gebhart/patrepeval huggingface dataset:
Multidimensional endotyping in patients with severe asthma reveals inflammatory heterogeneity in matrix metalloproteinases and chitinase 3–like protein 1 (2016)

In 2 distinct cohorts we have identified and replicated 6 clinicopathobiologic clusters based on blood and induced sputum measures. Our data underline a disconnect between clinical features and underlying inflammation, suggest IL-5 production is relatively steroid insensitive, and highlight the expression of YKL-40 in patients with neutrophilic inflammation and the expression of MMPs in patients with severe asthma.
Pulsatile microvascular blood flow imaging by short-time Fourier transform analysis of ultrafast laser holographic interferometry (2015)

We report on wide-field imaging of pulsatile microvascular blood flow in the exposed cerebral cortex of a mouse by holographic interferometry. We recorded interferograms of laser light backscattered by the tissue, beating against an off-axis reference beam with a 50 kHz framerate camera. Videos of local Doppler contrasts were rendered numerically by Fresnel transformation and short-time Fourier transform analysis. This approach enabled instantaneous imaging of pulsatile blood flow contrasts in superficial blood vessels over 256 × 256 pixels with a spatial resolution of 10 microns and a temporal resolution of 20 ms.
Condensed Thiophenes and Selenophenes: Thionyl Chloride and Selenium Oxychloride as Sulfur and Selenium Transfer Reagents. (2002)

Abstract For Abstract see ChemInform Abstract in Full Text.
Impact of different cellular-IP convergence strategies on mobile terminals (2002)

The last few years has seen a proliferation of the Internet, making it accessible to several millions of users worldwide. At the same time, the use of mobile devices such as cellular telephones and personal digital assistants (PDA) has been on the rise. Currently, we are beginning to see the convergence of these technologies whereby access to the Internet and other (potentially private) packet switched networks happens via mobile devices. The Internet protocol (IP) and the associated TCP/IP protocol suite - which is used in the Internet - is beginning to find its way into mobile devices as well. However, the cellular-IP convergence strategy and the extent to which the TCP/IP protocol suite is being embraced varies from one cellular standard to another. We compare differences in cellular-IP convergence strategies and discuss the impact that this has on cellular terminals.
Downregulation of bcl-2 by antisense oligonucleotides reduces tumor size and improves chemosensitivity of human melanoma in SCID mice (1997)

Jansen, B1,2; Wadl, H1,2; Brown, D B; Bryan, R; Wolff, K1; Eichler, H-G2; Pehamberger, H1 Author Information
Abstract 1943: miR-148a overexpression reduces TRAIL resistance and tumorigenesis in NSCLC. (2013)

Abstract Non-small cell lung cancer (NSCLC) is the leading cause of death from cancer throughout the world. Although some advances have been made in lung cancer therapy, patient survival is still poor. Tumor-necrosis factor related apoptosis-inducing ligand (TRAIL) has been shown to induce apoptosis in malignant cells without inducing significant toxicity in normal cells. However, several carcinomas, including lung cancer, remain resistant to TRAIL. MicroRNAs (miRNAs) are small non-coding RNAs of ∼24 nt that can block mRNA translation and/or negatively regulate its stability. miRNAs are often aberrantly expressed in cancer and their function is linked to the regulation of oncogenes and/or tumor suppressor genes involved in cell signaling pathways. Several miRNAs have been implicated in increasing susceptibility or resistance to TRAIL-induced apoptosis by inhibiting key functional proteins. In order to identify the miRNAs involved in TRAIL resistance in NSCLC, we evaluated the differential expression of miRNAs in H460 sensitive cells compared with H460R cells that have acquired TRAIL-resistance. MiR-148a was the most downregulated miR in the acquired resistant cells compared to the sensitive cells. Treatment of NSCLC cells with TRAIL after miR-148a overexpression decreased cell viability and increased apoptosis. Furthermore, miR-148a overexpression induced downregulation of matrix metalloproteinase 15 (MMP15) and Rho-associated kinase 1 (ROCK1) by targeting their 3’ untranslated regions as analysed by Western blot and luciferase reporter assay. Previous studies have shown that MMP15 acts as an anti-apoptotic factor involved in TRAIL resistance in cancer cells. Both, MMP15 and ROCK1 have been reported to be activators of tumor invasion and migration. Our preliminary functional studies using small interference RNA (siRNA) knockdowns of these genes in NSCLC cells support these data. A better understanding of the tumor-supressive role of miR-148a could be the key to developing an effective prognostic and therapeutic tool for treating NSCLC. Citation Format: Pooja Joshi, Michela Garofalo, Carlo M. Croce. miR-148a overexpression reduces TRAIL resistance and tumorigenesis in NSCLC. [abstract]. In: Proceedings of the 104th Annual Meeting of the American Association for Cancer Research; 2013 Apr 6-10; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2013;73(8 Suppl):Abstract nr 1943. doi:10.1158/1538-7445.AM2013-1943
Sea ice motion measurements from SEASAT SAR images (1983)

Satellite imaging radar is expected to become the prime instrument for mapping the distribution and motion of sea ice on a periodic basis, The observational independence from weather, fog, and clouds and the fact that it provides its own illumination are decisive advantages that imaging radar has in the remote sensing of sea ice. The SEASAT spacecraft launched in 1978 included such an imaging radar, and approximately one fourth of all SEASAT SAR observations are of sea ice in the Beaufort Sea. Data from seven sequential orbits of the satellite were selected to study the capabilities and limitations of spaceborne radar application to sea‐ice mapping. The results are encouraging: (1) There is no difficulty in identifying homologue ice features on sequential radar images; (2) The accuracy is entirely controlled by accuracy of the orbit data and the geometric calibration of the sensor; (3) Conventional radargrammetric methods serve well for satellite radar ice mapping; (4) Ground control points can be used to calibrate the ice location and motion measurements in the cases where orbit data and sensor calibration are lacking. Ice motion was found to be approximately 6.4±0.5 km per day. However, higher accuracies are feasible with better timing calibration of the sensor events and knowledge of the orbit. The accuracy of pixel location was also determined over land areas. It was found that with the use of one control point in 10,000 km 2 the accuracy is about ±150 m. With higher density of control points (7 in 1000km2) the location accuracy improves to the image resolution (i.e., ±25 m). This is applicable for both optical and digital data.
PubNet: a flexible system for visualizing literature derived networks (2005)

We have developed PubNet, a web-based tool that extracts several types of relationships returned by PubMed queries and maps them into networks, allowing for graphical visualization, textual navigation, and topological analysis. PubNet supports the creation of complex networks derived from the contents of individual citations, such as genes, proteins, Protein Data Bank (PDB) IDs, Medical Subject Headings (MeSH) terms, and authors. This feature allows one to, for example, examine a literature derived network of genes based on functional similarity.
Dual-Component Gelatinous Peptide/Reactive Oligomer Formulations as Conduit Material and Luminal Filler for Peripheral Nerve Regeneration (2017)

Toward the next generation of nerve guidance conduits (NGCs), novel biomaterials and functionalization concepts are required to address clinical demands in peripheral nerve regeneration (PNR). As a biological polymer with bioactive motifs, gelatinous peptides are promising building blocks. In combination with an anhydride-containing oligomer, a dual-component hydrogel system (cGEL) was established. First, hollow cGEL tubes were fabricated by a continuous dosing and templating process. Conduits were characterized concerning their mechanical strength, in vitro and in vivo degradation and biocompatibility. Second, cGEL was reformulated as injectable shear thinning filler for established NGCs, here tyrosine-derived polycarbonate-based braided conduits. Thereby, the formulation contained the small molecule LM11A-31. The biofunctionalized cGEL filler was assessed regarding building block integration, mechanical properties, in vitro cytotoxicity, and growth permissive effects on human adipose tissue-derived stem cells. A positive in vitro evaluation motivated further application of the filler material in a sciatic nerve defect. Compared to the empty conduit and pristine cGEL, the functionalization performed superior, though the autologous nerve graft remains the gold standard. In conclusion, LM11A-31 functionalized cGEL filler with extracellular matrix (ECM)-like characteristics and specific biochemical cues holds great potential to support PNR.
In Vivo Photopharmacology Enabled by Multifunctional Fibers (2020)

Photoswitchable ligands can add an optical switch to a target receptor or signaling cascade and enable reversible control of neural circuits. The application of this approach, termed photopharmacology, to behavioral experiments has been impeded by a lack of integrated hardware capable of delivering both light and compounds to deep brain regions in moving subjects. Here, we devise a hybrid photochemical genetic approach to target neurons using a photoswitchable agonist of the capsaicin receptor TRPV1, <i>red</i>-AzCA-4. Using multifunctional fibers with optical and microfluidic capabilities, we delivered a transgene coding for TRPV1 into the ventral tegmental area (VTA). This sensitized excitatory VTA neurons to <i>red</i>-AzCA-4, allowing us to optically control conditioned place preference in mice, thus extending applications of photopharmacology to behavioral experiments. Applied to endogenous receptors, our approach may accelerate future studies of molecular mechanisms underlying animal behavior.
Mutation of the Protein Kinase C Phosphorylation Site on Rat α1 Na+,K+-ATPase Alters Regulation of Intracellular Na+ and pH and Influences Cell Shape and Adhesiveness (1997)

The enzyme Na+,K+-ATPase creates the transmembrane Na+ gradient that is of vital importance for functioning of all eukaryotic cells. Na+, K+-ATPase can be phosphorylated by protein kinase A (PKA) and protein kinase C (PKC), and these sites of phosphorylation have been identified. In the present study, we have examined the physiological significance of PKC phosphorylation of rat Na+,K+-ATPase. In COS cells transfected with wild type rat Na+,K+-ATPase alpha1, intracellular Na+ was higher and pH was lower than in cells transfected with rat Na+,K+-ATPase alpha1 in which the PKC phosphorylation site, Ser-23, had been mutated into alanine. Phorbol dibutyrate inhibited Na+,K+-ATPase-dependent ATP hydrolysis and Rb+ uptake in cells expressing wild type Na+,K+-ATPase but not in cells expressing S23A Na+,K+-ATPase. Cells expressing the S23A mutant had a more rounded appearance and attached less well to fibronectin than did untransfected cells or cells transfected with wild type rat Na+, K+-ATPase alpha1. These results indicate a functional role for PKC-mediated phosphorylation of rat Na+,K+-ATPase alpha1 and suggest a connection between this enzyme and cell adhesion.
Binder‐Free and Full Electrical‐Addressing Free‐Standing Nanosheets with Carbon Nanotube Fabrics for Electrochemical Applications (2011)

A unique manufacturing route to build a layer-by-layer (LBL) structure of two-dimensionally ordered, free-standing β-nickel hydroxide nanosheets that are fully electrically addressed with single-wall carbon nanotube fabrics is demonstrated. The performance of the system is verified by a comparative study on the differences between simple bulky and LBL-structured electrochemical cathodes, representing two extreme cases. Detailed facts of importance to specialist readers are published as ”Supporting Information”. Such documents are peer-reviewed, but not copy-edited or typeset. They are made available as submitted by the authors. Please note: The publisher is not responsible for the content or functionality of any supporting information supplied by the authors. Any queries (other than missing content) should be directed to the corresponding author for the article.
Light-emitting diodes with integrated omnidirectionally reflective contacts (2004)

An electrically conductive omnidirectional reflector (ODR) is demonstrated as p-type ohmic contact for an AlGaInP light-emitting diode (LED). The ODR comprises the semiconductor, a metal layer and an intermediate low-refractive index dielectric layer. The SiO<sub>2</sub> dielectric layer, located between a GaP and a silver layer, is perforated by an array of AuZn micro-contacts thus enabling electrical conductivity. It is shown that the ODR-LED has a significantly higher light-extraction efficiency as compared to LEDs employing distributed Bragg reflectors (DBRs). For devices emitting in the red wavelength range, external quantum efficiencies of 18 % and 11 % are obtained for ODR- and DBR-LEDs, respectively. The performance of the ODR-LED can be further increased by replacing the SiO2 dielectric with materials having a refractive index << 1.45. Performance characteristics of such powerful reflectors will be presented.
Supplementary Methods from Phase I Basket Study of Taselisib, an Isoform-Selective PI3K Inhibitor, in Patients with <i>PIK3CA</i>-Mutant Cancers (2023)

&lt;p&gt;Supplementary Methods&lt;/p&gt;
Cutting Edge: Evidence of Direct TCR α-Chain Interaction with Superantigen (2007)

Superantigens are known to activate a large number of T cells. The SAg is presented by MHC class II on the APC and its classical feature is that it recognizes the variable region of the beta-chain of the TCR. In this article, we report, by direct binding studies, that staphylococcal enterotoxin (SE) H (SEH), a bacterial SAg secreted by Staphylococcus aureus, instead recognizes the variable alpha-chain (TRAV27) of TCR. Furthermore, we show that different SAgs (e.g., SEH and SEA) can simultaneously bind to one TCR by binding the alpha-chain and the beta-chain, respectively. Theoretical three-dimensional models of the penta complexes are presented. Hence, these findings open up a new dimension of the biology of the staphylococcal enterotoxins.
Hybrid Electrodeposition of Ag-Graphene Composite Films on Cu Alloys for High-Conductive and Wear-Resistive Automotive Connectors (2020)

In recent years, plug-in hybrid electric vehicles (PHEV) and plug-in hybrid vehicles (PHV) have become popular due to depletion of fossil fuels. At the tip of the wire harness, which is said to be the nerve of automobiles, there are numerous terminal connectors that are connected to various electronic devices, and the demand for their reliability is every increasing with the progress of PHEVs and PHVs. Considering the conductivity and heat generation, Cu alloys that plated with a highly conductive Ag film are commonly used. However, in addition to the problem of soaring costs due to the increased use of noble Ag, which is a, there is an important problem that the wear resistance of Ag is insufficient because of its adhesiveness during sliding and/or its soft nature, which has been unsolved yet. In this study, we are aimed at fabricating a novel Ag-graphene composite films on Cu alloys though a facile hybrid electrodeposition. Here, graphene is used to function as an effective solid lubricant, while maintaining the conductivity of Ag matrix plating films that are indispensable to various automotive connectors. A commercial Cu alloy sheet was used as the base material. Graphene was produced by electrolytically exfoliating Graphite. A cyan-free Ag plating solution containing home-made graphene nano-flakes was adopted in electrodeposition. The thickness of the deposited films was designed to be 5 mm and controlled by depositing conditions. The resultant specimens were investigated by FE-SEM, EDX, GD-OES, Raman spectroscopy. The properties such as hardness, resistivity, and wear resistance were also evaluated. Fig.1 shows the surface FE-SEM images of as-deposited pure Ag and Ag-graphene films. Both the pure Ag and the Ag-graphene composite film were smooth, consisting of nano-sized fine particles. It can be seen in the Ag-graphene composite film that, there were some areas where the particle size was slightly larger, and moreover, a hazy film-like material was observed on them, which was examined as C by EDS analysis. Fig. 2 shows the Raman spectroscopic measurement results of the pure Ag film and the Ag-graphene composite films. Compared to peak-less spectrum of pure Ag film, three typical peaks were detected in Ag-graphene composite film. The detected peaks are indexed to be D-band, G-band, and 2D-band from graphene, thus indicating the co-deposition of Ag and graphene flakes during the hybrid Ag electrodeposition and graphene electrophoretic deposition. Moreover, it was also found that the Ag-graphene composite films exhibited higher hardness and lower friction coefficient compared to the pure Ag film, thus confirming a promising candidate material for high-conductive and wear-resistive automotive connectors. Figure 1
SALSA VERDE: a machine learning attack on Learning With Errors with sparse small secrets (2023)

Learning with Errors (LWE) is a hard math problem used in post-quantum cryptography. Homomorphic Encryption (HE) schemes rely on the hardness of the LWE problem for their security, and two LWE-based cryptosystems were recently standardized by NIST for digital signatures and key exchange (KEM). Thus, it is critical to continue assessing the security of LWE and specific parameter choices. For example, HE uses secrets with small entries, and the HE community has considered standardizing small sparse secrets to improve efficiency and functionality. However, prior work, SALSA and PICANTE, showed that ML attacks can recover sparse binary secrets. Building on these, we propose VERDE, an improved ML attack that can recover sparse binary, ternary, and narrow Gaussian secrets. Using improved preprocessing and secret recovery techniques, VERDE can attack LWE with larger dimensions ($n=512$) and smaller moduli ($\log_2 q=12$ for $n=256$), using less time and power. We propose novel architectures for scaling. Finally, we develop a theory that explains the success of ML LWE attacks.
Two Types of Spheroid Bodies in the Nigral Neurons in Parkinson's Disease (1991)

Dendritic spheroid bodies (SBs) and Lewy bodies (LBs) were identified in comparable numbers in the substantia nigra pars compacta (SBC) of nine parkinsonian cases and one case of striatonigral degeneration but were not found in cases of Huntington's disease or neurologically normal controls. The immunohistochemical profile of the SBs in dystrophic dendrites of nigrostriatal dopaminergic neurons was remarkably similar to that of the LBs found within dendrites or free of the SNC neuropil. Both types of inclusions stained positively with antibodies to tyrosine hydroxylase, ubiquitin and microtubule-associated protein-2 (MAP2), and negatively for Tau-2, although they had different ultrastructural appearances. A few intracellular LBs were stained by antibodies to neurofilament proteins (NFs) 68, 160, and 200 kD, but dendritic SBs and extracellular LBs were not so stained. These data indicate that dendritic SBs and extracellular LBs may have a common molecular pathogenetic origin in Parkinson's disease. On the other hand, the SBs seen in the pars reticulata (SNR) and in the distal nigrostriatal axons even in control cases were generally stained by antibodies to NFs and ubiquitin but not to MAP2. This latter staining pattern in similar to that shown by SBs in the anterior horn in ALS and in the cerebellum of neurologically normal brains and is believed typical of axonal as opposed to dendritic SBs.
Endomagnet: Magnetic Compression Anastomosis by Therapeutic Endoscopy (2017)

Interest for magnetic solutions used for endoscopy has grown in the past years. Among those, magnetic pressure anastomosis has been already developed by different teams, but no solutions are yet available for physicians. This solution enables leakage- and bleeding free procedure, without surgery. Reasons – not exhaustive – for that is the need for two endoscopes, the necessity of using a laparoscopic camera to secure the procedure, and the difficulty to have a wide opening compared to the device. Our department is developing a new magnetic solution, avoiding the problems described above when creating anastomosis in the GI tract.
Visualizing and Quantifying Charge Distributions Correlated to Threshold Voltage Shifts in Lateral Organic Transistors (2014)

Lateral organic field-effect transistors (OFETs), consisting of a polystyrene (PS) polymer gate material and a pentacene organic semiconductor (OSC), were electrically polarized from bias stress during operation or in a separate charging step, and investigated with scanning Kelvin probe microscopy (SKPM) and current-voltage determinations. The charge storage inside the polymer was indicated, without any alteration of the OFET, as a surface voltage with SKPM, and correlated to a threshold voltage (VT) shift in the transistor operation. The SKPM method allows the gate material/OSC interface of the OFET to be visualized and the surface voltage variation between the two gate material interfaces to be mapped. The charge distribution for three samples was derived from the surface voltage maps using Poisson's equation. Charge densities calculated this way agreed with those derived from the VT shifts and the lateral gate-OSC capacitance. We also compared the behavior of two other polymers with PS: PS accepted the most static charge in its entire volume, poly(2-trifluoromethylstyrene) (F-PS) had the most stability to bias stress, and poly(methyl methacrylate) (PMMA) showed the most leakage current and least consistent response to static charging of the three polymers. This work provides a clear demonstration that surface voltage on a working OFET gate material can be related to the quantity of static charge responsible for bias stress and nonvolatility in OFETs.
Co-ion Effects in the Self-Assembly of Macroions: From Co-ions to Co-macroions and to the Unique Feature of Self-Recognition (2020)

Macroions, as soluble ions with a size on the nanometer scale, show unique solution behavior different from those of simple ions and large colloidal suspensions. In macroionic solutions, the counterions are known to be important and well-explored. However, the role of co-ions (ions carrying the same type of charge as the macroions) is often ignored. Here, through experimental and simulation studies, we demonstrate the role of co-ions as a function of co-ion size on their interaction with the macroions (using {Mo<sub>72</sub>Fe<sub>30</sub>} and {SrPd<sub>12</sub>} as models) and the related self-assembly into blackberry-type structures in dilute solutions. Several regimes of unique co-ion effects are clearly identified: small ions (halides, oxoacid ions), subnanometer-scaled bulky ions (lacunary Keggin and dodecaborate ions), and those with sizes comparable to the macroions. Small co-ions have no observable effect on the self-assembly of fully hydrophilic {Mo<sub>72</sub>Fe<sub>30</sub>}, while due to hydrophobic interaction and intermolecular hydrogen bonds, the small co-ions show influences on the self-assembly of hydrophobic {SrPd<sub>12</sub>}. Subnanometer ions, a.k.a. "superchaotropic ions", are still too small to assemble into a blackberry by themselves, but they can coassemble with the macroions, showing a strong interaction with the macroionic system. When the co-ion size is comparable to that of the macroions, they assemble independently instead of assembling with the macroions, leading to the previously reported unique self-recognition phenomenon for macroions.