gebhart/patrepeval huggingface dataset:
CNN‐based UGS method using Cartesian‐to‐polar coordinate transformation (2018)

The main concern of user‐guided segmentation (UGS) is to achieve high segmentation accuracy with minimal user interaction. A novel convolutional neural network (CNN)‐based UGS method is proposed, which employs a single click as the user interaction. In the proposed method, the input image in the Cartesian coordinate system is first converted into the polar transformed image with the user‐guided point (UGP) as the origin of the polar coordinate system. The transformed image not only effectively delivers the UGP to the CNN, but also enables a single‐scale convolution kernel to act as a multi‐scale kernel, whose receptive field in the Cartesian coordinate system is altered based on the UGP without any extra parameters. In addition, a feature selection module (FSM) is introduced and utilised to additionally extract radial and angular features from the polar transformed image. Experimental results demonstrate that the proposed CNN using the polar transformed image improves the segmentation accuracy (mean intersection over union) by 3.69% on PASCAL VOC 2012 dataset compared with the CNN using the Cartesian coordinate image. The FSM achieves additional performance improvement of 1.32%. Moreover, the proposed method outperforms the conventional non‐CNN‐based UGS methods by 12.61% on average.
System design considerations for a high-power aerospace resonant link converter (2003)

A novel variable-speed, constant-frequency (VSCF) 400 Hz aircraft generating system has been developed using an actively clamped resonant DC link converter. The design approach used to select the best configuration for the resonant converter power stage is described, including techniques for choosing power component values to meet key governing performance specifications. Interactions between the various converter components are discussed, suggesting approaches for selecting values which must meet multiple and sometimes conflicting system performance criteria. Verification is provided using a combination of simulation results and test data from a 60 kVA laboratory breadboard system.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
ChemInform Abstract: The Spongistatins: Architecturally Complex Natural Products. Part 2. Synthesis of the C(29—51) Subunit, Fragment Assembly, and Final Elaboration to (+)‐Spongistatin 2. (2001)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 100 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a “Full Text” option. The original article is trackable via the “References” option.
Sulfone-Based Electrolytes for Nonaqueous Li–O2 Batteries (2014)

We investigated the use of sulfone-based electrolytes for the Li–O2 battery. The study compared the behavior of three commercially available sulfones: ethyl vinyl sulfone (EVS), tetramethylene sulfone (TMS), also called sulfolane, and ethyl methyl sulfone (EMS). First, we carried out a preliminary investigation of the oxygen reduction reaction and oxygen evolution reaction (ORR/OER) as a function of solvent type and Li+ concentration. Then, TMS and EMS were tested (LiTFSI salt) in Li–O2 cells. The cells exhibited initial capacities around 1800 and 2000 mAh.g–1carbon, respectively. The capacity retention on cycling was quite low. We analyzed the reaction products during discharge and charge by means of powder X-ray diffraction, infrared spectroscopy, 1H-nuclear magnetic resonance, and mass spectrometry. Although EVS was at first sight the most attractive sulfone, since it is a liquid at room temperature, it was the least stable in the presence of oxygen; its vinyl group was attacked by reduced O2 species. On the other hand, both TMS and EMS performed better during the first five cycles; Li2O2 formation and decomposition was the main reaction, although some byproducts formed during cycling. After five cycles, there was still a considerable amount of Li2O2 formed, but decomposition to form Li2CO3 became significant, and it accumulated at the O2 electrode. This was the likely reason for capacity fading.
Ion Migration‐Induced Amorphization and Phase Segregation as a Degradation Mechanism in Planar Perovskite Solar Cells (2020)

Abstract The operation of halide perovskite optoelectronic devices, including solar cells and LEDs, is strongly influenced by the mobility of ions comprising the crystal structure. This peculiarity is particularly true when considering the long‐term stability of devices. A detailed understanding of the ion migration‐driven degradation pathways is critical to design effective stabilization strategies. Nonetheless, despite substantial research in this first decade of perovskite photovoltaics, the long‐term effects of ion migration remain elusive due to the complex chemistry of lead halide perovskites. By linking materials chemistry to device optoelectronics, this study highlights that electrical bias‐induced perovskite amorphization and phase segregation is a crucial degradation mechanism in planar mixed halide perovskite solar cells. Depending on the biasing potential and the injected charge, halide segregation occurs, forming crystalline iodide‐rich domains, which govern light emission and participate in light absorption and photocurrent generation. Additionally, the loss of crystallinity limits charge collection efficiency and eventually degrades the device performance.
Influence of Formic Acid Impurity on Proton Exchange Membrane Fuel Cell Performance (2010)

The effect of trace amounts of formic acid (HCOOH) in hydrogen fuel on proton exchange membrane fuel cell (PEMFC) performance is reported. Long-term stability tests (100 h), periodic cyclic voltammetry scans, and electrochemical impedance spectroscopy analyses are used to evaluate and characterize the effects of this impurity on fuel cell performance. The results show that trace amounts of HCOOH cause degradation in fuel cell performance and significantly contaminate the electrodes. Furthermore, full recovery from the contamination could not be achieved by applying pure hydrogen to the anode while operating the fuel cell. However, this degradation may also be caused by the coarsening or dissolution of Pt, in addition to any permanent effects of HCOOH contamination. Mechanisms of contamination of the electrodes and performance degradation of the PEMFC are also postulated.
Analysis of missense variation in human BRCA1 in the context of interspecific sequence variation (2004)

An internal test of the analysis is consistent with our classification of the variants designated probably deleterious; however, we must stress that this classification is tentative and does not have sufficient independent confirmation to serve as a clinically applicable stand alone method.
Accl polymorphism in von Willebrand factor (F8VWF) at codon 516 (1991)

The sequence of VWF (1) shows a potential dimorphism of the third base of codon 516. An AccI site is (+) when the sequence is TAC and (-) when it is TAT. Polymorphism: Using two 17 base primers starting 38 bp 5' and 118 bp 3' to the dimorphic site, genomic DNA was amplified 35 cycles as described (2) under these conditions: 30" at 920, 4' at 600, electrophoresis in 12% PAG. AccI (-,-) shows one 157 bp band (S1); (+,+) shows two (123, 34 bp) (S2) (+, -) shows all three (Fig.
Detection of the catalytic activities of DNA polymerases and their associated exonucleases following SDS-polyacrylamide gel electrophoresis (1981)

A method is described to detect DNA polymerases and nucleases in homogeneous or crude enzyme preparations after electrophoresis in SDS-polyacrylamide gels(2) containing the appropriate template or substrate. DNA polymerases are electrophoresed in a gel containing gapped calf thymus DNA and after a renaturation treatment, the gel is incubated in a reaction mixture in which one deoxyribonucleoside triphosphate is [alpha-32P]-labelled. Incorporation of radioactivity into DNA is detected at the vicinity of the polymerase band by autoradiography. An associated nuclease activity can be measured after electrophoresis in a gel containing 32P-labelled gapped DNA, when nucleolytic digestion is seen as a clear band in the resulting autoradiogram. The gels can subsequently be stained with Coomassie blue to establish identical molecular weights of polymerase, nuclease and protein bands. Applications of this technique are discussed.
Detection of the first charged states in ultrasmall Si single-hole transistor using dual-channel radio frequency reflectometry (2014)

Si CMOS single-electron transistors (SET) fabricated using fully depleted SOI [1] enable an understanding of charging mechanisms in ultimately scaled CMOS devices down to a transport through a single dopant [2]. A schematic representation of such a device is shown in Fig 1. Radio-frequency (RF) reflectometry [3] is an effective tool for charge detection in various single-electron systems. Since it does not require any DC current flow the detection of electrons passing even through a single tunnel junction [4] is possible. When a Si SET is populated with electrons, one intriguing question need to be answered: where do the first charge carriers spatially accumulate during the formation of the conducting “island”? To address this issue we use a dual channel technique that enables spatial identification of charging processes within the device. Here we present results obtained using this technique for single-hole transistors (SHT). A micrograph of a typical studied SHT device.
A conserved PI(4,5)P2–binding domain is critical for immune regulatory function of DOCK8 (2021)

DOCK8 is a Cdc42-specific guanine-nucleotide exchange factor that is essential for development and functions of various subsets of leukocytes in innate and acquired immune responses. Although DOCK8 plays a critical role in spatial control of Cdc42 activity during interstitial leukocyte migration, the mechanism remains unclear. We show that the DOCK homology region (DHR)-1 domain of DOCK8 binds specifically to phosphatidylinositol 4,5-bisphosphate (PI(4,5)P2) and is required for its recruitment to the plasma membrane. Structural and biochemical analyses reveal that DOCK8 DHR-1 domain consists of a C2 domain-like core with loops creating the upper surface pocket, where three basic residues are located for stereospecific recognition of phosphoinositides. Substitution of the two basic residues, K576 and R581, with alanine abolished PI(4,5)P2 binding in vitro, ablated the ability of DOCK8 to activate Cdc42 and support leukocyte migration in three-dimensional collagen gels. Dendritic cells carrying the mutation exhibited defective interstitial migration in vivo. Thus, our study uncovers a critical role of DOCK8 in coupling PI(4,5)P2 signaling with Cdc42 activation for immune regulation.
Transient X-ray Diffraction Reveals Nonequilibrium Phase Transition in Thin Films of CH3NH3PbI3 Perovskite (2022)

Advantageous optoelectronic properties of methylammonium lead triiodide likely arise from coupling between photogenerated charge-carriers and the soft, deformable lattice. We investigate structural dynamics of MAPbI3 films using time-resolved X-ray diffraction versus pump–probe time delay and pump intensity. During the first nanosecond, the lattice anisotropically distorts from tetragonal to cubic at excitation intensities that are insufficient to thermally induce the first-order thermodynamic phase transition at 330 K. The high-symmetry structure then relaxes back to the starting phase with 11 and 236 ns time constants via a different transition pathway than observed either in the first nanosecond or in previous reports for MAPbI3. Early time dynamics are consistent with polaron formation and lattice strain stabilization while the slower recovery dynamics outlive radiative recombination and relate metastability. Fluence-independence of these lattice deformations in the low-power regime conveys relevance to optoelectronics including photovoltaics and highlights sustained involvement of nonequilibrium, photoinduced lattice reorganization in MAPbI3 under functional conditions.
Exploring the Photodynamics of a New 2D-MOF Composite: Nile Red@Al–ITQ-HB (2018)

In this work, we unravel the photodynamics of Nile Red (NR) interacting with Al-ITQ-HB nanostructure, a new layer-type metal-organic framework (MOF) with potential catalytic and photonic applications. Steady-state spectroscopy reveals the presence of NR monomers and aggregates when interacting with the MOF structure. Time-resolved experiments provide emission lifetimes of the interacting monomers, H- and J-type aggregates. We observed contributions from two monomer populations having different environments. One monomer species emits from the local-excited state and another from a photoproduced charge-separated state resulting from an ultrafast intramolecular charge transfer (ICT). Femtosecond fluorescence experiments reveal that the ICT process occurs in ∼1 ps. Fluorescence microscopy on single crystals and agglomerates of the composites shows a homogenous distribution of the dye lifetimes within the material. This study shows that the photobehavior of NR in Al-ITQ-HB MOF is dictated by its location within the material. The reported findings using a well-known polarity probe and a new two-dimensional MOF provide information on the microenvironment of this material, which may help for designing smart MOFs with potential applications in photonics and nanocatalysis.
NIMG-74. RADIOMICS OF TUMOR INVASION 2.0: COMBINING MECHANISTIC TUMOR INVASION MODELS WITH MACHINE LEARNING MODELS TO ACCURATELY PREDICT TUMOR INVASION IN HUMAN GLIOBLASTOMA PATIENTS (2017)

In glioblastoma (GBM), contrast enhanced (CE)-MRI delineates bulk tumor with contrast-enhancement but poorly characterizes invasive tumor in the nonenhancing T2W abnormality. There is extensive literature in both machine-learning (ML) and mechanistic mathematical oncology seeking to accurately predict diffuse tumor invasion from multi-parametric MRI. ML offers strengths of a data-driven iterative approach, while mechanistic (proliferation-invasion, PI) modeling incorporates spatial relationships with expected drop-offs of tumor cell density from central regions of MRI enhancement. In this study, we build and cross-validate a first-of-its-kind hybrid (ML-PI) model. We collected 82 image-guided biopsies from 18 primary GBM patients throughout CE T1W and nonenhancing T2W regions. For each biopsy, we obtained neuropathologist estimates of tumor cell density and spatially matched MRI (CE T1W, T2W) from which we extracted texture features. PI maps of tumor invasion were generated from MRI-based patient-specific estimates of the net rates of invasion and proliferation. Then, the PI maps were incorporated with a ML model that uses texture features to predict cell density to minimize the prediction error on biopsy samples (ML strength) while making sure tumor-wide prediction (biopsied and unbiopsied regions) conformed with glioblastoma biology (PI strength). We optimized this hybrid ML-PI model using leave-one-out-cross-validation, and compared its performance with PI and ML alone. We used Pearson correlation (r) between cross-validated predicted tumor cell density and true tumor cell density. We focused on prediction within the nonenhancing zone (n=32) because accurate estimation of invasive tumor cell density in this zone has important clinical value for radiation and surgical planning. PI-ML showed significantly stronger correlation (r=0.76) compared to PI (r=0.44) and ML (r=0.04) models alone (p value<0.01). We present a first-of-its-kind hybrid model combining mechanistic modeling and machine learning approaches that accurately quantifies tumor cell gradients within the non-enhancing T2W zone of GBM.
150 × 120 Gb/s Field Trial over 1,504 km using All-Distributed Raman Amplification (2014)

An all-distributed Raman system is demonstrated to support high order modulation formats with coherent digital processing. We report the transmission of 150 channels × 120 Gb/s over 1,504 km field fiber with 5 dB Q margin.
Nano-pattern replication using parylene thin film for optical applications (2007)

We propose a nano-pattern replication method using a heat-resistant polymer film for optical applications, such as surface plasmon optics. Parylene was adopted as a replication material because of its good heat-resistance at metal evaporations. The replication preciseness was evaluated by investigating the size error between master patterns and replication patterns. The 5-mum-thick parylene film with line and space (L/S) patterns was used for the investigation. Although there was about 50-80 nm increase of line width at an edge of each parylene line pattern, the pattern transfer preciseness was sufficient for optical application in visible range. The parylene nano-pattern film also showed a good resistance to Au evaporation and strain due to heat was only 0.25%. As an example of an optical application, transmission enhancement from the aperture surrounded by nano-sized concentric corrugations was demonstrated with our parylene nano-pattern film.
Tetraspanin Protein CD9 Is a Novel Paranodal Component Regulating Paranodal Junctional Formation (2004)

The axoglial paranodal junction is essential for the proper localization of ion channels around the node of Ranvier. The integrity of this junction is important for nerve conduction. Although recent studies have made significant progress in understanding the molecular composition of the paranodal junction, it is not known how these membrane components are distributed to the appropriate sites and interact with each other. Here we show that CD9, a member of the tetraspanin family, is present at the paranode. CD9 is concentrated in the paranode as myelination proceeds, but CD9 clusters become diffuse, associated with disruption of the paranode, in cerebroside sulfotransferase-deficient mice. Immunohistochemical and Western blot analysis showed that CD9 is distributed predominantly in the PNS. Ablation of CD9 in mutant mice disrupts junctional attachment at the paranode and alters the paranodal components contactin-associated protein (also known as Paranodin) and neurofascin 155, although the frequency of such abnormalities varies among individuals and individual axons even in the same mouse. Electron micrographs demonstrated that compact myelin sheaths were also affected in the PNS. Therefore, CD9 is a myelin protein important for the formation of paranodal junctions. CD9 also plays a role in the formation of compact myelin in the PNS.
Malfunction analysis of SiC-SIT DC circuit breaker in 400V-DC power supply system (2011)

In DC power supply system, a fast response circuit breaker is required. Semiconductor DC circuit breaker is an important key technology in DC power supply system. This paper considers the malfunction issue of Silicon Carbide-Static Induction Transistor (SiC-SIT) based DC circuit breaker in DC power supply system. The malfunction mechanism is explained, and a solution methodology proposed. Investigations are achieved by MATLAB/Simulink and experimented work.
NFIL3 Suppresses Hypoxia‐induced Apoptotic Cell Death by Targeting the Insulin‐like Growth Factor 2 Receptor (2014)

The insulin-like growth factor-II/mannose 6-phosphate receptor (IGF2R) over-expression correlates with heart disease progression. The IGF2R is not only an IGF2 clearance receptor, but it also triggers signal transduction, resulting in cardiac hypertrophy, apoptosis and fibrosis. The present study investigated the nuclear factor IL-3 (NFIL3), a transcription factor of the basic leucine zipper superfamily, and its potential pro-survival effects in cardiomyocytes. NFIL3 might play a key role in heart development and act as a survival factor in the heart, but the regulatory mechanisms are still unclear. IGF2 and IGF2R protein expression were highly increased in rat hearts subjected to hemorrhagic shock. IGF2R protein expression was also up-regulated in H9c2 cells exposed to hypoxia. Over-expression of NFIL3 in H9c2 cardiomyoblast cells inhibited the induction of hypoxia-induced apoptosis and down-regulated IGF2R expression levels. Gel shift assay, double-stranded DNA pull-down assay and chromatin immune-precipitation analyses indicated that NFIL3 binds directly to the IGF2R promoter region. Using a luciferase assay, we further observed NFIL3 repress IGF2R gene promoter activity. Our results demonstrate that NFIL3 is an important negative transcription factor, which through binding to the promoter of IGF2R, suppresses the apoptosis induced by IGF2R signaling in H9c2 cardiomyoblast cells under hypoxic conditions.
Percolation in quantum computation and communication (2007)

This article is a draft of a book chapter of the book entitled "Quantum Percolation and Breakdown", to appear 2008.
MR imaging of Kallmann syndrome, a genetic disorder of neuronal migration affecting the olfactory and genital systems. (1993)

Previous investigators of patients with KS used axial MR images to demonstrate hypoplasia of the olfactory sulci but offered no assessment of the olfactory bulbs. In the present study we used coronal images to show hypoplasia of both olfactory sulci and bulbs. In addition, we found what we believe to be the radiologic correlate of arrested neuronal migration in KS.
Competition of Δ 9 -Tetrahydrocannabinol with Estrogen in Rat Uterine Estrogen Receptor Binding (1977)

Direct competition experiments with delta 9 -tetrahydrocannibinol (delta 9-THC) and estradiol in binding assays with rat uterine cytosol estrogen receptors showed that delta 9-THC was a weak, but nevertheless significant, competitor for binding to cytoplasmic estrogen receptors. These data support, at the molecular level, the observations that delta 9-THC has a weak estrogenic activity (at least the ability to bind to estrogen receptors). Moreover, estrogen-like binding suggests that delta 9-THC, acting at the level of estrogen receptor, causes a primary estrogenic effect rather than an indirect or secondary phenomenon.
Interplay between promoter methylation and chromosomal loss in gene silencing at 3p11-p14 in cervical cancer (2015)

Loss of 3p11-p14 is a frequent event in epithelial cancer and a candidate prognostic biomarker in cervical cancer. In addition to loss, promoter methylation can participate in gene silencing and promote tumor aggressiveness. We have performed a complete mapping of promoter methylation at 3p11-p14 in two independent cohorts of cervical cancer patients (n = 149, n = 121), using Illumina 450K methylation arrays. The aim was to investigate whether hyperm-ethylation was frequent and could contribute to gene silencing and disease aggressiveness either alone or combined with loss. By comparing the methylation level of individual CpG sites with corresponding data of normal cervical tissue, 26 out of 41 genes were found to be hypermethylated in both cohorts. The frequency of patients with hypermethylation of these genes was found to be higher at tumor stages of 3 and 4 than in stage 1 tumors. Seventeen of the 26 genes were transcriptionally downregulated in cancer compared to normal tissue, whereof 6 genes showed a significant correlation between methylation and expression. Integrated analysis of methylation, gene dosage, and expression of the 26 hypermethylated genes identified 3 regulation patterns encompassing 8 hypermethylated genes; a methylation driven pattern (C3orf14, GPR27, ZNF717), a gene dosage driven pattern (THOC7, PSMD6), and a combined methylation and gene dosage driven pattern (FHIT, ADAMTS9, LRIG1). In survival analysis, patients with both hypermethylation and loss of LRIG1 had a worse outcome compared to those harboring only hypermethylation or none of the events. C3orf14 emerged as a novel methylation regulated suppressor gene, for which knockdown was found to promote invasive growth in human papilloma virus (HPV)-transformed keratinocytes. In conclusion, hypermethylation at 3p11-p14 is common in cervical cancer and may exert a selection pressure during carcinogenesis alone or combined with loss. Information on both events could lead to improved prognostic markers.