gebhart/patrepeval huggingface dataset:
Abstract 2680: Characterization of tumor associated antigens using a recombinant expression of a patient derived breast cancer cDNA library and autologous serum using the SEREX technique (2011)

Abstract Autoantibodies to tumor proteins in patient serum may serve as biomarkers in breast cancer diagnosis or as a potential targeted therapeutic when conjugated to drugs or radiotherapies. The tumor associated antigens (TAAs) to which they bind may be of further diagnostic or prognostic value. In order to identify TAAs, a cDNA library was created from a patient breast tumor, recombinantly expressed with lambda phage in XL1-Blue cells, and tested against autologous patient serum to identify potential TAAs using a modified technique based on serological analysis of recombinant cDNA expression libraries (SEREX) that allows for much smaller quantities of source material and reduces library production time. Identified TAAs and serum autoantibody concentrations against those proteins will be presented in the context of developing a new customized therapy for patients with breast cancer. Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 102nd Annual Meeting of the American Association for Cancer Research; 2011 Apr 2-6; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2011;71(8 Suppl):Abstract nr 2680. doi:10.1158/1538-7445.AM2011-2680
Second harmonic generation imaging in muscle fibers (2003)

We have used second harmonic generation (SHG) imaging to quantify a strong intrinsic SHG-signal from cellular and subcellular muscle fibre preparations. In isolated single muscle cells, the intrinsic SHG-signal periodically follows the striation pattern and strongly depends on the sarcomere length and the polarization of the illuminating laser beam. At the subcellular level, the SHG signal seems to be located mainly at the overlapping region of the (thin) actin and (thick) myosin filaments. Thus, SHG imaging resolves the arrangement of the contractile structures with high resolution non-invasively and without chromophores. It may also allow to study dynamic molecular interactions of the motor protein myosin with actin filaments during force production and muscle shortening.
FlexiVia ROM Compiler Programmable on Different Via Layers Based on Top Metal Assignment (2006)

We present a ROM compiler programmable from via 1 to via n - 2, where n is the number of metal layers. The layer on which the code via is landed can be selected by the user. With the coding being able to take place as close to the topmost metal as possible, the turnaround time for a revision is shortened. In this paper, we discuss the array assembly scheme and its impacts on the design considerations by the choice of strapping period
Data associated with the manuscript "On Lake Methane: Spatial Variability in Stable Carbon Isotopic Composition and the Potential Importance of Groundwater Input" (2021)

Data associated with the manuscript On Lake Methane: Spatial Variability in Stable Carbon Isotopic Composition and the Potential Importance of Groundwater Input
Curcumin Suppresses Janus Kinase-STAT Inflammatory Signaling through Activation of Src Homology 2 Domain-Containing Tyrosine Phosphatase 2 in Brain Microglia (2003)

Curcumin has been strongly implicated as an anti-inflammatory agent, but the precise mechanisms of its action are largely unknown. In this study, we show that the inhibitory action of curcumin on Janus kinase (JAK)-STAT signaling can contribute to its anti-inflammatory activity in the brain. In both rat primary microglia and murine BV2 microglial cells, curcumin effectively suppressed the ganglioside-, LPS-, or IFN-gamma-stimulated induction of cyclooxygenase-2 and inducible NO synthase, important enzymes that mediate inflammatory processes. These anti-inflammatory effects appear to be due, at least in part, to the suppression of the JAK-STAT inflammatory signaling cascade. Curcumin markedly inhibited the phosphorylation of STAT1 and 3 as well as JAK1 and 2 in microglia activated with gangliosides, LPS, or IFN-gamma. Curcumin consistently suppressed not only NF binding to IFN-gamma-activated sequence/IFN-stimulated regulatory element, but also the expression of inflammation-associated genes, including ICAM-1 and monocyte chemoattractant protein 1, whose promoters contain STAT-binding elements. We further show that activation of Src homology 2 domain-containing protein tyrosine phosphatases (SHP)-2, a negative regulator of JAK activity, is likely to be one of the mechanisms underlying the curcumin-mediated inhibition of JAK-STAT signaling. Treatment of microglial cells with curcumin led to an increase in phosphorylation and association with JAK1/2 of SHP-2, which inhibit the initiation of JAK-STAT inflammatory signaling in activated microglia. Taken together, these data suggest curcumin suppresses JAK-STAT signaling via activation of SHP-2, thus attenuating inflammatory response of brain microglial cells.
Theory of the time evolution of exciton coherence in weakly disordered crystals (1980)

Coherent states in molecular crystals are described as minimum-uncertainty superpositions of all the crystal states that can interact with light, and their amplitude decay due to the presence of disorder is calculated through the time-dependent exciton Greens function. The functional form of the decay is investigated, and different methods for its calculation are compared. The decay obtainable for the k=0 vibrational exciton in α-N2 through direct time-domain approximations provides good agreement with experimental results.
Statins and Inflammation in Cardiovascular Disease (2017)

In this review article, we present the basic pathophysiologic data supporting the anti-inflammatory actions of statins in clinical and experimental settings and we link these mechanisms with confirmatory clinical data on the potent non lipid lowering effects of HMG-CoA reductase inhibitors.
Genome-Resolved Metagenomics and Detailed Geochemical Speciation Analyses Yield New Insights into Microbial Mercury Cycling in Geothermal Springs (2020)

Geothermal systems emit substantial amounts of aqueous, gaseous, and methylated mercury, but little is known about microbial influences on mercury speciation. Here, we report results from genome-resolved metagenomics and mercury speciation analysis of acidic warm springs in the Ngawha Geothermal Field (<55°C, pH <4.5), Northland Region, Aotearoa New Zealand. Our aim was to identify the microorganisms genetically equipped for mercury methylation, demethylation, or Hg(II) reduction to volatile Hg(0) in these springs. Dissolved total and methylated mercury concentrations in two adjacent springs with different mercury speciation ranked among the highest reported from natural sources (250 to 16,000 ng liter<sup>-1</sup> and 0.5 to 13.9 ng liter<sup>-1</sup>, respectively). Total solid mercury concentrations in spring sediments ranged from 1,274 to 7,000 μg g<sup>-1</sup> In the context of such ultrahigh mercury levels, the geothermal microbiome was unexpectedly diverse and dominated by acidophilic and mesophilic sulfur- and iron-cycling bacteria, mercury- and arsenic-resistant bacteria, and thermophilic and acidophilic archaea. By integrating microbiome structure and metagenomic potential with geochemical constraints, we constructed a conceptual model for biogeochemical mercury cycling in geothermal springs. The model includes abiotic and biotic controls on mercury speciation and illustrates how geothermal mercury cycling may couple to microbial community dynamics and sulfur and iron biogeochemistry.<b>IMPORTANCE</b> Little is currently known about biogeochemical mercury cycling in geothermal systems. The manuscript presents a new conceptual model, supported by genome-resolved metagenomic analysis and detailed geochemical measurements. The model illustrates environmental factors that influence mercury cycling in acidic springs, including transitions between solid (mineral) and aqueous phases of mercury, as well as the interconnections among mercury, sulfur, and iron cycles. This work provides a framework for studying natural geothermal mercury emissions globally. Specifically, our findings have implications for mercury speciation in wastewaters from geothermal power plants and the potential environmental impacts of microbially and abiotically formed mercury species, particularly where they are mobilized in spring waters that mix with surface or groundwaters. Furthermore, in the context of thermophilic origins for microbial mercury volatilization, this report yields new insights into how such processes may have evolved alongside microbial mercury methylation/demethylation and the environmental constraints imposed by the geochemistry and mineralogy of geothermal systems.
Uniform patchy and hollow rectangular platelet micelles from crystallizable polymer blends (2016)

The preparation of colloidally stable, self-assembled materials with tailorable solid or hollow two-dimensional (2D) structures represents a major challenge. We describe the formation of uniform, monodisperse rectangular platelet micelles of controlled size by means of seeded-growth methods that involve the addition of blends of crystalline-coil block copolymers and the corresponding crystalline homopolymer to cylindrical micelle seeds. Sequential addition of different blends yields solid platelet block comicelles with concentric rectangular patches with distinct coronal chemistries. These complex nano-objects can be subject to spatially selective processing that allows their disassembly to form perforated platelets, such as well-defined hollow rectangular rings. The solid and hollow 2D micelles provide a tunable platform for further functionalization and potential for a variety of applications.
Selective excitation luminescence and electronic Raman scattering study of the 78-meV acceptor in GaAs (1984)

We observe for the first time two excited states of the 78-meV acceptor in liquid encapsulated Czochralski GaAs with excitation energies of 62.9 and 66.9 meV above the ground state, respectively. These levels were observed in two different samples using selective excitation luminescence and electronic Raman scattering. We conclude that these levels could correspond to transitions from the 1s2 ground state to the split 1s12s1 excited state of a double acceptor.
Prevalence of Open-Angle Glaucoma Among Adults in the United States (2004)

Open-angle glaucoma affects more than 2 million individuals in the United States. Owing to the rapid aging of the US population, this number will increase to more than 3 million by 2020.
THE APPLICATION OF GUIDED WAVE TRAVEL TIME TOMOGRAPHY TO BENDS (2010)

The concept of predictive maintenance using permanent sensors that monitor the integrity of an installation is an interesting addition to the current method of periodic inspections. The method should be capable of providing quantitative wall thickness information for both straight pipes and bends. The wave propagation in bends is far more complicated than in straight pipes because natural focusing occurs due to geometrical path differences. Numerical simulations clearly show this effect. Travel time tomography requires accurate modeling of travel times that can be translated to spatial wall thickness variations. Therefore, a ray tracing algorithm has been developed to calculate travel times as part of the tomographic inversion kernel. Numerical results show that a tomographic inversion on simple simulated data provides accurate results. The focusing effect due to the shape of the bend yields a phase rotation of the wavelet, which complicates accurate timing picking. This effect was excluded in the simulated ray tracing data. Based on these observations it is concluded that a more accurate, wave equation based forward modeling algorithm is required to obtain accurate inversion results on realistic data.
Irisin prevents microgravity‐induced impairment of osteoblast differentiation in vitro during the space flight CRS‐14 mission (2020)

Understanding molecular mechanisms responsible for bone cells unbalance in microgravity would allow the development of better countermeasures for astronauts, and eventually advancing terrestrial osteoporosis treatments. We conduct a unique investigation by using a controlled 3D in vitro cell model to mimic the bone microenvironment in microgravity aboard the SpaceX Dragon cargo ferry to the ISS. Osteoblasts (OBs), osteoclasts (OCs), and endothelial cells (ECs), seeded on Skelite discs, were cultured w/ or w/o rec-Irisin and exposed to 14 days of microgravity in the eOSTEO hardware. Gene expression analysis was assessed, and results were compared to ground controls treated within identical payloads. Our results show that the microgravity-induced downregulation of mRNA levels of genes encoding for OB key transcription factors (Atf4 -75%, P < .01; RunX2 -87%, P < .001, Osterix -95%, P < .05 vs ground) and proteins (Collagen I -84%, P < .05; Osteoprotegerin -94%, P < .05) were prevented by irisin. Despite it was not effective in preventing Trap and Cathepsin K mRNA increase, irisin induced a 2.8-fold increase of Osteoprotegerin (P < .05) that might act for reducing osteoclastogenesis in microgravity. Our results provide evidence that irisin supports OB differentiation and activity in microgravity and it might represent a countermeasure to prevent bone loss in astronauts.
PDTD: a web-accessible protein database for drug target identification (2008)

PDTD serves as a comprehensive and unique repository of drug targets. Integrated with TarFisDock, PDTD is a useful resource to identify binding proteins for active compounds or existing drugs. Its potential applications include in silico drug target identification, virtual screening, and the discovery of the secondary effects of an old drug (i.e. new pharmacological usage) or an existing target (i.e. new pharmacological or toxic relevance), thus it may be a valuable platform for the pharmaceutical researchers. PDTD is available online at http://www.dddc.ac.cn/pdtd/.
Identification of GA-Binding Protein Transcription Factor Alpha Subunit (GABPA) as a Novel Bookmarking Factor (2019)

Mitotic bookmarking constitutes a mechanism for transmitting transcriptional patterns through cell division. Bookmarking factors, comprising a subset of transcription factors (TFs), and multiple histone modifications retained in mitotic chromatin facilitate reactivation of transcription in the early G1 phase. However, the specific TFs that act as bookmarking factors remain largely unknown. Previously, we identified the "early G1 genes" and screened TFs that were predicted to bind to the upstream region of these genes, then identified GA-binding protein transcription factor alpha subunit (GABPA) and Sp1 transcription factor (SP1) as candidate bookmarking factors. Here we show that GABPA and multiple histone acetylation marks such as H3K9/14AC, H3K27AC, and H4K5AC are maintained at specific genomic sites in mitosis. During the M/G1 transition, the levels of these histone acetylations at the upstream regions of genes bound by GABPA in mitosis are decreased. Upon depletion of GABPA, levels of histone acetylation, especially H4K5AC, at several gene regions are increased, along with transcriptional induction at 1 h after release. Therefore, we proposed that GABPA cooperates with the states of histone acetylation to act as a novel bookmarking factor which, may negatively regulate transcription during the early G1 phase.
An analytical solution for inverse kinematic of 7-DOF redundant manipulators with offset-wrist (2012)

A valid analytical inverse kinematics computation for seven-degree-of-freedom (7-DOF) redundant manipulators with offset-wrist is proposed. The method uses a virtual joint to replace the join offset from the wrist, and forms a virtual manipulator with a sphere-wrist. Assuming that the virtual manipulator and the real manipulator's joint angles keep the same all the time, the virtual manipulator seems to be driven by the real manipulator; meanwhile, the real manipulator seems to be driven by the virtual manipulator. There is an interesting relationship between these two manipulators: the pose of the virtual manipulator can be calculated if the pose and the 7th joint's angle of the real manipulator are given. It means that the virtual manipulator is driven to the calculated pose when the real manipulator moves to the given pose with the given 7th joint angle, meanwhile, the real manipulator will be driven to the to the given pose when the virtual manipulator moves to the calculated pose with the given 7th joint angle. Then the inverse kinematic solutions of real manipulator can be obtained through solving the inverse kinematic problems of virtual manipulator with a known 7th joint angle. They share the same solutions. In this paper, the manipulators' configuration is analyzed and the virtual joint method and its detailed solution processes were given. Lastly the method is verified by kinematic simulations. The results show that the virtual joint method behaves high precision in solving the inverse kinematic of 7-DOF redundant manipulator with offset-wrist.
Data from Targeted Chemotherapy for Head and Neck Cancer with a Chimeric Oncolytic Adenovirus Coding for Bifunctional Suicide Protein FCU1 (2023)

&lt;div&gt;Abstract&lt;p&gt;&lt;b&gt;Purpose:&lt;/b&gt; Transfer of prodrug activation systems into tumors by using replication-deficient viruses has been suggested to be an effective method for achieving high local and low systemic anticancer drug concentrations. However, most current suicide gene therapy strategies are still hindered by poor efficiency of &lt;i&gt;in vivo&lt;/i&gt; gene transfer, inefficient tumor penetration, limited bystander cell killing effect, and need of large prodrug doses. We hypothesized that local amplification provided by a replication competent platform would help overcome these limitations.&lt;/p&gt;&lt;p&gt;&lt;b&gt;Experimental Design:&lt;/b&gt; We generated a transductionally and &lt;i&gt;transcriptionally&lt;/i&gt; targeted oncolytic adenovirus Ad5/3-Δ24FCU1 expressing the fusion suicide gene &lt;i&gt;FCU1&lt;/i&gt;. &lt;i&gt;FCU1&lt;/i&gt; encodes a bifunctional fusion protein that efficiently catalyzes the direct conversion of 5-FC, a relatively nontoxic antifungal agent, into the toxic metabolites 5-fluorouracil and 5-fluorouridine monophosphate, bypassing the natural resistance of certain human tumor cells to 5-fluorouracil.&lt;/p&gt;&lt;p&gt;&lt;b&gt;Results:&lt;/b&gt; We examined the efficacy of Ad5/3-Δ24FCU1 and the replication-defective control Ad5/3-FCU1 with and without 5-FC. FCU1 expression was confirmed by Western blot, whereas enzymatic conversion levels &lt;i&gt;in vitro&lt;/i&gt; and &lt;i&gt;in vivo&lt;/i&gt; were determined by high-performance liquid chromatography separation. Significant antitumor effect was observed &lt;i&gt;in vitro&lt;/i&gt; and &lt;i&gt;in vivo&lt;/i&gt; in a murine model of head and neck squamous cell carcinoma. Although we observed a decrease in viral DNA copy number &lt;i&gt;in vitro&lt;/i&gt; and in tumors treated with Ad5/3-Δ24FCU1 and 5-FC, suggesting an effect on virus replication, the highest antitumor effect was observed for this combination.&lt;/p&gt;&lt;p&gt;&lt;b&gt;Conclusions:&lt;/b&gt; It seems feasible and efficacious to combine adenovirus replication to the FCU1 prodrug activation system. Clin Cancer Res; 16(9); 2540–9. ©2010 AACR.&lt;/p&gt;&lt;/div&gt;
Insulator-metal transition and anomalous sign reversal of the dominant charge carriers in perovskiteBaTiO3−δ (2008)

Dc resistivity, magnetic susceptibility, and Hall and Seebeck coefficients were measured in the 2--400 K range on perovskite ${\text{BaTiO}}_{3\ensuremath{-}\ensuremath{\delta}}$ single crystals with electron concentration of $9.8\ifmmode\times\else\texttimes\fi{}{10}^{17}\ensuremath{-}3.5\ifmmode\times\else\texttimes\fi{}{10}^{20}\text{ }{\text{cm}}^{\ensuremath{-}3}$. The insulator-metal transition in ${\text{BaTiO}}_{3\ensuremath{-}\ensuremath{\delta}}$ was found at critical electron concentration ${n}_{c}\ensuremath{\approx}1.6\ifmmode\times\else\texttimes\fi{}{10}^{20}\text{ }{\text{cm}}^{\ensuremath{-}3}$. In contrast to ${\text{SrTiO}}_{3\ensuremath{-}\ensuremath{\delta}}$, both Hall and Seebeck coefficients of metallic ${\text{BaTiO}}_{3\ensuremath{-}\ensuremath{\delta}}$ show strong temperature dependence below 290 K which culminates by a sign reversal from negative to positive. The temperature of the sign reversal anomaly is concentration dependent and increases with $n$. Magnetic susceptibility of metallic samples shows anomalous decrease upon cooling below 300 K. It is proposed that the low-temperature $p$-type conductivity in ${\text{BaTiO}}_{3\ensuremath{-}\ensuremath{\delta}}$ may be attributed to the charge-carrier contributions from the two electronic bands separated by a narrow (3--7 meV) energy gap.
Design of Low-Profile Microstrip Antenna with Enhanced Bandwidth and Reduced Size (2006)

An effective technique is presented to enhance the bandwidth and reduce the size of an ultralow-profile microstrip antenna. By loading multicouple staggered slots on the patch and using inset feed structure, two TM <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">10</sub> modes can be excited at two close frequencies and matched well simultaneously. Designs based on the structures with four-, five-, and six-couple staggered slots have been made to demonstrate the effective technique. To the best designed results, the presented ultralow-profile microstrip antenna obtains a bandwidth enhancement of about two times and a size reduction of about 60% compared with the ordinary one. The technique is suitable for radio-frequency front-end antenna integration and package in microwave and millimeter-wave bands
Bandwidths of orientation channels in human vision (1979)

The ability of observers to discriminate between stimuli differing in orientation was measured using low contrast, foveally viewed stimuli. Detection and discrimination performance were measured simultaneously. A model is presented which permits bandwidths of orientation-tuned mechanisms to be estimated from the data. In a group of five observers, half-amplitude bandwidths varied from 10 degrees to 20 degrees.
Supplementary Methods from Cancer-Associated Adipocytes Exhibit an Activated Phenotype and Contribute to Breast Cancer Invasion (2023)

Supplementary Methods from Cancer-Associated Adipocytes Exhibit an Activated Phenotype and Contribute to Breast Cancer Invasion
혼합수소발생기용 전력변환장치의 특성 (2007)

In this paper, the basic experiment, electrolytic cell design and basic manufacturing have been made to interpret the characteristics of Hydrogen-Oxygen-Gas-Generator. As for the detailed matters, the data research on basic technology on Hydrogen-Oxygen-Cas and analysis on characteristics of Hydrogen-Oxygen-Gas from basic experiment. Also the experiment of characteristics and comparative evaluation between constant current source using SCR converter from existing method and constant current source using new phase shift PWM control method converter. As results when it has injected constant DC current, we has compared Gas quantities by variable ripple frequencies using phase shift PWM control method converter. Therefore, in linear region, it has not different Gas quantities by constant DC current and by phase shift PWM control method converter. Also, it has increased Gas quantities wilder linear region when put ripple frequency at saturation region. Through, Gas quantities and input power, it has acquired higher input power per Gas quantities at put pulse curren. Therefore, when designing converter or inverter for electrolysis, which has ripple current.