gebhart/patrepeval huggingface dataset:
CRISPR-Cas9: Tool for Qualitative and Quantitative Plant Genome Editing (2016)

Recent developments in genome editing techniques have aroused substantial excitement among agricultural scientists. These techniques offer new opportunities for developing improved plant lines with addition of important traits or removal of undesirable traits. Increased adoption of genome editing has been geared by swiftly developing Clustered regularly interspaced short palindromic repeats (CRISPR). This is appearing as driving force for innovative utilization in diverse branches of plant biology. CRISPR-Cas9 mediated genome editing is being used for rapid, easy and efficient alteration of genes among diverse plant species. With approximate completion of conceptual work about CRISPR-Cas9, plant scientists are applying this genome editing tool for crop attributes enhancement. The capability of this system for performing targeted and efficient modifications in genome sequence as well as gene expression will certainly spur novel developments not only in model plants but in crop and ornamental plants as well. Additionally, due to non-involvement of foreign DNA, this technique may help alleviating regulatory issues associated with genetically modified plants. We expect that prevailing challenges in plant science like genomic region manipulation, crop specific vectors etc. will be addressed along with sustained growth of this genome editing tool. In this review, recent progress of CRISPR-Cas9 technology in plants has been summarized and discussed. We reviewed significance of CRISPR-Cas9 for specific and non-traditional aspects of plant life. It also covers strengths of this technique in comparison with other genome editing techniques, e.g., Zinc finger nucleases, Transcription activator-like effector nucleases and potential challenges in coming decades have been described.
iBump: Smartphone application to detect car accidents (2014)

Traffic accidents are a fact of life. While accidents are sometimes unavoidable, studies show that the long response time required for emergency responders to arrive is a primary reason behind increased fatalities in serious accidents. One way to reduce this response time is to reduce the amount of time it takes to report an accident. Smartphones are ubiquitous and with network connectivity are perfect devices to immediately inform relevant authorities about the occurrence of an accident. This paper presents the development of a system that uses smartphones to automatically detect and report car accidents in a timely manner. Data is continuously collected from the smartphone's accelerometer and analyzed using Dynamic Time Warping (DTW) to determine the severity of the accident, reduce false positives and to notify first responders of the accident location and owner's medical information. In addition, accidents can be viewed on the smartphone over the Internet offering instant and reliable access to the information concerning the accident. By implementing this application and adding a notification system, the response time required to notify emergency responders of traffic accidents can reduce the response time and perhaps help in reducing fatalities.
Genetic diagnosis of haemophilia and other inherited bleeding disorders (2006)

Inherited deficiencies of plasma proteins involved in blood coagulation generally lead to lifelong bleeding disorders, whose severity is inversely proportional to the degree of factor deficiency. Haemophilia A and B, inherited as X-linked recessive traits, are the most common hereditary hemorrhagic disorders caused by a deficiency or dysfunction of blood coagulation factor VIII (FVIII) and factor IX (FIX). Together with von Willebrand's disease, a defect of primary haemostasis, these X-linked disorders include 95% to 97% of all the inherited deficiencies of coagulation factors. The remaining defects, generally transmitted as autosomal recessive traits, are rare with prevalence of the presumably homozygous forms in the general population of 1:500,000 for FVII deficiency and 1 in 2 million for prothrombin (FII) and factor XIII (FXIII) deficiency. Molecular characterization, carrier detection and prenatal diagnosis remain the key steps for the prevention of the birth of children affected by coagulation disorders in developing countries, where patients with these deficiencies rarely live beyond childhood and where management is still largely inadequate. These characterizations are possible by direct or indirect genetic analysis of genes involved in these diseases, and the choice of the strategy depends on the effective available budget and facilities to achieve a large benefit. In countries with more advanced molecular facilities and higher budget resources, the most appropriate choice in general is a direct strategy for mutation detection. However, in countries with limited facilities and low budget resources, carrier detection and prenatal diagnosis are usually performed by linkage analysis with genetic markers. This article reviews the genetic diagnosis of haemophilia, genetics and inhibitor development, genetics of von Willebrand's disease and of rare bleeding disorders.
Data fusion (2009)

The amount of information produced in the world increases by 30% every year and this rate will only go up. With advanced network technology, more and more sources are available either over the Internet or in enterprise intranets. Modern data management applications, such as setting up Web portals, managing enterprise data, managing community data, and sharing scientific data, often require integrating available data sources and providing a uniform interface for users to access data from different sources; such requirements have been driving fruitful research on data integration over the last two decades [11, 13].
58.3: Fabrication of Zinc Tin Oxide TFTs by Self‐Aligned Imprint Lithography (SAIL) on Flexible Substrates (2009)

Abstract Zinc tin oxide (ZTO) thin‐film transistors (TFTs) provide attractive performance and are suitable for low‐temperature processes compatible with flexible “plastic” substrates. We report our progress in integrating ZTO into our SAIL process to produce high‐performance TFT on flexible substrates.
Superhydrophobicity on Two-Tier Rough Surfaces Fabricated by Controlled Growth of Aligned Carbon Nanotube Arrays Coated with Fluorocarbon (2005)

Considerable effort has been expended on theoretical studies of superhydrophobic surfaces with two-tier (micro and nano) roughness, but experimental studies are few due to the difficulties in fabricating such surfaces in a controllable way. The objective of this work is to experimentally study the wetting and hydrophobicity of water droplets on two-tier rough surfaces for comparison with theoretical analyses. To compare wetting on micropatterned silicon surfaces with wetting on nanoscale roughness surfaces, two model systems are fabricated: carbon nanotube arrays on silicon wafers and carbon nanotube arrays on carbon nanotube films. All surfaces are coated with 20 nm thick fluorocarbon films to obtain low surface energies. The results show that the microstructural characteristics must be optimized to achieve stable superhydrophobicity on microscale rough surfaces. However, the presence of nanoscale roughness allows a much broader range of surface design criteria, decreases the contact angle hysteresis to less than 1 degrees , and establishes stable and robust superhydrophobicity, although nanoscale roughness could not increase the apparent contact angle significantly if the microscale roughness dominates.
Structure of Thioaromatic Self-Assembled Monolayers on Gold and Silver (2001)

Self-assembled monolayers (SAMs) formed from thiophenol, 1,1‘-biphenyl-4-thiol, 1,1‘;4‘,1‘ ‘-terphenyl-4-thiol, and anthracene-2-thiol on polycrystalline Au and Ag were characterized by X-ray photoelectron spectroscopy and angle-resolved near-edge X-ray absorption fine structure spectroscopy. With the exception of the poorly defined thiophenol film on Au, all thioaromatic molecules were found to form highly oriented and densely packed SAMs on both substrates. The molecular orientation and orientational order of the adsorbed thioaromatic molecules depends on the number of aromatic rings, the substrate, and the rigidity of the aromatic system. The molecules, which on average are slightly inclined with respect to the surface normal, show a less tilted orientation with increasing length of the aromatic chain, and as observed for aliphatic SAMs, they exhibit smaller tilt angles on Ag than on Au. However, the difference in the tilt angles for aromatic SAMs on Au and Ag is smaller than that observed in the aliphatic films. A comparison of the monolayers formed from p-terphenylthiol and anthracenethiol films suggests that a higher molecular rigidity has only a slight effect on the final molecular orientation within the respective SAMs.
Cellular uptake and intracellular trafficking of long chain fatty acids (1999)

While aspects of cellular fatty acid uptake have been studied as early as 50 years ago, recent developments in this rapidly evolving field have yielded new functional insights on the individual mechanistic steps in this process. The extremely low aqueous solubility of long chain fatty acids (LCFA) together with the very high affinity of serum albumin and cytoplasmic fatty acid binding proteins for LCFA have challenged the limits of technology in resolving the individual steps of this process. To date no single mechanism alone accounts for regulation of cellular LCFA uptake. Key regulatory points in cellular uptake of LCFA include: the aqueous solubility of the LCFA; the driving force(s) for LCFA entry into the cell membrane; the relative roles of diffusional and protein mediated LCFA translocation across the plasma membrane; cytoplasmic LCFA binding protein-mediated uptake and/or intracellular diffusion; the activity of LCFA-CoA synthetase; and cytoplasmic protein mediated targeting of LCFA or LCFA-CoAs toward specific metabolic pathways. The emerging picture is that the cell has multiple, overlapping mechanisms that assure adequate uptake and directed intracellular movement of LCFA required for maintenance of physiological functions. The upcoming challenge is to take advantage of new advances in this field to elucidate the differential interactions between these pathways in intact cells and in tissues.
Control of fetal hemoglobin: new insights emerging from genomics and clinical implications (2009)

Increased levels of fetal hemoglobin (HbF, alpha(2)gamma(2)) are of no consequence in healthy adults, but confer major clinical benefits in patients with sickle cell anemia (SCA) and beta thalassemia, diseases that represent major public health problems. Inter-individual HbF variation is largely genetically controlled, with one extreme caused by mutations involving the beta globin gene (HBB) complex, historically referred to as pancellular hereditary persistence of fetal hemoglobin (HPFH). These Mendelian forms of HPFH are rare and do not explain the common form of heterocellular HPFH which represents the upper tail of normal HbF variation, and is clearly inherited as a quantitative genetic trait. Genetic studies have identified three major quantitative trait loci (QTLs) (Xmn1-HBG2, HBS1L-MYB intergenic region on chromosome 6q23, and BCL11A on chromosome 2p16) that account for 20-50% of the common variation in HbF levels in patients with SCA and beta thalassemia, and in healthy adults. Two of the major QTLs include oncogenes, emphasizing the importance of cell proliferation and differentiation as an important contribution to the HbF phenotype. The review traces the story of HbF quantitative genetics that uncannily mirrors the changing focus in genetic methodology, from candidate genes through positional cloning, to genome-wide association, that have expedited the dissection of the genetic architecture underlying HbF variability. These genetic results have already provided remarkable insights into molecular mechanisms that underlie the hemoglobin 'switch'.
Bamiphylline improves exercise-induced myocardial ischemia through a novel mechanism of action. (1993)

In patients with stable angina pectoris, oral administration of bamiphylline improves exercise capacity. Its anti-ischemic action does not appear to be mediated by systemic hemodynamic effects or by stenosis dilation. Therefore, the improvement of myocardial ischemia caused by bamiphylline is probably due to redistribution of coronary blood flow toward the underperfused subendocardium. This novel anti-ischemic action would appear to be mediated by antagonism of A1 receptors.
Novel and Emerging Drugs for Acute Myeloid Leukemia (2012)

Acute myeloid leukemia (AML) is a challenging disease to treat with the majority of patients dying from their illness. While overall survival has been markedly prolonged in acute promyelocytic leukemia (APL), survival in younger adults with other subtypes of AML has only modestly improved over the last twenty years. Physicians who treat AML eagerly await drugs like Imatinib for chronic myeloid leukemia, Cladribine for hairy cell leukemia, and Rituximab for non-Hodgkin Lymphoma which have had an important impact on improving outcome. Recent research efforts have focused on refining traditional chemotherapeutic agents to make them more active in AML, targeting specific genetic mutations in myeloid leukemia cells, and utilizing novel agents such as Lenalidomide that have shown activity in other hematologic malignancies. Here, we focus on reviewing the recent literature on agents that may assume a role in clinical practice for patients with AML over the next five years.
Probe labeling and hybridization techniques (1993)

7. Labelling of probes and their detection: 7.1 Choice of label and labelling method. 7.2 Radioisotopic labelling and detection of nucleic acids. 7.3 Non-radioactive primary labels. 7.4 Recognition systems. 7.5 Overview of enzymatic incorporation of labels into probes. 7.6 Uniform incorporation of labels in nucleic acids. 7.7 End-labelling of probes. 7.8 Chemical modification of probes to introduce labels. 7.9 Universal probes. 7.10 Biological probes. 8. Mixed-phase and solution hybridization formats: 8.1 Materials and solutions. 8.2 Slot/dot blot hybridization on membranes. 8.3 (Semi)-solution hybridization. 9. Hybridization after electrophoretic fractionation of nucleic acids: 9.1 Electrophoretic procedures. 9.2 Transfer procedures. 9.3 Hybridization in the gel or before electrophoresis. 10. Colony and plaque lift hybridization: 10.1 Colony and plaque hybridization - different approaches. 10.2 Colony hybridization. 10.3 Plaque hybridization. 10.4 Hybridization to colony or plaque nucleic acids. 10.5 Selection, packing and purification of clones. 11. In situ hybridization: 11.1 Theoretical considerations. 11.2 Cytological procedures 11.3 Hybridization procedures. 11.4 Emerging in situ hybridization techniques. 12. Selected applications of hybridization: 12.1 Aims of subtractive or suppression hybridization. 12.2 Hybrid selection of mRNA. 12.3 S1 analysis of mRNA and DNA probes. 12.4 RNase protection assays. 12.5 Triple helices. 12.6 Current developments and prospects.
Towards minimized gonadotropins with full bioactivity (1999)

Gonadotropins are highly complex glycoprotein hormones consisting of two noncovalently associated subunits, which are heavily glycosylated. Using the X-ray structure of human choriogonadotropin and structure/activity relationships we aimed to design 'minimized' gonadotropins of reduced complexity. Our results show that it is possible to reduce the size of natural human choriogonadotropin by one-third of its molecular weight while retaining its wild-type biopotency. To our knowledge, such 'mini'-human choriogonadotropins represent the smallest gonadotropins described so far with an lutropin/choriogonadotropin receptor affinity and in vitro biological activity comparable with that of natural human choriogonadotropin. It provides an important step towards the structure/function-based design of small molecule drugs to the human gonadotropin receptors.
Managing energy consumption costs in desktop PCs and LAN switches with proxying, split TCP connections, and scaling of link speed (2005)

Abstract The IT equipment comprising the Internet in the USA uses about $6 billion of electricity every year. Much of this electricity use is wasted on idle, but fully powered‐up, desktop PCs and network links. We show how to recover a large portion of the wasted electricity with improved power management methods that are focused on network issues. Copyright © 2005 John Wiley &amp; Sons, Ltd.
Tissue-Engineered Composites of Anulus Fibrosus and Nucleus Pulposus for Intervertebral Disc Replacement (2004)

These results demonstrate the feasibility of creating a composite intervertebral disc with both anulusfibrosus and nucleus pulposus for clinical applications.
Components of a system that ligates cyclin to ubiquitin and their regulation by the protein kinase cdc2. (1994)

Cyclin B, a positive regulatory subunit of the cdc2 protein kinase complex, is synthesized across the cell cycle and then rapidly degraded at the end of mitosis. Degradation of cyclin B is triggered by increased levels of active cdc2 and is required for exit from mitosis. It was shown previously that cyclin degradation is carried out by the ubiquitin system, but the components responsible for the specificity and regulation of cyclin-ubiquitin ligation have not been identified. The formation of ubiquitin-protein conjugates usually requires the sequential action of three enzymes: a ubiquitin-activating enzyme (E1), a ubiquitin-carrier protein (E2), and a ubiquitin-protein ligase (E3). In this work we employed a fractionation approach to identify the components of a clam oocyte system responsible for specific ubiquitination of cyclin and to determine which components are regulated by cdc2. Experimental conditions were established under which a fusion protein containing an amino-terminal fragment of cyclin B is ligated to ubiquitin only in extracts from M-phase but not from interphase cells. Fractionation of M-phase extracts by DEAE-cellulose and high speed centrifugation yielded three fractions that were all required for cell cycle stage-specific cyclin-ubiquitin ligation. Only one of these fractions could be replaced by a previously known enzyme of the ubiquitin system, E1. A second fraction contained a novel species of E2, termed E2-C, which acts in the ligation of ubiquitin to cyclin but not to other endogenous proteins. A third component is associated with particulate material. Whereas E2-C from either M-phase or interphase extracts is active, the particulate component is active only in M-phase. Incubation of the particulate fraction from interphase cells with the protein kinase cdc2 activates it for cyclin-ubiquitin ligation, after a lag of about 30 min. These findings suggest that the particulate fraction may contain an E3 enzyme that acts on cyclin, as well as additional factors activated by cdc2.
Calibrations and the measurement uncertainty of wide-band liquid crystal thermography (2009)

Wide-band liquid crystal thermography is a high-resolution, non-intrusive optical technique for full-field temperature measurement. The paper presents comprehensive experimental results on the calibration and the measurement uncertainty for a thermochromic liquid crystal (TLC) with a bandwidth of 20 °C, examining the effects of the use of an image noise reduction technique, the lighting angle, the TLC coating thickness and the coating quality on the hue–temperature curve and the measurement uncertainty. It is found that combined with the image noise reduction technique of a 5 × 5 median filter, the measurement accuracy of the TLC can be significantly improved, and the high-accuracy usable bandwidth of the TLC can be considerably enlarged. The lighting angle has distinctive effects on the hue curve and the measurement uncertainty of the TLC, and a smaller lighting angle provides a smaller measurement uncertainty. The coating thickness has an appreciable effect on the TLC hue–temperature curve, but has a non-distinctive effect on the measurement uncertainty providing the coating thickness is over 20 µm. It is also found that the TLC coating quality has distinctive effects on the TLC hue curve and the measurement uncertainty. A finely prepared TLC coating produces a wider range of hue over the active temperature range, a considerably smaller measurement uncertainty and a larger high-accuracy usable bandwidth than the roughly prepared coating.
A flow cytometric immune function assay for human peripheral blood dendritic cells (2000)

CD11c+ and CD11c- (CD123+) dendritic cells (DCs) have been described in blood. Both cell types express high levels of HLA-DR and lack the lineage markers CD3, CD14, CD19, CD20, CD16, and CD56. These immunophenotypic properties were used along with analysis of activation-related surface antigens and intracellular staining of cytokines to characterize functional responses of these DC subsets to stimuli in whole human blood (WB). Samples from healthy donors were activated with lipopolysaccharide (LPS) or phorbol 12-myristate 13-acetate plus ionomycin (PMA+I). The only distinct response in CD11c- DCs was the expression of CD25 upon PMA+I activation. CD11c+ cells responded to LPS stimulation by producing high levels of interleukin-1beta (IL-1beta) and tumor necrosis factor alpha (TNF-alpha), and lower levels of IL-6, IL-1Ra, and IL-8 and an increased expression of accessory molecules (CD25, CD40, CD80, CD86, HLA-DR, and HLA-DQ). PMA+I activation of CD11c+ cells resulted in high levels of IL-1beta and lower levels of IL-8, IL-1Ra, and TNF-alpha and up-regulation of CD80, CD86, HLA-DR, and HLA-DQ. Our data support prior observations of functional differences between peripheral blood DC subsets and demonstrate the power of multiparameter flow cytometry to characterize the pleiotropic responses of these cells to various stimuli.
Effects of fish oil on cytokines and immune functions of mice with murine AIDS (1998)

The effects of fish oil, which is rich in n-3 fatty acids, on cytokine levels in a murine model of acquired immune deficiency syndrome (AIDS) were studied. Thirty-two C57BL/6 female mice were divided into two dietary groups and fed either a corn oil diet or a fish oil diet. After 4 weeks, each diet group was further divided into two subgroups, and mice in one subgroup were injected i.p. with LP-BM5 murine retrovirus (MAIDS) stock. After 4 weeks, all mice were killed, blood samples were collected, and the spleens and the livers were excised. Splenocytes were isolated immediately and cultured in RPMI-1640 medium and stimulated by either lipopolysaccharide (LPS) or Concanavalin A (ConA) for 24 h. The supernatant was collected for cytokine assays. The results showed that MAIDS infection increased the levels of tumor necrosis factor-alpha (TNF-alpha) and interleukin-1-beta (IL-1beta), while fish oil partially prevented this elevation. MAIDS infection depressed interleukin-2 (IL-2) and interferon-gamma (IFNgamma), while fish oil partially prevented the depression of IL-2. In addition, MAIDS infection depressed LPS- and ConA-stimulated cell proliferation, while fish oil partially prevented the depression. The results suggest that fish oil may slow down the progression of murine AIDS by modulating levels of cytokines including TNF-alpha, IL-1beta, and IL-2.