gebhart/patrepeval huggingface dataset:
Ratiometric Molecular Microscopy: Towards Real-Time Quantitative Delineation of Brain Tumor Margins (2012)

In order to unambiguously distinguish between normal and malignant brain tissues in real-time, an achromatic version of a micro-mirror-scanned miniature dual-axis confocal microscope has been developed for ratiometric quantification of biomarker expression as revealed by the topical application of fluorescent contrast agents that are being developed using rational and combinatorial approaches.
Inside Cover: Photocatalytic Water Oxidation by a Mixed‐Valent MnIII3MnIVO3 Manganese Oxo Core that Mimics the Natural Oxygen‐Evolving Center (Angew. Chem. Int. Ed. 42/2014) (2014)

The engine of aerobic life on earth is a tetramanganese oxo cluster at the very heart of Photosystem II (PS II) in green plants, algae, and photosynthetic bacteria. In their Communication on page 11182 ff., F. Scandola, U. Kortz, M. Bonchio et al. have identified a unique hybrid set of ligands to provide the first functional analogue of the PS II oxygen-evolving center that works in an artificial environment (Cover picture: Rami Al-Oweini).
Information scrambling in quantum circuits (2021)

Interactions in quantum systems can spread initially localized quantum information into the exponentially many degrees of freedom of the entire system. Understanding this process, known as quantum scrambling, is key to resolving several open questions in physics. Here, by measuring the time-dependent evolution and fluctuation of out-of-time-order correlators, we experimentally investigate the dynamics of quantum scrambling on a 53-qubit quantum processor. We engineer quantum circuits that distinguish operator spreading and operator entanglement and experimentally observe their respective signatures. We show that whereas operator spreading is captured by an efficient classical model, operator entanglement in idealized circuits requires exponentially scaled computational resources to simulate. These results open the path to studying complex and practically relevant physical observables with near-term quantum processors.
Frequency dependent electrical measurements of amorphous GeSbSe chalcogenide thin films (2010)

A commercial bulk chalcogenide glass (Ge28Sb12Se60) was used as a source to fabricate amorphous thin films via thermal evaporation technique. At low frequencies (&amp;lt;1 MHz) impedance spectroscopy was performed to measure electrical properties. To measure ac conductivity at microwave frequencies, a split resonance cavity technique was applied for which a model based on parallel arrangement of substrate and film capacitors was developed. This model was used to extract tan δ and ac conductivity of the films. Microwave ac conductivity was correlated with the extrapolated low frequency conductivity data confirming applicability of the universal law commonly observed in amorphous semiconductors.
TIM-1 Signaling Is Required for Maintenance and Induction of Regulatory B Cells through Apoptotic Cell Binding or TIM-1 Ligation. (2014)

B cells can exhibit potent IL-10-dependent regulatory activity (Bregs). We previously demonstrated that TIM-1 is an inclusive marker for IL-10+ Bregs and these cells can directly transfer allograft tolerance. We now show that TIM-1 is not only a marker for Bregs, but is intimately involved in their induction and maintenance. Naïve TIM-1Δmucin (mucin domain deletion) mice exhibit an ˜40% baseline deficiency in IL-10+ B cells compared to wt mice. TIM-1Δmucin recipients of BM12 heart allografts are hyper-responsive and exhibit accelerated rejection (MST 27d vs. >60d in wt recipients; p,0.01). Moreover, CD4 cells from TIM-1Δmucin recipients exhibit increased IFNγ(3x), IL-6(2x), and IL-17(1.5x), and impaired IL-5(4x), and IL-13(10x).Transfer of alloimmunized wt TIM-1+ but not TIM-1- B cells into TIM-1Δmucin recipients prolonged GS (MST from 27 to 42d; p<0.05) suggesting that the relative Breg deficiency in TIM-1Δmucin mice contributes to their hyper-responsiveness. Next, we addressed the response of B cells from wt vs. TIM-1Δmucin mice to in vivo TIM-1 ligation with a tolerogenic anti-TIM-1(RMT1-10). Importantly, anti-TIM-1 binds with equivalent affinity to TIM-1 from both mice. Whereas anti-TIM-1 induces a 1.6-2X increase (to 22%) in TIM-1+IL-10+ Bregs in wt mice, this mAb had no affect on Bregs from TIM-1Δmucin mice. (10% = control levels). This suggests a defect in TIM-1 signaling. Finally, we asked whether the induction of IL-10+ Bregs in response to apoptotic cells (ACs) is dependent on intact TIM-1, a known phosphatidylserine(PS) receptor. wt and TIM-1Δmucin mice were treated with autologous ACs. ACs increased Bregs 2.5X in wt mice but had no effect in TIM-1Δmucin mice. Similarly, purified TIM-1+ (but not TIM-1- or TIM-1Δmucin) B cells upregulate IL-10 expression when they are directly cultured with ACs in vitro. Assessed by confocal microscopy, TIM-1+ TIM-1Δmucin B cells and TIM-1- wt B cells both bind 70% less PS-liposomes than TIM-1+ wt B cells. These data suggest that TIM-1 signaling plays a direct role in Breg maintenance and induction both under physiological conditions (in response to apoptotic cells) and in response to TIM-1 ligation. We hypothesize that AC:TIM-1 binding helps maintain basal Bregs and is defective in TIM-1Δmucin mice, contributing to their hyper-reactivity.
Synthesis and Pharmacological Evaluation of Novel Adenine–Hydrogen Sulfide Slow Release Hybrids Designed as Multitarget Cardioprotective Agents (2016)

This work deals with the design, synthesis, and evaluation of the cardioprotective properties of a number of novel hybrid compounds combining the adenine nucleus with a suitable H2S slow-releasing moiety, coupled via a stable ether bond. The H2S release rate of the hybrids and their ability to increase cGMP were estimated in vitro. The most promising derivatives 4 and 11, both containing 4-hydroxythiobenzamide moiety as H2S donor, were selected for further in vivo evaluation. Their ability to release H2S in vivo was recorded using a new fully validated UPLC-DAD method. Both compounds reduced significantly the infarct size when administered at the end of sustained ischemia. Mechanistic studies showed that they conferred enhanced cardioprotection compared to adenine or 4-hydroxythiobenzamide. They activate the PKG/PLN pathway in the ischemic myocardium, suggesting that the combination of both pharmacophores results in synergistic cardioprotective activity through the combination of both molecular pathways that trigger cardioprotection.
Apparatus and method for the production of gel beads containing a biocatalyst (2023)

An apparatus and method for the large-scale and continuous production of gel beads containing a biocatalyst. The apparatus is a columnar system based on the chemical cross-linking of hydrocolloidal gels that contain and immobilize a biocatalyst, the biocatalyst being a microorganism or an enzyme. Hydrocolloidal gels, such as alginate, carrageenan, and a mixture of bone gelatin and modified alginate, provide immobilization matrices that can be used to entrap and retain the biocatalyst while allowing effective contact with substrates and release of products. Such immobilized biocatalysts are generally formulated into small spheres or beads that have high concentrations of the biocatalyst within the gel matrix. The columnar system includes a gel dispersion nozzle submerged in a heated non-interacting liquid, typically an organic liquid, that is immiscible with water to allow efficient formation of spherical gel droplets, the non-interacting liquid having a specific gravity that is less than water so that the gel droplets will fall through the liquid by the force of gravity. The heated non-interacting liquid is in direct contact with a chilled upflowing non-interacting liquid that will provide sufficient residence time for the gel droplets as they fall through the liquid so that they will be cooled below the gelling temperature and form solid spheres. The upflowing non-interacting liquid is in direct contact with an upflowing temperature-controlled aqueous solution containing the necessary chemicals for cross-linking or fixing of the gel beads to add the necessary stability. The flow rates of the two liquid streams can be varied to control the proper residence time in each liquid section to accommodate the production of gel beads of differing settling velocities. A valve is provided for continuous removal of the stabilized gel beads from the bottom of the column.
Factors Associated With Positive D‐dimer Results in Patients Evaluated for Pulmonary Embolism (2010)

Many factors are associated with a positive D-dimer test. The effect of these factors on the usefulness of the test should be considered prior to ordering a D-dimer.
Preface (1994)

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Planetary Geochemical Investigations by Raman-LIBS Spectroscopy (RLS) (2013)

Abstract Not Provided
Circulating Cell-Free RNA in Blood as a Host Response Biomarker for the Detection of Tuberculosis (2023)

Tuberculosis (TB) remains a leading cause of death from an infectious disease worldwide. This is partly due to a lack of tools to effectively screen and triage individuals with potential TB. Whole blood RNA signatures have been extensively studied as potential biomarkers for TB, but they have failed to meet the World Health Organization's (WHOs) target product profiles (TPPs) for a non-sputum triage or diagnostic test. In this study, we investigated the utility of plasma cell-free RNA (cfRNA) as a host response biomarker for TB. We used RNA profiling by sequencing to analyze plasma samples from 182 individuals with a cough lasting at least two weeks, who were seen at outpatient clinics in Uganda, Vietnam, and the Philippines. Of these individuals, 100 were diagnosed with microbiologically-confirmed TB. Our analysis of the plasma cfRNA transcriptome revealed 541 differentially abundant genes, the top 150 of which were used to train 15 machine learning models. The highest performing model led to a 9-gene signature that had a diagnostic accuracy of 89.1% (95% CI: 83.6-93.4%) and an area under the curve of 0.934 (95% CI: 0.8674-1) for microbiologically-confirmed TB. This 9-gene signature exceeds the optimal WHO TPPs for a TB triage test (sensitivity: 96.2% [95% CI: 80.9-100%], specificity: 89.7% [95% CI: 72.4-100%]) and was robust to differences in sample collection, geographic location, and HIV status. Overall, our results demonstrate the utility of plasma cfRNA for the detection of TB and suggest the potential for a point-of-care, gene expression-based assay to aid in early detection of TB.
Machine learning for deep space network antenna motions detection (2022)

Highly stable frequency and timing standards are essential for deep-space missions and radio science. At the NASA Deep Space Network (DSN), these standards are distributed through a network of underground fiber cables to support several Goldstone antennas. Independently developed frequency-measuring instruments generate tremendous quantities of data to monitor and validate the antennas’ stringent frequency requirements. In this paper, we propose a lightweight processing tool capable of detecting disturbances on the frequency signal caused by DSN antenna motions. Our training data is sampled from the movement log of the antenna of interest and the generated data from the fiber optic metrology instrument linked to the antenna. We demonstrate that a convolutional neural network (CNN) model can achieve high accuracies on classifying instances of antenna movements and is an effective predictor when used iteratively on longer, variable stretches of metrology data. The simplicity, low training cost, and high accuracies of our model strongly suggest its efficacy in identifying and troubleshooting frequency disturbances caused by the antenna.
A Hardware Accelerator for JavaTM Platforms on a 130-nm Embedded Processor Core (2007)

We have developed a hardware accelerator for Java platforms, integrated on a SuperH microprocessor core, using a 130-nm CMOS process. The Java accelerator, a bytecode translation unit (BTU), is tightly coupled with the CPU to share resources. The BTU supports 159 basic bytecodes and 5 or 6 optional bytecodes. It. supports both connected device configuration (CDC) 1.0 and connected limited device configuration (CLDC) 1.0.4 technologies. The BTU corresponds to the dual-issued superscalar CPU and applies a new method, control-sharing. With this method, the BTU always grasps the pipeline status of the CPU, and the Java program is processed by both the BTU and the CPU. To implement this method, we developed some acceleration techniques: fast branch requests, enhanced CPU instructions, Java runtime exception detection hardware, and fewer overhead cycles of handover between the BTU and the CPU. In particular, the BTU can detect Java runtime exceptions in parallel with other processing, such as an array access. With previous methods, there is a disadvantage in that CPU efficiency decreases for Java-specific processing, such as array index bounds checking. The sample chip was fabricated in Renesas 130-nm, five-layer Cu, dual-vth -low-power CMOS technology. The chip runs at 216 MHz and 1.2 V. The BTU has 75 kG. The benchmark on an evaluation board showed 6.55 embedded caffeine marks (ECM)/MH/. on the CLDC 1.0.4 configuration, a tenfold speed increase without the BTU for roughly the same power consumption. In other words, power savings of 90 percent with the same performance were achieved.
Figure S3 from Cathepsin B Is Dispensable for Cellular Processing of Cathepsin B-Cleavable Antibody–Drug Conjugates (2023)

&lt;p&gt;Supplementary Figure 3: Effect of pharmacological inhibition of cathepsin B in KPL-4 cells. A) Loss of enzymatic activity with the addition of CA074-ME. B) Dose-titration curve for KPL-4 cells with and without CA074-ME in the presence of anti-HER2-VC(S)-MMAE. C) Free MMAE release in KPL-4 cells with and without CA074-ME.&lt;/p&gt;
Cover Picture: Macromol. Rapid Commun. 4/2007 (2007)

Cover: Microwave heating is already an established technique in organic chemistry, but polymer chemists are just starting to discover the advantages of microwave irradiation. The articles compiled in this Special Issue of Macromolecular Rapid Communications on “Microwaves and Polymers” give an overview about the state‐of‐the‐art of microwave assisted synthesis of polymers and address challenges that include gaining a better understanding of the effects of microwave irradiation on molecules and scale‐up issues.
Ultra Small OLEd Pico Projector (2009)

Abstract An ultra compact projection system based on a high brightness OLEd micro display is developed. System design and realization of a prototype are presented. This OLEd pico projector with a volume of about 10 cm 3 can be integrated into portable systems like mobile phones or PdAs. The Fraunhofer IPMS developed the high brightness monochrome OLEd micro display. The Fraunhofer IOF designed the specific projection lens [1] and integrated the OLEd and the projection optic to a full functional pico projection system. This article provides a closer look on the technology and its possibilities.
Framework composition and activity of platinum-containing high-silica zeolites in n-hexane isomerization (2009)

The conversion of n-hexane on Pt-containing dealuminated mordenites and ZSM-5 zeolites was studied. The framework composition and the concentrations of extraframework aluminum compounds in mordenites were determined by X-ray diffraction analysis. It was demonstrated that the aluminum content of the framework affected the activity in n-hexane isomerization. It was found that a Pt-mordenite catalyst containing a considerable amount of extraframework aluminum compounds exhibited maximum activity. A quantum-chemical study of the interaction of platinum with Brønsted and Lewis acid sites was performed. It was hypothesized that oxidized surface platinum nanoparticles were the active sites of Pt-containing high-silica zeolites. These nanoparticles were formed by the interaction of platinum clusters with proton sites or extraframework aluminum compounds. An alternative mechanism was proposed for the conversion of alkanes to exclude the direct participation of acid sites.
Practical Applications of Signal Processing and Machine Learning in a Dynamic Retail Environment (2018)

Presented on October 31, 2018 at 12:15 p.m. in the Marcus Nanotechnology Building, Room 1116.
1695: BIOREACTANCE CARDIOGRAPHY IN A PORCINE MODEL OF SUBCLINICAL HEMORRHAGE (2019)

Anderson, Justin; Hamlin, Alexandra; Joseph, Minichiello; Klein, Samuel; Lindqwister, Alexander; Halter, Ryan; Elliott, Jonathan; Vaze, Vikrant; Paradis, Norman Author Information
Anti-PD-1 to enhance NK-cell cytotoxicity towards CD30+ Hodgkin lymphoma induced by CD30/CD16A TandAb AFM13. (2016)

e14012 Background: AFM13 is an NK-cell engaging TandAb in Ph. 2 development in Hodgkin Lymphoma (HL) and CD30+ malignancies. As immune checkpoint modulators have demonstrated clinical efficacy in a various cancers we were prompted to investigate the combination of AFM13 with several immunomodulatory antibodies. In previous experiments, we demonstrated higher efficacy of AFM13 than such antibodies and strong synergy between AFM13 and an anti-PD1 antibody in vitro, and in vivo PDX models with human HL tumors. Methods: To further investigate the immunological mechanisms we used an autologous PDX mouse model with donor-matched tumors and PBMCs from HL patients. Animals were treated with AFM13 and in combination with anti-PD1. Tumor size, tumor-infiltrating human lymphoid cells, myeloid cells and intra-tumoral cytokines were evaluated at several time-points after treatment start. Results: While monotherapy with AFM13 was reproducibly more potent than anti-PD1 in controlling tumor growth, significant synergy was observed when both agents were combined. We observed a strong correlation between tumor growth inhibition and levels of tumor-infiltrating NK-cells, T-cells, myeloid cells and intra-tumoral cytokines. In contrast to anti-PD1 monotherapy, which only induced T-cell infiltration, AFM13 monotherapy was able to induce infiltration of both NK- and T-cells, which was further enhanced by the combination of both agents. Tumor analyses at earlier time-points showed that the initial immune response is characterized by infiltration of macrophages and activated NK-cells, whilst the adaptive immune response by T-cells and dendritic cells occurred later. These findings strongly support AFM13-mediated cross-talk between innate and adaptive immunity and a concerted role in tumor eradication. Conclusions: Our data support strong synergistic anti-tumor efficacy when AFM13 is combined with anti-PD1 checkpoint, mediated by tumor-infiltrating lymphoid and myeloid cells, providing strong evidence for cross-talk between innate and adaptive immunity induced by AFM13-recruited human NK-cells. A clinical study in r/r HL patients of AFM13 in combination with KEYTRUDA is currently in preparation.
Analysis of Omic Data (2015)

Since the late 1990s, there has been an explosion in the development of technologies that measure cellular content on a genome scale. These methods generate large amounts of data, generally referred to as omic data; sometimes referred to as content. The quality and coverage of omic data sets has improved steadily with time. Individual data points in omic data sets are treated as independent variables. They can then be correlated statistically to find patterns in the presence of cellular components. Such statistical correlations do not confer causality. GEMs, given their mechanism-based construction, can be used as a context for the analysis of polyomic data sets [358]. Such contextualization can lead to the establishment of causation. Furthermore, GEMs can integrate mechanistically multiple omic data sets, thus aiding in the determination of how various components come together to produce cellular functions and phenotypic states. For some, this big data to knowledge conversion represents a grand challenge in biology. Here we will cover the basic principles of omic data analysis using GEMs. More detailed reviews have appeared describing these data-mapping methods and their use [41, 175, 209, 232, 253].
The Total Cost to the Health Care System in Medicare and Medicaid Patients for the Treatment of Cervical Myelopathy (2018)

There is no significant difference in the total health care expenditures for operative versus nonoperative treatment of cervical myelopathy after 3 years. It is critical to understand that nonoperative treatment of this progressive disease leads to a substantial increase in total health care expenditures with increased risk of falls, injury, and further morbidity.
INFLUENCE OF BACTERIAL ENDOTOXIN ON RADIATION-INDUCED ACTIVATION OF HUMAN ENDOTHELIAL CELLS IN VITRO AND IN VIVO (1997)

To extend previous studies on the anti-inflammatory role of interleukin (IL)-10 in vivo, mice pretreated with IL-10 were subjected to ionizing radiation (IR), lipopolysaccharide (LPS), or both and assessed for the expression of the intercellular adhesion molecule 1 (ICAM-1) in immunohistochemical analyses. IL-10 was able to almost fully protect LPS+IR-treated animals against ICAM-1 up-regulation. Because LPS and IR also increased adhesion of peripheral blood mononuclear cells, transendothelial migration assays were performed to investigate the functional significance of these findings. IR was found to induce transendothelial migration, and this effect could be enhanced by cotreatment with LPS, in the same fashion as peripheral blood mononuclear cell adhesion. Also in this system, IL-10 proved to act as a potent LPS antagonist. Finally, in vivo immunohistochemical analyses revealed an infiltration of CD3+ T lymphocytes into organs that were the target of transplant-related complications after LPS+IR treatment. This infiltration could also be completely reversed by IL-10 pretreatment.
Parallel file striping on optical jukebox servers (2003)

In the near future, large digital media servers are expected to offer storage capacities in the order of petabytes. Servers made of clusters of PCs connected to jukeboxes may represent an interesting alternative compared with servers made of arrays of magnetic disks. However, due to disk exchange overhead, higher seek times and lower data transfer rates, access to data located on optical disks is significantly slower than access to data located on magnetic disks. In the present contribution, we analyze the benefits and limitations of striping files across multiple optical disks in order to speedup the retrieval of large pieces of information. We also show that server applications requiring both computer power and I/O bandwidth may be distributed over several processing nodes and access files striped over multiple optical disks. For such applications, as long as disk exchanges are not necessary, a predictable speedup can be obtained by ensuring a high enough number of server computers, optical disk drive units, and enough communication bandwidth.
External partial discharge resistance of polyethylene and crosslinked polyethylene containing voltage stabilizers (2002)

Anthracene and vinyl naphthalene were melt blended with a low density polyethylene grade at concentrations of 0.5 and 2 wt% respectively. The latter was mixed with dicumyl-peroxide and crosslinked. The resistance to external partial discharges was measured by recording time to breakdown in a needle-plane configuration. The external PD resistance was neither increased by crosslinking nor by the addition of aromatic additives at concentrations of up to a few percent by weight.