gebhart/patrepeval huggingface dataset:
Cell-Directed Integration into Three-Dimensional Lipid−Silica Nanostructured Matrices (2010)

We report a unique approach in which living cells direct their integration into 3D solid-state nanostructures. Yeast cells deposited on a weakly condensed lipid/silica thin film mesophase actively reconstruct the surface to create a fully 3D bio/nano interface, composed of localized lipid bilayers enveloped by a lipid/silica mesophase, through a self-catalyzed silica condensation process. Remarkably, this integration process selects exclusively for living cells over the corresponding apoptotic cells (those undergoing programmed cell death), via the development of a pH gradient, which catalyzes silica deposition and the formation of a coherent interface between the cell and surrounding silica matrix. Added long-chain lipids or auxiliary nanocomponents are localized within the pH gradient, allowing the development of complex active and accessible bio/nano interfaces not achievable by other synthetic methods. Overall, this approach provides the first demonstration of active cell-directed integration into a nominally solid-state three-dimensional architecture. It promises a new means to integrate "bio" with "nano" into platforms useful to study and manipulate cellular behavior at the individual cell level and to interface living organisms with electronics, photonics, and fluidics.
BriX: a database of protein building blocks for structural analysis, modeling and design (2010)

High-resolution structures of proteins remain the most valuable source for understanding their function in the cell and provide leads for drug design. Since the availability of sufficient protein structures to tackle complex problems such as modeling backbone moves or docking remains a problem, alternative approaches using small, recurrent protein fragments have been employed. Here we present two databases that provide a vast resource for implementing such fragment-based strategies. The BriX database contains fragments from over 7000 non-homologous proteins from the Astral collection, segmented in lengths from 4 to 14 residues and clustered according to structural similarity, summing up to a content of 2 million fragments per length. To overcome the lack of loops classified in BriX, we constructed the Loop BriX database of non-regular structure elements, clustered according to end-to-end distance between the regular residues flanking the loop. Both databases are available online (http://brix.crg.es) and can be accessed through a user-friendly web-interface. For high-throughput queries a web-based API is provided, as well as full database downloads. In addition, two exciting applications are provided as online services: (i) user-submitted structures can be covered on the fly with BriX classes, representing putative structural variation throughout the protein and (ii) gaps or low-confidence regions in these structures can be bridged with matching fragments.
Diffusion tensor imaging of left ventricular remodeling in response to myocardial infarction in the mouse (2008)

The cardiac muscle architecture lies at the basis of the mechanical and electrical properties of the heart, and dynamic alterations in fiber structure are known to be of prime importance in healing and remodeling after myocardial infarction. In this study, left ventricular remodeling was characterized using diffusion tensor imaging (DTI) in a mouse model of myocardial infarction. Myocardial infarction was induced in mice by permanent ligation of the left anterior descending coronary artery. Serial ex vivo DTI measurements were performed 7, 14, 28, and 60 days after ligation. Apparent diffusion coefficient, fractional anisotropy, the three eigenvalues of the diffusion tensor, and the myofiber disarray served as readout parameters. After myocardial infarction, the mouse hearts displayed extreme wall thinning in the infarcted area, which covered large parts of the apex and extended into the free wall up to the equator. Average heart mass increased by 70% 7-60 days after infarction. Histological analysis showed that the infarct at 7 days consisted of unstructured tissue with residual necrosis and infiltration of macrophages and myofibroblasts. At 14 days after infarction, the necrotic tissue had disappeared and collagen fibers were starting to appear. From 28 to 60 days, the infarct had fully developed into a mature scar. DTI parameters showed dynamic changes as a function of time after infarction. The apparent diffusion coefficient in the infarcted region was lower than in remote regions and increased as a function of time after infarction. The fractional anisotropy was higher in the infarcted region and was maximum at 28 days, which was attributed to the development of structured collagen fibers. Myofiber disarray, which was analyzed by considering the alignment of fibers in neighboring voxels, was significantly higher in infarcted regions. DTI provides a valuable non-destructive tool for characterizing structural remodeling in diseased myocardium.
A Comparison of the Cytolytic Properties of Murine Primary CD8+ Cytotoxic T Lymphocytes and Cloned Cytotoxic T Cell Lines (1988)

Lysates of many highly cytolytic murine primary CD8+ cytotoxic T lymphocytes (CTLs) have no detectable hemolytic activity and only traces of serine esterase activity, indicating a striking paucity or absence of the perforin-rich secretory granules that are abundant in the cytoplasm of murine cloned CTL cell lines. Nevertheless, the primary CTLs are almost as resistant to granule-mediated lysis as CTL cell lines. Moreover, target cells that are lysed by all CTLs so far tested, whether primary or cell lines, show similar rapid and marked increases in intracellular calcium and breakdown of DNA into nucleosome-sized fragments. A parsimonious explanation for all of these findings is that primary CTLs, like the CTL cell lines, exercise their cytolytic activity by means of perforin, but the amounts needed are extremely small and below the level of detection by the current relatively insensitive hemolytic assays.
3D Cell Culture in Alginate Hydrogels (2015)

This review compiles information regarding the use of alginate, and in particular alginate hydrogels, in culturing cells in 3D. Knowledge of alginate chemical structure and functionality are shown to be important parameters in design of alginate-based matrices for cell culture. Gel elasticity as well as hydrogel stability can be impacted by the type of alginate used, its concentration, the choice of gelation technique (ionic or covalent), and divalent cation chosen as the gel inducing ion. The use of peptide-coupled alginate can control cell-matrix interactions. Gelation of alginate with concomitant immobilization of cells can take various forms. Droplets or beads have been utilized since the 1980s for immobilizing cells. Newer matrices such as macroporous scaffolds are now entering the 3D cell culture product market. Finally, delayed gelling, injectable, alginate systems show utility in the translation of in vitro cell culture to in vivo tissue engineering applications. Alginate has a history and a future in 3D cell culture. Historically, cells were encapsulated in alginate droplets cross-linked with calcium for the development of artificial organs. Now, several commercial products based on alginate are being used as 3D cell culture systems that also demonstrate the possibility of replacing or regenerating tissue.
IN VITOR AND IN VIVO CYTOTOXICITY OF T CELLS CLONED FROM REJECTING ALLOGRAFTS (1986)

Epa-1 is a tissue-restricted, non-major histocompatibility (MHC) antigen that may be responsible for the extreme sensitivity of skin to allograft rejection and graft-versus-host disease (GVHD), especially with MHC-compatible donors and recipients. To confirm that Epa-1 serves as a target in allograft rejection and GVHD, we isolated Epa-1-specific cytotoxic T lymphocyte (CTL) clones completely in vivo from sponge-matrix allografts and from lymph nodes draining rejecting skin allografts. These clones induced GVHD-like skin lesions in antigen-specific, MHC-restricted fashion following intradermal inoculation into appropriate hosts. The in vivo-derived clones are conventional CTL since they are IL-2-dependent and express the Thy-1.2+, Lyt-1-, Lyt-2+, L3T4- phenotype. The results of this study also are pertinent to the controversy over which T-cell subset actually mediates allograft immunity, since the intragraft isolation and subsequent cloning of conventional CTL that induce necrotizing skin lesions are direct evidence that CTL are the proximal mediators of allograft rejection.
Localization of ventricular activation origin using patient‐specific geometry: Preliminary results (2018)

The novel pace-mapping approach to localizing the origin of ventricular activation offers an easily implementable supplement and/or alternative to the preprocedure inverse solution; its simplicity makes it suitable for real-time applications during clinical catheter-ablation procedures.
Spin lock and magnetization transfer imaging of head and neck tumors. (1996)

Low spin lock and magnetization transfer effects are characteristic of benign tumors. High spin lock and magnetization transfer effects were associated with malignancy, but there were overlapping values for salivary gland infections, some benign tumors, and malignancies. The spin lock technique seems to be an effective method for generating magnetization transfer-based contrast in the head and neck tumors.
Transport of diatom and dinoflagellate resting spores in ships' ballast water: implications for plankton biogeography and aquaculture (1992)

Diatom and dinoflagellate species that are not endemic to a region can be inadvertently introduced when their resistant resting stages are discharged with the ballast-tank waters and sediments of bulk cargo vessels. A survey of 343 cargo vessels entering 18 Australian ports showed that 65% of ships were carrying significant amounts of sediment on the bottom of their ballast tanks. All of these samples contained diatoms, including species that are not endemic to Australian waters. Diatom resting spores, especially of Chaetoceros, were also detected. Dinoflagellate resting spores (cysts) were present in 50% of the sediment samples. Of the 53 cyst species identified, 20 (including Diplopelta, Diplopsalopsis, Gonyaulax, Polykrikos, Protoperidinium, Scrippsiella and Zygabikodinium spp.) were successfully germinated to produce viable cultures. Such diversity of diatom and dinoflagellate species in ships' ballast water suggests that the apparent cosmopolitanism of many coastal phytoplankton species may be due partly to the global transport of seawater ballast. Of considerable concern was the detection in 16 ships of cysts of the toxic dinoflagellates Alexandrium catenella, Alexandrium tamarense and Gymnodinium catenatum. One single ballast tank was estimated to contain >300 million viable A.tamarense cysts, some of which were successfully germinated in the laboratory to produce toxic cultures. These toxic dinoflagellate species, which can contaminate shellfish with paralytic shellfish poisons, pose a serious threat to human health and the aquaculture industry. Ballast-water quarantine measures recently introduced in Australia are discussed. Mid-ocean exchange of ballast water is only partially effective in removing dinoflagellate cysts which have settled to the bottom of ballast tanks. The present work indicates that the most effective measure to prevent the spreading of toxic dinoflagellate cysts via ships' ballast water would be to avoid taking on ballast water during dinoflagellate blooms in the water column of the world's ports.
Synthesis and Structure−Activity Relationships of 6,7-Disubstituted 4-Anilinoquinoline-3-carbonitriles. The Design of an Orally Active, Irreversible Inhibitor of the Tyrosine Kinase Activity of the Epidermal Growth Factor Receptor (EGFR) and the Human Epidermal Growth Factor Receptor-2 (HER-2) (2002)

A series of of 6,7-disubstituted-4-anilinoquinoline-3-carbonitrile derivatives that function as irreversible inhibitors of EGFR and HER-2 kinases have been prepared. These inhibitors have, at the 6-position, butynamide, crotonamide, and methacrylamide Michael acceptors bearing water-solublilizing substituents. These compounds were prepared by acylation of 6-amino-4-(arylamino)quinoline-3-carbonitriles with unsaturated acid chlorides or mixed anhydrides. We performed competitive reactivity studies showing that attaching a dialkylamino group onto the end of the Michael acceptor results in compounds with greater reactivity due to intramolecular catalysis of the Michael addition. This, along with improved water-solubility results in compounds with enhanced biological properties. We present molecular modeling results consistent with the proposed mechanism of inhibition. One compound, 5 (EKB-569), which shows excellent oral in vivo activity, was selected for further studies and is currently in phase I clinical trials for the treatment of cancer.
Practice Parameters for the Treatment of Restless Legs Syndrome and Periodic Limb Movement Disorder (1999)

These are the first clinical guidelines published for the treatment of Restless Legs Syndrome (RLS) and Periodic Limb Movement Disorder (PLMD) providing evidence-based practice parameters. They were developed by the Standards of Practice Committee and reviewed and approved by the Board of Directors of the American Academy of Sleep Medicine. The guidelines provide recommendations for the practice of sleep medicine in North America regarding the treatment of RLS and PLMD. Recommendations are based on the accompanying comprehensive review of the medical literature regarding treatment of RLS and PLMD which was developed by a task force commissioned by the American Academy of Sleep Medicine. Recommendations are identified as standards, guidelines, or options, based on the strength of evidence from published studies that meet criteria for inclusion. Dopaminergic agents are the best studied and most successful agents for treatment of RLS and PLMD. Specific recommendations are also given for the use of opioid, benzodiazepine, anticonvulsant, and adrenergic medications, and for iron supplementation. In general, pharmacological treatment should be limited to individuals who meet diagnostic criteria and especially who experience insomnia and/or excessive sleepiness that is thought to occur secondary to RLS or PLMD. Individuals treated with medication should be followed by a physician and monitored for clinical response and adverse effects. It would be desirable for future investigations to employ multicenter clinical trials, with expanded numbers of subjects using double-blind, placebo-controlled designs, and an assessment of long-term response, side effects, and impact of treatment on quality of life. Evaluation of special groups such as children, pregnant women, and the elderly is warranted.
Auditory Masking and the Critical Band (1961)

Masked audiograms were studied as a function of the bandwidth, level, and frequency of a masking noise. In a reverse procedure, audiograms were determined when a movable, narrow, and approximately rectangular band of noise was used as signal in the presence of one or more masking tones. In both cases changes in the masked audiograms as a function of bandwidth made it possible to measure critical bandwidth. When masked audiograms were studied as a function of level, discontinuous changes in their height and shape occurred when the masking stimulus reached a certain “transition” level. If masking noises of subcritical or critical width were used, the growth of masking with level contained a discontinuity at a level of the masking stimulus equal to about 50 db SL. An abrupt change in the shape of the masked audiograms occurred at the same level. The change of shape when a pure tone was the masking stimulus consisted in the appearance of a “notch” one critical bandwidth above the frequency of the masking tone. Findings associated with the bandwidth parameter suggest interpretations of the critical band and of masking. The changes occurring at the transition level may indicate the threshold of the inner haircells.
Microstructure fabrication with a CO2 laser system (2003)

In this paper, we investigate the use of a commercial CO2 laser system for fabrication of microfluidic systems in polymers. We discuss the cutting process with the laser system and present a straightforward model for the channel depth of microchannels dependent on the fabrication parameters. In particular, we examine the influence of the cutting sequence, the number of cut passes, the laser beam velocity and the laser radiant flux. The model allows the prediction of microchannel depths within a maximum deviation of 8 µm for channels that are up to 210 µm in depths. It was shown that, at constant channel depth, the channel width could be varied by 27% by using different cutting parameters. The optimum cutting sequence for the production of a channel -junction is also presented in the paper. The laser system is shown to be a flexible and rapid tool for the production of polymer microfluidic prototypes.
Music on the Internet and the intellectual property protection problem (2002)

Recent advances in audio compression technology coupled with trends toward higher network bandwidth, lower memory costs and lower storage costs indicate that the obstacles to music distribution on the Internet will soon be overcome. Because it provides benefits to consumers and to music content owners alike, networked music distribution may become one of the first compelling Internet consumer services. At the same time, these technological advances create opportunities for pirates. The authors believe that the music industry must prepare for network music distribution or face widespread theft of its music. In this paper, they first review the technological advances that are driving a change in the industry's business model. They then discuss the opportunities that these advances allow. Finally they focus on the dangers to content owners and discuss various ways to protect music content.
Automating and Analyzing Whole-Farm Carbon Models (2020)

A whole farm carbon model estimates the emissions of greenhouse gasses (GHGs) based on information for a farm. We analyzed two models, Holos whole-farm and COMET-Farm, by running the models on random inputs and building predictive models from the runs. Holos estimates GHG emissions for a particular year based on crop and animal agriculture input, while COMET-farm adds past and future farm management practices. Users of the models must manually enter farm data through a graphical user interface (GUI), which is a good method for a single farm, but makes it infeasible to calculate GHG emissions over hundreds to thousands of farms. So we automated the interface and generated random farm scenarios within ranges given by experts. We scraped the estimated carbon footprint from thousands of runs of the models and used algorithms to build predictive models that have high accuracy. By reverse engineering the whole-farm carbon models we were able to determine which farm management practices in each whole farm carbon model have the biggest impact on GHG emissions. This can help farmers and rural planners change farm management practices to decrease GHG emissions.
Wide-range tunable Fabry–Perot array filter for wavelength-division multiplexing applications (2005)

A new design for a Fabry-Perot-based array filter for wavelength-division multiplexing (WDM) applications is proposed. The device is composed of two partially reflective mirrors; the surface of one of the mirrors is stepwise. Not only does the configuration of multiple air-gap cavities into a single unit provide wavelength tunability but the channel numbers can be expanded. A four-channel multiplexer has been demonstrated. The results revealed that a compact and cost-effective WDM device should be easily attainable.
Micrometastases and isolated tumor cells: relevant and robust or rubbish? (MIRROR): preliminary results of the MIRROR study from the Dutch breast cancer trialists' group (BOOG). (2009)

Abstract Abstract #23 Background&amp;#x2028; The sentinel lymph node procedure (SNP) has largely replaced axillary lymph node dissection (ALND) in patients with early breast cancer (BC). Intensified examination of the sentinel node (SN) results in the detection of isolated tumor cells (ITCs) and micrometastases, whereas its relevance is still debated. This retrospective cohort study is the first study on this topic which includes only patients who underwent a SNP, with central review of all SN slides, and with separate analyses for the impact of administration of adjuvant systemic therapy.&amp;#x2028; Methods&amp;#x2028; Patients operated for BC in all Dutch hospitals in the years 1998-2005, having favourable tumor characteristics (&amp;gt; 35 year; tumor size 1-3 cm and differentiation grade I-II OR tumor size ≤ 1 cm irrespective of grade), having undergone a SNP with pN0(i-), pN0(i+), or pN1mi as final N-stage were selected. Patients were classified in cohort I in case of pN0(i-) and no adjuvant systemic therapy (AST), in cohort II in case of pN0(i+)/pN1mi and no AST, and in cohort III in case of pN0(i+)/pN1mi with AST. SNs were centrally reviewed and restaged according to 6th TNM classification. The 5-year disease-free survival (DFS) was analysed for the 3 different cohorts.&amp;#x2028; Results&amp;#x2028; So far, data are available for 1,744 of the 3,240 selected patients (cohort I n=935; cohort II n=340, cohort III n=469) with a median follow-up of 5.5 years. At diagnosis median age was 58, 56 and 56 years (p &amp;lt; 0.01) and median tumor size was 1.2, 1.4 and 1.5 cm (p &amp;lt; 0.0001). Differentiation grade and hormone receptor status were equally distributed among the three cohorts. Adjuvant systemic therapy in cohort III consisted of chemotherapy (10%), hormonal therapy (63%), or both (27%). The 5-yr DFS is 84% in cohort I, 73% in cohort II, and 86% in cohort III (p = 0.003 cohort I vs II; p &amp;lt; 0.0001 cohort II vs III). Correction for baseline characteristics did not lead to a relevant change in the results.&amp;#x2028; Conclusion&amp;#x2028; BC patients with ITCs or micrometastases as final N-stage after SNP have a significantly worse 5-yr DFS as compared to patients having no ITCs or micrometastases, independent of primary tumor characteristics. Adjuvant systemic therapy significantly improves the 5-yr DFS in the group of patients with ITCs or micrometastases in the lymph node(s). At the meeting, updated analyses will be available for the entire MIRROR study population.&amp;#x2028; Support: The Netherlands organization for health research and development (ZonMw) and all Dutch CCCs. Citation Information: Cancer Res 2009;69(2 Suppl):Abstract nr 23.
Hybrid Nanogenerator for Concurrently Harvesting Biomechanical and Biochemical Energy (2010)

Harvesting energy from multiple sources available in our personal and daily environments is highly desirable, not only for powering personal electronics, but also for future implantable sensor-transmitter devices for biomedical and healthcare applications. Here we present a hybrid energy scavenging device for potential in vivo applications. The hybrid device consists of a piezoelectric poly(vinylidene fluoride) nanofiber nanogenerator for harvesting mechanical energy, such as from breathing or from the beat of a heart, and a flexible enzymatic biofuel cell for harvesting the biochemical (glucose/O2) energy in biofluid, which are two types of energy available in vivo. The two energy harvesting approaches can work simultaneously or individually, thereby boosting output and lifetime. Using the hybrid device, we demonstrate a "self-powered" nanosystem by powering a ZnO nanowire UV light sensor.
Detection of TV commercials (2004)

This paper presents a system that labels TV shots either as commercial or program shots. The system uses two observations: logo presence and shot duration. These observations are modeled using HMMs, and a Viterbi decoder is finally used for shot labeling. The system has been tested on several hours of real video, achieving more than 99% correct labeling.