. This paper presents some issues concerning the use of scanning micro‐mirrors for such applications, and explains how to overcome image distortions that emerge when micro‐mirrors are used for projection of light.
Editing Templates: A User Interface Generation Tool (1986)

This article discusses a basic architecture for a user interface management system and the problem of updating a display in response to interactive commands. The basic architecture is then extended to include basic editing and browsing processes on arbitrary data structures. Editing templates are presented as a technique embodying the entire manipulation process for a particular data structure/data display combination. In conjuction with the user interface management system, Such templates are able to automatically provide a majority of the code required in an interactive applicaton.
Supplementation of Infant Formula With the Probiotic Lactobacillus reuteri and Zinc: Impact on Enteric Infection and Nutrition in Infant Rhesus Monkeys (2002)

-supplementation of infant formula is safe, improves iron status and decreases diarrhea severity in infant rhesus monkeys and thus may help protect formula-fed human infants from infection and nutritional deficiencies.
Repertoire selection by pre‐B‐cell receptors and B‐cell receptors, and genetic control of B‐cell development from immature to mature B cells (2000)

During B-cell development the surrogate light (SL) chain is selectively expressed in progenitor and precursor B cells during the developmental stages of D(H) to J(H) and V(H) to D(H)J(H) rearrangements. Approximately half of all muH chains produced by these rearrangements cannot pair with SL chains and cannot form a pre-B-cell receptor (pre-BCR). A spectrum of affinities between VpreB and individual V(H) domains generates preB cells with pre-BCR of different fitness which, in turn, determines the extent of the pre-B II-cell proliferation and the fidelity of allelic exclusion of the H chain locus. Once pre-BCR is expressed, SL chain expression is turned off. As pre-B II cells proliferate, SL is diluted out, thus limiting pre-BCR formation. As a consequence, pre-B II cells stop proliferating, become small and resting and begin to rearrange the L chain loci. Multiple rearrangements of the kappaL chain alleles are often detected in wild-type small pre-B II cells. Around 20% of the muH chain-expressing small pre-B II cells also express L chains but do not display the Ig on the surface. Hence, it is likely that not all L chains originally generated in resting pre-B II cells can pair with the muH chain previously present in that cell. The best fitting ones are selected preferentially to generate sIg+ B cells. Furthermore, the transition of immature B cells from the bone marrow to spleen and their development to mature cells appear as two separate steps controlled by different genes.
Factors affecting the dissolution rate of novolac resins II: developer composition effects (1996)

Resist function depends upon photoinduced changes in the dissolution rate of phenolic polymer films in aqueous base. The events that occur as the molecules in these films move from the glassy state into solution are not well understood. This paper presents an extensive study of the influence of developer composition and concentration on the dissolution rate of novolac films in aqueous base. The dissolution rate is shown to be a function of both the cation and anion composition and concentration in the developer at a constant pH. When salts are added to the base, the rate first increases, reaches a maximum, and then decreases with increasing salt concentration. In the concentration regime below the maximum, the rate increases linearly with cation concentration and is independent of anion composition. The dissolution of novolac is dependent on cation concentration and not ionic strength in this regime. In the concentration regime above the maximum, the composition of the anion has a marked influence on the rate.
Chondrocyte-mediated depletion of articular cartilage proteoglycans <i>in vitro</i> (1985)

The degradation of proteoglycan was examined in cultured slices of pig articular cartilage. Pig leucocyte catabolin (10 ng/ml) was used to stimulate the chondrocytes and induce a 4-fold increase in the rate of proteoglycan loss from the matrix for 4 days. Material in the medium of both control and depleted cultures was mostly a degradation product of the aggregating proteoglycan. It was recovered as a very large molecule slightly smaller than the monomers extracted with 4M-guanidinium chloride and lacked a functional hyaluronate binding region. The size and charge were consistent with a very limited cleavage or conformational change of the core protein near the hyaluronate binding region releasing the C-terminal portion of the molecule intact from the aggregate. The 'clipped' monomer diffuses very rapidly through the matrix into the medium. The amount of proteoglycan extracted with 4M-guanidinium chloride decreased during culture from both the controls and depleted cartilage, and the average size of the molecules initially remained the same. However, the proportion of molecules with a smaller average size increased with time and was predominant in explants that had lost more than 70% of their proteoglycan. All of this material was able to form aggregates when mixed with hyaluronate, and glycosaminoglycans were the same size and charge as normal, indicating either that the core protein had been cleaved in many places or that larger molecules were preferentially released. A large proportion of the easily extracted and non-extractable proteoglycan remained in the partially depleted cartilage and the molecules were the same size and charge as those found in the controls. There was no evidence of detectable glycosidase activity and only very limited sulphatase activity. A similar rate of breakdown and final distribution pattern was found for newly synthesized proteoglycan. Increased amounts of latent neutral metalloproteinases and acid proteinase activities were present in the medium of depleted cartilage. These were not thought to be involved in the breakdown of proteoglycan. Increased release of proteoglycan ceased within 24h of removal of the catabolin, indicating that the effect was reversible and persisted only while the stimulus was present.
Carbohydrate‐deficient transferrin in galactosaemia (1997)

Carbohydrate-deficient isoforms of transferrin (CDT) were examined in Guthrie cards from patients with galactosaemia before and during dietary treatment for up to 9 y. In untreated patients the CDT values were elevated due to abnormal asialo- and/or disialotransferrin. During treatment, the CDT levels were normal except on a few temporary occasions. Galactose or its close metabolites did not inhibit two relevant glycosyltransferases in vitro, and their levels were not correlated to the CDT values. The transferrin isoform changes in untreated patients were similar to, but less pronounced than in CDG syndrome type I.
Development of Re-based diffusion barrier coatings on nickel based superalloys (2005)

A diffusion barrier type coating with a duplex layer structure, an inner σ-(Re, W, Cr, Ni) as a diffusion barrier and outer Ni-aluminide as an Al reservoir, was formed on a Nickel based, single crystal, superalloy (TMS-82 +) and on Hastelloy X. Oxidation properties of both the alloys with or without the diffusion barrier coating were investigated in air under thermal cycling between room temperature and 1423 K for up to 360 ks. The inner σ layer with a composition (at%) of (35–40) Re, (15–20) W, (15–25) Cr and (15–25) Ni was produced by electrodeposition of Ni-70Re and Ni-20W films from aqueous solutions followed by Cr-pack cementation at temperatures between 1473 and 1573 K, and the outer Ni-aluminides of β-(Ni,Cr)Al + γ′-(Ni,Cr)3Al was formed by electrodeposition of a Ni film, followed by Al pack cementation. After the 360 ks oxidation it was found that the structure and composition of both σ layer and alloy substrate were retained with little change. Furthermore, there was little Al in the σ layer. It could be concluded that the Re-based alloys such as σ (Re(W),Cr,Ni) are very promising candidates as a diffusion barrier between the outer Al-reservoir layer and alloy substrate at temperature of 1423 K. It was found that the Re(W)-Cr-Ni acts as a diffusion barrier for both inward diffusion of Al and outward diffusion of alloying elements in the alloy substrate.
Validation of the Embryonic Stem Cell Test in the International ECVAM Validation Study on Three <i>In Vitro</i> Embryotoxicity Tests (2004)

A detailed report is presented on the performance of the embryonic stem cell test (EST) in a European Centre for the Validation of Alternative Methods (ECVAM)-sponsored formal validation study on three in vitro tests for embryotoxicity. Twenty coded test chemicals, classified as non-embryotoxic, weakly embryotoxic or strongly embryotoxic on the basis of their in vivo effects in animals and/or humans, were tested in four laboratories. The outcome showed that the EST can be considered to be a scientifically validated test, which is ready for consideration for use in assessing the embryotoxic potentials of chemicals for regulatory purposes.
Enhancing security of Pass Points system using variable tolerance (2010)

Passpoints system is one of the techniques used in Authentication using Graphical Images. In this method users click on images rather than typing a long and complex alphanumeric password with the computer keyboard. Psychological studies have shown that people can remember pictures better than text. During the time of registration a user may choose several areas (click points) on an image. In order to log in the user has to click close to the chosen click points, e.g. within.25 to.50cm from the click point, because users cannot click exactly on the same pixel on which they have clicked at the time of registration. This margin of error around the click point is called Tolerance. Existing Passpoints scheme uses the same tolerance ( 20X20 pixels) over a number of clicks by the user. But by varying the tolerance (i.e. decrementing the tolerance level) as users click on more points, the information left to an attacker is reduced. Hence, the security of the system is increased. In this paper we described how the level of security is increased.
Transcriptome-based cancer type prediction for tumors of unknown origin. (2019)

3081 Background: Tumors of unknown origin occur in approximately 5% of newly diagnosed cancers and are difficult to treat without establishing the tissue type from which they derive. Establishing tumor origin guides standard of care treatment for several NCCN targeted therapy guidelines. Leveraging tissue specificity in gene expression profiles, classification models based on RNA expression offer a promising approach to identify the likely primary cancer site in tumors of unknown origin. Methods: In this study, we developed a transcriptome-based cancer type classifier trained on over 10,000 tissue samples annotated by pathologists and sequenced for RNA expression to identify conserved patterns of expression characteristic of 30 tumor types across primary and metastatic tissue sites. The classifier probabilistically ranks cancer of origin. Results: Overall, the accuracy of the most probable cancer prediction was 85%, 88% within primary tumors and 77% within metastatic tumors. The top three cancers types with the highest accuracy were colorectal (accuracy in metastatic: 93%, accuracy in primary tumors: 99%), breast (95%, 96%) and lung (87%, 94%). Classifier performance was lower in low-purity metastatic tumors where the surrounding normal tissue obscures the tumor transcriptional profile, though the classifier still achieves 71% accuracy on metastatic tumors with less than 50% purity. Conclusions: We present a novel method to probabilistically predict tumor type for cancers of unknown origin using RNA-Seq. Our method achieves robust classification that is applicable to primary and metastatic tumors and demonstrates the value of utilizing RNA-Seq to aid cancer diagnosis and treatment decisions.
Imaging of Cell–Cell Communication in a Vertical Orientation Reveals High-Resolution Structure of Immunological Synapse and Novel PD-1 Dynamics (2015)

The immunological synapse (IS) is one of the most pivotal communication strategies in immune cells. Understanding the molecular basis of the IS provides critical information regarding how immune cells mount an effective immune response. Fluorescence microscopy provides a fundamental tool to study the IS. However, current imaging techniques for studying the IS cannot sufficiently achieve high resolution in real cell-cell conjugates. In this study, we present a new device that allows for high-resolution imaging of the IS with conventional confocal microscopy in a high-throughput manner. Combining micropits and single-cell trap arrays, we have developed a new microfluidic platform that allows visualization of the IS in vertically "stacked" cells. Using this vertical cell pairing (VCP) system, we investigated the dynamics of the inhibitory synapse mediated by an inhibitory receptor, programed death protein-1, and the cytotoxic synapse at the single-cell level. In addition to the technique innovation, we have demonstrated novel biological findings by this VCP device, including novel distribution of F-actin and cytolytic granules at the IS, programed death protein-1 microclusters at the NK IS, and kinetics of cytotoxicity. We propose that this high-throughput, cost-effective, easy-to-use VCP system, along with conventional imaging techniques, can be used to address a number of significant biological questions in a variety of disciplines.
Electrochemically Promoted Tyrosine-Click-Chemistry for Protein Labeling (2018)

The development of new bio-orthogonal ligation methods for the conjugation of native proteins is of particular importance in the field of chemical biology and biotherapies. In this work, we developed a traceless electrochemical method for protein bioconjugation. The electrochemically promoted tyrosine-click (e-Y-CLICK) allowed the chemoselective Y-modification of peptides and proteins with labeled urazoles. A low potential is applied in an electrochemical cell to activate urazole anchors in situ and on demand, without affecting the electroactive amino acids from the protein. The versatility of the electrosynthetic approach was shown on biologically relevant peptides and proteins such as oxytocin, angiotensin 2, serum bovine albumin, and epratuzumab. The fully conserved enzymatic activity of a glucose oxidase observed after e-Y-CLICK further highlights the softness of the method. The e-Y-CLICK protocols were successfully performed in pure aqueous buffers, without the need for co-solvents, scavenger or oxidizing chemicals, and should therefore significantly broaden the scope of bioconjugation.
Endothelin1 activates and sensitizes human C-nociceptors (2007)

Microneurography was used to record action potentials from afferent C-fibers in cutaneous fascicles of the peroneal nerve in healthy volunteers. Afferent fibers were classified according to their mechanical responsiveness to von Frey stimulation (75g) into mechano-responsive and mechano-insensitive nociceptors. Various concentrations of Endothelin1 (ET1) and Histamine were injected into the receptive fields of C-fibers. Activation and heat sensitization were monitored. Axon reflex flare and psychophysical ratings were assessed after injection of ET1 and codeine into the forearms after pre-treatment with an H1 blocker or sodium chloride. 65% of mechanosensitive nociceptors were activated by ET1. One-third showed long lasting responses (>15min). In contrast, none of thirteen mechano-insensitive fibers were activated. Sensitization to heat was observed in 62% of mechanosensitive and in 46% of mechano-insensitive fibers. Injection of ET1 produced a widespread axon reflex flare, which was suppressed by pre-treatment with an H1 receptor blocker. In addition, pain sensations were induced more often than itching by ET1 in contrast to codeine. No wheal was observed after injection of ET1. Both itching and pain were decreased after H1 blocker treatment. In summary: (1) In humans ET1 activates mechanosensitive, but not mechano-insensitive, nociceptors. (2) Histamine released from mast cells is not responsible for all effects of ET1 on C-nociceptors. (3) ET1 could have a differential role in pain compared to other chemical algogens which activate additionally or even predominantly mechano-insensitive fibers.
Wing Mechanization Design and Analysis for a Perching Micro Air Vehicle (2008)

This paper describes the development of a mechanized wing concept for a perching micro air vehicle. The wings are capable of rotating at two spanwise joints to simulate the motion of a bird’s wings during a perching maneuver. This project focuses on the wing mechanization design and analysis as well as the structure/mechanism integration. The advantage of a perching type of landing is that it allows the vehicle to land with approximately zero vertical and horizontal velocity on a tree branch, power line, or ledge. The requirements to perform this maneuver were investigated, the structural design was developed, and the mechanization integration to achieve this motion was determined. A model was designed and manufactured to demonstrate the kinematic mechanism making this wing motion possible. Wind tunnel testing and analytical simulation were also completed to further develop the model.
Simian virus 40 large T-antigen point mutants that are defective in viral DNA replication but competent in oncogenic transformation. (1984)

The large T antigen of simian virus 40 (SV40) is a multifunctional protein that is essential in both the virus lytic cycle and the oncogenic transformation of cells by SV40. To investigate the role of the numerous biochemical and physiological activities of T antigen in the lytic and transformation processes, we have studied DNA replication-deficient, transformation-competent large T-antigen mutants. Here we describe the genetic and biochemical analyses of two such mutants, C2/SV40 and C11/SV40. The mutants were isolated by rescuing the integrated SV40 DNA from C2 and C11 cells (CV-1 cell lines transformed with UV-irradiated SV40). The mutant viral early regions were cloned into the plasmid vector pK1 to generate pC2 and pC11. The mutations that are responsible for the deficiency in viral DNA replication were localized by marker rescue. Subsequent DNA sequencing revealed point mutations that predict amino acid substitutions in the carboxyl third of the protein in both mutants. The pC2 mutation predicts the change of Lys----Arg at amino acid 516. pC11 has two mutations, one predicting a change of Pro----Ser at residue 522, and another predicting a Pro----Arg change at amino acid 549. The two C11 mutations were separated from each other to form two distinct viral genomes in pC11A and pC11B. pC2, pC11, pC11A, and pC11B are able to transform both primary and established rodent cell cultures. The C11 and C11A T antigens are defective in ATPase activity, suggesting that wild-type levels of ATPase activity are not necessary for the oncogenic transformation of cells by T antigen.
WASP: Protecting Web Applications Using Positive Tainting and Syntax-Aware Evaluation (2008)

Many software systems have evolved to include a web-based component that makes them available to the public via the Internet and can expose them to a variety of web-based attacks. One of these attacks is SQL injection, which can give attackers unrestricted access to the databases underlying web applications and has become increasingly frequent and serious. This paper presents a new, highly automated approach for protecting web applications against SQL injection that has both conceptual and practical advantages over most existing techniques. From a conceptual standpoint, the approach is based on the novel idea of positive tainting and on the concept of syntax-aware evaluation. From a practical standpoint, our technique is precise and efficient and has minimal deployment requirements. We also present an extensive empirical evaluation of our approach performed using WASP, a tool that implements our technique. In the evaluation, we used WASP to protect a wide range of web applications while subjecting them to a large and varied set of attacks and legitimate accesses. WASP was able to stop all attacks and did not generate any false positives. Our studies also show that the overhead imposed by WASP was negligible in most cases.
An investigation of the diffusion‐limited growth of animal cells around single hollow fibers (1992)

To compare modeling with experimental data of cell growth surrounding individual fibers, the growth profiles of hybridoma cells in the extracapillary space of single hollow fiber bioreactors were examined. Agarose was provided in the extracapillary space to provide support and minimize convection. By sacrificing bioreactors at various time intervals, the growth profiles of cells surrounding a single hollow fiber could be monitored with increasing time. Using photomicroscopy and viable staining, areas of viable and nonviable cell growth were examined at various stages of development ranging from initial seeding to stable growth conditions. Cells were found to act as nucleation sites for the growth of individual colonies within the agarose. Profiles at stable growth conditions resulted in a thick cell mass near the surface of the fiber wall followed by cell colonies of decreasing size with increasing radial distance. A simplified theoretical model for cell growth was developed using mass balance equations for substrate penetration into individual cell colonies as well as away from the wall of a single fiber. The resulting profiles derived from theory were compared with experiments and found to be in good agreement for entering oxygen concentrations of 5% and 20%.