gebhart/patrepeval huggingface dataset:
Characterization of zebrafish mutants with defects in embryonic hematopoiesis (1996)

As part of a large scale chemical mutagenesis screen of the zebrafish (Danio rerio) genome, we have identified 33 mutants with defects in hematopoiesis. Complementation analysis placed 32 of these mutants into 17 complementation groups. The allelism of the remaining 1 blood mutant is currently unresolved. We have categorized these blood mutants into four phenotypic classes based on analyses of whole embryos and isolated blood cells, as well as by in situ hybridization using the hematopoietic transcription factors GATA-1 and GATA-2. Embryos mutant for the gene moonshine have few if any proerythroblasts visible on the day circulation begins and normal erythroid cell differentiation is blocked as determined by staining for hemoglobin and GATA-1 expression. Mutations in five genes, chablis, frascati, merlot, retsina, thunderbird and two possibly unique mutations cause a progressive decrease in the number of blood cells during the first 5 days of development. Mutations in another seven genes, chardonnay, chianti, grenache, sauternes, weiflherbst and zinfandel, and two additional mutations result in hypochromic blood cells which also decrease in number as development proceeds. Several of these mutants have immature cells in the circulation, indicating a block in normal erythroid development. The mutation in zinfandel is dominant, and 2-day old heterozygous carriers fail to express detectable levels of hemoglobin and have decreasing numbers of circulating cells during the first 5 days of development. Mutations in two genes, freixenet and yquem, result in the animals that are photosensitive with autofluorescent blood, similar to that found in the human congenital porphyrias. The collection of mutants presented here represent several steps required for normal erythropoiesis. The analysis of these mutants provides a powerful approach towards defining the molecular mechanisms involved in vertebrate hematopoietic development.
A framework for information quality assessment (2007)

Abstract One cannot manage information quality (IQ) without first being able to measure it meaningfully and establishing a causal connection between the source of IQ change, the IQ problem types, the types of activities affected, and their implications. In this article we propose a general IQ assessment framework. In contrast to context‐specific IQ assessment models, which usually focus on a few variables determined by local needs, our framework consists of comprehensive typologies of IQ problems, related activities, and a taxonomy of IQ dimensions organized in a systematic way based on sound theories and practices. The framework can be used as a knowledge resource and as a guide for developing IQ measurement models for many different settings. The framework was validated and refined by developing specific IQ measurement models for two large‐scale collections of two large classes of information objects: Simple Dublin Core records and online encyclopedia articles.
Mesoporous silica nanoparticles in biomedical applications (2012)

This tutorial review provides an outlook on nanomaterials that are currently being used for theranostic purposes, with a special focus on mesoporous silica nanoparticle (MSNP) based materials. MSNPs with large surface area and pore volume can serve as efficient carriers for various therapeutic agents. The functionalization of MSNPs with molecular, supramolecular or polymer moieties, provides the material with great versatility while performing drug delivery tasks, which makes the delivery process highly controllable. This emerging area at the interface of chemistry and the life sciences offers a broad palette of opportunities for researchers with interests ranging from sol-gel science, the fabrication of nanomaterials, supramolecular chemistry, controllable drug delivery and targeted theranostics in biology and medicine.
The tomato resistance protein Bs4 is a predicted non‐nuclear TIR‐NB‐LRR protein that mediates defense responses to severely truncated derivatives of AvrBs4 and overexpressed AvrBs3 (2003)

The Lycopersicon esculentum Bs4 resistance (R) gene specifies recognition of Xanthomonas campestris pv. vesicatoria (Xcv) strains that express the cognate AvrBs4 avirulence protein. Bs4 was isolated by positional cloning and is predicted to encode a nucleotide-binding leucine-rich repeat (NB-LRR) protein that is homologous to tobacco N and potato Y-1 resistance proteins. Xcv infection tests demonstrate that Bs4 confers perception of AvrBs4 but not the 97% identical AvrBs3 protein. However, when delivered via Agrobacterium T-DNA transfer, both, avrBs4 and avrBs3 trigger a Bs4-dependent hypersensitive response, indicating that naturally occurring AvrBs3-homologues provide a unique experimental platform for molecular dissection of recognition specificity. Transcript studies revealed intron retention in Bs4 transcripts. Yet, an intron-deprived Bs4 derivative still mediates AvrBs4 detection, suggesting that the identified splice variants are not crucial to resistance. The L. pennellii bs4 allele, which is >98% identical to L. esculentum Bs4, has a Bs4-like exon-intron structure with exception of a splice polymorphism in intron 2 that causes truncation of the predicted bs4 protein. To test if the receptor-ligand model is a valid molecular description of Bs4-mediated AvrBs4 perception, we conducted yeast two-hybrid studies. However, a direct interaction was not observed. Defense signaling of the Bs4-governed reaction was studied in Nicotiana benthamiana by virus-induced gene silencing and showed that Bs4-mediated resistance is EDS1- and SGT1-dependent.
Nanofluidic Devices and Their Applications (2008)

Recent developments in micro- and nanotechnologies made possible the fabrication of devices integrating a deterministic network of nanochannels, i.e., with at least one dimension in a range from 1 to 100 nm. The proximity of this dimension and the Debye length, the size of biomolecules such as DNA or proteins, or even the slip length, added to the excellent control on the geometry gives unique features to nanofluidic devices. This new class of devices not only finds applications wherever less well-defined porous media, such as electrophoresis gels, have been traditionally used but also give a new insight into the sieving mechanisms of biomolecules and the fluid flow at the nanoscale. Beyond this, the control on the geometry allows smarter design resulting, among others, in new separation principles by taking advantage of the anisotropy. This perspective gives an overview on the fabrication technologies of nanofluidic devices and their applications. In the first part, the current state of the art of nanofluidic fabrication is presented. The second part first discusses the key transport phenomena in nanochannels. Current applications of nanofluidic devices are next discussed. Finally, future challenges and possible applications are highlighted.
Thermal-energy storage in crosslinked pellets of high-density polythylene for home heating and cooling via off-peak electric power utilization (1983)

Electron beam crosslinking of high-denisty polyethylene (HDPE) was studied to obtain pellets for phase-change thermal-energy storage that retain their original shape and form through repeated melt/freeze cycles, and thus “serve as their own container.” Electron-beam voltage, amperage, atmosphere, pellet-bed depth, traverse rate, and total dose were varied to establish cost/effective conditions for adequate thermal from stability combined with highest retention of heat of fusion. The results of electron beam crosslinking are compared with chemical crosslinking in cost and effectiveness. Utility of the electron-beam crosslinked HDPE pellets in a low-cost, efficient pellet-bed heat exchanger was demonstrated. Potential applications discussed include thermal storage for home heating and cooling, industrial processing, and off-peak electric utilization for load leveling.
Syk and ZAP-70 mediate recruitment of p56lck/CD4 to the activated T cell receptor/CD3/zeta complex. (1995)

During antigen recognition by T cells, CD4 and the T-cell receptor (TCR)/CD3/zeta complex are thought to interact with the same major histocompatibility complex II molecule in a stable ternary complex. Evidence has suggested that the association of CD4 with TCR/CD3/zeta requires the interaction of the protein tyrosine kinase p56lck with CD4. We have taken a biochemical approach to understand the mechanism by which p56lck and, in particular, its src homology (SH) 2 domain contributes to the association of CD4 with TCR/CD3/zeta during activation. We have previously shown that the p56lck SH2 domain binds directly to tyrosine-phosphorylated ZAP-70. Here we formally demonstrate the in vivo association of p56lck with the homologous protein tyrosine kinases Syk and ZAP-70 after CD3 stimulation of Jurkat cells. A tyrosine-phosphorylated peptide containing the sequence predicted to be optimal for binding to the SH2 domain of src family kinases specifically competes for this association, indicating that tyrosine-phosphorylated ZAP-70 and Syk bind to p56lck by an SH2-mediated interaction. We also show that the same peptide is able to compete for the activation-dependent TCR/CD4 association in Jurkat cells. Moreover, ZAP-70 and CD4 cocap only after CD3 stimulation in human T lymphoblasts. We propose that the interaction of the p56lck SH2 domain with zeta-associated tyrosine-phosphorylated ZAP-70 and/or Syk enables CD4 to associate with antigen-stimulated TCR/CD3/zeta complexes.
Differential Effects of DX-9065a, Argatroban, and Synthetic Pentasaccharide on Tissue Thromboplastin Inhibition Test and Dilute Russell's Viper Venom Test (2003)

New synthetic direct and indirect factor Xa or factor IIa inhibitors are increasingly used for the prevention and treatment of thrombotic disorders, including patients suffering from antiphospholipid syndrome. In this study, the effects of the synthetic direct factor Xa inhibitor DX-9065a, the indirect synthetic heparinomimetic pentasaccharide, and the direct factor IIa inhibitor Argatroban were studied. These two widely used assays for the detection of lupus anticoagulant, namely the tissue thromboplastin inhibition (TTIT) and the dilute Russell viper venom tests (DRWT) proved useful. The drugs were added to a normal human plasma pool ranging in concentration from 0.04 to 10 microg/mL. Using the two tests named above, DX-9065a and Argatroban showed a dose-related prolongation of TTIT and DRWT in the concentration range from 0.04 to 5 micromol/mL, but the pentasaccharide only slightly prolonged the clotting times of these assays even at high concentrations. Argatroban had the more pronounced effect on both tests when compared with DX-9065a (p < 0.001). The most responsive assay for DX-9065a up to a concentration of 2.5 micromol/mL was the DRWT. For Argatroban both TTIT and DRWT were equally responsive. Patients whose plasma was tested for suspected lupus anticoagulant and who have been given DX-9065a or Argatroban may have false-positive results with the TTIT tests and DRWT. This effect should be considered during patient management. These results indicate that these assays could be used for the effective quantitation of the direct factor Xa or factor IIa inhibitors when suitable controls are used.
Lung parenchyma: projection reconstruction MR imaging. (1991)

Magnetic resonance (MR) imaging of lung parenchyma is limited by the low proton density and short T2 in the lung as well as the effects of susceptibility and motion. The MR imaging appearance of lung parenchyma was investigated with a pulse sequence that offers some solutions to these problems. This sequence employs projection reconstruction (PR) acquisition gradients and a section-selective excitation pulse designed to eliminate the need to refocus and to allow low-frequency k-space data to be collected with minimal delay. Echo times as short as 50 microseconds can be achieved, producing a proton-density-weighted image. An excised inflated lung specimen and specimens from human subjects with normal lungs (n = 3), pulmonary arteriovenous malformations (n = 1), bronchogenic carcinoma (n = 1), and bullous lung disease with lung metastases (n = 1) were examined. Signal intensity from lung parenchyma and visibility of pulmonary structures were superior on images obtained with the PR MR imaging technique compared with spin-echo images.
Preparation and Evaluation of a Sustained Naloxone Delivery System in Rats (1975)

The use of a non-biodegradable polymer system to provide a sustained release of the narcotic antagonist naloxone in rats is described. The kinetics of morphine analgesia (measured by the hot-plate test) in the presence of the naloxone implant, and the urinary excretion of radiolabeled naloxone were measured. The shift of the morphine dose-response curve to the right is expressed in terms of dose ratios, which were calculated from the ED50 values for morphine obtained 9 days before, and 1, 8, 15, 22 and 29 days after implantation of the polymer. Our experiments indicate that effective levels of antagonist were maintained for 3-4 weeks after implantation of a polymer system containing 16 mg of naloxone. After 29 days, more than 95% of the absorbed drug had been released, with 16% of the implanted radioactivity appearing in the urine. These results demonstrate the feasibility of using a sustained release form of a narcotic antagonist to block the effects of morphine.
Genetic Polymorphisms and Oxidative Stress in Heart Failure (2002)

Heart failure results from various known cardiovascular diseases, such as coronary artery disease, or can be the result of an idiopathic dilated cardiomyopathy. It is of utmost importance for diagnostic, preventive, and therapeutic purposes to understand the cellular events that trigger the cascade of functional and structural changes that result in the development and progression of heart failure. Progress in unraveling the genetic background in both ischemic and nonischemic cardiomyopathies has been slow compared with that for monogenic diseases, such as some forms of hypertrophic cardiomyopathy or familial dilated cardiomyopathies. It is likely that susceptibility to and risk of progression of heart failure are both influenced by many genes acting in concert or independently. Among the diverse subcellular mechanisms implicated in the pathogenesis and progression of heart failure, reactive oxygen species play a major role. The search for genetic polymorphisms in clinical association studies in order to identify genotypes susceptible to develop and affect the progression to heart failure has been the focus of many investigations over the past several years. In this review, the authors summarize the current data in support of the role of various polymorphisms of genes related to oxidative stress in the susceptibility to develop heart failure, and its progression.
TEXT DETECTION WITH CONVOLUTIONAL NEURAL NETWORKS (2008)

Text detection is an important preliminary step before text can be recognized in unconstrained image environments. We present an approach based on convolutional neural networks to detect and localize horizontal text lines from raw color pixels. The network learns to extract and combine its own set of features through learning instead of using hand-crafted ones. Learning was also used in order to precisely localize the text lines by simply training the network to reject badly-cut text and without any use of tedious knowledge-based postprocessing. Although the network was trained with synthetic examples, experimental results demonstrated that it can outperform other methods on the real-world test set of ICDAR’03.
Infections after lung transplantation (2018)

The good clinical result of lung transplantation is constantly undermined by the high incidence of infection, which negatively impacts on function and survival. Moreover, infections may also have immunological interactions that play a role in the acute rejection and in the development of chronic lung allograft dysfunction. There is a temporal sequence in the types of infection that affects lung allograft: in the first postoperative month bacteria are the most frequent cause of infection; following this phase, cytomegalovirus and Pneumocystis carinii are common. Fungal infections are particularly feared due to their association with bronchial complication and high mortality. Scrupulous postoperative surveillance is mandatory for the successful management of lung transplantation patients with respect to early detection and treatment of infections. This paper is aimed to address clinicians in the management of the major infectious complications that affect the lung transplant population.
Transfers of 2-inch GaN films onto sapphire substrates using Smart Cut TM technology (2005)

For the first time, transfers of thin GaN films by means of the Smart Cut technology were demonstrated. Full wafer transfer of a 2-inch GaN layer from its original substrate onto a carrier sapphire wafer is reported.
THE ACID HYDROLYSIS OF GLYCOSIDES: I. GENERAL CONDITIONS AND THE EFFECT OF THE NATURE OF THE AGLYCONE (1964)

First-order rate coefficients and energies and entropies of activation have been determined for the acid-catalyzed hydrolysis of a number of methyl D-glycopyranosides and disaccharides. The relation between the logarithm of the rate coefficients and values for Hammett's acidity function was linear, although different for different acids. All compounds had entropies of activation indicating a unimolecular reaction mechanism. Glucosides of tertiary alcohols were hydrolyzed very rapidly, triethylmethyl β-D-glucopyranoside, for example, 30,000 times taster than the corresponding methyl compound.Increase in size of the aglycone caused a slight increase in the rate of hydrolysis of β-D-glucopyranosides, steric hindrance thus being of no significance. Electron-attracting substituents in the aglycone had little or no influence on the rate of hydrolysis, obviously because they would tend to lower the equilibrium concentration of the conjugate acid, while facilitating the subsequent heterolysis, the two opposing effects more or less cancelling out. These results were discussed in connection with recent studies on the acid hydrolysis of various phenyl glycopyranosides and with reference to the postulated occurrence of an activating inductive effect in oligo- and poly-saccharides containing carboxyl or other electronegative groups at C-5. It was concluded that there is little evidence for the existence of any such effect and that, for example, pseudoaldobiouronic acids should be hydrolyzed at the same rate as corresponding neutral disaccharides.
Muscarinic M1 agonists in the treatment of Alzheimer’s disease (2000)

The treatment of Alzheimer’s disease attempts to correct cholinergic deficiency in the brain. In addition to the established, but restricted, efficacy of acetylcholinesterase inhibitors, attempts are being made to develop agents which will stimulate muscarinic receptors directly. This approach is logical and was found efficacious in several animal models of the disease; however none of these agents succeeded in clinical studies. Several reasons might account for this failure, which are discussed, as well as the prospects for the future.
Truncated forms of human complement factor H (1989)

By the use of Western-blot analyses with polyclonal anti-(Factor H) antibodies, two low-Mr protein species of Mr 41,000 and 37,000 under non-reducing conditions and 43,000 and 40,000 under reducing conditions are consistently detected together with the well-known 155,000-Mr Factor H in human plasma and serum. These two additional species are also found in plasma, urine and synovial fluids. The 41,000-Mr species but not the 37,00-Mr species is detected by a monoclonal anti-(Factor H) antibody directed at the N-terminal part of Factor H. The 37,000-Mr species but not the 41,000-Mr species is detected by a monoclonal anti-(Factor H) antibody directed at the C-terminal part of Factor H. The 41,000-Mr and 37,000-Mr species are different from the well-characterized 36,000-Mr N-terminal tryptic fragment of Factor H. They are likely to represent translational products of the short Factor H mRNA species of 1.8 kb and 1.2-1.5 kb occurring in human liver that we have recently described.
As-rigid-as-possible shape interpolation (2000)

We present an object-space morphing technique that blends the interiors of given two- or three-dimensional shapes rather than their boundaries. The morph is rigid in the sense that local volumes are least-distorting as they vary from their source to target configurations. Given a boundary vertex correspondence, the source and target shapes are decomposed into isomorphic simplicial complexes. For the simplicial complexes, we find a closed-form expression allocating the paths of both boundary and interior vertices from source to target locations as a function of time. Key points are the identification of the optimal simplex morphing and the appropriate definition of an error functional whose minimization defines the paths of the vertices. Each pair of corresponding simplices defines an affine transformation, which is factored into a rotation and a stretching transformation. These local transformations are naturally interpolated over time and serve as the basis for composing a global coherent least-distorting transformation.
The "bystander effect": tumor regression when a fraction of the tumor mass is genetically modified. (1993)

Tumor cells expressing the herpes simplex virus thymidine kinase (HSV-TK) gene are sensitive to the drug ganciclovir (GCV). We demonstrate here that HSV-TK-positive cells exposed to GCV were lethal to HSV-TK-negative cells as a result of a "bystander effect." HSV-TK-negative cells were killed in vitro when the population of cultured cells contained only 10% HSV-TK-positive cells. The mechanism of this "bystander effect" on HSV-TK-negative cells appeared to be related to the process of apoptotic cell death when HSV-TK-positive cells were exposed to GCV. Flow cytometric and electron microscopic analyses suggested that apoptotic vesicles generated from the dying gene-modified cells were phagocytized by nearby, unmodified tumor cells. Prevention of apoptotic vesicle transfer prevented the bystander effect. The toxic effect of HSV-TK-positive cells on HSV-TK-negative cells was reproduced in an in vivo model. A mixed population of tumor cells consisting of HSV-TK-positive and HSV-TK-negative cells was inoculated s.c. into mice. Regression of the tumor mass occurred when the inoculum consisted of as few as 10% HSV-TK-expressing tumor cells. The bystander effect was also demonstrated in i.p. tumor studies. Initial experiments demonstrated that prolonged survival (> 70 days) occurred when a mixture containing 50% HSV-TK-positive and 50% HSV-TK-negative cells was injected i.p. followed by GCV treatment. Further, survival was prolonged for mice with a preexisting HSV-TK-negative i.p. tumor burden by injecting HSV-TK-positive cells and GCV. These results suggest that genetic modification of tumor cells may be useful for developing cancer therapies.