gebhart/patrepeval huggingface dataset:
Regulation of mTORC1 and its impact on gene expression at a glance (2013)

The mechanistic (or mammalian) target of rapamycin (mTOR) is a kinase that regulates key cellular functions linked to the promotion of cell growth and metabolism. This kinase, which is part of two protein complexes termed mTOR complex 1 (mTORC1) and 2 (mTORC2), has a fundamental role in coordinating anabolic and catabolic processes in response to growth factors and nutrients. Of the two mTOR complexes, mTORC1 is by far the best characterized. When active, mTORC1 triggers cell growth and proliferation by promoting protein synthesis, lipid biogenesis, and metabolism, and by reducing autophagy. The fact that mTORC1 deregulation is associated with several human diseases, such as type 2 diabetes, cancer, obesity and neurodegeneration, highlights its importance in the maintenance of cellular homeostasis. Over the last years, several groups observed that mTORC1 inhibition, in addition to reducing protein synthesis, deeply affects gene transcription. Here, we review the connections between mTORC1 and gene transcription by focusing on its impact in regulating the activation of specific transcription factors including including STAT3, SREBPs, PPARγ, PPARα, HIF1α, YY1–PGC1α and TFEB. We also discuss the importance of these transcription factors in mediating the effects of mTORC1 on various cellular processes in physiological and pathological contexts.
On conditions for uniqueness in sparse phase retrieval (2014)

The phase retrieval problem has a long history and is an important problem in many areas of optics. Theoretical understanding of phase retrieval is still limited and fundamental questions such as uniqueness and stability of the recovered solution are not yet fully understood. This paper provides several additions to the theoretical understanding of sparse phase retrieval. In particular we show that if the measurement ensemble can be chosen freely, as few as 4k - 1 phaseless measurements suffice to guarantee uniqueness of a k-sparse M-dimensional real solution. We also prove that 2(k <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sup> - k + 1) Fourier magnitude measurements are sufficient under rather general conditions.
Fabrication of Ultrasmall Silicon Waveguide Lenses Designed by Wavefront-Matching Method (2019)

We design and fabricate ultrasmall silicon waveguide lenses designed by a wavefront-matching (WFM) method by a standard CMOS process. It is experimentally demonstrated that a low-loss several micron free-space light propagation is possible by using the waveguide lens designed by the WFM method.
Controlled Growth of Ordered Nanopore Arrays in GaN (2010)

High-quality, ordered nanopores in semiconductors are attractive for numerous biological, electrical, and optical applications. Here, GaN nanorods with continuous pores running axially through their centers were grown by organometallic vapor phase epitaxy. The porous nanorods nucleate on an underlying (0001)-oriented GaN film through openings in a SiN(x) template that are milled by a focused ion beam, allowing direct placement of porous nanorods. Nanopores with diameters ranging from 20-155 nm were synthesized with crystalline sidewalls.
Nano-Biomechanical Study of Spatio-Temporal Cytoskeleton Rearrangements that Determine Subcellular Mechanical Properties and Endothelial Permeability (2015)

The endothelial cell (EC) lining of the pulmonary vascular system forms a semipermeable barrier between blood and the interstitium and regulates various critical biochemical functions. Collectively, it represents a prototypical biomechanical system, where the complex hierarchical architecture, from the molecular scale to the cellular and tissue level, has an intimate and intricate relationship with its biological functions. We investigated the mechanical properties of human pulmonary artery endothelial cells (ECs) using atomic force microscopy (AFM). Concurrently, the wider distribution and finer details of the cytoskeletal nano-structure were examined using fluorescence microscopy (FM) and scanning transmission electron microscopy (STEM), respectively. These correlative measurements were conducted in response to the EC barrier-disrupting agent, thrombin, and barrier-enhancing agent, sphingosine 1-phosphate (S1P). Our new findings and analysis directly link the spatio-temporal complexities of cell re-modeling and cytoskeletal mechanical properties alteration. This work provides novel insights into the biomechanical function of the endothelial barrier and suggests similar opportunities for understanding the form-function relationship in other biomechanical subsystems.
Tuning the hole injection barrier height at organic/metal interfaces with (sub-) monolayers of electron acceptor molecules (2005)

We demonstrate that the insertion of an electron acceptor molecular (sub-) monolayer at organic/metal interfaces enables systematic tuning of the hole injection barrier height (Δh). Ultraviolet photoemission spectroscopy results show that Δh for α-sexithiophene thin films deposited on Ag(111) can be reduced from 1.3to1.0eV by introducing a chemisorbed monolayer of 11,11,12,12-tetracyano-9,10-anthraquinodimethane (TCAQ) on the metal surface. Fine-tuning of Δh within the interval of 0.3eV is achieved by using TCAQ coverages in the submonolayer range.
Practical amino acid-catalyzed asymmetric synthesis pf protected α-hydroxy-amino aldehydes and acids (2010)

Practical amino acid-catalyzed asymmetric synthesis pf protected α-hydroxy-amino aldehydes and acids
High sensitive magnetic sensor using symmetric response GMR (2021)

High-sensitive magnetoresistance (MR) sensors have attracted much attention as an Internet of Things sensor. To improve the sensitivity, a new high-sensitive magnetic sensor which is referred to a symmetric response magnetoresistance (SRMR) sensor is proposed. This sensor uses giant magnetoresistance (GMR) elements which have symmetric field response. An ac magnetic field with frequency f is applied to the GMR elements in order to modulate a small detecting magnetic field. Due to the symmetric response of the MR element, a carrier signal of the ac magnetic field is converted to 2 f and the detecting signal is converted to f. By using a full bridge circuit, where two pairs of GMR elements have opposite phase of the applied ac field, the 2 f components can be eliminated at the differential output terminal of the bridge. Since this system converts the frequency range of the detecting magnetic field to higher one, its noise level, which is dominated by the 1/ f noise, can be decreased. The effect of noise reduction and carrier signal suppression were confirmed by a circuit simulation. Moreover, the SRMR sensor with the antiphase ac modulation bridge was fabricated. It was confirmed that the detectivity of the magnetic field was obtained around 75 pT at 60 Hz. Improvement of the noise reduction and the magnetic field concentrator system, a perspective of the sensitivity less than picotesla might be possible.
Preliminary studies into the direct interfacing of a microreactor to a gas chromatographic instrument (2001)

The paper reports on a preliminary study into the coupling of a microreactor to a GC-FID, using a standard GC needle as the interface between the microreactor and the injection port of a conventional GC. Using the injection needle as the ground electrode, electroosmotic flow was used to control the injection of reagent/sample into the GC. Photolithographic and wet etching techniques were used to fabricate the microreactor (channels 200 microns id, 100 microns deep) in a borosilicate glass substrate. The results of the effects of voltage and injection times on the response signal are presented. The critical obstacles to overcome were the backpressure posed by the carrier gas disrupting the liquid flow in the channels and reservoirs of the microreactor and the need to thermally insulate the microreactor, to prevent evaporation of solvent and reagents from the device.
Intrahepatic Markers of Hepatitis Delta Virus Infection: A Study By In Situ Hybridization (1989)

The intrahepatic distribution of hepatitis delta virus RNA was studied by in situ hybridization in 33 formalin-fixed, paraffin-embedded biopsies from 17 chronic hepatitis B virus carriers superinfected with hepatitis delta virus. The findings were correlated with the expression of the hepatitis delta antigen, the duration of the hepatitis delta virus infection and the eosinophilic degeneration of the hepatocytes. Intranuclear hepatitis delta virus RNA and antigen were found in 28 specimens, whereas the remaining five were negative for both markers. Hepatitis delta virus RNA and antigen were mostly found within the same cell. In 20 specimens, however, a variable number of hepatocytes showed the presence of hepatitis delta virus RNA alone. The percentage of these over the total number of infected cells was higher in the specimens taken within 1 year from the acute delta hepatitis, whereas their absence was invariably associated with a long-established hepatitis delta virus infection. Interestingly, the vast majority of hepatocytes undergoing eosinophilic degeneration, a change significantly associated with hepatitis delta virus infection, did not show the presence of either hepatitis delta virus RNA or the viral antigen, suggesting a lack of association, at the cellular level, between viral replication and cytopathological change. The specificity of the detection of hepatitis delta virus RNA was confirmed by negative findings in nine specimens from seven chronic hepatitis B virus carriers without evidence of past or current hepatitis delta virus infection. The loss in sensitivity due to the formalin fixation was estimated to be 50% of that obtained in frozen biopsies, as determined by counting autoradiographic grains over infected cells.(ABSTRACT TRUNCATED AT 250 WORDS)
An Evaluation of Automated Electric Transportation Deployment Strategies: Discreet vs. Organic (2011)

This paper proposes a deployment path for automated vehicles, arguing for an evolutionary process of discreet deployment where fully functioning systems are developed from the ground up in areas with the greatest opportunity and expand to become interconnected. This is an alternative to the organic deployment strategies developed during work on the Automated Highway Systems (AHS) program, whereby the technology progresses over time from manual driving to full automation. This paper compares the two approaches, arguing that organic deployment is fundamentally hampered by institutional hurdles and the difficulty of encouraging the large-scale adoption necessary to achieve the most significant benefits of automation, including increased lane capacity and vehicle speed. Discrete deployment is an especially attractive scenario for Automated Electric Transportation (AET), and different communities could develop different forms of AET, varying vehicle and service types to suit its particular needs.
Designing a vision-based mobile interface for in-store shopping (2008)

Due to the situated nature of mobile applications, designing them requires more emphasis on users' cognitive load and interaction style. Considering that users can only devote limited and fragmented attention to mobile interface when moving between locations, what interaction-styles and services are appropriate to a specific user scenario? To explore this issue for in-store shopping, we designed a vision-based mobile interface for supporting shopper's communicational and organizational requirements on-the-go. With this interface, the physical objects can be automatically recognized by the camera phone in real time, so that shoppers can easily access related internet services. In this paper, we present an ethnographic study from which the design rationale is generated, and a formative evaluation to understand how mobile visual interface can be used in the field. The issues uncovered and lessons learned are applicable to our design improvement. Moreover, we use this to motivate the discussion on vision-based mobile interfaces in general, including embodied interaction and alternate interfaces.
LOX/Methane Engine Utilizing Liquid/Liquid Co-axial Swirl Injector (2011)

The propellant combination of liquid methane and liquid oxygen has been the focus of many research and design programs in the past few years. This paper focuses on the investigation of an increase in performance of a liquid oxygen (LOX) / liquid methane (LCH4) engine through the use of a liquid/liquid co-axial swirl injector. This injection scheme is an unlike impinging type which uses concentric injection orifices that inject both propellants in the liquid phase and with a designed angular momentum. This creates a swirling cone of each propellant which will then impinge together. The engine developed uses multiple injection elements of this type to generate 2200 N (495 lbf) of thrust. To investigate the performance of the engine, the engine is scheduled to be hot fire tested early next summer. The data collected will then be compared to a reference engine that has a configuration which is extremely similar except for the injection method. This will allow for the quantification of the change in performance of the engine caused by the injection method. Future uses of this engine include a potential flight test in the fall of 2010. The same team that is developing the engine is also part of a CSULB project to design and manufacturing a high performance light weight rocket which is base lined to use this engine.
Cutaneous immunosurveillance by self-renewing dermal γδ T cells (2011)

The presence of γδ T cell receptor (TCR)-expressing cells in the epidermis of mice, termed dendritic epidermal T cells (DETCs), is well established. Because of their strict epidermal localization, it is likely that DETCs primarily respond to epithelial stress, such as infections or the presence of transformed cells, whereas they may not participate directly in dermal immune responses. In this study, we describe a prominent population of resident dermal γδ T cells, which differ from DETCs in TCR usage, phenotype, and migratory behavior. Dermal γδ T cells are radioresistant, cycle in situ, and are partially depend on interleukin (IL)-7, but not IL-15, for their development and survival. During mycobacterial infection, dermal γδ T cells are the predominant dermal cells that produce IL-17. Absence of dermal γδ T cells is associated with decreased expansion in skin draining lymph nodes of CD4(+) T cells specific for an immunodominant Mycobacterium tuberculosis epitope. Decreased CD4(+) T cell expansion is related to a reduction in neutrophil recruitment to the skin and decreased BCG shuttling to draining lymph nodes. Thus, dermal γδ T cells are an important part of the resident cutaneous immunosurveillance program. Our data demonstrate functional specialization of T cells in distinct microcompartments of the skin.
Low-threshold photonic crystal laser (2003)

We have fabricated planar photonic crystal nanocavity lasers, based on our new high-quality factor design that incorporates fractional edge dislocations in triangular lattice photonic crystal cavities. Lasers with InGaAsP quantum well active material emitting at 1550nm were optically pumped with 10ns pulses, and lase at room temperature at threshold pumping powers below 220 microWatt. We have attributed this to the small mode volume and the high Q factors inherent to our device design. We have performed detailed numerical analysis of our structures, and have found an excellent agreement between theoretical predictions and experimental results. The optical field of the lasing mode in our nano-laser is localized in the air-hole region and therefore the laser can be used to investigate interaction between light and matter introduced in the cavity and nanospectroscopy.
LaAlO3/SrTiO3-based device concepts (2012)

Abstract This chapter discusses a variety of device concepts that are based on the conductive interface between LaAlO3 and SrTiO3. The interface between these two insulating oxides spontaneously forms a high mobility, two dimensional electron gas when the LaAlO3 thickness exceeds a critical value. At the critical thickness, the insulator-metal transition can be reversibly controlled using externally applied fields, and furthermore can be defined on the extreme nanoscale using a conducting AFM probe. After an initial discussion of macroscopic field effects at this interface, the chapter describes the use of conducting AFM lithography to fabricate nanoscale devices. Nanoscale wires, diodes, transistors, and photodetectors can be created, modified, and erased. Possible future integration with silicon-based electronics is discussed, along with possible applications in the fields of spintronics, quantum information processing, and quantum simulation.
Linkage of the late onset autosomal dominant familial spastic paraplegia (DFSPII) to chromosome 2p markers (1994)

Pure familial spastic paraplegias (FSP) is a neurodegenerative disease characterized by spasticity of lower limbs. FSP in inherited as an autosomal dominant (DFSP) or an autosomal recessive (RFSP) trait. DFSP has been classified into early onset (DFSPI) and late onset (DFSPII) based on the mean age of onset in families. A locus for RFSP has been mapped to chromosome 8, while a locus for DFSPI has been mapped to chromosome 14q. Genetic locus heterogeneity was observed in both of these forms. The location of DFSPII locus (or loci) is unknown. We collected DNA samples from 81 individuals including 26 affecteds from three DFSPII families (9998, 840, 581). The mean age of onset of systems was 26.5, 42.5, and 35.2 years, respectively. We first tested 156 DNA markers distributed throughout the human 22 autosomes with family 9998 and positive lod scores were obtained with chromosome 2p markers D2S174 (Z({theta})=2.93 at {theta}=0.00), D2S146 (Z({theta})=1.03 at {theta}=0.00) and D2S177 (Z({theta})=1.04 at {theta}=0.00). Analysis of the 2 additional families confirmed the linkage with a peak lod score of Z({theta})=4.62 at {theta}=0.105 with D2S174. The multipoint linkage analysis using the map D2S175-10cM-D2S174-14cM-D2DS177 suggested that the DFSPII locus most likely maps between D2S174 and D2S177 withmore » Z({theta})=6.11. There was no evidence in our data supporting genetic locus heterogeneity for the DFSPII.« less
Heart RateVariability Analysis of Effect of Nicotine using Lomb-Welch Periodograms (2004)

Heart rate variability (HRV) is frequently used to measure autonomic nervous system (ANS) activity. However, little is known about the mechanism underlying pharmacologically induced changes in HRV. Previous research has shown that nicotine exposure stimulates the ANS, mediating a wide spectrum of physiological and behavioral effects, including altered respiratory sinus arrhythmia and enhanced arousal and attention. Using Lomb-Welch periodograms, the effect of nicotine on the ANS in 14 nicotine- naive human subjects are studied. Results showed an increase in the low frequency (LF) to high frequency (HF) ratio with little change in mean heart rate. Results suggest that nicotine affects both sympathetic and parasympathetic reactivities and that the LF/HF best characterizes early ANS activated nicotine changes in HRV. The Lomb-Welch periodogram of the HRV is also compared to the conventional interpolated Welch periodogram. The attenuation of the high frequency components due to interpolation of the non-uniform R-R intervals is found to be a function of the power of the high frequency components, increasing with increasing power. Thus analyses using Welch periodograms that make use of the high frequency components may yield erroneous results.
Declarative failure recovery for sensor networks (2007)

Wireless sensor networks consist of a system of distributed sensors embedded in the physical world, and promise to allow observation of previously unobservable phenomena. Since they are exposed to unpredictable environments, sensor-network applications must handle a wide variety of faults: software errors, node and link failures, and network partitions. The code to manually detect and recover from faults crosscuts the entire application, is tedious to implement correctly and efficiently, and is fragile in the face of program modifications. We investigate language support for modularly managing faults. Our insight is that such support can be naturally provided as an extension to existing "macroprogramming" systems for sensor networks. In such a system, a programmer describes a sensor network application as a centralized program; a compiler then produces equivalent node-level programs. We describe a simple checkpoint API for macroprograms, which can be automatically implemented in a distributed fashion across the network. We also describe declarative annotations that allow programmers to specify checkpointing strategies at a higher level of abstraction. We have implemented our approach in the Kairos macroprogramming system. Experiments show it to improve application availability by an order of magnitude and incur low messaging overhead.
Mixed plate bending elements based on least‐squares formulation (2004)

Abstract A finite element formulation for the bending of thin and thick plates based on least‐squares variational principles is presented. Finite element models for both the classical plate theory and the first‐order shear deformation plate theory (also known as the Kirchhoff and Mindlin plate theories, respectively) are considered. High‐order nodal expansions are used to construct the discrete finite element model based on the least‐squares formulation. Exponentially fast decay of the least‐squares functional, which is constructed using the L 2 norms of the equations residuals, is verified for increasing order of the nodal expansions. Numerical examples for the bending of circular, rectangular and skew plates with various boundary conditions and plate thickness are presented to demonstrate the predictive capability and robustness of the new plate bending elements. Plate bending elements based on this formulation are shown to be insensitive to both shear‐locking and geometric distortions. Copyright © 2004 John Wiley &amp; Sons, Ltd.
Activating STING1-dependent immune signaling inTP53mutant and wild-type acute myeloid leukemia (2022)

DNA methyltransferase inhibitors (DNMTis) reexpress hypermethylated genes in cancers and leukemias and also activate endogenous retroviruses (ERVs), leading to interferon (IFN) signaling, in a process known as viral mimicry. In the present study we show that in the subset of acute myeloid leukemias (AMLs) with mutations in <i>TP53</i>, associated with poor prognosis, DNMTis, important drugs for treatment of AML, enable expression of ERVs and IFN and inflammasome signaling in a STING-dependent manner. We previously reported that in solid tumors poly ADP ribose polymerase inhibitors (PARPis) combined with DNMTis to induce an IFN/inflammasome response that is dependent on STING1 and is mechanistically linked to generation of a homologous recombination defect (HRD). We now show that STING1 activity is actually increased in <i>TP53</i> mutant compared with wild-type (WT) <i>TP53</i> AML. Moreover, in <i>TP53</i> mutant AML, STING1-dependent IFN/inflammatory signaling is increased by DNMTi treatment, whereas in AMLs with WT <i>TP53</i>, DNMTis alone have no effect. While combining DNMTis with PARPis increases IFN/inflammatory gene expression in WT <i>TP53</i> AML cells, signaling induced in <i>TP53</i> mutant AML is still several-fold higher. Notably, induction of HRD in both <i>TP53</i> mutant and WT AMLs follows the pattern of STING1-dependent IFN and inflammatory signaling that we have observed with drug treatments. These findings increase our understanding of the mechanisms that underlie DNMTi + PARPi treatment, and also DNMTi combinations with immune therapies, suggesting a personalized approach that statifies by <i>TP53</i> status, for use of such therapies, including potential immune activation of STING1 in AML and other cancers.