gebhart/patrepeval huggingface dataset:
A gel‐free MS‐based quantitative proteomic approach accurately measures cytochrome P450 protein concentrations in human liver microsomes (2008)

The human cytochrome P450 (P450) superfamily consists of membrane-bound proteins that metabolize a myriad of xenobiotics and endogenous compounds. Quantification of P450 expression in various tissues under normal and induced conditions has an important role in drug safety and efficacy. Conventional immunoquantification methods have poor dynamic range, low throughput, and a limited number of specific antibodies. Recent advances in MS-based quantitative proteomics enable absolute protein quantification in a complex biological mixture. We have developed a gel-free MS-based protein quantification strategy to quantify CYP3A enzymes in human liver microsomes (HLM). Recombinant protein-derived proteotypic peptides and synthetic stable isotope-labeled proteotypic peptides were used as calibration standards and internal standards, respectively. The lower limit of quantification was approximately 20 fmol P450. In two separate panels of HLM examined (n = 11 and n = 22), CYP3A, CYP3A4 and CYP3A5 concentrations were determined reproducibly (CV <or=27%). The MS-based method strongly correlated with the immunoquantification method (r(2)>or=0.87) and marker activities (r(2)>or=0.88), including testosterone 6beta-hydroxylation (CYP3A), midazolam 1'-hydroxylation (CYP3A), itraconazole 6-hydroxylation (CYP3A4) and CYP3A5-mediated vincristine M1 formation (CYP3A5). Taken together, our MS-based method provides a specific, sensitive and reliable means of P450 protein quantification and should facilitate P450 characterization during drug development, especially when specific substrates and/or antibodies are unavailable.
Cryogenic sensor enabling broad-band and traceable power measurements (2021)

Recently, great progress has been made in the field of ultrasensitive microwave detectors, reaching even the threshold for utilization in circuit quantum electrodynamics. However, cryogenic sensors lack the compatibility with broad-band metrologically traceable power absorption measurements at ultralow powers, which limits their scope of applications. Here, we demonstrate such measurements using an ultralow-noise nanobolometer which we extend by an additional direct-current (dc) heater input. The tracing of the absorbed power relies on comparing the response of the bolometer between radio frequency (rf) and dc-heating powers traced to the Josephson voltage and quantum Hall resistance. To illustrate this technique, we demonstrate methods to calibrate the power that is delivered to the base temperature stage of a dilution refrigerator using our in-situ power sensor. As an example, we demonstrate the ability to measure accurately the attenuation of a coaxial input line between the frequencies of 50 MHz and 7 GHz with an uncertainty down to 0.1 dB at typical input power of -114 dBm.
SLLISWD Sequence in the 10FNIII Domain Initiates Fibronectin Fibrillogenesis (2013)

Fibronectin (FN) assembly into extracellular matrix is tightly regulated and essential to embryogenesis and wound healing. FN fibrillogenesis is initiated by cytoskeleton-derived tensional forces transmitted across transmembrane integrins onto RGD binding sequences within the tenth FN type III (10FNIII) domains. These forces unfold 10FNIII to expose cryptic FN assembly sites; however, a specific sequence has not been identified in 10FNIII. Our past steered molecular dynamics simulations modeling 10FNIII unfolding by force at its RGD loop predicted a mechanical intermediate with a solvent-exposed N terminus spanning the A and B β-strands. Here, we experimentally confirm that the predicted 23-residue cryptic peptide 1 (CP1) initiates FN multimerization, which is mediated by interactions with 10FNIII that expose hydrophobic surfaces that support 8-anilino-1-napthalenesulfonic acid binding. Localization of multimerization activity to the C terminus led to the discovery of a minimal 7-amino acid "multimerization sequence" (SLLISWD), which induces polymerization of FN and the clotting protein fibrinogen in addition to enhancing FN fibrillogenesis in fibroblasts. A point mutation at Trp-6 that reduces exposure of hydrophobic sites for 8-anilino-1-napthalenesulfonic acid binding and β-structure formation inhibits FN multimerization and prevents physiological cell-based FN assembly in culture. We propose a model for cell-mediated fibrillogenesis whereby cell traction force initiates a cascade of intermolecular exchange starting with the unfolding of 10FNIII to expose the multimerization sequence, which interacts with strand B of another 10FNIII domain via a Trp-mediated β-strand exchange to stabilize a partially unfolded intermediate that propagates FN self-assembly.
Pharmacokinetics and clinical response to single agent rucaparib in a dialysis dependent patient with BRCA associated breast and recurrent ovarian cancer (2018)

A 56-year old woman with BRCA-associated breast cancer and recurrent ovarian cancer was treated with a poly (ADP-ribose) polymerase enzyme (PARP) inhibitor, rucaparib, in the setting of dialysis-dependence which required dose modification. Rucaparib trough levels were obtained before and after dialysis and a clinically significant disease response was appreciated.
Optimization of C-11 DPA713 PET for pediatric patients with epilepsy: appropriate scan protocol for lesion detection (2018)

1592 Objectives: Neuroinflammation is known to be one of major pathological abnormalities of epilepsy. Translocator protein (TSPO) ligand PET imaging has been suggested as a functional imaging for detection of epileptogenic foci in patients with intractable epilepsy. Especially the second-generation TSPO radioligands like C-11 DPA713 are known to have high specific binding than prototypical agent PK11195. The utility of PET by such agents, however, has never be examined for pediatric patients with epilepsy. Although the distribution volume of the tracer is usually used as an index of specific binding, invasive arterial sampling and long duration of scanning are necessary to calculate the parameter. The purpose of this study is to suggest the minimum invasive scan protocol of C-11 DPA713 PET to identify the lesions in pediatric patients with intractable epilepsy.
Seven patients (age: 8.9 ± 6.2 years old, male/female: 5/2) with intractable epilepsy whose foci or cause had already been diagnosed were included in this study. (The patients’ genotype affecting the affinity of radioligand binding to TSPO were all homozygous high-affinity binders.) For all the patients, C-11 DPA was intravenously injected over 30 seconds by the infusion pump and, at the same time as injection start, dynamic PET scan was started. Dynamic PET image of each patient was co-registered to MRI. In each patient, volume of interest were located on the epileptogenic foci resected by surgery or on the pathological lesion determined by MRI and on the corresponding region in the contralateral hemisphere. The difference in time activity curve between the ipsilateral and contralateral volume of interest (dTAC) was assessed. As the result, the dTACs reached a plateau and the maximum within 60 minutes after injection in all the patients irrespective of pathological features. As far as pediatric patients with epilepsy are concerned, static scanning of C-11 DPA713 PET should be performed around 60 minutes after injection.
Thermal Stability of Na 3– x V 2 (PO 4 ) 2 F 3– y O y : Influence of F – for O 2– Substitution and Degradation Mechanisms (2023)

The Na-ion battery technology appears as a reliable, sustainable, and environmentally friendly alternative to the Li-ion one, especially for stationary energy storage. As for the Li-ion technology, the safety aspect is of high importance to ensure large-scale development. In this work, we studied the thermal stability and decomposition mechanisms of carbon-coated Na3V2(PO4)2F3 and two fluorine-rich phases belonging to the solid-solution Na3V3+2–yV4+y(PO4)2F3–yOy (y = 0.07 and y = 0.12), that family of compounds being often considered among the most promising positive electrode materials for Na-ion batteries. This study shows the good thermal stability of these polyanionic materials and reveals that a low O2– for F– substitution has a very limited effect on the thermal stability of fully reintercalated materials recovered in the discharged state of the battery, whereas it has a beneficial impact for highly deintercalated ones, obtained by in-depth charges. Furthermore, whatever the state of charge and the oxygen content in NaxV2(PO4)2F3–yOy (1 ≤ x ≤ 3 and y = 0, 0.07 and 0.12), the thermal degradation leads, quite unexpectedly, to the formation of crystalline Na3V3+2(PO4)2F3 in addition to an amorphous phase. The fluorination of the partial oxygen for fluorine substituted material was clearly demonstrated by X-ray diffraction (XRD) and solid state nuclear magnetic resonance spectroscopy (NMR) on materials recovered after differential scanning calorimetry (DSC) analyses. The formation of a fully sodiated crystalline phase from the thermal degradation of the material obtained in charged states of the battery, with or without the presence of electrolyte, was never reported before.
The optimum automatic thresholding using the phase of zernike moments (2004)

A new technique for automatic thresholding of images has been introduced. This technique is based on maximizing the correlation between Zernike moments' phases of the gray-level and binary images of the same objects. This technique of gray level thresholding is unimodal. Thresholding using Zernike moments would be of interest to pattern recognition applications where Zernike moments are used as features. The experimental results show that correlating the phases of Zernike moments yields the optimal threshold values. These results also indicate the robustness and stability of the technique when dealing with noisy sample images.
1125: Identification of A Novel Missense Mutation of SLC7A9 Frequent in Japanese Cystinuria Population that Cause Membrane Targeting Defect of the Transporter Protein by Introducing A Bulky Side Chain on its C -Terminus (2004)

You have accessJournal of UrologyDiscussed Poster, Monday, May 10, 2004, Monday, May 10, 2004 1:00 - 5:00 pm1 Apr 20041125: Identification of A Novel Missense Mutation of SLC7A9 Frequent in Japanese Cystinuria Population that Cause Membrane Targeting Defect of the Transporter Protein by Introducing A Bulky Side Chain on its C -Terminus Shinichi Sakamoto, Yasuhiro Shigeta, Takeshi Ueda, Arthit Chairoungdua, Masanori Fujimura, Yusuke Awa, Yukio Naya, Koichiro Akakura, Tomohiko Ichikawa, Tatsuo Igarashi, Yoshikatsu Kanai, Hitoshi Endou, and Haruo Ito Shinichi SakamotoShinichi Sakamoto More articles by this author , Yasuhiro ShigetaYasuhiro Shigeta More articles by this author , Takeshi UedaTakeshi Ueda More articles by this author , Arthit ChairoungduaArthit Chairoungdua More articles by this author , Masanori FujimuraMasanori Fujimura More articles by this author , Yusuke AwaYusuke Awa More articles by this author , Yukio NayaYukio Naya More articles by this author , Koichiro AkakuraKoichiro Akakura More articles by this author , Tomohiko IchikawaTomohiko Ichikawa More articles by this author , Tatsuo IgarashiTatsuo Igarashi More articles by this author , Yoshikatsu KanaiYoshikatsu Kanai More articles by this author , Hitoshi EndouHitoshi Endou More articles by this author , and Haruo ItoHaruo Ito More articles by this author View All Author Informationhttps://doi.org/10.1016/S0022-5347(18)38362-9AboutPDF ToolsAdd to favoritesDownload CitationsTrack CitationsPermissionsReprints ShareFacebookLinked InTwitterEmail "1125: Identification of A Novel Missense Mutation of SLC7A9 Frequent in Japanese Cystinuria Population that Cause Membrane Targeting Defect of the Transporter Protein by Introducing A Bulky Side Chain on its C -Terminus." The Journal of Urology, 171(4S), pp. 296–297 © 2016 by American Urological AssociationFiguresReferencesRelatedDetails Volume 171Issue 4SApril 2004Page: 296-297 Advertisement Copyright & Permissions© 2016 by American Urological AssociationMetricsAuthor Information Shinichi Sakamoto More articles by this author Yasuhiro Shigeta More articles by this author Takeshi Ueda More articles by this author Arthit Chairoungdua More articles by this author Masanori Fujimura More articles by this author Yusuke Awa More articles by this author Yukio Naya More articles by this author Koichiro Akakura More articles by this author Tomohiko Ichikawa More articles by this author Tatsuo Igarashi More articles by this author Yoshikatsu Kanai More articles by this author Hitoshi Endou More articles by this author Haruo Ito More articles by this author Expand All Advertisement PDF downloadLoading ...
Fast constant modulus adaptive algorithm (1991)

An exact block formulation of the constant modulus algorithm (CMA) is presented, in which a reduction of arithmetic complexity is achieved. Two types of fast algorithms are explained, either in time-domain or in frequencydomain. The first one is of greater interest for small block lengths and the second one, using the FFT as an intermediate step, has greater advantage for large blocks. Due to the equivalence between the original CMA formulation and this one, the convergence properties of the CMA are maintained, which is not the case in the Treichler et al. implementation in frequency domain of this algorithm. Furthermore, this approach allows the use of very small block lengths (e.g. N = 2), the reduction of the arithmetic complexity increasing with the block size.
Performance Analysis of Primary User Detection in a Multiple Antenna Cognitive Radio (2007)

We consider the problem of detecting a primary user signal over a wireless channel by a cognitive radio with multiple antennas. We present a multiple antenna processing based energy detector. In this detection method, the multiple copies of the primary user signal at the antennas of the cognitive radio receiver are combined and input to an energy detector. We consider two multiple antenna processing methods and analyze their detection performance - the achieved probability of detection for a pre-specified probability of false alarm and given signal-to-noise ratio. We derive closed-form expressions for the probabilities for detection and false alarm for each of the processing schemes. Finally, we show through numerical results the potential improvement in primary user detection with multiple antenna processing based energy detection at the cognitive radio receiver.
Digital microbiology: detection and classification of unknown bacterial pathogens using a label-free laser light scatter-sensing system (2011)

The majority of tools for pathogen sensing and recognition are based on physiological or genetic properties of microorganisms. However, there is enormous interest in devising label-free and reagentless biosensors that would operate utilizing the biophysical signatures of samples without the need for labeling and reporting biochemistry. Optical biosensors are closest to realizing this goal and vibrational spectroscopies are examples of well-established optical label-free biosensing techniques. A recently introduced forward-scatter phenotyping (FSP) also belongs to the broad class of optical sensors. However, in contrast to spectroscopies, the remarkable specificity of FSP derives from the morphological information that bacterial material encodes on a coherent optical wavefront passing through the colony. The system collects elastically scattered light patterns that, given a constant environment, are unique to each bacterial species and/or serovar. Both FSP technology and spectroscopies rely on statistical machine learning to perform recognition and classification. However, the commonly used methods utilize either simplistic unsupervised learning or traditional supervised techniques that assume completeness of training libraries. This restrictive assumption is known to be false for real-life conditions, resulting in unsatisfactory levels of accuracy, and consequently limited overall performance for biodetection and classification tasks. The presented work demonstrates preliminary studies on the use of FSP system to classify selected serotypes of non-O157 Shiga toxin-producing E. coli in a nonexhaustive framework, that is, without full knowledge about all the possible classes that can be encountered. Our study uses a Bayesian approach to learning with a nonexhaustive training dataset to allow for the automated and distributed detection of unknown bacterial classes.
Weakly But Deeply Supervised Occlusion-Reasoned Parametric Road Layouts (2021)

We propose an end-to-end network that takes a single perspective RGB image of a complex road scene as input, to produce occlusion-reasoned layouts in perspective space as well as a parametric bird's-eye-view (BEV) space. In contrast to prior works that require dense supervision such as semantic labels in perspective view, our method only requires human annotations for parametric attributes that are cheaper and less ambiguous to obtain. To solve this challenging task, our design is comprised of modules that incorporate inductive biases to learn occlusion-reasoning, geometric transformation and semantic abstraction, where each module may be supervised by appropriately transforming the parametric annotations. We demonstrate how our design choices and proposed deep supervision help achieve meaningful representations and accurate predictions. We validate our approach on two public datasets, KITTI and NuScenes, to achieve state-of-the-art results with considerably less human supervision.
Heart-lung interactions in acute respiratory distress syndrome: pathophysiology, detection and management strategies (2018)

Acute respiratory distress syndrome (ARDS) is the most severe form of acute respiratory failure characterized by diffuse alveolar and endothelial damage. The severe pathophysiological changes in lung parenchyma and pulmonary circulation together with the effects of positive pressure ventilation profoundly affect heart lung interactions in ARDS. The term pulmonary vascular dysfunction (PVD) refers to the specific involvement of the vascular compartment in ARDS and is expressed clinically by an increase in pulmonary arterial (PA) pressure and pulmonary vascular resistance both affecting right ventricular (RV) afterload. When severe, PVD can lead to RV failure which is associated to an increased mortality. The effect of PVD on RV function is not only a consequence of increased pulmonary vascular resistance as afterload is a much more complex phenomenon that includes all factors that oppose efficient ventricular ejection. Impaired pulmonary vascular mechanics including increased arterial elastance and augmented wave-reflection phenomena are commonly seen in ARDS and can additionally affect RV afterload. The use of selective pulmonary vasodilators and lung protective mechanical ventilation strategies are therapeutic interventions that can ameliorate PVD. Prone positioning and the open lung approach (OLA) are especially attractive strategies to improve PVD due to their effects on increasing functional lung volume. In this review we will describe some pathophysiological aspects of heart-lung interactions during the ventilatory support of ARDS, its clinical assessment and discuss therapeutic interventions to prevent the occurrence and progression of PVD and RV failure.
GNN-RE: Graph Neural Networks for Reverse Engineering of Gate-Level Netlists (2021)

This work introduces a generic, machine learning (ML)-based platform for functional reverse engineering (RE) of circuits. Our proposed platform <monospace xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">GNN-RE</monospace> leverages the notion of graph neural networks (GNNs) to: 1) represent and analyze flattened/unstructured gate-level netlists; 2) automatically identify the boundaries between the modules or subcircuits implemented in such netlists; and 3) classify the subcircuits based on their functionalities. For GNNs in general, each graph node is tailored to learn about its own features and its neighboring nodes, which is a powerful approach for the detection of any kind of subgraphs of interest. For <monospace xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">GNN-RE</monospace> , in particular, each node represents a gate and is initialized with a feature vector that reflects on the functional and structural properties of its neighboring gates. <monospace xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">GNN-RE</monospace> also learns the global structure of the circuit, which facilitates identifying the boundaries between subcircuits in a flattened netlist. Initially, to provide high-quality data for training of <monospace xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">GNN-RE</monospace> , we deploy a comprehensive dataset of foundational designs/components with differing functionalities, implementation styles, bit widths, and interconnections. <monospace xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">GNN-RE</monospace> is then tested on the unseen shares of this custom dataset, as well as the EPFL benchmarks, the ISCAS-85 benchmarks, and the 74X series benchmarks. <monospace xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">GNN-RE</monospace> achieves an average accuracy of 98.82% in terms of mapping individual gates to modules, all without any manual intervention or postprocessing. We also release our code and source data.
Passive Prosthetic Foot Shape and Size Optimization Using Lower Leg Trajectory Error (2017)

A method is presented to optimize the shape and size of a passive prosthetic foot using the Lower Leg Trajectory Error (LLTE) as the design objective. The LLTE is defined as the root-mean-square error between the lower leg trajectory calculated for a given prosthetic foot by finding the deformed shape of the foot under typical ground reaction forces and a target physiological lower leg trajectory obtained from published gait data for able-bodied walking. In previous work, the design of simple two degree-of-freedom analytical models consisting of rigid structures, rotational joints with constant stiffness, and uniform cantilevered beams, have been optimized for LLTE. However, prototypes built to replicate these simple models were large, heavy, and overly complex. In this work, the size and shape of a single-part compliant prosthetic foot keel made out of nylon 6/6 was optimized for LLTE to produce a light weight, low cost, and easily manufacturable prosthetic foot design. The shape of the keel was parameterized as a wide Bézier curve, with constraints ensuring that only physically meaningful shapes were considered. The LLTE value for each design was evaluated using a custom MATLAB script, which ran ADINA finite element analysis software to find the deformed shape of the prosthetic keel under multiple loading scenarios. The optimization was performed by MATLAB’s built-in genetic algorithm. After the optimal design for the keel was found, a heel was added to structure, sized such that when the user’s full weight acted on the heel, the structure had a factor of safety of two. The resulting optimal design has a lower LLTE value than the two degree-of-freedom analytical models, at 0.154 compared to 0.172, 0.187, and 0.269 for the two degree-of-freedom models. At 412 g, the optimal wide curve foot is nearly half the mass of the lightest prototype built from the previous models, which was 980 g. The design found through this compliant mechanism optimization method is thus far superior to the two degree-of-freedom models previously considered.