gebhart/patrepeval huggingface dataset:
Systematically Prioritizing Functional Differentially Methylated Regions (fDMRs) by Integrating Multi-omics Data in Colorectal Cancer (2015)

While genome-wide differential DNA methylation regions (DMRs) have been extensively identified, the comprehensive prioritization of their functional importance is still poorly explored. Here, we aggregated multiple data resources rooted in the genome, epigenome and transcriptome to systematically prioritize functional DMRs (fDMRs) in colorectal cancer (CRC). As demonstrated, the top-ranked fDMRs from all of the data resources showed a strong enrichment for known methylated genes. Additionally, we analyzed those top 5% DMR-coupled coding genes using functional enrichment, which resulted in significant disease-related biological functions in contrast to the tail 5% genes. To further confirm the functional importance of the top-ranked fDMRs, we applied chromatin modification alterations of CRC cell lines to characterize their functional regulation. Specifically, we extended the utility of the top-ranked DMR-coupled genes to serve as classification and survival biomarkers, which showed a robust performance across diverse independent data sets. Collectively, our results established an integrative framework to prioritize fDMRs, which could help characterize aberrant DNA methylation-induced potential mechanisms underlying tumorigenesis and uncover epigenome-based biomarkers for clinical diagnosis and prognosis.
Mucosal nasopharyngeal immune responses of horses to protein antigens of Streptococcus equi (1985)

Mucosal nasopharyngeal immunoglobulin A (IgA) and IgG responses to proteins of Streptococcus equi were studied in horses after the experimental production of strangles. S. equi-specific IgA and IgG titers in nasopharyngeal mucus were much higher in samples from animals 1 to 2 weeks after challenge than in samples from control animals. Although IgA was the major immunoglobulin in nasal mucus, there was more antibody activity associated with IgG as measured by radioimmunoassay. Great differences between the specificities of antibodies in nasal mucus and in serum were detected. IgA and IgG of mucus origin recognized only two major proteins with molecular weights of about 41,000 and 46,000 in acid extracts of S. equi and gave no detectable reaction with culture supernatant proteins. Only one protein of about 62,000 molecular weight was recognized in acid extracts of an equine strain of S. zooepidemicus. In contrast, immunoglobulins in serum recognized a great variety of proteins in culture supernatants and acid extracts of S. equi and S. zooepidemicus which did not include those proteins recognized by immunoglobulins in mucus. These findings provide good evidence for the independence of the local and systemic immune responses of the horse to S. equi. Horses rechallenged shortly after recovery from the first infection were resistant to challenge with an inoculum of S. equi 10 times greater than that to which they were originally susceptible. This resistance appeared to be independent of the levels of bactericidal antibody in serum. We therefore suggest that immunity to S. equi infection is mediated by locally produced nasopharyngeal antibodies.
Development and in vitro evaluation of an acid buffering bioadhesive vaginal gel for mixed vaginal infections (2008)

An acid buffering bioadhesive vaginal (ABBV) gel was developed for the treatment of mixed vaginal infections. Different bioadhesive polymers were evaluated on the basis of their bioadhesive strength, stability and drug release properties. Bioadhesion and release studies showed that guar gum, xanthan gum and hydroxypropyl methylcelullose K4M formed a good combination of bioadhesive polymers to develop the ABBV gel. Monosodium citrate was used as an acid buffering agent to provide acidic pH (4.4). The drugs clotrimazole (antifungal) and metronidazole (antiprotozoal as well as antibacterial) were used in the formulation along with Lactobacillus spores to treat mixed vaginal infections. The ex vivo retention study showed that the bioadhesive polymers hold the gel for 12-13 hours inside the vaginal tube. Results of the in vitro antimicrobial study indicated that the ABBV gel had better antimicrobial action than the commercial intravaginal drug delivery systems and retention was prolonged in an ex vivo retention experiment.
Fluorescent Aptaswitch for Detection of Lead Ions (2022)

Detection of metal ions has essential roles in biology, food industry, and environmental sciences. In this work, we developed a Pb<sup>2+</sup> detection strategy based on a fluorophore-tagged Pb<sup>2+</sup>-binding aptamer. The DNA aptamer changes its conformation on binding Pb<sup>2+</sup>, switching from an "off" state (low fluorescence) to an "on" state (high fluorescence). This method provides a quantitative readout with a detection limit of 468 nM, is highly specific to Pb<sup>2+</sup> when tested against other metal ions, and is functional in complex biofluids. Such metal sensing DNA aptamers could be coupled with other biomolecules for sense-and-actuate mechanisms in biomedical and environmental applications.
Influence of P on Solubility of C and on Snoek Peak in Low Carbon Steels (1991)

The influence of P on the solubility of C in ferrite equilibrium with cementite was investigated in low carbon steels containing P ranging from 0 to 0.21 mass% over a temperature from 573 to 973 K. Internal friction method was employed together with chemical analysis of C by means of the infrared absorption method after combustion.It has been clarified that P increases the solubility of C in ferrite in equilibrium with cementite, whereas P reduces the Snoek peak height despite the fact that the amount of C in solid solution is constant. The proportionality constant K in the equation, Sol. C (mass ppm)=K×Qmax−1(10−4), was experimentally determined as a function of P content and it was clarified that K increases with increasing P content.Taking into account the fact that the reduction of Sneok peak height increases with Co, Mn, and P addition in this order, the elastic strain around the substitutional atom due to the diffrence in atomic radius is postulated to be the main reason why Snoek peak height decreases with the addition of alloying elements. Here, the solute C in the lattice-strained region is supposed to be unable to contribute to the Snoek peak.
Cyber-enhanced canine suit with wide-view angle for three-dimensional LiDAR SLAM for indoor environments (2020)

Understanding the topographical information of the disaster site can enhance the efficiency and safety of search and rescue missions. This study describes the development of a cyber-enhanced canine suit for three-dimensional (3D) simultaneous localization and mapping within indoor environments. The suit's weight was approximately 3.0 kg and was compatible with large dogs (>30.0 kg). It could collect dense, wide view-angle, and long-range 3D point clouds. The collected point clouds were processed offline to create 3D maps. The suit was equipped with a protective cover that could prevent physical damage to the light imaging detection and ranging (LiDAR) sensor from collision. The protective cover was designed to (a) eliminate any effects on the performance of the 3D LiDAR and (b) sustain the stress from the impact at the velocity of 20.0 m/s with no physical damage. Additionally, the canine suit was also modified for better fitting and stability of the LiDAR on a wider range of dog bodies. The performance of the suit was demonstrated on real dogs in four different scenarios in areas with different space sizes, dog gait patterns, and ground layouts. The space size and position errors observed did not exceed 0.80% and 1.13%, respectively.
On the conformation of benzo-annelated bicyclo[4.4.1]undecanes, bicyclo[5.5.1]tridecanes, and a bicyclo[5.4.1]dodecane (1986)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTOn the conformation of benzo-annelated bicyclo[4.4.1]undecanes, bicyclo[5.5.1]tridecanes, and a bicyclo[5.4.1]dodecaneShuntaro Mataka, Kazufumi Takahashi, Toshizumi Hirota, Keisuke Takuma, Hiroshi Kobayashi, Masashi Tashiro, Kiyohisa Imada, and Minoru KuniyoshiCite this: J. Org. Chem. 1986, 51, 24, 4618–4622Publication Date (Print):November 1, 1986Publication History Published online1 May 2002Published inissue 1 November 1986https://pubs.acs.org/doi/10.1021/jo00374a023https://doi.org/10.1021/jo00374a023research-articleACS PublicationsRequest reuse permissionsArticle Views200Altmetric-Citations20LEARN 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 Get e-Alerts
Comparison of GEANT4 and MCNPX-PoliMi fission models (2012)

The detection and characterization of special nuclear material (SNM) is of significant importance for nonproliferation applications. For neutron energies <;1 eV, fission is the dominating interaction process of all possible neutron-nucleus interactions, hence thermal neutron induced fission is one of the techniques that can be utilized for the characterization of the SNM. Prompt and delayed neutrons and gamma-rays are emitted per fission event. These multiplicities can be modeled using Monte Carlo techniques. However, the modeling of multiplicity distributions of prompt fission neutrons and gamma-rays is dependent not only upon statistical models but also upon tracking fission neutrons and gamma-rays on an event-by-event basis. Both Geant4 and MCNPX-PoliMi are capable of simulating particles on an event-by-event basis. In Geant4, the neutron and gamma-ray multiplicity distributions are computed using a customized fission library developed by the Lawrence Livermore National Laboratory (LLNL). The neutron and gamma-ray multiplicity distributions are also computed with MCNPX-PoliMi, which is a modified version of MCNP code. Simulations show that there is very good agreement in neutron multiplicities generated with these codes. Furthermore, various fission models can be simulated in these respective Monte Carlo codes.
Upregulation of striatal adenosine A2A receptor mRNA in 6‐hydroxydopamine‐lesioned rats intermittently treated with L‐DOPA (2004)

To determine whether the adenosine A2A receptor might play a role in L-DOPA-induced dyskinesia in Parkinson's disease, we analyzed changes in the expression of A2A receptor mRNA in response to intermittent treatment with L-DOPA in rats with dopaminergic denervation by 6-hydroxydopamine (OHDA) infusion into the medial forebrain bundle. Intermittent treatment with L-DOPA increased A2A receptor mRNA levels in the dopamine-depleted striatum of 6-OHDA-lesioned rats exhibiting behavioral sensitization to L-DOPA. These results suggest that A2A receptor activation is associated with the development of motor complications induced by L-DOPA treatment.
Microwave-Irradiated Transition-Metal Catalysis: Rapid and Efficient Dehydrative Carbon-Carbon Coupling of Alcohols with Active Methylenes (2008)

A rapid and highly productive synthetic microwave-irradiation­ protocol for transition-metal-catalyzed carbon-carbon coupling of a wide range of benzylic/allylic alcohols with β-diones, β-keto esters, and dialkyl malonates is reported. In a representative screening of transition-metal catalysts, salts of Zn, Cu, Fe, Sc, Ru, Pt, Ta, and Mo were found to furnish the coupling products. In light of the results obtained, among all of these catalysts copper(II) triflate was found to be relatively more effective compared to other catalysts even in the case of a less reactive benzyl alcohol or diester. Interestingly, these MW-irradiated reactions are performed in a more or less MW-transparent medium, such as toluene, having a very low tanδ, or under neat conditions.
High-throughput formation of lipid bilayer membrane arrays with an asymmetric lipid composition (2014)

We present a micro-device in which more than 10,000 asymmetric lipid bilayer membranes are formed at a time on micro-chamber arrays. The arrayed asymmetric lipid bilayers, where lipid compositions are different between the inner and outer leaflets, are formed with high efficiency of over 97% by injecting several types of liquids into a micro-device that has hydrophilic-in-hydrophobic surfaces. The lipid compositional asymmetry is an intrinsic property of bio-membranes, and therefore, this micro-device extends the versatility of artificial lipid-bilayer systems, which were previously limited to symmetric bilayer formation, and could contribute to the understanding of the role of lipid compositional asymmetry in cell physiology and also to further analytical and pharmacological applications.
Photonic Crystals Fabricated by Two-Photon Polymerization with Mechanical Defects (2023)

One-dimensional photonic crystals have been used in sensing applications for decades, due to their ability to induce highly reflective photonic bandgaps. In this study, one-dimensional photonic crystals with alternating low- and high-density layers were fabricated from a single photosensitive polymer (IP-Dip) by two-photon polymerization. The photonic crystals were modified to include a central defect layer with different elastic properties compared to the surrounding layers, for the first time. It was observed that the defect mode resonance can be controlled by compressive force. Very good agreement was found between the experimentally measured spectra and the model data. The mechanical properties of the flexure design used in the defect layer were calculated. The calculated spring constant is of similar magnitude to those reported for microsprings fabricated on this scale using two-photon polymerization. The results of this study demonstrate the successful control of a defect resonance in one-dimensional photonic crystals fabricated by two-photon polymerization by mechanical stimuli, for the first time. Such a structure could have applications in fields, such as micro-robotics, and in micro-opto–electro–mechanical systems (MOEMSs), where optical sensing of mechanical fluctuations is desired.
Electroless Deposition of Ag Nanoparticles on SiNx:H and SiOx Solar Cell Coatings (2010)

We report about a new low cost, fast and large area electroless technique for the formation of Ag nanoparticles with controlled size and density on the surface of SiNx:H and SiOx layers at room temperature and on the time scale of several minutes. The influence of the SiNx:H and SiOx layer stoechiometries on the size and density on Ag nanoparticles are discussed in details.
Adaptive Frequency-Domain Channel Estimator in 4$ \,\times \,$4 MIMO-OFDM Modems (2009)

This work presents an adaptive frequency-domain channel estimator (FD-CE) for equalization of space-time block code multiple-input multiple-output (MIMO) orthogonal frequency-division multiplexing (OFDM) systems in time-varying frequency-selective fading. The proposed adaptive FD-CE ensures the channel estimation accuracy in each set of four MIMO-OFDM symbols. Performance evaluation shows that the proposed method achieved a 10% packet error rate of 64 quadrature amplitude modulation (QAM) at 29.5 dB SNR under 120 km/h (Doppler shift is 266 Hz) in 4 times 4 MIMO-OFDM systems. To decrease complexity, the rich feature of Alamouti-like matrix is exploited to derive an efficient very large-scale integration (VLSI) solution. Finally, this adaptive FD-CE using an in-house 0.13-mu m CMOS library occupies an area of 3 times 3.1 mm <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sup> , and the 4 times 4 MIMO-OFDM modem consumes about 62.8 mW at 1.2 V supply voltage.
Low-cost active optical system for fire surveillance (2009)

Detection of smoke plumes using active optical sensors provides many advantages with respect to passive methods of fire surveillance. However, the price of these sensors is often too high as compared to passive fire detection instruments, such as infrared and video cameras. This article describes robust and cost effective diode-laser optical sensor for automatic fire surveillance in industrial environment. Physical aspects of the sensing process allowing to simplify the hardware and software design, eventually leading to significant reduction of manufacturing and maintenance costs, are discussed.
Abstract 2677: A detailed analysis of protein binding and biological activity of methoxy-substituted resorcinylic isoxazole amide HSP90 inhibitors (2010)

Abstract The molecular chaperone Heat Shock Protein 90 (HSP90) has emerged as an exciting biological target in cancer therapy. HSP90 regulates the conformation, stability and activity of several client proteins such as ERBB2, BRAF, CRAF, AKT and mutant p53, many of which are associated with the six hallmarks of cancer. Inhibition of HSP90 results in the degradation of these clients by the 26S proteasome, leading to cell cycle arrest and apoptosis. Resorcinylic isoxazole amide HSP90 inhibitors show considerable promise and NVP-AUY922 is currently in Phase I clinical trials. Our previous studies have reported that one or both of the phenolic groups on the resorcinol ring are important for HSP90 inhibitory activity (Brough et al J Med Chem 51 196-218 2008). To explore the mechanisms underlying the importance of the phenol groups on protein binding and biological activity, a series of monomethoxy- and dimethoxy-substituted resorcinylic 5′-ethyl isoxazole amides were synthesized and compared with the 2′,4′-dihydroxy compound by protein X-ray crystal structure and biological techniques. The most potent HSP90 inhibitors in this series in terms of binding to the HSP90 target and inhibiting cancer cell proliferation was the 2′,4′-dihydroxy-5′ethyl isoxazole CCT239215, followed by the 2′-hydroxy-4′methoxy-5′ethyl isoxazole CCT078722. In contrast, 2′,4′-dimethoxy and 2′-methoxy, 4′-hydroxy derivatives showed no binding to HSP90 or antiproliferative activity. This structure-activity relationship was also maintained with respect to biomarkers of HSP90 target inhibition, as measured by depletion of HSP90 client proteins and induction of HSP72. In HCT116 human colon cells treatment with 350nM of CCT239215 and CCT078722 for 4hr caused a loss of HSP90 from P23 immunoprecipitates, demonstrating dissociation between P23 and HSP90, thereby confirming on-target effects. No dissociation was observed with the inactive 2′-methoxy, 4′-hydroxy or 2′,4′-dimethoxy analogs. These results confirm that the hydroxy group at the 2′ position on the resorcinol ring is crucial for HSP90 inhibitory activity. X-ray crystal structures showed that for CCT078722, the 4′-methoxy group of the resorcinol ring disrupts the hydrogen bonding that is seen with 2′,4′-dihydroxy CCT239215 and with the clinical candidate NVP-AUY922, and instead is involved in van der Waals contacts. Thus the results provide a structural explanation for the reduced but still significant activity of the 2′-methoxy-subtituted analog and the lack of activity of the 2′,4′-dimethoxy-substituted compound. Note: This abstract was not presented at the AACR 101st Annual Meeting 2010 because the presenter was unable to attend. Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 101st Annual Meeting of the American Association for Cancer Research; 2010 Apr 17-21; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2010;70(8 Suppl):Abstract nr 2677.
Frequency Selective Hybrid Precoding for Limited Feedback Millimeter Wave Systems (2016)

Hybrid analog/digital precoding offers a compromise between hardware complexity and system performance in millimeter wave (mmWave) systems. This type of precoding allows mmWave systems to leverage large antenna array gains that are necessary for sufficient link margin, while permitting low cost and power consumption hardware. Most prior work has focused on hybrid precoding for narrow-band mmWave systems, with perfect or estimated channel knowledge at the transmitter. MmWave systems, however, will likely operate on wideband channels with frequency selectivity. Therefore, this paper considers wideband mmWave systems with a limited feedback channel between the transmitter and receiver. First, the optimal hybrid precoding design for a given RF codebook is derived. This provides a benchmark for any other heuristic algorithm and gives useful insights into codebook designs. Second, efficient hybrid analog/digital codebooks are developed for spatial multiplexing in wideband mmWave systems. Finally, a low-complexity yet near-optimal greedy frequency selective hybrid precoding algorithm is proposed based on Gram-Schmidt orthogonalization. Simulation results show that the developed hybrid codebooks and precoder designs achieve very-good performance compared with the unconstrained solutions while requiring much less complexity.
Chalcogenide microstructured optical fibers (2012)

Chalcogenide glasses are known for their large transparency in the mid-infrared and their high linear refractive index (>;2). They present also a high non-linear coefficient (n <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sub> ), 100 to 1000 times larger than for silica, depending on the composition. we have developed a casting method to prepare the chalcogenide preform. This method allows optical losses as low as 0.4 dB/m at 1.55 μm and less than 0.05 dB/m in the mid IR. Our group has prepared various chalcogenide MOFs operating in the IR range in order to associate the high non-linear properties of these glasses and the original MOF properties. For example, small core fibers have been drawn to enhance the non linearities for telecom applications such as signal regeneration and generation of supercontinuum sources. On another hand, in the 3-12 μm window, single mode fibers and exposed core fibers have been realized for Gaussian beams propagation and sensors applications respectively.