gebhart/patrepeval huggingface dataset:
A Heritable Recombination System for Synthetic Darwinian Evolution in Yeast (2012)

Genetic recombination is central to the generation of molecular diversity and enhancement of evolutionary fitness in living systems. Methods such as DNA shuffling that recapitulate this diversity mechanism in vitro are powerful tools for engineering biomolecules with useful new functions by directed evolution. Synthetic biology now brings demand for analogous technologies that enable the controlled recombination of beneficial mutations in living cells. Thus, here we create a Heritable Recombination system centered around a library cassette plasmid that enables inducible mutagenesis via homologous recombination and subsequent combination of beneficial mutations through sexual reproduction in Saccharomyces cerevisiae. Using repair of nonsense codons in auxotrophic markers as a model, Heritable Recombination was optimized to give mutagenesis efficiencies of up to 6% and to allow successive repair of different markers through two cycles of sexual reproduction and recombination. Finally, Heritable Recombination was employed to change the substrate specificity of a biosynthetic enzyme, with beneficial mutations in three different active site loops crossed over three continuous rounds of mutation and selection to cover a total sequence diversity of 10(13). Heritable Recombination, while at an early stage of development, breaks the transformation barrier to library size and can be immediately applied to combinatorial crossing of beneficial mutations for cell engineering, adding important features to the growing arsenal of next generation molecular biology tools for synthetic biology.
P630 Development and evaluation of BioCLIA-Tracker infliximab kit: A fast and innovative chemiluminescent assay for the monitoring of patients treated with infliximab (2018)

Infliximab, a monoclonal antibody directed against TNFa, is a drug widely used for the treatment of inflammatory diseases, including Crohn’s disease and ulcerative colitis. Therapeutic drug monitoring (TDM) appears to be a cost-effective tool proposed to facilitate treatment adjustment and improve efficacy of biologics therapies. Rapid and accurate results are needed for appropriate use of TDM. We present here the analytical performances of the newly developed BioCLIA-TRACKER Infliximab assay, allowing fast and fully automated quantification of Infliximab on the random access BioCLIA 1200 chemiluminescent analyser. The infliximab assays use TNFα-coupled magnetic beads. A monoclonal antibody directed against human IgG conjugated to alkaline phosphatase and a high sensitive chemiluminescent substrate are used for the detection of Infliximab. Light emission is linked to the quantity of Infliximab present in the sample. Analytical performances were assessed using two types of serum samples: human serum spiked with Infliximab, and samples from inflammatory bowel disease patients treated with Infliximab (n = 33). Theradiag BioCLIA-TRACKER Infliximab assay presents a large dynamic range from 0.5 to 32 µg/ml. Infliximab measurement shows high accuracy (80% < % recovery < 120%) and high precision (6.4% < CV < 15.6% for intra-precision, 4.0% < CV < 19.5% for inter-run precision). None interference were observed with biologic agents (bilirubin, haemoglobin, lipids, and rheumatoïd factors). BioCLIA-TRACKER Infliximab assay was compared with LISA-TRACKER Infliximab assay and showed good correlation (R² = 0.94, slope = 1.00). BioCLIA-TRACKER Infliximab kit is an innovative assay which exhibits fast, accurate and reproducible results. Excellent agreements were observed with LISA-TRACKER Infliximab assay. BioCLIA-TRACKER kit is a valuable tool for the monitoring of patients treated with Infliximab and allowing rapid treatment adjustment.
DENDRIMER-ENHANCED MRI AS A DIAGNOSTIC AND PROGNOSTIC BIOMARKER OF SEPSIS IN AGED MICE (2004)

SOCIETY OF CRITICAL CARE MEDICINE 34TH CRITICAL CARE CONGRESS PHOENIX, ARIZONA, USA JANUARY 15-19, 2005: Poster Presentation: Basic Scnence: Sepsis/Inflammation/Infection I
Efficient Self-Calibrated Convolution for Real-Time Image Super-Resolution (2022)

With the recent advancements in Convolutional Neural Net-work (CNN) architectures designs, many image processing tasks benefited from the design of such deep and complex networks including image super-resolution (SR). While deep and complex models achieve improved SR reconstruction, they lack the practicality in implementation for real-time applications, such as in mobile phones or online conferencing. This is due to the large number of parameters and excessive required multiply-accumulate operations (MACs). In this paper, an accurate real-time SR model structure is proposed. The proposed structure reduces the required number of MACs by performing all operations on low dimensional feature maps and reduces the model parameters by utilizing depthwise separable convolutional (DSC) layers. An efficient version of the recently introduced self-calibrated convolution with pixel attention (SC-PA) is introduced to further improve feature representation. Experimental results show that the proposed model improves performance in objective metrics, such as Peak Signal-to-Noise Ratio (PSNR) and Structural Similarity (SSIM) index, over similar complexity real-time SR models.
High‐Z Sensitized Plastic Scintillators: A Review (2018)

The need for affordable and reliable radiation detectors has prompted significant investment in new radiation detector materials, due to concerns about national security and nuclear nonproliferation. Plastic scintillators provide an affordable approach to large volume detectors, yet their performance for high-energy gamma radiation is severely limited by the small radiation stopping power inherent to their low atomic number. Although some sensitization attempts with organometallics were made in the 1950s to 1960s, the concomitant decrease in light yield has limited the usefulness of these sensitized detectors. Recently, with new knowledge gained during the rapid development of organic optoelectronics and nanotechnology, there has been a revived interest in the field of heavy element sensitized plastic scintillators. Here, the recent efforts on sensitized plastic scintillators are summarized. Basic scintillator physics is first reviewed. The discussion then focuses on two major thrusts in the field: sensitization with: (1) organometallics and (2) oxide and fluoride nanoparticles. The design rationales and major results are examined in detail, with existing limitations and possible future pathways discussed. Special attention is paid to the underlying energy deposition and transfer processes, as these determine the key performance metrics such as light yield and radioluminescence decay lifetime.
Addressing the Rising Prices of Disease-Modifying Therapies for Multiple Sclerosis (2019)

Our website uses cookies to enhance your experience. By continuing to use our site, or clicking "Continue," you are agreeing to our Cookie Policy | Continue JAMA Neurology HomeNew OnlineCurrent IssueFor Authors Podcast Publications JAMA JAMA Network Open JAMA Cardiology JAMA Dermatology JAMA Health Forum JAMA Internal Medicine JAMA Neurology JAMA Oncology JAMA Ophthalmology JAMA Otolaryngology–Head & Neck Surgery JAMA Pediatrics JAMA Psychiatry JAMA Surgery Archives of Neurology & Psychiatry (1919-1959) JN Learning / CMESubscribeJobsInstitutions / LibrariansReprints & Permissions Terms of Use | Privacy Policy | Accessibility Statement 2023 American Medical Association. All Rights Reserved Search All JAMA JAMA Network Open JAMA Cardiology JAMA Dermatology JAMA Forum Archive JAMA Health Forum JAMA Internal Medicine JAMA Neurology JAMA Oncology JAMA Ophthalmology JAMA Otolaryngology–Head & Neck Surgery JAMA Pediatrics JAMA Psychiatry JAMA Surgery Archives of Neurology & Psychiatry Input Search Term Sign In Individual Sign In Sign inCreate an Account Access through your institution Sign In Purchase Options: Buy this article Rent this article Subscribe to the JAMA Neurology journal
Universal Chiplet Interconnect Express (UCIe): An Open Industry Standard for Innovations With Chiplets at Package Level (2022)

Universal Chiplet Interconnect Express (UCIe) is an open industry standard interconnect for developing an open chiplet ecosystem, where chiplets from any supplier can be packaged anywhere in an interoperable manner. This article delves into the architectural, circuit, channel, and packaging aspects that we developed that has been adopted in the UCIe 1.0 Specification. We present our results based on our channel and circuit implementation studies.
OXYGEN PERMEATION IN THE MEMBRANE OF POLY(OCTYLMETHACRYLATE-co-4-VINYLPYRIDINE)-SALICYLALDEHYDEETHYLENEDIIMINE COBALT COMPLEX (1986)

Abstract Oxygen-binding and -permeation in the membrane prepared from the poly(octylmethacrylate-co-4-vinylpyridine) complexed with salicylaldehydeethylenediimine cobalt was studied by spectroscopic and permeability measurements. The cobalt complex in the membrane effectively acted as a fixed carrier on oxygen permeation.
Sorting points into neighborhoods (SPIN): data analysis and visualization by ordering distance matrices (2005)

Software package will be available for academic users upon request.
Development of Survey Instruments to Guide the Design of Health Status Monitoring Systems for the Elderly: Content Validity Evaluation (2006)

The development of technologies for monitoring the health status of older adults in their living settings is a long and expensive process that involves multiple stakeholders. If the technology is to be mass produced, widely deployed and utilized by different user groups, the technology has to meet certain feasibility criteria, including being acceptable, useful, and potentially beneficial to all the different users. This paper describes the development, content and content validity evaluation results of three custom survey instruments designed to assess the feasibility of using in-home health status, monitoring technologies. The instruments were designed to solicit input from three primary stakeholders in the care process: the monitoring candidate older adults, professional caregivers, and informal caregiver. The validity of the instruments content was evaluated by ten field experts who were asked to score each question in each of the three survey instruments on a 4-point Likert scale on relevance, clarity, and simplicity. All three survey instruments received significantly high overall mean content validity scores. The content validity evaluation results indicated that these instruments are ready to be used to solicit users' requirements from the user groups to guide the refinement of monitoring technologies.
Electromagnetic-SPICE modeling and analysis of 3D power network (2011)

Accurate modeling and estimation of 3D power network electrical performance are vitally important to aid the 3D integration and packaging design. In order to achieve high accuracy, we combine the electromagnetic (EM) and analytic simulations in this work to evaluate the electrical performance of a 3D power network, which consists of Cu through-strata-vias (TSVs), solders, micro-solders, and on-chip power grids. We intentionally partition the real stack-up structure of 3D power network into separated components, electromagnetically extract all the passive elements (resistance, inductance, conductance, and capacitance, i.e., RLGC) for each component at certain frequency points of interest. We then assemble all the components again into a corresponding SPICE model of 3D power network and import EM-extracted RLGC values to analyze the overall 3D system power performance. The number of stacked ICs, floorplanning of TSV/micro-solders, operating frequency of 3D system, and characteristics of decoupling capacitance are examined to unveil several 3D power delivery design implications.
Embryo Implantation (2021)

A lesson learned from modern developmental biology is the striking degree of conservation of strategies and molecules used to program developmental events in species as diverse as insects, birds, amphibians, and mammals. Nonetheless, mammals retain distinctions with regard to the strategies used to protect and nourish their offspring during development, namely the processes of implantation and placentation. While involving relatively few cell types, placentation is a complex process. Furthermore, genes associated with this process display remarkably high spontaneous mutational rates, suggesting a strong adaptive/selection pressure on this tissue (Roberts et al., 1999). In the case of implantation, a highly coordinated process is set into motion hereby specialized cells of the embryo, the trophectoderm and trophoblast, establish contact with a specialized tissue of the mother, the uterus. The exquisite coordination involves the regulated production of growth factors, cytokines, and hormones by embryonic as well as maternal tissues of both uterine and extrauterine origins. In concert, complementary receptors for these factors must be expressed by the appropriate tissues to propagate implantation signals. In addition, cell surface components must become functionally available to support attachment of trophectoderm/trophoblast and uterine cells. To add to the challenge, it has been shown that, in most mammals, there is only a restricted time during the uterine cycle during which implantation can occur (Psychoyos, 1986). Failure to initiate the critical early events of implantation during this “window of receptivity” results in early pregnancy failure.
Cold‐induced Glutamate Releasein vivofrom the Magnocellular Region of the Paraventricular Nucleus is Involved in Ovarian Sympathetic Activation (2010)

We previously reported that centrally-induced sympathetic activation in response to cold stress is associated with a polycystic ovarian condition in rats, and thyrotrophin-releasing hormone (TRH) released locally from the magnocellular region of the paraventricular nucleus (PVN) appears to be involved in this activation. Because TRH neurones express NMDA glutamate receptors, in the present study, we investigated the role of glutamate in the increased release of TRH from magnocellular neurones induced by cold stress and its relationship to ovarian neurotransmission. Animals with a push-pull cannula stereotaxically implanted into the magnocellular portion of the PVN were exposed to cold stress (4 degrees C for 64 h) and subjected to intracerebral perfusion. Perfusate fractions were obtained and analysed by high-performance liquid chromatography to measure glutamate and GABA levels. Glutamate, but not GABA, release increased significantly in animals perfused under cold exposure. In vivo administration of glutamate to the PVN increased TRH release. Injection of MK-801 into the magnocellular portion of the PVN reduced ovarian noradrenaline turnover and led to an increase in catecholamine concentration from the adrenal glands and celiac ganglia. Taken together, the results obtained in the present study strongly suggest that glutamate release from the magnocellular PVN is sensitive to cold stress and that glutamate acts through the NMDA receptor to mediate cold-induced TRH release. This in turn triggers hypothalamic-ovarian pathway activation, which might be responsible for the polycystic condition induced by cold stress and other ovarian pathologies characterised by increased sympathetic discharge.
Development of photostable proximity bioassays (2006)

We are developing a novel reporter for proximity assays based on enhanced lanthanide luminescence promoted by metal nanoparticles. This method should provide high on/off ratios using photostable labels.
Effect of errors in reangulation on planar and tomographic thallium-201 washout profile curves. (1985)

Cardiac phantom studies were performed with and without a defect present to test the hypothesis that myocardial 201TI quantitative circumferential washout profile curves calculated from planar and rotating slant hole (RSH) collimator tomographic images are equally affected by errors in axial repositioning. Simulated stress images were acquired with the long axis of the phantom perpendicular to the camera surface and redistribution images were acquired to represent 50% 201TI washout with axial repositioning errors relative to the stress position ranging from 0 to 20 degrees in 5 degrees increments. There was a decrease in the 201TI washout profile curves compared to that expected (50%) in the wall tilted away from the camera surface, and a reciprocal increase in the 201TI washout profile curves in the wall tilted towards the camera surface for both imaging techniques whether a lesion was present or not. This effect became more pronounced as the error in axial repositioning was increased for both the planar (p less than 0.001) and the RSH tomographic (p less than 0.001) techniques. However, the deviation of the 201TI washout profile curves from that expected (50%) was greater for the planar imaging technique with or without a lesion (p less than 0.05 to 0.001). Thus, we conclude that 201TI quantitative circumferential washout profile curves calculated using this tomographic imaging technique are less affected by errors in axial repositioning than those calculated using an equivalent projection by standard planar imaging methods. These data emphasize the importance which must be placed on the repositioning of patients to obtain valid 201TI washout profile curves for the detection and localization of coronary artery disease.
Use of oral sodium polyacrylate in rat gastrointestinal alkali burns. (1988)

Alkali-induced injuries of the esophagus and stomach are currently medically managed with steroids and antibiotics. We investigated whether treatment with sodium polyacrylate (PANa), a proposed mucosal protectant, could decrease the deleterious effect of alkali injuries or prevent alkali injuries. Rats were randomized in 4 groups. Group I (control; n = 7) received 0.1 ml normal saline via gastric gavage. Groups II-IV received 0.1 ml 25% NaOH. Group II (n = 22) received no further treatment. Group III (n = 9) received 0.25% PANa ad lib in drinking water for 3 days prior to NaOH. Group IV received 0.25% PANa for 6 days after NaOH. Animals were weighed daily. At 6 days post NaOH, stomachs were removed from animals in Groups II-IV and burn lesions were outlined on tracing paper. 1 x 1 cm sections of burned areas were fixed, stained with H&E and histologically evaluated. In another study, 0.1 ml of 10% NaOH was given to 2 groups of animals. Group I (n = 22) received no other treatment, while Group II (n = 13) received PANa ad lib in drinking water for 3 days prior to NaOH. Of the animals treated with 25% NaOH, only those in Group II showed a decrease mean weight which was statistically significant on Day 4, p = 0.016. Mean burn areas were statistically greater in Group II than in Group IV (p = 0.025), while histologically, lesions were similar. Pretreatment with PANa prior to 10% NaOH prevented the weight loss which occurred daily in the control animals.(ABSTRACT TRUNCATED AT 250 WORDS)
Aminolysis of low‐molecular‐weight and polymeric 4‐nitrophenyl esters (1988)

Abstract 4‐Nitrophenyl methacrylate (1a), 4‐nitrophenyl esters of some N ‐methacryloyl‐ω‐amino acids (1b −d) and 4‐nitrophenyl esters of N ‐acetyl‐ and N ‐methacryloyltryptophane (2a and 2b) were prepared and characterized. Copolymers of 1 a −d and 2 b with N ‐2‐hydroxypropylmethacrylamide (HPMA), N ‐isopropylmethacrylamide (iPMA) and N ‐ethylmethacrylamide (EMA) were also prepared. The 4‐nitrophenyl ester content of the copolymers was determined spectrophotometrically from their UV absorption and from the UV absorption of the 4‐nitrophenolate ion which is released upon hydrolysis of the active esters with 0,1 M sodium hydroxide. The difference between these values depends on both the type of polymerizable active ester used and the comonomer. The proportion of non‐hydrolyzable structure is especially high in the case of copolymers containing 4‐nitrophenyl esters of the methacryloylated α‐amino acids 1b and 2b . The formation of non‐hydrolyzable structures is likely due to side reactions which occur during polymerization. The polymers prepared by copolymerization of the polymerizable 4‐nitrophenyl esters were not found to be suitable for the preparation of polymeric fluorescent probes by a chemical modification route. It was found that the rate of aminolysis of low‐molecular‐weight and polymeric activated esters increases with increasing the number of methylene groups in the N ‐(ω‐aminoalkyl)‐5‐dimethylamino‐1‐ naphthalenesulfonamides (dansylamines) 3a–f .
Parkin ubiquitination of Kindlin-2 enables mitochondria-associated metastasis suppression (2023)

Mitochondria are signaling organelles implicated in cancer, but the mechanisms are elusive. Here, we show that Parkin, an E3 ubiquitination (Ub) ligase altered in Parkinson's disease, forms a complex with the regulator of cell motility, Kindlin-2 (K2), at mitochondria of tumor cells. In turn, Parkin ubiquitinates Lys581 and Lys582 using Lys48 linkages, resulting in proteasomal degradation of K2 and shortened half-life from ∼5 h to ∼1.5 h. Loss of K2 inhibits focal adhesion turnover and β1 integrin activation, impairs membrane lamellipodia size and frequency, and inhibits mitochondrial dynamics, altogether suppressing tumor cell-extracellular matrix interactions, migration, and invasion. Conversely, Parkin does not affect tumor cell proliferation, cell cycle transitions, or apoptosis. Expression of a Parkin Ub-resistant K2 Lys581Ala/Lys582Ala double mutant is sufficient to restore membrane lamellipodia dynamics, correct mitochondrial fusion/fission, and preserve single-cell migration and invasion. In a 3D model of mammary gland developmental morphogenesis, impaired K2 Ub drives multiple oncogenic traits of EMT, increased cell proliferation, reduced apoptosis, and disrupted basal-apical polarity. Therefore, deregulated K2 is a potent oncogene, and its Ub by Parkin enables mitochondria-associated metastasis suppression.
Insulin-Dependent Diabetes in the Nod Mouse Model I. Detection and Characterization of Autoantibody Bound to the Surface of Pancreatic Beta Cells Prior to Development of the insulitis Lesion in Prediabetic Nod Mice (1993)

Type I, insulin-dependent diabetes (IDD) results from an autoimmune response against the insulin producing pancreatic beta cells. This autoimmune reaction involves both humoral and cell-mediated factors; nevertheless, the relative role of each remains unresolved. Furthermore, while adoptive transfer experiments have provided evidence for the role of T cells in beta cell destruction, the specific events which initiate leukocyte migration into the islets (insulitis) are unknown. Earlier studies indicated that NOD pancreatic beta cells may bind small amounts of autoantibody. Because of the possible importance of an early humoral response to the initiation of insulitis and subsequent disease, we have investigated a number of aspects of this phenomenon to determine the nature and specificity of the early autoantibodies as well as the time at which autoantibody binds to beta cells. Results of this study demonstrate that NOD/Uf mice are sensitized to islet-cell associated antigens, including GAD, prior to the first appearance of insulitis; that a small percentage of the beta cells of NOD/Uf mice have autoantibody bound to their surface prior to insulitis; that sera collected from preinsulitis NOD/Uf mice contain autoantibodies which will bind to beta cells of both IDD-prone and IDD-resistant mice; and that the autoantibodies which bind pancreatic beta cells are predominantly IgM with lesser amounts of IgG and IgA. These findings suggest that, in the natural course of IDD, insulitis may develop in response to an initial autoantibody-mediated injury of beta cells.