gebhart/patrepeval huggingface dataset:
Involvement of photobleaching and inhibition of protochlorophyll(ide) accumulation in tentoxin effects on greening of mung bean seedlings (1982)

Several types of evidence indicate that tentoxin‐caused reduction of chlorophyll accumulation in greening primary leaves of mung bean [ Vigna radiata (L.) Wilczek cv. Berken] is due to both photobleaching and decreased protochlorophyll(ide) synthesis. Greening was greater under dim (2.5 μmol m ‐2 s ‐1 ) far‐red or white light than under bright (180 to 200 μmol m ‐2 s ‐1 ) white light in tentoxin‐treated tissues, whereas there was a positive correlation between fluence rate and greening in control tissues. Under continuous white light (100 μmol m ‐2 s ‐1 ) chorophyll(ide) accumulation was slower in tentoxin‐treated than in control tissues. This was caused by greater photobleaching of newly formed chlorophyll(ide), as well as by decreased protochlorophyll(ide) synthesis. Photobleaching did not affect protochlorophyll(ide) synthesis in control or tentoxin‐treated tissues. Chlorophyll(ide) was less stable in tentoxin‐treated than in control tissues during a 24 h period of darkness. Plastids of tentoxin‐treated tissues had all of the chlorophyll‐proteins of control plants. Etioplasts of tentoxin‐treated plants contained normal galactolipid contents, but galactolipids in these plants were greatly reduced in white light. Reduced chlorophyll accumulation caused by tentoxin is apparently the result of both photodestruction and of reduced synthesis of chlorophyll.
Demonstration of a four-channel WDM/OCDMA system using 255-chip 320-Gchip/s quarternary phase coding gratings (2002)

In this letter, we report the fabrication and application of 255-chip 320 Gchip/s quaternary phase superstructure fiber Bragg gratings (SSFBGs) for optical code generation and recognition in a four-channel wavelength-division-multiplexing (WDM)/optical code-division-multiplexing (OCDM) experiment. Individual users of the system operate with different coding schemes, repetition rates, and wavelengths. Our experiments show that a single SSFBG can be used to perform simultaneous optical decoding and wavelength channel selection.
Multishot diffusion‐weighted FSE using PROPELLER MRI (2001)

A method for obtaining diffusion-weighted images that are free from the artifacts associated with echo-planar acquisitions, such as signal pile-up and geometric warping, is introduced. It uses an ungated, multishot fast spin-echo (FSE) acquisition that is self-navigated. The phase of the refocusing pulses is alternated to minimize non-Carr-Purcell-Meiboom-Gill (CPMG) artifacts. Several reconstruction methods are combined to make this method robust against motion artifacts. Examples are shown of clinical diffusion-weighted imaging and high-resolution diffusion tensor imaging.
Radiological analysis of idiopathic pulmonary hemosiderosis in children (2011)

Objective To study the imaging characteristics and pathologic findings of idiopathic pulmonary hemosiderosis(IPH).Methods The clinical datas and imaging findings of 23 cases of IPH treated in our hospital between 2000 and 2010 were retrospectively analyzed.Results On plain film,flake consolidation and ground -glass shadows( n =16),diffuse miliary and micronodular shadows( n =8),and difuse reticular shadows( n =5 )were demonstrated in both lungs.On HRCT,diffuse flake consolidation and ground - glass shadows ( n =7 ),diffuse miliary and mieronodular shadows ( n =5 ) and multiple follicular and reticular shadows ( n =4)were displayed in both lungs.Air bronchogram was seen in 2 and thickened interlobular septum in 3 cases.Conclusions Chest film is the important method to detect IPH.Combined analysis of imaging findings(HRCT),clinical manifestation,and laboratory results,particularly the presence of hemosider in macrophagocyte in sputum,gastric juice or lung tissue may provide a confirmed diagnosis of IPH.

Key words: 
Children ;  Idiopathic pulmonary hemosiderosis ;  Imaging diagnosis
Data from Tumor Genetic Analyses of Patients with Metastatic Renal Cell Carcinoma and Extended Benefit from mTOR Inhibitor Therapy (2023)

&lt;div&gt;Abstract&lt;p&gt;&lt;b&gt;Purpose:&lt;/b&gt; Rapalogs are allosteric mTOR inhibitors and approved agents for advanced kidney cancer. Reports of clonal heterogeneity in this disease challenge the concept of targeted monotherapy, yet a small subset of patients derives extended benefit. Our aim was to analyze such outliers and explore the genomic background of extreme rapalog sensitivity in the context of intratumor heterogeneity.&lt;/p&gt;&lt;p&gt;&lt;b&gt;Experimental Design:&lt;/b&gt; We analyzed archived tumor tissue of 5 patients with renal cell carcinoma, who previously achieved durable disease control with rapalogs (median duration, 28 months). DNA was extracted from spatially separate areas of primary tumors and metastases. Custom target capture and ultradeep sequencing was used to identify alterations across 230 target genes. Whole-exome sequence analysis was added to investigate genes beyond this original target list.&lt;/p&gt;&lt;p&gt;&lt;b&gt;Results:&lt;/b&gt; Five long-term responders contributed 14 specimens to explore clonal heterogeneity. Genomic alterations with activating effect on mTOR signaling were detected in 11 of 14 specimens, offering plausible explanation for exceptional treatment response through alterations in two genes (TSC1 and MTOR). In two subjects, distinct yet functionally convergent alterations activated the mTOR pathway in spatially separate sites. In 1 patient, concurrent genomic events occurred in two separate pathway components across different tumor regions.&lt;/p&gt;&lt;p&gt;&lt;b&gt;Conclusions:&lt;/b&gt; Analysis of outlier cases can facilitate identification of potential biomarkers for targeted agents, and we implicate two genes as candidates for further study in this class of drugs. The previously reported phenomenon of clonal convergence can occur within a targetable pathway which might have implications for biomarker development beyond this disease and this class of agents. &lt;i&gt;Clin Cancer Res; 20(7); 1955–64. ©2014 AACR&lt;/i&gt;.&lt;/p&gt;&lt;/div&gt;
Ladder-shaped microfluidic system for rapid antibiotic susceptibility testing (2023)

Data for publication.
Out-of-Distribution Detection for Dermoscopic Image Classification (2021)

Medical image diagnosis can be achieved by deep neural networks, provided there is enough varied training data for each disease class. However, a hitherto unknown disease class not encountered during training will inevitably be misclassified, even if predicted with low probability. This problem is especially important for medical image diagnosis, when an image of a hitherto unknown disease is presented for diagnosis, especially when the images come from the same image domain, such as dermoscopic skin images. Current out-of-distribution detection algorithms act unfairly when the in-distribution classes are imbalanced, by favouring the most numerous disease in the training sets. This could lead to false diagnoses for rare cases which are often medically important. We developed a novel yet simple method to train neural networks, which enables them to classify in-distribution dermoscopic skin disease images and also detect novel diseases from dermoscopic images at test time. We show that our BinaryHeads model not only does not hurt classification balanced accuracy when the data is imbalanced, but also consistently improves the balanced accuracy. We also introduce an important method to investigate the effectiveness of out-of-distribution detection methods based on presence of varying amounts of out-of-distribution data, which may arise in real-world settings.
Long‐term Lamivudine Therapy for Chronic Hepatitis B Infection in Children Unresponsive to Interferon (2006)

Four years after starting lamivudine treatment, most children from this study were off lamivudine, mainly because of lack of compliance and poor HBe seroconversion. These findings suggest that continuing treatment with lamivudine for undefined periods is hard to implement and does not improve HBe seroconversion.
Fast single-frequency time-of-flight range imaging (2015)

This paper proposes a solution to the 2-D phase unwrapping problem, inherent to time-of-flight range sensing technology due to the cyclic nature of phase. Our method uses a single frequency capture period to improve frame rate and decrease the presence of motion artifacts encountered in multiple frequency solutions. We present an illumination model that considers intensity image and estimates of the surface normal in addition to the phase image. Considering the number of phase wrap as the `label', the likelihood of each label is estimated at each pixel, and support for the labeling is shared between pixels throughout the image by Non-Local Cost Aggregation. Comparative experimental results confirm the effectiveness of the proposed approach.
RESOLUTION AND ETCH RESISTANCE OF A FAMILY OF 193nm POSITIVE RESISTS (1995)

Our approach to the design of positive, single layer resists for 193nm lithography will be discussed. Phenolic resins, the archetype in positive photoresist materials, cannot be used at this wavelength due to optical opacity. Acrylic polymers combine the required optical transparency at 193nm with easily tailored properties. With a design based on methacrylate terpolymers, we developed a high resolution positive resist for 193nm lithography with excellent imaging at both 193 and 248nm. Our recent work has centered on gaining further insight into methacrylate polymer structure/property relationships, improving the imaging performance and finally increasing the etch resistance. Towards that end, we have employed a class of dissolution inhibitors for 193 nm resists that are combined with methacrylate polymers to provide 3-component resists.[1] A family of 5B-steroid dissolution inhibitors that also increase etch resistance will be described. Imaging and etch performance of four versions of our resist will be disclosed. These methac ylate resists show resolution capability below 0.25 micron, etch rates 20% higher than novolak resins, good environmental stability in contrast to traditional DUV resists and dual wavelength (193/248nm) imaging.
Exploring Simple Siamese Representation Learning (2020)

Siamese networks have become a common structure in various recent models for unsupervised visual representation learning. These models maximize the similarity between two augmentations of one image, subject to certain conditions for avoiding collapsing solutions. In this paper, we report surprising empirical results that simple Siamese networks can learn meaningful representations even using none of the following: (i) negative sample pairs, (ii) large batches, (iii) momentum encoders. Our experiments show that collapsing solutions do exist for the loss and structure, but a stop-gradient operation plays an essential role in preventing collapsing. We provide a hypothesis on the implication of stop-gradient, and further show proof-of-concept experiments verifying it. Our "SimSiam" method achieves competitive results on ImageNet and downstream tasks. We hope this simple baseline will motivate people to rethink the roles of Siamese architectures for unsupervised representation learning. Code will be made available.
Increased Lung Metastasis in Transgenic NM23-Null/SV40 Mice with Hepatocellular Carcinoma (2005)

The lack of NM23-M1 expression promotes metastasis in the SV40 animal model of liver carcinogenesis.
Necroptosis Is Active in Children With Inflammatory Bowel Disease and Contributes to Heighten Intestinal Inflammation (2013)

We show for the first time that necroptosis is strongly associated with intestinal inflammation in children with IBD and contributes to strengthen the inflammatory process. We believe that RIP3 and MLKL could represent attractive targets for the management of human IBD.
Temporal Detection Threshold of Audio-Tactile Delays With Virtual Button (2023)

Synchronization of audio-tactile stimuli represents a key feature of multisensory interactions. However, information on stimuli synchronization remains scarce, especially with virtual buttons. This work used a click sensation produced with traveling waves and auditory stimulus (a bip-like sound) related to a virtual click for a psychological experiment. Participants accomplish a click gesture and judge if the two stimuli were synchronous or asynchronous. Delay injection was performed on the audio (haptic first) or the click (audio first). In both sessions, one stimulus follows the other with a delay ranging from 0-700 ms. We use weighted and transformed 3-up/1-down staircase procedures to estimate people's sensitivity. We found a threshold of 179 ms and 451 ms for the auditory first and haptic first conditions, respectively. Statistical analysis revealed a significant effect between the two stimuli' order for threshold. Participants' acceptable asynchrony decreased when the delay was on the haptic rather than on the audio. This effect could be due to the natural experience in which the stimuli tend to be first tactile and then sonorous rather than the other way around. Our findings will help designers to create multimodal virtual buttons by managing audio-tactile temporal synchronization.
Order-independent constraint-based causal structure learning (2014)

We consider constraint-based methods for causal structure learning, such as the PC-, FCI-, RFCI- and CCD- algorithms (Spirtes et al., 1993, 2000; Richardson, 1996; Colombo et al., 2012; Claassen et al., 2013). The first step of all these algorithms consists of the adjacency search of the PC-algorithm. The PC-algorithm is known to be order-dependent, in the sense that the output can depend on the order in which the variables are given. This order-dependence is a minor issue in low-dimensional settings. We show, however, that it can be very pronounced in high-dimensional settings, where it can lead to highly variable results. We propose several modifications of the PC-algorithm (and hence also of the other algorithms) that remove part or all of this order-dependence. All proposed modifications are consistent in high-dimensional settings under the same conditions as their original counterparts. We compare the PC-, FCI-, and RFCI-algorithms and their modifications in simulation studies and on a yeast gene expression data set. We show that our modifications yield similar performance in low-dimensional settings and improved performance in high-dimensional settings. All software is implemented in the R-package pcalg.
Localized Radon transform-based detection of ship wakes in SAR images (1995)

Presents a Radon transform-based approach to the detection of ship wakes in synthetic aperture radar (SAR) images. The key element of this technique is a localization of the Radon transform, whereby the intensity integration is performed over short line segments rather than across the entire image. A linear feature detection algorithm, which utilizes this localized Radon transform, is then developed. In this algorithm, referred to as the feature space line detector algorithm, the transform space is subjected to processing which serves to isolate and locate the response of linear features and suppresses the response of false alarms. This algorithm is tested on both synthetic images corrupted by various levels of Weibull multiplicative noise and on actual SAR images of ship wakes. The results of this testing demonstrate the algorithm's robustness in the presence of noise, as well as its ability to detect and localize linear features that are significantly shorter than the image dimensions.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Asymmetric Synthesis of Fluorophenylalanines and (Trifluoromethyl)phenylalanines; the Use of Chiral Pyridoxamine-Like Pyridinophane-Zinc Complex as an Enzyme Mimic (1990)

Abstract Transamination reactions in the presence of zinc(II) ion between (R)- or (S)-15-aminomethyl-14-hydroxy-5,5-dimethyl-2,8-dithia[9](2,5)pyridinophane, pyridoxamine analog with planar chirality, and o-, m-, and p-fluorophenylpyruvic acids or o-, m-, and p-(trifluoromethyl)phenylpyruvic acids gave the corresponding fluorophenylalanines or (trifluoromethyl)phenylalanines with 33–66% enantiomeric excess in moderate yields. The observed rate constants of these transaminations, kobsd, were determined with a concomitant observation of of a linear relationship between logkobsd and Hammett’s constant, σ0.
Enhancement of dentin bond strength of resin cement using new resin coating materials (2019)

The purpose of this study was to investigate combinations of resin coating materials with a dual-cure resin cement for indirect restorations by evaluating microtensile bond strengths (μTBS). Dentin surfaces of human molars were bonded with either a direct or an indirect resin composite with/without the resin coating technique. For the resin coating material, Clearfil SE Bond 2 and either one of Clearfil Protect Liner F, Clearfil Majesty LV, Panavia V5 or an experimental light-cure coating material were used. For the dual-cure resin cement, either Panavia V5 or Panavia F2.0 were used with Panavia V5 Tooth Primer or ED Primer II. Resin coating does not always contribute to the enhancement of μTBS. The highest μTBS was obtained with the resin coating combination of Clearfil SE Bond 2 and Panavia V5, and cementation with Panavia F2.0, which was identical to that of the direct resin composite bonded with Clearfil SE Bond 2.
Chemical composition distribution study in ethylene/1‐hexene copolymerization to produce LLDPE material using MgCl2‐TiCl4‐based Ziegler‐Natta catalysts (2009)

Abstract The characteristic features of LLDPE polymerization with ZN catalyst are the time drift effect during polymerization and the bending effect when trying to decrease density of the copolymer by adding more comonomer to the polymerization. The time drift in LLDPE polymerization is revealed by a constant decrease of comonomer incorporation during polymerization time. The bending is revealed by difficulties in lowering the density of LLDPE material below the density of 920 kg/m 3 . With increasing comonomer content during polymerization, the density does not decrease, but the soluble fraction increases. To try to observe if these phenomena are connected, two types of catalysts, SiO 2 supported and precipitated MgCl 2 ZN catalysts, were studied. A short time (10 min) and an extended time (60 min) copolymerization test series where the polymerizations were performed in the presence of a gradually increasing comonomer amount. Both catalysts show a strong bending when density is presented as a function of 1‐hexene both in 10‐ and 60‐min polymerization, indicating no connection between time drift and bending. The density, melting point, and crystallinity results all indicate that both catalysts are making similar copolymer material with identical chemical composition distribution. © 2009 Wiley Periodicals, Inc. J Appl Polym Sci, 2010
Real-Time Pseudo-Random Representation of Urban Sprawl (2001)

Abstract : The Department of Defense (DoD) has identified the need for simulation representations of urban sprawl, and has open actions reviewing urban sprawl simulation capabilities. The essence of the problem is the large terrain database development and subsequent terrain complexity that is required for representation of large urban and suburban areas. A further complexity is the need to simulate the interior structure of a large number of buildings for dismounted combat. This need for suburban representations impacts directly upon the ability of the Department to simulate urban combat and unconventional warfare.
Abstract 3404: Identifying genes involved in retinoic-acid-mediated breast tumor progression by total-genome-knockdown screen (2014)

Abstract Despite numerous advances in cancer care, breast cancer remains one of the leading causes of cancer-related death among Canadian women. Previous work by our lab has identified aldehyde dehydrogenase 1A3 (ALDH1A3) as a breast cancer stem cell marker, and patients with high levels of ALDH1A3 in their tumors have worse outcomes. Furthermore, we found that via its retinoic acid (RA) production function, ALDH1A3 also contributes to breast tumor growth and metastasis in a murine xenograft model. RA induces transcription of many genes (directly and indirectly), initiates cell signaling and regulates many cellular processes involved in cell growth and differentiation. To identify the key RA-inducible genes which mediate breast cancer progression we performed a genome-wide lentiviral-based shRNA screen using MDA-MB-231 breast cancer cells xenotransplanted into NOD/SCID mice with or without RA treatment. From the in vivo screen, 50 genes were identified as being putatively involved in RA-mediated breast tumor growth. 14 genes have been confirmed in vitro as differentially expressed in the presence of RA. We have generated individual shRNA knockdown clones of the genes and are validating their involvement in RA-mediated breast cancer progression in vivo. Analysis of the genes identified by this screen revealed potential interactions between RA and Wnt signaling, implicating extensive cross-talk between these two pathways. Completion of this study will define the mechanism of RA-mediated breast cancer progression and potentially identify new therapeutic targets for breast cancer treatment. Citation Format: Krysta M. Coyle, Cheryl Dean, Lu-Zhe Pan, Dae-Gyun Ahn, Mohammad Sultan, Jayme Salsman, Graham Dellaire, Carman Giacomantonio, Patrick W. Lee, Paola Marcato. Identifying genes involved in retinoic-acid-mediated breast tumor progression by total-genome-knockdown screen. [abstract]. In: Proceedings of the 105th Annual Meeting of the American Association for Cancer Research; 2014 Apr 5-9; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2014;74(19 Suppl):Abstract nr 3404. doi:10.1158/1538-7445.AM2014-3404
Study of a Fractional Slot Concentrated Winding Double Rotor Permanent Magnet Synchronous Motor for In-Wheel Direct-Drive Applications (2020)

Simulation results of a double rotor permanent magnet synchronous motor with fractional slot concentrated winding for in-wheel direct-drive applications, in two different configurations, are presented in this paper. Finite element method is used to predict the motor working characteristics and performances for both structures, under different working conditions, and to find the optimal solution for the experimental demonstrator. The main goal is to achieve a high torque and power density over a large speed operation domain.
Infiltrating CTLs are bothered by HLA-E on tumors (2012)

We recently described the upregulation of HLA-E in ovarian and cervical cancers. Instead of interacting with natural killer cells, HLA-E appeared to inhibit intratumoral cytotoxic T lymphocytes (CTL) via the receptor CD94/NKG2A. Strikingly, the survival benefit of intraepithelial infiltrating CTL was lost in those cancers with high HLA-E expression.
Tight-binding equations for longitudinally driven waveguides: Lieb and Kagome lattices (2018)

A tight-binding approximation is developed for longitudinally driven photonic lattices with three lattice sites per unit cell. Two cases are considered in detail: Lieb and Kagome lattices. The lattice is decomposed into three sublattices each of which are allowed move independently of one another. Emphasis is placed on periodic driving induced by laser-etched helical coils along the direction of propagation. The linear Floquet bands are constructed for various sublattice rotation patterns such as: phase offset, different radii, different frequency, and a quasi one-dimensional motion. Depending on the nature of the band structure, edge states can move unidirectionally. In this case they move effectively across defects due to underlying topological protection. On the other hand, non-topological edge waves are found to reflect off defects.