gebhart/patrepeval huggingface dataset:
Novel cancer subtyping method based on patient-specific gene regulatory network (2021)

ABSTRACT The identification of cancer subtypes is important for the understanding of tumor heterogeneity. In recent years, numerous computational methods have been proposed for this problem based on the multi-omics data of patients. It is widely accepted that different cancer subtypes are induced by different molecular regulatory networks. However, only a few incorporate the differences between their molecular systems into the classification processes. In this study, we present a novel method to classify cancer subtypes based on patient-specific molecular systems. Our method quantifies patient-specific gene networks, which are estimated from their transcriptome data. By clustering their quantified networks, our method allows for cancer subtyping, taking into consideration the differences in the molecular systems of patients. Comprehensive analyses of The Cancer Genome Atlas (TCGA) datasets applied to our method confirmed that they were able to identify more clinically meaningful cancer subtypes than the existing subtypes and found that the identified subtypes comprised different molecular features. Our findings show that the proposed method, based on a simple classification using the patient-specific molecular systems, can identify cancer subtypes even with single omics data, which cannot otherwise be captured by existing methods using multi-omics data.
A theoretical study of H2O2 as the surrogate of dose in minibeam radiotherapy, with a diffusion model considering radical removal process (2023)

DMCR is a more realistic model for H<sub>2</sub> O<sub>2</sub> simulation than the FDM. In addition, the H<sub>2</sub> O<sub>2</sub> distribution can be a good surrogate of dose distribution when the minibeam effect could be observed.
Fragment-based drug discovery applied to heat shock protein 90 (HSP90) (2011)

Acinetobacter baumannii is one of the species most commonly isolated from clinical specimens and it can be the cause of severe and sometimes lethal, nosocomial infections. It colonizes patients in Intensive Care Units and contaminates inanimate hospital surfaces [1].
Synthesis, characterization and unusual near-infrared luminescence of 1,1,4,4-tetracyanobutadiene derivatives (2020)

Two 1,1,4,4-tetracyanobutadiene (TCBD) derivatives were prepared by [2+2]cycloaddition-retroelectrocyclization from ynamides bearing either a pyrene (1) or a perylene unit (2). In addition to panchromatic absorptions in 2, in the solid state, both compounds unexpectedly display NIR photoluminescence that could be detected up to about 1350 nm.
Performance Evaluation of Location Management Techniques in PCS Network (2011)

Location management being a major part of cellular network provides mobility to mobile subscribers. The current location information is required to route the call correctly to the recipient irrespective of its current location. The current HLR/VLR architecture for location management in standards like IS-41 & GSM suffers from call setup delay due to network congestion and also prone to failure due to its centralized nature. This paper attempts to make an evaluation of the optimized location management techniques suggesting fully distributed, hierarchical and multi HLR approach against the conventional one and also highlights the pros and cons of all the reviewed techniques.
Simultaneous Computation of the External Flow around a Car Body and the Internal Flow Through its Engine Compartment (1992)

&lt;div class="htmlview paragraph"&gt;Both the external and internal flows of cars are simulated simultaneously. A third-order upwind-difference scheme is used in these simulations. Computational grids are generated by a multi-block transformation and a trans-finite method. Engine compartments are modeled by grid systems but the heat exchanger is simulated as a pressure loss proportional to the dynamic pressure of the flow passing through it.&lt;/div&gt; &lt;div class="htmlview paragraph"&gt;First, the flow for a very simple test model with no wheels and nothing in its engine compartment is simulated and compared with experimental results in order to validate a simulation method for the engine compartment. Pressure distributions on the inner surfaces agree very well with measured values, while pressure distributions on the external surfaces show reasonable agreement except for the roof end and the leading edge of the floor. The predicted drag coefficient is 7% larger than the experimental value.&lt;/div&gt; &lt;div class="htmlview paragraph"&gt;This method is next applied to a prototype car. A grid system is generated including an engine block, a transmission, an air-cleaner and suspension arms. Both the drag coefficient and the airflow rate through the radiator are calculated. These values are compared with experimental results and the agreement is good. We conclude that the present method is quite useful for predicting and optimizing both the drag coefficient and the airflow rate through the radiator.&lt;/div&gt;
Optical Design and Optimization of Translational Reflective Adaptive Optics Ophthalmoscopes (2014)

Thesis (Ph. D.)--University of Rochester. Institute of Optics, 2014.
Functional analysis of aromatic biosynthetic pathways in Pseudomonas putida KT2440 (2008)

Pseudomonas putida KT2440 is a non-pathogenic prototrophic bacterium with high potential for biotechnological applications. Despite all that is known about this strain, the biosynthesis of essential chemicals has not been fully analysed and auxotroph mutants are scarce. We carried out massive mini-Tn5 random mutagenesis and screened for auxotrophs that require aromatic amino acids. The biosynthesis of aromatic amino acids was analysed in detail including physical and transcriptional organization of genes, complementation assays and feeding experiments to establish pathway intermediates. There is a single pathway from chorismate leading to the biosynthesis of tryptophan, whereas the biosynthesis of phenylalanine and tyrosine is achieved through multiple convergent pathways. Genes for tryptophan biosynthesis are grouped in unlinked regions with the trpBA and trpGDE genes organized as operons and the trpI, trpE and trpF genes organized as single transcriptional units. The pheA and tyrA gene-encoding multifunctional enzymes for phenylalanine and tyrosine biosynthesis are linked in the chromosome and form an operon with the serC gene involved in serine biosynthesis. The last step in the biosynthesis of these two amino acids requires an amino transferase activity for which multiple tyrB-like genes are present in the host chromosome.
HAADF-STEM Study of Filament Material in Hot Filament CVD Diamond Films (2019)

was identified in these scans. However, due to the sporadic distribution of the impurities it is possible that none was present in any of the regions scanned.
Structure-Based Design of a Potent and Selective Covalent Inhibitor for SRC Kinase That Targets a P-Loop Cysteine (2020)

SRC is a major regulator of many signaling pathways and contributes to cancer development. However, development of a selective SRC inhibitor has been challenging, and FDA-approved SRC inhibitors, dasatinib and bosutinib, are multitargeted kinase inhibitors. Here, we describe our efforts to develop a selective SRC covalent inhibitor by targeting cysteine 277 on the P-loop of SRC. Using a promiscuous covalent kinase inhibitor (CKI) <b>SM1-71</b> as a starting point, we developed covalent inhibitor <b>15a</b>, which discriminates SRC from other covalent targets of <b>SM1-71</b> including TAK1 and FGFR1. As an irreversible covalent inhibitor, compound <b>15a</b> exhibited sustained inhibition of SRC signaling both <i>in vitro</i> and <i>in vivo</i>. Moreover, <b>15a</b> exhibited potent antiproliferative effects in nonsmall cell lung cancer cell lines harboring SRC activation, thus providing evidence that this approach may be promising for further drug development efforts.
Towards Gradient Free and Projection Free Stochastic Optimization (2018)

This paper focuses on the problem of \emph{constrained} \emph{stochastic} optimization. A zeroth order Frank-Wolfe algorithm is proposed, which in addition to the projection-free nature of the vanilla Frank-Wolfe algorithm makes it gradient free. Under convexity and smoothness assumption, we show that the proposed algorithm converges to the optimal objective function at a rate $O\left(1/T^{1/3}\right)$, where $T$ denotes the iteration count. In particular, the primal sub-optimality gap is shown to have a dimension dependence of $O\left(d^{1/3}\right)$, which is the best known dimension dependence among all zeroth order optimization algorithms with one directional derivative per iteration. For non-convex functions, we obtain the \emph{Frank-Wolfe} gap to be $O\left(d^{1/3}T^{-1/4}\right)$. Experiments on black-box optimization setups demonstrate the efficacy of the proposed algorithm.
Splashing onset in dense suspension droplets (2013)

We investigate the impact of droplets of dense suspensions onto a solid substrate. We show that a global hydrodynamic balance is unable to predict the splash onset and propose to replace it by an energy balance at the level of the particles in the suspension. We experimentally verify that the resulting, particle-based Weber number gives a reliable, particle size and density dependent splash onset criterion. We further show that the same argument also explains why in bimodal systems smaller particles are more likely to escape than larger ones.
Accumulation of Defective Neuraminidase (NA) Genes by Influenza A Viruses in the Presence of NA Inhibitors as a Marker of Reduced Dependence on NA (2002)

With the use of neuraminidase (NA) inhibitors (BCX-1812, oseltamivir, or zanamivir), drug-resistant variants of influenza A viruses were generated that lacked characteristic markers of resistance, such as substitutions in the NA active center or in the hemagglutinin. Drug resistance was associated with the accumulation of defective (Delta) RNA segments encoding NA. This phenomenon could be explained by reduced dependence of the virus on its NA activity. Analysis of the last isolates recovered from 11 volunteers, experimentally infected with influenza virus and treated with BCX-1812, revealed that they maintained full susceptibility to the drug in the NA inhibition assay (50% inhibitory concentration, 0.35-0.5 nM). The presence of DeltaRNA segments was detected in 1 of these isolates but was not found in the isolates recovered from placebo recipients (n = 8). Because of a lack of cell culture-based assays for susceptibility testing of human influenza viruses, detection of DeltaRNA segments should be considered an additional assay for monitoring of NA inhibitor resistance.
Cobaloxime‐Based Photocatalytic Devices for Hydrogen Production (2007)

It is the dawning of the age of supramolecular photocatalysts for H2 production using first-row transition-metal catalytic centers. These catalysts consist of a ruthenium tris(diimine) light-harvesting unit covalently linked to various catalytic cobaloxime centers (see picture). The catalyst stability, CoII/CoI redox potential, and nucleophilicity of the cobaloxime moiety all affect the photocatalytic properties.
Multiphysics Integrated Computational Materials Engineering Linking Additive Manufacturing Process Parameters with Part Performance (2021)

The central goal of this chapter is to present an outline of the plan and current status of an effort to connect Additive Manufacturing (AM) process parameters with parameters describing the functional performance of produced parts. The term “functional performance” here represents primarily mechanical or thermal or electrochemical performance. The described effort represents an overview of the main research activities within a new multi-year grand-challenge project initiated at the US Naval Research Laboratory (US-NRL) in late 2016, in collaboration with groups from various academic institutions.
MYC paralog-dependent apoptotic priming orchestrates a spectrum of vulnerabilities in small cell lung cancer (2019)

MYC paralogs are frequently activated in small cell lung cancer (SCLC) but represent poor drug targets. Thus, a detailed mapping of MYC-paralog-specific vulnerabilities may help to develop effective therapies for SCLC patients. Using a unique cellular CRISPR activation model, we uncover that, in contrast to MYCN and MYCL, MYC represses BCL2 transcription via interaction with MIZ1 and DNMT3a. The resulting lack of BCL2 expression promotes sensitivity to cell cycle control inhibition and dependency on MCL1. Furthermore, MYC activation leads to heightened apoptotic priming, intrinsic genotoxic stress and susceptibility to DNA damage checkpoint inhibitors. Finally, combined AURK and CHK1 inhibition substantially prolongs the survival of mice bearing MYC-driven SCLC beyond that of combination chemotherapy. These analyses uncover MYC-paralog-specific regulation of the apoptotic machinery with implications for genotype-based selection of targeted therapeutics in SCLC patients.
Reply to the Comment on “Identification of Precursor Species in the Formation of MFI Zeolite in the TPAOH−TEOS−H2O System” (2002)

ADVERTISEMENT RETURN TO ISSUEPREVCommentReply to the Comment on "Identification of Precursor Species in the Formation of MFI Zeolite in the TPAOH−TEOS−H2O System"Christine E. A. Kirschhock, Raman Ravishankar, Frederik Verspeurt, Piet J. Grobet, Pierre A. Jacobs, and Johan A. MartensView Author Information Centrum voor Oppervlaktechemie en Katalyse, K.U. Leuven, Kasteelpark Arenberg 23, B-3001 Leuven, Belgium Cite this: J. Phys. Chem. B 2002, 106, 12, 3333–3334Publication Date (Web):February 28, 2002Publication History Received31 December 2001Revised12 January 2002Published online28 February 2002Published inissue 1 March 2002https://pubs.acs.org/doi/10.1021/jp0146521https://doi.org/10.1021/jp0146521article-commentaryACS PublicationsCopyright © 2002 American Chemical Society. This publication is available under these Terms of Use. Request reuse permissions This publication is free to access through this site. Learn MoreArticle Views453Altmetric-Citations37LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InRedditEmail PDF (18 KB) Get e-AlertscloseSUBJECTS:Aggregation,Chemical structure,Nanoparticles,Precursors,Silicon Get e-Alerts
Contrast‐enhanced Ultrasound in Urology (2018)

In contrast-enhanced ultrasonography (CEUS), micrometer-sized, encapsulated, gas-filled microbubbles are employed to enhance the signals in ultrasound imaging. Since the microbubbles remain intravascular, CEUS is able to visualize perfusion of various tissues. This is particularly useful for imaging malignancies of prostate and kidney, for example, as these exhibit altered perfusion behavior due to angiogenesis and neovascularization. CEUS can also be used to visualize the treatment effects of focal and ablative therapy. Current CEUS research focuses on its use for biopsy targeting and for diagnosis of renal abnormalities. Future advances are expected in the objective quantification of contrast enhancement, molecular imaging with so-called targeted microbubbles that specifically accumulate in the tissue of interest, and fusion techniques combining CEUS with CT or MRI. As a consequence, CEUS is gaining attention in current clinical practice.
Recent and future progress on advanced ceramics sintering by Spark Plasma Sintering (2015)

This article describes recent trends in Spark Plasma Sintering (SPS) technology. The SPS method is widely recognized as a useful sintering technique to develop various kinds of attractive ceramics, metals, and composite materials due to its excellent features of rapid heating, electromagnetic field effect, and a well-controlled microstructure.
Interaction between dislocations and Σ = 51 and Σ = 19 tilt grain boundaries in germanium: Study by in-situ, TEM and HREM (1993)

International audience
Real-Time Monitoring of Aluminum Oxidation Through Wide Band Gap MgF2 Layers for Protection of Space Mirrors (2019)

Because of its extraordinary and broad reflectivity, aluminum is the only logical candidate for advanced space mirrors that operate deep into the UV. However, aluminum oxidizes rapidly in the air, and even a small amount of oxide (as little as a nanometer) can have a noticeable, detrimental impact on its reflectivity at short wavelengths. Thin films of wide band gap materials like MgF2 have previously been used to protect aluminum surfaces. Here we report the first real-time, spectroscopic ellipsometry (SE) study of aluminum oxidation as a function of MgF2 over layer thickness, which ranged from 0 – 6 nm. SE data analysis was performed vis-à-vis a multilayer optical model that included a thick silicon nitride layer. The optical constants for evaporated aluminum were initially determined using a multi-sample analysis (MSA) of SE data from MgF2 protected and bare Al surfaces. Two models were then considered for analyzing the real-time data obtained from Al/MgF2 stacks. The first used the optical constants of aluminum obtained in the MSA with two adjustable parameters: the thicknesses of the aluminum and aluminum oxide layers. The thicknesses obtained from this model showed the expected trends (increasing Al2O3 layer thickness and decreasing Al layer thickness with time), but some of the Al2O3 thicknesses were unphysical (negative). Because the optical constants of very thin metals films depend strongly on their structures and deposition conditions, a second, more advanced model was employed that fit the optical constants for Al, and also the Al and Al2O3 thicknesses, for each data set. In particular, the Al and Al2O3 thicknesses and optical constants of Al were determined in an MSA for each of 50 evenly spaced analyses in each four-hour dynamic run performed. The resulting optical constants for Al were then fixed for that sample and the thicknesses of the Al and Al2O3 layers were determined. While the first and second models yielded similar Al and Al2O3 thickness vs. time trends, the film thicknesses obtained in this manner were more physically reasonable. Thicker MgF2 layers slow the oxidation rate of aluminum. The results from this work should prove useful in protecting space mirrors prior to launch.
Simulation Meets Experiment: Unraveling the Properties of Water in Metal-Organic Frameworks Through Vibrational Spectroscopy (2021)

In nanoporous materials, guest–host interactions affect the properties and function of both adsorbent and adsorbate molecules. Due to their structural and chemical diversity, metal-organic frameworks (MOFs), a common class of nanoporous materials, have been shown to be able to efficiently and, often, selectively adsorb various types of guest molecules. In this study, we characterize the structure and dynamics of water confined in ZIF-90. Through the integration of experimental and computational infrared (IR) spectroscopy, we probe the structure of heavy water (D2O) adsorbed in the pores, disentangling the fundamental framework–water and water–water interactions. The experimental IR spectrum of D2O in ZIF-90 displays a blue-shifted OD-stretch band compared to liquid D2O. The analysis of the IR spectra simulated at both classical and quantum levels indicates that the D2O molecules preferentially interact with the carbonyl groups of the framework and highlights the importance of including nuclear quantum effects and taking into account Fermi resonances for a correct interpretation of the OD-stretch band in terms of the underlying hydrogen-bonding motifs. Through a systematic comparison with the experimental spectra, we demonstrate that computational spectroscopy can be used to gain quantitative, molecular-level insights into framework–water interactions that determine the water adsorption capacity of MOFs as well as the spatial arrangements of the water molecules inside the MOF pores which, in turn, are key to the design of MOF-based materials for water harvesting.
A monolithically integrated optical heterodyne receiver (2005)

We demonstrate a monolithically integrated optical heterodyne receiver consisting of an input fiber waveguide, a single frequency distributed Bragg reflector (DBR) laser, a multimode interferometer-based 3-dB coupler, and a pair of semiconductor optical amplifier (SOA)/p-i-n modules using a single epitaxial growth based on asymmetric twin-waveguide (ATG) technology. The input signal was coupled into a fiber waveguide and mixed with the DBR local oscillator laser through the 3-dB coupler, and then coupled into the SOA/p-i-n modules for detection. Using this monolithically integrated optical receiver with a wide-band rectifier narrow-band amplifier receiver, a 3-GHz frequency modulated coherent analog optical link is demonstrated.
The S-ROM hydroxyapatite proximally-coated modular femoral stem in revision hip replacement (2014)

We report on 397 consecutive revision total hip replacements in 371 patients with a mean clinical and radiological follow-up of 12.9 years (10 to 17.7). The mean age at surgery was 69 years (37 to 93). A total of 28 patients (8%) underwent further revision, including 16 (4%) femoral components. In all 223 patients (56%, 233 hips) died without further revision and 20 patients (5%, 20 hips) were lost to follow-up. Of the remaining patients, 209 (221 hips) were available for clinical assessment and 194 (205 hips) for radiological review at mean follow-up of 12.9 years (10 to 17.7). The mean Harris Hip Score improved from 58.7 (11 to 92) points to 80.7 (21 to 100) (p < 0.001) and the mean Merle d'Aubigné and Postel hip scores at final follow-up were 4.9 (2 to 6), 4.5 (2 to 6) and 4.3 (2 to 6), respectively for pain, mobility and function. Radiographs showed no lucencies around 186 (90.7%) femoral stems with stable bony ingrowth seen in 199 stems (97%). The survival of the S-ROM femoral stem at 15 years with revision for any reason as the endpoint was 90.5% (95% confidence interval (CI) 85.7 to 93.8) and with revision for aseptic loosening as the endpoint 99.3% (95% CI 97.2 to 99.8). We have shown excellent long-term survivorship and good clinical outcome of a cementless hydroxyapatite proximally-coated modular femoral stem in revision hip surgery.
Amino‐Acid‐Based Polymerizable Surfactants for the Synthesis of Chiral Nanoparticles (2016)

Amino-acid-based chiral surfactants with polymerizable moieties are synthesized, and a versatile approach to prepare particles thereof with a chiral surface functionality is presented. As an example of an application, the synthesized particles are tested for their ability as nucleating agents in the enantioselective crystallization of amino acid conglomerate systems, taking rac-asparagine as a model system. Particles resulting from chiral surfactants with different tail groups are compared and the results demonstrate that only the chiral nanoparticles made of the polymerizable surfactant are able to act efficiently as nucleation agent in enantioselective crystallization.
Correction: Oxidative dehydrogenation of propane over transition metal sulfides using sulfur as an alternative oxidant (2021)

Correction for ‘Oxidative dehydrogenation of propane over transition metal sulfides using sulfur as an alternative oxidant’ by Allison M. Arinaga <italic>et al.</italic>, <italic>Catal. Sci. Technol.</italic>, 2020, <bold>10</bold>, 6840–6848, DOI: 10.1039/D0CY01039A.