gebhart/patrepeval huggingface dataset:
Distinct RNA degradation pathways and 3' extensions of yeast non-coding RNA species (2011)

Non-coding transcripts originating from bidirectional promoters have been reported in a wide range of organisms. In yeast, these divergent transcripts can be subdivided into two classes. Some are designated Cryptic Unstable Transcripts (CUTs) because they are terminated by the Nrd1-Nab3-Sen1 pathway and then rapidly degraded by the nuclear exosome. This is the same processing pathway used by yeast snoRNAs. Whereas CUTs are only easily observed in cells lacking the Rrp6 or Rrp47 subunits of the nuclear exosome, Stable Uncharacterized Transcripts (SUTs) are present even in wild-type cells. Here we show that SUTs are partially susceptible to the nuclear exosome, but are primarily degraded by cytoplasmic 5' to 3' degradation and nonsense-mediated decay (NMD). Therefore, SUTs may be processed similarly to mRNAs. Surprisingly, both CUTs and SUTs were found to produce 3' extended species that were also subject to cytoplasmic degradation. The functions, if any, of these extended CUTs and SUTs are unknown, but their discovery suggests that yeasts generate transcripts reminiscent of long non-coding RNAs found in higher eukaryotes.
Distributed control in adaptive optics: deformable mirror and turbulence modeling (2006)

Future large optical telescopes require adaptive optics (AO) systems whose deformable mirrors (DM) have ever more degrees of freedom. This paper describes advances that are made in a project aimed to design a new AO system that is extendible to meet tomorrow's specifications. Advances on the mechanical design are reported in a companion paper [6272-75], whereas this paper discusses the controller design aspects. The numerical complexity of controller designs often used for AO scales with the fourth power in the diameter of the telescope's primary mirror. For future large telescopes this will undoubtedly become a critical aspect. This paper demonstrates the feasibility of solving this issue with a distributed controller design. A distributed framework will be introduced in which each actuator has a separate processor that can communicate with a few direct neighbors. First, the DM will be modeled and shown to be compatible with the framework. Then, adaptive turbulence models that fit the framework will be shown to adequately capture the spatio-temporal behavior of the atmospheric disturbance, constituting a first step towards a distributed optimal control. Finally, the wavefront reconstruction step is fitted into the distributed framework such that the computational complexity for each processor increases only linearly with the telescope diameter.
Efficiency Improvement of GaN-Based LEDs With a $ \hbox{SiO}_{2}$ Nanorod Array and a Patterned Sapphire Substrate (2010)

The enhancement of light extraction from GaN-based light-emitting diodes (LEDs) with a patterned sapphire substrate (PSS) and a SiO <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sub> 12-fold photonic quasi-crystal (PQC) structure using nanoimprint lithography is presented. At a driving current of 20 mA on transistor-outline-can package, the light output powers of LED with a PSS and LED with a PSS and a SiO <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sub> PQC structure are enhanced by 35% and 48%, compared with the conventional LED. In addition, the higher output power of the LED with a PSS and a SiO <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sub> PQC structure is due to better reflectance on PSS and higher epitaxial quality on an n-GaN using a SiO <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sub> 12-fold PQC structure pattern. These results provide promising potential to increase output powers of commercial light-emitting devices.
Electron irradiation damage and sputtering from oxidized silicon particles supported on amorphous carbon (1991)

Abstract It is found that electron irradiation, in an electron microscope, of oxidized silicon small particles (nanometers to microns in size) supported on amorphous carbon films, produce extensive surface damage of the oxide layer. During irradiation, the sputtering of the entire thickness (many nanometers) of the silica layer was observed except for a thin (∽ 1 nm) uniform layer which remained stable to further irradiation. The sputtered silica came off and deposited on the nearby carbon film, and was identified using electron energy loss spectroscopy. The carbon film surrounding the particles was seen to damage drastically during irradiation. The damage of the oxide layer seems to be catalyzed by the carbon film at the SiO2/C interface since the rate of removal of the oxide layer decreases as the supporting carbon film disintegrates and is much slower for particles that are not supported.
Pressure-induced polyamorphism in a main-group metallic glass (2016)

The mechanism of pressure-induced amorphous-to-amorphous transitions (AATs) in metallic glasses (MGs) has been a subject of intense research. Most AATs in MGs were found in lanthanide-based alloys and shown to originate from $4f$ orbital delocalization. Recently, evidence of an unexpected AAT in the main-group Ca-Al MGs was reported without a satisfactory explanation. Here, based on the results of first-principles molecular dynamics calculations, the suggested AAT at 12--15 GPa in the $\mathrm{C}{\mathrm{a}}_{72.7}\mathrm{A}{\mathrm{l}}_{27.3}$ MG is confirmed. Contrary to the common belief that the coordinate of metallic glasses with close packing cannot be increased further, the coordination around Al atoms is found to increase suddenly at the transition as a consequence of atomic migration and the aggregation of Al atoms. This transition originates from pressure-enhanced bonding between Ca $3d$ and Al $3p$ orbitals and is confirmed by the good agreement on the predicted and measured electrical conductivities. The theoretical analysis not only uncovers a mechanism of pressure-induced AAT in main-group MGs, but it can be generalized to establish a different perspective to guide the understanding of transformation phenomena in compressed MGs.
The Influence of UV Irradiation on Ketonic Defect Emission in Fluorene‐Based Copolymers (2008)

Abstract The influence of UV irradiation in inert atmosphere on the emission spectrum of fluorenone containing poly[9,9‐bis(2‐ethyl)hexylfluorene] (PF2/6) has been investigated by means of optical absorption, photoluminescence (PL) and Fourier transform infrared (FTIR) spectroscopy. It is shown that a substantial reduction of green emission arising from ketonic defect sites can be achieved by irradiation of thin films with UV light. This is found to be accompanied by partial cross‐linking of the films. FTIR measurements show no reduction of the C=O stretching mode upon irradiation, and, moreover, the degree of cross‐linking does not scale with the relative fluorenone content (0.1, 0.5, and 5%). Therefore, the reduced emission intensity in the green spectral region is rather associated with the occurrence of interruptions in the polymer backbone, which reduce the effective conjugation length and subsequently inhibit the energy transfer onto the ketonic defect sites. The found results enabled us to build organic light emitting devices (OLEDs) that can be structured by selective illumination of the emitting layer with an intense UV light source. This method allows for the fabrication of rather efficient (2000 cd m −2 at 7 V) two‐color OLEDs.
PORTABLE ENERGY-DISPERSIVE X-RAY FLUORESCENCE INTEGRATES MINERALOGY AND CHEMOSTRATIGRAPHY INTO REAL-TIME FORMATION EVALUATION (2011)

Our objective is to unlock the wealth of information contained in drill cuttings in real-time for complementing petrophysical characterization while drilling. The approach is to integrate the direct measurement from drill cuttings with Logging While Drilling (LWD) data to support drilling, geosteering and formation evaluation. In this framework, an accurate mineralogical and lithological characterization of drill cuttings is a key issue. Visual determination of mineralogy via microscopy often substantially varies between analysts, e.g., various mud-logging personnel at the wellsite and geologists in the office. Further, modern polycrystalline diamond compact (PDC) bits may produce paste or powder, rather than regular drill cuttings, and may be unsuitable for visual/microscopic determination of mineralogy and lithology. A way to tackle the above challenge is to perform a geochemical elemental analysis, by means of Energy-Dispersive X-Ray Fluorescence (ED-XRF). A reliable, portable ED-XRF instrument, robust enough for rig site employment is routinely used for a wellsite chemostratigraphy service. The instrument produces accurate elemental data, which can, in addition to its chemostratigraphic applications, be used for mineral and lithology modeling. A methodology has been developed to convert the elemental analysis into a mineralogical composition of the rock sample that is comparable to measurements from full scale X-Ray Diffraction (XRD) laboratory equipment. An experimental setup was deployed to assess the ability of modeling mineralogy from geochemical analysis (wellsite ED-XRF) of a set of rock samples in a blind test (Marsala et al., 2011). The analytical results were compared to results obtained from the same samples through state-of-the-art laboratory ED-XRF and wave-length dispersive XRF (WD-XRF) instruments. The geochemical data from the wellsite and the two lab-based instruments show good agreement. Finally, the modeled mineral compositions from whole-rock geochemical data were compared with the mineralogy determined from XRD analysis and showed good agreement. Modeled mineralogy from whole-rock geochemical data has been utilized in a wide range of applications ranging from mineralogy and lithology, to brittleness index determination for frac design in shale gas reservoirs.
Supplementary Figure and Table from iPSC-Derived Neoantigen-Specific CTL Therapy for Ewing Sarcoma (2023)

&lt;p&gt;Supplementary Figure 1 with legend and Supplementary Table 1&lt;/p&gt;
Modeling of Field Dependent Maxwell-Wagner Interfacial Capacitance for Bilayer Metal-Insulator-Metal (MIM) Capacitors (2018)

In this letter, we have presented the modeling of field dependent Maxwell-Wagner interfacial capacitance for bilayer Metal-Insulator-Metal (MIM) capacitors. The model was verified with measured capacitance–voltage characteristics of fabricated bilayer Al 2 O 3 /TiO 2 MIM capacitors. The model reveals the origin of voltage linearity of MIM capacitors at low frequencies (&lt;10 kHz). The proposed model for bilayer/multilayer MIM capacitors is very useful tool to design circuits for mixed signal, analog and digital circuits with low variation of capacitance for change in voltage.
Computergestützte Visualisierung digitaler Mammogramme (1999)

Computer-assisted visualization and interpretation of digital mammography images using a dedicated workstation can be performed with sufficiently high diagnostic accuracy.
Feed-Forward Networks with Attention Can Solve Some Long-Term Memory Problems (2015)

We propose a simplified model of attention which is applicable to feed-forward neural networks and demonstrate that the resulting model can solve the synthetic "addition" and "multiplication" long-term memory problems for sequence lengths which are both longer and more widely varying than the best published results for these tasks.
Impact of the Backgate on the Performance of SOI UTBB nMOSFETs at Cryogenic Temperatures (2021)

In this paper we present an experimental investigation on SOI UTBB n-MOSFETs at cryogenic temperatures. The device has a silicide source/drain with dopant segregation formed by "Implantation Into Silicide" (IIS) process. The controllability of the back-gate (V <inf xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">back</inf> ) on the device performance is characterized, showing that Vback is essential to tune the threshold voltage Vth and improve the subthreshold swing SS, Drain-Induced Barrier Lowering DIBL and mobility at cryogenic temperatures. The cryogenic effect on V <inf xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">th</inf> , SS and DIBL with different V <inf xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">back</inf> is also studied. Furthermore, using the V <inf xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">back</inf> and quantization effect at cryogenic temperature, we can optimize the SS to a lower value, providing a potential way to get ideal value of SS at cryogenic temperature.
Detection of mouse IL-8 receptor homologue expression on peripheral blood leukocytes and mature myeloid lineage cells in bone marrow (1996)

Interleukin-8 (IL-8) exhibits activities on bone marrow progenitor cells such as regulation of their growth and their mobilization into peripheral blood. In order to clarify the molecular mechanism of the effects of IL-8 on mouse bone marrow cells, we examined the cellular distribution of mouse IL-8 receptor homologue by an immunofluorescence analysis. Peripheral blood Gr-1+ mature granulocytes, and a substantial portion of NK1.1+ natural killer cells in peripheral blood and spleen were stained positively with anti-mouse IL-8 receptor homologue antibody, whereas CD4+, CD8+, or B220+ lymphocytes in peripheral blood and spleen, and thymocytes were not. Moreover, a small portion of ER-MP20+ monocytes in peripheral blood but neither peritoneal resident nor bone marrow macrophages were stained with anti-IL-8 receptor homologue antibody. In bone marrow, mature granulocytes and to a lesser degree, metamyelocytes and myelocytes expressed IL-8 receptor homologue. Moreover, lineage marker (Lin)-c-kit+ bone marrow progenitor cells started to express IL-8 receptor homologue only 5 days after in vitro culture with IL-3 and stem cell factor when metamyelocytes and myelocytes appeared. These results indicated that myeloid lineage cells express a substantial number of IL-8 receptor homologues only at the stage of myelocytes.
Active Plasma Loading of HPM Devices (2009)

This chapter contains sections titled: Introduction Overview of Earlier Results Recent Advances in Plasma-Filled HPM Sources Summary and Open Issues Acknowledgments This chapter contains sections titled: References 
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Abstract 11912: Glycocalyx Shedding is Markedly Increased During Acute Phase of Takotsubo Cardiomyopathy (2016)

Introduction: Acute myocardial infarction (AMI) and other forms of myocardial acute oxidative stress are associated with variable “shedding” of vascular and other glycocalyx. This glycocalyx shedding (GCS) can be quantitated by release into plasma of glycocalyx components such as Syndecan-1 (SD1), which is the most prevalent proteoglycan. Previous in vitro studies have implicated both catecholamines and BNP release as potential accentuating factors in GCS: since these are prominent aspects of the pathogenesis of Takotsubo cardiomyopathy (TTC), we hypothesised that TTC (i) would be associated with increased GCS both acutely and during subsequent 3 months of continued myocardial inflammation and (ii) extent of GCS would be predictable on the basis of NT-proBNP and catecholamine releases. Methods: SD1 concentrations were measured in 49 TTC patients acutely and after 3 months in comparison with 12 normal age-matched controls and 10 myocardial infarct patients. Correlations between SD1 and (i) acute LV function, (ii) lowest BP on admission, (iii) peak catecholamine release, and (iv) extent of systemic and myocardial inflammatory activation [measured by high sensitive C-reactive protein (hsCRP), NT-proBNP concentrations, and myocardial T2 signal intensity on cardiac MRI] were sought. Results: Acute SD1 concentrations in TTC patients were significantly elevated compared to 3 month and control values (2-way ANOVA) (Figure). However, there was no significant difference between acute TTC and MI levels. In addition, there were no correlations between SD1 concentrations and extent of severity of acute episode. Conclusions: 1. TTC, despite minimal associated myocardial necrosis, is associated with marked increase in GCS. 2. Extent of GCS in TTC is not closely related to either release of NT-proBNP or normetanephrine. We postulate that GCS may contribute to some of the clinical features of TTC, such as development of pulmonary oedema without marked increases in PCWP.
Nonlinear Plasma Dynamics at High Intensity Laser Interaction (1980)

Some aspects of progress in laser fusion are briefly reviewed which indicate that experiments are on the threshold of entering a regime where nonlinear dynamics will become important. Recent studies of the general nonlinear force that include additional nonponderomotive terms are reviewed. Computer calculations that provide a detailed knowledge of the transfer of optical energy into a plasma corona by nonlinear forces are then described. Two key regimes are observed: 1) early production of fast moving cold blocks of plasma followed by 2) a decay of the corona where the plasma velocity obeys a Kortweg-de-Vries equation. This soliton decay corresponds to a fast thermalization of laser radiation in the corona at perpendicular incidence, i.e., without asymmetries of laser incidence as in the case of resonance absorption or striated motion. This permits a short pulse high intensity irradiation to achieve conditions equivalent to an ideal gasdynamic ablation compression.
Inhibition of the neuromuscular acetylcholine receptor with atracurium activates FOXO/DAF‐16‐induced longevity (2021)

Abstract Transcriptome‐based drug screening is emerging as a powerful tool to identify geroprotective compounds to intervene in age‐related disease. We hypothesized that, by mimicking the transcriptional signature of the highly conserved longevity intervention of FOXO3 ( daf ‐ 16 in worms) overexpression, we could identify and repurpose compounds with similar downstream effects to increase longevity. Our in silico screen, utilizing the LINCS transcriptome database of genetic and compound interventions, identified several FDA‐approved compounds that activate FOXO downstream targets in mammalian cells. These included the neuromuscular blocker atracurium, which also robustly extends both lifespan and healthspan in Caenorhabditis elegans . This longevity is dependent on both daf ‐ 16 signaling and inhibition of the neuromuscular acetylcholine receptor subunit unc ‐ 38 . We found unc ‐ 38 RNAi to improve healthspan, lifespan, and stimulate DAF‐16 nuclear localization, similar to atracurium treatment. Finally, using RNA‐seq transcriptomics, we identify atracurium activation of DAF‐16 downstream effectors. Together, these data demonstrate the capacity to mimic genetic lifespan interventions with drugs, and in doing so, reveal that the neuromuscular acetylcholine receptor regulates the highly conserved FOXO/DAF‐16 longevity pathway.
High-density magneto-optical recording using a blue laser and CAD-MSR media (2000)

We have investigated high density magneto-optical recording on a center aperture detection (CAD) type of magnetically induced super resolution (MSR) disk using a GaN blue laser diode. The substrate treatment by an ultraviolet rays irradiation, the optimum thermal structure, and the stabilization of copy process by tripled layer recording films were applied to improve the CAD-MSR media for a blue laser. The carrier to noise ratio of 0.227 micrometers mark length was 43 dB and the jitter without cross-talk from adjacent tracks was 10.3% at the areal density of 10.8 Gbit/in<SUP>2</SUP>. We confirmed that a blue laser is the most promising method in order to realize the higher areal density for CAD-MSR disk.
Diffusion‐Mediated Growth and Size‐Dependent Nanoparticle Reactivity during Ruthenium Atomic Layer Deposition on Dielectric Substrates (2018)

Abstract Understanding the growth mechanisms during the early stages of atomic layer deposition (ALD) is of interest for several applications including thin film deposition, catalysis, and area‐selective deposition. The surface dependence and growth mechanism of (ethylbenzyl)(1‐ethyl‐1,4‐cyclohexadienyl)ruthenium and O 2 ALD at 325 °C on HfO 2 , Al 2 O 3 , OH, and SiOSi terminated SiO 2 , and organosilicate glass (OSG) are investigated. The experimental results show that precursor adsorption is strongly affected by the surface termination of the dielectric, and proceeds most rapidly on OH terminated dielectrics, followed by SiOSi and finally SiCH 3 terminated dielectrics. The initial stages of growth are characterized by the formation and growth of Ru nanoparticles, which is mediated by the diffusion of Ru species. Mean‐field and kinetic Monte Carlo modeling show that ALD on OSG is best described when accounting for (1) cyclic generation of new nanoparticles at the surface, (2) surface diffusion of both atomic species and nanoparticles, and (3) size‐dependent nanoparticle reactivity. In particular, the models indicate that precursor adsorption initially occurs only on the dielectric substrate, and occurs on the Ru nanoparticles only when these reach a critical size of about 0.85 nm. This phenomenon is attributed to the catalytic decomposition of oxygen requiring a minimum Ru nanoparticle size.
Metathesis of Hex‐1‐ene in Ionic Liquids. (2004)

Abstract For Abstract see ChemInform Abstract in Full Text.
Structure of 2,3-dihydro-1H-imidazo[1,2-b]pyrazole (IMPY), an inhibitor of DNA synthesis, C5H7N3 (1983)

Mr= 109.13, orthorhombic, P212121, a= 7.098 (1), b=7.225 (1), c= 10.980 (3)A, V= 563.09A 3, Z-4, D m=1.29, D x=l.29Mgm -a, 2(CuKs)=l.54178A, p=0.70mm -~. Final R= 0.059 for 425 significant reflections measured at 298 K. The pyrazole portion is planar, while the dihydroimidazole group has a shallow half-chair conformation with C(4) deviating by 0.136 (4) A out of the plane of this ring.