gebhart/patrepeval huggingface dataset:
Cancerization of the Pancreatic Ducts (2018)

Invasive pancreatic ductal adenocarcinoma (PDAC) can infiltrate back into and spread along preexisting pancreatic ducts and ductules in a process known as cancerization of ducts (COD). Histologically COD can mimic high-grade pancreatic intraepithelial neoplasia (HG-PanIN). We reviewed pancreatic resections from 100 patients with PDAC for the presence or absence of ducts with histologic features of COD. Features supporting COD included adjacent histologically similar invasive PDAC and an abrupt transition between markedly atypical intraductal epithelium and normal duct epithelium or circumferential involvement of a duct. As the TP53 and SMAD4 genes are frequently targeted in invasive PDAC but not HG-PanIN, paired PDAC and histologically suspected COD lesions were immunolabeled with antibodies to the p53 and Smad4 proteins. Suspected COD was identified on hematoxylin and eosin sections in 89 (89%) of the cases. Immunolabeling for p53 and Smad4 was performed in 68 (76%) of 89 cases. p53 was interpretable in 55 cases and all 55 (100%) cases showed concordant labeling between COD and invasive PDAC. There was matched aberrant p53 immunolabeling in 37 (67%) cases including overexpression in 30 (55%) cases and lack of expression in 7 (13%) cases. Smad4 immunolabeling was interpretable in 61 cases and 59 (97%) cases showed concordant labeling between COD and invasive PDAC. Matched loss of Smad4 was seen in 28 (46%) cases. The immunolabeling of invasive PDAC and COD for p53 and Smad4 supports the high prevalence of COD observed on hematoxylin and eosin and highlights the utility of p53 and Smad4 immunolabeling in differentiating COD and HG-PanIN.
Neuronostatin Encoded by the Somatostatin Gene Regulates Neuronal, Cardiovascular, and Metabolic Functions (2008)

Somatostatin is important in the regulation of diverse neuroendocrine functions. Based on bioinformatic analyses of evolutionarily conserved sequences, we predicted another peptide hormone in pro-somatostatin and named it neuronostatin. Immuno-affinity purification allowed the sequencing of an amidated neuronostatin peptide of 13 residues from porcine tissues. In vivo treatment with neuronostatin induced c-Fos expression in gastrointestinal tissues, anterior pituitary, cerebellum, and hippocampus. In vitro treatment with neuronostatin promoted the migration of cerebellar granule cells and elicited direct depolarizing actions on paraventricular neurons in hypothalamic slices. In a gastric tumor cell line, neuronostatin induced c-Fos expression, stimulated SRE reporter activity, and promoted cell proliferation. Furthermore, intracerebroventricular treatment with neuronostatin increased blood pressure but suppressed food intake and water drinking. Our findings demonstrate diverse neuronal, neuroendocrine, and cardiovascular actions of a somatostatin gene-encoded hormone and provide the basis to investigate the physiological roles of this endogenously produced brain/gut peptide.
Computation of Apparent Formation Dip From Single Azimuth Sensor Data Having Different Depths of Investigation (2015)

Abstract A typical gamma-gamma density tool used for making borehole geophysical measurements has a source and two in-line detectors at different distances from the source which results in each having unique effective penetration lengths (EPLs). Gamma-gamma tools typically have internal shielding so that the measurement is primarily influenced by the formation directly in front of the detectors. In high angle and horizontal wells, the difference in EPL creates an offset in measured depth (MD) between the two measurements when crossing a boundary between two layers having a density contrast. In a wellbore drilling down-section with the logging tool oriented toward the bottom of the wellbore, the detector with the deeper EPL senses the boundary at a shallower measured depth while the shallower-sensing one senses the boundary at a deeper measured depth. For a wellbore drilling up-section, the detection order and measured depths are reversed. This effect has been verified using Monte-Carlo N-Particle (MCNP) modeling code (Radtke 2006). This offset in measured depth is a function of the relative difference in EPL, the azimuthal orientation/relative bearing of the detectors with respect to top of hole, and the relative angle between the wellbore and the formation boundary. By knowing the respective tool EPL's and the relative bearing of the detectors, and measuring/determining the offset in measured depth where the detectors have responsed to the bed boundaries, the incident angle or angle of attack can be calculated. The depth shifts can be calucaled by auto-correlation techniques or manually. The incident angle can be combined with the trajectory inclination to compute the apparent formation dip in the azimuth of the wellbore. The incident angle gives us the indication of whether we are drilling up-section or down-section and how quickly we are cutting through the beds. These are a critical factors when determining the position of the wellbore relative to the geological layers while geosteering or when doing post drill look backs (correlation studies) and attempting to determine where the well was placed. A sinusoid fitting technique is typically used with azimuthal image data to determine formation dip and azimuth. The advantage of the new method is that sinusoids are not required. Only two or more single, oriented nonrotating measurements are needed. The method is validated with a full azimuthal density data set and then demonstrated in a second well with a commercial density logging tool that is conveyed through-the-bit. These tools are designed such that the density pad faces downward toward the bottom of the hole during logging operations and is not rotated azimuthally. Since azimuthal data is not acquired, one limitation of the technique is that the azimuth of the formation boundary cannot be computed.
An 11 GHz Contiguous Band Output Multiplexing Network for INTELSAT VI Spacecraft (2005)

Measured data of a 5-Channel 11GHz Contiguous Band Multiplexer meeting INTELSAT VI requirements is presented. No compensating networks or dummy channels are used in the physical realization of the multiplexer, thus advancing the state-of-the-art.
Diisobutylaluminum Hydride Reductions Revitalized: A Fast, Robust, and Selective Continuous Flow System for Aldehyde Synthesis (2011)

A continuous flow system for the multiparameter (flow rate, temperature, residence time, stoichiometry) optimization of the DIBALH reduction of esters to aldehydes is described. Incorporating an in-line quench (MeOH), these transformations are generally complete in fewer than 60 s. Mixing of the DIBALH and ester solutions was observed to be an exceptionally critical parameter for optimum results. This system thus provides general guidelines based on the structure of the ester for selective reduction of an ester without overreduction.
Emergency Tourniquet Effectiveness in Four Positions on the Proximal Thigh (2014)

The present study found that tourniquet effectiveness rates were uniformly 100% irrespective of whether the windlass position was medial, lateral, anterior, or posterior. These excellent clinical and statistical results indicate that users may continue to place the tourniquets as they prefer upon the proximal thigh.
Scanning two-photon continuous flow lithography for the fabrication of multi-functional microparticles (2020)

In this work, we demonstrate the high-throughput fabrication of 3D microparticles using a scanning two-photon continuous flow lithography (STP-CFL) technique in which microparticles are shaped by scanning the laser beam at the interface of laminar co-flows. The results demonstrate the ability of STP-CFL to manufacture high-resolution complex geometries of cell carriers that possess distinct regions with different functionalities. A new approach is presented for printing out-of-plane features on the microparticles. The approach eliminates the use of axial scanning stages, which are not favorable since they induce fluctuations in the flowing polymer media and their scanning speed is slower than the speed of galvanometer mirror scanners.
Imeglimin Amplifies Glucose-Stimulated Insulin Release from Diabetic Islets via a Distinct Mechanism of Action (2020)

ABSTRACT Pancreatic islet β-cell dysfunction is characterized by defective glucose-stimulated insulin secretion (GSIS) and is a predominant component of the pathophysiology of diabetes. Imeglimin, a novel first-in-class small molecule tetrahydrotriazine drug candidate, improves glycemia and GSIS in preclinical models and clinical trials in patients with type 2 diabetes; however, the mechanism by which it restores β-cell function is unknown. Here, we show that Imeglimin acutely and directly amplifies GSIS in islets isolated from rodents with Type 2 diabetes via a mode of action that is distinct from other known therapeutic approaches. The underlying mechanism involves increases in the cellular nicotinamide adenine dinucleotide (NAD + ) pool – potentially via the salvage pathway and induction of nicotinamide phosphoribosyltransferase (NAMPT) along with augmentation of glucose-induced ATP levels. Further, additional results suggest that NAD + conversion to a second messenger, cyclic ADP ribose (cADPR), via cyclic ADP ribose hydrolase (CD38) is required for Imeglimin’s effects in islets, thus representing a potential link between increased NAD + and enhanced glucose-induced Ca2+ mobilization which - in turn - is known to drive insulin granule exocytosis. Collectively, these findings implicate a novel mode of action for Imeglimin that explains its ability to effectively restore β-cell function and provides for a new approach to treat patients suffering from Type 2 diabetes.
Real‐Time and Continuous Sensors of Protein Kinase Activity Utilizing Chelation‐Enhanced Fluorescence (2014)

Protein kinases, the enzymes responsible for phosphoryl transfer from a chemical donor such as adenosine triphosphate (ATP) to a peptide or a protein acceptor, are integral enzymes in signaling cascades, play crucial roles in numerous cellular processes, and are of fundamental importance in systems biology. In addition, aberrant kinase activities are commonly associated with disease states, making kinases important therapeutic targets in current drug development initiatives. Therefore, understanding kinase activation dynamics is of utmost biological and clinical importance. Accurate and physiologically relevant methods to quantify kinase activities are needed to understand the intricate dynamics of kinase activation and inactivation. This chapter describes the design, evolution, and application of fluorescent-based Ser/Thr/Tyr kinase activity sensors that take advantage of chelation-enhanced fluorescence (CHEF). These sensors are compatible with physiological conditions, are selective for specific protein kinases, and provide real-time kinetic information regarding kinase activity.
Conjugation of biotin-coated luminescent quantum dots with single domain antibody-rhizavidin fusions (2016)

Straightforward and effective methods are required for the bioconjugation of proteins to surfaces and particles. Previously we demonstrated that the fusion of a single domain antibody with the biotin binding molecule rhizavidin provided a facile method to coat biotin-modified surfaces with a highly active and oriented antibody. Here, we constructed similar single domain antibody-rhizavidin fusions as well as unfused rhizavidin with a His-tag. The unfused rhizavidin produced efficiently and its utility for assay development was demonstrated in surface plasmon resonance experiments. The single domain antibody-rhizavidin fusions were utilized to coat quantum dots that had been prepared with surface biotins. Preparation of antibody coated quantum dots by this means was found to be both easy and effective. The prepared single domain antibody-quantum dot reagent was characterized by surface plasmon resonance and applied to toxin detection in a fluoroimmunoassay sensing format.
The elliptic curve discrete logarithm problem and equivalent hard problems for elliptic divisibility sequences (2008)

We define three hard problems in the theory of elliptic divisibility sequences (EDS Association, EDS Residue and EDS Discrete Log), each of which is solvable in sub-exponential time if and only if the elliptic curve discrete logarithm problem is solvable in sub-exponential time. We also relate the problem of EDS Association to the Tate pairing and the MOV, Frey-Rück and Shipsey EDS attacks on the elliptic curve discrete logarithm problem in the cases where these apply.
A replica technique for wordline and sense control in low-power SRAM's (1998)

With the migration toward low supply voltages in low-power SRAM designs, threshold and supply voltage fluctuations will begin to have larger impacts on the speed and power specifications of SRAM's. We present techniques based on replica circuits which minimize the effect of operating conditions' variability on the speed and power. Replica memory cells and bitlines are used to create a reference signal whose delay tracks that of the bitlines. This signal is used to generate the sense clock with minimal slack time and control wordline pulsewidths to limit bitline swings. We implemented the circuits for two variants of the technique, one using bitline capacitance ratioing in a 1.2-/spl mu/m 8-kbyte SRAM, and the other using cell current ratioing in a 0.35-/spl mu/m 2-kbyte SRAM. Both the RAM's were measured to operate over a wide range of supply voltages, with the latter dissipating 3.6 mW at 150 MHz at 1 V and 5.2 /spl mu/W at 980 kHz at 0.4 V.
Mechanical Properties of a Series of Macro- and Nanodimensional Organic Cocrystals Correlate with Atomic Polarizability (2015)

A correlation between Young's modulus, as determined by using nanoindentation atomic force microscopy (AFM), and atomic polarizability is observed for members of a series of cocrystals based on systematic changes to one cocrystal component. Time domain spectroscopy over terahertz frequencies (THz-TDS) is used for the first time to directly measure the polarizability of macro- and nanosized organic solids. Cocrystals of both macro- and nanodimensions with highly polarizable atoms result in softer solids and correspondingly higher polarizabilities.
Figure S1 from Folate Receptor Beta Designates Immunosuppressive Tumor-Associated Myeloid Cells That Can Be Reprogrammed with Folate-Targeted Drugs (2023)

&lt;p&gt;supplemental figure 1&lt;/p&gt;
Cold denaturation of ubiquitin at high pressure (2006)

Cold-induced conformational transition of ubiquitin was studied at pH 4.5 under a constant pressure of 2 kbar using variable pressure one-dimensional 1H and two-dimensional 15N/1H NMR spectroscopy as well as IR spectroscopy. Although a tendency for preferential stabilization of a peculiar locally disordered and partially hydrated conformer I, identical with that previously found with variable-pressure NMR at 0 degrees C, is recognized, the transition of the folded conformer N to the unfolded conformer U occurs largely cooperatively with decreasing temperature, reaching near completion at - 21 degrees C. NMR spectral features as well as the analysis of NMR relaxation parameters indicate that the polypeptide chain is almost fully unfolded, fairly well-hydrated and floppy at - 21 degrees C, whereas the IR spectrum shows a substantial decrease of the beta-sheet. The Gibbs energy change from the folded state (a mixture of N and I) to the unfolded state at 2 kbar obtained from the 1H NMR data is fitted well with a single DeltaCp value of 2.43 +/- 0.13 (kJ/K mol) for the entire temperature range between - 21 and 90 degrees C, covering both the cold denaturation and heat denaturation, showing that the two denatured states actually belong to a single thermodynamic phase of the protein. The DeltaCp value determined at 2 kbar is substantially smaller than the DeltaCp determined at 1 bar (3.8-5.8 (kJ/Kmol), which is consistent with the fact that the denaturation takes place from a mixture of N and I at 2 kbar rather than from pure N at 1 bar.
N-Protected Tripeptide Inhibitors of Angiotensin Converting Enzyme (1990)

Journal Article N-Protected Tripeptide Inhibitors of Angiotensin Converting Enzyme Get access Hiroshi Kayahara, Hiroshi Kayahara Laboratory of Chemical Control, Department of Bioscience and Biotechnology, Shinshu University, 8304 Minamiminowa, Kamiina, Nagano 399-45, Japan Search for other works by this author on: Oxford Academic Google Scholar Akio Ohashi, Akio Ohashi Laboratory of Chemical Control, Department of Bioscience and Biotechnology, Shinshu University, 8304 Minamiminowa, Kamiina, Nagano 399-45, Japan Search for other works by this author on: Oxford Academic Google Scholar Koji Tadasa, Koji Tadasa Laboratory of Chemical Control, Department of Bioscience and Biotechnology, Shinshu University, 8304 Minamiminowa, Kamiina, Nagano 399-45, Japan Search for other works by this author on: Oxford Academic Google Scholar Shozo Kato Shozo Kato Laboratory of Chemical Control, Department of Bioscience and Biotechnology, Shinshu University, 8304 Minamiminowa, Kamiina, Nagano 399-45, JapanTokuyama Soda Co., Ltd., 2051 Endo, Fujisawa, Kanagawa 252, Japan Search for other works by this author on: Oxford Academic Google Scholar Agricultural and Biological Chemistry, Volume 54, Issue 5, 1 May 1990, Pages 1325–1326, https://doi.org/10.1080/00021369.1990.10870107 Published: 01 May 1990 Article history Received: 15 December 1989 Published: 01 May 1990
Flexible Low‐Voltage Organic Complementary Circuits: Finding the Optimum Combination of Semiconductors and Monolayer Gate Dielectrics (2014)

Low-voltage p-channel and n-channel organic transistors with channel lengths down to 0.5 μm using four small-molecule semiconductors and ultra-thin dielectrics based on two different phosphonic acid monolayers are fabricated on plastic substrates and studied in terms of effective mobility, intrinsic mobility and contact resistance. For the optimum materials combination, flexible complementary circuits have signal delays of 3.1 μs at 5 V.
Molecular Identification of Cytokinin-specific Binding Protein (1999)

Synthetic phenylurea derivatives such as N-phenyl-N'-(4-pyridyl)urea (4PU) and N-(2-chloro-4-pyridyl)-N'-phenylurea (4PU30) have strong cytokinin activities. Using tritiated 4PU30 as a probe, we found the presence of a cytokinin-specific binding protein (CSBP) with high affinity for 4PU30 (Ka for 4PU30 = 4 x 10(10) M-1) in the soluble fraction of etiolated mung bean seedlings. We purified CSBP by the use of 4PU-Sepharose 4B, an affinity gel ligated with 4PU. Analysis of its cDNA revealed that CSBP was a novel member of a major pollen allergen/pathogenesis-related protein family with a calculated molecular weight of 17 kDa. Recombinant CSBP was expressed in Escherichia coli was confirmed to bind specifically to cytokinins.
The prognostic significance of RUNX2 and miR-10a/10b and their inter-relationship in breast cancer (2014)

These findings indicate that higher expression of RUNX2 and miR-10a/b was associated with adverse outcome of breast cancer. Expression levels of RUNX2 and miR-10a/b individually or jointly are potential prognostic factors for predicting breast cancer recurrence. Data from in vitro studies support the notion that RUNX2 promoted cell motility by upregulating miR-10a/b.
Surrogate-Based Modeling and Dimension-Reduction Techniques for Thermo-Fluid and Energy Systems (2011)

Successful modeling and/or design of thermo-fluid and energy systems often requires one to address the impact of multiple “design variables” on the prescribed outcome. There are often multiple, competing objectives based on which we assess the outcome of optimization. Since accurate, high fidelity models are typically time consuming and computationally expensive, comprehensive evaluations can be conducted only if an efficient framework is available. Furthermore, informed decisions of model/hardware’s overall performance rely on an adequate understanding of the global, not local, sensitivity of the individual design variables on the objectives. The surrogate-based approach, which involves approximating the objectives as continuous functions of design variables from limited data, offers a rational framework to reduce the number of important input variables, i.e., the dimension of a design or modeling space. In this paper, we discuss the fundamental issues that arise in surrogate-based analysis and optimization, highlighting concepts, methods, techniques, as well as practical implications. To aid the discussions of the issues involved, we will summarize recent efforts in investigating cryogenic cavitating flows, active flow control based on dielectric barrier discharge concepts, and Li-ion batteries.
One-pot synthesis of 1-exo-alkylidene-2,3-anhydro furanoses: convenient precursors for exo-glycals and functionalized C-glycals (2002)

1-exo-Methylene-2,3-anhydro furanoses, obtained from C-glycals in a one-pot, three step operation can be readily transformed into functionalized C-glycals by palladium-catalyzed nucleophilic addition.
Supplementary Figures from Real-time Genomic Characterization of Advanced Pancreatic Cancer to Enable Precision Medicine (2023)

&lt;p&gt;Supplementary Figure S1: Overview of workflow and data generation. Supplementary Figure S2: Analysis of neoplastic cellularity. Supplementary Figure S3: Recurrent copy number alterations. Supplementary Figure S4: Mutational signature analysis. Supplementary Figure S5: Analysis of PDAC gene expression signatures. Supplementary Figure S6: Clinically relevant alterations in the cohort.&lt;/p&gt;
Hathi (2012)

Recent architectural trends---cheap, fast solid-state storage, inexpensive DRAM, and multi-core CPUs---provide an opportunity to rethink the interface between applications and persistent storage. To leverage these advances, we propose a new system architecture called Hathi that provides an in-memory transactional heap made persistent using high-speed flash drives. With Hathi, programmers can make consistent concurrent updates to in-memory data structures that survive system failures.
A high-resolution analog-to-digital converter design for sub-100 nm technology using folding-integration technique (2014)

To design a low-power, high-speed and high-resolution analog-to-digital converter (ADC) in sub-100 nm technology, this paper presents a technique using folding integration (F. I.) and digital calibration. We have compared the circuit simulation results with the ideal case (Matlab simulation results) and have done nonlinearity analysis. The effectiveness of the digital error correction is confirmed by simulations.
Uplink performance optimization in relay enhanced LTE-Advanced networks (2009)

Relaying concept has been proposed to satisfy the demanding requirements of LTE-Advanced which was recently agreed by 3GPP as an evolution of LTE. Relay enhanced networks are expected to enhance the coverage and capacity in a cost efficient way. Yet, transmit power of UE should be optimized in a relay based scenario where interference increases by additional RNs. New cell edges introduced by RNs increase the number of users that transmit with high power. This leads to severe interference, in particular when a large number of RNs are deployed in a cell with reuse one. In this paper, performance evaluation of relay based deployment within the LTE-Advanced uplink framework is carried out by applying the standardized LTE power control scheme both at eNBs and RNs. The importance of power control parameter settings is examined to achieve optimal performance in relay scenarios.