gebhart/patrepeval huggingface dataset:
Optical coherence tomography to detect acute esophageal radiation‐induced damage in mice: A validation study (2019)

Radiation therapy for patients with non-small-cell lung cancer is hampered by acute radiation-induced toxicity in the esophagus. This study aims to validate that optical coherence tomography (OCT), a minimally invasive imaging technique with high resolution (~10 μm), is able to visualize and monitor acute radiation-induced esophageal damage (ARIED) in mice. We compare our findings with histopathology as the gold standard. Irradiated mice receive a single dose of 40 Gy at proximal and distal spots of the esophagus of 10.0 mm in diameter. We scan mice using OCT at two, three, and seven days post-irradiation. In OCT analysis, we define ARIED as a presence of distorted esophageal layering, change in backscattering signal properties, or change in the esophageal wall thickness. The average esophageal wall thickness is 0.53 mm larger on OCT when ARIED is present based on histopathology. The overall sensitivity and specificity of OCT to detect ARIED compared to histopathology are 94% and 47%, respectively. However, the overall sensitivity of OCT to assess ARIED is 100% seven days post-irradiation. We validate the capability of OCT to detect ARIED induced by high doses in mice. Nevertheless, clinical studies are required to assess the potential role of OCT to visualize ARIED in humans.
Supramolecular chemistry with ureido-benzoic acids (2014)

A novel, complementary quadruple hydrogen-bonding motif is presented that shows very strong dimerization and is switchable with pH.
Low-temperature sintering of zirconia ceramics. (1986)

Well-sintered zirconia ceramics are hardly obtained by conventional solid state reaction below 1500°C.However, it was found that the sinterability of the zirconia ceramics can be enhanced by using the mixed powders composed of ZrO2 raw powder and a pulverized calcined ZrO2 powder containing high concentrations of Y2O3. For example, the well-sintered partially stabilized zirconia ceramics containing 5 mol% Y2O3 was able to be prepared by firing even at 1300°C using the ZrO2 powder containing 40 mol% Y2O3 and ZrO2 raw powders.
Dual Protonophore–Chitinase Inhibitors Dramatically Affect O. volvulus Molting (2014)

The L3-stage-specific chitinase OvCHT1 has been implicated in the development of Onchocerca volvulus, the causative agent of onchocerciasis. Closantel, a known anthelmintic drug, was previously discovered as a potent and specific OvCHT1 inhibitor. As closantel is also a known protonophore, we performed a simple scaffold modulation to map out the structural features that are relevant for its individual or dual biochemical roles. Furthermore, we present that either OvCHT1 inhibition or protonophoric activity was capable of affecting O. volvulus L3 molting and that the presence of both activities in a single molecule yielded more potent inhibition of the nematode's developmental process.
Waveform optimization for large-scale multi-antenna multi-sine wireless power transfer (2016)

Wireless power transfer (WPT) is expected to be a technology reshaping the landscape of low-power applications such as the Internet of Things, machine-to-machine communications and radio frequency identification networks. Although there has been some progress towards multi-antenna multi-sine WPT design, the large-scale design of WPT, reminiscent of massive multiple-input multiple-output (MIMO) in communications, remains an open problem. Considering the nonlinear rectifier model, a multiuser waveform optimization algorithm is derived based on successive convex approximation (SCA). A lower-complexity algorithm is derived based on asymptotic analysis and sequential approximation (SA). It is shown that the difference between the average output voltage achieved by the two algorithms can be negligible provided the number of antennas is large enough. The performance gain of the nonlinear model based design over the linear model based design can be large, in the presence of a large number of tones.
Ligand binding kinetics of IL-2 and IL-15 to heteromers formed by extracellular domains of the three IL-2 receptor subunits (1995)

Studies on the binding of IL-2 to its receptor (IL-2R) have generally been limited to receptors expressed on cell surfaces. This has hampered detailed kinetic and mechanistic studies at the molecular level. We have prepared the soluble extracellular domains of all three receptor subunits (called alpha, beta and gamma) by recombinant techniques and have used these to perform detailed kinetic studies of their binding properties using the technique of surface plasmon resonance. We describe a novel approach whereby the receptors are assembled on an antibody surface, being held by an epitope engineered into the C-terminus of each of these domains. Thus the receptors are oriented naturally leading to homogeneous ligand binding kinetics. We have characterized the interactions of the heteromeric complexes of these subunits with mouse and human IL-2 and their analogs, as well as the recently discovered cytokine, IL-15. We have also studied the extracellular domains of the mouse receptor subunits for the first time and have used these as well as mouse-human hybrid receptors to probe the mechanism of assembly of these complexes. We show that no additional proteins are required to reproduce the properties of these complexes in vitro. In addition, kinetic studies with site-specific analogs of IL-2 and the mouse-human receptor hybrids clearly indicate that the extracellular domains of alpha and beta can together readily bind ligand with kinetic properties distinct from those of the constituent subunits. In contrast, a complex containing ligand and the extracellular domains of beta and gamma was comparatively difficult to assemble and required prolonged exposure to IL-2. Our method enabled us to calculate the stoichiometry of these complexes and to determine that anchoring these subunits is necessary to efficiently drive complex formation. The kinetic and equilibrium differences between the mouse and human receptor complexes, and between IL-2 and IL-15 binding to these receptors clarify the roles of the alpha and gamma subunits in the differential response of cells to different cytokines that may be present simultaneously in the environment.
Supplementary Figure 2 from Breast Field Cancerization: Isolation and Comparison of Telomerase-Expressing Cells in Tumor and Tumor Adjacent, Histologically Normal Breast Tissue (2023)

&lt;p&gt;PDF file - 57K, hTERT promoter reporter (Green Vector) effectively separates mixed populations of cells based on telomerase activity. HEK293 cells (telomerase positive) and WI-38 cells (telomerase negative) were infected separately with "Green Virus", mixed in a 1:1 ratio and sorted based on "high" (R1) or "low" (R2) green fluorescence. Gel-based TRAP analysis was performed on sorted populations. Densitometry analysis demonstrated a 4.2 fold increase in telomerase activity in the High population.&lt;/p&gt;
Abstract A163: A diverse array of mutations in MTOR are hyperactivating and correlate with rapamycin sensitivity. (2013)

Abstract Components of the PI3K-Akt-mTOR signaling axis are frequently mutated in cancer but relatively few mutations have been observed in the MTOR gene itself, which encodes the mTOR kinase. We used cancer genome sequencing data to generate a catalogue of over 450 MTOR point mutations found in cancer and from these identified a set of over 25 that cause mTOR pathway hyperactivation in cells. Mutations occur in multiple cancer types and cluster in several distinct regions in the C-terminal half of mTOR. The distribution and diversity of hyperactivating mutations is distinct from those found in kinases such as AKT1 or BRAF but similar to the pattern seen in PIK3CA. The mutations do not affect the sub-cellular localization of mTOR or its capacity to nucleate the mTORC1 and mTORC2 complexes, but the mutants do bind less DEPTOR, an mTOR inhibitor. In kinetic analyses, several of the most frequently recurrent mutations demonstrate increased K-cat over wild-type mTOR, suggesting that these mutations alter the mTOR kinase itself. Lastly, cancer cell lines with naturally arising mTOR mutations that fall within the clusters exhibited hypersensitivity to mTOR inhibitors. Thus, a diverse set of mutations in mTOR can activate the mTOR pathway and may predict which patients are most likely to respond to rapamycin-based therapies. Citation Information: Mol Cancer Ther 2013;12(11 Suppl):A163. Citation Format: Brian Grabiner, David Sabatini. A diverse array of mutations in MTOR are hyperactivating and correlate with rapamycin sensitivity. [abstract]. In: Proceedings of the AACR-NCI-EORTC International Conference: Molecular Targets and Cancer Therapeutics; 2013 Oct 19-23; Boston, MA. Philadelphia (PA): AACR; Mol Cancer Ther 2013;12(11 Suppl):Abstract nr A163.
High-throughput validation of ceRNA regulatory networks (2017)

Abstract Background MicroRNAs (miRNAs) play multiple roles in tumor biology. Interestingly, reports from multiple groups suggest that miRNA targets may be coupled through competitive stoichiometric sequestration. Specifically, computational models predicted and experimental assays confirmed that miRNA activity is dependent on miRNA target abundance, and consequently, changes in the abundance of some miRNA targets lead to changes to the regulation and abundance of their other targets. The resulting indirect regulatory influence between miRNA targets resembles competition and has been dubbed competitive endogenous RNA (ceRNA). Recent studies have questioned the physiological relevance of ceRNA interactions, our ability to accurately predict these interactions, and the number of genes that are impacted by ceRNA interactions in specific cellular contexts. Results To address these concerns, we reverse engineered ceRNA networks (ceRNETs) in breast and prostate adenocarcinomas using context-specific TCGA profiles, and tested whether ceRNA interactions can predict the effects of RNAi-mediated gene silencing perturbations in PC3 and MCF7 cells._ENREF_22 Our results, based on tests of thousands of inferred ceRNA interactions that are predicted to alter hundreds of cancer genes in each of the two tumor contexts, confirmed statistically significant effects for half of the predicted targets. Conclusions Our results suggest that the expression of a significant fraction of cancer genes may be regulated by ceRNA interactions in each of the two tumor contexts.
Development of Scanning µ-RHEED Microscopy for Imaging Polycrystal Grain Structure in LSI (1989)

A new type of scanning µ-RHEED (reflection high energy electron diffraction) microscope has been developed. Three diffraction spots of a RHEED pattern were simultaneously selected for imaging. The scanning µ-RHEED images were obtained from the intensity change of the diffraction spots. The distribution of normally rotated micrograins inside the same plane's grain parallel to the surface was successfully observed from the scanning µ-RHEED images. Micrograin structures of poly-Si and Cu thin films were observed with a resolution of less than one micron.
Decomposition of surface EMG signals using non-linear LMS optimisation of higher-order cumulants (2003)

Deals with the problem of decomposition of surface electromyograms (SEMG). According to the physiological facts, a multiple-input multiple-output (MIMO) is used. The measured signals are taken as the channel responses corresponding to the motor-unit action potentials (MUAPs) convolution by the innervation pulse trains. The decomposition is based on the third-order cumulants whose values enter as coefficients of nonlinear system of equations. The system is solved by nonlinear least mean square (LMS) optimisation. Synthetic SEMG signals from a MIMO(2,3) with additive Gaussian noise with SNRs of 10 and 0 dB prove that a successful multichannel decomposition is possible also in very noisy environments.
[Measuring scheme for the determination of residual energy of the urinary stream]. (1980)

A measuring arrangement is described for the measurement of the urinary jet pressure on the urethral external meatus in male individuum. The residue energy can be calculated by means of simultaneous urinary flow measurement.
Efficient Timing and Frequency Offset Estimation in OFDM Systems (2006)

Orthogonal frequency division multiplexing (OFDM) is a bandwidth efficient modulation scheme used widely for high speed data communication. Fast and ro- bust synchronization algorithms are necessary for OFDM systems operating in burst mode like WLANs. In this paper, we propose an efficient timing and carrier frequency synchronization method for OFDM. The proposed scheme needs only one OFDM symbol for both symbol/frame timing and frequency offset estimation, while previous synchronization algorithms need more than two OFDM symbols as a training sequence. Numerical analysis shows that the proposed frequency estimator nearly achieves the Cramer-Rao lower bound for the variance of the frequency offset estimate, despite the reduction in the training sequence length.
Local pressure and matrix component effects on verteporfin distribution in pancreatic tumors (Conference Presentation) (2017)

Pancreatic tumors are characterized by large interstitial hypertension from enhanced deposition of extracellular matrix components, resulting in widespread vascular collapse and reduced molecular uptake of systemically delivered therapies. Although the origins of hypoperfusion is debated amongst researchers, spatial distribution of collagen density and hyaluronic acid content have shown to be a key metric in understanding the lack of efficacy for both acute and chronic therapies in these tumors. In this study, the AsPC-1 tumor model was used both subcutaneously and orthotopically to study the measurable factors which are related to this. A conventional piezoelectric pressure catheter was used to measure total tissue pressure (TTP), defined as a combination of solid stress (SS) and interstitial fluid pressure (IFP), TTP = SS + IFP, in multiple locations within the tumor interstitium. Matrix components such as collagen and hyaluronic acid were scored using masson’s trichrome stain and hyaluronic acid binding protein (HABP), respectively, and co-registered with values of TTP. The results show that these key measurements are related to the spatial distribution of verteporfin in the same tumors. Photodynamic treatment with verteporfin is known to ablate large regions of tumor tissue and also allow better permeability for chemotherapies. The study of spatial distribution of verteporfin in relation to stromal content and TTP will help us better control these types of combination therapies.
Influence of Defects in 4H-SiC Avalanche Photodiodes on Geiger-Mode Dark Count Probability (2009)

4H-SiC single photon avalanche diodes are reported. A separate absorption and multiplication non-reach through device structure was optimized for operation in Geiger mode. An estimated dark current at a gain of 1000 was ranging between 0.4 pA (0.75 nA/cm2) and 20nA (38 A/cm2) on devices with an effective mesa diameter of 260 m. The electron beam induced current technique was used to image defects in the active region of studied devices. Increased reverse bias leakage current and increased Geiger mode dark count probability were correlated with the presence of large number of defects. Single photon detection efficiencies of up to 11% were measured at a wavelength of 266 nm in Geiger mode.
The jPET-D4: Detector Calibration and Acquisition System of the 4-Layer DOI-PET Scanner (2006)

We are developing a high-performance brain PET scanner, JPET-D4. This scanner is designed to achieve not only high spatial resolution but also high sensitivity using four-layered depth-of-interaction (DOI) detectors. The scanner has five detector rings with the ring diameter of 390 mm and each detector ring consists of 24 DOI detectors. In order to identify the crystal of interaction and its energy from PMT output, we have previously proposed the DOI detector calibration method. This method creates position and energy look-up-tables (LUTs) from the uniform irradiation. The position LUT converts location of 2D position histograms to crystal addresses. The energy LUT corrects light output of each crystal. Five detector rings have been installed and calibrated. The average energy resolution for 120 DOI detectors is optimized to 17% plusmn 1.4%. The scatter fraction for this system is 38% with energy window of 400-600 keV. The sensitivity for point source is 112 kcps/MBq with a 250 keV LLD
Reduction of HARQ memory in low mobility LTE systems (2013)

Hybrid ARQ (HARQ) combines Automatic Repeat Request (ARQ) and Forward Error Correction (FEC) to exploit information from erroneous packets after retransmissions. Due to its superior reliability, HARQ became a crucial component of several important 3G and 4G systems such as Long Term Evolution (LTE) and LTE-Advanced. Although the performance advantage is very attractive, implementing HARQ is challenging with emerging high throughput communication systems. Knowing that LTE and LTE-A systems would provide Gbps or hundreds of Mbps, a straightforward implementation would require around 10 Mbit memory for a HARQ buffer. With cost and power-limited wireless terminals, the available memory size to support HARQ requires an efficient implementation. In this paper we propose a novel method to exploit the time coherence of the wireless channel in order to reduce the memory storage for HARQ. This method has been evaluated with a full LTE MIMO simulation chain. Compared to state-of-the-art solutions, we show a promising memory compression factor close to 4, whereas performance degradation is marginal.
Differentiating Microbial Forensic qPCR Target and Control Products by Electrospray Ionization Mass Spectrometry (2013)

Molecular bioforensic research is dependent on rapid and sensitive methods such as real-time PCR (qPCR) for the identification of microorganisms. The use of synthetic positive control templates containing small modifications outside the primer and probe regions is essential to ensure all aspects of the assay are functioning properly, including the primers and probes. However, a typical qPCR or reverse transcriptase qPCR (qRT-PCR) assay is limited in differentiating products generated from positive controls and biological samples because the fluorescent probe signals generated from each type of amplicon are indistinguishable. Additional methods used to differentiate amplicons, including melt curves, secondary probes, and amplicon sequencing, require significant time to implement and validate and present technical challenges that limit their use for microbial forensic applications. To solve this problem, we have developed a novel application of electrospray ionization mass spectrometry (ESI-MS) to rapidly differentiate qPCR amplicons generated with positive biological samples from those generated with synthetic positive controls. The method has sensitivity equivalent to qPCR and supports the confident and timely determination of the presence of a biothreat agent that is crucial for policymakers and law enforcement. Additionally, it eliminates the need for time-consuming methods to confirm qPCR results, including development and validation of secondary probes or sequencing of small amplicons. In this study, we demonstrate the effectiveness of this approach with microbial forensic qPCR assays targeting multiple biodefense agents (bacterial, viral, and toxin) for the ability to rapidly discriminate between a positive control and a positive sample.
Increasing bandwidth of orthogonally polarised omnidirectional antenna composed of halo and sleeve antennas (2023)

Abstract In this study, we developed and investigated a small‐diameter, low‐profile, wideband orthogonal‐polarisation multiple‐input multiple‐output (MIMO) antenna. A polarisation MIMO antenna is a combination of a modified sleeve antenna for vertical polarisation and a halo antenna with four parasitic elements for horizontal polarisation. Four parasitic elements vertically were loaded above and below the halo antenna, and a sleeve antenna with an upper sleeve structure was inserted inside the halo antenna to achieve a low profile, wideband antenna with a small diameter. Simulation and measurement results showed that the proposed antenna achieved a relative bandwidth of 10.1% (| S 11 | and | S 22 | ≤ −10 dB). For the lower frequency wavelength ( λ min ) in the required bandwidth, the diameter and height of the proposed antenna are 0.14 λ min and 0.57 λ min respectively. Additionally, it is capable of orthogonal‐polarisation isolation of approximately 20 dB within the operating frequency bandwidth.
Demonstration of a mode-conversion cavity add–drop filter (2011)

We experimentally demonstrate a new type of add–drop filter incorporating an asymmetric Y-branch waveguide coupler and a shifted-grating mode-conversion cavity. The device relies on mode separation in the asymmetric Y-branch and wavelength-selective mode conversion upon reflection from the shifted-grating cavity. Add–drop functionality is demonstrated in a three-port integrated silicon-on-insulator device.
Both complete and correct? (2014)

Correcting erroneous input (i.e., correction) and completing a word based on partial input (i.e., completion) are two important "smart" capabilities of a modern intelligent touchscreen keyboard. However little is known whether these two capabilities are conflicting or compatible with each other in the keyboard parameter tuning. Applying computational optimization methods, this work explores the optimality issues related to them. The work demonstrates that it is possible to simultaneously optimize a keyboard algorithm for both correction and completion. The keyboard simultaneously optimized for both introduces no compromise to correction and only a slight compromise to completion when compared to the keyboards exclusively optimized for one objective. Our research also demonstrates the effectiveness of the proposed optimization method in keyboard algorithm design, which is based on the Pareto multi-objective optimization and the Metropolis algorithm. For the development and test datasets used in our experiments, computational optimization improved the correction accuracy rate by 8.3% and completion power by 17.7%.
All-lignin approach to prepare cationic colloidal lignin particles: stabilization of durable Pickering emulsions (2017)

Adsorption of cationic lignin on colloidal lignin particles is a green route to new types of Pickering emulsion applications.