gebhart/patrepeval huggingface dataset:
Serdab: An IoT Framework for Partitioning Neural Networks Computation across Multiple Enclaves (2020)

Recent advances in Deep Neural Networks (DNN) and Edge Computing have made it possible to automatically analyze streams of videos from home/security cameras over hierarchical clusters that include edge devices, close to the video source, as well as remote cloud compute resources. However, preserving the privacy and confidentiality of users' sensitive data as it passes through different devices remains a concern to most users. Private user data is subject to attacks by malicious attackers or misuse by internal administrators who may use the data in activities that are not explicitly approved by the user. To address this challenge, we present Serdab, a distributed orchestration framework for deploying deep neural network computation across multiple secure enclaves (e.g., Intel SGX). Secure enclaves provide a guarantee on the privacy of the data/code deployed inside it. However, their limited hardware resources make them inefficient when solely running an entire deep neural network. To bridge this gap, Serdab presents a DNN partitioning strategy to distribute the layers of the neural network across multiple enclave devices or across an enclave device and other hardware accelerators. Our partitioning strategy achieves up to 4.7x speedup compared to executing the entire neural network in one enclave.
Failure Mechanism Study of GaAs MODFET Devices and Integrated Circuits (1985)

GaAs Modulation Doped Field Effect Transistor (MOD-FET) integrated circuits have been accelerated stress tested under bias at 150°C, 200°C, 210°C. The failure mode has been identified to be a diffusion controlled degradation of the 2 DEC layers. Alpha particle irradiation resulted in a decrease in charge collection efficiency, and catastrophic gate burnout.
Translational regulation of lipoprotein lipase in adipocytes: depletion of cellular protein kinase Cα activates binding of the C subunit of protein kinase A to the 3′-untranslated region of the lipoprotein lipase mRNA (2008)

Adipose LPL (lipoprotein lipase) plays an important role in regulating plasma triacylglycerols and lipid metabolism. We have previously demonstrated that PKCalpha (protein kinase Calpha) depletion inhibits LPL translation in 3T3-F442A adipocytes. Using in vitro translation experiments, the minimum essential region on the 3'UTR (3'-untranslated region) of LPL mRNA required for the inhibition of translation was identified as the proximal 39 nt. These results were confirmed by RNase protection analysis using cytoplasmic proteins isolated from the adipocytes treated with PKCalpha antisense oligomers and the LPL 3'UTR transcript (LPL 3'UTR nt: 1512-1640). The protein components involved in this RNA-binding interaction from PKCalpha depletion were passed through an affinity column containing a sequence of the LPL 3'UTR and, after Western blotting, the RNA-binding proteins were identified as the catalytic and the regulatory subunits of PKA (protein kinase A), Calpha and RIIbeta, and AKAP (A-kinase-anchoring protein) 121. This RNA inhibitory complex consisted of the same RNA-binding proteins that have been identified previously as mediators of LPL translational inhibition by PKA activation, suggesting that PKCalpha depletion inhibits LPL translation through PKA activation. In additional experiments, PKC depletion by prolonged PMA treatment or PKCalpha antisense oligomers resulted in an increase in PKA activity in 3T3-F442A adipocytes, comparable with PKA activation with adrenaline (epinephrine) treatment. These results demonstrate that LPL translational inhibition occurs through an RNA-binding complex involving PKA subunits and AKAP121, and this complex can be activated either through traditional PKA activation methods or through the depletion of PKCalpha.
HPLC/Tandem Electrospray Mass Spectrometry for the Determination of Sub-ppb Levels of Pacific and Caribbean Ciguatoxins in Crude Extracts of Fish (1998)

Ciguatera is a significant food-borne disease caused by potent polyether toxins (ciguatoxins) which accumulate in the flesh of ciguateric reef fish at risk levels > 0.1 ppb for Pacific ciguatoxins. Research on ciguatera has been severely hindered by the lack of analytical methods that detect and characterize low levels of ciguatoxin in crude extracts of fish. Here we report a new procedure for ciguatoxin analysis based on gradient reversed-phase HPLC/tandem mass spectrometry (HPLC/MS/MS). The method gave a linear response to pure Pacific and Caribbean ciguatoxins (P-CTX-1 and C-CTX-1) and the structurally related brevetoxin (PbTx-2) spiked into crude extracts of fish. Levels equivalent to 40 ppt P-CTX-1, 100 ppt C-CTX-1, and 200 ppt PbTx-2 in fish flesh could be detected by HPLC/MS/MS. Using P-CTX-1 as an internal standard, the analysis of extracts of 30 ciguateric fish from the Caribbean Sea (8 toxic, 12 borderline, and 10 nontoxic by mouse bioassay) confirmed the reliability of the method and allowed an estimated risk level of > 0.25 ppb C-CTX-1 to be established. HPLC/MS/MS provides a sensitive analytical approach, not previously available, for the determination of Pacific and Caribbean ciguatoxins at sub-ppb levels in fish flesh.
Factors That Determine the Adhesive Strength in a Bioinspired Bone Tissue Adhesive (2020)

Phosphoserine-modified cements (PMCs) are a family of wet-field tissue adhesives that bond strongly to bone and biomaterials. The present study evaluated variations in the adhesive strength using a scatter plot, failure mode, and a regression analysis of eleven factors. All single-factor, continuous-variable correlations were poor (R2 &lt; 0.25). The linear regression model explained 31.6% of variation in adhesive strength (R2 = 0.316 p &lt; 0.001), with bond thickness predicting an 8.5% reduction in strength per 100 μm increase. Interestingly, PMC adhesive strength was insensitive to surface roughness (Sa 1.27–2.17 μm) and the unevenness (skew) of the adhesive bond (p &gt; 0.167, 0.171, ANOVA). Bone glued in conditions mimicking the operating theatre (e.g., the rapid fixation and minimal fixation force in fluids) produced comparable adhesive strength in laboratory conditions (2.44 vs. 1.96 MPa, p &gt; 0.986). The failure mode correlated strongly with the adhesive strength; low strength PMCs (&lt;1 MPa) failed cohesively, while high strength (&gt;2 MPa) PMCs failed adhesively. Failure occurred at the interface between the amorphous surface layer and the PMC bulk. PMC bonding is sufficient for clinical application, allowing for a wide tolerance in performance conditions while maintaining a minimal bond strength of 1.5–2 MPa to cortical bone and metal surfaces.
Effect of lattice deformation on photoinduced phase transition process in RbMn[Fe(CN)6] (2010)

Abstract Structural transformation effect on a photoinduced (PI) charge‐transfer process leading to a phase transition in RbMn[Fe(CN) 6 ], which exhibits a magnetic phase transition with a hysteresis loop between 230 and 300 K, has been investigated by Raman spectroscopy. The valence states of the transition metal ions and the lattice symmetry are reflected in the vibrational frequency of the adjacent CN ions. The charge‐transfer phase transition from the high‐temperature (HT) phase to low‐temperature (LT) phase can be induced by the photo‐excitation with 395 nm light in resonance with the ligand‐to‐metal charge transfer (LMCT) band. The conversion efficiency is lowered with decreasing temperature within the hysteresis loop. However, upon further lowering the temperature, the photo‐conversion restarts in the residual HT configuration units and domains around 50 K. The behavior is ascribed to the change of the potential curves in the excited electronic state due to the lattice deformation caused by the cubic‐to‐tetragonal phase transition in the surrounding lattice.
A QCM study of ORR-OER and an in situ study of a redox mediator in DMSO for Li–O2 batteries (2015)

The oxygen reduction reaction and oxygen evolution reaction (ORR-OER) in DMSO were investigated by cyclic voltammetry and potentiostatic methods. A quartz crystal microbalance (QCM) was used to detect which products are formed during reduction and to evaluate the reversibility of the reactions. The studied parameters include the scan rate and the applied cathodic potential. We confirm by the QCM that LiO2 is soluble: this conclusion comes from the time delay we observed between the deposition of the expected mass (based on Faraday's law) and the measured mass. Ambiguity in reported literature values for the slope of the deposited mass per electron M/z is due to the negligence in considering this time delay. The average M/z value versus cathodic charge indicates that soluble LiO2 is the first product of the ORR which reacts further to form Li2O2, either via a disproportionation reaction or via further electrochemical reduction of LiO2. For strong negative potentials and thus large depths of discharge, Li2O is the main discharge product. The reaction pathways hence strongly depend on the experimental conditions applied; especially the reduction potential. The redox mediator tetrathiafulvalene (TTF) was investigated and its influence on reversibility was confirmed by cycling at moderate depths of discharge, where Li2O2 is the main discharge product.
Neutron-induced thermoluminescence properties of Tb 3+ -doped Ca 2 B 2 O 5 ceramics (2021)

Abstract We fabricated 10 B-enriched ( 10 B ceramics) and 11 B-enriched ( 11 B ceramics) Ca 2 B 2 O 5 :Tb ceramics as thermoluminescence (TL) materials for neutron detection applications. The TL properties of the ceramics after X-ray irradiation, particle beam irradiation, and neutron irradiation were investigated. The TL properties of the 10 B ceramics and 11 B ceramics after X-ray irradiation were similar, whereas the neutron-induced TL intensity of the 10 B ceramics was significantly higher than that of the 11 B ceramics. The different TL properties of these ceramics are due to the α -rays, Li ions, and γ -rays generated during the 10 B( n , α ) 7 Li reaction. The lower limit of neutron detection by the ceramics was less than 2 × 10 7 neutrons cm −2 , which was lower than those of several previously reported TL materials. Therefore, these ceramics can be applied as TL dosimetry materials for neutron detection.
Discovery and Optimization of Isoquinoline Ethyl Ureas as Antibacterial Agents (2017)

Our strategy to combat resistant bacteria consisted of targeting the GyrB/ParE ATP-binding sites located on bacterial DNA gyrase and topoisomerase IV and not utilized by marketed antibiotics. Screening around the minimal ethyl urea binding motif led to the identification of isoquinoline ethyl urea 13 as a promising starting point for fragment evolution. The optimization was guided by structure-based design and focused on antibacterial activity in vitro and in vivo, culminating in the discovery of unprecedented substituents able to interact with conserved residues within the ATP-binding site. A detailed characterization of the lead compound highlighted the potential for treatment of the problematic fluoroquinolone-resistant MRSA, VRE, and S. pneumoniae, and the possibility to offer patients an intravenous-to-oral switch therapy was supported by the identification of a suitable prodrug concept. Eventually, hERG K-channel block was identified as the main limitation of this chemical series, and efforts toward its minimization are reported.
A Microfabricated High-speed GCxGC System. (2012)

Abstract not provided.
Physical Properties of Intercalated Inorganic Nanotubes (2002)

Recently synthesized single‐wall MoS2 nanotubes were electrochemically doped with Li and then studied by X‐band electron spin resonance (ESR). We demonstrate, that on average 2.3 mole of Li per MoS2 unit can be intercalated into the bundles of MoS2 nanotubes. The ESR results show that most of the Li is intercalated into the channels between the individual nanotubes. The electronic properties of charged MoS2 nanotubes are largely determined by the defects, either by paramagnetic or topological. We found also evidence for the presence of small Li metallic particles in our sample.
Longitudinal study on circulating miRNAs in patients after lung cancer resection (2015)

There is an urgent need of comprehensive longitudinal analyses of circulating miRNA patterns to identify dynamic changes of miRNAs in cancer patients after surgery. Here we provide longitudinal analysis of 1,205 miRNAs in plasma samples of 26 patients after lung cancer resection at 8 time points over a period of 18 months and compare them to 12 control patients. First, we report longitudinal changes with respect to the number of detected miRNAs over time and identified a significantly increased number of miRNAs in patients developing metastases (p = 0.0096). A quantitative analysis with respect to the expression level of the detected miRNAs revealed more significant changes in the miRNA levels in samples from patients without metastases compared to the non-cancer control patients. This analysis provided further evidence of miRNA plasma levels that are changing over time after tumor resection and correlate to patient outcome. Especially hsa-miR-197 could be validated by qRT-PCR as prognostic marker. Also for this miRNA, patients developing metastases had levels close to that of controls while patients that did not develop metastases showed a significant up-regulation.In conclusion, our data indicate that the overall miRNome of a patient that later develops metastases is less affected by surgery than the miRNome of a patient who does not show metastases. The relationship between altered plasma levels of specific miRNAs with the development of metastases would partially have gone undetected by an analysis at a single time point only.
ChemInform Abstract: Sialylation of Oligosaccharide on a Protein by Chemoenzymatic Method (2001)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 100 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a “Full Text” option. The original article is trackable via the “References” option.
Structure of aspartate racemase complexed with a dual substrate analogue, citric acid, and implications for the reaction mechanism (2007)

Pyrococcus horikoshii OT3 aspartate racemase (PhAspR) catalyzes the interconversion between L- and D-aspartate. The X-ray structure of PhAspR revealed a pseudo mirror-symmetric distribution of the residues around its active site, which is very reasonable for its chiral substrates, L-aspartate and D-aspartate. In this study, we have determined the crystal structure of an inactive mutant PhAspR complexed with a citric acid (Cit) at a resolution of 2.0 A. Cit contains the substrate analogue moieties of both L- and D-aspartate and exhibits a low competitive inhibition activity against PhAspR. In the structure, Cit binds to the catalytic site of PhAspR, which induced the conformational change to close the active site. The distance between the thiolates was estimated to be 7.4 A, representing a catalytic state and the substrate binding modes of PhAspR. Two conserved basic residues, Arg48 and Lys164, seem to be indispensable for PhAspR activity. Arg48 is thought to be responsible for recognizing carboxyl groups of the substrates L-/D-aspartates and stabilizing a reaction intermediate, and Lys164 is responsible for stabilizing a closed state structure. In this structure, the L-aspartate moiety of Cit is likely to take the substrate position of the PhAspR-substrate complex, which is very similar to that of Glutamate racemase. There is also another possibility that the two substrate analogue moieties of the bound Cit reflect the binding modes of both L- and D-aspartates. Based on the PhAspR-Cit complex structure, the reaction mechanism of aspartate racemase was elucidated.
Full Functional Knockout of Placental Growth Factor by Knockin with an Inactive Variant Able to Heterodimerize with VEGF-A (2018)

Placental growth factor (PlGF) is a proangiogenic member of the vascular endothelial growth factor (VEGF) family playing a central role in pathological angiogenesis. PlGF-DE is a PlGF variant unable to bind vascular endothelial growth factor receptor 1 (VEGFR-1) but still able to generate heterodimer with VEGF-A. We have generated PlGF-DE knockin mice that are vital and fertile and show unaltered expression of Plgf, Vegf-a, Vegfr-1, and Vegfr-2 compared with wild-type mice. Interestingly, these mutants showed additional and remarkable angiogenesis impairment in tumor growth, hindlimb ischemia, and choroidal neovascularization compared with both PlGF knockout and wild-type mice. These findings provided insights on VEGF-A/PlGF heterodimer function, which was able to rescue neovascularization and vascular leakage in PlGF-DE knockin mice. Collectively, these data show that PlGF-DE knockin mouse could be considered the full functional knockout of PlGF, suggesting a reassessment of the phenotypes of knockout mice for the genes whose products are able to generate heterodimeric proteins.
SPACE-TIME CODING FOR INFORMED TRANSMITTERS (2003)

All the discussion so far in this book (with the exception of Sections 3.3 and 6.1) has focused on the case when the channel is unknown to the transmitter. In this chapter, we will briefly study how partial channel knowledge at the transmitter can be used to improve the system performance. In particular we will study linearly precoded STBC.
The Role of Multidrug Resistance Efflux Pumps in Cancer: Revisiting a JNCI Publication Exploring Expression of the MDR1 (P-glycoprotein) Gene (2015)

The Journal of the National Cancer Institute published our paper entitled “Expression of a Multidrug Resistance Gene in Human Cancers” (1) 26 years ago. It was the first systematic determination of whether the energy-dependent multidrug efflux pump P-glycoprotein (P-gp), the product of the ABCB1 (MDR1) gene, was expressed in human cancers and has been cited over 1200 times. Four hundred cancers were studied, and the conclusion was that expression was widespread both in intrinsically drug-resistant cancers such as colon, pancreatic, liver, adrenocortical, and kidney cancers, and in some cancers that acquired resistance, such as leukemias, lymphomas, breast cancer, and neuroblastoma. Other cancers at the time of initial presentation, such as lung cancers (except for neuroendocrine tumors), ovarian cancer, esophageal cancer, and mesothelioma expressed little or no P-glycoprotein. The major conclusions of this paper, which have withstood the test of time (see below) were: 1) that P-gp was expressed at levels sufficient to confer drug resistance in many different difficult-to-treat cancers, 2) that its expression appeared during the acquisition of resistance for some cancers, indicating a possible role for P-gp in acquired resistance, 3) that many cancers did not appear to express P-gp mRNA at detectable levels and therefore efforts to inhibit P-gp and reverse resistance in these cancers were unlikely to succeed, and 4) that it remained to be proven whether P-gp expression, though perhaps sufficient for drug resistance in cancers, was the main cause of resistance in any cancer. Considerable effort has been devoted to answer this last question: Are P-gp or other multidrug transporters discovered since (see below) useful targets for drug development with the possible outcome of reversing multidrug resistance in cancer?
THE LATARJET PROCEDURE FOR ANTERIOR SHOULDER INSTABILITY: A PROSPECTIVE SERIES OF 50 CONSECUTIVE PATIENTS (2013)

The Latarjet procedure is a successful primary and revision option for anterior shoulder instability; however recent reports have highlighted varying complication rates. Our aim was to prospectively study clinical, functional and radiological outcomes of patients undergoing this procedure. 50 consecutive patients underwent a Latarjet coracoid transfer between 2006 and 2012. Mean age was 27 years (17–63), 48 were male. Pre-/post-operative imaging, Oxford Shoulder Instability Score (OISS), American Shoulder & Elbow Surgeons score (ASES), Subjective Shoulder Value score (SSV) and clinical evaluation were documented. Mean follow up was 32 months (6–74). There were no dislocations or revision procedures. Subluxation occurred in one patient only. 95% of shoulders were subjectively graded “excellent” or “good;” 5% “fair;” and none as “poor”. The mean pre-op ASES was 58(50–66) and 95(92–98) post-operatively (p These results suggest that the Latarjet procedure is safe and reliable with low complication rates.
CCR3 is a target for age-related macular degeneration diagnosis and therapy (2020)

Age-related macular degeneration (AMD), a leading cause of blindness worldwide, is as prevalent as cancer in industrialized nations. Most blindness in AMD results from invasion of the retina by choroidal neovascularisation (CNV). Here we show that the eosinophil/mast cell chemokine receptor CCR3 is specifically expressed in choroidal neovascular endothelial cells in humans with AMD, and that despite the expression of its ligands eotaxin-1, -2 and -3, neither eosinophils nor mast cells are present in human CNV. Genetic or pharmacological targeting of CCR3 or eotaxins inhibited injury-induced CNV in mice. CNV suppression by CCR3 blockade was due to direct inhibition of endothelial cell proliferation, and was uncoupled from inflammation because it occurred in mice lacking eosinophils or mast cells, and was independent of macrophage and neutrophil recruitment. CCR3 blockade was more effective at reducing CNV than vascular endothelial growth factor A (VEGF-A) neutralization, which is in clinical use at present, and, unlike VEGF-A blockade, is not toxic to the mouse retina. In vivo imaging with CCR3-targeting quantum dots located spontaneous CNV invisible to standard fluorescein angiography in mice before retinal invasion. CCR3 targeting might reduce vision loss due to AMD through early detection and therapeutic angioinhibition.
Coffee-Ring Structure from Dried Graphene Derivative Solutions: A Facile One-Step Fabrication Route for All Graphene-Based Transistors (2014)

We demonstrated a coffee-ring structure of graphene derivatives as a one-step solution fabrication route for graphene-based transistors. The key finding is that the coffee-ring structure formed after solvent evaporation of chemically modified graphene nanosheet solutions has an equivalent structure to all graphene-based transistors, the source/drain electrodes and semiconducting channel of which consisted monolithically of graphene nanosheets. These transistors have a thick stack of reduced graphene oxide at the edge of the coffee-ring structure, providing highly conductive thick graphite-like contact as the source and drain electrodes, and the thin film in the midsection of the coffee-ring pattern can simultaneously behave as the semiconducting channel. Here, we provide a holistic approach for achieving coffee-ring graphene-based transistors addressing the entire process flow starting with the coffee-ring structure formation from aqueous graphene oxide dispersion, proceeding through a rapid photoreduction using intensely pulsed white light, and finally a simple cutting of the edge line connections. The degree of graphene oxide reduction was precisely controlled by varying the irradiation energy of pulsed light, which allowed us to systematically investigate its effect on the transistor performances. We confirmed the feasibility of a coffee-ring graphene-based transistor using inkjet printing technique and using chemically reduced graphene oxide dispersions.