gebhart/patrepeval huggingface dataset:
Characterization and differentiation of high energy amine peroxides by direct analysis in real time TOF/MS (2007)

Characterization of hexamethelene triperoxide diamine (HMTD), tetramethylene diperoxide dicarbamide (TMDD) and tetramethylene diperoxide acetamide (TMDA) has been carried out using Direct Analysis in Real Time/Time of Flight Mass Spectrometry (DART-TOF/MS). The study also centered in the detection of their precursors such as hexamine and formaldehyde. Analysis of the compounds by GC-MS was also conducted. HMTD shows a clear peak at 209 m/z that allowed its detection in standard solutions and lab made standards. TATP samples with deuterium enrichment are being analyzed to compare results that could differentiate from HMTD and similar substances. All samples were characterized by Raman and FT-IR to confirm the DART results. Some of the vibrations observed were in the &#957;(O-O), &#957;(N-C), &#957;(N-H), &#957;(C-O), &#948;(CH<sub>3</sub>-C) and &#948;(C-O). Development methodology for trace detection was compared with GC/MS and HPLC-MS results previously presented for HMTD and TATP.
Performance and Reliability Impact of Copper Plasticity in Backside TSV-Last Fabrication Process (2016)

The effects of copper permanent deformation during thermal cycles in backside through-silicon via (TSV)-last fabrication process are studied using an advanced 3-D simulator. The plasticity and creep model parameters are chosen to match experimental data. Two sets of different TSV configurations and back end of line (BEOL) layouts are utilized to examine TSV reliability, BEOL reliability, and front-end device performance after postplating thermal excursion. The results indicate that the copper plasticity deformation affects TSV stress distributions for TSV-last fabrication process. The configuration employing a thicker liner made of a softer material shows better TSV and BEOL reliability and lower TSV stress-induced device performance impact. It is also observed that the BEOL layout near the TSV edge needs to be optimized as the BEOL structures in this region experience larger mechanical stress and lower reliability.
SCAPULAR NOTCHING IN REVERSE SHOULDER ARTHROPLASTY (2009)

Scapular notching is of concern in reverse shoulder arthroplasty and has been suggested as a cause of glenoid loosening. Our purpose was to analyze in a large series the characteristics and the consequences of the notch and then to enlighten the causes in order to seek some solutions to avoid it. 430 consecutive patients (457 shoulders) were treated by a reverse prosthesis for various etiologies between 1991 and 2003 and analyzed for this retrospective multicenter study. Adequate evaluation of the notch was available in 337 shoulders with a follow-up of 47 months (range, 24–120 months). The notch has been diagnosed in 62% cases at the last follow-up. Intermediate reviews show that the notch is already visible within the first postoperative year in 82% of these cases. Frequency and grade extension of the notch increase significantly with follow-up (p< 0.0001) but notch, when present, is not always evolutive. At this point of follow-up, scapular notch is not correlated with clinical outcome. There is a corr...
Reducing Refresh Power in Mobile Devices with Morphable ECC (2015)

Energy consumption is a primary consideration that determines the usability of emerging mobile computing devices such as smartphones. Refresh operations for main memory account for a significant fraction of the overall energy consumption, especially during idle periods, when processor can be switched off quickly, however, memory contents continue to get refreshed to avoid data loss. Given that mobile devices are idle most of the times, reducing refresh power in idle mode is critical to maximize the duration for which the device remains usable. The frequency of refresh operations in memory can be reduced significantly by using strong multi-bit error correction codes (ECC). Unfortunately, strong ECC codes incur high latency, which causes significant performance degradation (as high as 21%, and on average 10%). To obtain both low refresh power in idle periods and high performance in active periods, this paper proposes Morphable ECC (MECC). During idle periods, MECC keeps the memory protected with 6-bit ECC (ECC-6) and employs a refresh period of 1 second, instead of the typical refresh period of 64ms. During active operation, MECC reduces the refresh interval to 64ms, and converts memory from ECC-6 to weaker ECC (single-bit error correction) on a demand-basis, thus avoiding the high latency of ECC-6, except for the first access during the active mode. Our proposal reduces refresh operations during idle mode by 16x, memory power in idle mode by 2X, while retaining performance within 2% of a system that does not use any ECC.
Grid applications---High-performance dynamic graphics streaming for scalable adaptive graphics environment (2006)

The Scalable Adaptive Graphics Environment (SAGE) is specialized middleware for enabling data, high-definition video and extremely high-resolution graphics to be streamed in real-time from remotely distributed rendering and storage clusters to scalable display walls over ultra-high-speed networks. In this paper, we present the SAGE architecture, focusing on its dynamic graphics streaming capability. In the SAGE framework, multiple visualization applications can be streamed to large tiled displays and viewed at the same time. The application windows can be moved, resized and overlapped like any standard desktop window manager. Every window movement or resize operation requires dynamic and non-trivial reconfiguration of the involved graphics streams. This approach has been successfully shown to scale to support streaming on the LambdaVision 100 Megapixel display wall. SAGE is now being extended to support distance collaboration with multiple endpoints by streaming visualization to all the participants.
An independent assessment of an artificial intelligence system for prostate cancer detection shows strong diagnostic accuracy (2021)

Prostate cancer is a leading cause of morbidity and mortality for adult males in the US. The diagnosis of prostate carcinoma is usually made on prostate core needle biopsies obtained through a transrectal approach. These biopsies may account for a significant portion of the pathologists' workload, yet variability in the experience and expertise, as well as fatigue of the pathologist may adversely affect the reliability of cancer detection. Machine-learning algorithms are increasingly being developed as tools to aid and improve diagnostic accuracy in anatomic pathology. The Paige Prostate AI-based digital diagnostic is one such tool trained on the digital slide archive of New York's Memorial Sloan Kettering Cancer Center (MSKCC) that categorizes a prostate biopsy whole-slide image as either "Suspicious" or "Not Suspicious" for prostatic adenocarcinoma. To evaluate the performance of this program on prostate biopsies secured, processed, and independently diagnosed at an unrelated institution, we used Paige Prostate to review 1876 prostate core biopsy whole-slide images (WSIs) from our practice at Yale Medicine. Paige Prostate categorizations were compared to the pathology diagnosis originally rendered on the glass slides for each core biopsy. Discrepancies between the rendered diagnosis and categorization by Paige Prostate were each manually reviewed by pathologists with specialized genitourinary pathology expertise. Paige Prostate showed a sensitivity of 97.7% and positive predictive value of 97.9%, and a specificity of 99.3% and negative predictive value of 99.2% in identifying core biopsies with cancer in a data set derived from an independent institution. Areas for improvement were identified in Paige Prostate's handling of poor quality scans. Overall, these results demonstrate the feasibility of porting a machine-learning algorithm to an institution remote from its training set, and highlight the potential of such algorithms as a powerful workflow tool for the evaluation of prostate core biopsies in surgical pathology practices.
VVC in the cloud and browser playback (2022)

The most recent international video coding standard that was developed jointly by the ITU-T and ISO/IEC is Versatile Video Coding (VVC). While VVC contains a feature set for a very wide range of applications it also allows for significant bit-rate reductions of around 50% for the same subjective video quality compared to its predecessor, High Efficiency Video Coding (HEVC). After the standardization was finished in July 2020, many activities were started to allow integration of VVC into practical applications.
High-Efficiency 250–320 GHz Power Amplifiers Using InP-based MOS-HEMTs (2022)

This study presents a broadband, high-efficiency power amplifier (PA) monolithic microwave integrated circuit (MMIC) that uses InP-based metal-oxide-semiconductor high-electron-mobility transistors (MOS-HEMTs) with an extended drain-side access region and a broadband conjugate matching topology. Advanced device technologies such as double-side-doped structures, MOS gate structures, and asymmetric gate recess were adopted, and the length of the drain side access region was optimized to simultaneously obtain high power and efficiency. A common-source PA MMIC was fabricated, and an interstage circuit was designed to maximize the S21 per unit stage in the broadband, resulting in a record-high PAE and wide bandwidth.
A novel mechanism for regulating the activity of proliferating cell nuclear antigen by a small protein (2014)

Proliferating cell nuclear antigen (PCNA) forms a trimeric ring that associates with and influences the activity of many proteins participating in DNA metabolic processes and cell cycle progression. Previously, an uncharacterized small protein, encoded by TK0808 in the archaeon Thermococcus kodakarensis, was shown to stably interact with PCNA in vivo. Here, we show that this protein, designated Thermococcales inhibitor of PCNA (TIP), binds to PCNA in vitro and inhibits PCNA-dependent activities likely by preventing PCNA trimerization. Using hydrogen/deuterium exchange mass spectrometry and site-directed mutagenesis, the interacting regions of PCNA and TIP were identified. Most proteins bind to PCNA via a PCNA-interacting peptide (PIP) motif that interacts with the inter domain connecting loop (IDCL) on PCNA. TIP, however, lacks any known PCNA-interacting motif, suggesting a new mechanism for PCNA binding and regulation of PCNA-dependent activities, which may support the development of a new subclass of therapeutic biomolecules for inhibiting PCNA.
Abstract 4233: Wnt pathway antagonist ipafricept (FZD8-Fc, OMP-54F28) inhibits tumor growth and reduces tumor-initiating cell frequency in ovarian patient-derived xenograft models (2015)

Abstract Ovarian cancer is the deadliest gynecologic malignancy and the fifth leading cause of death from cancer in women in the U.S. The Wnt/beta-catenin pathway, which signals through the Frizzled (FZD) receptor family and several co-receptors, has long been implicated in cancer. We have developed ipafricept (FZD8-Fc, OMP-54F28), a recombinant fusion protein consisting of the ligand-binding domain of FZD8 and a human IgG1 Fc fragment. This fusion protein blocks Wnt signaling induced by multiple Wnt family members by binding and sequestering WNT. Using minimally passaged ovarian patient-derived xenograft tumors (PDX), we demonstrate that ipafricept is efficacious in combination with chemotherapy in four of eight ovarian cancer PDX tumors examined. Utilizing an in vivo serial transplantation assay, we quantified a reduction of the tumor initiating cell frequency by ipafricept in combination with paclitaxel. Additionally, we have discovered that pre-treatment with ipafricept several days prior to paclitaxel therapy enhances the activity of both agents when compared to delivering the drugs simultaneously. The anti-tumor effect observed is directly associated with a modulation of Wnt pathway gene sets. In responsive tumors, we discovered that a large number of WNT target genes were significantly down-regulated by ipafricept (e.g, AXIN2, LRP5/6, and FZD8). Conversely, in non-responsive tumors, these genes were either unchanged or up-regulated by the combination therapy. Histologic analysis revealed that total beta-catenin protein levels were reduced by ipafricept alone and in combination with paclitaxel in responsive tumors but were unchanged in non-responsive tumors. We are using these tumors to develop biomarkers that can be used clinically. Our data demonstrates the potential therapeutic benefit of targeting Wnt signaling in ovarian cancer. A Phase 1b clinical trial is currently examining ipafricept in combination with paclitaxel and carboplatin in patients with recurrent platinum-sensitive ovarian cancer. Citation Format: Marcus M. Fischer, Wan-Ching Yen, Chun Zheng, Randall Henner, Fiore Cattaruzza, Tracy Tang, Pete Yeung, Tanuka Biswas, John Lewicki, Austin Gurney, Ann M. Kapoun, Timothy Hoey. Wnt pathway antagonist ipafricept (FZD8-Fc, OMP-54F28) inhibits tumor growth and reduces tumor-initiating cell frequency in ovarian patient-derived xenograft models. [abstract]. In: Proceedings of the 106th Annual Meeting of the American Association for Cancer Research; 2015 Apr 18-22; Philadelphia, PA. Philadelphia (PA): AACR; Cancer Res 2015;75(15 Suppl):Abstract nr 4233. doi:10.1158/1538-7445.AM2015-4233
Superbase‐Catalyzed Addition of Methanol to Propyne and Allene: An Expedient Synthesis of 2‐Methoxypropene. (2006)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 200 leading journals. To access a ChemInform Abstract, please click on HTML or PDF.
Electrophile scanning by chemical proteomics reveals a potent pan-active DUB probe for investigation of deubiquitinase activity in live cells (2022)

ABSTRACT Deubiquitinases (DUBs) are proteases that hydrolyze isopeptide bonds linking ubiquitin to protein substrates, which can lead to reduced substrate degradation through the ubiquitin proteasome system. Deregulation of DUB activity has been implicated in many disease states, including cancer, neurodegeneration and inflammation, making them potentially attractive targets for therapeutic intervention. The &gt;100 known DUB enzymes have been classified primarily by their conserved active sites, but we are still building our understanding of their substrate profiles, localization and regulation of DUB activity in diverse contexts. Ubiquitin-derived covalent activity-based probes (ABPs) are the premier tool for DUB activity profiling, but their large recognition element impedes cellular permeability and presents an unmet need for small molecule ABPs which account for local DUB concentration, protein interactions, complexes, and organelle compartmentalization in intact cells or organisms. Here, through comprehensive warhead profiling we identify cyanopyrrolidine (CNPy) probe IMP-2373 ( 12 ), a small molecule pan-DUB ABP to monitor DUB activity in physiologically relevant live cell systems. Through chemical proteomics and targeted assays we demonstrate that IMP-2373 quantitatively engages more than 35 DUBs in live cells across a range of non-toxic concentrations, and in diverse cell lines and disease models, and we demonstrate its application to quantification of changes in intracellular DUB activity during MYC deregulation in a model of B cell lymphoma. IMP-2373 thus offers a complementary tool to ubiquitin ABPs to monitor dynamic DUB activity in the context of disease-relevant phenotypes. SYNOPSIS TOC Graphical Abstract
Linear Viscoelastic Properties of Regular- and Reduced-Fat Pasteurized Process Cheese During Heating and Cooling (2006)

The rheology of process cheese during heating and cooling was examined by measuring the transient and dynamic linear viscoelastic properties of regular fat, lower moisture and an 80% reduced-fat, higher moisture pasteurized process cheese from 10 to 50°C. The dynamic (stress and frequency sweep) and transient (creep and recovery) rheological properties of the reduced-fat process cheese were found to be higher than that of regular-fat process cheese, indicating that fat content changed rheological properties more than moisture content. The temperature-dependent frequency dispersions of storage and loss moduli (dynamic mechanical spectra) were fitted with a power-law model, and master curves (at a reference temperature of 30°C) and shift factors were obtained by shifting the temperature-dependent frequency dispersion of dynamic mechanical spectra. The relaxation spectra (moduli, viscosities and relaxation times) of both cheeses were obtained from the master curves using the generalized Maxwell model and nonlinear regression. The viscosity distribution of corresponding Maxwell model elements were higher for the reduced-fat cheese by a factor of 1.6–4.7 compared to the regular-fat cheese, indicating that the higher moisture content in the reduced-fat process cheese did not loosen the protein matrix or soften the cheese even though higher moisture is recommended to cheese manufacturers in order to compensate for some textural defects in reduced-fat cheeses.
Rain attenuation prediction for the design of site-diversity LEO/SMS Gateway configuration in the tropics (2002)

This paper presents a propagation analysis regarding the set up of a LEO/SMS Gateway in a tropical region. The propagation effects considered are rain induced attenuation and gaseous absorption. The study is based on five years measurements of point rainfall rate and slant-path rain attenuation at 12 GHz performed in Rio de Janeiro. A method was developed and applied to scale the measured attenuation results to 19 and 29 GHz, the down and up-link frequencies of the Gateway.
The Time Is Right to Focus on Model Organism Metabolomes (2016)

Model organisms are an essential component of biological and biomedical research that can be used to study specific biological processes. These organisms are in part selected for facile experimental study. However, just as importantly, intensive study of a small number of model organisms yields important synergies as discoveries in one area of science for a given organism shed light on biological processes in other areas, even for other organisms. Furthermore, the extensive knowledge bases compiled for each model organism enable systems-level understandings of these species, which enhance the overall biological and biomedical knowledge for all organisms, including humans. Building upon extensive genomics research, we argue that the time is now right to focus intensively on model organism metabolomes. We propose a grand challenge for metabolomics studies of model organisms: to identify and map all metabolites onto metabolic pathways, to develop quantitative metabolic models for model organisms, and to relate organism metabolic pathways within the context of evolutionary metabolomics, i.e., phylometabolomics. These efforts should focus on a series of established model organisms in microbial, animal and plant research.
Light-driven retinal ganglion cell responses in blind rd mice after neural retinal transplantation. (2001)

This study demonstrates the presence of light-driven ganglion cell responses after subretinal transplantation in a retinal degenerate model. This finding may reflect functional integration of the transplant with the host, but a rescue effect on remaining host photoreceptors cannot be ruled out. The findings suggest, however, that modification of host parameters, such as host age, may be important approaches for improving the functional success of retinal transplantation.
Intraneural ganglia in the hip and pelvic region (2009)

To the authors' knowledge, these are the first cases of intraneural ganglia demonstrated to have a connection to the hip joint. This finding at a rare site provides further evidence for the unifying articular (synovial) theory for the formation of intraneural ganglia and reveals a shared mechanism for their propagation. Furthermore, understanding the pathogenesis of these lesions provides insight into their successful treatment and their recurrence.
Lagrangian coherent structures in the flow field of a fluidic oscillator (2016)

This paper is associated with a video winner of a 2015 APS/DFD Gallery of Fluid Motion Award. The original video is available from the Gallery of Fluid Motion, http://dx.doi.org/10.1103/APS.DFD.2015.GFM.V0015
Cardiomyocytes derived from human embryonic and induced pluripotent stem cells: comparative ultrastructure (2011)

Induced pluripotent stem cells (iPSC) are generated from fully differentiated somatic cells that were reprogrammed into a pluripotent state. Human iPSC which can be obtained from various types of somatic cells such as fibroblasts or keratinocytes can differentiate into cardiomyocytes (iPSC-CM), which exhibit cardiac-like transmembrane action potentials, intracellular Ca(2+) transients and contractions. While major features of the excitation-contraction coupling of iPSC-CM have been well-described, very little is known on the ultrastructure of these cardiomyocytes. The ultrastructural features of 31-day-old (post-plating) iPSC-CM generated from human hair follicle keratinocytes (HFKT-iPSC-CM) were analysed by electron microscopy, and compared with those of human embryonic stem-cell-derived cardiomyocytes (hESC-CM). The comparison showed that cardiomyocytes from the two sources share similar proprieties. Specifically, HFKT-iPSC-CM and hESC-CM, displayed ultrastructural features of early and immature phenotype: myofibrils with sarcomeric pattern, large glycogen deposits, lipid droplets, long and slender mitochondria, free ribosomes, rough endoplasmic reticulum, sarcoplasmic reticulum and caveolae. Noteworthy, the SR is less developed in HFKT-iPSC-CM. We also found in both cell types: (1) 'Ca(2+)-release units', which connect the peripheral sarcoplasmic reticulum with plasmalemma; and (2) intercellular junctions, which mimic intercalated disks (desmosomes and fascia adherens). In conclusion, iPSC and hESC differentiate into cardiomyocytes of comparable ultrastructure, thus supporting the notion that iPSC offer a viable option for an autologous cell source for cardiac regenerative therapy.
HIV-1-Specific T Cell-Dependent Natural Killer (NK) Cell Activation: Major Contribution by NK Cells to Interferon-γ Production in Response to HIV-1 Antigens (2009)

Natural killer (NK) cells can directly recognize virus-infected cells. Here, we demonstrate that NK cells also produce interferon (IFN)-gamma in an HIV-1-specific, T cell-dependent manner. After stimulation of peripheral blood mononuclear cells (PBMCs) from HIV-1-infected individuals with HIV-1-derived peptides, up to half of the IFN-gamma-producing PBMCs are NK cells. These results indicate that T cell-dependent NK cell IFN-gamma production can be important for immune control of HIV-1, and have implications for the interpretation of data from vaccine trials using ELISPOT and ELISA.
Der virtuelle Patient (2014)

The subject of this book is the virtualization of people and the impact of the virtual patient on medicine and health care. Using case examples, the authors illustrate the options and prospects for virtual patient models and simulations, and describe their application in clinical care and in training.