gebhart/patrepeval huggingface dataset:
Bias-dependent carrier dynamics studied by Laser Terahertz Emission Microscopy with nanometer resolution (2017)

Laser Terahertz Emission Microscopy (LTEM) is a method which has been developed in order to study intrinsic carrier dynamics in semiconductors with a spatial resolution which is only limited by the wavelength of the incident fs laser [1]. More recently, it has been shown that the spatial resolution in a terahertz (THz) spectroscopy experiment can be improved even further by utilizing plasmonic coupling of the incident THz field to a subwavelength metal tip, which has resulted in resolutions on the order of 10 nm [2]. As previously proposed [3] we here present our first results on LTEM with nanometer resolution by combining the two methods mentioned above as illustrated in Fig. 1 (a) where the incident fs laser pulses (100 fs, 800 nm, 80 MHz) are coupled to a sharp metal tip with a spatial diameter of sub-20 nm. The THz pulses emerging from the sample are detected by eO sampling in a 2 mm thick ZnTe crystal with lockin detection to the tapping frequency of the AFM probe (20 kHz). The tapping amplitude of the AFM probe is approximately 40 nm and the length of the probe is 80 μm ± 20% (Rocky Mountain Nanotechnology). In addition, we demonstrate how the detected LTEM signal can be modulated by applying a bias on the AFM probe while keeping the sample on a ground plane.
3p Arm Loss and Survival in Head and Neck Cancer: An Analysis of TCGA Dataset (2021)

Loss of the 3p chromosome arm has previously been reported to be a biomarker of poorer outcome in both human papillomavirus (HPV)-positive and HPV-negative head and neck cancer. However, the precise operational measurement of 3p arm loss is unclear and the mutational profile associated with the event has not been thoroughly characterized. We downloaded the clinical, single nucleotide variation (SNV), copy number aberration (CNA), RNA sequencing, and reverse phase protein assay (RPPA) data from The Cancer Genome Atlas (TCGA) and The Cancer Proteome Atlas HNSCC cohorts. Survival data and hypoxia scores were downloaded from published studies. In addition, we report the inclusion of an independent Memorial Sloan Kettering cohort. We assessed the frequency of loci deletions across the 3p arm separately in HPV-positive and -negative disease. We found that deletions on chromosome 3p were almost exclusively an all or none event in the HPV-negative cohort; patients either had <1% or >97% of the arm deleted. 3p arm loss, defined as >97% deletion in HPV-positive patients and >50% in HPV-negative patients, had no impact on survival (<i>p</i> > 0.05). However, HPV-negative tumors with 3p arm loss presented at a higher N-category and overall stage and developed more distant metastases (<i>p</i> < 0.05). They were enriched for SNVs in TP53, and depleted for point mutations in CASP8, HRAS, HLA-A, HUWE1, HLA-B, and COL22A1 (false discovery rate, FDR < 0.05). 3p arm loss was associated with CNAs across the whole genome (FDR < 0.1), and pathway analysis revealed low lymphoid-non-lymphoid cell interactions and cytokine signaling (FDR < 0.1). In the tumor microenvironment, 3p arm lost tumors had low immune cell infiltration (FDR < 0.1) and elevated hypoxia (FDR < 0.1). 3p arm lost tumors had lower abundance of proteins phospho-HER3 and ANXA1, and higher abundance of miRNAs hsa-miR-548k and hsa-miR-421, which were all associated with survival. There were no molecular differences by 3p arm status in HPV-positive patients, at least at our statistical power level. 3p arm loss is largely an all or none phenomenon in HPV-negative disease and does not predict poorer survival from the time of diagnosis in TCGA cohort. However, it produces tumors with distinct molecular characteristics and may represent a clinically useful biomarker to guide treatment decisions for HPV-negative patients.
Poly‐gene fusion transcripts and chromothripsis in prostate cancer (2012)

Complex genome rearrangements are frequently observed in cancer but their impact on tumor molecular biology is largely unknown. Recent studies have identified a new phenomenon involving the simultaneous generation of tens to hundreds of genomic rearrangements, called chromothripsis. To understand the molecular consequences of these events, we sequenced the genomes and transcriptomes of two prostate tumors exhibiting evidence of chromothripsis. We identified several complex fusion transcripts, each containing sequence from three different genes, originating from different parts of the genome. One such poly-gene fusion transcript appeared to be expressed from a chain of small genomic fragments. Furthermore, we detected poly-gene fusion transcripts in the prostate cancer cell line LNCaP, suggesting they may represent a common phenomenon. Finally in one tumor with chromothripsis, we identified multiple mutations in the p53 signaling pathway, expanding on recent work associating aberrant DNA damage response mechanisms with chromothripsis. Overall, our data show that chromothripsis can manifest as massively rearranged transcriptomes. The implication that multigenic changes can give rise to poly-gene fusion transcripts is potentially of great significance to cancer genetics.
Epicardial wavefronts arise from widely distributed transient sources during ventricular fibrillation in the isolated swine heart (2008)

It has been proposed that VF waves emanate from stable localized sources, often called "mother rotors." However, evidence for the existence of these rotors is conflicting. Using a new panoramic optical mapping system that can image nearly the entire ventricular epicardium, we recently excluded epicardial mother rotors as the drivers of Wiggers' stage II VF in the isolated swine heart. Furthermore, we were unable to find evidence that VF requires sustained intramural sources. The present study was designed to test the following hypotheses: 1. VF is driven by a specific region, and 2. Rotors that are long-lived, though not necessarily permanent, are the primary generators of VF wavefronts. Using panoramic optical mapping, we mapped VF wavefronts from 6 isolated swine hearts. Wavefronts were tracked to characterize their activation pathways and to locate their originating sources. We found that the wavefronts that participate in epicardial reentry were not confined to a compact region; rather they activated the entire epicardial surface. New wavefronts feeding into the epicardial activation pattern were generated over the majority of the epicardium and almost all of them were associated with rotors or repetitive breakthrough patterns that lasted for less than 2 s. These findings indicate that epicardial wavefronts in this model are generated by many transitory epicardial sources distributed over the entire surface of the heart.
Preclinical swine joint imaging using forward-viewing spectrally encoded endoscopy (Conference Presentation) (2019)

Utilizing spatial wavelength encoding, spectrally encoded endoscopy (SEE) makes it possible to create miniature, small diameter endoscopic probes that can allow easy access to hard-to-reach locations within the body. Previously described SEE probes have been side-viewing, which limits their use for guiding the navigation of narrow passages. Forward-viewing SEE (FVSEE) probes are advantageous as they provide a look ahead that facilitates navigation and surveillance of a wider field of view (FOV). In this work, we present a novel FVSEE probe. The 500-µm illumination optics are designed in such a way that the shortest wavelength (460 nm) propagates along the optical axis, while an angle of approximately 56° is formed between the longest wavelength (720 nm) and the optical axis. Two-dimensional illumination was accomplished by rotating the illumination optics at a speed of 15 rps using a miniature torque coil. Reflected light from the sample was collected by 8 multimode detection fibers that were arranged into a circular array around the illumination optics. The proximal ends of the detection fibers were polished at a 17° angle, resulting in a total angle of detection of approximately 100°. Light coming out from the distal end of the detection fibers, which were rearranged into a linear array, was detected using a custom spectrometer with a tall-pixel linear CCD camera. The FVSEE probe was used to conduct a preclinical imaging of a swine joint. The results were compared to a commercial chip-on-the-tip mini-endoscope and showed a better spatial resolution and a wider FOV using the FVSEE probe.
Increasing the breadth and potency of response to the seasonal influenza virus vaccine by immune complex immunization (2017)

The main barrier to reduction of morbidity caused by influenza is the absence of a vaccine that elicits broad protection against different virus strains. Studies in preclinical models of influenza virus infections have shown that antibodies alone are sufficient to provide broad protection against divergent virus strains in vivo. Here, we address the challenge of identifying an immunogen that can elicit potent, broadly protective, antiinfluenza antibodies by demonstrating that immune complexes composed of sialylated antihemagglutinin antibodies and seasonal inactivated flu vaccine (TIV) can elicit broadly protective antihemagglutinin antibodies. Further, we found that an Fc-modified, bispecific monoclonal antibody against conserved epitopes of the hemagglutinin can be combined with TIV to elicit broad protection, thus setting the stage for a universal influenza virus vaccine.
Temperature-Dependent Optical Properties of Single Crystalline and Polycrystalline Silver Thin Films (2017)

Silver holds a unique place in plasmonics compared to other noble metals owing to its low losses in the visible and near-IR wavelength ranges. With a growing interest in local heating and high temperature applications of plasmonics, it is becoming critical to characterize the dielectric function of nanometer-scale thin silver films at higher temperatures, especially near the breakdown temperature, which depends on the film thickness and crystallinity. So far, such a comprehensive study has been missing. Here we report the in situ high temperature ellipsometry measurements of ultrasmooth and epitaxial quality crystalline silver films, along with electron beam evaporated polycrystalline silver films at temperatures up to 700 °C, in the wavelength range of 330–2000 nm. Our findings show that the dielectric function of all the films changes remarkably at elevated temperatures with larger relative changes observed in polycrystalline films. In addition, low-loss epitaxial films were found to be thermally more stable at elevated temperatures. We demonstrate the importance of our findings for high temperature applications with a numerical simulation of field enhancement in a bow-tie nanoantenna, a near field transducer commonly used for heat-assisted magnetic recording. The simulated field profiles at elevated temperatures showed significant deviations compared to those at room temperature, clearly suggesting that the use of room temperature optical properties in modeling elevated temperature applications can be misleading due to the thermal deviations in the Ag dielectric function. We also provide causal analytical models describing the elevated temperature Ag dielectric functions.
Contextual AI - The Next Frontier Towards Human-Centric Artificial Intelligence (2019)

Presented on February 28, 2019 at 4:30 p.m. in the Clough Undergraduate Learning Commons, Room 152.
Nanoscale Structural and Chemical Segregation in Pt50Ru50 Electrocatalysts (2001)

Abstract To address how the chemical and structural heterogeneity of Pt50Ru50 nanoparticles affects methanol oxidation activity, we have employed an arsenal of transmission electron microscopy techniques (conventional bright field-imaging, selected area diffraction, atomic-resolution lattice imaging, electron-energy loss spectroscopy, and energy-dispersive x-ray spectroscopy) to characterize 2.5-nm particles in differing oxidation and hydration states. Our studies demonstrate that electrocatalysts containing a high fraction of Ru-rich hydrous oxide, as apposed to the anhydrous PtRu bimetallic alloy, have as much as 250x higher methanol oxidation activity The nominally 2.5-nm Pt50Ru50 particles were studied in as-received, reduced and reoxidized forms. The reducing treatment consisted of 2 h at 100 °C in flowing 10% PL/argon mixture. For re-oxidation, the reduced particles were heated for 20 h at 100 °C in an H2O-saturated oxygen atmosphere. The particles were suspended in methanol, and pipetted onto holey-carboncoated Cu grids for TEM studies.
Mildronate: An Antiischemic Drug for Neurological Indications (2005)

Mildronate (3-(2,2,2-trimethylhydrazinium)propionate; MET-88; meldonium, quaterine) is an antiischemic drug developed at the Latvian Institute of Organic Synthesis. Mildronate was designed to inhibit carnitine biosynthesis in order to prevent accumulation of cytotoxic intermediate products of fatty acid beta-oxidation in ischemic tissues and to block this highly oxygen-consuming process. Mildronate is efficient in the treatment of heart ischemia and its consequences. Extensive evaluation of pharmacological activities of mildronate revealed its beneficial effect on cerebral circulation disorders and central nervous system (CNS) functions. The drug is used in neurological clinics for the treatment of brain circulation disorders. It appears to improve patients' mood; they become more active, their motor dysfunction decreases, and asthenia, dizziness and nausea become less pronounced. Since the brain does not utilize fatty acids as fuel other mechanisms of action of mildronate in CNS should be considered. Several reports indicate the possible existence of an alternative, non-carnitine dependent mechanism of action of mildronate. Our recent findings suggest that CNS effects of mildronate could be mediated by stimulation of the nitric oxide production in the vascular endothelium by modification of the gamma-butyrobetaine and its esters pools. It is hypothesized that mildronate may increase the formation of the gamma-butyrobetaine esters. The latter are potent cholinomimetics and may activate eNOS via acetylcholine receptors or specific gamma-butyrobetaine ester receptors. This article summarizes known pharmacological effects of mildronate, its pharmacokinetics, toxicology, as well as the proposed mechanisms of action.
Linear Programming Models for Jamming Attacks on Network Traffic Flows (2008)

We present a new class of network attacks, referred to as flow-jamming attacks, in which an adversary with multiple jammers throughout the network jams packets to reduce traffic flow. We propose a linear programming framework for flowjamming attacks, providing a foundation for the design of future
Figure S10 from Inhibiting ERK5 Overcomes Breast Cancer Resistance to Anti-HER2 Therapy By Targeting the G<sub>1</sub>–S Cell-Cycle Transition (2023)

&lt;p&gt;Inhibition of ERK5 by AX-15836 or MEK5 by BIX-02189 enhance HER2+ breast cancer cell sensitivity to trastuzumab through decreasing RB phosphorylation.&lt;/p&gt;
Comparison of conductivity measured hematocrit to microhematocrit. (1992)

Two electrical conductivity methods of hematocrit (H) measurement, Coulter Counter (CCH) and lonometer (IH), were compared to the microhematocrit (MH) with two different anticoagulants, Li Heparin (Li) and EDTA. The results showed MH-Li is higher than MH-EDTA (mean difference 1.7 vol%). The IH-Li is 1.8 vol% higher than CC H-EDTA. These differences are attributed to osmotic shrinking of red cells by EDTA. The MH-Li and IH-Li correlate very closely (r = .992), and are considered to provide the truest hematocrit values.
Development and Evaluation of Quality Control Methods in a Microtask Crowdsourcing Platform (2014)

Open Crowdsourcing platforms like Amazon Mechanical Turk provide an attractive solution for process of high volume tasks with low costs. However problems of quality control is still of major interest. In this paper, we design a private crowdsourcing system, where we can devise methods for the quality control. For the quality control, we introduce four worker selection methods, each of which we call preprocessing filtering, real-time filtering, post processing filtering, and guess processing filtering. These methods include a novel approach, which utilizes a collaborative filtering technique in addition to a basic approach of initial training or gold standard data. For an use case, we have built a very large dictionary, which is necessary for Large Vocabulary Continuous Speech Recognition and Text-to-Speech. We show how the system yields high quality results for some difficult tasks of word extraction, part-of-speech tagging, and pronunciation prediction to build a large dictionary.
Sensitization of Europium(III) Luminescence by Benzophenone-Containing Ligands:  Regioisomers, Rearrangements and Chelate Ring Size, and Their Influence on Quantum Yields (2007)

A series of europium(III) complexes based on the macrocyclic azacarboxylate structure, DO3A, have been investigated, incorporating benzophenone appended at N10 of the macrocycle via linkers containing amide bonds (H3DO3A = 1,4,7,10-tetraazacyclododecane-1,4,7-tris-acetic acid). Complexes [EuL(1-3)] incorporate N10-CH2CONH-BP linkers (BP = benzophenone), which allow formation of a five-membered chelate ring containing the metal ion upon chelation of the amide oxygen; these three isomeric complexes differ from one another in the substitution position of the BP unit, namely para, meta, and ortho for L1, L2, and L3 respectively. The quantum yields of europium luminescence sensitized via the chromophore are found to be highly dependent upon the position of substitution, being 20 times smaller for the ortho compared to the para-substituted complex. A related para-substituted BP complex [EuL(4)], prepared by an unusual Michael reaction of the azamacrocycle with a BP-containing acrylamide, incorporates an additional methylene unit in the linker, namely N10-CH2CH2CONH-BP. Despite the longer linker, this complex equals the luminescence quantum yield achieved with [EuL(1)] (Phi(lum) = 0.097 and 0.095, respectively, in H2O at 298 K). Analysis of the pertinent kinetics reveals that the decreased energy transfer efficiency in this complex, arising from the longer donor-acceptor distance, is compensated by an increased radiative rate constant. Under basic conditions, the ortho-substituted complex [EuL(3)] undergoes an intramolecular rearrangement to generate an unprecedented complex [EuL(5)] incorporating a 4-phenyl-2-hydroxyquinoline unit directly bound to the ring nitrogen. Although this complex is a poor emitter, an analogous complex obtained from 2-amino-acetophenone, which generates 4-methyl-2-hydroxyquinoline during the corresponding rearrangement, is an order of magnitude more emissive while still benefiting from relatively long-wavelength absorption. The emission from this complex is pH sensitive, being dramatically quenched under mildly basic conditions.
Potassium currents in the heart: functional roles in repolarization, arrhythmia and therapeutics (2016)

This is the second of the two White Papers from the fourth UC Davis Cardiovascular Symposium Systems Approach to Understanding Cardiac Excitation-Contraction Coupling and Arrhythmias (3-4 March 2016), a biennial event that brings together leading experts in different fields of cardiovascular research. The theme of the 2016 symposium was 'K<sup>+</sup> channels and regulation', and the objectives of the conference were severalfold: (1) to identify current knowledge gaps; (2) to understand what may go wrong in the diseased heart and why; (3) to identify possible novel therapeutic targets; and (4) to further the development of systems biology approaches to decipher the molecular mechanisms and treatment of cardiac arrhythmias. The sessions of the Symposium focusing on the functional roles of the cardiac K<sup>+</sup> channel in health and disease, as well as K<sup>+</sup> channels as therapeutic targets, were contributed by Ye Chen-Izu, Gideon Koren, James Weiss, David Paterson, David Christini, Dobromir Dobrev, Jordi Heijman, Thomas O'Hara, Crystal Ripplinger, Zhilin Qu, Jamie Vandenberg, Colleen Clancy, Isabelle Deschenes, Leighton Izu, Tamas Banyasz, Andras Varro, Heike Wulff, Eleonora Grandi, Michael Sanguinetti, Donald Bers, Jeanne Nerbonne and Nipavan Chiamvimonvat as speakers and panel discussants. This article summarizes state-of-the-art knowledge and controversies on the functional roles of cardiac K<sup>+</sup> channels in normal and diseased heart. We endeavour to integrate current knowledge at multiple scales, from the single cell to the whole organ levels, and from both experimental and computational studies.
A theoretical study of resonant cavity-enhanced photodectectors with Ge and Si active regions (1992)

An integration of Ge or Si with compound semiconductors is considered for optical detectors at wavelengths ranging from the visible to 1.55 μm. Both Ge and Si are indirect band gap materials with relatively small absorption coefficients but very long carrier lifetimes. Using a resonant cavity formed by large band gap compound semiconductor mirrors surrounding Ge and Si active layers, high photosensitivity for thin (&amp;lt;0.5 μm) absorbing layers can be achieved. Two different methods are discussed and compared for the calculation of the photosensitivity of resonant cavity enhanced detectors. The standing wave effect and its dependence on cavity parameters are analyzed. Design rules for such resonant cavity enhanced photodetectors are presented. The spectral response of some device designs to achieve high quantum efficiency and wavelength selectivity has also been theoretically investigated.
Measurement Uncertainty Propagation in Transistor Model Parameters via Polynomial Chaos Expansion (2017)

We present an analysis of the propagation of measurement uncertainty in microwave transistor nonlinear models. As a case study, we focus on residual calibration uncertainty and its effect on modeled nonlinear capacitances extracted from small-signal microwave measurements. We evaluate the uncertainty by means of the polynomial chaos expansion (PCE) method and compare the results with the NIST Microwave Uncertainty Framework, which enables both sensitivity and Monte Carlo (MC) analyses for uncertainty quantification in microwave measurements. We demonstrate that, for the considered application, PCE provides results in agreement with classical MC simulations but with a significant reduction of the computational effort.
A novel solution for decoupling of two closely spaced antennas at low frequencies (2011)

In this paper, we present a novel technique to increase the isolation between two very closely spaced planar inverted F antennas (PIFA) on a common ground-plane. The proposed decoupling structure consists of thin wire (TW) array and two Z elements. For the proposed antenna at low band, the improved isolation between the antennas is from 3.1 dB (for the initial PIFA) to 10.8 dB. Further, the proposed technique has been proven to be efficient in the presence of the user.