gebhart/patrepeval huggingface dataset:
An In Vivo Screen Identifies PYGO2 as a Driver for Metastatic Prostate Cancer (2018)

Advanced prostate cancer displays conspicuous chromosomal instability and rampant copy number aberrations, yet the identity of functional drivers resident in many amplicons remain elusive. Here, we implemented a functional genomics approach to identify new oncogenes involved in prostate cancer progression. Through integrated analyses of focal amplicons in large prostate cancer genomic and transcriptomic datasets as well as genes upregulated in metastasis, 276 putative oncogenes were enlisted into an <i>in vivo</i> gain-of-function tumorigenesis screen. Among the top positive hits, we conducted an in-depth functional analysis on Pygopus family PHD finger 2 (<i>PYGO2</i>), located in the amplicon at 1q21.3. PYGO2 overexpression enhances primary tumor growth and local invasion to draining lymph nodes. Conversely, PYGO2 depletion inhibits prostate cancer cell invasion <i>in vitro</i> and progression of primary tumor and metastasis <i>in vivo</i> In clinical samples, PYGO2 upregulation associated with higher Gleason score and metastasis to lymph nodes and bone. Silencing PYGO2 expression in patient-derived xenograft models impairs tumor progression. Finally, PYGO2 is necessary to enhance the transcriptional activation in response to ligand-induced Wnt/β-catenin signaling. Together, our results indicate that PYGO2 functions as a driver oncogene in the 1q21.3 amplicon and may serve as a potential prognostic biomarker and therapeutic target for metastatic prostate cancer.<b>Significance:</b> Amplification/overexpression of PYGO2 may serve as a biomarker for prostate cancer progression and metastasis. <i>Cancer Res; 78(14); 3823-33. ©2018 AACR</i>.
Computational polarized Raman microscopy on sub-surface nanostructures with sub-diffraction-limit resolution (2021)

Raman microscopy with resolution below the diffraction limit is demonstrated on sub-surface nanostructures. Unlike most other modalities for nanoscale measurements, our approach is able to image nanostructures buried several microns below the sample surface while still extracting details about the chemistry, strain, and temperature of the nanostructures. In this work, we demonstrate that combining polarized Raman microscopy adjusted to optimize edge enhancement effects and nanostructure contrast with fast computational deconvolution methods can improve the spatial resolution while preserving the flexibility of Raman microscopy. The cosine transform method demonstrated here enables significant computational speed-up from O(N<sup>3</sup>) to O(Nlog N) - resulting in computation times that are significantly below the image acquisition time. CMOS poly-Si nanostructures buried below 0.3 - 6 µm of complex dielectrics are used to quantify the performance of the instrument and the algorithm. The relative errors of the feature sizes, the relative chemical concentrations and the fill factors of the deconvoluted images are all approximately 10% compared with the ground truth. For the smallest poly-Si feature of 230 nm, the absolute error is approximately 25 nm.
GPS SBAS L1/L5 bistatic radar altimeter (2014)

GNSS bistatic radar offers a low cost alternative for ocean altimetry. It can also be used to measure wind speed, wind direction and modeling of the ocean surface state. A bistatic configuration, using one right-handed circular polarized and one left-handed circular polarized antenna, was built in 2012 and installed in the NOAA hurricane hunter in order to measure direct and reflected L1 and L5 signals. The direct and reflected signals were compared and the path difference between them calculated, leading to altitude measurements of the receiver using both SBAS L1 and L5 signals. Compared to publicly available signals on L1, the higher code rate of L5 provides higher measurement sensitivity. The estimated altitude of the airplane receiver was compared to a radar altimeter and an onboard GPS receiver was used as truth reference.
Faculty Opinions recommendation of Photosystem I/molecular wire/metal nanoparticle bioconjugates for the photocatalytic production of H2. (2008)

Photosystem I (PS I) is a robust photosynthetic complex that adeptly captures photons to create a charge-separated state with a quantum efficiency that approaches 1.0. This charge-separated state is stable for approximately 100 ms, and the low-potential reductant that is produced is poised at a redox potential favorable for H2 evolution. PS I has been covalently linked to Pt and Au nanoparticle surfaces by 1,6-hexanedithiol which serves as a molecular wire to both connect PS I to the particles and transfer electrons from the terminal electron transfer cofactor of PS I, FB, to the nanoparticle. Illumination of these Photosystem I/molecular wire/nanoparticle bioconjugates is able to catalyze the reaction: 2H+ + 2e(-)--> H2. Transfer of the electrons from PS I to the nanoparticle through the molecular wire is not rate-limiting for H2 evolution. Supplying the system with more efficient donor-side electron donating species results in a 5-fold increase in the rate of H2 evolution. PMID: 18439011
Second and Third Virial Coefficients for Methane + Ethane and Methane + Ethane + Carbon Dioxide at (300 and 320) K (1996)

Measurements of pVT made using the Burnett technique at (300 and 320) K are reported for methane, ethane, three x1 methane + (1 − x1) ethane mixtures with x1 = 0.30623, 0.49971, and 0.70090, and two x1 methane + x2 ethane + (1 − x1 − x2) carbon dioxide mixtures with x1 = 0.32125, x2 = 0.34099 and x1 = 0.24759, x2 = 0.56013. Second virial coefficients have been calculated from these results for the pure fluids, and the binary and ternary mixtures. Cross second and third virial coefficients have been derived, including the cross third virial coefficient which describes the simultaneous unlike interaction between methane, ethane, and carbon dioxide. The experimental results were used to test an approximation to the virial equation which greatly simplifies calculations for multicomponent mixtures and which requires only experimental virial coefficients for binary mixtures. Values calculated using the model agree with experimental values within the estimated uncertainties. The results are compared with literature values, where available.
Label-free nanoscopy enabled by coherent imaging with photonic waveguides (2019)

In this project it was found that Fourier ptychographic microscopy can be improved far beyond its conventional limits via waveguide-based optical systems. Extensive in silico studies showed that images obtained on highrefractive index material waveguide chips in conjunction with hyperspectral illumination light and ﬁnely designed waveguide geometries can be combined via a modiﬁed phase-retrieval algorithm to yield a resolution below 150 nm.
Effects of solvent addition to acetylation medium on cellulose triacetate prepared from low‐grade hardwood dissolving pulp (1998)

As cellulose triacetate was prepared from low-grade hardwood-dissolving pulp, a considerable amount of the insoluble residue was present in the acetylation medium of the acetic acid/acetic anhydride/sulfuric acid system, and it consisted mainly of cellulose triacetate (CTA) and xylan diacetate (XDA). As one of the remedies for reducing the insoluble residue, a solvent was added to the acetylation medium and the effects of the solvent addition on the amount of insoluble residue formed were studied. To do so, 17 different solvents were selected so as to cover a wide range of solubility parameters. The obtained results clearly indicated that the addition of the solvent affects the amount of insoluble residue and that, excluding dichloroacetic acid, nitromethane was effective for its reduction, but that neither methylene chloride nor nitroethane were in spite of their effectiveness for softwood-dissolving pulp, which would be due to the intrinsic properties of XDA on the solubility in the acetylation medium. A new acetylation system with such an appropriate solvent would, therefore, provide a clue as to an industrial usage of the low-grade hardwood-dissolving pulps for cellulose acetate production. © 1998 John Wiley & Sons, Inc. J Appl Polym Sci 69: 1445–1449, 1998
Eye Tracking for Deep Learning Segmentation Using Convolutional Neural Networks (2019)

Deep learning with convolutional neural networks (CNNs) has experienced tremendous growth in multiple healthcare applications and has been shown to have high accuracy in semantic segmentation of medical (e.g., radiology and pathology) images. However, a key barrier in the required training of CNNs is obtaining large-scale and precisely annotated imaging data. We sought to address the lack of annotated data with eye tracking technology. As a proof of principle, our hypothesis was that segmentation masks generated with the help of eye tracking (ET) would be very similar to those rendered by hand annotation (HA). Additionally, our goal was to show that a CNN trained on ET masks would be equivalent to one trained on HA masks, the latter being the current standard approach. Step 1: Screen captures of 19 publicly available radiologic images of assorted structures within various modalities were analyzed. ET and HA masks for all regions of interest (ROIs) were generated from these image datasets. Step 2: Utilizing a similar approach, ET and HA masks for 356 publicly available T1-weighted postcontrast meningioma images were generated. Three hundred six of these image + mask pairs were used to train a CNN with U-net-based architecture. The remaining 50 images were used as the independent test set. Step 1: ET and HA masks for the nonneurological images had an average Dice similarity coefficient (DSC) of 0.86 between each other. Step 2: Meningioma ET and HA masks had an average DSC of 0.85 between each other. After separate training using both approaches, the ET approach performed virtually identically to HA on the test set of 50 images. The former had an area under the curve (AUC) of 0.88, while the latter had AUC of 0.87. ET and HA predictions had trimmed mean DSCs compared to the original HA maps of 0.73 and 0.74, respectively. These trimmed DSCs between ET and HA were found to be statistically equivalent with a p value of 0.015. We have demonstrated that ET can create segmentation masks suitable for deep learning semantic segmentation. Future work will integrate ET to produce masks in a faster, more natural manner that distracts less from typical radiology clinical workflow.
Fast spin‐echo triple‐echo dixon (fTED) technique for efficientT2‐weighted water and fat imaging (2007)

Previously published fast spin-echo (FSE) implementations of a Dixon method for water and fat separation all require multiple scans and thus a relatively long scan time. Further, the minimum echo spacing (esp), a time critical for FSE image quality and scan efficiency, often needs to be increased in order to bring about the required phase shift between the water and fat signals. This work proposes and implements a novel FSE triple-echo Dixon (fTED) technique that can address these limitations. In the new technique, three raw images are acquired in a single FSE scan by replacing each frequency-encoding gradient in a conventional FSE with three consecutive gradients of alternating polarity. The timing of the three gradients is adjusted by selecting an appropriate receiver bandwidth (RBW) so that the water and fat signals for the three corresponding echoes have a relative phase shift of -180 degrees , 0 degrees , and 180 degrees , respectively. A fully automated postprocessing algorithm is then used to generate separate water-only and fat-only images for each slice. The technique was implemented with and without parallel imaging. We demonstrate that the new fTED technique enables both uniform water/fat separation and fast scanning with uncompromised scan parameters, including applications such as T(2)-weighted separate water and fat imaging of the abdomen during breath-holding.
A Molecular Model To Explain and Predict the Stereoselectivity in Rhodium-Catalyzed Hydroformylation (1998)

By example of the bidentate phosphine−phosphite ligand BINAPHOS 1, [(2-diphenylphosphino)-1,1‘-binaphthalen-2‘-yl)(1,1‘-binaphthalen-2,2‘-diyl)phosphite], a semiquantitative theoretical model elucidates the origin of stereodifferentiation in rhodium-catalyzed hydroformylation. It is demonstrated that the outstanding properties of 1 are due to the synergistic combination of three factors: (i) pronounced coordination preferences for steric and electronic reasons; (ii) adequate number of chirality centers; (iii) correct configuration of the binaphthyl fragments. The model is, in principle, applicable to all kinds of bidentate phosphine ligands.
A generalizable protocol for expression and purification of membrane-bound bacterial phosphoglycosyl transferases in liponanoparticles (2023)

Abstract Phosphoglycosyl transferases (PGTs) are among the first membrane-bound enzymes involved in the biosynthesis of bacterial glycoconjugates. Robust expression and purification protocols for an abundant subfamily of PGTs remains lacking. Recent advancements in detergent-free methods for membrane protein solubilization open the door for purification of difficult membrane proteins directly from cell membranes into native-like liponanoparticles. By leveraging autoinduction, in vivo SUMO tag cleavage, styrene maleic acid co-polymer liponanoparticles (SMALPs), and Strep-Tag purification, we have established a robust workflow for expression and purification of previously unobtainable PGTs. The material generated from this workflow is extremely pure and can be directly visualized by Cryogenic Electron Microscopy (CryoEM). The methods presented here promise to be generalizable to additional membrane proteins recombinantly expressed in E. coli and should be of interest to the greater membrane proteomics community. Highlights Expression and purification of full-length Lg-PGTs has proven challenging. Autoinduction and in vivo Ulp1 cleavage produces active full-length Lg-PGTs. SMA and DIBMA are vastly superior to DDM for Lg-PGT solubilization. Strep-tag purification yields SMALPs suitable for CryoEM characterization.
UNDER DEVELOPMENTRaising a billion voices (2008)

research-article Share on UNDER DEVELOPMENTRaising a billion voices Authors: Sheetal K. Agarwal IBM India Research Laboratory (New Delhi) IBM India Research Laboratory (New Delhi)View Profile , Arun Kumar IBM India Research Laboratory (New Delhi) IBM India Research Laboratory (New Delhi)View Profile , Sougata Mukherjea IBM India Research Laboratory (New Delhi) IBM India Research Laboratory (New Delhi)View Profile , Amit A. Nanavati IBM India Research Laboratory (New Delhi) IBM India Research Laboratory (New Delhi)View Profile , Nitendra Rajput IBM India Research Laboratory (New Delhi) IBM India Research Laboratory (New Delhi)View Profile Authors Info & Claims InteractionsVolume 15Issue 2March + April 2008 pp 76–79https://doi.org/10.1145/1340961.1340981Online:01 March 2008Publication History 0citation439DownloadsMetricsTotal Citations0Total Downloads439Last 12 Months112Last 6 weeks6 Get Citation AlertsNew Citation Alert added!This alert has been successfully added and will be sent to:You will be notified whenever a record that you have chosen has been cited.To manage your alert preferences, click on the button below.Manage my AlertsNew Citation Alert!Please log in to your account Save to BinderSave to BinderCreate a New BinderNameCancelCreateExport CitationPublisher SiteGet Access
The Association Between Schizophrenia and Rheumatoid Arthritis: A Nationwide Population-Based Swedish Study on Intraindividual and Familial Risks (2014)

Numerous studies have reported a reduced risk of rheumatoid arthritis (RA) in schizophrenia. The mechanisms are unknown, but recent genome-wide association studies of schizophrenia have shown strong associations with markers spanning the major histocompatibility complex region, indicating a possible role for adaptive immunity also in schizophrenia. In this population-based cohort study, we assess the associations between RA and schizophrenia and the extent to which any observed associations are specific to RA/schizophrenia. We then extend the assessments per RA subtype and to risks in first-degree relatives. The study population included every individual identified in the Swedish Population Register born in Sweden between 1932 and 1989. The risk for RA in schizophrenia was significantly decreased (hazard ratio [HR] = 0.69, 95% CI = 0.59-0.80), but similar reductions were noted for osteoarthritis (a noninflammatory joint disorder) and ankylosing spondylitis (a non-RA inflammatory disorder). Comparable associations were seen in schizoaffective subjects while no significant associations were observed in bipolar disorder. Overall, first-degree relatives of schizophrenia patients were not at reduced risk of RA, but the risk for seronegative RA was significantly decreased in children and siblings of schizophrenia probands (HR = 0.13, 95% CI = 0.02-0.95 and HR = 0.67, 95% CI = 049-0.92, respectively). In conclusion, our intraindividual analyses suggest that differential misclassification bias is an important factor for the observed inverse association and emphasize the need of optimized care-provision for nonpsychiatric symptoms in schizophrenia patients. Our familial analyses indicted the possibility of an inverse coinheritance of schizophrenia and seronegative RA.
Tumor necrosis factor receptor regulation of peripheral node addressin biosynthetic components in tumor endothelial cells (2022)

Tumor-associated tertiary lymphoid structures are ectopic lymphoid aggregates that have considerable morphological, cellular, and molecular similarity to secondary lymphoid organs, particularly lymph nodes. Tumor vessels expressing peripheral node addressin (PNAd) are hallmark features of these structures. Previous work from our laboratory demonstrated that PNAd is displayed on intratumoral vasculature of murine tumors, and its expression is controlled by the engagement of lymphotoxin-α<sub>3</sub>, secreted by effector CD8 T cells, with tumor necrosis factor receptors (TNFR) on tumor endothelial cells (TEC). The goals of the present work were: 1) to identify differences in expression of genes encoding the scaffolding proteins and glycosyl transferases associated with PNAd biosynthesis in TEC and lymph node blood endothelial cells (LN BEC); and 2) to determine which of these PNAd associated components are regulated by TNFR signaling. We found that the same genes encoding scaffolding proteins and glycosyl transferases were upregulated in PNAd<sup>+</sup> LN BEC and PNAd<sup>+</sup> TEC relative to their PNAd<sup>neg</sup> counterparts. The lower level of PNAd expression on TEC vs LN BEC was associated with relatively lower expression of these genes, particularly the carbohydrate sulfotransferase <i>Chst4</i>. Loss of PNAd on TEC in the absence of TNFR signaling was associated with lack of upregulation of these same genes. A small subset of PNAd<sup>+</sup> TEC remaining in the absence of TNFR signaling showed normal upregulation of a subset of these genes, but reduced upregulation of genes encoding the scaffolding proteins podocalyxin and nepmucin, and carbohydrate sulfotransferase Chst2. Lastly, we found that checkpoint immunotherapy augmented both the fraction of TEC expressing PNAd and their surface level of this ligand. This work points to strong similarities in the regulation of PNAd expression on TEC by TNFR signaling and on LN BEC by lymphotoxin-β receptor signaling, and provides a platform for the development of novel strategies that manipulate PNAd expression on tumor vasculature as an element of cancer immunotherapy.
Endorectal surface coil MR imaging of prostatic carcinoma with the inversion‐recovery sequence (1991)

The value of inversion-recovery (IR) sequences in the diagnosis and staging of prostatic carcinoma with magnetic resonance (MR) imaging was studied. Twenty-six patients with carcinoma of the prostate were imaged at 1.5 T with an endorectal surface coil and with a variety of IR sequences and a set of spin-echo (SE) sequences for comparison. Ex vivo prostate specimens were imaged again at the same field strength. The two images were correlated with histologic sections. Cancer was identified with MR imaging in 96% of patients. Of the tumors more than 4 mm in diameter, 87% were identified on T2-weighted SE images, whereas only 26% were identified on IR images. However, IR images may be more useful in local staging of carcinoma. Gross capsular infiltration was present in only two patients; however, it was detectable (and excluded in five other patients) by means of IR images. It was not detectable on SE images. The high quality of images obtained with the endorectal coil was confirmed. The authors conclude that addition of the IR sequence to MR imaging with the endorectal coil may improve the usefulness of this examination.
Elastic properties, thermal stability, and thermodynamic parameters of MoAlB (2017)

MoAlB is the first and, so far, the only transition-metal boride that forms alumina when heated in air and is thus potentially useful for high-temperature applications. Herein, the thermal stability in argon and vacuum atmospheres and the thermodynamic parameters of bulk polycrystalline MoAlB were investigated experimentally. At temperatures above 1708 K, in vacuum and inert atmospheres, this compound incongruently melts into the binary MoB and liquid aluminum metal as confirmed by differential thermal analysis, quenching experiments, x-ray diffraction, and scanning electron microscopy. Making use of that information together with heat-capacity measurements in the 4--1000-K temperature range---successfully modeled as the sum of lattice, electronic, and dilation contributions---the standard enthalpy, entropy, and free energy of formation are computed and reported for the full temperature range. The standard enthalpy of formation of MoAlB at 298 K was found to be $\ensuremath{-}132\ifmmode\pm\else\textpm\fi{}3.2$ kJ/mol. Lastly, the thermal conductivity values are computed and modeled using a variation of the Slack model in the 300--1600-K temperature range.
<title>Pasotron high-power microwave source performance</title> (1996)

The PASOTRON (Plasma Assisted Slow-wave Oscillator) high- power microwave source utilizes a unique plasma-cathode electron gun and self-generated plasma channel to inject a long-pulse electron beam into a variety of slow-wave structures for microwave generation. The plasma-channel beam transport eliminates the need for an externally-applied axial magnetic field to confine the beam, which results in a very compact, low weight HPM source compared to conventional technologies. The Pasotron has been configured as both a backward-wave oscillator (BWO) and a traveling-wave amplifier, and has produced up to 20-MW of peak power and >= 500 Joules per pulse during operation as a BWO. In this paper, we will present the performance of the Pasotron device for a variety of rippled-wall and helix slow-wave structures. The advantages of each slow-wave structure will be discussed, and the output couplers and mode-converters used with each structure to obtain TE-mode outputs are described. The device configurations used for operation in C-band and in L-band will be shown. Long-pulse (approximately equals 100 microsecond(s) ec), plasma-cathode electron-guns operating at 30-to- 200 kV and currents of 50-to-1000 A will also be described. Finally, we will present and discuss pulse shortening that has been observed in these plasma-filled devices.
Ultra-Fast Diffractive Optical Micro-Trap Arrays for Neutral Atom Quantum Computing. (2016)

Abstract not provided.
Aromatic Hydroxylation by H2O2 and O2 Catalyzed by a μ‐Oxo Diiron(III) Complex (1996)

An excellent functionalized enzyme model for the active site of methane monooxygenase and ribonucleotide reductase is represented by the μ-ace-tato- and μ-oxo-bridged diiron complex 1. Reaction with H2O2 or O2 in the presence of ascorbate leads to hydroxylation of one phenyl ring to a phenol. This then coordindates to the metal center with formation of a mononuclear complex.