gebhart/patrepeval huggingface dataset:
P3–419: Identification of presenilin–associated proteins and potential regulators of the gamma–secretase complex (2006)

The presenilins, NCT, aph–1 and pen–2 form a series of high molecular weight complexes that are necessary for gamma– and epsilon–secretase cleavage of selected Type 1 transmembrane proteins, including APP, Notch and cadherins. However, questions concerning the biology of the presenilin complexes remain to be resolved. These include how their activity is modulated in terms of substrate specificity, what are the relative activities of the gamma– and epsilon–sites, and whether or not additional proteins in the presenilin complexes might subsume these putative regulatory functions. To investigate the possible presence of additional co–factors, we sought to apply an in situ cross–linking method that maintains the microenvironment of the presenilin complex. PS1 immuno–affinity purification using a novel in vivo formaldehyde cross–linked has been used in wild–type and PS1/ PS2 double knockout blastocyst–derived cells. This has revealed that all four known constituents of the presenilin complex (nicastrin, aph–1, pen–2 and PS1) were present as shown by mass spectrometry. A few other possible candidates were also identified in the immunoprecipitates from wild–type cells. We are following up on that the confirmation experiments on their interaction with presenilin complex by co–immunoprecipitation, glycerol velocity gradients and on native/2D gel chromatography. This has been complemented by functional examination of gamma–secretase activity by determination of Abeta and ICD production in whole cells and cell–free gamma–secretase assays. This has led to the identification of several potential modulators of the presenilin complex that may have functional significance.
3D Camera Calibration Using Gray Code Patterns (2008)

This DOI is not currently attached to any metadata records. DOIs can’t actually ever be deleted (they’re persistent), but sometimes our members create DOIs in error. We do have a process to approximate deletion which we follow only in rare cases where the DOI has been genuinely created in error, and most crucially, if the DOI has never been published anywhere online or in print and never otherwise distributed to or communicated with anyone (authors, readers, reviewers, etc.
Thorough characterization of an EUV mask (2009)

We reported that we were successful in our 45nm technology node device demonstration in February 2008 and 22nm node technology node device patterning in February 2009 using ASML's Alpha Demo Tool (ADT).1, 2, 3 In order to insert extreme ultraviolet (EUV) lithography at the 15nm technology node and beyond, we have thoroughly characterized one EUV mask, a so-called NOVACD mask. In this paper, we report on three topics. The first topic is an analysis of line edge roughness (LER) using a mask Scanning Electron Microscope (SEM), an Atomic Force Microscope (AFM) and the Actinic Inspection Tool (AIT) to compare resist images printed with the ASML ADT. The results of the analysis show a good correlation between the mask AFM and the mask SEM measurements. However, the resist printing results for the isolated space patterns are slightly different. The cause of this discrepancy may be resist blur, image log slope and SEM image quality and so on. The second topic is an analysis of mask topography using an AFM and relative reflectivity of mirror and absorber surface using the AIT. The AFM data show 6 and 7 angstrom rms roughness for mirror and absorber, respectively. The reflectivity measurements show that the mirror reflects EUV light about 20 times higher than absorber. The last topic is an analysis of a 32nm technology node SRAM cell which includes a comparison of mask SEM image, AIT image, resist image and simulation results. The ADT images of the SRAM pattern were of high quality even though the mask patters were not corrected for OPC or any EUV-specific effects. Image simulation results were in good agreement with the printing results.
Using Wavelength Splitting at the Remote Node to Mitigate Rayleigh Backscattering for Optical Wired and Wireless Access Networks (2010)

We demonstrate an optical wired and wireless access network using wavelength-splitting (WS) at remote-node. A pair of CW carriers is generated from each laser source for wired and wireless applications respectively for effective Rayleigh-backscattering mitigation.
External-heater-induced negative capacitance in electronic devices (2021)

Abstract Negative capacitance (NC) is considered an extraordinary phenomenon although it is observed in various electronic devices. Based on device-specific properties, numerous mechanisms have been proposed for decades to explain how ordinary positive capacitance values reach negative values at low frequencies under a high voltage bias. In a previous study, we demonstrated that ubiquitous self-heating of devices is a source of NC in organic light-emitting diodes (OLEDs) and hole-only devices. The principal mechanism of the NC is the nonlinear coupling of the real and imaginary parts of admittance, caused by AC temperature modulation. In this study, a simple test applicable to various devices was conducted to monitor the effects of heating on capacitance. External heating by nichrome wires, rather than self-heating, induced NC, which reflected the heat transfer characteristics of the devices considered: an OLED and a Schottky barrier diode. The heating effect was shown to be a basic and common mechanism of NC, independent of device-specific electronic properties. Therefore, self-heating effects must be considered prior to exploring device-specific NC sources in electronic devices.
Reducing delays to lung cancer treatment through systematic consult scheduling: A multidisciplinary quality improvement initiative at a safety-net hospital. (2021)

e18640 Background: Delays in diagnosis and treatment have been identified as practice gaps in lung cancer management. At our large safety-net hospital, 2016-2018 data provided by the Commission on Cancer (CoC) indicated that 58-66% of lung cancer patients began treatment &gt; 30 days after their diagnosis, compared to a median of 30 days for CoC-accredited hospitals. A quality improvement (QI) project was performed to identify causes for treatment delays, and to implement changes to reduce the median time from diagnosis to treatment to &lt; 30 days. Methods: Root cause analysis was performed on a cohort of lung cancer patients identified and abstracted by the CoC Registry with diagnosis in October 2018-September 2019, to provide more recent data on treatment delays and to identify actionable interventions. Subsequently, a multidisciplinary QI initiative through Thoracic Surgery, Hematology Oncology, and Radiation Oncology was implemented using the Plan-Do-Study-Act (PDSA) tool. The initiative was tracked for 6 months starting in August 2020, with time from referral to consult and time from diagnosis to treatment calculated via chart review. Results: For the root cause analysis, 36 patients were identified. Eleven cases were excluded as they did not receive treatment at our institution. For the remaining 25 patients, the median time from referral to consult across all three oncology specialties was 13 days. The most common barriers to initiating treatment were appointment scheduling delays (37.5%), patient factors including synchronous malignancies or insurance, geographic or cultural barriers (31.3%), and multiple factors including appointment scheduling delays (25%). Median time from diagnosis to treatment was 31 days, with 36% (N = 9) starting treatment in &lt; 30 days. While appointment scheduling delays included both work-up (imaging, procedures) and consults as well as follow-ups, multidisciplinary discussions identified time from referral to consult as the most actionable QI initiative. With support from Patient Navigation, the three oncology specialties jointly implemented a system whereby suspected or confirmed new lung cancer patients were scheduled for consult ideally in &lt; 7 days, and no more than 14 days from the referral date. Of 28 new lung cancer patients who started treatment after the QI intervention, median time from referral to consult decreased to 7 days. Median time from diagnosis to treatment decreased to 26.5 days, with 53.6% (N = 15) of patients starting treatment in &lt; 30 days. Conclusions: By decreasing time from referral to consult, this multidisciplinary QI intervention facilitated earlier initiation of treatment for lung cancer patients. Similar actions to decrease other scheduling delays and mitigate the impact of social determinants of health could further promote improvements in timely patient care.
In vivo and in vitro imaging of I2imidazoline receptors in the monkey brain (2010)

I₂ imidazoline receptors (I₂Rs) are associated with depression, Alzheimer's disease, and Huntington's disease. However, in vivo imaging of I₂Rs in the monkey brain has not been reported until now. We performed in vitro and in vivo imaging of (I₂Rs) in the monkey brain using ¹¹C-labeled 2-(3-fluoro-4-tolyl)-4,5-dihydro-1H-imidazole ([¹¹C]FTIMD) which has high and selective affinity of I₂Rs. In an auto-radiography (ARG) study, the distribution pattern of [¹¹C]FTIMD in the monkey brain was similar to that of [³H]idazoxan binging to I₂Rs in the human brain, which was previously described. The specific binding of [¹¹C]FTIMD accounted for >97% of total binding in brain regions existing I₂ Rs. In positron emission tomography (PET) studies, the radioactivity was accumulated in brain regions existing I₂Rs ligand BU224, the accumulated radioactivity was decreased to approximately 66%-75% of the baseline measurement at 15-45 min after injection of [¹¹C]FTIMD. These results suggest that [¹¹C]FTIMD shows the specific-binging to I₂Rs in the monkey brain as depicted by PET and ARG. We performed the first in vivo imaging of I₂Rs using [¹¹C]FTIMD in the monkey brain.
Ultrasensitive Capture of Human Herpes Simplex Virus Genomes Directly from Clinical Samples Reveals Extraordinarily Limited Evolution in Cell Culture (2018)

Herpes simplex viruses (HSVs) are difficult to sequence due to their large DNA genome, high GC content, and the presence of repeats. To date, most HSV genomes have been recovered from culture isolates, raising concern that these genomes may not accurately represent circulating clinical strains. We report the development and validation of a DNA oligonucleotide hybridization panel to recover nearly complete HSV genomes at abundances up to 50,000-fold lower than previously reported. Using copy number information on herpesvirus and host DNA background via quantitative PCR, we developed a protocol for pooling for cost-effective recovery of more than 50 HSV-1 or HSV-2 genomes per MiSeq run. We demonstrate the ability to recover >99% of the HSV genome at >100× coverage in 72 h at viral loads that allow whole-genome recovery from latently infected ganglia. We also report a new computational pipeline for rapid HSV genome assembly and annotation. Using the above tools and a series of 17 HSV-1-positive clinical swabs sent to our laboratory for viral isolation, we show limited evolution of HSV-1 during viral isolation in human fibroblast cells compared to the original clinical samples. Our data indicate that previous studies using low-passage-number clinical isolates of herpes simplex viruses are reflective of the viral sequences present in the lesion and thus can be used in phylogenetic analyses. We also detect superinfection within a single sample with unrelated HSV-1 strains recovered from separate oral lesions in an immunosuppressed patient during a 2.5-week period, illustrating the power of direct-from-specimen sequencing of HSV.<b>IMPORTANCE</b> Herpes simplex viruses affect more than 4 billion people across the globe, constituting a large burden of disease. Understanding the global diversity of herpes simplex viruses is important for diagnostics and therapeutics as well as cure research and tracking transmission among humans. To date, most HSV genomics has been performed on culture isolates and DNA swabs with high quantities of virus. We describe the development of wet-lab and computational tools that enable the accurate sequencing of near-complete genomes of HSV-1 and HSV-2 directly from clinical specimens at abundances >50,000-fold lower than previously sequenced and at significantly reduced cost. We use these tools to profile circulating HSV-1 strains in the community and illustrate limited changes to the viral genome during the viral isolation process. These techniques enable cost-effective, rapid sequencing of HSV-1 and HSV-2 genomes that will help enable improved detection, surveillance, and control of this human pathogen.
NO More Dogma (2009)

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Supplementary Figure and Table Legends from Identification of Hypermethylated Genes Associated with Cisplatin Resistance in Human Cancers (2023)

Supplementary Figure and Table Legends from Identification of Hypermethylated Genes Associated with Cisplatin Resistance in Human Cancers
Seismic Determination of Reservoir Heterogeneity: Application to the Characterization of Heavy Oil Reservoirs (2003)

The objective of the project was to examine how seismic and geologic data could be used to improve characterization of small-scale heterogeneity and their parameterization in reservoir models. Performed a theoretical and numerical study to examine which subsurface features the surface seismic method actually resolves.
Fundamental limitations of power control and radio resource management in wireless networks: Research Articles (2004)

The ultimate resource in wireless networks is transmission power. The system stability and the resource sharing algorithms all rely on well functioning power control. To realistically address resource management algorithms, it is important to consider fundamental limitations of the radio resource and of power control. Exact and approximate capacity expressions are derived and related to Quality of Service (QoS) requirements of services. Power control is subject to limited update rate, limited feedback bandwidth, time delays, measurement errors, feedback errors and filtering effects which all affect the resulting performance. Simulations further illustrate the hampering effects and motivates models of power control inaccuracies. Copyright © 2004 John Wiley & Sons, Ltd.
Bioinspired Materials: Bio‐inspired Design of Submerged Hydrogel‐Actuated Polymer Microstructures Operating in Response to pH (Adv. Mater. 12/2011) (2011)

The cover depicts polymer “microfins” embedded in pH-responsive gel and submerged in water. Actuation of the fins driven by volume phase transitions in a pH-responsive hydrogel “muscle” may be able to drive the flow of particles in solution, as proposed on p. 1442 by Joanna Aizenberg and co-workers. The system is designed to provide uniform directional bending actuation over a large area and integrated with electrochemical and microfluidic cells.
Thymus machinery for T-cell selection (2018)

An immunocompetent and self-tolerant pool of naive T cells is formed in the thymus through the process of repertoire selection. T cells that are potentially capable of responding to foreign antigens are positively selected in the thymic cortex and are further selected in the thymic medulla to help prevent self-reactivity. The affinity between T-cell antigen receptors expressed by newly generated T cells and self-peptide-major histocompatibility complexes displayed in the thymic microenvironments plays a key role in determining the fate of developing T cells during thymic selection. Recent advances in our knowledge of the biology of thymic epithelial cells have revealed unique machinery that contributes to positive and negative selection in the thymus. In this article, we summarize recent findings on thymic T-cell selection, focusing on the machinery unique to thymic epithelial cells.
HOT (2011)

We introduce Hodge-optimized triangulations (HOT), a family of well-shaped primal-dual pairs of complexes designed for fast and accurate computations in computer graphics. Previous work most commonly employs barycentric or circumcentric duals; while barycentric duals guarantee that the dual of each simplex lies within the simplex, circumcentric duals are often preferred due to the induced orthogonality between primal and dual complexes. We instead promote the use of weighted duals ("power diagrams"). They allow greater flexibility in the location of dual vertices while keeping primal-dual orthogonality, thus providing a valuable extension to the usual choices of dual by only adding one additional scalar per primal vertex. Furthermore, we introduce a family of functionals on pairs of complexes that we derive from bounds on the errors induced by diagonal Hodge stars, commonly used in discrete computations. The minimizers of these functionals, called HOT meshes, are shown to be generalizations of Centroidal Voronoi Tesselations and Optimal Delaunay Triangulations, and to provide increased accuracy and flexibility for a variety of computational purposes.
In VivoApplications of Bioorthogonal Chemistries (2017)

This chapter reviews the development and optimization of four bioorthogonal reactions: the Staudinger ligation, copper-catalyzed azide-alkyne cycloaddition, copper-free click chemistry, and the tetrazine ligation. It highlights the efforts of researchers to enhance the pharmacokinetic properties of bioorthogonal reagents, thereby enabling their use in vivo and opening the door to exciting new applications of these unique chemistries. In order for a bioorthogonal reaction to be successful in vivo, one of the reaction partners must be somehow integrated into the target biomolecule. The chapter presents examples in which metabolic glycan engineering is used to install reactive bioorthogonal handles into the glycomes of living animals. Most of the in vivo metabolic labeling experiments presented in the chapter employ peracetylated versions of the sugar analogs, which readily penetrate cell membranes and are deacetylated by cytosolic esterases.
Ultrasound Molecular Imaging of Angiogenesis Using Vascular Endothelial Growth Factor-Conjugated Microbubbles (2017)

Imaging of angiogenesis receptors could provide a sensitive and clinically useful method for detecting neovascularization such as occurs in malignant tumors, and responses to antiangiogenic therapies for such tumors. We tested the hypothesis that microbubbles (MB) tagged with human VEGF<sub>121</sub> (MB<sub>VEGF</sub>) bind to the kinase insert domain receptor (KDR) in vitro and angiogenic endothelium in vivo, and that this specific binding can be imaged on a clinical ultrasound system. In this work, targeted adhesion of MB<sub>VEGF</sub> was evaluated in vitro using a parallel plate flow system containing adsorbed recombinant human KDR. There was more adhesion of MB<sub>VEGF</sub> to KDR-coated plates when the amount of VEGF<sub>121</sub> on each MB or KDR density on the plate was increased. MB<sub>VEGF</sub> adhesion to KDR-coated plates decreased with increasing wall shear rate. On intravital microscopic imaging of bFGF-stimulated rat cremaster muscle, there was greater microvascular adhesion of MB<sub>VEGF</sub> compared to that of isotype IgG-conjugated control MB (MB<sub>CTL</sub>). To determine if MB<sub>VEGF</sub> could be used to ultrasonically image angiogenesis, ultrasound imaging was performed in mice bearing squamous cell carcinoma after intravenous injection of MB<sub>VEGF</sub>. Ultrasound videointensity enhancement in tumor was significantly higher for MB<sub>VEGF</sub> (17.3 ± 9.7 dB) compared to MB<sub>CTL</sub> (3.8 ± 4.4 dB, n = 6, p < 0.05). This work demonstrates the feasibility of targeted ultrasound imaging of an angiogenic marker using MB<sub>VEGF</sub>. This approach offers a noninvasive bedside method for detecting tumor angiogenesis and could be extended to other applications such as molecular monitoring of therapeutic angiogenesis or antiangiogenic therapies in cardiovascular disease or cancer.
Electrical stimulation of the eighth nerve in cat: Temporal properties of unit responses in the large spherical cell region of the AVCN (1981)

Single-unit responses to intracochlear electrical stimulation were studied. Responses were highly phase-locked to sinusoidal stimulation at frequencies less than 4 kHz. At any given stimulus frequency, synchronization indexes were greater than those that have been reported for eighth nerve responses to acoustic stimuli. At the onset of a low-frequency (i.e., below 800 Hz) sinusoidal stimulus, firing rate gradually increased over many tens of milliseconds. Rise times were as long as 50–100 ms for low-intensity, low-frequency sinusoidal stimulus bursts. At greater intensities and/or higher stimulus frequencies, the response rise times were considerably shorter. Preliminary results indicate that responses to trains of short-duration biphasic pulses do not exhibit such slow rise times. These results may relate to Eddington's [Ann. Otol. Rhinol. Laryngol. 87 (Suppl. 53), 1–37 (1978)] finding that behavioral threshold increases sharply as the burst duration of a sinusoidal stimulus is decreased. However, threshold is only a weak function of the duration of a train of short-duration biphasic pulses. For sinusoids below 300 Hz, multiple discharges per cycle were common at levels considerably above threshold. [Work supported by NIH.]
Competition between Depletion Effects and Coupling in the Plasmon Modulation of Doped Metal Oxide Nanocrystals (2019)

Degenerately doped semiconductor nanocrystals (NCs) exhibit strong light-matter interactions due to localized surface plasmon resonance (LSPR) in the near- to mid-infrared region. Besides being readily tuned through dopant concentration introduced during synthesis, this LSPR can also be dynamically modulated by applying an external electrochemical potential. This characteristic makes these materials candidates for electrochromic window applications. Here, using prototypical doped indium oxide NCs as a model system, we find that the extent of electrochemical modulation of LSPR frequency is governed by the depletion width and the extent of inter-NC LSPR coupling, which are indirectly controlled by the dopant density, size, and packing density of the NCs. The depletion layer is a near-surface region with a sharply reduced free carrier population that occurs whenever the surface potential lies below the Fermi level. Changes in the depletion width under applied bias substantially control the spectral modulation of the LSPR of individual NCs and also modify the inter-NC LSPR coupling, which additionally modulates the LSPR absorption on the NC film scale. Here, we show that both of these effects must be considered primary factors in determining the extent of LSPR frequency modulation and that the dominant factor depends on NC size. For a constant doping concentration, depletion effects govern LSPR modulation for smaller NCs, while LSPR coupling is prevalent in larger NCs. Consequently, as the size of the NCs is increased while keeping the doping concentration constant, we observe a reversal in the sign of the LSPR frequency modulation from positive to negative.