gebhart/patrepeval huggingface dataset:
Performance of deep learning to detect mastoiditis using multiple conventional radiographs of mastoid (2020)

The deep learning algorithm trained by multiple views showed better performance than that trained by single view. The diagnostic performance of the algorithm for detecting mastoiditis on mastoid series was similar to or higher than that of radiologists.
Structural and Spectroscopic Study of Reactions between Chelating Zinc-Binding Groups and Mimics of the Matrix Metalloproteinase and Disintegrin Metalloprotease Catalytic Sites:  The Coordination Chemistry of Metalloprotease Inhibition (2005)

To understand the coordination chemistry of zinc-binding groups (ZBGs) with catalytic zinc centers in matrix metalloproteinases (MMPs) and disintegrin metalloproteases (ADAMs), we have undertaken a model compound study centered around tris(3,5-methylphenypyrazolyl)hydroboratozinc(II) hydroxide and aqua complexes ([Tp(Ph,Me)ZnOH] and [Tp(Ph,Me)Zn(OH2)]+, respectively, wherein (Tp(Ph,Me))- = hydrotris(3,5-methylphenylpyrazolyl)borate) and the products of their reactions with a class of chelating Schiff's base ligands. The results show that the protic ligands, HL (HL = N-propyl-1-(5-methyl-2-imidazolyl)methanimine (5-Me-4-ImHPr), N-propyl-1-(4-imidazolyl)methanimine (4-ImHPr), and N-propyl-1-(2-imidazolyl)methanimine (2-ImHPr)), react with [Tp(Ph,Me)ZnOH] and give products with the general formula [Tp(Ph,Me)ZnL], whereas reactions with neutral aprotic ligands, L' (L' = N-propyl-1-(1-methyl-2-imidazolyl)methanimine (1-Me-2-ImPr) and N-propyl-1-(2-thiazolyl)methanimine (2-TaPr)), yield the corresponding [Tp(Ph,Me)ZnL]+ complexes. Although the phenol group of N-propyl-1-(2-hydroxyphenyl)methanimine (2-HOPhPr) is protic, this ligand forms a cationic four-coordinate complex containing an intraligand hydrogen bond. The solid-state structures of these complexes were determined by single-crystal X-ray diffraction, and the results showed that the protic ligands form five-membered chelates of the Zn2+ ion. All ligands displace the aqua ligand in [Tp(Ph,Me)Zn(OH2)]+ to yield complexes having 1H NMR spectra consistent with the formation of five membered chelates. The 1H resonance frequencies of the chelating ligands typically shift upfield upon coordination to the zinc center, due to ring current effects from the pendant phenyl groups of the (Tp(Ph,Me))- ligand. Thus, the 1H NMR spectra provide a convenient and sensitive means of tracking the solution reactions by titration. The resulting series of spectra showed that the stabilities of the chelates in solution depend on the propensity of the ligands to deprotonate upon chelation of the zinc center. The behaviors of these bidentate ZBGs provide insight into the structural and electronic factors that contribute to the stabilities of inhibited MMPs and ADAMs and suggest that the proton acidity of the coordinated ZBG may be a crucial criterion for inhibitor design.
Evaluation of one year of frequent dialysis on fluid load and body composition using calf bioimpedance technique (2019)

Reduction of fluid overload with no alteration of body composition was observed in this study. Accordingly, improving fluid status was confirmed by reducing BP and use of antihypertensive drugs together with increase in CNR. Measurement of fluid status by CNR in hemodialysis patients is a new method to quantitatively assess hydration potentially creating a target for volume of fluid removal.
FDG PET/CT Imaging of Oropharyngeal Squamous Cell Carcinoma (2013)

Index morphologic and glycolytic parameters as measured in FDG PET/CT are significantly larger in HPV-negative as compared with HPV-positive primary oropharyngeal carcinoma. In contrast, the same parameters trended to be larger in HPV-positive regional nodal disease.
Room-temperature macromolecular crystallography using a micro-patterned silicon chip with minimal background scattering (2016)

Recent success at X-ray free-electron lasers has led to serial crystallography experiments staging a comeback at synchrotron sources as well. With crystal lifetimes typically in the millisecond range and the latest-generation detector technologies with high framing rates up to 1 kHz, fast sample exchange has become the bottleneck for such experiments. A micro-patterned chip has been developed from single-crystalline silicon, which acts as a sample holder for up to several thousand microcrystals at a very low background level. The crystals can be easily loaded onto the chip and excess mother liquor can be efficiently removed. Dehydration of the crystals is prevented by keeping them in a stream of humidified air during data collection. Further sealing of the sample holder, for example with Kapton, is not required. Room-temperature data collection from insulin crystals loaded onto the chip proves the applicability of the chip for macromolecular crystallography. Subsequent structure refinements reveal no radiation-damage-induced structural changes for insulin crystals up to a dose of 565.6 kGy, even though the total diffraction power of the crystals has on average decreased to 19.1% of its initial value for the same dose. A decay of the diffracting power by half is observed for a dose of <i>D</i><sub>1/2</sub> = 147.5 ± 19.1 kGy, which is about 1/300 of the dose before crystals show a similar decay at cryogenic temperatures.
Requirement-Guided Model Refinement (2014)

Medical device is a typical Cyber-Physical System and ensuring the safety and efficacy of the device requires closed-loop verification. Currently closed-loop ver-ifications of medical devices are performed in the form of clinical trials in which the devices are tested on the patients. Using clinical trials as closed-loop verifi-
A shear wave elastography system for cetacean tissues and its potential application in fish bioacoustics. (2011)

A system is being developed to determine the in vivo, low-frequency elastic properties of cetacean head soft tissues. The system consists of two ultrasound-based components: a shear wave generation source and a vibrometer that monitors the induced tissue motions. Processing of the tissue motion data yields estimates of the frequency dependent shear speed and loss as a function of tissue depth. This work builds upon developments by other researchers in the area of radiation force elastography, with the addition of novel design features intended to enable the examination of tissue volumes that are relatively thick and/or obstructed by bone. Potential applications of the technology to fish bioacoustics investigations will be discussed. [Work supported by ONR.]
Escherichia coli aspartate carbamoyltransferase: the probing of crystal structure analysis via site-specific mutagenesis (1991)

Crystal structures are known for aspartate carbamoyltransferase (ATCase) in the T and R states, with and without the allosteric activator adenosine triphosphate (ATP) or inhibitor cytidine triphosphate (CTP). Visual inspection of X-ray crystal structures does not provide all of the information necessary for the determination of structure--function relationships in protein molecules. This problem is compounded because the crystalline states of the molecule may introduce effects due to crystal packing, restricted flexibility and less than optimum enzymatic conditions. Therefore, alternative techniques are required to test mechanisms conjectured from three-dimensional crystal structures of proteins. The technique of site-specific mutagenesis allows the researcher to test structure--function models based on three-dimensional structures and to obtain further insight into characteristics of the enzyme. Site-specific mutagenesis has been used to probe residues believed to be critical in the structure and function of ATCase. Selection of residues to be mutated has depended extensively on three-dimensional crystal structures of the enzyme. To date, 48 site-specific mutations at 37 different amino acid sites have been published. Although a total of 118 mutants at 58 different sites has been communicated to our laboratory, only published mutants will be considered in this review. In this paper, we compile for the first time, review, and analyze the site-specific mutants of ATCase. Site-specific mutagenesis of proteins has become a powerful technique in modern-day molecular biology, especially in studying a molecule as large as aspartate carbamoyltransferase. In this review, the role of site-specific mutagenesis of ATCase is discussed and improvements in the analysis are suggested.
Author response: Origin of wiring specificity in an olfactory map revealed by neuron type–specific, time-lapse imaging of dendrite targeting (2023)

Advanced genetics and imaging reveal wiring logic underlying the olfactory map organization in the developing fruit fly brain, and strategies employed by projection neurons to target dendrites to specific locations in a timely manner.
Instability of superconducting state in Josephson tunnel junctions (1984)

Experiments on low-resistance Josephson Sn--I--Sn tunnel junctions have shown the superconductor to exhibit an instability that manifests itself on the current--voltage characteristic (IVC) in the form of a jumplike decrease of the voltage when it reaches a value 2..delta../e. When a weak magnetic field H is applied parallel to the junction plane and suppresses the nonstationary Josephson effect, the negative-slope IVC section vanishes. The H-dependent instability-current component, as well as the dc component of the Josephson current near 2..delta../e, can be approximated by a function of H/sup -2/. The singularity observed is attributed to the presence of a maximum of the superconducting component, due to the Riedel singularity, at V = 2..delta../e.
<title>At-wavelength characterization of DUV-radiation-induced damage in fused silica</title> (2000)

Fused silica is the optical material of choice for deep ultraviolet (DUV) lithographic systems. However, this material is subject to irradiation-induced compaction with ArF excimer radiation. Here we report direct, at-wavelength, wavefront measurements of DUV-laser-damaged fused silica samples performed using phase-shifting point diffraction interferometry (PS/PDI). Experimental results show that the damage anneals in the temperature range of 200 to approximately 600 degrees Celsius. Finally, the interferometric measurements are compared to birefringence studies performed on the same samples.
Granule Exocytosis Assay of CTL Activation (1993)

Granule exocytosis assay for cytotoxic T lymphocyte (CTL) activation has become an important additional method of evaluating activating stimuli and of studying cell surface receptors and transmembrane signaling. It also provides the opportunity to study the effects of enhancing and inhibiting agents on the exocytic response by predictably manipulating the intensity of granule exocytosis which can be triggered by immobilized monoclonal antibody (mAb) or by the antigen (Ag)-bearing target cell. This assay is based on the ability of CTL to release cytoplasmic granules into the culture medium that contain the easily detectable enzyme serine esterase (Pasternack et al., 1986; Takayama and Sitkovsky, 1987). We describe here the granule exocytosis assay in response to immobilized anti-T-cell receptor (TCR) mAb and to Ag-bearing target cells. For more details the reader is directed to (Taffs and Sitkovsky (1991).
Advances in extracellular vesicle isolation methods: a path towards cell-type specific EV isolation (2023)

Extracellular vesicles are small, heterogenous, phospholipid-rich vesicles that are secreted by all cells into the extracellular space. They play a key role in intercellular communication because they can transport a variety of biomolecules such as proteins, lipids, and nucleic acids between cells. As categorized by the International Society of Extracellular Vesicles (ISEV), the term EV encompasses different sub-types, including exosomes, microvesicles, and apoptotic bodies, which differ in their size, origin, and cargo. EVs can be isolated from biological fluids such as blood, urine, and cerebrospinal fluid, and their biomolecular content can be analyzed to monitor the progression of certain diseases. Therefore, EVs can be used as a new source of liquid biomarkers for advancing novel diagnostic and therapeutic tools. Isolating and analyzing EVs can be challenging due to their nanoscopic size and low abundance. Several techniques have been developed for the isolation and characterization of EVs, including ultracentrifugation, density gradient separation, size-exclusion chromatography, microfluidics, and magnetic bead-based/affinity methods. This review highlights advances in EV isolation techniques in the last decade and provides a perspective on their advantages, limitations, and potential application to cell-type specific EV isolation in the future.
Octahedron-based Projections as Intermediate Representations for Computer Imaging: TOAST, TEA, and More (2019)

This paper defines and discusses a set of rectangular all-sky projections that have no singular points, notably the Tesselated Octahedral Adaptive Spherical Transformation (or TOAST) developed initially for the WorldWide Telescope. These have proven to be useful as intermediate representations for imaging data where the application transforms dynamically from a standardized internal format to a specific format (projection, scaling, orientation, etc.) requested by the user. TOAST is strongly related to the Hierarchical Triangular Mesh pixelization and is particularly well adapted to situations where one wishes to traverse a hierarchy of images increasing in resolution. Because it can be recursively computed using a very simple algorithm it is particularly adaptable to use with graphical processing units.
Negative feedback control design for a PWM-buck converter (2002)

This paper uses a conventional pulse width modulator (PWM) control method to design a negative feedback controller for the PWM-buck converter. The main objective in using the conventional control is to design a stable compensator in the closed loop to provide stability and improve the performance for the power supply for the parameter variations, load changes, and the equivalent series resistance (ESR) effects. This is done by adding a compensator in the feedback loop of the switching power supply. The performance of the PWM-buck converter is improved. The simulation program PSPICE is used to verify the theoretical analysis of the converter.
Local superconducting coupling in the strong-localization limit of ultrathin granular metal films (1989)

The onset of fluctuations into the superconducting state, as identified by the appearance of a local minimum in the resistance versus temperature, is found to be coincident with the characteristic activation energy of normal-state conduction falling to a value of the order of the superconducting energy gap of the material at T=0. The model of conduction used is variable-range hopping with a Coulomb gap, appropriate to granular metals.
Protein–protein interaction network analysis applied to DNA copy number profiling suggests new perspectives on the aetiology of Mayer–Rokitansky–Küster–Hauser syndrome (2021)

Mayer-Rokitansky-Küster-Hauser (MRKH) syndrome is a rare disease, characterised by the aplasia of vagina and uterus in women with a 46,XX karyotype. Most cases are sporadic, but familial recurrence has also been described. Herein, we investigated an Italian cohort of 36 unrelated MRKH patients to explore the presence of pathogenic copy number variations (CNVs) by array-CGH and MLPA assays. On the whole, aberrations were found in 9/36 (25%) patients. Interestingly, one patient showed a novel heterozygous microduplication at Xp22.33, not yet described in MRKH patients, containing the PRKX gene. Moreover, a novel duplication of a specific SHOX enhancer was highlighted by MLPA. To predict the potential significance of CNVs in MRKH pathogenesis, we provided a network analysis for protein-coding genes found in the altered genomic regions. Although not all of these genes taken individually showed a clear clinical significance, their combination in a computational network highlighted that the most relevant biological connections are related to the anatomical structure development. In conclusion, the results described in the present study identified novel genetic alterations and interactions that may be likely involved in MRKH phenotype determination, so adding new insights into the complex puzzle of MRKH disease.
Tanshinone IIA Prevents Leu27IGF-II-Induced Cardiomyocyte Hypertrophy Mediated by Estrogen Receptor and Subsequent Akt Activation (2015)

IGF-IIR plays important roles as a key regulator in myocardial pathological hypertrophy and apoptosis, which subsequently lead to heart failure. Salvia miltiorrhiza Bunge (Danshen) is a traditional Chinese medicinal herb used to treat cardiovascular diseases. Tanshinone IIA is an active compound in Danshen and is structurally similar to 17[Formula: see text]-estradiol (E[Formula: see text]. However, whether tanshinone IIA improves cardiomyocyte survival in pathological hypertrophy through estrogen receptor (ER) regulation remains unclear. This study investigates the role of ER signaling in mediating the protective effects of tanshinone IIA on IGF-IIR-induced myocardial hypertrophy. Leu27IGF-II (IGF-II analog) was shown in this study to specifically activate IGF-IIR expression and ICI 182,780 (ICI), an ER antagonist used to investigate tanshinone IIA estrogenic activity. We demonstrated that tanshinone IIA significantly enhanced Akt phosphorylation through ER activation to inhibit Leu27IGF-II-induced calcineurin expression and subsequent NFATc3 nuclear translocation to suppress myocardial hypertrophy. Tanshinone IIA reduced the cell size and suppressed ANP and BNP, inhibiting antihypertrophic effects induced by Leu27IGF-II. The cardioprotective properties of tanshinone IIA that inhibit Leu27IGF-II-induced cell hypertrophy and promote cell survival were reversed by ICI. Furthermore, ICI significantly reduced phospho-Akt, Ly294002 (PI3K inhibitor), and PI3K siRNA significantly reduced the tanshinone IIA-induced protective effect. The above results suggest that tanshinone IIA inhibited cardiomyocyte hypertrophy, which was mediated through ER, by activating the PI3K/Akt pathway and inhibiting Leu27IGF-II-induced calcineurin and NFATC3. Tanshinone IIA exerted strong estrogenic activity and therefore represented a novel selective ER modulator that inhibits IGF-IIR signaling to block cardiac hypertrophy.
BJT Device and Circuit Co-Optimization Enabling Bandgap Reference and Temperature Sensing in 7-nm FinFET (2018)

Caused by the increased power density and strong thermal gradients in today's large SoC/FPGAs in scaled process technologies, high-precision bandgap references and temperature sensors have become some of the most critical analog blocks. BJT devices form core components of such benchmark analog circuitry, thanks to their linear dependence on temperature. This paper discusses BJT device modeling and characterization results in 7-nm FinFET CMOS technology with regard to the BJT's variability and process spread. It provides guidance useful for the circuit implementation and quantifies the circuit application performance. Two test-chip device arrays are presented to demonstrate the feasibility of using BJTs in FinFET CMOS. A bandgap reference circuit is designed using the developed SPICE model. It shows measured max inaccuracy of ±\pmb0.2%. The presented merged layout structure further saves 20% of area.
Mechanism of Date Retention Improvement by High Temperature Annealing of Al2O3Blocking Layer in Flash Memory Device (2011)

The mechanism underlying improved data retention via high-temperature oxygen annealing of the Al2O3 blocking layer in a charge-trap type flash memory device is investigated in comparison with the case of high-temperature nitrogen annealing. The results show that significant improvement of the retention property can be achieved by oxygen annealing at 1100 °C, compared to nitrogen annealing. Experimental evidence indicated that the underlying mechanism does not arise from suppression of the trap-assisted tunneling current through the blocking oxide; instead it is caused by a reduction of the thermionic emission component of the charge loss factor. This is possibly due to changes of the conduction band offset of the crystallized Al2O3.
PTPN22 Alters the Development of Regulatory T Cells in the Thymus (2012)

PTPN22 encodes a tyrosine phosphatase that inhibits Src-family kinases responsible for Ag receptor signaling in lymphocytes and is strongly linked with susceptibility to a number of autoimmune diseases. As strength of TCR signal is critical to the thymic selection of regulatory T cells (Tregs), we examined the effect of murine PTPN22 deficiency on Treg development and function. In the thymus, numbers of pre-Tregs and Tregs increased inversely with the level of PTPN22. This increase in Tregs persisted in the periphery and could play a key part in the reduced severity observed in the PTPN22-deficient mice of experimental autoimmune encephalomyelitis, a mouse model of multiple sclerosis. This could explain the lack of association of certain autoimmune conditions with PTPN22 risk alleles.
The Nanoscopic Organization of Synapse Structures: A Common Basis for Cell Communication (2021)

Synapse structures, including neuronal and immunological synapses, can be seen as the plasma membrane contact sites between two individual cells where information is transmitted from one cell to the other. The distance between the two plasma membranes is only a few tens of nanometers, but these areas are densely populated with functionally different proteins, including adhesion proteins, receptors, and transporters. The narrow space between the two plasma membranes has been a barrier for resolving the synaptic architecture due to the diffraction limit in conventional microscopy (~250 nm). Various advanced super-resolution microscopy techniques, such as stimulated emission depletion (STED), structured illumination microscopy (SIM), and single-molecule localization microscopy (SMLM), bypass the diffraction limit and provide a sub-diffraction-limit resolving power, ranging from 10 to 100 nm. The studies using super-resolution microscopy have revealed unprecedented details of the nanoscopic organization and dynamics of synaptic molecules. In general, most synaptic proteins appear to be heterogeneously distributed and form nanodomains at the membranes. These nanodomains are dynamic functional units, playing important roles in mediating signal transmission through synapses. Herein, we discuss our current knowledge on the super-resolution nanoscopic architecture of synapses and their functional implications, with a particular focus on the neuronal synapses and immune synapses.
Rapid Removal of Benzyloxycarbonyl Groups from 1,4,7,10‐Tetraazacyclododecane Derivatives by Catalytic Transfer Hydrogenation. (2003)

Abstract For Abstract see ChemInform Abstract in Full Text.