gebhart/patrepeval huggingface dataset:
Coupled Analysis Dictionary Learning to inductively learn inversion: Application to real-time reconstruction of Biomedical signals (2018)

This work addresses the problem of reconstructing biomedical signals from their lower dimensional projections. Traditionally Compressed Sensing (CS) based techniques have been employed for this task. These are transductive inversion processes; the problem with these approaches is that the inversion is time-consuming and hence not suitable for real-time applications. With the recent advent of deep learning, Stacked Sparse Denoising Autoencoder (SSDAE) has been used for learning inversion in an inductive setup. The training period for inductive learning is large but is very fast during application - capable of real-time speed. This work proposes a new approach for inductive learning of the inversion process. It is based on Coupled Analysis Dictionary Learning. Results on Biomedical signal reconstruction show that our proposed approach is very fast and yields result far better than CS and SSDAE.
Nanocomposite Ionogel Electrolytes for Solid‐State Rechargeable Batteries (2020)

Abstract Ionogels composed of ionic liquids and gelling solid matrices offer several advantages as solid‐state electrolytes for rechargeable batteries, including safety under diverse operating conditions, favorable electrochemical and thermal properties, and wide processing compatibility. Among gelling solid matrices, nanoscale materials have shown particular promise due to their ability to concurrently enhance ionogel mechanical properties, thermal stability, ionic conductivity, and electrochemical stability. These beneficial attributes suggest that ionogel electrolytes are not only of interest for incumbent lithium‐ion batteries but also for next‐generation rechargeable battery technologies. Herein, recent advances in nanocomposite ionogel electrolytes are discussed to highlight their advantages as solid‐state electrolytes for rechargeable batteries. By exploring a range of different nanoscale gelling solid matrices, relationships between nanoscale material structure and ionogel properties are developed. Furthermore, key research challenges are delineated to help guide and accelerate the incorporation of nanocomposite ionogel electrolytes in high‐performance solid‐state rechargeable batteries.
ChemInform Abstract: Synthesis of Methyl 3‐Amino‐4‐aryl(or methyl)sulfonyl‐2‐thiophenecarboxylates from 3‐Alkoxy‐2‐aryl(or methyl)sulfonylacrylonitriles. (1999)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 100 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a “Full Text” option. The original article is trackable via the “References” option.
Cinnamaldehyde hydrogenation using Au–Pd catalysts prepared by sol immobilisation (2018)

We report the catalytic performance of Au–Pd nanoparticles prepared <italic>via</italic> a sol immobilisation technique for the catalytic hydrogenation of cinnamaldehyde under mild reaction conditions.
The 43rd Annual Meeting of the Canadian College of Neuropsychopharmacology, November 4, 2021 (2022)

Background: Depression is a prevalent psychiatric disorder characterized by heterogeneous symptoms that can last a lifetime and remain even after several courses of antidepressant treatments. Vulnerability to depression is associated with long-lasting changes in the transcriptional profile of the nucleus accumbens (NAcc), a brain region involved in reward and mood regulation. Methods: Here, we characterized the enduring changes in histone modifications in the NAcc of mice exposed to chronic social defeat stress (CSDS), a validated model for the study of depression-like behaviours that separates mouse populations into susceptible (SUS) and resilient (RES) based on a social interaction test (SIT). Tissue from the NAcc of control, SUS, and RES mice was collected either 24 hours or 4 weeks after the SIT and processed for histone profiling via mass spectrometry. In parallel, we mapped the genome-wide enrichment of the most changed histone modifications using CUT&RUN and assessed for chromatin accessibility in a cell-specific manner using ATAC-Seq. Results: CSDS alters the methylation (me) dynamics of lysine (K) 27 of the histone variant H3.3 -the predominant form of H3 present in adult brain neurons. Specifically, we observed an increase in the abundance of H3.3K27me1 and a decrease in the abundance of H3.3K27me2 in the NAcc of SUS mice. Gen omic distribution shows that H3.3K27me1 is primarily enriched in gene bodies and proximal promoters, suggesting its crucial role in determining stress-induced transcriptional profiles. In contrast, H3.3K27me2 is weakly deposited across intergenic regions. Using bioinformatics, we are currently identifying changes of chromatin accessibility and functional regulatory elements that coincide with H3.3K27me1 enrichment. Conclusion: Our results suggest that H3.3K27me1 and H3.3K27me2 are important chromatin "scars" that mediate enduring susceptibility to stress in the NAcc. Understanding the molecular basis of these adaptations and identifying the genomic regions affected will shed new light on persisting forms of stress-induced pathology.
Design and Analysis of IoT Applications: A Model-Driven Approach (2016)

The Internet of Things (IoT) is a new paradigm consisting of heterogeneous entities that communicate with each other by sending and receiving messages in heterogeneous formats through heterogeneous protocols to achieve a common goal. When designing IoT applications, there are two main challenges: the complexity to represent such heterogeneous entities, message formats, and protocols in an unambiguous manner, and the lack of methodologies to verify QoS (Quality of Service) properties. This paper introduces a design and analysis process supported by a framework to assist IoT application engineers to precisely model IoT applications and verify their properties. The framework is composed of the SysML4IoT, a SysML profile based on the IoT-A Reference Model, and the SysML2NuSMV, a model-to-text translator that converts the model and QoS properties specified on it to be executed by NuSMV, a mature model checker that allows entering a system model comprising a number of communicating Finite State Machines (FSM) and automatically checks its properties specified as Computational Tree Logic (CTL) or Linear Temporal Logic (LTL) formulas. Our approach is evaluated through a proof of concept implementation that analyzes the QoS property of reliability in a Building Energy Conservation (BEC) IoT application.
Immobilizing Reporters for Molecular Imaging of the Extracellular Microenvironment in Living Animals (2011)

We report here an immobilization strategy using a collagen binding protein to deliver and confine synthetic reporters to the extracellular microenvironment in vivo for noninvasively imaging the activity of targets in the microenvironment. We show that the immobilization of reporters on collagens in the local microenvironment is highly efficient and physiologically stable for repetitive, long-term imaging. By using this strategy we successfully developed an immobilized bioluminescent activatable reporter and a dual-modality reporter to map and quantitatively image the activity of extracellular matrix metalloproteinases (MMP) in tumor-bearing mice. The inhibition of MMP activity by chemical inhibitor was also demonstrated in living subjects. We further demonstrated the general applicability of this immobilization strategy by imaging MMP activity at the inflammation site in a mouse model. Our results show that the in vivo immobilization of reporters can be used as a general strategy for probing the local extracellular microenvironment.
Disease-associated dendritic cells respond to disease-specific antigens through the common heat shock protein receptor (2003)

The most abundant intracellular proteins, heat shock proteins (HSPs), serve as molecular chaperones for regulatory and maturation pathways. Diverse families of HSPs have been shown to bind antigenic peptides and to play major roles in innate and adaptive immune responses through the common HSP receptor, CD91. HIV-1+ patients with Kaposi sarcoma (KS) were matched for CD4 count and HIV-1 RNA viral load to HIV-1+ patients without Kaposi sarcoma (and negative for Kaposisarcoma-associated herpesvirus). We then investigated the pathways used by tumor lysates, viral lysates, and viral particles in their activation. In particular, we observed immune responses after HSP depletion using antitumor antibiotics and blockade of the common HSP receptor, CD91. Despite the impaired functional capacity of dendritic cells (DCs) derived from patients with KS, DCs retain the ability to prime the adaptive arm of the immune system through the common HSP receptor, leading to phenotypic activation and stimulation of tetramer-positive CD8+ cytotoxic T cells. We also show that interferon-producing plasmacytoid DCs are selectively depleted in KS-positive compared with matched KS-negative HIV-1-infected patients. Functionally impaired DCs can effectively cross-present immune responses through the common HSP receptor. These results have important implications for the etiopathogenesis of KS and for the development and design of any compounds, including vaccines, derived from cellular lysates.
Self-assembled nanoparticle antiglare coatings (2012)

Here we report a simple and scalable bottom-up technology for assembling close-packed nanoparticle monolayers on both sides of a glass substrate as high-quality antiglare coatings. Optical measurements show that monolayer coatings consisting of 110 nm silica nanoparticles can significantly reduce optical reflectance and enhance specular transmittance of the glass substrate for a broad range of visible wavelengths. Both experiments and numerical simulations reveal that the antiglare properties of the self-assembled colloidal monolayers are significantly affected by the size of the colloidal particles.
ChemInform Abstract: Mild Synthesis of Asymmetric 2′‐Carboxyethyl‐Substituted Fluoresceins. (2008)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 200 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a “Full Text” option. The original article is trackable via the “References” option.
Mutant LV476-7AA of A-subunit of Enterococcus hirae V1-ATPase: High affinity of A3B3 complex to DF axis and low ATPase activity (2013)

Vacuolar ATPase (V-ATPase) of Enterococcus hirae is composed of a soluble functional domain V1 (A3B3DF) and an integral membrane domain Vo (ac), where V1 and Vo domains are connected by a central stalk, composed of D-, F-, and d-subunits; and two peripheral stalks (E- and G-subunits). We identified 120 interacting residues of A3B3 heterohexamer with D-subunit in DF heterodimer in the crystal structures of A3B3 and A3B3DF. In our previous study, we reported 10 mutants of E. hirae V1-ATPase, which showed lower binding affinities of DF with A3B3 complex leading to higher initial specific ATPase activities compared to the wild-type. In this study, we identified a mutation of A-subunit (LV(476-7)AA) at its C-terminal domain resulting in the A3B3 complex with higher binding affinities for wild-type or mutant DF heterodimers and lower initial ATPase activities compared to the wild-type A3B3 complex, consistent with our previous proposal of reciprocal relationship between the ATPase activity and the protein-protein binding affinity of DF axis to the A3B3 catalytic domain of E. hirae V-ATPase. These observations suggest that the binding of DF axis at the contact region of A3B3 rotary ring is relevant to its rotation activity.
Polarization dependence of avalanche multiplication factor in 1.5 μm quantum dot waveguide photodetector (2016)

Get PDF Email Share Share with Facebook Tweet This Post on reddit Share with LinkedIn Add to CiteULike Add to Mendeley Add to BibSonomy Get Citation Copy Citation Text T. Umezawa, K. Akahane, A. Matsumoto, A. Kanno, N. Yamamoto, and T. Kawanishi, "Polarization dependence of avalanche multiplication factor in 1.5 μm quantum dot waveguide photodetector," in Conference on Lasers and Electro-Optics, OSA Technical Digest (2016) (Optica Publishing Group, 2016), paper SM4E.8. Export Citation BibTex Endnote (RIS) HTML Plain Text Citation alert Save article
Single-cell analysis of Schistosoma mansoni reveals a conserved genetic program controlling germline stem cell fate (2020)

Abstract Schistosomes are parasitic flatworms causing one of the most prevalent infectious diseases from which millions of people are currently suffering. Their germline outputs many fertilized eggs, which are both the transmissible agents and the cause of the infection-associated pathology. Given its significance, the schistosome germline has been a research focus for more than a century. Nonetheless, little is known about the molecular mechanisms that regulate its development. Here, we construct a transcriptomic cell type atlas of juvenile schistosomes. This allows us to capture germline stem cells (GSCs) during de novo gonadal development. We identify a genetic program that balances the fate of GSC between proliferation and differentiation. This program is controlled by onecut , a homeobox transcription factor, and boule , an mRNA binding protein. Evaluating this genetic program in schistosome’s free-living evolutionary cousin, the planarian, shows that this germline-specific regulatory program is conserved but its function has changed significantly during evolution.
Supramolecular Zinc Phthalocyanine–Imidazolyl Perylenediimide Dyad and Triad: Synthesis, Complexation, and Photophysical Studies (2011)

Two new supramolecular architectures based on zinc phthalocyanine (Pc) and imidazolyl-substituted perylenediimide (PDI), ZnPc/DImPDI/ZnPc 1 and ZnPc/ImPDI 2, have been prepared. A strong electron-donor, ZnPc-8, which contained eight tert-octylphenoxy groups was synthesized to ensure high solubility, thereby reducing aggregation in solution and providing σ-donor features while avoiding regioisomeric mixtures. Also, PDI units were functionalized with tert-octylphenoxy groups at the bay positions, which provide solubility to avoid aggregation in solution, together with one and two imidazole moieties in the amide position, PDI-6 and PDI-4, respectively, to be able to strongly coordinate with the ZnPc complex. Supramolecular complexation studies by (1)H NMR spectroscopy and ESI-MS demonstrate a high coordinative binding constant between imidazole-substituted PDI-4 or PDI-6 and ZnPc-8. The same results were confirmed by UV/Vis and fluorescence titration studies. UV/Vis titration studies revealed the formation of a 1:1 complex ZnPc/ImPDI 2 for the systems ZnPc-8 and PDI-6 and a 2:1 complex ZnPc/DImPDI/ZnPc 1 for the interaction of ZnPc-8 and PDI-4. The binding constant in both cases was determined to be on the order of 10(5) M(-1). Femtosecond laser flash photolysis measurements provided a direct proof of the charge-separated state within both supramolecular assemblies by observing the transient absorption band at 820 nm due to the zinc phthalocyanine radical cation. The lifetimes of charge-separated states are (9.8±3) ns for triad 1 and (3±1) ns for dyad 2. As far as we know, this is the first time that a radical ion pair has been detected in a supramolecular assembled ZnPc-PDI system and has obtained the longest lifetime of a charge-separated state published for ZnPc-PDI assemblies.
Development of Related HCV Protease Inhibitors: Macrocyclization of Two Highly Functionalized Dienyl-ureas via Ring-Closing Metathesis (2013)

A novel assembly of two structurally related 14-membered ring macrocyclic hepatitis C virus protease inhibitors is presented. Key to their successful construction was an ultimate ring-closing metathesis step on the respective highly functionalized dienyl-ureas. In the case of IDX316, this procedure significantly outperformed the original macrocyclizations in terms of reaction conditions, impurity profile, product isolation, and basic efficiency metrics. Simple nonchromatographic purification methods achieved sub-10-ppm ruthenium content in the isolated product. Overall yields to IDX316 from all five starting materials ranged from 11 to 40%, and the estimated process mass intensity was improved by a factor of 50 relative to the original unscalable discovery-based routes. Application of similar methodology in the case of IDX320 and first scale-up to half-kilogram batch sizes was demonstrated.
The Carbon Dioxide Laser as an Aid in Apicoectomy: An in Vitro Study (1997)

CO2 laser treatment optimally prepares the tooth for final intraoperative filling because of sealing of the dentinal tubules, the resultant elimination of niches for bacteria and the sterilizing effect of the laser.
Clonal Hematopoiesis with Oncogenic Potential (CHOP): Separation from CHIP and Roads to AML (2019)

The development of leukemia is a step-wise process that is associated with molecular diversification and clonal selection of neoplastic stem cells. Depending on the number and combinations of lesions, one or more sub-clones expand/s after a variable latency period. Initial stages may develop early in life or later in adulthood and include premalignant (indolent) stages and the malignant phase, defined by an acute leukemia. We recently proposed a cancer model in which the earliest somatic lesions are often age-related early mutations detectable in apparently healthy individuals and where additional oncogenic mutations will lead to the development of an overt neoplasm that is usually a preleukemic condition such as a myelodysplastic syndrome. These neoplasms may or may not transform to overt acute leukemia over time. Thus, depending on the type and number of somatic mutations, clonal hematopoiesis (CH) can be divided into CH with indeterminate potential (CHIP) and CH with oncogenic potential (CHOP). Whereas CHIP mutations <i>per se</i> usually create the molecular background of a neoplastic process, CHOP mutations are disease-related or even disease-specific lesions that trigger differentiation and/or proliferation of neoplastic cells. Over time, the acquisition of additional oncogenic events converts preleukemic neoplasms into secondary acute myeloid leukemia (sAML). In the present article, recent developments in the field are discussed with a focus on CHOP mutations that lead to distinct myeloid neoplasms, their role in disease evolution, and the impact of additional lesions that can drive a preleukemic neoplasm into sAML.
Data from A Cryptic Vascular Endothelial Growth Factor T-Cell Epitope: Identification and Characterization by Mass Spectrometry and T-Cell Assays (2023)

&lt;div&gt;Abstract&lt;p&gt;Vascular endothelial growth factor (VEGF) is involved in various physiologic processes, such as angiogenesis or wound healing, but is also crucial in pathologic events, such as tumor growth. Thus, clinical anti-VEGF treatments have been developed that could already show beneficial effects for cancer patients. In this article, we describe the first VEGF-derived CD8&lt;sup&gt;+&lt;/sup&gt; T-cell epitope. The natural HLA ligand SRFGGAVVR was identified by differential mass spectrometry in two primary renal cell carcinomas (RCC) and was significantly overpresented on both tumor tissues. SRFGGAVVR is derived from a cryptic translated region of VEGF presumably by initiation of translation at the nonclassic start codon CUG&lt;sup&gt;499&lt;/sup&gt;. SRFGGAVVR-specific T cells were generated &lt;i&gt;in vitro&lt;/i&gt; using peptide-loaded dendritic cells or artificial antigen-presenting cells. SRFGGAVVR-specific CD8&lt;sup&gt;+&lt;/sup&gt; T cells, identified by HLA tetramer analysis after &lt;i&gt;in vitro&lt;/i&gt; stimulation, were fully functional T effector cells, which were able to secrete IFN-γ on stimulation and killed tumor cells &lt;i&gt;in vitro&lt;/i&gt;. Additionally, we have quantitatively analyzed VEGF mRNA and protein levels in RCC tumor and normal tissue samples by gene chip analysis, quantitative reverse transcription-PCR, &lt;i&gt;in situ&lt;/i&gt; hybridization, and bead-based immunoassay. In the future, T cells directed against VEGF as a tumor-associated antigen may represent a possible way of combining peptide-based anti-VEGF immunotherapy with already existent anti-VEGF cancer therapies. [Cancer Res 2008;68(7):2447–54]&lt;/p&gt;&lt;/div&gt;
Distributed Multiple Access and Flow Control for Wireless Network Coding (2010)

In this paper we propose network coding to perform multi-hop multicast wireless transmissions. More specifically, we address the problem of reducing redundancy in the completely distributed operation of network coding, so as to increase network throughput. In order to do so, we propose a distributed system where network nodes autonomously make decisions with respect to the packets to encode and forward, with the goal of maximizing the data detection probability and minimizing the overhead of transmitted packets. Our setup consists of a Slotted Aloha network where nodes inject packets at a rate which depends on how useful these packets are to other nodes. We model the selection of transmission probabilities by means of a game theoretic approach, in which nodes reach the desired transmission probabilities as an equilibrium solution to the game. Simulation results show that the proposed scheme outperforms a Slotted Aloha system with optimal uniform retransmission probability.
Purification and Properties of 3‐Hexulosephosphate Synthase from Methylomonas M 15 (1976)

3‐Hexulosephosphate synthase, the first enzyme of the ribulose monophosphate cycle, was purified 15‐fold from methanol‐grown Methylomonas M 15. The purification procedure involved chromatography on DEAE‐cellulose, Sephadex G‐75, and DEAE‐Sephadex A‐50. The purified enzyme was more than 95% pure as judged by analytical polyacrylamide gel electrophoresis. The molecular weight was calculated to be 43000 from sedimentation equilibrium experiments. Electrophoresis in sodium dodecylsulfate gels gave a single band corresponding to a molecular weight of 22000. The enzyme catalyzes specifically the condensation of formaldehyde with ribulose 5‐phosphate to yield d ‐ arabino ‐3‐hexulose 6‐phosphate. The K m values were found to be 1.1 mM for formaldehyde and 1.6 mM for ribulose 5‐phosphate. A bivalent cation is essential for activity and stability of the enzyme, Mg 2+ and Mn 2+ serve best for this purpose. The optimum of pH for enzyme activity is 7.5–8.0.
Demand-supply matching through auctioning for the circular economy (2021)

The circular economy aims to reduce the consumption of resources and energy by exploiting multiple use-cycles of components and materials. The creation of new circular businesses hinges on efficient alignment between market demands of circular products with the supply of End-of-life components and materials. In this paper, we address the digitization of a matchmaking tool for the circular economy by defining demand-supply matching (DSM) in context of business link identification and cross-sectorial matchmaking. We further specify a DSM process and p resent our DSM tool, which facilitates publication and search for supplier offerings and demander needs, selection of auctioning candidates, and digitized auctioning and contract definition. By that, this tool supports the alignment of market demands with matching supply offerings. In particular, it combines the steps of publishing, searching, selecting, auctioning and contract definition into one tool, which we argue can make matchmaking more efficient compared to addressing these steps separately. Finally, we present the design of the tool and discuss its merits in light of the needed acceptance for automating business link identification and contractual interactions.