gebhart/patrepeval huggingface dataset:
Mortality-based Quantification of Injury Severity for Frequently Occurring Motor Vehicle Crash Injuries. (2013)

The study purpose was to develop mortality-based metrics of injury severity for frequent motor vehicle crash (MVC) injuries. Injury severity was quantified with mortality-based metrics for 240 injuries comprising the top 95% most frequently occurring AIS 2+ injuries in the National Automotive Sampling System - Crashworthiness Data System (NASS-CDS) 2000-2011. Mortality risk ratios (MRRs) were computed by dividing the number of deaths by occurrences for each of the 240 injuries using National Trauma Data Bank Research Data System (NTDB-RDS) MVC cases. MRRMAIS was computed using only patients with a maximum AIS (MAIS) equal to the AIS severity of a given injury. Each injury had an associated MRR and MRRMAIS which ranged from zero (0% mortality representing low severity) to one (100% or universal mortality representing high severity). Injuries with higher MRR and MRRMAIS values are considered more severe because they resulted in a greater proportion of deaths among injured patients. The results illustrated an overall positive trend between AIS severity and the MRR and MRRMAIS values as expected, but showed large variations in MRR and MRRMAIS for some injuries of the same AIS severity. Mortality differences up to 83% (MRR) and 54% (MRRMAIS) were observed for injuries of the same AIS severity. The MRR-based measures of injury severity indicate that some lower AIS severity injuries may result in as many deaths as higher AIS severity injuries. This data-driven determination of injury severity using MRR and MRRMAIS provides a supplement or an alternative to AIS severity classification.
Editorial: Purinergic Pharmacology (2019)

The purine nucleotides and nucleosides constitute important extracellular signaling molecules acting as neurotransmitters and neuromodulators. Indeed, extracellular adenosine 5′-triphosphate (ATP) and adenosine, tightly controlled by nucleotidases, ribokinases, deaminases, and transporters, signal through a rich array of purinergic receptors. These receptors, which emerged early in evolution, are among the most abundant in living organisms controlling many physiological actions, thus becoming promising therapeutic targets in a wide range of pathological conditions. Thus, while P1 receptors are selective for adenosine, a breakdown product of ATP, P2 receptors are activated by purine nucleotides, as well as P2Y receptors being activated by pyrimidine nucleotides. Interestingly, purinergic receptors, both G protein-coupled (i.e., P1 and P2Y) and ligand-gated ion channel (i.e., P2X) receptors, are involved in many neuronal and non-neuronal mechanisms, including pain, immune responses, exocrine and endocrine secretion, platelet aggregation, endothelial-mediated vasodilatation and inflammation, among others.
Measurement of Temperature and Reaction Species in the Cathode Diffusion Layer of a Free-Convection Fuel Cell (2007)

Micron- and millimeter-scale sensors were employed to acquire first-of-their-kind experimental measurements of the spatial and temporal distributions of temperature, oxygen partial pressure, and relative humidity in the mass transport layer immediately above the planar, horizontal cathode of polymer electrolyte membrane fuel cell (PEMFC) driven by natural convection. The sensors provide approximately (or better) spatial resolution and temporal resolution. Substantial changes in temperature and reaction species concentrations were observed with increasing current density during a current-voltage scan. A linear decrease in oxygen partial pressure and a linear increase in water vapor partial pressure were observed with increasing current density, consistent with a flux balance analysis. Spatially resolved profiles normal to the surface indicate that thermal and reaction species gradients extend up to above the horizontal cathode surface. Complementary horizontal profiles (parallel to the surface) reveal that the cell's cathode rib structure visibly influences oxygen distribution. Most significantly, these data show that thermal and species concentration effects are not confined to the gas diffusion layer (GDL), but extend well beyond the cathode surface, into the surrounding space. The measurements were used to estimate diffusion and/or convection mass transfer coefficients above the cathode surface. Transient data reveal substantial differences in the time constants associated with oxygen, water, and heat transport. The insights provided by this study should prove useful to inform and validate future physical models of air-breathing fuel cell systems.
The role of quantum chemistry in covalent inhibitor design (2021)

Abstract The recent ascent of targeted covalent inhibitors (TCI) in drug discovery brings new opportunities and challenges to quantum chemical reactivity calculations supporting discovery efforts. TCIs typically form a covalent bond with the targeted nucleophilic amino acid side chain. Their reactivity that can be both computed and experimentally measured is therefore one of the key factors in determining inhibitory potency. Calculation of relevant quantum chemical descriptors and corresponding reaction barriers of model reactions represent efficient ways to predict intrinsic reactivities of covalent ligands. A more comprehensive description of covalent ligand binding is offered by mixed quantum mechanical/molecular mechanical (QM/MM) potentials. Reaction mechanisms can be investigated by the exploration of the potential energy surface as a function of suitable reaction coordinates, and free energy surfaces can also be calculated with molecular dynamics based simulations. Here we review the methodological aspects and discuss applications with primary focus on high‐end QM/MM simulations to illustrate the current status of quantum chemical support to covalent inhibitor design. Available QM approaches are suitable to identify likely reaction mechanisms and rate determining steps in the binding of covalent inhibitors. The efficient QM/MM prediction of ligand reactivities complemented with the computational description of the recognition step makes these computations highly useful in covalent drug discovery.
BiCMOS versus CMOS technology in fully differential OTA designs (2002)

A design program evaluates CMOS and BiCMOS fully differential OTA's performance independently of the application. As a validation an amplifier has been realized. Measurements and simulations are shown and compared. Finally, a comparison is presented between CMOS and BiCMOS OTAs when long, or short transistor lengths are used.
Real-time administration of indocyanine green in combination with computer vision and artificial intelligence for the identification and delineation of colorectal liver metastases (2023)

ML accurately identifies CRLMs from surrounding liver tissue enabling representative 2D mapping of such lesions from their fluorescence perfusion patterns using AIM. This may assist in reducing positive margin rates at metastatectomy and in identifying unexpected/occult malignancies.
Heterogeneous Enhancement Patterns of Tumor-adjacent Parenchyma at MR Imaging Are Associated with Dysregulated Signaling Pathways and Poor Survival in Breast Cancer (2017)

Purpose To identify the molecular basis of quantitative imaging characteristics of tumor-adjacent parenchyma at dynamic contrast material-enhanced magnetic resonance (MR) imaging and to evaluate their prognostic value in breast cancer. Materials and Methods In this institutional review board-approved, HIPAA-compliant study, 10 quantitative imaging features depicting tumor-adjacent parenchymal enhancement patterns were extracted and screened for prognostic features in a discovery cohort of 60 patients. By using data from The Cancer Genome Atlas (TCGA), a radiogenomic map for the tumor-adjacent parenchymal tissue was created and molecular pathways associated with prognostic parenchymal imaging features were identified. Furthermore, a multigene signature of the parenchymal imaging feature was built in a training cohort (n = 126), and its prognostic relevance was evaluated in two independent cohorts (n = 879 and 159). Results One image feature measuring heterogeneity (ie, information measure of correlation) was significantly associated with prognosis (false-discovery rate < 0.1), and at a cutoff of 0.57 stratified patients into two groups with different recurrence-free survival rates (log-rank P = .024). The tumor necrosis factor signaling pathway was identified as the top enriched pathway (hypergeometric P < .0001) among genes associated with the image feature. A 73-gene signature based on the tumor profiles in TCGA achieved good association with the tumor-adjacent parenchymal image feature (R<sup>2</sup> = 0.873), which stratified patients into groups regarding recurrence-free survival (log-rank P = .029) and overall survival (log-rank P = .042) in an independent TCGA cohort. The prognostic value was confirmed in another independent cohort (Gene Expression Omnibus GSE 1456), with log-rank P = .00058 for recurrence-free survival and log-rank P = .0026 for overall survival. Conclusion Heterogeneous enhancement patterns of tumor-adjacent parenchyma at MR imaging are associated with the tumor necrosis signaling pathway and poor survival in breast cancer. <sup>©</sup> RSNA, 2017 Online supplemental material is available for this article.
A Temperature and Supply Independent Bias Circuit and MMIC Power Amplifier Implementation for W-CDMA Applications (2005)

A novel bias circuit providing a stable quiescent current for temperature and supply voltage variations is proposed and implemented to a W-CDMA MMIC power amplifier. The power amplifier with the proposed bias circuit has the quiescent current variation of only 6% for the -30°C to 90°C temperature change, and 8.5% for the 2.9 V to 3.1V supply voltage change, and the variation of the power gain at the 28 dBm output power is less than ±0.8 (0.05) dB for the ±0.1 V of supply voltage (±60°C of temperature) variation.
Two-dimensional cantilever array with varying spring constants and tip radii for life-science applications (2012)

A fabrication process for realising two-dimensional cantilever arrays for parallel force spectroscopy of biological samples is presented. The parallel optical atomic force microscopy readout system has been developed and presented elsewhere. The arrays are designed either for (i) force-indentation onto living cells to obtain stiffness mapping or (ii) cell adhesion experiments. Both experiments require very different spring constants and tip radii of curvature. The arrays are based on silicon nitride cantilevers with molded tips. The fabrication process includes an advanced molding process and a thermocompression bonding of two silicon wafers. V-groove structures along the cantilevers, which increase the area moment of inertia, were introduced in the cantilever design. This feature enables the fabrication of cantilevers with different spring constants but same footprint from one wafer. An analytical model and experimental results confirmed that the spring constant of the cantilever (200×50×0.45 µm) could be increased up to two decades (0.03–5 N/m) by changing the depth of the V-grooves. To realise the large tip radius required for cell adhesion experiments, an enlarging/rounding procedure has been applied to a truncated pyramidal tip mold. With this process, the authors obtained tips with a radius up to 4 µm.
Association Between Interstitial Lung Abnormalities and All-Cause Mortality (2016)

In 4 separate research cohorts, interstitial lung abnormalities were associated with a greater risk of all-cause mortality. The clinical implications of this association require further investigation.
Disaster Microbiology—a New Field of Study (2022)

Natural and human-made disasters can cause tremendous physical damage, societal change, and suffering. In addition to their effects on people, disasters have been shown to alter the microbial population in the area affected. Alterations for microbial populations can lead to new ecological interactions, with additional potentially adverse consequences for many species, including humans. Disaster-related stressors can be powerful forces for microbial selection. Studying microbial adaptation in disaster sites can reveal new biological processes, including mechanisms by which some microbes could become pathogenic and others could become beneficial (e.g., used for bioremediation). Here we survey examples of how disasters have affected microbiology and suggest that the topic of "disaster microbiology" is itself a new field of study. Given the accelerating pace of human-caused climate change and the increasing encroachment of the natural word by human activities, it is likely that this area of research will become increasingly relevant to the broader field of microbiology. Since disaster microbiology is a broad term open to interpretation, we propose criteria for what phenomena fall under its scope. The basic premise is that there must be a disaster that causes a change in the environment, which then causes an alteration to microbes (either a physical or biological adaptation), and that this adaptation must have additional ramifications.
VLSI Yield Prediction and Estimation: A Unified Framework (1986)

In this paper we present a unified framework for prediction and estimation of the manufacturing yield of VLSI circuits. We formally introduce a number of yield measures that are useful both during the design process and during the manufacturing process. This framework is general enough to bridge the gap between the traditional concepts of parametric and catastrophic yield. We provide a classification of causes of yield loss which is essential for efficient yield estimation. Finally, we relate yield to manufacturing costs which provides a common denominator for the discussion of the manufacturing process efficiency.
Targeting microbubbles with Shiga-Toxin B-subunit (2009)

The targeting moiety (B-subunit) of the Shiga toxin (STxB) is a very potent ligand for the glycolipid Gb3, which is expressed in ovarian, colorectal and breast carcinomas. It is also present on endothelial cells of tumor neovascularization. This study demonstrates the use of STxB for targeting microbubbles onto cancerous cells. STxB-functionalized microbubbles and biotinylated controls were incubated with colorectal carcinoma HT29 in opticell plates. The culture plates were observed by fluorescence microscopy. The plates were then installed in a water-bath under a 8 MHz transducer array. STxB and control microbubbles were also injected in nude mice with subcutaneous breast tumors, before ultrasound imaging. FACS analysis demonstrated that STxB was stably associated with the microbubbles. Fluorescence microscopy showed that STxB-functionalized microbubbles adhered favorably to the Gb3 expressing cells, as compared to cells in which Gb3 expression was inhibited. Disruption ultrasonography of the culture plates showed a 12 dB difference in average backscatter intensity of the surface of Gb3 expressing cells, compared to Gb3-negative cells. An intensity difference of 18 dB was also observed between cells that were incubated with STxB-functionalized-microbubbles, as compared to unspecific microbubbles. The experiment in mice showed a significant increase in microbubble-signal intensity within gb3-positive tumors after being injected with STxBmicrobubbles. These in vitro and in vivo experiments showed that STxBfunctionalized microbubbles bind specifically to cells expressing the Gb3 glycolipid. The targeting moieties of toxins are a new group of ligands for microbubbles and have several advantages compared to antibodies and small peptides.
Aspheric V-groove reflector design with the SMS method in two dimensions (2010)

The Simultaneous Multiple Surface design method in two dimensions (SMS2D) is applied to the design of aspheric V-groove reflectors. The general design problem is to achieve perfect coupling of two wavefronts after two reflections at the groove, no matter which side of the groove the rays hit first. Two types of configurations are identified, and several symmetric and asymmetric design examples are given. Computer simulations with a commercial simulation package are also shown.
Effects of a novel Nodal-targeting monoclonal antibody in melanoma (2015)

Nodal is highly expressed in various human malignancies, thus supporting the rationale for exploring Nodal as a therapeutic target. Here, we describe the effects of a novel monoclonal antibody (mAb), 3D1, raised against human Nodal. In vitro treatment of C8161 human melanoma cells with 3D1 mAb shows reductions in anchorage-independent growth and vasculogenic network formation. 3D1 treated cells also show decreases of Nodal and downstream signaling molecules, P-Smad2 and P-ERK and of P-H3 and CyclinB1, with an increase in p27. Similar effects were previously reported in human breast cancer cells where Nodal expression was generally down-regulated; following 3D1 mAb treatment, both Nodal and P-H3 levels are reduced. Noteworthy is the reduced growth of human melanoma xenografts in Nude mice treated with 3D1 mAb, where immunostaining of representative tumor sections show diminished P-Smad2 expression. Similar effects both in vitro and in vivo were observed in 3D1 treated A375SM melanoma cells harboring the active BRAF(V600E) mutation compared to treatments with IgG control or a BRAF inhibitor, dabrafenib. Finally, we describe a 3D1-based ELISA for the detection of Nodal in serum samples from cancer patients. These data suggest the potential of 3D1 mAb for selecting and targeting Nodal expressing cancers.
A proposal of coupled resonator optical waveguides based on slotted nanobeam cavities (2013)

We propose coupled resonator optical waveguides based on slotted nanobeam cavities. Numerical results show that our proposed structure can achieve a high effective nonlinear coefficient because of small group velocity and small effective mode area.
High-Q suspended optical resonators in 3C silicon carbide obtained by thermal annealing (2020)

We fabricate suspended single-mode optical waveguides and ring resonators in 3C silicon carbide (SiC) that operate at telecommunication wavelength, and leverage post-fabrication thermal annealing to minimize optical propagation losses. Annealed optical resonators yield quality factors of over 41,000, which corresponds to a propagation loss of 7 dB/cm, and is a significant improvement over the 24 dB/cm in the case of the non-annealed chip. This improvement is attributed to the enhancement of SiC crystallinity and a significant reduction of waveguide surface roughness, from 2.4 nm to below 1.7 nm. The latter is attributed to surface layer oxide growth during the annealing step. We confirm that the thermo-optic coefficient, an important parameter governing high-power and temperature-dependent performance of SiC, does not vary with annealing and is comparable to that of bulk SiC. Our annealing-based approach, which is especially suitable for suspended structures, offers a straightforward way to realize high-performance 3C-SiC integrated circuits.
Monodisperse Polystyrene Latex Particles Functionalized by the Macromonomer Technique (1998)

Monodisperse core−shell latex particles functionalized with surface groups that were introduced by the macromonomer technique were obtained by means of a two-step emulsion polymerization process in a batch reactor at 70 °C. In the first step the cores were synthesized by means of a batch emulsion polymerization of styrene (St), and in the second step, the shells were formed by batch emulsion copolymerizations of St and different macromonomers using the seeds obtained previously. Macromonomers were synthesized by anionic “living” polymerization. They are constituted of a poly(ethylene oxide) hydrophilic block and a hydrophobic block or sequence end-fitted with an unsaturation. The latexes were characterized by gravimetry, transmission electron microscopy (TEM), and conductometric titrations to obtain the conversion, the particle size distribution (PSD), and the surface charge density (σ), respectively. The colloidal stability of the cores and final latexes were determined by measuring the critical coagulation concentration (CCC) at two pHs (7 and 2) using KBr as electrolyte. The surface charges of the latexes were moderately low, with corresponding moderately low CCCs. The presence of spacers, confirmed with a disk centrifuge photosedimentometer (DCP) and photon correlation spectrophotometer (PCS), did not increase the CCC. During the CCC measurements, at high electrolyte concentrations, the reduced solubility of the spacer PEO moiety in the solution resulted in its collapse on the particle surface.
Hardware acceleration of compression and encryption in SAP HANA (2022)

With the advent of cloud computing, where computational resources are expensive and data movement needs to be secured and minimized, database management systems need to reconsider their architecture to accommodate such requirements. In this paper, we present our analysis, design and evaluation of an FPGA-based hardware accelerator for offloading compression and encryption for SAP HANA, SAP's Software-as-a-Service (SaaS) in-memory database. Firstly, we identify expensive data-transformation operations in the I/O path. Then we present the design details of a system consisting of compression followed by different types of encryption to accommodate different security levels, and identify which combinations maximize performance. We also analyze the performance benefits of offloading decryption to the FPGA followed by decompression on the CPU. The experimental evaluation using SAP HANA traces shows that analytical engines can benefit from FPGA hardware offloading. The results identify a number of important trade-offs (e.g., the system can accommodate low-latency secured transactions to high-performance use cases or offer lower storage cost by also compressing payloads for less critical use cases), and provide valuable information to researchers and practitioners exploring the nascent space of hardware accelerators for database engines.
Lysophosphatidic acid-1-receptor targeting agents for fibrosis (2011)

Experiments in animal models clearly demonstrate that LPA1R antagonists have interesting anti-fibrotic potencies. This reveals promising perspectives for the design of new therapeutic approaches to prevent fibrosis-associated diseases. Nevertheless, the number of efficient LPA1R antagonists currently available is still low, and none of them has been used in clinical trials so far.
Influence of Stack Orientations on the Static Strengths of SPR Joints (2017)

To improve fuel efficiency and reduce greenhouse gas emissions, lightweight materials, such as aluminium alloys, are used increasingly in automotive manufacturing. Currently, self-piercing riveting (SPR) is a major technology used by manufacturers to join aluminium body structures due to its advantages over other joining technologies. When different materials are joined together, different stack orientations can be used. To find out the influence of stack orientations on joint strength for further structure optimization, in this paper the joint quality and the static strengths of three pairs of twothickness stacks with different orientations were studied. The results showed that by joining the thicker material as a bottom material rather than a top material, joint interlocks were improved. As to the mechanical strength, for the stacks with both top and bottom sheets as AA5754, when a thicker sheet was joined as a bottom material, the joints had stronger static strength, and for stacks with 3.0 mm AA5754 and 2.0 mm AA6008T61, when the 3.0 mm AA5754 was joined as a bottom material, the joints had stronger static lap shear strength but weaker static T peel strength.