gebhart/patrepeval huggingface dataset:
Ruthenium-caged antisense morpholinos for regulating gene expression in zebrafish embryos (2015)

Photochemical approaches afford high spatiotemporal control over molecular structure and function, for broad applications in materials and biological science. Here, we present the first example of a visible light responsive ruthenium-based photolinker, Ru(bipyridine)<sub>2</sub>(3-ethynylpyridine)<sub>2</sub> (RuBEP), which was reacted stoichiometrically with a 25mer DNA or morpholino (MO) oligonucleotide functionalized with 3' and 5' terminal azides, via Cu(I)-mediated [3+2] Huisgen cycloaddition reactions. RuBEP-caged circular morpholinos (Ru-MOs) targeting two early developmental zebrafish genes, <i>chordin</i> and <i>notail</i>, were synthesized and tested <i>in vivo</i>. One-cell-stage zebrafish embryos microinjected with Ru-MO and incubated in the dark for 24 h developed normally, consistent with caging, whereas irradiation at 450 nm dissociated one 3-ethynylpyridine ligand (ϕ = 0.33) and uncaged the MO to achieve gene knockdown. As demonstrated, Ru photolinkers provide a versatile method for controlling structure and function of biopolymers.
Integration of light delivery for heat assisted magnetic recording (2009)

Light delivery with spot size converter (SSC) and optical fiber for heat assisted magnetic recording is proposed. It has an advantage in optical efficiency and integration tolerance. SSC was fabricated and confirmed its operation. Fly-ability of pico slider with optical fiber was also demonstrated.
CD20-Directed Serotherapy in Patients With Multiple Myeloma: Biologic Considerations and Therapeutic Applications (2002)

Clonotypic B cells circulating in patients with multiple myeloma (MM) express CD20, and it has been suggested that these cells may be clonogenic. Furthermore, 20% of patients with MM express CD20 on their bone marrow plasma cells (BMPCs). Therefore, the authors began a phase II clinical study to determine the activity of the anti-CD20 monoclonal antibody rituximab in MM patients. Nineteen previously treated MM patients received 375 mg/m2 rituximab per week for 4 weeks. Three months after initiation of treatment, patients were assessed for response and received a second course of therapy if their disease was stable (SD) or they achieved a partial response (PR). Six of 19 (32%) patients had either a PR (n = 1) or SD (n = 5), with a median time to treatment failure of 5.5 months (mean, 10.3 months; range, 3-27+ months). All six patients who had a PR or SD had CD20+ BMPC. Overall, rituximab therapy was well tolerated. Because most patients with MM poorly express CD20 on their BMPCs, the authors evaluated agents for their ability to induce CD20 expression and thereby facilitate rituximab binding on MM cells. These studies show that interferon-gamma (IFN-y) induced CD20 expression on MM BMPCs, MM B cells, and healthy donor BMPCs. In contrast, CD20 expression on chronic lymphocytic leukemia, follicular non-Hodgkin's lymphoma, healthy donor B cells, and progenitor cells was unaffected by IFN-y. Rituximab binding to the BMPCs of MM patients was also increased after culture with pharmacologically attainable levels of IFN-gamma (1-100 U/mL). In conclusion, these studies suggest that MM patients with CD20+ BMPCs may benefit from rituximab therapy. Furthermore, IFN-gamma induces CD20 expression on MM BMPCs and B cells and facilitates rituximab binding to MM BMPCs, providing the rationale for clinical trials to examine its use with CD20-directed serotherapies in MM.
Modified FDR Controlling Procedure for Multi-Stage Analyses (2009)

Multiple testing has become an integral component in genomic analyses involving microarray experiments where a large number of hypotheses are tested simultaneously. However, before applying more computationally intensive methods, it is often desirable to complete an initial truncation of the variable set using a simpler and faster supervised method such as univariate regression. Once such a truncation is completed, multiple testing methods applied to any subsequent analysis no longer control the appropriate Type I error rates. Here we propose a modified marginal Benjamini & Hochberg step-up FDR controlling procedure for multi-stage analyses (FDR-MSA), which correctly controls Type I error in terms of the entire variable set when only a subset of the initial set of variables is tested. The method is presented with respect to a variable importance application. As the initial subset size increases, we observe convergence to the standard Benjamini & Hochberg step-up FDR controlling multiple testing procedures. We demonstrate the power and Type I error control through simulation and application to the Golub Leukemia data from 1999.
Cyanine Nanocages Activated by Near-Infrared Light for the Targeted Treatment of Traumatic Brain Injury (2020)

Traumatic brain injury (TBI) is a common and prevalent condition that affects large numbers of people across a range of ages. Individuals engaging in physical activities and victims of accidents are at a higher risk for TBI. There is a lack of available treatment specifically for TBI. Given the difficulty to determine its precise location in the brain, TBI remains difficult to fully diagnose or treat. Herein, we disclose a novel strategy for directing therapeutic agents to TBI sites, without the need to determine the precise location of the TBI activity in the brain. This novel approach is based on the use of a cyanine dye nanocage carrying Gabapentin, a known TBI therapeutic agent. Upon exposure of the cyanine nanocage to near-infrared light, the local release of Gabapentin is triggered, selectively at the TBI-affected site.
Dynamic kelvinlets (2018)

We introduce Dynamic Kelvinlets , a new analytical technique for real-time physically based animation of virtual elastic materials. Our formulation is based on the dynamic response to time-varying force distributions applied to an infinite elastic medium. The resulting displacements provide the plausibility of volumetric elasticity, the dynamics of compressive and shear waves, and the interactivity of closed-form expressions. Our approach builds upon the work of de Goes and James [2017] by presenting an extension of the regularized Kelvinlet solutions from elastostatics to the elastodynamic regime. To finely control our elastic deformations, we also describe the construction of compound solutions that resolve pointwise and keyframe constraints. We demonstrate the versatility and efficiency of our method with a series of examples in a production grade implementation.
Evaluation of wavelength dependence of integrated MZM using balanced-bridge and asymmetric X waveguide structures for high extinction ratio modulation (2017)

In this study, we measure the wavelength dependence on the device operation of integrated Mach-Zehnder modulators in cascade. We use a balanced-bridge and asymmetric X coupler. We investigate the extinction ratio and bias voltage of these structures, and calculate the relationship between the phase change and the imperfect-bias extinction ratio.
A robust image watermarking using DWT, SVD and Torus automorphism (2013)

Digital watermarking is a process to provide authenticity by hiding a data into an image or audio or document. Hiding of data in an image can be done in frequency domain. Since frequency domain based techniques are more robust against signal processing and geometric attacks than time domain techniques. One such frequency domain technique is developed based on combination of discrete wavelet transform, singular value decomposition and torus automorphism and is presented in this paper. This results prove that this method robust against different attacks and has good PSNR ratio.
Diagnosis of Acute Pulmonary Embolism in Outpatients: Comparison of Thin-Collimation Multi–Detector Row Spiral CT and Planar Ventilation-Perfusion Scintigraphy (2003)

Thin-collimation multi-detector row CT is more accurate than V-P scintigraphy in the diagnosis of acute PE in outpatients. Furthermore, CT provides alternative diagnoses for patients without PE on high-quality transverse or near-isotropic reformatted images.
Interleukins 4 and 13 modulate gene expression and promote proliferation of primary human tenocytes (2010)

Stimulation with IL-4 or IL-13 could be used to facilitate tendon repair in vivo or to aid in tendon tissue engineering, through stimulation of tenocyte proliferation.
Modulation of NMDA receptors by prion proteins (2007)

Background: The precise physiological function of endogenous cellular prion protein (PrPC) remains unclear. It has been shown that PrP-null mice exhibit reduced LTP and greater susceptability to seizure mortality in several in vivo (e.g. kainic acid) models of epilepsy. In addition, PrP-null mice exhibit greater exctitotoxic cell death in response to kainic acid exposure. Methods: In our study we investigated the synaptic properties of WT and PrP-null mice. &#x0D; Results: Recordings in the CA1 layer of adult hippocampal slices showed that PrP-null mice exhibit a reduced threshold to evoked responses and no difference in paired-pulse facilitation relative to WT animals. In addition, greater excitability was observed in PrP-null slices in response to zero-Mg2+ induced seizure-like events. Recordings from mature hippocampal cultures showed slightly altered AMPA and GABAA miniature synaptic currents. NMDA mEPSCs were observed to be increased in amplitude and significantly prolonged in decay time. NMDA-evokved currents also exhibited markedly prolonged deactivation kinetics. This effect on evoked NMDA currents was reproduced in WT neurons by PrP-RNAi transfection, and eliminated by PrPC transfection into PrP-null neurons. &#x0D; Conclusions: These data suggest enhanced NMDA activity in PrP-null neurons. Consistent with this finding, in vitro and in vivo excitotoxicity assays demonstrated increased neuronal cell death in PrP-null cultures and animals upon transient exposure to NMDA. The prolonged deactivation kinetics were most consistent with functional activity/augmentation of NR2D NMDA receptor subunits, and PrP coimmunoprecipiated with NR2D NMDA receptor subunits. This enhanced NMDA receptor function was paralleleld by increased excitotoxicy in Prp-null mice. Our findings demonstrate a novel functional role for PrP as a modulator of synaptic NMDA currents and attributes a neuroprotective function to PrP.
Harnessing brain waves: a review of brain magnetic resonance elastography for clinicians and scientists entering the field (2021)

Brain magnetic resonance elastography (MRE) is an imaging technique capable of accurately and non-invasively measuring the mechanical properties of the living human brain. Recent studies have shown that MRE has potential to provide clinically useful information in patients with intracranial tumors, demyelinating disease, neurodegenerative disease, elevated intracranial pressure, and altered functional states. The objectives of this review are: (1) to give a general overview of the types of measurements that have been obtained with brain MRE in patient populations, (2) to survey the tools currently being used to make these measurements possible, and (3) to highlight brain MRE-based quantitative biomarkers that have the highest potential of being adopted into clinical use within the next 5 to 10 years. The specifics of MRE methodology strategies are described, from wave generation to material parameter estimations. The potential clinical role of MRE for characterizing and planning surgical resection of intracranial tumors and assessing diffuse changes in brain stiffness resulting from diffuse neurological diseases and altered intracranial pressure are described. In addition, the emerging technique of functional MRE, the role of artificial intelligence in MRE, and promising applications of MRE in general neuroscience research are presented.
COMPETING CAUSES OF MORTALITY IN PATIENTS WITH T1B RENAL CELL CARCINOMA: ADDITIONAL EVIDENCE TO EXPAND THE INDICATIONS FOR NEPHRON SPARING SURGERY (2009)

You have accessJournal of Urology1 Apr 2009COMPETING CAUSES OF MORTALITY IN PATIENTS WITH T1B RENAL CELL CARCINOMA: ADDITIONAL EVIDENCE TO EXPAND THE INDICATIONS FOR NEPHRON SPARING SURGERY David J Kaplan, Robert G Uzzo, Brian L Egleston, David Y.T. Chen, and Stephen A Boorjian David J KaplanDavid J Kaplan More articles by this author , Robert G UzzoRobert G Uzzo More articles by this author , Brian L EglestonBrian L Egleston More articles by this author , David Y.T. ChenDavid Y.T. Chen More articles by this author , and Stephen A BoorjianStephen A Boorjian More articles by this author View All Author Informationhttps://doi.org/10.1016/S0022-5347(09)60909-5AboutPDF ToolsAdd to favoritesDownload CitationsTrack CitationsPermissionsReprints ShareFacebookLinked InTwitterEmail "COMPETING CAUSES OF MORTALITY IN PATIENTS WITH T1B RENAL CELL CARCINOMA: ADDITIONAL EVIDENCE TO EXPAND THE INDICATIONS FOR NEPHRON SPARING SURGERY." The Journal of Urology, 181(4S), pp. 319–320 © 2009 by American Urological AssociationFiguresReferencesRelatedDetails Volume 181Issue 4SApril 2009Page: 319-320 Advertisement Copyright & Permissions© 2009 by American Urological AssociationMetricsAuthor Information David J Kaplan More articles by this author Robert G Uzzo More articles by this author Brian L Egleston More articles by this author David Y.T. Chen More articles by this author Stephen A Boorjian More articles by this author Expand All Advertisement PDF downloadLoading ...
An updated and simplified method for bile duct cannulation of rats (2010)

The single bile duct cannulated rat model was used for short-term intestinal absorption studies. Rats were randomly assigned to three groups: (A) bile duct cannulated, (B) control laparotomy and (C) no treatment. The body weight and health of the rats were monitored before and until day 5 after surgery, while bile flow was measured in group A on day 2. On the fifth day, tail vein blood was harvested, and alanine aminotransferase, aspartate aminotransferase, alkaline phosphatase and total bilirubin were quantified. Analysis of variance showed no significant difference between the groups for these parameters. This study demonstrated the suitability of a surgical rat model feasible for evaluation of the impact of bile in pharmacokinetic studies.
Approaching the TW-regime with mJ-class picosecond pulses post-compressed to 13 fs (2023)

We demonstrate efficient post compression of 9.45 mJ, 1.2 ps pulses to 13 fs at 1 kHz repetition rate using a two stage gas filled multi pass cell system reaching near terawatt peak power.
Friction-induced fluctuation of cutting forces in the diamond turning of aluminium single crystals (2003)

This paper presents a multidisciplinary approach to the analysis of the fluctuation of cutting forces in the diamond turning of crystalline materials. The analysis is based on a microplasticity model for shear angle prediction and a cutting force model incorporating a friction variable which is estimated from the power spectrum analysis. The results reveal that the pattern of periodic fluctuation of the microcutting forces is not only due to the crystallographic orientation of the materials being cut but also to the friction between the chip and the tool face. The frictional effect is found to cause a change in the pattern and the periodicity of the fluctuation of the cutting force. The power spectrum predicted from the cutting force model incorporates a friction variable which can be chosen to match the experimental power spectrum, thus providing a new way to assess the frictional condition, and can be used as a diagnostic tool to monitor the tool wear and cutting conditions during diamond turning.
Porous Nanomaterials for Ultrabroadband Omnidirectional Anti‐Reflection Surfaces with Applications in High Concentration Photovoltaics (2016)

Materials for nanoporous coatings that exploit optimized chemistries and self‐assembly processes offer capabilities to reach ≈98% transmission efficiency and negligible scattering losses over the broad wavelength range of the solar spectrum from 350 nm to 1.5 µm, on both flat and curved glass substrates. These nanomaterial anti‐reflection coatings also offer wide acceptance angles, up to ±40°, for both s‐ and p‐polarization states of incident light. Carefully controlled bilayer films have allowed for the fabrication of dual‐sided, gradient index profiles on plano‐convex lens elements. In concentration photovoltaics platforms, the resultant enhancements in the photovoltaics efficiencies are ≈8%, as defined by experimental measurements on systems that use microscale triple‐junction solar cells. These materials and their applications in technologies that require control over interface reflections have the potential for broad utility in imaging systems, photolithography, light‐emitting diodes, and display technologies.
The Logbook, A Publication of the Wayne E. Meyer Institute of Systems Engineering / October 2003 (2003)

www.nps.navy.mil/meyerinstitute Email:MeyerInst@nps.navy.mil Phone:(831) 656-7847 Fax:(831) 656-2336 Naval Postgraduate School, 777 Dyer Rd., Mail Code 97, Monterey, CA
Dehydrogenation Mechanism of Liquid Organic Hydrogen Carriers: Dodecahydro‐N‐ethylcarbazole on Pd(111) (2013)

Dodecahydro-N-ethylcarbazole (H12-NEC) has been proposed as a potential liquid organic hydrogen carrier (LOHC) for chemical energy storage, as it combines both favourable physicochemical and thermodynamic properties. The design of optimised dehydrogenation catalysts for LOHC technology requires a detailed understanding of the reaction pathways and the microkinetics. Here, we investigate the dehydrogenation mechanism of H12-NEC on Pd(111) by using a surface-science approach under ultrahigh vacuum conditions. By combining infrared reflection-absorption spectroscopy, density functional theory calculations and X-ray photoelectron spectroscopy, surface intermediates and their stability are identified. We show that H12-NEC adsorbs molecularly up to 173 K. Above this temperature (223 K), activation of C-H bonds is observed within the five-membered ring. Rapid dehydrogenation occurs to octahydro-N-ethylcarbazole (H8-NEC), which is identified as a stable surface intermediate at 223 K. Above 273 K, further dehydrogenation of H8-NEC proceeds within the six-membered rings. Starting from clean Pd(111), C-N bond scission, an undesired side reaction, is observed above 350 K. By complementing surface spectroscopy, we present a temperature-programmed molecular beam experiment, which permits direct observation of dehydrogenation products in the gas phase during continuous dosing of the LOHC. We identify H8-NEC as the main product desorbing from Pd(111). The onset temperature for H8-NEC desorption is 330 K, the maximum reaction rate is reached around 550 K. The fact that preferential desorption of H8-NEC is observed even above the temperature threshold for H8-NEC dehydrogenation on the clean surface is attributed to the presence of surface dehydrogenation and decomposition products during continuous reactant exposure.
ChemInform Abstract: Total Synthesis of Pinnatoxin A. (1998)

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.
Hycanthone Inhibits Inflammasome Activation and Neuroinflammation-Induced Depression-Like Behaviors in Mice (2022)

Despite the various medications used in clinics, the efforts to develop more effective treatments for depression continue to increase in the past decades mainly because of the treatment-resistant population, and the testing of several hypotheses- and target-based treatments. Undesirable side effects and unresponsiveness to current medications fuel the drive to solve this top global health problem. In this study, we focused on neuroinflammatory response-mediated depression which represents a cluster of depression etiology both in animal models and humans. Several meta-analyses reported that proinflammatory cytokines such as interleukin 6 (IL-6) and tumor necrosis factor-α (TNF-α) were increased in major depressive disorder patients. Inflammatory mediators implicated in depression include type-I interferon and inflammasome pathways. To elucidate the molecular mechanisms of neuroinflammatory cascades underlying the pathophysiology of depression, we introduced hycanthone, an antischistosomal drug, to check whether it can counteract depressive-like behaviors <i>in vivo</i> and normalize the inflammation-induced changes <i>in vitro</i>. Lipopolysaccharide (LPS) treatment increased proinflammatory cytokine expression in the murine microglial cells as well as the stimulation of type I interferon-related pathways that are directly or indirectly regulated by Janus kinase-signal transducer and activator of transcription (JAK-STAT) activation. Hycanthone treatment attenuated those changes possibly by inhibiting the JAK-STAT pathway and inflammasome activation. Hycanthone also ameliorated depressive-like behaviors by LPS. Taken together, we suggest that the inhibitory action of hycanthone against the interferon pathway leading to attenuation of depressive-like behaviors can be a novel therapeutic mechanism for treating depression.
Mucosal cytokine imbalance in irritable bowel syndrome (2008)

Despite the expected heterogeneity of the disorder, differences in mucosal chemokine signalling were evident in this cross-sectional study of IBS patients at the level of both gene expression and protein secretion, with IBS patients demonstrating a consistent deficit in the expression and secretion of chemokines known to play a critical role in mucosal defence.
“Haunted by the Aboriginal”: Theory and Its Other (2016)

Postmodern and postcolonial theories are especially sensitive to the question 
of otherness . They are intensely aware of their social, historical, institutional 
and geo-political formation and location, and express this refl exive awareness by taking an ethical stance towards otherness that can be described as 
anti-ethnocentric and anti-assimilative. The assimilative impulse that leads 
to the logic of identity and the ethnocentrism that can only see the Other in 
its own image are staunchly opposed by these theories which, instead, aim 
to value and preserve the Other as unbridgeable difference or absolute alterity. But I want to argue in this essay that in adopting an ethics of alterity, in 
showing sensitivity to otherness and in strongly opposing any aggressive 
appropriation of the Other, postmodern and postcolonial theories often 
encounter a problem in which their ethical approach to the Other ends up 
using the Other to prop up their own theoretical enterprise.
1P-046 Ligand Recognition of Lipocalin-type Prostaglandin D Synthase(The 46th Annual Meeting of the Biophysical Society of Japan) (2008)

TheBiophysicalSociety of
Tritium Effects on Aromatic Carbon–Loaded Polymers (2020)

By incorporating carbon nanotubes (CNTs) and graphene nanomaterials with aromatic sp2 carbon structures, we have specifically tuned filled ethylene propylene diene monomer elastomer (EPDM) seal and gasket composite materials for radiation resistance. Our results show that CNTs and graphene have an increased ability to stabilize the EPDM matrix compared to standard carbon black (CB) as a radiation-resistant filler. Graphene outperforms both CNT and CB fillers when considering surface damage under conditions where beta exposure is an issue. Both graphene and CNT fillers offer significantly reduced changes in glass transition temperature under prolonged exposure to tritium compared to CB-filled standards, with a 2.5-fold and almost 5-fold reduction, respectively. Thus, CNT- and graphene-filled O-ring materials could be designed that would maintain acceptable seals significantly longer than currently used composites.