gebhart/patrepeval huggingface dataset:
An adaptive decorrelation method removes Illumina DNA base-calling errors caused by crosstalk between adjacent clusters (2017)

Base-calling accuracy is crucial for high-throughput DNA sequencing and downstream analysis such as read mapping and genome assembly. Accordingly, we made an endeavor to reduce DNA sequencing errors of Illumina systems by correcting three kinds of crosstalk in the cluster intensity data. We discovered that signal crosstalk between adjacent clusters accounts for a large portion of sequencing errors in Illumina systems, even after correcting color crosstalk caused by the overlap of dye emission spectra and phasing/pre-phasing caused by out-of-step nucleotide synthesis. Interestingly and importantly, spatial crosstalk between adjacent clusters is cluster-specific and often asymmetric, which cannot be corrected by existing deconvolution methods. Therefore, we introduce a novel mathematical method able to estimate and remove spatial crosstalk, thereby reducing base-calling errors by 44-69% at a given mapping rate from Illumina systems. Furthermore, the resolution gained from this work provides new room for higher throughput of DNA sequencing and of general measurement systems using fluorescence-based imaging technology. The resulting base-caller 3Dec is available for academic users at http://github.com/flishwnag/3dec. Not only does it reduce 62.1% errors compared to the standard pipeline, but also its implementation is fast enough for daily sequencing.
Developmental Normative Data on The Test of Variables of Attention (T.O.V.A.™) (1993)

Developmental normative data for 775 children aged 6-16 are presented for the Test of Variables of Attention (T.O.V.A.), a 23-minute fixed-interval visual Continuous Performance Test with minimal language demands and no left-right discrimination. The target is presented on 22.5% and 77.5% of the trials during the first and second halves, respectively, T.O.V.A. indices include omission and commission errors, response time means and standard deviations, and anticipatory responses. Attention and impulse control developed in a non-linear manner, changing rapidly in early childhood and leveling off during later childhood and adolescence.
Cloning of an Interleukin-3 Receptor Gene: a Member of a Distinct Receptor Gene Family (1990)

Interleukin-3 (IL-3) binds to its receptor with high and low affinities, induces tyrosine phosphorylation, and promotes the proliferation and differentiation of hematopoietic cells. A binding component of the IL-3 receptor was cloned. Fibroblasts transfected with the complementary DNA bound IL-3 with a low affinity [dissociation constant (Kd) of 17.9 +/- 3.6 nM]. No consensus sequence for a tyrosine kinase was present in the cytoplasmic domain. Thus, additional components are required for a functional high affinity IL-3 receptor. A sequence comparison of the IL-3 receptor with other cytokine receptors (erythropoietin, IL-4, IL-6, and the beta chain IL-2 receptor) revealed a common motif of a distinct receptor gene family.
EESEN: End-to-End Speech Recognition using Deep RNN Models and WFST-based Decoding (2015)

The performance of automatic speech recognition (ASR) has improved tremendously due to the application of deep neural networks (DNNs). Despite this progress, building a new ASR system remains a challenging task, requiring various resources, multiple training stages and significant expertise. This paper presents our Eesen framework which drastically simplifies the existing pipeline to build state-of-the-art ASR systems. Acoustic modeling in Eesen involves learning a single recurrent neural network (RNN) predicting context-independent targets (phonemes or characters). To remove the need for pre-generated frame labels, we adopt the connectionist temporal classification (CTC) objective function to infer the alignments between speech and label sequences. A distinctive feature of Eesen is a generalized decoding approach based on weighted finite-state transducers (WFSTs), which enables the efficient incorporation of lexicons and language models into CTC decoding. Experiments show that compared with the standard hybrid DNN systems, Eesen achieves comparable word error rates (WERs), while at the same time speeding up decoding significantly.
Mammalian cell biotechnology. A practical approach. (1991)

M. Butler: The characteristics and growth of cultured cells A. MacLeod: Serum and its fractionation N. Jenkins: Growth factors C. MacDonald: Genetic engineering of animal cells A. Dickson: Protein expression and processing C. Harbour & A. Fletcher: Hybridomas: production and selection A. Handa-Corrigan: Bioreactor design D. Kilburn: Monitoring and control of bioreactors A. Lyddiatt: Downstream processing protein recovery B. Griffiths: Products from animal cells
Simultaneous Mechanical Loading and Confocal Reflection Microscopy for Three-Dimensional Microbiomechanical Analysis of Biomaterials and Tissue Constructs (2003)

At present, mechanisms by which specific structural and mechanical properties of the three-dimensional extracellular matrix microenvironment influence cell behavior are not known. Lack of such knowledge precludes formulation of engineered scaffolds or tissue constructs that would deliver specific growth-inductive signals required for improved tissue restoration. This article describes a new mechanical loading-imaging technique that allows investigations of structural-mechanical properties of biomaterials as well as the structural-mechanical basis of cell-scaffold interactions at a microscopic level and in three dimensions. The technique is based upon the integration of a modified, miniature mechanical loading instrument with a confocal microscope. Confocal microscopy is conducted in a reflection and/or fluorescence mode for selective visualization of load-induced changes to the scaffold and any resident cells, while maintaining each specimen in a "live," fully hydrated state. This innovative technique offers several advantages over current biomechanics methodologies, including simultaneous visualization of scaffold and/or cell microstructure in three dimensions during mechanical loading; quantification of macroscopic mechanical parameters including true stress and strain; and the ability to perform multiple analyses on the same specimen. This technique was used to determine the structural-mechanical properties of three very different biological materials: a reconstituted collagen matrix, a tissue-derived biomaterial, and a tissue construct representing cells and matrix.
Chiral Heterocylic Carbenes in Asymmetric Homogeneous Catalysis (1996)

The ee values of the hydrosilylation of acetophenone with the rhodium catalyst 1 are only small; nevertheless, the robustness of the catalyst is impressive: The chiral carbene ligand, which is readily available and can be easily varied, remains bound to the metal in solution to over 100°C. Thus, no excess of ligand is necessary in the catalytic reactions.
Macrophage uptake of cholesterol-containing particles derived from LDL and isolated from atherosclerotic lesions (1990)

A variety of different cholesterol-rich particles with different physical and chemical structures can be isolated from human atherosclerotic lesions. Many of these particles are internalized in an unregulated fashion by macrophages in culture, leading to lipid loading of these cells. However, the in vivo relevance of this uptake is still uncertain. In this overview, we have summarized data obtained primarily in our laboratory on low density lipoprotein (LDL)-like particles (A-LDL) and large cholesterol-rich droplets isolated from human atherosclerotic lesions. Based on our studies, we propose a variety of different mechanisms of uptake. A-LDL can be internalized by the LDL receptor or the scavenger receptor on macrophages in culture; the latter uptake mechanism can lead to lipid loading. In addition, at high concentrations A-LDL can undergo aggregation, possibly due to intermolecular cross-bridging by aldehydes released during oxidation of these particles. The aggregates are subsequently internalized by macrophages by phagocytosis, a process which appears to be independent of the LDL or scavenger receptor. By contrast, arterial smooth muscle cells do not take up these aggregates. Large cholesteryl ester-rich particles isolated from human lesions, and derived from LDL that had been degraded by hydrolytic enzymes in the extracellular space of the arterial wall, or from inclusions released from lysed foam cells, are also internalized via phagocytosis by macrophages in culture. Since some of these particles contain apoliproteins and/or proteins that are ligands for receptors on macrophages, initial receptor-mediated binding may precede and facilitate subsequent phagocytosis in some cases. Uptake of the diverse group of cholesteryl ester-rich particles in plaques can induce lipid loading of macrophages and therefore may lead to further growth of the atherosclerotic plaque.
New Flu Antiviral Candidate May Thwart Drug Resistance (2020)

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 HomeNew OnlineCurrent IssueFor Authors Podcasts Clinical Reviews Editors' Summary Medical News Author Interviews More 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 journal
Effect of Clostridium difficile toxin A on human intestinal epithelial cells: induction of interleukin 8 production and apoptosis after cell detachment. (1996)

Clostridium difficile is the aetiological agent of pseudomembranous colitis, and animal studies suggest the essential role of secreted toxin A in inducing disease. This study examined the biological responses to toxin A by human intestinal epithelial cells. Confluent monolayers of Caco2, HT29, and T84 cells and primary epithelial cells in organ cultures of human colonic biopsy specimens and after detachment with EDTA were studied. Interleukin 8 was assayed using enzyme linked immunosorbent assay (ELISA). Purified C difficile toxin A induced cell rounding and detachment of monolayers of the epithelial cell lines. Cells in detached monolayers initially remained viable while adherent to each other. Subsequently, an increasing number of apoptotic cells appeared in suspension. Exposure to toxin A for 24 hours induced interleukin 8 production in T84 and HT29 cells. Toxin A also induced epithelial cell rounding, detachment, and apoptosis in organ cultures of human colonic biopsy specimens. During culture (in medium only), EDTA detached colonic epithelial cells produced interleukin 8 and cell death occurred by apoptosis. Colonic disease by C difficile may be initiated by toxin A mediated induction of epithelial cell interleukin 8 production and apoptosis after cell detachment from the basement membrane. Studies on isolated (toxin untreated) colonic epithelial cells suggest that interleukin 8 production and apoptosis occur as a consequence of cell injury and detachment.
Noninvasive FFR derived from coronary CT angiography in the management of coronary artery disease: technology and clinical update (2016)

After a decade of clinical use of coronary computed tomographic angiography (CCTA) to evaluate the anatomic severity of coronary artery disease, new methods of deriving functional information from CCTA have been developed. These methods utilize the anatomic information provided by CCTA in conjunction with computational fluid dynamics to calculate fractional flow reserve (FFR) values from CCTA image data sets. Computed tomography-derived FFR (CT-FFR) enables the identification of lesion-specific drop noninvasively. A three-dimensional CT-FFR modeling technique, which provides FFR values throughout the coronary tree (HeartFlow FFRCT analysis), has been validated against measured FFR and is now approved by the US Food and Drug Administration for clinical use. This technique requires off-site supercomputer analysis. More recently, a one-dimensional computational analysis technique (Siemens cFFR), which can be performed on on-site workstations, has been developed and is currently under investigation. This article reviews CT-FFR technology and clinical evidence for its use in stable patients with suspected coronary artery disease.
Transcriptional Profiling of Cross Pathway Control in Neurospora crassa and Comparative Analysis of the Gcn4 and CPC1 Regulons (2007)

Identifying and characterizing transcriptional regulatory networks is important for guiding experimental tests on gene function. The characterization of regulatory networks allows comparisons among both closely and distantly related species, providing insight into network evolution, which is predicted to correlate with the adaptation of different species to particular environmental niches. One of the most intensely studied regulatory factors in the yeast Saccharomyces cerevisiae is the bZIP transcription factor Gcn4p. Gcn4p is essential for a global transcriptional response when S. cerevisiae experiences amino acid starvation. In the filamentous ascomycete Neurospora crassa, the ortholog of GCN4 is called the cross pathway control-1 (cpc-1) gene; it is required for the ability of N. crassa to induce a number of amino acid biosynthetic genes in response to amino acid starvation. Here, we deciphered the CPC1 regulon by profiling transcription in wild-type and cpc-1 mutant strains with full-genome N. crassa 70-mer oligonucleotide microarrays. We observed that at least 443 genes were direct or indirect CPC1 targets; these included 67 amino acid biosynthetic genes, 16 tRNA synthetase genes, and 13 vitamin-related genes. Comparison among the N. crassa CPC1 transcriptional profiling data set and the Gcn4/CaGcn4 data sets from S. cerevisiae and Candida albicans revealed a conserved regulon of 32 genes, 10 of which are predicted to be directly regulated by Gcn4p/CPC1. The 32-gene conserved regulon comprises mostly amino acid biosynthetic genes. The comparison of regulatory networks in species with clear orthology among genes sheds light on how gene interaction networks evolve.
Cyclosporin A in rheumatoid arthritis: overview of efficacy. (1993)

Five clinical trials of cyclosporin A (CyA) in the treatment of RA were reviewed and an initial evaluation made of clinical endpoints across the studies. A composite effect score for efficacy and the rates of dropout due to toxicity were each compared to earlier meta-analyses evaluating the relative efficacy and toxicity of second-line drugs for RA. The overall percentage improvements over a 6-month assessment period for the various clinical endpoints were all found to meet a minimal clinical improvement of 20%: tender joints, 20%; grip strength, 22%; swollen joints, 29%; functional index, 29%; morning stiffness, 40%; and CRP, 45%. The exception was ESR (16%). The composite effect for CyA indicated significant improvement over placebo (P < 0.001). This effect in excess of placebo was in the range of that found for antimalarial drugs. The toxicity associated with CyA was similar to that found with drugs with low toxicity, such as auranofin. A more detailed analysis using individual patient data and the results of two studies is planned.
The PFA-100 (2005)

The PFA-100 is a laboratory test designed to measure platelet function. Adequate platelet function depends upon the platelet's ability to adhere to the site of endothelial injury, activate surface receptors to attract other platelets and aggregate or clump together to form a platelet plug. This process is necessary to stop bleeding but may be harmful if it causes occlusion of a vessel. Platelet altering medication therapy is widely used in the prevention and treatment of coronary artery disease, peripheral arterial occlusive disease, and cerebrovascular ischemia. The PFA-100 provides the clinician with valuable information about platelet function. This information is helpful in determining the therapeutic effectiveness of antiplatelet medications, assisting in evaluating risk of bleeding and identifying primary platelet dysfunction.
The Non-JAZ TIFY Protein TIFY8 from Arabidopsis thaliana Is a Transcriptional Repressor (2014)

Jasmonate (JA) signalling is mediated by the JASMONATE-ZIM DOMAIN (JAZ) repressor proteins, which are degraded upon JA perception to release downstream responses. The ZIM protein domain is characteristic of the larger TIFY protein family. It is currently unknown if the atypical member TIFY8 is involved in JA signalling. Here we show that the TIFY8 ZIM domain is functional and mediated interaction with PEAPOD proteins and NINJA. TIFY8 interacted with TOPLESS through NINJA and accordingly acted as a transcriptional repressor. TIFY8 expression was inversely correlated with JAZ expression during development and after infection with Pseudomonas syringae. Nevertheless, transgenic lines with altered TIFY8 expression did not show changes in JA sensitivity. Despite the functional ZIM domain, no interaction with JAZ proteins could be found. In contrast, TIFY8 was found in protein complexes involved in regulation of dephosphorylation, deubiquitination and O-linked N-acetylglucosamine modification suggesting an important role in nuclear signal transduction.
A Prospective, Randomized Trial of Autologous Bone Marrow Transplantation and Chemotherapy in Multiple Myeloma (1996)

High-dose therapy combined with transplantation improves the response rate, eventfree survival, and overall survival in patients with myeloma.
Progressive multifocal leukoencephalopathy in transplant recipients (2011)

The risk of PML exists throughout the posttransplantation period. Bone marrow recipients survive longer than solid organ recipients but may have a lower median time to first symptoms of PML. Posttransplantation PML has a higher case fatality and may have a higher incidence than reported in human immunodeficiency virus (HIV) patients on highly-active antiretroviral therapy (HAART) or multiple sclerosis patients treated with natalizumab.
Pilot Testing of a Radio Frequency Heating System for Enhanced Oil Recovery From Diatomaceous Earth (1994)

Abstract This paper describes a high power, full scale field demonstration of a radio frequency (RF) downhole applicator system which has the objective of ultimately expanding the scope of Texaco’s thermal operations beyond conventional operations. Field testing of KAI Technologies radio frequency heating system was performed in the Texaco Denver Producing Division’s Midway area, N. Midway field, CA, in a shallow diatomite reservoir during the summer of 1992. Two tests (a low power test and a high power test), gave every indication that RF technology is a viable way of heating a formation.
Receptor Binding Transforms the Surface Subunit of the Mammalian C-Type Retrovirus Envelope Protein from an Inhibitor to an Activator of Fusion (2001)

The envelope protein (Env) of murine leukemia viruses (MLVs) is composed of a surface subunit (SU) and a transmembrane subunit (TM), which mediates membrane fusion, resulting in infection. SU contains a discrete N-terminal receptor binding domain (RBD) that is connected to the remainder of Env by a short, proline-rich segment. Previous studies suggest that after receptor binding, the RBD interacts directly with the remainder of Env to trigger fusion (A. L. Barnett, R. A. Davey, and J. M. Cunningham, Proc. Natl. Acad. Sci. USA 98:4113-4118, 2001). To investigate the role of the RBD in activating fusion, we compared infection by several MLVs that are defective unless rescued in trans by the addition of soluble RBD to the culture medium. Infection by MLV lacking a critical histidine residue near the N terminus of the viral RBD is dependent on the expression of receptors for both the RBD in the viral Env and the soluble RBD supplied in trans. However, infection by MLVs in which the RBD has been deleted or replaced by the ligand erythropoietin are dependent only on expression of the receptor for the soluble RBD. We were able to expand the host range of xenotropic MLV to nonpermissive murine fibroblasts only if the RBD was deleted from the xenotropic viral envelope and the soluble RBD from ecotropic Friend MLV was supplied to the culture medium. These findings indicate that receptor binding transforms the RBD from an inhibitor to an activator of the viral fusion mechanism and that viruses lacking the critical histidine residue at the N terminus of the RBD are impaired at the activation step.
Rate conversion of MPEG coded video by re-quantization process (2002)

We propose rate conversion method by re-quantization in which MPEG coded video at high bit rate is converted into the MPEG bitstream at a lower bit rate without decoding to obtain the reconstructed picture. The quantization step required for re-quantization is determined by the local and global quantization steps which are closely related to the activities in the pixel domain. The simulation results show that very similar rate distortion curves to those of transcoding have been obtained, and the difference in SNR is relatively small, about 0.4 dB at 1 Mbit/s in MPEG1 using a master bitstream at 4 Mbit/s, and 1 dB at 3 Mbit/s in MPEG2 using a master at 9 Mbit/s. Since the proposed method is very simple and requires much less hardware implementation cost than transcoding, it has a significant advantage as a rate conversion tool.
Patterned Delivery of Immunoglobulins to Surfaces Using Microfluidic Networks (1997)

Microfluidic networks (microFNs) were used to pattern biomolecules with high resolution on a variety of substrates (gold, glass, or polystyrene). Elastomeric microFNs localized chemical reactions between the biomolecules and the surface, requiring only microliters of reagent to cover square millimeter-sized areas. The networks were designed to ensure stability and filling of the microFN and allowed a homogeneous distribution and robust attachment of material to the substrate along the conduits in the microFN. Immunoglobulins patterned on substrates by means of microFNs remained strictly confined to areas enclosed by the network with submicron resolution and were viable for subsequent use in assays. The approach is simple and general enough to suggest a practical way to incorporate biological material on technological substrates.
PROPERTIES OF THE RETINAL BINDING SITE IN BACTERIORHODOPSIN. USE OF RETINOL AND RETINYL MOIETIES AS FLUORESCENT PROBES (1978)

Abstract— The fluorescence spectra of various reduced bacteriorhodopsin chromophore species indicate energy transfer from aromatic amino acid side chains of the protein to the retinyl moiety. Binding studies with retinol reveal that energy transfer occurs only when the retinyl moiety is bound in the chromophoric site of the protein. Retroretinol is a fluorescent probe for the binding site.