gebhart/patrepeval huggingface dataset:
Multiple comparisons permutation test for image based data mining in radiotherapy (2013)

: Comparing incidental dose distributions (i.e. images) of patients with different outcomes is a straightforward way to explore dose-response hypotheses in radiotherapy. In this paper, we introduced a permutation test that compares images, such as dose distributions from radiotherapy, while tackling the multiple comparisons problem. A test statistic Tmax was proposed that summarizes the differences between the images into a single value and a permutation procedure was employed to compute the adjusted p-value. We demonstrated the method in two retrospective studies: a prostate study that relates 3D dose distributions to failure, and an esophagus study that relates 2D surface dose distributions of the esophagus to acute esophagus toxicity. As a result, we were able to identify suspicious regions that are significantly associated with failure (prostate study) or toxicity (esophagus study). Permutation testing allows direct comparison of images from different patient categories and is a useful tool for data mining in radiotherapy.
Predicting host immune cell dynamics using tissue gene expression (2018)

Immune cell dynamics are critical to disease pathology. Deconvolution algorithms attempt to predict cell quantities based on gene expression profiles derived from diseased tissue and are evaluated using artificial or simple samples. We tested their capability of estimating cell counts given data from influenza-infected lung sampled over time post infection. Our findings suggest that current methods must be improved in order to characterize disease-associated immune cell dynamics.
Demonstration of electrooptic modulation at 2165nm using a silicon Mach-Zehnder interferometer (2012)

We demonstrate electrooptic modulation at a wavelength of 2165nm, using a free-carrier injection-based silicon Mach-Zehnder modulator. The modulator has a V(π)∙L figure of merit of 0.12V∙mm, and an extinction ratio of -23dB. Optical modulation experiments are performed at bitrates up to 3Gbps. Our results illustrate that optical modulator design methodologies previously developed for telecom-band devices can be successfully applied to produce high-performance devices for a silicon nanophotonic mid-infrared integrated circuit platform.
Cross-Layer Strategic Ensemble Defense Against Adversarial Examples (2020)

Deep neural network (DNN) has demonstrated its success in multiple domains. However, DNN models are inherently vulnerable to adversarial examples, which are generated by adding adversarial perturbations to benign inputs to fool the DNN model to misclassify. In this paper, we present a cross-layer strategic ensemble framework and a suite of robust defense algorithms, which are attack-independent, and capable of auto-repairing and auto-verifying the target model being attacked. Our strategic ensemble approach makes three original contributions. First, we employ input-transformation diversity to design the input-layer strategic transformation ensemble algorithms. Second, we utilize model-disagreement diversity to develop the output-layer strategic model ensemble algorithms. Finally, we create an input-output cross-layer strategic ensemble defense that strengthens the defensibility by combining diverse input transformation based model ensembles with diverse output verification model ensembles. Evaluated over 10 attacks on ImageNet dataset, we show that our strategic ensemble defense algorithms can achieve high defense success rates and are more robust with high attack prevention success rates and low benign false negative rates, compared to existing representative defenses.
Multimedia streaming via TCP (2004)

TCP is widely used in commercial media streaming systems, with recent measurement studies indicating that a significant fraction of Internet streaming media is currently delivered over HTTP/TCP. These observations motivate us to develop analytic performance models to systematically investigate the performance of TCP for both live and stored media streaming. We validate our models via ns simulations and experiments conducted over the Internet. Our models provide guidelines indicating the circumstances under which TCP streaming leads to satisfactory performance, showing, for example, that TCP generally provides good streaming performance when the achievable TCP throughput is roughly twice the media bitrate, with only a few seconds of startup delay.
937-P: Self-Reported Acute Psychological Stress Is Associated with CGM-Based Hyperglycemia in Type 1 Diabetes (2019)

Objective: There have been no clear data describing the association between acute psychological stress and glycemic variability (GV) in people with type 1 diabetes (T1D). Patients self-report that acute stress leads to hyperglycemia. Methods: Twenty adults with T1D on CGM augmented insulin pump completed self-reported psychological stress diaries for a period of 5 weeks at 2 clinical research centers. Participants reported intensity of stress on a 7-point scale, with 1 indicating mild stress and 7 severe stress, and duration of each stress episode. CGM data were analyzed for week 1 and week 5. Results: Baseline characteristics were age 44.9±15.0 years, F/M 12/8, HbA1c 6.8±0.7%, and diabetes duration 22.9±15.9 years. Total number of stress events reported was 126 over the two-week period. Subjects reported stress on average of 9±2.2 days representing 64.2%±28.2% of days. GV was compared on days of stress vs. days without stress for each subject. Mean BG did not differ; however, % time spent above 250 mg/dl was less in patients who did not report stress events during the day (6.1± 9.8%) compared to patients with stressful episodes (10.1±17.6%) (p=0.02) (Table). Discussion: Acute stress in patients with T1D was associated with certain measures of GV. We are currently analyzing GV based on duration and intensity of stress and the time between reported stress and change in glucose. Disclosure V. Dadlani: None. J.E. Pinsker: Research Support; Self; Ascensia Diabetes Care, Dexcom, Inc., Insulet Corporation, LifeScan, Inc., Roche Diabetes Care, Tandem Diabetes Care. Speaker's Bureau; Self; Tandem Diabetes Care. K. Kumari: None. C.C. Andre: None. M. Cescon: None. C. Reid: None. S.K. McCrady-Spitzer: None. P. Thapa: None. M. Church: None. D. Choudhary: None. F.J. Doyle: Consultant; Self; ModeAGC. Other Relationship; Self; Insulet Corporation. E. Dassau: Consultant; Self; Eli Lilly and Company, Insulet Corporation. Research Support; Self; Dexcom, Inc., DreaMed Diabetes, Ltd., Insulet Corporation, Roche Diabetes Care, Tandem Diabetes Care, Xeris Pharmaceuticals, Inc. Speaker's Bureau; Self; Roche Diabetes Care. Other Relationship; Self; ModAGC. Y.C. Kudva: Advisory Panel; Self; Novo Nordisk Inc. Other Relationship; Self; Dexcom, Inc., Roche Diabetes Care, Tandem Diabetes Care. Funding JDRF; The Leona M. and Harry B. Helmsley Charitable Trust (2-SRA-2017-503-M-B); Dexcom, Inc. (IIS-2017-043)
Weighted-least-squares multi-filter phase imaging with partially coherent light: characteristics of annular illumination (2018)

Multi-filter phase imaging with partially coherent light (MFPI-PC) is a promising microscopic quantitative phase imaging (QPI) method that measures the phase of a transparent object. In the present work, a weighted-least-squares version is developed and applied to the important case of annular illumination. The resulting improved algorithms have largely solved the noise magnification problem associated with the original MFPI-PC in annular illumination. Simulation and microlens experiments are used to validate the new QPI method for the case of annular illumination.
GRAPHENE-BASED TRANSPARENT CONDUCTIVE FILMS (2013)

Graphene is a promising alternative to indium tin oxide for use in transparent conducting electrodes. We review recent progress in production methods of graphene and its applications in optoelectronic devices such as touch panel screens, organic photovoltaic cells, organic light emitting diodes and thin film transistors. In addition, we discuss important criteria such as optical transmittance, electrical conductivity and work function, which are critical considerations in the integration of graphene conductive films with optoelectronic devices.
MFS1, a Pleiotropic Transporter in Dermatophytes That Plays a Key Role in Their Intrinsic Resistance to Chloramphenicol and Fluconazole (2021)

A recently identified <i>Trichophyton rubrum</i> major facilitator superfamily (MFS)-type transporter (TruMFS1) has been shown to give resistance to azole compounds and cycloheximide (CYH) when overexpressed in <i>Saccharomyces cerevisiae</i>. We investigated the roles of MFS1 in the intrinsic resistance of dermatophytes to CYH and chloramphenicol (CHL), which are commonly used to isolate these fungi, and to what extent MFS1 affects the susceptibility to azole antifungals. Susceptibility to antibiotics and azoles was tested in <i>S. cerevisiae</i> overexpressing MFS1 and ΔMFS1 mutants of <i>Trichophyton benhamiae</i>, a dermatophyte that is closely related to <i>T. rubrum</i>. We found that TruMFS1 functions as an efflux pump for CHL in addition to CYH and azoles in <i>S. cerevisiae</i>. In contrast, the growth of <i>T. benhamiae</i> ΔMFS1 mutants was not reduced in the presence of CYH but was severely impaired in the presence of CHL and thiamphenicol, a CHL analog. The suppression of MFS1 in <i>T. benhamiae</i> also increased the sensitivity of the fungus to fluconazole and miconazole. Our experiments revealed a key role of MFS1 in the resistance of dermatophytes to CHL and their high minimum inhibitory concentration for fluconazole. Suppression of MFS1 did not affect the sensitivity to CYH, suggesting that another mechanism was involved in resistance to CYH in dermatophytes.
Field responsive mechanical metamaterials (2018)

Typically, mechanical metamaterial properties are programmed and set when the architecture is designed and constructed, and do not change in response to shifting environmental conditions or application requirements. We present a new class of architected materials called field responsive mechanical metamaterials (FRMMs) that exhibit dynamic control and on-the-fly tunability enabled by careful design and selection of both material composition and architecture. To demonstrate the FRMM concept, we print complex structures composed of polymeric tubes infilled with magnetorheological fluid suspensions. Modulating remotely applied magnetic fields results in rapid, reversible, and sizable changes of the effective stiffness of our metamaterial motifs.
Transmission of multidrug-resistant Campylobacter jejuni to children from different sources in Pakistan (2019)

A high prevalence of multidrug-resistant C. jejuni among paediatric diarrhoeal patients was observed. Moreover, the association of these isolates to livestock clades suggests transmission to human populations via the food chain. The presence of imipenem-resistant MBL-producing C. jejuni can lead to serious public health concerns.
ChemInform Abstract: Futalosine and Its Derivatives, New Nucleoside Analogues. (1999)

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.
Discovery of 5-(4-Chlorophenyl)-1-(2,4-dichlorophenyl)-3-hexyl-1H-1,2,4-triazole, a Novel in Vivo Cannabinoid Antagonist Containing a 1,2,4-Triazole Motif (2004)

A new series of 1,2,4-triazoles have been prepared and the evaluation of their cannabinoid properties have been carried out. Compound 8 showed cannabinoid silent antagonist activity in mouse vas deferens and guinea pig ileum preparations and in vivo assays (cannabinoid tetrad) in mouse. It did not have intrinsic activity in these bioassays, and therefore, it did not behave as a partial agonist or an inverse agonist.
Advanced oxidation processes of decomposing dichloroacetic acid and trichloroacetic acid in water (2008)

We studied the decomposition of two haloacetic acids (HAAs), dichloroacetic acid (DCAA) and trichloroacetic acid (TCAA), in water by single oxidants ozone (O3) and ultraviolet radiation (UV) and the advanced oxidation processes (AOPs) constituted by the combinations of O3/UV, H2O2/UV, O3 /H2O2, and O3/H2O2/UV. The concentrations of HAAs were analyzed at specified time intervals to track their decomposition. Except for O3 and UV, the four combined oxidation processes remarkably enhance the decomposition of DCAA and TCAA owing to the generated very reactive hydroxyl radicals. The fastest decomposition process is O3/H2O2/UV, closely followed by O3/UV. DCAA is much easier to decompose than TCAA. The kinetics of HAA decomposition by O3/UV can be described well by a pseudo first-order reaction model under a constant initial dissolved O3 concentration and fixed UV radiation. Humic acids and HCO3 - in the reaction system both decrease the decomposition rate constants for DCAA and TCAA. The amount of H2O2 accumulates in the presence of humic acids in the O3/UV process.
Complex Modal Decomposition Applied to Nematode Posturing (2009)

The complex orthogonal decomposition (COD), a process of extracting complex modes from complex ensemble data, is summarized, as is the use of complex modal coordinates. A brief assessment is made on how small levels of noise affect the decomposition. The decomposition is applied to the posturing of a wild Caenorhabditis elegans nematode. The decomposition indicates that the worm has a multi-modal posturing behavior, involving at least a dominant locomotion mode and a secondary, steering mode. The locomotion mode is closer to a pure traveling waveform than the steering mode. The characteristic wavelength of the primary mode was estimated in the complex plane. Frequency was obtained from the complex modal coordinate’s complex whirl rate of the complex modal coordinate, and from its fast Fourier transform.
Effects of Pad Temperature on the Chemical Mechanical Polishing of Tungsten (2014)

In this study, the effects of pad temperature on the chemical mechanical polishing (CMP) of tungsten were investigated. During polishing, the pad temperature was monitored and the removal rate behavior with respect to the pad temperature evolution was explored. The pad temperature was increased during tungsten CMP, and the tungsten removal rate increased accordingly. Further, it was found that the two had a strong correlation. Although tetraethyl orthosilicate (TEOS) polishing experiment showed that the pad temperature increased similarly under various experimental conditions, the TEOS removal rate did not change for all conditions. A novel pad-cooling nozzle effectively reduced the pad temperature during tungsten polishing and influenced the tungsten removal rate drop. Table motor current monitoring revealed that friction forces were almost identical under all experimental conditions for tungsten polishing regardless of the application of pad cooling. On the basis of pad temperature and table motor current data, it was clear that the tungsten removal rate was determined by temperature, indicating that the tungsten removal mechanism was mostly driven by a chemical reaction. Further, the pad cooling function can be used to control the tungsten removal rate effectively, resulting in a stable tungsten CMP process.
Synthesis of medium-entropy (Zr<sub>1/3</sub>Hf<sub>1/3</sub>Ta<sub>1/3</sub>)B<sub>2</sub> using the spark plasma consolidation of diboride powders (2020)

In this study, we introduce a simple and effective method for producing a ternary solid-solution of diborides, a medium-entropy Zr1/3Hf1/3Ta1/3B2. Using commercially available diboride powders with equimolar ratio and performing spark plasma consolidation at 1927 °C we demonstrate that single-phase medium-entropy ceramic can be consolidated using an hour-long procedure. The flexural strength and fracture toughness at room temperature were 318 ± 14 MPa and 2.9 MPa m1/2, respectively.
HAXPES evaluation of ferroelectric HfSiO MIM capacitor (2018)

We present direct evaluation of a buried ferroelectric HfSiO layer beneath a top TiN electrode with MIM capacitor structure. Since inelastic mean free path for HAXPES is several times deeper than that for conventional XPS, we clearly measured Hf4f spectrum of HfSiO and revealed that chemical bonding state varied after thermal annealing of the HfSiO for crystallization. The method provides powerful assistance for such process optimization.
Decoration of Porous Silicon with Gold Nanoparticles via Layer-by-Layer Nanoassembly for Interferometric and Hybrid Photonic/Plasmonic (Bio)sensing (2019)

Gold nanoparticle layers (AuNPLs) enable the coupling of morphological, optical, and electrical properties of gold nanoparticles (AuNPs) with tailored and specific surface topography, making them exploitable in many bioapplications (e.g., biosensing, drug delivery, and photothermal therapy). Herein, we report the formation of AuNPLs on porous silicon (PSi) interferometers and distributed Bragg reflectors (DBRs) for (bio)sensing applications via layer-by-layer (LbL) nanoassembling of a positively charged polyelectrolyte, namely, poly(allylamine hydrochloride) (PAH), and negatively charged citrate-capped AuNPs. Decoration of PSi interferometers with AuNPLs enhances the Fabry-Pérot fringe contrast due to increased surface reflectivity, resulting in an augmented sensitivity for both bulk and surface refractive index sensing, namely, about 4.5-fold using NaCl aqueous solutions to infiltrate the pores and 2.6-fold for unspecific bovine serum albumin (BSA) adsorption on the pore surface, respectively. Sensitivity enhancing, about 2.5-fold, is also confirmed for affinity and selective biosensing of streptavidin using a biotinylated polymer, namely, negatively charged poly(methacrylic acid) (b-PMAA). Further, decoration of PSi DBR with AuNPLs envisages building up a hybrid photonic/plasmonic optical sensing platform. Both photonic (DBR stop-band) and plasmonic (localized surface plasmon resonance, LSPR) peaks of the hybrid structure are sensitive to changes of bulk (using glucose aqueous solutions) and surface (due to BSA unspecific adsorption) refractive index. To the best of our knowledge, this is the first report about the formation of AuNPLs via LbL nanoassembly on PSi for (i) the enhancing of the interferometric performance in (bio)sensing applications and (ii) the building up of hybrid photonic/plasmonic platforms for sensing and perspective biosensing applications.
Heat shock factor 1 induces cancer stem cell phenotype in breast cancer cell lines (2015)

Heat shock factor 1 (HSF1) has long been recognized as the master transcription factor that regulates heat shock proteins (HSPs). More recently HSF1 has been associated with a broader role in regulating response to a variety of cellular stresses beyond heat-shock. We previously found that high HSF1 expression is associated with poor outcome in lung, breast and colon cancers. Importantly, however, the HSF1 signature correlated with poor outcome in these studies was not related to the heat shock response, which suggested that tumor outcome associated with high HSF expression may be due to processes other than stress response. Hence, we explored the question whether high HSF1 expression might be associated with the cancer stem cell (CSC) phenotype. To do so, we examined the association of HSF1 with CSC phenotype by FACS and immunofluorescence. In addition, we evaluated the effects of HSF1 over-expression and knock-down on sphere formation and CSC marker expression in breast cancer cell lines. Here, we report results demonstrating that high HSF1 not only correlates with CSC marker expression, but inducible HSF1 over-expression augments and HSF1 knock-down inhibits CSC phenotype. Furthermore, HSF1 expression confers resistance to chemotherapeutic drugs and increases CSC frequency. In conclusion, our study indicates that one of the potential HSP-independent HSF1 driven mechanisms that may contribute to poor outcome in human tumors involves regulation of the CSC phenotype. Hence, therapeutic inhibition of HSF1 may be one route to target CSCs in human tumors.
ChemInform Abstract: Towards the Optimal Screening Collection: A Synthesis Strategy. (2008)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 200 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.
Evaluation of 3-Dimensionality in Approved and Experimental Drug Space (2020)

The 3-dimensional (3D) structure of therapeutics and other bioactive molecules is an important factor in determining the strength and selectivity of their protein-ligand interactions. Previous efforts have considered the strain introduced and tolerated through conformational changes induced upon protein binding. Herein, we present an analysis of 3-dimentionality for energy-minimized structures from the DrugBank and ligands bound to proteins identified in the Protein Data Bank (PDB). This analysis reveals that the majority of molecules found in both the DrugBank and the PDB tend toward linearity and planarity, with few molecules having highly 3D conformations. Decidedly 3D geometries have been historically difficult to achieve, likely due to the synthetic challenge of making 3D organic molecules, and other considerations, such as adherence to the 'rule-of-five'. This has resulted in the dominance of planar and/or linear topologies of the molecules described here. Strategies to address the generally flat nature of these data sets are explored, including the use of 3D organic fragments and inorganic scaffolds as a means of accessing privileged 3D space. This work highlights the potential utility of libraries with greater 3D topological diversity so that the importance of molecular shape to biological behavior can be more fully understood in drug discovery campaigns.
Li-O2 Battery Discharge Redox Mediation by Triarylmethyl Cations (2022)

Abstract Low discharge capacities resulting from electronically insulating Li 2 O 2 film growth on carbon electrodes is a major impediment to Li-O 2 battery commercialization. Redox mediation is an effective strategy to drive oxygen chemistry into solution, avoiding surface-mediated Li 2 O 2 film growth and extending discharge lifetimes. However, in order to continue improving upon prior research, exploration of more redox mediators and discovery of new redox mediator selection criteria is required. Herein, we report a new class of triarylmethyl cations which are effective at enhancing discharge capacities up to 26-fold. We observe that more positive redox mediator reduction potentials, and thus more sluggish kinetics for reaction of redox mediator and oxygen, leads to larger discharge capacities because of their improved ability to suppress the surface-mediated reduction pathway. Furthermore, we find that redox mediation may be achieved with redox mediator reduction potentials significantly more positive than what has been explored, an insight which should help guide future redox mediator exploration.