gebhart/patrepeval huggingface dataset:
[Not Available]. (2009)

The scale-free and small-world network models reflect the functional units of networks. However, when we investigated the network properties of a signaling pathway using these models, no significant differences were found between the original undirected graphs and the graphs in which inactive proteins were eliminated from the gene expression data. We analyzed signaling networks by focusing on those pathways that best reflected cellular function. Therefore, our analysis of pathways started from the ligands and progressed to transcription factors and cytoskeletal proteins. We employed the Python module to assess the target network. This involved comparing the original and restricted signaling cascades as a directed graph using microarray gene expression profiles of late onset Alzheimer's disease. The most commonly used method of shortest-path analysis neglects to consider the influences of alternative pathways that can affect the activation of transcription factors or cytoskeletal proteins. We therefore introduced included k-shortest paths and k-cycles in our network analysis using the Python modules, which allowed us to attain a reasonable computational time and identify k-shortest paths. This technique reflected results found in vivo and identified pathways not found when shortest path or degree analysis was applied. Our module enabled us to comprehensively analyse the characteristics of biomolecular networks and also enabled analysis of the effects of diseases considering the feedback loop and feedforward loop control structures as an alternative path.
An Improved Industrial Synthesis of Florfenicol plus an Enantioselective Total Synthesis of Thiamphenicol and Florfenicol (1997)

ADVERTISEMENT RETURN TO ISSUEPREVNoteNEXTAn Improved Industrial Synthesis of Florfenicol plus an Enantioselective Total Synthesis of Thiamphenicol and FlorfenicolGuangzhong Wu, Doris P. Schumacher, Wanda Tormos, Jon E. Clark, and Bruce L. MurphyView Author Information Chemical Process Research and Development, Schering-Plough Research Institute, 2015 Galloping Hill Road, Kenilworth, New Jersey 07033 Cite this: J. Org. Chem. 1997, 62, 9, 2996–2998Publication Date (Web):May 2, 1997Publication History Received1 August 1996Revised11 February 1997Published online2 May 1997Published inissue 1 May 1997https://doi.org/10.1021/jo961479+Copyright © 1997 American Chemical SocietyRIGHTS & PERMISSIONSArticle Views1252Altmetric-Citations37LEARN 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 InReddit Read OnlinePDF (182 KB) Get e-AlertsSupporting Info (1)»Supporting Information Supporting Information SUBJECTS:Alcohols,Anions,Enantioselective synthesis,Ethers,Organic reactions Get e-Alerts
Distill: Domain-Specific Compilation for Cognitive Models (2022)

Computational models of cognition enable a better understanding of the human brain and behavior, psychiatric and neurological illnesses, clinical interventions to treat illnesses, and also offer a path towards human-like artificial intelligence. Cognitive models are also, however, laborious to develop, requiring composition of many types of computational tasks, and suffer from poor performance as they are generally designed using high-level languages like Python. In this work, we present Distill, a domain-specific compilation tool to accelerate cognitive models while continuing to offer cognitive scientists the ability to develop their models in flexible high-level languages. Distill uses domain-specific knowledge to compile Python-based cognitive models into LLVM IR, carefully stripping away features like dynamic typing and memory management that add performance overheads without being necessary for the underlying computation of the models. The net effect is an average of 27 × performance improvement in model execution over state-of-the-art techniques using Pyston and PyPy. Distill also repurposes classical compiler data flow analyses to reveal properties about data flow in cognitive models that are useful to cognitive scientists. Distill is publicly available, integrated in the PsyNeuLink cognitive modeling environment, and is already being used by researchers in the brain sciences.
Fundamental Study on Reflection Property of Radiated Noise against Ground Floor in Semi-Anechoic Chamber for EMC Test of Inverter (2022)

Radiated electromagnetic (EM) noise caused by fast-changing voltage and currents is one of the important issues for developing inverters. However, the complex structure of the inverter made it difficult to investigate its radiated EM noise. The source part, radiation part, and radiation property should be considered to predict the radiated EM noise of the inverter unit. This paper deals with the polarization and reflection properties of the simple dipole model based on EM theory and experimental results in the semi-anechoic chamber to explain the radiation property of EM noise from the inverter unit.
Scalability and Yield in Elastomer Stamp Micro-Transfer-Printing (2017)

Elastomer stamp micro-transfer-printing is a highly scalable method for the assembly of microscale components onto non-native substrates. One of the key value propositions of micro-transfer-printing is that the transfer stamp can be scaled to wafer-dimensions and can transfer tens to thousands of micro-devices in a single step, equating to multiple millions of units per hour. Here, we report on the results of systematically scaling the stamp from 12.8 mm × 12.8 mm to a full 150 mm stamp, capable of transferring all the required devices to a 150 mm receiving wafer in one operation. The 150 mm stamp is designed to transfer more than 80,000 chips in one print cycle. This study was carried out using silicon nitride test vehicles that were specially designed for this project. We will discuss how stamp scaling impacts transfer yield and the implications for ultra-high throughput assembly of micro-devices. In addition, we will explore the capability to transfer very small devices down to 3 μm × 3 μm.
Macrocyclization of enzyme-based supramolecular polymers (2010)

AB type monomers for supramolecular polymers have been developed based on the strong and reversible noncovalent interaction between ribonuclease S-peptide (A) and S-protein (B), resulting in an active enzyme complex as the linking unit. Two AB-type protein constructs are synthesized differing in the length of the flexible oligo(ethylene glycol) spacer separating the two end groups. Using an experimental setup where size exclusion chromatography is directly coupled to Q-TOF mass spectrometry, we have analyzed the self-assembled architectures as a function of concentration. The theory of macrocyclization under thermodynamic control is used to quantitatively analyze the experimental data. Using this theory, we show that AB-type monomers linked by flexible linkers grow reversibly via ring–chain competition. Inherently the formation of linear polymeric assemblies is beyond the capability of these types of building blocks due to concentration limits of proteins. The results therefore contribute to the general understanding of supramolecular polymerization with biological building blocks and demonstrate design requirements for monomers if linear polymerization is desired.
Physical Solvents that are Alternatives for PEGDME in CO{sub 2} Absorption (2011)

Advanced gasification power plants will employ the water-gas shift reaction producing a high pressure gas-phase mixture containing CO{sub 2}, H{sub 2} and water. This gas mixture at elevated pressures provides ample driving force in order to use a physical solvent that will selectively absorb, not chemically bind, to the CO{sub 2}. Potential physical absorbers include (a) liquid mixtures of CO{sub 2}-philic polydisperse oligomers, (b) small, volatile, liquid CO{sub 2}-philic solvents, and (c) CO{sub 2}-philic solids capable of melting in the presence of CO{sub 2}. The objective of this study was to identify alternative physical solvents that would selectively dissolve only CO{sub 2} from this mixture. The first phase of our research involved the comparison of the CO{sub 2} solvent strength of PEGDME with that of other low volatility oligomers that are known to be “CO{sub 2}-philic”. Small volatile CO{sub 2} solvents were also examined in the second phase of this work. Lastly, solid CO{sub 2}-philes have been investigated as a potential CO{sub 2} solvent.
Estimation of Glottal Closing and Opening Instants in Voiced Speech Using the YAGA Algorithm (2011)

Accurate estimation of glottal closing instants (GCIs) and opening instants (GOIs) is important for speech processing applications that benefit from glottal-synchronous processing including pitch tracking, prosodic speech modification, speech dereverberation, synthesis and study of pathological voice. We propose the Yet Another GCI/GOI Algorithm (YAGA) to detect GCIs from speech signals by employing multiscale analysis, the group delay function, and <i xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">N</i> -best dynamic programming. A novel GOI detector based upon the consistency of the candidates' closed quotients relative to the estimated GCIs is also presented. Particular attention is paid to the precise definition of the glottal closed phase, which we define as the analysis interval that produces minimum deviation from an all-pole model of the speech signal with closed-phase linear prediction (LP). A reference algorithm analyzing both electroglottograph (EGG) and speech signals is described for evaluation of the proposed speech-based algorithm. In addition to the development of a GCI/GOI detector, an important outcome of this work is in demonstrating that GOIs derived from the EGG signal are not necessarily well-suited to closed-phase LP analysis. Evaluation of YAGA against the APLAWD and SAM databases show that GCI identification rates of up to 99.3% can be achieved with an accuracy of 0.3 ms and GOI detection can be achieved equally reliably with an accuracy of 0.5 ms.
Effect of Hemodiafiltration on Self-Reported Sleep Duration: Results from a Randomized Controlled Trial (2019)

In our RCT, the dialysis modality (HDF vs. HD) had no effect on self-reported sleep duration. In both groups, dialysis in the 1st shift adversely affected self reported sleep duration.
Caractérisation de nouveaux dérivés et analogues de la nétropsine et identification de leurs intermédiaires de synthèse par spectrométrie de masse FAB (1991)

Abstract The fast‐atom bombardment (FAB) mass spectra of a series of netropsin derivatives and analogues were examined in positive‐ion and when necessary negative‐ion modes. Behaviour of these derivatives was related to that of oligopeptides. Some compounds protected by t ‐butoxycarbonyl groups were also investigated using this technique and showed characteristic fragmentations.
Cofilin hyperactivation in HIV infection and targeting the cofilin pathway using an anti-α 4 β 7 integrin antibody (2019)

A functional HIV cure requires immune reconstitution for lasting viremia control. A major immune dysfunction persisting in HIV infection is the impairment of T helper cell migration and homing to lymphoid tissues such as GALTs (gut-associated lymphoid tissues). ART (antiretroviral therapy) does not fully restore T cell motility for tissue repopulation. The molecular mechanism dictating this persistent T cell dysfunction is not understood. Cofilin is an actin-depolymerizing factor that regulates actin dynamics for T cell migration. Here, we demonstrate that blood CD4 T cells from HIV-infected patients (<i>n</i> = 193), with or without ART, exhibit significantly lower levels of cofilin phosphorylation (hyperactivation) than those from healthy controls (<i>n</i> = 100; ratio, 1.1:2.3; <i>P</i> < 0.001); cofilin hyperactivation is also associated with poor CD4 T cell recovery following ART. These results suggest an HIV-mediated systemic dysregulation of T cell motility that cannot be repaired solely by ART. We further demonstrate that stimulating blood CD4 T cells with an anti-human α<sub>4</sub>β<sub>7</sub> integrin antibody can trigger signal transduction and modulate the cofilin pathway, partially restoring T cell motility in vitro<i>.</i> However, we also observed that severe T cell motility defect caused by high degrees of cofilin hyperactivation was not repairable by the anti-integrin antibody, demonstrating a mechanistic hindrance to restore immune functions in vivo. Our study suggests that cofilin is a key molecule that may need to be therapeutically targeted early for T cell tissue repopulation, immune reconstitution, and immune control of viremia.
Controlled Occlusion of Proteins: A Tool for Modulating the Properties of Skeletal Elements (1994)

Abstract Composite materials in which the organic host is stiffened by guest particles, are widely used in nature and are produced synthetically by man. Organisms also produce a different type of composite in which the host is a crystal and the guests are macromolecules occluded in an orderly fashion within the crystal. The best studied examples, to date, are biogenic calcite crystals, and in particular those formed by the echinoderms. In vitro experiments with calcite crystals grown in the presence of echnioderm intracrystalline proteins, show that these macromolecules are occluded inside the crystal on specific planes, and their presence alters the mechanical properties of the crystal host. Furthermore, the proteins also influence the crystal textural properties. Model studies using crystals of dicarboxylic acid salts grown in the presence of intracrystalline proteins show that the coherence length is reduced in directions perpendicular to the planes on which the proteins adsorb. We found anisotropic effects in almost all the biogenic calcite crystals we examined. Furthermore, we noted an interesting relationship between the variations in coherence length in the different crystallographic directions and the gross morphology of the single crystal elements, suggesting that these proteins may also function in determining the morphology of the crystal during growth. These novel single crystalprotein composites may be just one example of strategies used in nature for producing materials with special properties.
OnabotulinumtoxinA alters inflammatory gene expression and immune cells in chronic headache patients (2021)

Occipital headache, the perception of pain in the back of the head, is commonly described by patients diagnosed with migraine, tension-type headache, and occipital neuralgia. The greater and lesser occipital nerves play central role in the pathophysiology of occipital headache. In the clinical setup, such headaches are often treated with onabotulinumtoxinA, a neurotoxin capable of disrupting ability of nociceptors to get activated and/or release proinflammatory neuropeptides. Attempting to understand better onabotulinumtoxinA mechanism of action in reducing headache frequency, we sought to determine its effects on expression of inflammatory genes in injected occipital tissues. To achieve this goal, we injected 40 units of onabotulinumtoxinA into four muscle groups (occipitalis, splenius capitis, semispinalis capitis, and trapezius muscles-all located on one side of the occiput) of patients with chronic bilateral occipital headache scheduled for occipital nerve decompression surgery 1 month later. At the time of surgery, we collected discarded muscle, fascia and periosteum tissues from respective locations on both sides of the neck and occiput and performed targeted transcriptome analyses to determine expression level of inflammatory genes in onabotulinumtoxinA-injected and onabotulinumA-uninjected tissues. We found that (i) onabotulinumtoxinA alters expression of inflammatory genes largely in periosteum, minimally in muscle and not at all in fascia; (ii) expression of inflammatory genes in uninjected periosteum and muscle is significantly higher in historical onabotulinumA responders than historical non-responders; (iii) in historical responders' periosteum, onabotulinumA decreases expression of nearly all significantly altered genes, gene sets that define well recognized inflammatory pathways (e.g. pathways involved in adaptive/innate immune response, lymphocyte activation, and cytokine, chemokine, NF-kB, TNF and interferon signalling), and abundance of 12 different immune cell classes (e.g. neutrophils, macrophages, cytotoxic T-, NK-, Th1-, B- and dendritic-cells), whereas in historical non-responders it increases gene expression but to a level that is nearly identical to the level observed in the uninjected periosteum and muscle of historical responders; and surprisingly (iv) that the anti-inflammatory effects of onabotulinumA are far less apparent in muscles and absent in fascia. These findings suggest that in historical responders' periosteum-but not muscle or fascia-inflammation contributes to the pathophysiology of occipital headache, and that further consideration should be given to the possibility that onabotulinumA mechanism of action in migraine prevention could also be achieved through its ability to reduce pre-existing inflammation, likely through localized interaction that lead to reduction in abundance of immune cells in the calvarial periosteum.
Identification of N2-(1-Carboxyethyl)guanine (CEG) as a Guanine Advanced Glycosylation End Product (1995)

Reducing sugars such as glucose react nonenzymatically with protein amino groups to initiate a posttranslational modification process known as advanced glycosylation. Nucleotide bases also participate in advanced glycosylation reactions, producing DNA-linked advanced glycosylation endproducts (AGEs) that cause mutations and DNA transposition. Although several protein-derived AGEs have been isolated and structurally characterized, AGE-modified nucleotides have not yet been reported. We systematically examined the reactivities of the model nucleotide bases 9-methylguanine (9-mG), 9-methyladenine (9-mA), and 1-methylcytosine (1-mC) toward glucose and several glucose-derived reactants. In "fast" reactions performed at refluxing temperature and physiological pH, 1 equiv of nucleotide base was reacted with 10 equiv of D-glucose, D-glucose 6-phosphate (G-6-P), D-glucose 6-phosphate/lysine (G-6-P/Lys), the Schiff base 1-n-propylamino-N-D-glucoside (SB), or the Amadori product 1-n-propylamino-N-D-fructose (AP). In every reaction involving 9-mG, N2-(1-carboxyethyl)-9-methylguanine (CEmG) was a major product which was produced. N2-(1-carboxyethyl)-9-methylguanine also formed from 9-mG and AP in long-term incubations performed at 37 degrees C. Direct treatment of 9-mG with methylglyoxal (MG), a Maillard reaction propagator that forms from the decomposition of AP, also produced CEmG in high yield. N2-(1-Carboxyethyl)-9-methylguanine appears to result from the nucleophilic addition of the primary amino group of guanine to the ketone group of MG followed by an intramolecular rearrangement. Methylglyoxal is a known prokaryotic mutagen and was shown additionally to be mutagenic in a eukaryotic shuttle vector assay system.(ABSTRACT TRUNCATED AT 250 WORDS)
Learned Hand Gesture Classification Through Synthetically Generated Training Samples (2018)

Hand gestures are a natural component of human-human communication. Simple hand gestures are intuitive and can exhibit great lexical variety. It stands to reason that such a user input mechanism can have many benefits, including seamless interaction, intuitive control and robustness to physical constraints and ambient electrical, light and sound interference. However, while semantic and logical information encoded via hand gestures is readily decoded by humans, leveraging this communication channel in human-machine interfaces remains a challenge. Recent data-driven deep learning approaches are promising towards uncovering abstract and complex relationships that manual and direct rule-based classification schemes fail to discover. Such an approach is amenable towards hand gesture recognition, but requires myriad data which can be collected physically via user experiments. This process, however, is onerous and tedious. A streamlined approach with less overhead is sought. To that end, this work presents a novel method of synthetic hand gesture dataset generation that leverages modern gaming engines. Furthermore, preliminary results indicate that the dataset, despite being synthetic and requiring no physical data collection, is both accurate and rich enough to train a real-world hand gesture classifier that operates in real-time.
Real-Time Temperature Detection Via Quantum Dots for Photothermal Cellular Actuation (2021)

Plasmonic heating finds multiple applications in cell manipulation and stimulation, where heat generated by metal nanoparticles can be used to modify cell adhesion, control membrane currents, and suppress neuronal action potentials among others. Metal nanoparticles can also be easily integrated in artificial extracellular matrices to provide tunable, thermal cueing functionalities with nanometer spatial resolution. In this contribution, we present a platform enabling the combination of plasmonic heating with localized temperature sensing using quantum dots (QDs). Specifically, a functional nanocomposite material was designed with gold nanorods (AuNRs) and QDs incorporated in a cell-permissive hydrogel (e.g., collagen) as well as an optical set-up combining optical heating and temperature imaging, respectively. Specific area stimulation/readout can be realized through structured illumination using digital micromirror device (DMD) projection.
Dynamic Factors Controlling Targeting Nanocarriers to Vascular Endothelium (2011)

Endothelium lining the luminal surface of blood vessels is the key target and barrier for vascular drug delivery. Nanocarriers coated with antibodies or affinity peptides that bind specifically to endothelial surface determinants provide targeted delivery of therapeutic cargoes to these cells. Endothelial targeting consists of several phases including circulation in the bloodstream, anchoring on the endothelial surface and, in some cases, intracellular uptake and trafficking of the internalized materials. Dynamic parameters of the vasculature including the blood hydrodynamics as well as surface density, accessibility, membrane mobility and clustering of target determinants modulate these phases of the targeting, especially anchoring to endothelium. Further, such controlled parameters of design of drug nanocarriers such as affinity, surface density and epitope specificity of targeting antibodies, carrier size and shape also modulate endothelial targeting and resultant sub-cellular addressing. This article reviews experimental and computational approaches for analysis of factors modulating targeting nanocarriers to the endothelial cells.