gebhart/patrepeval huggingface dataset:
Significance Analysis of Spectral Count Data in Label-free Shotgun Proteomics (2008)

Spectral counting has become a commonly used approach for measuring protein abundance in label-free shotgun proteomics. At the same time, the development of data analysis methods has lagged behind. Currently most studies utilizing spectral counts rely on simple data transforms and posthoc corrections of conventional signal-to-noise ratio statistics. However, these adjustments can neither handle the bias toward high abundance proteins nor deal with the drawbacks due to the limited number of replicates. We present a novel statistical framework (QSpec) for the significance analysis of differential expression with extensions to a variety of experimental design factors and adjustments for protein properties. Using synthetic and real experimental data sets, we show that the proposed method outperforms conventional statistical methods that search for differential expression for individual proteins. We illustrate the flexibility of the model by analyzing a data set with a complicated experimental design involving cellular localization and time course.
Wafer-scale MoS2 thin layers prepared by MoO3 sulfurization (2012)

Atomically thin molybdenum disulfide (MoS(2)) layers have attracted great interest due to their direct-gap property and potential applications in optoelectronics and energy harvesting. Meanwhile, they are extremely bendable, promising for applications in flexible electronics. However, the synthetic approach to obtain large-area MoS(2) atomic thin layers is still lacking. Here we report that wafer-scale MoS(2) thin layers can be obtained using MoO(3) thin films as a starting material followed by a two-step thermal process, reduction of MoO(3) at 500 °C in hydrogen and sulfurization at 1000 °C in the presence of sulfur. Spectroscopic, optical and electrical characterizations reveal that these films are polycrystalline and with semiconductor properties. The obtained MoS(2) films are uniform in thickness and easily transferable to arbitrary substrates, which make such films suitable for flexible electronics or optoelectronics.
Comparative analysis of the isovolume calibration method for non-invasive respiratory monitoring techniques based on area transduction versus circumference transduction using the connected cylinders model (2011)

An analytical formalism developed previously to examine the robustness of the isovolume calibration technique for non-invasive respiratory monitoring devices based on measurements of torso circumference (e.g. fibre-optic respiratory plethysmography) is extended here to techniques based on area measurement (e.g. respiratory inductive plethysmography), and the results are compared. The earlier perturbation approach is adopted, and an exact method is also presented. It is demonstrated that the area-based techniques have less dependence on the cylindrical compartmental parameters of radius and height, and are independent of compartmental volume if height variations are negligible, in contrast to circumference-based techniques. It is also demonstrated that both the area- and the circumference-based techniques provide similar inferences of volume when calibrated using the isovolume method under reasonable assumptions for the dimensions of the compartments that constitute a model of the torso.
Potential antitumor agents. 25 [1]. Synthesis and cytotoxic activity of 3-(2-chloro-3-indolylmethylene)1,3-dihydroindol-2-ones. (1997)

The Knoevenagel reaction between 2-indolinones and 2-chloroindolaldehydes gave 3-(2-chloro-3-indolylmethylene)1,3-dihydroindol-2-ones which were tested as potential antitumor agents on cultures of HeLa cells. 2-Chloro derivatives with at least one unsubstituted NH group, are promising candidates for further investigation.
Recent advances in diagnosis and treatment of gliomas using chlorotoxin-based bioconjugates. (2014)

Malignant gliomas, especially glioblastoma multiforme, are the most widely distributed and deadliest brain tumors because of their resistance to surgical and medical treatment. Research of glioma-specific bioconjugates for diagnosis and therapy developed rapidly during the past several years. Many studies have demonstrated that chlorotoxin (CTX) and Buthus martensii Karsch chlorotoxin (BmK CT) specifically inhibited glioma cells growth and metastasis, and accelerated tumor apoptosis. The bioconjugates of CTX or BmK CT with other molecules have played an increasing role in diagnostic imaging and treatment of gliomas. To date, CTX-based bioconjugates have achieved great success in phase I/II clinical trials about safety profiles. Here, we will provide a review on the important role of ion channels in the underlying mechanisms of gliomas invasive growth and how CTX suppresses gliomas proliferation and migration. We will summarize the recent advances in the applications of CTX bioconjugates for gliomas diagnosis and treatment. In addition, we will review recent studies on BmK CT bioconjugates and compare their efficacies with CTX derivatives. Finally, we will address advantages and challenges in the use of CTX or BmK CT bioconjugates as specific agents for theranostic applications in gliomas.
A Double-blind Placebo Controlled Trial of Fluoxetine in Fibromyalgia (1994)

42 women were randomized to receive either placebo or fluoxetine at 20 mgs per day. Inter and intra group differences in clinical variables were evaluated after 3 and 6 weeks of treatment. Except for self rated anxiety which improved in the placebo treated group at 3 weeks, no differences between groups were noted. For those receiving fluoxetine both AIMS Anxiety (4.0 baseline vs. 3.3, p = 0.04) and Depression scores (2.6 baseline vs. 1.9, p = 0.03) improved at 3 weeks; however, improvement in the Beck Depression Scale did not reach significance (11.8 vs. 9.4, p = 0.34). At 6 weeks, both AIMS Depression (2.6 at baseline and 1.5 at 6 weeks, p = 0.03) and Beck Depression Scales (11.8 at baseline vs. 8.3 at 6 weeks, p = 0.04) showed improvement, as did sleep quality (9.6 vs. 7.6, p = 0.03). But no other variable had a significant change from baseline at either the 3 or 6 week point. Our data do not suggest that fluoxetine improves the signs and symptoms of fibromyalgia.
Adaptive Filters Theory and Applications (1999)

From the Publisher:
Adaptive filtering is an advanced and growing field in signal processing. A filter is a transmission network used in electronic circuits for the selective enhancement or reduction of specified components of an input signal. Filtering is achieved by selectively attenuating those components of the input signal which are undesired, relative to those which it is desired to enhance. This comprehensive book is both a valuable student resource and a useful technical reference for signal processing engineers in industry. The author is experienced in teaching graduates and practicing engineers and the text offers good theoretical coverage complemented by plenty of application examples.
Lithium Aluminum Hydride Reductions; A New Hydrolysis Method for Intractable Products (1986)

A new hydrolysis procedure is described for lithium aluminum hydride reductions which allows for simpler technique and markedly improved yields in the synthesis of multifunctional products. The procedure is illustrated by the reduction of a series of formamides and amino-esters to give various propanolamines.
Regulation of Protein Kinase B/Akt-Serine 473 Phosphorylation by Integrin-linked Kinase (2001)

Protein kinase B (PKB/Akt) is a regulator of cell survival and apoptosis. To become fully activated, PKB/Akt requires phosphorylation at two sites, threonine 308 and serine 473, in a phosphatidylinositol (PI) 3-kinase-dependent manner. The kinase responsible for phosphorylation of threonine 308 is the PI 3-kinase-dependent kinase-1 (PDK-1), whereas phosphorylation of serine 473 has been suggested to be regulated by PKB/Akt autophosphorylation in a PDK-1-dependent manner. However, the integrin-linked kinase (ILK) has also been shown to regulate phosphorylation of serine 473 in a PI 3-kinase-dependent manner. Whether ILK phosphorylates this site directly or functions as an adapter molecule has been debated. We now show by in-gel kinase assay and matrix-assisted laser desorption-ionization time-of-flight mass spectrometry that biochemically purified ILK can phosphorylate PKB/Akt directly. Co-immunoprecipitation analysis of cell extracts demonstrates that ILK can complex with PKB/Akt as well as PDK-1 and that ILK can disrupt PDK-1/PKB association. The amino acid residue serine 343 of ILK within the activation loop is required for kinase activity as well as for its interaction with PKB/Akt. Mutational analysis of ILK further shows a crucial role for arginine 211 of ILK within the phosphoinositide phospholipid binding domain in the regulation of PKB- serine 473 phosphorylation. A highly selective small molecule inhibitor of ILK activity also inhibits the ability of ILK to phosphorylate PKB/Akt in vitro and in intact cells. These data demonstrate that ILK is an important upstream kinase for the regulation of PKB/Akt.
Prevention of motoneuron death by adenovirus-mediated neurotrophic factors (1997)

Amyotrophic lateral sclerosis (ALS) is a fatal neurodegenerative disease characterized by progressive loss of motoneurons, and has no effective treatment. Experimental studies in rodents have shown that motoneurons respond to a variety of molecules including brain-derived neurotrophic factor (BDNF). and the glial-cell line-derived neurotrophic factor (GDNF). Here we investigated the neuroprotective effect of these growth factors, encoded by an adenovirus, on the death of axotomized facial motoneurons in newborn rats. We used a new gene therapy strategy that involves gene transfer to motoneurons by intramuscular injection of an adenoviral vector, which is retrogradely transported from injected target muscle (Finiels et al.,: NeuroReport 7:373-378, 1995). A significant increased survival of motoneurons was observed in animals pretreated with adenovirus encoding BDNF (34.5%, P < 0.05) ou GDNF (41.9%, P < 0.05) 1 week after axotomy. These results indicate that pretreatment with BDNF or GDNF, using this therapeutic strategy, is able to prevent the massive death of motoneurons that normally follows axotomy in the neonatal period, opening new perspectives to limit neuronal death in degenerative disorders.
Model driven development for distributed real-time and embedded systems (2005)

The major histocompatibility complex (MHC) class I (MHC-I) region contains a multitude of genes relevant to immune response. Multiple E3 ubiquitin ligase genes, including tripartite motif 10 (<i>TRIM10</i>), <i>TRIM15</i>, <i>TRIM26</i>, <i>TRIM27</i>, <i>TRIM31</i>, <i>TRIM38</i>, <i>TRIM39</i>, <i>TRIM40</i>, and RING finger protein 39 (<i>RNF39</i>), are organized in a tight cluster, and an additional two TRIM genes (namely <i>TRIM38</i> and <i>TRIM27</i>) telomeric of the cluster within the MHC-I region. The E3 ubiquitin ligases encoded by these genes possess important roles in controlling the intensity of innate immune responses. In this review, we discuss the E3 ubiquitin ligases encoded within the MHC-I region, highlight their regulatory roles in innate immunity, and outline their potential functions in infection, inflammatory and autoimmune diseases.
Mechanism of Ribonuclease Cytotoxicity (1995)

Bovine seminal ribonuclease (BS-RNase), a dimeric homolog of bovine pancreatic ribonuclease A (RNase A), is toxic to mammalian cells. In contrast to dimeric BS-RNase, a monomeric BS-RNase and RNase A are not cytotoxic and are bound tightly by cytosolic ribonuclease inhibitor. To elucidate the mechanism of ribonuclease cytotoxicity, we constructed a series of hybrid and semisynthetic enzymes and examined their properties. In five hybrid enzymes, divergent residues in BS-RNase were replaced with the analogous residues of RNase A so as to diminish an interaction with a putative cellular receptor. In a semisynthetic enzyme, the disulfide bonds that cross-link the monomeric subunits of dimeric BS-RNase were replaced with thioether bonds, which can withstand the reducing environment of the cytosol. Each hybrid and semisynthetic enzyme had ribonucleolytic and cytotoxic activities comparable with those of wild-type BS-RNase. These results suggest that dimeric BS-RNase (pI = 10.3) enters cells by adsorptive rather than receptor-mediated endocytosis and then evades cytosolic ribonuclease inhibitor so as to degrade cellular RNA. This mechanism accounts for the need for a cytosolic ribonuclease inhibitor and for the cytotoxicity of other homologs of RNase A.
Frame-rate up-conversion using transmitted motion and segmentation fields for very low bit-rate video coding (2002)

We present a motion-compensated interpolation scheme that allows recovery of skipped frames at the receiver. The interpolation is performed based on an object-based interpretation of the video. The main advantage of the scheme is that the decoded motion and segmentation information is used without refinement. This is attributable to the fact that the object-based representation is true to the "real" motion. We present simulation results in a very low bit-rate coding environment, where multiple frames need to be skipped. The interpolated frames show good reconstruction quality, whereas standard block-based methods lead to unacceptable artifacts.
Modular design of permanent-magnetgenerators for wind turbines (1996)

Radial-field, multipole, permanent-magnet, synchronous machines may be used as direct-coupled generators for large grid-connected wind turbines. Power ratings from below 100 kW to more than 1 MW and pole numbers of 100 to 300 may be required. Modular construction reduces the detail design effort, and the number of drawings and tools needed. Module designs are presented which can be used for a wide range of machine designs. The rotor modules use standard ferrite magnet blocks. The stator modules are simple E cores each carrying a single rectangular coil. The arrangement eases assembly of the magnetised parts and creates a machine with low reactances and high efficiency.
The Intensity of Hemodialysis and the Response to Erythropoietin in Patients with End-Stage Renal Disease (1996)

In patients with end-stage renal disease, inadequate hemodialysis is associated with a suboptimal response to erythropoietin therapy. Increasing the intensity of dialysis in patients with anemia who are receiving inadequate dialysis results in a significant increase in the hematocrit.
Making Gold Nanoparticles Glow:  Enhanced Emission from a Surface-Bound Fluoroprobe (2000)

ADVERTISEMENT RETURN TO ISSUEPREVCommunicationNEXTMaking Gold Nanoparticles Glow: Enhanced Emission from a Surface-Bound FluoroprobeK. George Thomas and Prashant V. KamatView Author Information Notre Dame Radiation Laboratory University of Notre Dame Notre Dame, Indiana 46556-0579 Cite this: J. Am. Chem. Soc. 2000, 122, 11, 2655–2656Publication Date (Web):March 4, 2000Publication History Received30 November 1999Published online4 March 2000Published inissue 1 March 2000https://pubs.acs.org/doi/10.1021/ja9941835https://doi.org/10.1021/ja9941835rapid-communicationACS PublicationsCopyright © 2000 American Chemical SocietyRequest reuse permissionsArticle Views3322Altmetric-Citations209LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InRedditEmail Other access optionsGet e-AlertscloseSupporting Info (1)»Supporting Information Supporting Information SUBJECTS:Aromatic compounds,Fluorescence,Gold,Hydrocarbons,Metal nanoparticles Get e-Alerts
An algebraic method for public-key cryptography (1999)

Algebraic key establishment protocols based on the difficulty of solving equations over algebraic structures are described as a theoretical basis for constructing public-key cryptosystems.
Metal‐Free Polymerization of Phenylsilane: Tris(pentafluorophenyl)borane‐Catalyzed Synthesis of Branched Polysilanes at Elevated Temperatures (2013)

The strong organoborane Lewis acid B(C6F5)3 catalyzes the polymerization of phenylsilane at elevated temperatures forming benzene and SiH4 as side-products. The resulting polymer is a branched polysilane with an irregular substitution pattern, as revealed by 2D NMR spectroscopy. Having explored the mechanism of this novel metal-free polymerization by computational chemistry methods at the DFT level, we have suggested that unusual cationic active species, namely monomer-stabilized silyl cations, propagate the polymerization. Hydride abstraction of SiH3 moiety by the catalyst in the initiation step was found to be kinetically preferred by around 9 kcal mol(-1) over activation by coordination of the monomer at the aromatic ring. The formation of linear Si-Si bonds during propagation was calculated to be less favorable than branching and ligand scrambling, which accounts for the branched and highly substituted form of the polymer that was obtained. This novel type of polymerization bears the potential for further optimization with respect to degree of polymerization and structure control for both primary as well as secondary silanes, which can be polymerized by sterically less hindered boranes.
A multi-layer video browsing system (1995)

The paper proposes an effective and efficient browsing system which is capable of representing the contents of a video sequence in a multi-layer manner. In this system, users can rapidly preview some preprocessed video shots, based on some simple scene change detection algorithm, to find out the particular video segments which are of interest. Because users just preview some video shots instead of examining all the video frames, this shot-based browsing method is superior to the conventional frame-based browsing one from the view points of the network bandwidth, user friendliness, and/or browsing efficiency. Based on the proposed browsing tool, a video-on-demand (VOD) prototype system has been implemented in the Communication and Multimedia Laboratory of National Taiwan University in an Ethernet LAN environment.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
e-DASH: Modelling an energy-aware DASH player (2017)

Dynamic Adaptive Streaming over HTTP (DASH) is one of the most popular ways to stream videos at present. In this work, we propose a DASH player energy-aware plugin (eDASH) for mobile devices which help reduce the battery consumption of the device. The eDASH player utilises a novel bitrate and video brightness adaptation algorithm to determine the next chunk to download. This algorithm utilises an energy-aware QoE model which factors in power consumption of the device in conjunction with existing bitrate adaptation logic to determine the next chunk. We also propose a new DASH architecture which could be easily integrated with the existing one. Macro-benchmarking of energy consumption of a mobile device while streaming and playing back video is conducted to obtain energy profiles of various video qualities. This energy data is then used along with real world network traces to drive simulations to evaluate energy savings that could be achieved using eDASH. We observe that up to 45% energy savings could be achieved with minimal reduction is QoE. We also find that up to 80% data transfer savings could also be achieved with an eDASH client.
Investigation of the Diffusion Process in Cross-Linked Polystyrenes by Means of NMR Imaging and Solid-State NMR Spectroscopy (1994)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTInvestigation of the Diffusion Process in Cross-Linked Polystyrenes by Means of NMR Imaging and Solid-State NMR SpectroscopyMartin Ilg, Bettina Pfleiderer, Klaus Albert, Wolfgang Rapp, and Ernst BayerCite this: Macromolecules 1994, 27, 10, 2778–2783Publication Date (Print):May 1, 1994Publication History Published online1 May 2002Published inissue 1 May 1994https://pubs.acs.org/doi/10.1021/ma00088a019https://doi.org/10.1021/ma00088a019research-articleACS PublicationsRequest reuse permissionsArticle Views112Altmetric-Citations25LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InRedditEmail Other access optionsGet e-Alertsclose Get e-Alerts
Determination of optical properties of human blood in the spectral range 250 to 1100 nm using Monte Carlo simulations with hematocrit-dependent effective scattering phase functions (2006)

The absorption coefficient mu(a), scattering coefficient mu(s), and anisotropy factor g of diluted and undiluted human blood (hematocrit 0.84 and 42.1%) are determined under flow conditions in the wavelength range 250 to 1100 nm, covering the absorption bands of hemoglobin. These values are obtained by high precision integrating sphere measurements in combination with an optimized inverse Monte Carlo simulation (IMCS). With a new algorithm, appropriate effective phase functions could be evaluated for both blood concentrations using the IMCS. The best results are obtained using the Reynolds-McCormick phase function with the variation factor alpha = 1.2 for hematocrit 0.84%, and alpha = 1.7 for hematocrit 42.1%. The obtained data are compared with the parameters given by the Mie theory. The use of IMCS in combination with selected appropriate effective phase functions make it possible to take into account the nonspherical shape of erythrocytes, the phenomenon of coupled absorption and scattering, and multiple scattering and interference phenomena. It is therefore possible for the first time to obtain reasonable results for the optical behavior of human blood, even at high hematocrit and in high hemoglobin absorption areas. Moreover, the limitations of the Mie theory describing the optical properties of blood can be shown.