gebhart/patrepeval huggingface dataset:
Development of Porosimetry Techniques for the Characterization of Plasma-Treated Porous Ultra Low-k Materials (2011)

For the sub-32 nm node, porous SiCOH dielectrics (p-SiCOH) are integrated using dual damascene patterning by etching trenches and vias into the porous material. One challenge is to control the process conditions to minimize the plasma-induced damage of p-SiCOH materials at the bottom and at the sidewall of the trenches. Ellipsometric Porosimetry has been adapted to characterize the plasma-treated materials for both horizontal and vertical surfaces. Since surface modifications can cause adsorption and desorption delays and hydrophobicity loss, porosimetry measurements operated with multi-solvent and kinetic protocols are required. Quantitative measurements of vertically patterned materials are demonstrated using periodic structures of porous material and a Scatterometric Porosimetry analysis. Results show a good sensitivity of the measurement to the different process conditions but also highlight a different impact of the plasma processes on patterned materials compared with blanket films.
Redox-responsive targeted gelatin nanoparticles for delivery of combination wt-p53 expressing plasmid DNA and gemcitabine in the treatment of pancreatic cancer (2014)

Gene/drug combination treatment significantly improves the therapeutic performance of the delivery system compared to the gene or drug alone treated groups. Anti-tumor activity of the thiolated gelatin loaded wt-p53 plasmid or gemcitabine-based therapy was attributed to their ability to induce cell apoptosis, which was confirmed by a marked increase in mRNA level of proapoptotic transcription factors, as well as, protein apoptotic biomarker expression and significant decrease in the anti-apoptotic transcription factors.
Hypoalbuminemia is an independent prognostic factor for overall survival in myelodysplastic syndromes (2012)

We hypothesized that hypoalbuminemia is an independent prognostic factor in patients with myelodysplastic syndromes (MDS). We analyzed records of 767 patients treated at Moffitt Cancer Center between January 2001 and December 2009 to evaluate the relationship between serum albumin (SA) at the time of presentation and overall survival (OS). Patients (median age of 69 years) were stratified into three groups based on SA concentration (≤3.5, 3.6-4.0, and >4.0 g/dL). Two-thirds of the patients had low or intermediate-1 International Prognostic Scoring System (IPSS)-based risk for MDS. Median OS by SA concentration of ≤3.5, 3.6-4.0, and >4.0 g/dL was 11, 23, and 34 months, respectively (P < 0.005), whereas rate of acute myeloid leukemia progression was highest in patients with low SA (≤3.5 g/dL). The SA level offered prognostic discrimination for outcomes within the lower and higher IPSS risk groups, as well as with the MD Anderson risk model. In multivariable analysis, SA was a significant independent co-variate for OS after adjustment for IPSS, age, serum ferritin, and transfusion dependence (hazard ratio = 0.8; 95% CI 0.6-0.9; P = 0.004). Our findings indicate that hypoalbuminemia is an independent prognostic biomarker that may serve as a surrogate representative of disease biology or comorbidities in patients with MDS.
EPID-22. CHARACTERIZATION OF RADIATION-INDUCED MENINGIOMAS IN A BRAIN TUMOR DATABASE (2020)

Abstract PURPOSE Radiation-induced meningiomas (RIMs) are associated with previous exposure to therapeutic irradiation. RIMs are rare and have not been well characterized relative to spontaneous meningiomas (SMs). METHODS 1003 patients with proven or presumed meningiomas were identified from the VCU brain tumor database. Chart review classified RIM patients and their characteristics. RESULTS Of the 1003 total patients, 76.47% were female with a mean ± SD age of 67.55 ± 15.50 years. 15 RIM patients were identified (66.67% female), with a mean ± SD age of 52.67 ± 15.46 years, 5 were African American and 10 were Caucasian. The incidence of RIMs was 1.49% in our data set. The mean age at diagnosis was 43.27 ± 15.06 years. The mean latency was 356.27 ± 116.96 months. The mean initiating dose was 44.28 ± 14.68 Gy. There was a significant difference between mean latency period and ethnicity, 258.3 months for African American population, and 405.2 months for Caucasian population (p = 0.003). There was a significant difference between the mean number of lesions in females (2.8) versus males (1.2; p = 0.046). Of the RIMs with characterized histology, 6 (55%) were WHO grade II and 5 (45%) were WHO grade I, demonstrating a prevalence of grade II tumors approximately double that found with SMs. RIMs were treated with combinations of observation, surgery, radiation, and medical therapy. Of the 8 patients treated with radiation, 4 demonstrated response. 8 of the 15 patients (53%) demonstrated recurrence/progression despite treatment. CONCLUSION RIMs are important because of the associated higher grade histology, gender, and ethnic incidences, and increased recurrence/progression compared to SMs. Despite the presumed contributory role of prior radiation, RIMs demonstrate a significant rate of responsiveness to radiation treatment.
Contribution of NAADP to Glutamate-Evoked Changes in Ca2+ Homeostasis in Mouse Hippocampal Neurons (2020)

Nicotinic acid adenine dinucleotide phosphate (NAADP) is a second messenger that evokes calcium release from intracellular organelles by the engagement of calcium release channels, including members of the Transient Receptor Potential (TRP) family, such as TRPML1, the (structurally) related Two Pore Channel type 1 (TPC1) and TPC2 channels as well as Ryanodine Receptors type 1 (RYR1; Guse, 2012). NAADP evokes calcium release from acidic calcium stores of many cell types (Guse, 2012), and NAADP-sensitive Ca<sup>2+</sup> stores have been described in hippocampal neurons of the rat (Bak et al., 1999; McGuinness et al., 2007). Glutamate triggers Ca<sup>2+</sup>-mediated neuronal excitotoxicity in inflammation-induced neurodegenerative pathologies such as Multiple Sclerosis (MS; Friese et al., 2014), and when applied extracellularly to neurons glutamate can elevate NAADP levels in these cells. Accordingly, glutamate-evoked Ca<sup>2+</sup> signals from intracellular organelles were inhibited by preventing organelle acidification (Pandey et al., 2009). Analysis of reported RNA sequencing experiments of cultured hippocampal neurons revealed the abundance of Mcoln1 (encoding TRPML1), Tpcn1, and Tpcn2 (encoding TPC1 and TPC2, respectively) as potential NAADP target channels in these cells. Transcripts encoding Ryr1 were not found in contrast to Ryr2 and Ryr3. To study the contribution of NAADP signaling to glutamate-evoked calcium transients in murine hippocampal neurons we used the NAADP antagonists Ned-19 (Naylor et al., 2009) and BZ194 (Dammermann et al., 2009). Our results show that both NAADP antagonists significantly reduce glutamate-evoked calcium transients. In addition to extracellular glutamate application, we studied synchronized calcium oscillations in the cells of the neuronal cultures evoked by addition of the GABA<sub>A</sub> receptor antagonist bicuculline. Pretreatment with Ned-19 (50 μM) or BZ194 (100 μM) led to an increase in the frequency of bicuculline-induced calcium oscillations at the cost of calcium transient amplitudes. Interestingly, Ned-19 triggered a rise in intracellular calcium concentrations 25 min after bicuculline stimulation, leading to the question whether NAADP acts as a neuroprotective messenger in hippocampal neurons. Taken together, our results are in agreement with the concept that NAADP signaling significantly contributes to glutamate evoked Ca<sup>2+</sup> rise in hippocampal neurons and to the amplitude and frequency of synchronized Ca<sup>2+</sup> oscillations triggered by spontaneous glutamate release events.
CLTR: An End-to-End, Transformer-Based System for Cell Level Table Retrieval and Table Question Answering (2021)

We present the first end-to-end, transformer-based table question answering (QA) system that takes natural language questions and massive table corpus as inputs to retrieve the most relevant tables and locate the correct table cells to answer the question. Our system, CLTR, extends the current state-of-the-art QA over tables model to build an end-to-end table QA architecture. This system has successfully tackled many real-world table QA problems with a simple, unified pipeline. Our proposed system can also generate a heatmap of candidate columns and rows over complex tables and allow users to quickly identify the correct cells to answer questions. In addition, we introduce two new open-domain benchmarks, E2E_WTQ and E2E_GNQ, consisting of 2,005 natural language questions over 76,242 tables. The benchmarks are designed to validate CLTR as well as accommodate future table retrieval and end-to-end table QA research and experiments. Our experiments demonstrate that our system is the current state-of-the-art model on the table retrieval task and produces promising results for end-to-end table QA.
A portable gamma camera for radiation monitoring (2002)

A compact gamma camera capable of imaging high energy gamma rays (up to 2 MeV) is currently being developed. This camera uses a three inch square Position Sensitive Photomultiplier Tube (PSPMT) [Hamamatsu, R-2487-05] coupled to a NaI(Tl) scintillator. The incoming gamma ray direction is determined by a segmented collimator. The camera exhibits energy resolutions of 17% FWHM at 122 keV and 12% FWHM at 662 keV. A spatial resolution of 3 mm is achieved at the center of the tube. Images have been obtained using gamma ray sources up to 1 MeV in energy using this system. The image reconstruction technique used here is presented in detail. Corrections for the non-uniformities across the face of the PSPMT are implemented to improve the spatial and spectral information content in the final image.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
An integer programming model for the weekly tour scheduling problem (2001)

Abstract We study a workforce planning and scheduling problem in which weekly tours of agents must be designed. Our motivation for this study comes from a call center application where agents serve customers in response to incoming phone calls. Similar to many other applications in the services industry, the demand for service in call centers varies significantly within a day and among days of the week. In our model, a weekly tour of an agent consists of five daily shifts and two days off, where daily shifts within a tour may be different from each other. The starting times of any two consecutive shifts, however, may not differ by more than a specified bound. Furthermore, a tour must also satisfy constraints regarding the days off, for example, it may be required that one of the days off is on a weekend day. The objective is to determine a collection of weekly tours that satisfy the demand for agents' services, while minimizing the total labor cost of the workforce. We describe an integer programming model where a weekly tour is obtained by combining seven daily shift scheduling models and days‐off constraints in a network flow framework. The model is flexible and can accommodate different daily models with varying levels of detail. It readily handles different days‐off rules and constraints regarding start time differentials in consecutive days. Computational results are also presented. © 2001 John Wiley &amp; Sons, Inc. Naval Research Logistics 48: 607–624, 2001.
Fuzzy Ranking of Financial Statements for Fraud Detection (2006)

Automatic detection of anomalies in financial statements can decrease the risk of exposure to fraudulent corporate behavior. This paper proposes a method to convert fraud classification rules learned from a genetic algorithm to a fuzzy score representing the degree to which a company's financial statements match those rules. Applying the method to financial data in real time can lead to the early detection of potentially fraudulent corporate behavior.
The contribution of rare variants to risk of schizophrenia in individuals with and without intellectual disability (2017)

By performing a meta-analysis of rare coding variants in whole-exome sequences from 4,133 schizophrenia cases and 9,274 controls, de novo mutations in 1,077 family trios, and copy number variants from 6,882 cases and 11,255 controls, we show that individuals with schizophrenia carry a significant burden of rare, damaging variants in 3,488 genes previously identified as having a near-complete depletion of loss-of-function variants. In patients with schizophrenia who also have intellectual disability, this burden is concentrated in risk genes associated with neurodevelopmental disorders. After excluding known risk genes for neurodevelopmental disorders, a significant rare variant burden persists in other genes intolerant of loss-of-function variants; although this effect is notably stronger in patients with both schizophrenia and intellectual disability, it is also seen in patients with schizophrenia who do not have intellectual disability. Together, our results show that rare, damaging variants contribute to the risk of schizophrenia both with and without intellectual disability and support an overlap of genetic risk between schizophrenia and other neurodevelopmental disorders.
Porous Glass‐Ceramic in the CαO–TiO 2 –P 2 O 5 System (1989)

A porous glass‐ceramic in the CaO–TiO 2 —P 2 O 5 system has been prepared by crystallization and subsequent chemical leaching of the corresponding glass. By applying a two‐step heat treatment to 45CaO · 25TiO 2 · 30P 2 O 5 glasses containing a few mol% of Na 2 O, volume crystallization results in the formation of dense glass‐ceramics composed of CaTi 4 (PO 4 ) 6 and β‐Ca 3 (PO 4 ) 2 phases. By leaching the resultant glass ceramics with HCI, β‐Ca 3 (PO 4 ) 2 is selectively dissolved out, leaving a crystalline CaTi 4 (PO 4 ) 6 skeleton. The surface area and mean pore radius of the porous glass‐ceramics were approximately 40 m 2 /g and 13 nm, respectively.
The Antioxidant and Anti-Inflammatory Activities of 8-Hydroxydaidzein (8-HD) in Activated Macrophage-Like RAW264.7 Cells (2018)

8-Hydroxydaidzein (8-HD) is a daidzein metabolite isolated from soybeans. This compound has been studied for its anti-proliferation, depigmentation, and antioxidant activities. However, the anti-inflammatory activities of 8-HD are not well-understood. Through its antioxidant effects in ABTS and DPPH assays, 8-HD reduces the production of sodium nitroprusside (SNP)-induced radical oxygen species (ROS). By triggering various Toll-like receptors (TLRs), 8-HD suppresses the inflammatory mediator nitric oxide (NO) without cytotoxicity. We examined the regulatory mechanism of 8-HD in lipopolysaccharide (LPS)-induced conditions. We found that 8-HD diminishes inflammatory gene expression (e.g., inducible nitric oxide synthase (iNOS), cyclooxygenase (COX)-2, and tumor necrosis factor (TNF)-&alpha;) by regulating the transcriptional activities of nuclear factor (NF)-κB and activator protein 1 (AP-1). To find the potential targets of 8-HD, signaling pathways were investigated by immunoblotting analyses. These analyses revealed that 8-HD inhibits the activation of TAK1 and that phosphorylated levels of downstream molecules decrease in sequence. Together, our results demonstrate the antioxidant and anti-inflammatory actions of 8-HD and suggest its potential use in cosmetics or anti-inflammatory drugs.
Analysis of Joint Impact of Optical Refractivity and Turbulence on Laser Beam and Image Characteristics (2018)

The results of numerical analysis demonstrate that an inverse temperature layer (ITL) located in the vicinity of a propagation path could significantly impact the laser beam statistical characteristics and image formation.
ChemInform Abstract: Total Synthesis of (+)‐Ambruticin S. (2002)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 100 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a “Full Text” option. The original article is trackable via the “References” option.
Ultrastructure and Mechanical Properties of Populus Wood with Reduced Lignin Content Caused by Transgenic Down-Regulation of Cinnamate 4-Hydroxylase (2010)

Several key enzymes in lignin biosynthesis of Populus have been down-regulated by transgenic approaches to investigate their role in wood lignification and to explore their potential for lignin modification. Cinnamate 4-hydroxylase is an enzyme in the early phenylpropanoid pathway that has not yet been functionally analyzed in Populus . This study shows that down-regulation of cinnamate 4-hydroxylase reduced Klason lignin content by 30% with no significant change in syringyl to guaiacyl ratio. The lignin reduction resulted in ultrastructural differences of the wood and a 10% decrease in wood density. Mechanical properties investigated by tensile tests and dynamic mechanical analysis showed a decrease in stiffness, which could be explained by the lower density. The study demonstrates that a large modification in lignin content only has minor influences on tensile properties of wood in its axial direction and highlights the usefulness of wood modified beyond its natural variation by transgene technology in exploring the impact of wood biopolymer composition and ultrastructure on its material properties.
Self-Trapping of “Necklace” Beams in Self-Focusing Kerr Media (1998)

We show that an azimuthally periodically modulated bright ring ``necklace'' beam can self-trap in self-focusing Kerr media and can exhibit stable propagation for very large distances. These are the first bright $(2+1)\mathrm{D}$ beams to exhibit stable self-trapping in a system described by the cubic $(2+1)\mathrm{D}$ nonlinear Schr\"odinger equation.
Novel Fourier transform infrared spectrometer architecture based on cascaded Fabry-Perot interferometers (2016)

In this work, we present a novel architecture for Fourier transform spectrometers based on cascaded low-finesse FP interferometers. One of the interferometers has fixed path length while the second is a scanning one using a relatively large stroke electrostatic comb-drive actuator. The fixed interferometer results in a spectrum modulation and, hence, a shifted version of the interferogram away from the point of the zero spacing between the two mirrors. The shifted interferogram can then be used with the Fourier transform algorithm to obtain the spectrum of the measured light. This cascaded FP configuration results in a simple arrangement of mirrors on a line, which makes it much tolerant to misalignment errors. The proposed configuration is implemented using the MEMS DRIE technology on an SOI wafer with a simple MEMS process flow without metallization or dielectric coating of the vertical optical surface. The fabricated compact structure is measured with both a laser source with narrow spectrum at 1550 nm and a wide spectrum source composed of an SLED and the ASE of a semiconductor optical amplifier source. The obtained results validate the concept of the new configuration.
Abstract 233: Bispecific HER2 ADC: Making more potent HER2 ADC by improving target internalization (2019)

Trastuzumab-emtansine (T-DM1) targets the well-characterized breast cancer oncogene HER2, and has shown success in the clinic, but tumors expressing intermediate levels of HER2 remain resistant to T-DM1 therapy, apparently due to insufficient lysosomal trafficking of T-DM1. Here, we engineered bispecific HER2-DM1 conjugates that bridge HER2 with the rapidly internalizing receptor APLP2. The high affinity arm of HER2xAPLP2 bispecific antibodies mediates surface binding to HER2+ tumor cells (but not to HER2- normal cells). After binding to HER2, the low affinity APLP2 arm promotes antibody internalization and lysosomal degradation. The strength of the APLP2 arm allows for modulation of the degree of internalization, degradation and killing. In in vitro killing assays, HER2xAPLP2-DM1 were significantly more potent than T-DM1 in cell lines expressing high (IHC3+) and intermediate (IHC 2+) levels of HER2, albeit induced little or no killing in cell lines expressing low HER2 levels (IHC 1+). Monovalent APLP2-ADCs induced little or no killing in all cell lines tested. Selected HER2xAPLP2-DM1 conjugates had acceptable PK profile in APLP2 humanized mice while significantly outperforming T-DM1 in inhibiting growth of IHC2+ tumor xenografts. These data pave the way to generate clinical candidate ADCs that will improve on T-DM1. In addition, our study opens up a possibility to exploit internalizing proteins such as APLP2 in combination with bispecific antibodies to enhance efficacy of ADCs.Citation Format: Andres Perez Bay, Anuj Kalsy, Shiwani Tiwari, Bo Luan, Art Kunz, Zhaoyuan Chen, Li Zhang, Terra Potocky, Thomas Nittoli, Gavin Thurston, Christopher Daly, Julian Andreev. Bispecific HER2 ADC: Making more potent HER2 ADC by improving target internalization [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2019; 2019 Mar 29-Apr 3; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2019;79(13 Suppl):Abstract nr 233.
Small-Molecule Inducer of β Cell Proliferation Identified by High-Throughput Screening (2013)

The identification of factors that promote β cell proliferation could ultimately move type 1 diabetes treatment away from insulin injection therapy and toward a cure. We have performed high-throughput, cell-based screens using rodent β cell lines to identify molecules that induce proliferation of β cells. Herein we report the discovery and characterization of WS6, a novel small molecule that promotes β cell proliferation in rodent and human primary islets. In the RIP-DTA mouse model of β cell ablation, WS6 normalized blood glucose and induced concomitant increases in β cell proliferation and β cell number. Affinity pulldown and kinase profiling studies implicate Erb3 binding protein-1 and the IκB kinase pathway in the mechanism of action of WS6.
A back biasing voltage generator for 28nm UTBB-FDSOI RVT CMOS digital circuits (2018)

This paper presents a Back-Biasing regulation module developed for the next-generation of 28nm UTBB FDSOI (Ultra-Thin Box and Body Fully Depleted Silicon On Insulator) IOT microcontroller products. The module enables both Reverse Back Biasing (RBB) and Forward Back Biasing (FBB) of a standard digital logic region with programmable voltage levels. Main design requirements and regulator load characteristics are analyzed. A description of the load model is also included. Silicon results from a circuit implementation included in i.MX7ULP™ low-power microcontroller are presented. The circuit occupies an area of 0.2mm <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sup> with negligible power consumption compared to the total system.
Using phase space diagrams to interpret multiple frequency drive sonoluminescence (1999)

The recent experimental results of J. Holzfuss, M. Rüggeberg, and R. Mettin [Phys. Rev. Lett. 81, 1961 (1998)] in which a second harmonic drive system was used to generate sonoluminescence (SL) have been analyzed in the context of the dissociation hypothesis (DH) of D. Lohse and S. Hilgenfeldt [J. Chem. Phys. 107, 6986 (1997)]. The second harmonic introduces two more variables that are under experimental control: a phase and an additional pressure term to the acoustic drive pressure. Diffusive equilibrium curves for a fixed gas concentration were calculated as was the Mach criterion. A phase space diagram was constructed to permit the prediction of regions of stable SL, unstable SL, stable non-SL, and unstable non-SL. These were compared to Holzfuss’ experimental observations, and excellent quantitative agreement was seen. The results provide further evidence that the underlying assumptions of DH are sound. They also indicate the utility of DH for determining appropriate experimental conditions to achieve SL and for optimizing an experimental system.