gebhart/patrepeval huggingface dataset:
Substratification of 70-gene high-risk breast cancers with a validated 80-gene molecular subtyping profile. (2010)

10615 Background: Classifying breast cancer into molecular subtypes has previously shown to be of potential use for further treatment guidance. Here we demonstrate how patients classified as high (or low) risk by MammaPrint can be further stratified into molecular subgroups by a newly developed and validated 80-gene molecular subtyping profile (BluePrint). Methods: This validation study was carried out on a gene expression dataset (Desmedt et al., ClinCRes 2007) of 198 frozen archival breast cancer samples that were also part of the TRANSBIG MammaPrint independent validation study (Buyse et al., JNCI 2006). These patients from 5 European hospitals had T1-2N0M0 invasive breast cancer, median age 47 years, median follow-up 14 years, without adjuvant treatment. Results: The 70-gene MammaPrint profile classified 124 out of 187 breast tumors (66%) as high risk and 63 (34%) as low risk. The 124 MammaPrint high-risk tumors were then further substratified with BluePrint into 48% (60) luminal-type, 21% (26) as ERBB2-type and 31% (38) as basal-type. Kaplan Meier analysis of these substratified groups shows nearly identical 10 year DMFS rates: luminal-type tumors 66%, ERBB2-type tumors 53%, basal-type tumors 62%, respectively, a similar survival as the original unstratified MammaPrint high-risk group (64%). Similarly, BluePrint stratified low-risk MammaPrint patients (63) all showed invariable good outcome (10 yr DMFS > 95%), including no distant metastases for basal and ERBB2-type (small) subgroups for a 10-year time period. Conclusions: The molecular subtyping profile BluePrint can classify MammaPrint high-risk breast tumors into biologically different molecular subgroups. We and others have shown that breast tumors of distinct molecular subtype have different benefit from (neo)adjuvant chemotherapy, ranging from minimal response in luminal- to substantial response for ERBB2- and basal-type tumors. Further substratification of MammaPrint high-risk patients may therefore be useful for developing subtype specific treatment regimens and potentially useful for future treatment decisions. Author Disclosure Employment or Leadership Position Consultant or Advisory Role Stock Ownership Honoraria Research Funding Expert Testimony Other Remuneration Agendia
Supramolecular Organization of C60 into Linear Columns of Five-Fold, Z-Shaped Strands (2001)

When cocrystallized with calix[5]arene, C60 arranges to form linear, 5-fold, Z-shaped columns consisting of molecular spheres that are in van der Waals contact with one another. The fullerene molecules are present in three completely different environments with regard to their supramolecular association with the calixarene molecules.
Low-Power Neuromorphic Hardware for Signal Processing Applications (2019)

Machine learning has emerged as the dominant tool for implementing complex cognitive tasks that require supervised, unsupervised, and reinforcement learning. While the resulting machines have demonstrated in some cases even super-human performance, their energy consumption has often proved to be prohibitive in the absence of costly super-computers. Most state-of-the-art machine learning solutions are based on memory-less models of neurons. This is unlike the neurons in the human brain, which encode and process information using temporal information in spike events. The different computing principles underlying biological neurons and how they combine together to efficiently process information is believed to be a key factor behind their superior efficiency compared to current machine learning systems. Inspired by the time-encoding mechanism used by the brain, third generation spiking neural networks (SNNs) are being studied for building a new class of information processing engines. Modern computing systems based on the von Neumann architecture, however, are ill-suited for efficiently implementing SNNs, since their performance is limited by the need to constantly shuttle data between physically separated logic and memory units. Hence, novel computational architectures that address the von Neumann bottleneck are necessary in order to build systems that can implement SNNs with low energy budgets. In this paper, we review some of the architectural and system level design aspects involved in developing a new class of brain-inspired information processing engines that mimic the time-based information encoding and processing aspects of the brain.
On Carbon doping to improve GeTe-based Phase-Change Memory data retention at high temperature (2010)

This paper investigates material and electrical properties of a new chalcogenide alloy for Phase-Change Memories (PCM): Carbon-doped GeTe (named GeTeC). First, several physico-chemical, optical and electrical analyses have been performed on full-sheet chalcogenide depositions in order to understand the intrinsic GeTeC phase-change behavior, and to characterize structure and composition of amorphous and crystalline states. Then, GeTeC with two different Carbon doping (4% and 10%) has been integrated in pillar-type analytical PCM cells. Physico-chemical and electrical data indicate that GeTeC is characterized by a much more stable amorphous phase compared to undoped GeTe. Thus, GeTeC offers a slower programming speed versus GeTe, but an improved data retention at high temperature. Finally, we argue that GeTeC alloy is a promising candidate for future developments of PCM technologies for embedded applications.
Scaling the Power Wall: A Path to Exascale (2014)

Modern scientific discovery is driven by an insatiable demand for computing performance. The HPC community is targeting development of supercomputers able to sustain 1 ExaFlops by the year 2020 and power consumption is the primary obstacle to achieving this goal. A combination of architectural improvements, circuit design, and manufacturing technologies must provide over a 20× improvement in energy efficiency. In this paper, we present some of the progress NVIDIA Research is making toward the design of Exascale systems by tailoring features to address the scaling challenges of performance and energy efficiency. We evaluate several architectural concepts for a set of HPC applications demonstrating expected energy efficiency improvements resulting from circuit and packaging innovations such as low-voltage SRAM, low-energy signalling, and on-package memory. Finally, we discuss the scaling of these features with respect to future process technologies and provide power and performance projections for our Exascale research architecture.
The efficacy of tixagevimab–cilgavimab prophylaxis against Omicron BA.5 variants in patients with hematological malignancies: insights from the Leukemia and Lymphoma Society Registry (2023)

Click to increase image sizeClick to decrease image size AcknowledgementsWe acknowledge that the Leukemia and Lymphoma Society Registry is supported by BeiGene, Pharmacyclics, an AbbVie Company, Kite, a Gilead Company, and Janssen Biotech.Disclosure statementNo potential conflict of interest was reported by the author(s).Author contributorsL.M.G. and L.A.S. designed and conducted the survey and participated in data collection. L.G., A.N., E.L., and V.S. performed the analysis. A.N. and E.L. wrote the manuscript. All authors provided critical feedback and reviewed the final manuscript. A.N. – Grant/Research: Pharmacyclics/AbbVie; Kite/Gilead, Cornerstone. Consultant: Janssen, Morphosys, Cornerstone, Epizyme, EUSA, Recordati, TG therapeutics, ADC therapeutics, AstraZeneca, Kite/Gilead, Honoraria: Pharmacyclics/AbbVie.Additional informationFundingThis study was supported by the Leukemia and Lymphoma Society.
TIJO: Trigger Inversion with Joint Optimization for Defending Multimodal Backdoored Models (2023)

We present a Multimodal Backdoor Defense technique TIJO (Trigger Inversion using Joint Optimization). Recent work arXiv:2112.07668 has demonstrated successful backdoor attacks on multimodal models for the Visual Question Answering task. Their dual-key backdoor trigger is split across two modalities (image and text), such that the backdoor is activated if and only if the trigger is present in both modalities. We propose TIJO that defends against dual-key attacks through a joint optimization that reverse-engineers the trigger in both the image and text modalities. This joint optimization is challenging in multimodal models due to the disconnected nature of the visual pipeline which consists of an offline feature extractor, whose output is then fused with the text using a fusion module. The key insight enabling the joint optimization in TIJO is that the trigger inversion needs to be carried out in the object detection box feature space as opposed to the pixel space. We demonstrate the effectiveness of our method on the TrojVQA benchmark, where TIJO improves upon the state-of-the-art unimodal methods from an AUC of 0.6 to 0.92 on multimodal dual-key backdoors. Furthermore, our method also improves upon the unimodal baselines on unimodal backdoors. We present ablation studies and qualitative results to provide insights into our algorithm such as the critical importance of overlaying the inverted feature triggers on all visual features during trigger inversion. The prototype implementation of TIJO is available at https://github.com/SRI-CSL/TIJO.
Selective Formation of Isopropyl alfa- and beta-Glucofuranosides in One Pot Reaction from D-Glucose and Propanol-2 Promoted by V2O5 (2004)

Reaction of D-glucose with propanol-2 promoted by V 2 O 5 gives rise exclusively to isopropylglucofuranosides. Their tetraacetates were prepared; X-ray structure of one of tetraacetates was determined. 1 H and 1 3 C NMR signals assignment was done by COSY and GMBC techniques. Mechanism of selective glucosidation was discussed.
Microserver System Use of Optical Technologies (2016)

The DOME microserver project achieves best operations per Joule thanks to ultra-dense packaging and the use of a suitable Server-on-a-Chip. Dense packaging eliminates many PHY chips and also replaces many off-board photonic links with on-board electronic links. Photonic links are, however, required at high density (32 ports) and high speed (40 Gbps) at the rack-unit edge.
ChemInform Abstract: 3‐Acetyl‐2,3‐dihydro‐2,2‐dimethyloxazole; Synthesis, Properties and Its Application as Olefinic Partner in the Paterno‐Bνchi Reaction. (1987)

Abstract The title compound (IV) is synthesized from the oxazolidine (I) via the mixture (IIIa)‐(IIId).
Fully integrated distributed power amplifier in CMOS technology, optimized for UWB transmitters (2004)

A power amplifier (PA) using the distributed amplifier technique for the ultra wideband (UWB) standard is presented. The amplifier is fabricated in a standard 0.13 /spl mu/m CMOS technology and comes with on-chip biasing circuitry and a non-distributed input stage. Measurement results are given for a chip-on-board module to take any influence of product assembly into account. It achieves a transmission coefficient S/sub 21/ = 17 dB, a corner frequency of f/sub c/ = 8 GHz and a 1 dB compression point of A/sub 1dB/ = 3.5 dBm. The output impedance is matched to 50 /spl Omega/ so that external matching circuitry can be omitted. With these features, it is customized to be integrated with other building blocks to a fully integrated CMOS UWB transmitter product.
Towards a Framework for Evaluating and Reporting Hansen Solubility Parameters: Applications to Nano and Micron Scale Particle Dispersions (2021)

A thorough understanding of complex interactions within particulate systems is a key for knowledge-based formulations. Hansen solubility parameters (HSP) are widely used to assess the compatibility of the dispersed phase with the continuous phase. At present, the determination of HSP is often based on a liquid ranking list obtained by evaluating a pertinent dispersion parameter using only one pre-selected characterization method. Furthermore, one cannot rule out the possibility of subjective judgment especially for liquids for which it is difficult to decipher the compatibility or underlying interactions. As a result, the end value of HSP might be of little or no information. To overcome these issues, we introduce a generalized technology-agnostic combinatorics-based approach. We discuss the principles of the approach and the implications of evaluating and reporting particle HSP values. We demonstrate the approach by using SiNx particles. We leverage the analytical centrifugation data to evaluate stability trajectories of SiNx dispersions in various liquids to deduce particle-liquid compatibility.
Boron Nitride Surface Activity as Route to Composite Dielectric Films (2015)

The propensity of boron nitride sheets to stack creates obstacles for their application as multifunctional materials despite their unique thermal, mechanical, and electrical properties. To address this challenge, we use a combination of molecular dynamics simulations and experimental techniques to demonstrate surfactant-like properties of BN sheets at the interface between immiscible solvents. The spreading of two-dimensional BN sheets at a high-energy oil/water interface lowers the free energy of the system, creating films of overlapping BN sheets that are more thermodynamically favorable than stacked sheets. Coating such films onto polymers results in composite materials with exceptional barrier and dielectric properties.
Impact of Nonfullerene Molecular Architecture on Charge Generation, Transport, and Morphology in PTB7‐Th‐Based Organic Solar Cells (2018)

Abstract Despite the rapid development of nonfullerene acceptors (NFAs), the fundamental understanding on the relationship between NFA molecular architecture, morphology, and device performance is still lacking. Herein, poly[[4,8‐bis[5‐(2‐ethylhexyl)thiophene‐2‐yl]benzo[1,2‐b:4,5‐b0]dithiophene‐2,6‐diyl][3‐fluoro‐2‐[(2‐ethylhexyl)carbonyl]‐thieno[3,4‐b]thiophenediyl]] (PTB7‐Th) is used as the donor polymer to compare an NFA with a 3D architecture (SF‐PDI4) to a well‐studied NFA with a linear acceptor–donor–acceptor (A–D–A) architecture (ITIC). The data suggest that the NFA ITIC with a linear molecular structure shows a better device performance due to an increase in short‐circuit current ( J sc ) and fill factor (FF) compared to the 3D SF‐PDI4. The charge generation dynamics measured by femtosecond transient absorption spectroscopy (TAS) reveals that the exciton dissociation process in the PTB7‐Th:ITIC films is highly efficient. In addition, the PTB7‐Th:ITIC blend shows a higher electron mobility and lower energetic disorder compared to the PTB7‐Th:SF‐PDI4 blend, leading to higher values of J sc and FF. The compositional sensitive resonant soft X‐ray scattering (R‐SoXS) results indicate that ITIC molecules form more pure domains with reduced domain spacing, resulting in more efficient charge transport compared with the SF‐PDI4 blend. It is proposed that both the molecular structure and the corresponding morphology of ITIC play a vital role for the good solar cell device performance.
Mechanistic Insights into IscU Conformation Regulation for Fe–S Cluster Biogenesis Revealed by Variable Temperature Electrospray Ionization Native Ion Mobility Mass Spectrometry (2022)

Iron-sulfur (Fe-S) cluster (ISC) cofactors are required for the function of many critical cellular processes. In the ISC Fe-S cluster biosynthetic pathway, IscU assembles Fe-S cluster intermediates from iron, electrons, and inorganic sulfur, which is provided by the cysteine desulfurase enzyme IscS. IscU also binds to Zn, which mimics and competes for binding with the Fe-S cluster. Crystallographic and nuclear magnetic resonance spectroscopic studies reveal that IscU is a metamorphic protein that exists in multiple conformational states, which include at least a structured form and a disordered form. The structured form of IscU is favored by metal binding and is stable in a narrow temperature range, undergoing both cold and hot denaturation. Interestingly, the form of IscU that binds IscS and functions in Fe-S cluster assembly remains controversial. Here, results from variable temperature electrospray ionization (vT-ESI) native ion mobility mass spectrometry (nIM-MS) establish that IscU exists in structured, intermediate, and disordered forms that rearrange to more extended conformations at higher temperatures. A comparison of Zn-IscU and apo-IscU reveals that Zn(II) binding attenuates the cold/heat denaturation of IscU, promotes refolding of IscU, favors the structured and intermediate conformations, and inhibits the disordered high charge states. Overall, these findings provide a structural rationalization for the role of Zn(II) in stabilizing IscU conformations and IscS in altering the IscU active site to prepare for Zn(II) release and cluster synthesis. This work highlights how vT-ESI-nIM-MS can be applied as a powerful tool in mechanistic enzymology by providing details of relationships among temperature, protein conformations, and ligand/protein binding.
Noncanonical Activation of β-Catenin by Porphyromonas gingivalis (2015)

Porphyromonas gingivalis is an established pathogen in periodontal disease and an emerging pathogen in serious systemic conditions, including some forms of cancer. We investigated the effect of P. gingivalis on β-catenin signaling, a major pathway in the control of cell proliferation and tumorigenesis. Infection of gingival epithelial cells with P. gingivalis did not influence the phosphorylation status of β-catenin but resulted in proteolytic processing. The use of mutants deficient in gingipain production, along with gingipain-specific inhibitors, revealed that gingipain proteolytic activity was required for β-catenin processing. The β-catenin destruction complex components Axin1, adenomatous polyposis coli (APC), and GSK3β were also proteolytically processed by P. gingivalis gingipains. Cell fractionation and Western blotting demonstrated that β-catenin fragments were translocated to the nucleus. The accumulation of β-catenin in the nucleus following P. gingivalis infection was confirmed by immunofluorescence microscopy. A luciferase reporter assay showed that P. gingivalis increased the activity of the β-catenin-dependent TCF/LEF promoter. P. gingivalis did not increase Wnt3a mRNA levels, a finding consistent with P. gingivalis-induced proteolytic processing causing the increase in TCF/LEF promoter activity. Thus, our data indicate that P. gingivalis can induce the noncanonical activation of β-catenin and disassociation of the β-catenin destruction complex by gingipain-dependent proteolytic processing. β-Catenin activation in epithelial cells by P. gingivalis may contribute to a proliferative phenotype.
New Frequency Temperature Characteristics of Miniaturized GT-Cut Quartz Resonators (1980)

Summary This paper describes the shape, size and frequency-temperature characteristics c.f a miniaturized GT cut quartz resonator. We have developed a ne.w GT cut quartz resonator, which is greatly miniaturized, highly shock resistant and has excellent frequency-temperature characteristics cver a wide temperature range. In order to obtain sufficient processing accuracy, this quartz resonator is u.anufactured by a lithographic process, and, by means of a one-body formation of a vibrational portion and supporting portions of the quartz resonator, it can be made small. To describe it in still more detail, in order to minimize the energy losses caused by vibrations of the supporting portions, the quartz resonator has been designed such that the amplitude of vibrations, derived from the vibrational portion and transmitted to the supporting portions, which have the function of changing the length-extensioral vibration derived from the vibrational. portion into a flexural mode vibration, is minimized at the end of the sc.pporting portions and thus there is h.ardly any distortion.
Super Boiler 2<sup>nd</sup> Generation Technology for Watertube Boilers (2012)

This report describes Phase I of a proposed two phase project to develop and demonstrate an advanced industrial watertube boiler system with the capability of reaching 94% (HHV) fuel-to-steam efficiency and emissions below 2 ppmv NOx, 2 ppmv CO, and 1 ppmv VOC on natural gas fuel. The boiler design would have the capability to produce >1500 F, >1500 psig superheated steam, burn multiple fuels, and will be 50% smaller/lighter than currently available watertube boilers of similar capacity. This project is built upon the successful Super Boiler project at GTI. In that project that employed a unique two-staged intercooled combustion system and an innovative heat recovery system to reduce NOx to below 5 ppmv and demonstrated fuel-to-steam efficiency of 94% (HHV). This project was carried out under the leadership of GTI with project partners Cleaver-Brooks, Inc., Nebraska Boiler, a Division of Cleaver-Brooks, and Media and Process Technology Inc., and project advisors Georgia Institute of Technology, Alstom Power Inc., Pacific Northwest National Laboratory and Oak Ridge National Laboratory. Phase I of efforts focused on developing 2nd generation boiler concepts and performance modeling; incorporating multi-fuel (natural gas and oil) capabilities; assessing heat recovery, heat transfer and steam superheating approaches; and developing the overall conceptual engineering boiler design. Based on our analysis, the 2nd generation Industrial Watertube Boiler when developed and commercialized, could potentially save 265 trillion Btu and $1.6 billion in fuel costs across U.S. industry through increased efficiency. Its ultra-clean combustion could eliminate 57,000 tons of NOx, 460,000 tons of CO, and 8.8 million tons of CO2 annually from the atmosphere. Reduction in boiler size will bring cost-effective package boilers into a size range previously dominated by more expensive field-erected boilers, benefiting manufacturers and end users through lower capital costs.
Lossless coding support in VVC (2020)

This Conference Presentation, Lossless coding support in VVC was recorded for the Optics + Photonics Digital Forum.
Morph-to-word transduction for accurate and efficient automatic speech recognition and keyword search (2017)

Word units are a popular choice in statistical language modelling. For inflective and agglutinative languages this choice may result in a high out of vocabulary rate. Subword units, such as morphs, provide an interesting alternative to words. These units can be derived in an unsupervised fashion and empirically show lower out of vocabulary rates. This paper proposes a morph-to-word transduction to convert morph sequences into word sequences. This enables powerful word language models to be applied. In addition, it is expected that techniques such as pruning, confusion network decoding, keyword search and many others may benefit from word rather than morph level decision making. However, word or morph systems alone may not achieve optimal performance in tasks such as keyword search so a combination is typically employed. This paper proposes a single index approach that enables word, morph and phone searches to be performed over a single morph index. Experiments are conducted on IARPA Babel program languages including the surprise languages of the OpenKWS 2015 and 2016 competitions.