gebhart/patrepeval huggingface dataset:
Elephant APOBEC3A cytidine deaminase induces massive double-stranded DNA breaks and apoptosis (2019)

The incidence of developing cancer should increase with the body mass, yet is not the case, a conundrum referred to as Peto's paradox. Elephants have a lower incidence of cancer suggesting that these animals have probably evolved different ways to protect themselves against the disease. The paradox is worth revisiting with the realization that most mammals encode an endogenous APOBEC3 cytidine deaminase capable of mutating single stranded DNA. Indeed, the mutagenic activity of some APOBEC3 enzymes has been shown to introduce somatic mutations into genomic DNA. These enzymes are now recognized as causal agent responsible for the accumulation of CG- > TA transitions and DNA breaks leading to chromosomal rearrangements in human cancer genomes. Here, we identified an elephant A3Z1 gene, related to human APOBEC3A and showed that it could efficiently deaminate cytidine, 5-methylcytidine and produce DNA breaks leading to massive apoptosis, similar to other mammalian APOBEC3A enzymes where body mass varies by up to four orders of magnitude. Consequently, it could be considered that eAZ1 might contribute to cancer in elephants in a manner similar to their proposed role in humans. If so, eAZ1 might be particularly well regulated to counter Peto's paradox.
Representative demonstrator of a matched illumination radar (2017)

An adaptive (or cognitive) radar operates by sensing the environment and accordingly adopts an optimal transmit-receive structure. To this end, in the literature, matched illumination (MI) principles have been investigated to realize this concept, algorithms have been developed for the different components in such radars, and the entire framework validated through numerical simulations. However, these algorithms need to be verified for real-time operation in a hardware environment before being deployed in an actual radar. This paper describes the implementation of a representative demonstrator of a cognitive radar using two National instruments vector signal transceivers. The main objective is to validate the performance in terms of SINR by comparing to the numerical simulations and identify the real-time constraints for realizing a hardware prototype of a cognitive radar.
Optimization of the Solubility of HIV-1-Neutralizing Antibody 10E8 through Somatic Variation and Structure-Based Design (2016)

Antibody 10E8 could be used to prevent HIV-1 infection, if manufactured and delivered economically. It suffers, however, from issues of solubility, which impede manufacturing. We hypothesized that the physical characteristic of 10E8 could be improved through rational design, without compromising breadth and potency. We used structural biology to identify hydrophobic patches on 10E8, which did not appear to be involved in 10E8 function. Reversion of hydrophobic residues in these patches to their hydrophilic germ line counterparts increased solubility. Next, clues from somatic variants of 10E8, identified by next-generation sequencing, were incorporated. A combination of structure-based design and somatic variant optimization led to 10E8v4, with substantially improved solubility and similar potency compared to the parent 10E8. The cocrystal structure of antibody 10E8v4 with its HIV-1 epitope was highly similar to that with the parent 10E8, despite 26 alterations in sequence and substantially improved solubility. Antibody 10E8v4 may be suitable for manufacturing.
Loranthus longiflorus protect central nervous system against oxidative damages of electromagnetic radiation on rat (2013)

Background: The interaction of mobile phone radio‑frequency electromagnetic radiation (RF‑EMR) with the brain is a serious concern of our society. In this study, we aimed to experiment on the anti‑oxidative property of a parasitic plant Loranthus longiflorus (Loranthaceae) to protect central nervous system against oxidative damages of mobile phone electromagnetic field (EMF). Materials and Methods: Healthy male albino wistar rats were exposed to RF‑EMR by giving 5 min calling/5 min interval for 1 hour per day for 2 months, keeping a GSM (0.9/1.8 GHz) mobile phone in silent mode (no ring tone) in the cage. After 15, 30, 45, 60 days exposure, three randomly picked animals from each group were tested with using behavioural model of CNS on rats. Results and Conclusion: Loranthus longiflorus bark extract could be effective in decreasing immobility (P < 0.05) and increased locomotor activity (P < 0.05). This result indicates the protective effect of Loranthus longiflorus bark against EMF induced oxidative damage of central nervous system. Key words: Depression, electromagnetic radiation, locomotor, Loranthus longiflorus bark, mobile phone
Q-band micro-patch antennas implemented on a high resistivity silicon substrate using the surface micromachining technology (2004)

Using the surface micromachining technology composed of thick photoresist patterning and Cu-metal plating process, Q-band micro-patch antennas were implemented on high resistivity silicon (HRS) substrate. Because the application frequency is sufficiently high, the monolithically integrated, miniaturized micro antennas find applications in many systems. 42-GHz micro-patch antennas were fed by the coupling from the micro-strip feeder under the patch part. Using the parasitic capacitance in the posts contacted with HRS substrate, the patch sizes were decreased with slight decreasing of the bandwidth of antennas. Implemented patch antennas have 3 or 4 posts and their size was decreased with the increasing post capacitance in the radiating edges. Implemented patch sizes were 2.12, 1.78, and 1.41-mm with rectangular shape and the measured bandwidth under -10 dB of S11 was about 6 GHz(/spl sim/15%) with center frequency of 41.5 GHz in the case of 2.12 mm patch length.
External Support for Saphenous Vein Grafts in Coronary Artery Bypass Surgery (2022)

ClinicalTrials.gov Identifier: NCT03209609.
Targeted Learning of the Mean Outcome under an Optimal Dynamic Treatment Rule (2014)

We consider estimation of and inference for the mean outcome under the optimal dynamic two time-point treatment rule defined as the rule that maximizes the mean outcome under the dynamic treatment, where the candidate rules are restricted to depend only on a user-supplied subset of the baseline and intermediate covariates. This estimation problem is addressed in a statistical model for the data distribution that is nonparametric beyond possible knowledge about the treatment and censoring mechanism. This contrasts from the current literature that relies on parametric assumptions. We establish that the mean of the counterfactual outcome under the optimal dynamic treatment is a pathwise differentiable parameter under conditions, and develop a targeted minimum loss-based estimator (TMLE) of this target parameter. We establish asymptotic linearity and statistical inference for this estimator under specified conditions. In a sequentially randomized trial the statistical inference relies upon a second-order difference between the estimator of the optimal dynamic treatment and the optimal dynamic treatment to be asymptotically negligible, which may be a problematic condition when the rule is based on multivariate time-dependent covariates. To avoid this condition, we also develop TMLEs and statistical inference for data adaptive target parameters that are defined in terms of the mean outcome under the estimate of the optimal dynamic treatment. In particular, we develop a novel cross-validated TMLE approach that provides asymptotic inference under minimal conditions, avoiding the need for any empirical process conditions. We offer simulation results to support our theoretical findings.
Multisite Kinetic Modeling of13C Metabolic MR Using [1-13C]Pyruvate (2014)

Hyperpolarized (13)C imaging allows real-time in vivo measurements of metabolite levels. Quantification of metabolite conversion between [1-(13)C]pyruvate and downstream metabolites [1-(13)C]alanine, [1-(13)C]lactate, and [(13)C]bicarbonate can be achieved through kinetic modeling. Since pyruvate interacts dynamically and simultaneously with its downstream metabolites, the purpose of this work is the determination of parameter values through a multisite, dynamic model involving possible biochemical pathways present in MR spectroscopy. Kinetic modeling parameters were determined by fitting the multisite model to time-domain dynamic metabolite data. The results for different pyruvate doses were compared with those of different two-site models to evaluate the hypothesis that for identical data the uncertainty of a model and the signal-to-noise ratio determine the sensitivity in detecting small physiological differences in the target metabolism. In comparison to the two-site exchange models, the multisite model yielded metabolic conversion rates with smaller bias and smaller standard deviation, as demonstrated in simulations with different signal-to-noise ratio. Pyruvate dose effects observed previously were confirmed and quantified through metabolic conversion rate values. Parameter interdependency allowed an accurate quantification and can therefore be useful for monitoring metabolic activity in different tissues.
Development and Application of m Health Based on Smart Phone and Tablet APP (2015)

Compared with traditional medical treatment, mobile medical system has the advantages of convenient, efficient, and significantly reducing the cost of medicine and its rapid development promotes the medical and health care of China. In this paper, the significance and status of smart phone, tablet APP to m Health were introduced and the classification of mHealth was conducted. Then, the problem and challenge in mHealth were pointed out. Finally, the future of mHealth was prospected.
Zero TCF ZnO/quartz SAW structure for gas sensing applications (2005)

A zero TCF SAW device was developed for a temperature selfcompensated gas sensor. The device is based on the combination of a ZnO film and a quartz substrate with the appropriate cut and propagation angle. The developed structure IDT/ZnO/quartz, using ST-cut 35/spl deg/ X propagation quartz, presents a zero power flow angle, a very low temperature coefficient of frequency (TCF) value, and a relatively high electromechanical coupling factor. In this structure, the ZnO film is used simultaneously as gas sensitive layer and as TCF compensation layer. As ZnO is a very promising material for the application as gas sensor, the main interaction mechanisms between the acoustic wave and gaseous species (CO/sub 2/, ethanol, butanol) are reviewed. Detailed results for the sensitivity of different acoustic modes are presented.
Search Party: Using Randomcast for Reliable Multicast with Local (1998)

IP multicast is an efficient means of sending to a group, but the packets are sent unreliably. Some applications, like distributed whiteboard and news articles, require detection and retransmission of lost packets. In order to scale to large groups, local recovery is necessary to avoid involving the entire group in the repair process for packet losses affecting small regions of the distribution tree. While many current research efforts have attempted to devise local recovery schemes that rely only on the existing service model, we believe that extending the multicast forwarding service could enable viable and highly scalable local recovery mechanisms. To investigate this open issue, we propose a new randomized forwarding service called randomcast, and build upon it a loss recovery protocol called Search Party. Starting with the local recovery structure of the very scalable LMS scheme, we use randomized forwarding to greatly improve robustness at a modest cost in overhead and/or retransmission delay (the trade-off between the two costs is fine-tunable). Analysis predicts that as the group size N increases, overhead will increase by at most log(N) and retransmission delay will be unaffected. Simulation experiments show that both increase very little as N grows from 8 to 64, and confirm the tunability of the trade-off.
Nonreciprocal microdisk resonators utilizing magnetic bubble domains in garnet film for ultra-compact optical waveguide isolators (2007)

The three-dimensional characteristics of magneto-optical microresonators are presented, leading to a guideline for the design of nonreciprocal circuits. This involves a demonstration of how the resonators with selected parameters are practical for miniaturized nonreciprocal circuits. (2 pages)
Organic Electronics: Ultrathin and Stretchable Rechargeable Devices with Organic Polymer Nanosheets Conformable to Skin Surface (Small 13/2019) (2019)

In article number 1805296, Kenichi Oyaizu, Hiroyuki Nishide, and co-workers report 100 nmthick, organic robust redox-active polymer/carbon nanotube hybrid nanosheets as rechargeable power sources. The use of the mechanically robust yet intrinsically soft nanosheets enable the fabrication of organic polymer-based batteries with only 1 μm thickness and stretchable properties. The devices are highly conformable to skin surfaces.
Lateral interdot carrier transfer in an InAs quantum dot cluster grown on a pyramidal GaAs surface (2010)

InAs quantum dot clusters (QDCs), which consist of three closely spaced QDs, are formed on nano-facets of GaAs pyramidal structures by selective-area growth using metal-organic chemical vapor deposition. Photoluminescence (PL) and time-resolved PL (TRPL) experiments, measured in the PL linewidth, peak energy and QD emission dynamics indicate lateral carrier transfer within QDCs with an interdot carrier tunneling time of 910 ps under low excitation conditions. This study demonstrates the controlled formation of laterally coupled QDCs, providing a new approach to fabricate patterned QD molecules for optical computing applications.
Resequencing delay for a queueing system with two heterogeneous servers under a threshold-type scheduling (1988)

In service centers with multiple-parallel servers, jobs may complete their service in a different order from the one in which they enter the center. In order to reestablish the original order, resequencing protocols need to be implemented. It is shown that under a threshold-type policy, the resequencing delay depends on the strategy by which customers are selected and dispatched to the servers. Two selection strategies are developed, and the delay characteristics corresponding to the two strategies are studied. Existing methods for finding the sequencing delay are extended to cover the threshold-type policy. Closed-form solutions for the resequencing delay distributions under both selection policies are derived. To characterize the performance of the system under the two policies, two optimization criteria are introduced, namely, the fraction of customers that experience resequencing delay and the mean resequencing delay. These quantities are calculated explicitly, and their comparison reveals that the optimal decision is independent of the load on the system. The selection of the optimal policy under the first criterion depends only on the service rates, whereas for the second criterion the optimal selection depends on the threshold value and the ratio of the service rates.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Color and Fluorescence Imaging with t-Boc-protected Dihydroxynaphthacenedione (2000)

Abstract In recent years, generation of patterned images in polymer films has become a central focus in a variety fields of chemistry. Recently, generation of functional images by selective immobilization of organic dyes in the polymer film has been reported.1-3 Selective removal of acid labile protecting groups through photoinduced chemical transformation followed by chemisorption of organic dyes from solution into the patterned polymer film afforded µm-scale functional images.
First Contemporary Case of Human Infection with Cryptococcus gattii in Puget Sound: Evidence for Spread of the Vancouver Island Outbreak (2007)

We report a case of cryptococcosis due to C. gattii which appears to have been acquired in the Puget Sound region, Washington State. Genotyping confirmed identity to the predominant Vancouver Island genotype. This is the first documented case of human disease by the major Vancouver Island emergence strain acquired within the United States.
Fabrication and Replication of Arrays of Single- or Multicomponent Nanostructures by Replica Molding and Mechanical Sectioning (2010)

This paper describes the fabrication of arrays of nanostructures (rings, crescents, counterfacing split rings, cylinders, coaxial cylinders, and other structures) by a four-step process: (i) molding an array of epoxy posts by soft lithography, (ii) depositing thin films on the posts, (iii) embedding the posts in epoxy, and (iv) sectioning in a plane parallel to the plane defined by the array of posts, into slabs, with an ultramicrotome ("nanoskiving"). This work demonstrates the combination of four capabilities: (i) formation of structures that are submicrometer in all dimensions; (ii) fabrication of 3D structures, and arrays of structures, with gradients of height; (iii) patterning of arrays containing two or more materials, including metals, semiconductors, oxides, and polymers; and (iv) generation of as many as 60 consecutive slabs bearing contiguous arrays of nanostructures. These arrays can be transferred to different substrates, and arrays of gold rings exhibit plasmonic resonances in the range of wavelengths spanning 2-5 microm.
Tractable policy management framework for IoT (2017)

Due to the advancement in the technology, hype of connected devices (hence forth referred to as IoT) in support of automating the functionality of many domains, be it intelligent manufacturing or smart homes, have become a reality. However, with the proliferation of such connected and interconnected devices, efficiently and effectively managing networks manually becomes an impractical, if not an impossible task. This is because devices have their own obligations and prohibitions in context, and humans are not equip to maintain a bird’s-eye-view of the state. Traditionally, policies are used to address the issue, but in the IoT arena, one requires a policy framework in which the language can provide sufficient amount of expressiveness along with efficient reasoning procedures to automate the management. In this work we present our initial work into creating a scalable knowledge-based policy framework for IoT and demonstrate its applicability through a smart home application.
Cascade Palladium Catalysis: A Predictable and Selectable Regiocontrolled Synthesis of N‐Arylbenzimidazoles (2013)

Nach Wahl: Eine palladiumkatalysierte Reaktionskaskade baut N-Arylbenzimidazole direkt aus 2-Chlorarylsulfonaten, Arylaminen und Amidnucleophilen auf. Die Heterocyclen entstehen dabei über eine chemoselektive oxidative Addition. Mit 2-Chloraryltriflaten (Tf) wird gezielt ein Regioisomer erhalten, mit den entsprechenden 2-Chlorarylmesylaten (Ms) das andere.
717: ULTRASHORT-COURSE ANTIBIOTICS FOR SUSPECTED VAP WITH MINIMAL AND STABLE VENTILATOR SETTINGS (2016)

Copyright © 2016 by the Society of Critical Care Medicine and Wolters Kluwer Health, Inc. All Rights Reserved.
Two Coupled Rejection Metrics Can Tell Adversarial Examples Apart (2022)

Correctly classifying adversarial examples is an essential but challenging requirement for safely deploying machine learning models. As reported in RobustBench, even the state-of-the-art adversarially trained models struggle to exceed 67% robust test accuracy on CIFAR-10, which is far from practical. A complementary way towards robustness is to introduce a rejection option, allowing the model to not return predictions on uncertain inputs, where confidence is a commonly used certainty proxy. Along with this routine, we find that confidence and a rectified confidence (R-Con) can form two coupled rejection metrics, which could provably distinguish wrongly classified inputs from correctly classified ones. This intriguing property sheds light on using coupling strategies to better detect and reject adversarial examples. We evaluate our rectified rejection (RR) module on CIFAR-10, CIFAR-10-C, and CIFAR-100 under several attacks including adaptive ones, and demonstrate that the RR module is compatible with different adversarial training frameworks on improving robustness, with little extra computation.
SLP-2 regulates T cell activation by optimizing cardiolipin compartmentalization in mitochondrial membranes and enhancing cellular respiration (178.7) (2012)

Abstract Stomatin-like protein 2 (SLP-2) is a mitochondrial protein of the highly conserved Stomatin, Prohibitin, Flotillin, HflC/K superfamily. The function of SLP-2 has remained unclear but members of this superfamily have been linked to membrane organization. We have previously reported that SLP-2 partitions within glycolipid-enriched, detergent-insoluble microdomains, and its expression is up-regulated upon T cell activation. This correlates with increased mitochondrial biogenesis and function. Using human inducible over-expression/down-regulation systems and newly generated T cell-specific SLP-2 knockout mice, we now report that SLP-2 binds directly and selectively to cardiolipin (CL) and interacts with prohibitins. Overexpression of SLP-2 leads to increased recruitment of prohibitins to mitochondrial membranes. This translates into optimal assembly and function of complexes I and II+III of the respiratory chain. SLP-2 deficiency in T cells is associated with abnormal CL compartmentalization and decreased respiration, which correlates with a selective post-transcriptional defect in the production of IL-2 and defective T cell (mostly CD4+) responses. Therefore, we propose that SLP-2 functions as an organizer of cardiolipin-enriched domains in mitochondrial membranes. These domains are required for optimal respiration and metabolic capacity during T cell activation. Our work also reveals a novel post-transcriptional checkpoint for IL-2 production under metabolic control.
Towards improved HIV-microbicide activity through the co-encapsulation of NRTI drugs in biocompatible metal organic framework nanocarriers (2017)

The efficacy of the routinely used anti-HIV (Human Immunodeficiency Virus) therapy based on nucleoside reverse transcriptase inhibitors (NRTIs) is limited by the poor cellular uptake of the active triphosphorylated metabolites and the low efficiency of intracellular phosphorylation of their prodrugs. Nanoparticles of iron(iii) polycarboxylate Metal-Organic Frameworks (nanoMOFs) are promising drug nanocarriers. In this study, two active triphosphorylated NRTIs, azidothymidine triphosphate (AZT-Tp) and lamivudine triphosphate (3TC-Tp), were successfully co-encapsulated into the biocompatible mesoporous iron(iii) trimesate MIL-100(Fe) nanoMOF in order to improve anti-HIV therapies. The drug loaded nanoMOFs could be stored for up to 2-months and reconstituted after freeze drying, retaining similar physicochemical properties. Their antiretroviral activity was evidenced in vitro on monocyte-derived macrophages experimentally infected with HIV, making these co-encapsulated nanosystems excellent HIV-microbicide candidates.