gebhart/patrepeval huggingface dataset:
Abstract 5757: A new functional classification of lung and breast cancers based on siRNA mediated knockdown of 48 NRs and 72 CoRegulators (2012)

Abstract Introduction: Nuclear receptors (NRs) and their co-regulators (CoRegs) are master regulators of key transcriptional processes important in cancer pathogenesis and could provide molecular biomarkers for prognosis and personalizing new cancer targeted therapy. Aims and Methods: Our goal is to functionally classify a panel of 54 lung cancer, 20 breast cancer, and several immortalized human lung and breast epithelial cell strains based on their growth and survival response to siRNA mediated knockdown of 48 NRs and 72 CoRegs. Following knockdown of individual NR/CoRegs, changes in growth patterns are quantified and statistical methods are used to identify disease subgroups of similar responders. These subgroups are then integrated with our legacy datasets for clinical demographics, cancer cell oncogenotype and genome wide molecular characterization, and responses to standard and targeted chemotherapy. Results and Conclusions: A diverse, representative panel consisting of lung cancer, breast cancer, and normal epithelial cell lines was tested by siRNA transfection. After optimization to determine transfection conditions, all cell lines were screened using a focused siRNA library targeting all 48 NRs and 72 CoRegs (each gene is targeted by pools of 4 different siRNAs, Qiagen). Screening experiments were performed in triplicate, in 96 well plates, in a five-day MTS assay and assays were repeated 3 times. Correlation between replicates for the same cell line is &amp;gt;0.84 and knockdowns were validated by qRT-PCR. We found: 1) NR/CoReg-specific knockdown could have no effect, increase, or decrease tumor cell viability in a cell line dependent manner. 2) Overall ∼70% of the NRs or CoRegs reduced cell viability in at least one tumor line when their expression was knocked down (examples included NURR1, PRMT1, RXRalpha, BRCA1). 3) NR/CoReg-specific tumor cell toxicity was validated independently by siRNA knockdown combined with a liquid colony formation assay. 4) Knockdown of several NR/CoRegs selectively killed tumor but not normal epithelial cells. 5) Tumor cell lines could be stratified into functionally unique categories based on their changes in growth following NR/CoReg-specific knockdowns. We conclude that siRNA mediated knockdown of a large number of NRs and their CoRegs identifies genes that show tumor cell selective toxicity, and that tumor lines vary in their siRNA response phenotypes. These data strengthen the concept for NR/CoReg targeted therapy of lung and breast cancer and also the need to “personalize” such therapy. Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 103rd Annual Meeting of the American Association for Cancer Research; 2012 Mar 31-Apr 4; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2012;72(8 Suppl):Abstract nr 5757. doi:1538-7445.AM2012-5757
Testing the monocyte-macrophage system in human cancer. (1980)

The participation of the monocyte-macrophages cells in the host immune defence mechanisms against cancer has been recognized since a few years. Testing this component of host homeostasis appears as an additional tool necessary for evaluation of immune deficiency in cancer patient. We review here the most current tests used in the frame of such an evaluation, and also the most interesting results.
ChemInform Abstract: Ti2‐Containing 18‐Tungsto‐2‐Arsenate(III) Monolacunary Host and the Incorporation of a Phenylantimony(III) Guest. (2016)

Abstract Compounds (IV) and (VII) are characterized in the solid state by single crystal XRD and FTIR spectroscopy, and in solution by UV/VIS and NMR spectroscopy and electrochemical measurements.
Non-Data-Aided I/Q Imbalance Compensation Using Measured Receiver Front-End Signals (2006)

The direct-conversion or homodyne receiver principle has received lots of interest in recent years for building flexible and compact radios. The homodyne architecture is, however, found to be rather sensitive to certain non-idealities of the analog front-end components. One big concern here is the amplitude and phase mismatches of the I and Q signal branches, resulting in insufficient rejection of the mirror frequency band. This paper presents an efficient low-order statistics based method (stat) for digital I/Q mismatch compensation, and compares the proposed technique with the blind signal separation (BSS) and hard decision (HD) based compensators proposed earlier by the authors. In addition to algorithm developments, big emphasis in the paper is on performance measurements and verifications carried out using measured true-world receiver front-end signals obtained from a laboratory homodyne measurement system. In general, the obtained results indicate that I/Q imbalance can be efficiently compensated using the proposed ideas. Even with really high-order modulation techniques, such as 64-QAM, close-to additive noise bound compensator performance is demonstrated using the measured signals
Blue-emitting bolaamphiphilic zwitterionic iridium(iii) complex (2019)

Aggregation induced emission is a very interesting phenomenon that recently has attracted a lot of interest. Most of the examples deal with organic molecules or flat metal complexes. Here we demonstrate that, by design, even iridium compounds can display this process without shifting the emission energy. In order to enhance the aggregation properties we have focussed on amphiphilic complexes. We report the synthesis and photophysical characterisation of a blue-emitting bolaamphiphilic zwitterionic Ir(iii) complex and an analogous cationic amphiphilic compound, used as a reference. The bolaamphiphile exhibited blue (λmax = 450 nm) emission in dilute, deaerated solution with a photoluminescence quantum yield (PLQY) of 22%, similar to the related cationic amphiphilic complex. The bolaamphiphile displayed significant emission enhancement in the solid state, with an emission quantum yield that reach 52%. Interestingly, the emission of the cationic analogue suffers from aggregation quenching in the solid state, (PLQY = 3%) as is common for these type of complexes. A correlation between the photophysical data and the arrangement in the solid state is discussed.
Coupled Thermo-Mechanical Simulation (2017)

Ultrasonic welding is a solid-state bond created using ultrasonic energy. It has been used in the semiconductor industry for several decades, and more recently, in the automotive industry such as for battery welding. Even though there existed several numerical simulations on ultrasonic welding, the models were too simplistic, in both theory and welding configuration, to present the multiple sheet, dissimilar metal ultrasonic welding. In this study, theories and a finite element procedure for the ultrasonic welding process are developed. The procedure invokes both Abaqus/Standard and Abaqus/Explicit to simulate the mechanical-thermal coupled phenomena over the entire weld duration with moderate computational cost. The procedure is verified and used to simulate selected specific cases involving multiple sheets and dissimilar materials, i.e., copper and aluminum. The simulation procedure demonstrates its capability to predict welding energy, temperature distribution, and fracture/distortion of the workpieces toward the goal of improving welding quality.
Process Control and Statistical Inference (1997)

Click to increase image sizeClick to decrease image sizeView correction statement:Corrigenda Additional informationNotes on contributorsStephen V. CrowderDr. Crowder is a Senior Member of the Technical Staff.Douglas M. HawkinsDr. Hawkins is a Professor in the Department of Applied Statistics. He is a Senior Member of ASQC.Marion R. ReynoldsDr. Reynolds is a Professor in the Departments of Statistics and Forestry. He is a Member of ASQC.Emmanuel YashchinDr. Yashchin is a Research Staff Member in the Statistics Group. He is a Member of ASQC.
Sorting bacteria by chain length - A factor of virulence? (2016)

Using Deterministic Lateral Displacement (DLD), we are able to separate bacteria by their size and their chain length. This separation enables the study of these properties as factors of virulence.
A tri-layer approach to controlling nanopore formation in oxide supports (2019)

A novel tri-layer approach for immobilizing metal nanoparticles in SiO2 supports is presented. In this work, we show that under rapid heating to temperatures of approximately 1,000 °C, metal nanoparticles less than 15 nm in size will entrench in the SiO2 layer on a silicon wafer to create pores as deep as 250 nm. We studied and characterized this entrenching behavior and subsequent nanopore formation for a wide variety of metal nanoparticles, including Au, Ag, Pt, Pd, and Cu. We also demonstrate that an Al2O3 layer acts as a barrier to such pore formation. Thus, by creating a tri-layer architecture consisting of SiO2 on Al2O3 on silicon wafers, we can control the depth to which nanoparticles entrench between 3–5 nm. This small range allows one to entrench particles for the purpose of immobilization but still present them above the surface. The two advances of moving into the sub-15 nm size regime and of controlled particle immobilization through entrenchment have important implications in studying site-isolated and stabilized metal nanoparticles for applications in sensing, separations, and catalysis.
Baw components for PCS-CDMA applications (2006)

Bulk Acoustic Wave (BAW) technology is highly investigated due to its silicon-based technology for further integration in the RF part of e.g. mobile phones. This paper shows the current performance of various components suitable for the US PCS-CDMA band. In particular, new results of a duplexer are presented as well as new designs for a transmit filter and a receive filter. Besides the transfer functions, measurements of the temperature coefficient for left and right skirts are shown as well. The presented results show clearly our improvements within solidly-mounted-resonator (SMR) -BAW technology. Our process flow using a 200 mm manufacturing line uses only the minimum required process steps by still keeping a high yield in combination with high process stability and high process robustness.
Effects of Iron, Nickel, and Cobalt on Precipitation Hardening of Alloy 718 (1991)

to evaluate the effects of nickel and cobalt substitutions
Understanding Reservoir Architecture: Combining Continuous Fluid Facies Mapping, Pressure Measurements, Downhole Fluid Analysis, and Geochemical Analyses* (2007)

Identifying compartmentalization and understanding reservoir structure are of critical importance to reservoir development. Traditional methods of identifying reservoir compartmentalization, such as drill stem tests and extended well tests, often become impractical in deepwater settings with costs approaching the costs of new wells and
The Future of Quantum Computing with Superconducting Qubits (2022)

For the first time in history, we are seeing a branching point in computing paradigms with the emergence of quantum processing units (QPUs). Extracting the full potential of computation and realizing quantum algorithms with a super-polynomial speedup will most likely require major advances in quantum error correction technology. Meanwhile, achieving a computational advantage in the near term may be possible by combining multiple QPUs through circuit knitting techniques, improving the quality of solutions through error suppression and mitigation, and focusing on heuristic versions of quantum algorithms with asymptotic speedups. For this to happen, the performance of quantum computing hardware needs to improve and software needs to seamlessly integrate quantum and classical processors together to form a new architecture that we are calling quantum-centric supercomputing. Long term, we see hardware that exploits qubit connectivity in higher than 2D topologies to realize more efficient quantum error correcting codes, modular architectures for scaling QPUs and parallelizing workloads, and software that evolves to make the intricacies of the technology invisible to the users and realize the goal of ubiquitous, frictionless quantum computing.
A multiview boosting approach to tissue segmentation (2014)

Digitized histopathology images have a great potential for improving or facilitating current assessment tools in cancer pathology. In order to develop accurate and robust automated methods, the precise segmentation of histologic objects such epithelium, stroma, and nucleus is necessary, in the hopes of information extraction not otherwise obvious to the subjective eye. Here, we propose a multivew boosting approach to segment histology objects of prostate tissue. Tissue specimen images are first represented at different scales using a Gaussian kernel and converted into several forms such HSV and La*b*. Intensity- and texture-based features are extracted from the converted images. Adopting multiview boosting approach, we effectively learn a classifier to predict the histologic class of a pixel in a prostate tissue specimen. The method attempts to integrate the information from multiple scales (or views). 18 prostate tissue specimens from 4 patients were employed to evaluate the new method. The method was trained on 11 tissue specimens including 75,832 epithelial and 103,453 stroma pixels and tested on 55,319 epithelial and 74,945 stroma pixels from 7 tissue specimens. The technique showed 96.7% accuracy, and as summarized into a receiver operating characteristic (ROC) plot, the area under the ROC curve (AUC) of 0.983 (95% CI: 0.983-0.984) was achieved.
Plasma-surface interaction during ITER transient events: simulation with QSPA Kh-50 and GOL-3 facilities (2008)

The paper presents experimental investigations of plasma-surface interaction (PSI) and materials behavior under plasma loads relevant to giant ELMs in ITER. The experiments were performed with QSPA Kh-50 and GOL-3 devices located in Kharkov, (Ukraine) and Novosibirsk (Russia) respectively. QSPA provided repetitive plasma pulses of the duration of 0.25 ms and the energy density up to 2.5 MJ/m². In GOL-3 multimirror trap the impacting plasma was heated up to 2…4 keV temperature by a high power relativistic electron beam (0.8 MeV, ~30 kA, ~12 µs, ~120 kJ). Surface morphology of the targets exposed to QSPA and GOL-3 plasma is analyzed. Development of cracking on the tungsten surface and droplets splashing are discussed.
In search of effective text input interfaces for off the desktop computing (2004)

It is generally recognized that today's frontier of HCI research lies beyond the traditional desktop computers whose GUI interfaces were built on the foundation of display-pointing device-full keyboard. Many interface challenges arise without such a physical UI foundation. Text writingranging from entering URLs and search queries, filling forms, typing commands, to taking notes and writing emails and chat messages-is one of the hard problems awaiting for solutions in off-desktop computing. This paper summarizes and synthesizes a research program on this topic at the IBM Almaden Research Center. It analyzes various dimensions that constitute a good text input interface; briefly reviews related literature; discusses the evaluation methodology issues of text input; presents the major ideas and results of two systems, ATOMIK and SHARK; and points out current and future directions in the area from our current vantage point.
Alloying at a Subnanoscale Maximizes the Synergistic Effect on the Electrocatalytic Hydrogen Evolution (2022)

Abstract Bonding dissimilar elements to provide synergistic effects is an effective way to improve the performance of metal catalysts. However, as the properties become more dissimilar, achieving synergistic effects effectively becomes more difficult due to phase separation. Here we describe a comprehensive study on how subnanoscale alloying is always effective for inter‐elemental synergy. Thirty‐six combinations of both bimetallic subnanoparticles (SNPs) and nanoparticles (NPs) were studied systematically using atomic‐resolution imaging and catalyst benchmarking based on the hydrogen evolution reaction (HER). Results revealed that SNPs always produce greater synergistic effects than NPs, the greatest synergistic effect was found for the combination of Pt and Zr. The atomic‐scale miscibility and the associated modulation of electronic states at the subnanoscale were much different from those at the nanoscale, which was observed by annular‐dark‐field scanning transmission electron microscopy (ADF‐STEM) and X‐ray photoelectron spectroscopy (XPS), respectively.
A CDC7 inhibitor sensitizes DNA-damaging chemotherapies by suppressing homologous recombination repair to delay DNA damage recovery (2021)

Cell division cycle 7 (CDC7), a serine/threonine kinase, plays important roles in DNA replication. We developed a highly specific CDC7 inhibitor, TAK-931, as a clinical cancer therapeutic agent. This study aimed to identify the potential combination partners of TAK-931 for guiding its clinical development strategies. Unbiased high-throughput chemical screening revealed that the highest synergistic antiproliferative effects observed were the combinations of DNA-damaging agents with TAK-931. Functional phosphoproteomic analysis demonstrated that TAK-931 suppressed homologous recombination repair activity, delayed recovery from double-strand breaks, and led to accumulation of DNA damages in the combination. Whole-genome small interfering RNA library screening identified sensitivity-modulating molecules, which propose the experimentally predicted target cancer types for the combination, including pancreatic, esophageal, ovarian, and breast cancers. The efficacy of combination therapy in these cancer types was preclinically confirmed in the corresponding primary-derived xenograft models. Thus, our findings would be helpful to guide the future clinical strategies for TAK-931.
The Long Road to a Universal Influenza Virus Vaccine (2020)

Seasonal and pandemic influenza virus infections can cause significant disease worldwide. Current vaccines only provide limited, short-lived protection, and antigenic drift/shift in the hemagglutinin (HA) surface glycoprotein necessitates their annual reformulation and re-administration. To overcome these limitations, universal influenza virus vaccine strategies aim at eliciting broadly protective antibodies to conserved epitopes of the HA. We have developed two approaches. (1) The first is based on “chimeric” HA constructs that retain the conserved stalk domain of the HA and have exotic HA heads. Vaccination and boosting with such constructs successfully redirects the immune system in animals and in humans towards the conserved immune sub-dominant domains of the HA stalks; this results in an antigenic silencing of the HA heads and a protective immune response facilitated by the conserved HA stalks. In mice and ferrets, such a strategy protects the animals against homo-subtypic and hetero-subtypic challenge with influenza A strains as well as against influenza B variants. It is hoped that vaccine constructs expressing three components (i.e., conserved group 1 HA stalks, conserved group 2 HA stalks, and conserved influenza B HA stalks) will be protective against all future seasonal and pandemic strains. (2) The “mosaic” HA approach is based on antigenic silencing of the major immunodominant antigenic sites of the HA heads by only replacing those epitopes with corresponding sequences of exotic avian HAs, yielding “mosaic” HAs. In mice, a prime-boost vaccination regime with inactivated viruses expressing “mosaic” HAs elicited highly cross-reactive antibodies against the stalk domain of the HAs that were capable of eliciting Fc-mediated effector functions in vitro. Extensive trials will be necessary in the future in order to identify the optimal vaccination regime (“chimeric” HA-based versus “mosaic” HA-based) in humans.
Engineered DNA Vaccination against Follicle-Stimulating Hormone Receptor Delays Ovarian Cancer Progression in Animal Models (2018)

Ovarian cancer presents in 80% of patients as a metastatic disease, which confers it with dismal prognosis despite surgery and chemotherapy. However, it is an immunogenic disease, and the presence of intratumoral T cells is a major prognostic factor for survival. We used a synthetic consensus (SynCon) approach to generate a novel DNA vaccine that breaks immune tolerance to follicle-stimulating hormone receptor (FSHR), present in 50% of ovarian cancers but confined to the ovary in healthy tissues. SynCon FSHR DNA vaccine generated robust CD8<sup>+</sup> and CD4<sup>+</sup> cellular immune responses and FSHR-redirected antibodies. The SynCon FSHR DNA vaccine delayed the progression of a highly aggressive ovarian cancer model with peritoneal carcinomatosis in immunocompetent mice, and it increased the infiltration of anti-tumor CD8<sup>+</sup> T cells in the tumor microenvironment. Anti-tumor activity of this FSHR vaccine was confirmed in a syngeneic murine FSHR-expressing prostate cancer model. Furthermore, adoptive transfer of vaccine-primed CD8<sup>+</sup> T cells after ex vivo expansion delayed ovarian cancer progression. In conclusion, the SynCon FSHR vaccine was able to break immune tolerance and elicit an effective anti-tumor response associated with an increase in tumor-infiltrating T cells. FSHR DNA vaccination could help current ovarian cancer therapy after first-line treatment of FSHR<sup>+</sup> tumors to prevent tumor recurrence.
Three-dimensional Contrast-enhanced MR Angiography with Real-time Fluoroscopic Triggering: Design Specifications and Technical Reliability in 330 Patient Studies (2000)

Technical reliability was determined for triggering three-dimensional (3D) contrast material-enhanced magnetic resonance (MR) angiography with MR fluoroscopy. Technical requirements for high reliability were also identified. Reliability was evaluated in 330 consecutive patient studies of the neck, thorax, abdomen, and pelvis. Contrast material arrival was detected fluoroscopically in 325 of the 330 studies (98.5%), and the 3D sequence was successfully triggered in 321 of 330 studies (97.3%). Fluoroscopic triggering of centrically encoded 3D MR angiographic acquisitions is a highly reliable means of obtaining 3D MR angiograms with high spatial resolution.
Supplementary Material from A Tricin Derivative from <i>Deschampsia antarctica</i> Desv. Inhibits Colorectal Carcinoma Growth and Liver Metastasis through the Induction of a Specific Immune Response (2023)

&lt;p&gt;Information about experimental procedure to obtain Antartina&lt;/p&gt;
Note: Influence of rinsing and drying routines on growth of multilayer thin films using automated deposition system (2010)

A versatile, high speed robot for layer-by-layer deposition of multifunctional thin films, which integrates concepts from previous dipping systems, has been designed with dramatic improvements in software, positioning, rinsing, drying, and waste removal. This system exploits the electrostatic interaction of oppositely charged species to deposit nanolayers (1-10 nm thick) from water onto the surface of a substrate. Dip times and number of deposited layers are adjustable through a graphical user interface. In between dips the system spray rinses and dries the substrate by positioning it in the two-tiered rinse-dry station. This feature significantly reduces processing time and provides the flexibility to choose from four different procedures for rinsing and drying. Assemblies of natural montmorillonite clay and polyethylenimine are deposited onto 175 microm poly(ethylene terephthalate) film to demonstrate the utility of this automated deposition system. By altering the type of rinse-dry procedure, these clay-based assemblies are shown to exhibit variations in film thickness and oxygen transmission rate. This type of system reproducibly deposits films containing 20 or more layers and may also be useful for other types of coatings that make use of dipping.