gebhart/patrepeval huggingface dataset:
Safety and MRI Artifact Evaluation at 1.5 T of Metallic Mounting Sheath of a Marking Clip Inadvertently Deployed at Stereotactic Biopsy (2004)

In case of inadvertent deployment of the sheath, a delay of 6-8 weeks before MRI is recommended as a conservative approach to ensure tissue ingrowth and to minimize the chance of harm to the patient. In the case of metallic clips used for breast biopsy, caution is warranted when a portion of the device unintended for placement is introduced into the breast.
On the steering of sound energy through a supercritical plate by a near-field transducer array (2008)

The ability to direct sound energy through the flexural vibrations of a submerged plate at various angles of incidence using a near-field transducer array is investigated. An alumina bar is placed in front of a one-dimensional, eight-element transducer array, between the array and the water. Operating in a receive mode, data were taken as a function of angle of incidence and compared to data taken without the presence of the alumina bar. The array was also operated in transmit mode and results were compared to corresponding receive mode data, showing that reciprocity holds. Results show that in fact sound energy can be steered through a plate, and that the measurement method used provides a convenient method of measuring the angular dependence of transmission through a plate, including measurements at frequencies above the plate's critical frequency. Experimental results of sound transmission versus angle of incidence of finite sized plates agree qualitatively with theoretical results from an analysis of the transmission through an unbounded flexible partition.
Visual Analytics for Topic Model Optimization based on User-Steerable Speculative Execution (2018)

To effectively assess the potential consequences of human interventions in model-driven analytics systems, we establish the concept of speculative execution as a visual analytics paradigm for creating user-steerable preview mechanisms. This paper presents an explainable, mixed-initiative topic modeling framework that integrates speculative execution into the algorithmic decisionmaking process. Our approach visualizes the model-space of our novel incremental hierarchical topic modeling algorithm, unveiling its inner-workings. We support the active incorporation of the user's domain knowledge in every step through explicit model manipulation interactions. In addition, users can initialize the model with expected topic seeds, the backbone priors. For a more targeted optimization, the modeling process automatically triggers a speculative execution of various optimization strategies, and requests feedback whenever the measured model quality deteriorates. Users compare the proposed optimizations to the current model state and preview their effect on the next model iterations, before applying one of them. This supervised human-in-the-loop process targets maximum improvement for minimum feedback and has proven to be effective in three independent studies that confirm topic model quality improvements.
Variable expression of mental retardation, autism, seizures, and dystonic hand movements in two families with an identical ARX gene mutation (2002)

Two families, originally diagnosed as having nonsyndromic X-linked mental retardation (NSXLMR), were reviewed when it was shown that they had a 24-bp duplication (428-45 1dup(24bp)) in the ARX gene [Stromme et al., 2002: Nat Genet 30:441-445]. This same duplication had also been found in three other families: one with X-linked infantile spasms and hypsarrhythmia (X-linked West syndrome, MIM 308350) and two with XLMR and dystonic movements of the hands (Partington syndrome, MIM 309510). On review, manifestations of both West and Partington syndromes were found in some individuals from both families. In addition, it was found that one individual had autism and two had autistic behavior, one of whom had epilepsy. The degree of mental retardation ranged from mild to severe. A GCG trinucleotide expansion (GCG)10+7 and a deletion of 1,517 bp in the ARX gene have also been found in association with the West syndrome, and a missense mutation (1058C>T) in a family with a newly recognized form of myoclonic epilepsy, severe mental retardation, and spastic paraplegia [Scheffer et al., 2002: Neurology, in press]. Evidently all these disorders are expressions of mutations in the same gene. It remains to be seen what proportions of patients with infantile spasms, focal dystonia, autism, epilepsy, and nonsyndromic mental retardation are accounted for by mutations in the ARX gene.
Measurement of W± and Z-boson production cross sections in pp collisions at s=13 TeV with the ATLAS detector (2016)

Measurements of the W and Z + -production cross sections (where = e , ) in proton-proton collisions at s = 13 TeV are presented using data recorded by the ATLAS experiment at the Large Hadron Collider, corresponding to a total integrated luminosity of 81 pb -1 . The total inclusive W -boson production cross sections times the single-lepton-flavour branching ratios are tot
Gut-Liver physiomimetics reveal paradoxical modulation of IBD-related inflammation by short-chain fatty acids (2019)

Summary Association between the microbiome, IBD and liver diseases are known, yet cause and effect remain elusive. By connecting human microphysiological systems of the gut, liver and circulating Treg/Th17 cells, we modeled progression of ulcerative colitis (UC) ex vivo. We show that microbiome-derived short-chain fatty acids (SCFA) may either improve or worsen disease severity, depending on the activation state of CD4 T cells. Employing multiomics, we found SCFA increased production of ketone bodies, glycolysis and lipogenesis, while markedly reducing innate immune activation of the UC gut. However, during acute T cell-mediated inflammation, SCFA exacerbated CD4 + T cell effector function, partially through metabolic reprograming, leading to gut barrier disruption and hepatic injury. These paradoxical findings underscore the emerging utility of human physiomimetic technology in combination with systems immunology to study causality and the fundamental entanglement of immunity, metabolism and tissue homeostasis.
Optimum decode-and-forward relay-assisted combining scheme with relay decision information (2015)

Diversity combining is a form of spatial diversity which is of primary importance in wireless communications. Maximum Ratio Combining (MRC) is known as the best combining scheme because it effectively uses the Channel State Information (CSI) at the receiver in the combining process. However, in cooperative relay-based systems employing relay detection, MRC performance is limited by the fact that the CSI is insufficient to optimize the combining process due to hard decisions performed by some signaling methods at the relay such as Decode-and-Forward (DF). In this paper, we propose a new optimum combining scheme for DF cooperative systems in which the performance gain is achieved through the use of relay decision information along with the CSI in the combining process. The proposed optimum combining is a general scheme, where MRC and other combining schemes are considered to be special cases of optimum combining. Results show that optimum combining significantly improves the system throughput and reduces the error probability. Moreover, it enhances the system robustness due to the adaptivity of the combiner with the change in cooperative channel conditions and packet size.
Identification of (E)‐4‐hydroxy‐3‐methyl‐but‐2‐enyl pyrophosphate as a major activator for human γδ T cells in Escherichia coli (2001)

The gcpE and lytB gene products control the terminal steps of isoprenoid biosynthesis via the 2-C-methyl-D-erythritol 4-phosphate pathway in Escherichia coli. In lytB-deficient mutants, a highly immunogenic compound accumulates significantly, compared to wild-type E. coli, but is apparently absent in gcpE-deficient mutants. Here, this compound was purified from E. coli DeltalytB mutants by preparative anion exchange chromatography, and identified by mass spectrometry, (1)H, (13)C and (31)P NMR spectroscopy, and NOESY analysis as (E)-4-hydroxy-3-methyl-but-2-enyl pyrophosphate (HMB-PP). HMB-PP is 10(4) times more potent in activating human Vgamma9/Vdelta2 T cells than isopentenyl pyrophosphate.
Violation-Aware Contextual Bayesian Optimization for Controller Performance Optimization with Unmodeled Constraints (2023)

We study the problem of performance optimization of closed-loop control systems with unmodeled dynamics. Bayesian optimization (BO) has been demonstrated to be effective for improving closed-loop performance by automatically tuning controller gains or reference setpoints in a model-free manner. However, BO methods have rarely been tested on dynamical systems with unmodeled constraints and time-varying ambient conditions. In this paper, we propose a violation-aware contextual BO algorithm (VACBO) that optimizes closed-loop performance while simultaneously learning constraint-feasible solutions under time-varying ambient conditions. Unlike classical constrained BO methods which allow unlimited constraint violations, or 'safe' BO algorithms that are conservative and try to operate with near-zero violations, we allow budgeted constraint violations to improve constraint learning and accelerate optimization. We demonstrate the effectiveness of our proposed VACBO method for energy minimization of industrial vapor compression systems under time-varying ambient temperature and humidity.
Structure of the NADPH-Binding Motif of Glutathione Reductase: Efficiency Determined by Evolution (1994)

The role of the second glycine residue (Gly-176) of the conserved GXGXXA "fingerprint" motif in the NADPH-binding domain of Escherichia coli glutathione reductase has been studied by means of site-directed mutagenesis. This glycine residue occurs at the N-terminus of the alpha-helix in the beta alpha beta fold that characterizes the dinucleotide-binding domain, in close proximity to the pyrophosphate bridge of the bound coenzyme. Introducing an alanine residue (G176A), the minimum possible change, at this position virtually inactivated the enzyme, as did the introduction of valine, leucine, isoleucine, glutamic acid, histidine, or arginine residues. Only the replacement by serine--a natural substitute for this glycine residue in some forms of mercuric reductase, a related flavoprotein disulfide oxidoreductase--produced a mutant enzyme (G176S) that retained significant catalytic activity. It is conceivable that this is due to a favorable hydrogen bond being formed between the serine hydroxyl and a pyrophosphate oxygen atom. In most of the mutant enzymes, the Km for NADPH was substantially greater than that found for wild-type glutathione reductase, as expected, but this was accompanied by an unexpected decrease in the Km for GSSG. The latter can be explained by the observation that the reduction of the enzyme by NADPH, the first half-reaction of the ping-pong mechanism, had become a rate-limiting step of the overall reaction catalyzed, albeit poorly, by the mutant enzymes.(ABSTRACT TRUNCATED AT 250 WORDS)
Schemes for cubature over the unit disk found via numerical optimization (2022)

Cubature schemes, in this case for uniformly weighted integration over the unit disk, enable exact evaluation of numerical integrals of polynomials but have been explicitly constructed for only low or moderate degrees. In this paper, cubature formulae are discovered for a wider range of degrees by leveraging numerical optimization. These results include a degree-17 cubature scheme with fewer points than existing solutions and up to a degree-77 solution with 1021 cubature points. Optimization heuristics and patterns in the distributions of cubature points are discussed, which serve as vital guides in this work. For example, these heuristics leverage a connection to circle-packing configurations to facilitate the discovery of fully symmetric cubature schemes.
ChemInform Abstract: Discrete and Infinite Host Frameworks Based Upon Resorcin[4]arenes by Design (2000)

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.
Linearization of a 65nm CMOS Power Amplifier with a Cartesian Feedback for W-CDMA Standard (2009)

International audience
A rapid and non-invasive proteomic analysis using DBS and buccal swab for multiplexed second-tier screening of Pompe disease and Mucopolysaccharidosis type I (2022)

Direct quantification of endogenous GAA and IDUA peptides in DBS by Immuno-SRM can be used for second-tier screening to rapidly identify severe PD and MPS I patients with a turnaround time of <1 week. Such patients could benefit from immediate clinical follow up and possibly earlier treatment.
Interference Steering to Manage Interference in IoT (2019)

Internet of Things (IoT) is a new paradigm that involves the interconnection of thousands of devices and home appliances. Due to the scarcity of the spectrum suitable for wireless electromagnetic transmission, many communication systems and devices are close to each other, or even overlapping in spectrum, thus incurring complicated interference situations. Therefore, interference in IoT is worthy of thorough investigation and should be well addressed. There have been numerous interference management (IM) proposals at the interfering transmitter or the interfered transmitter/receiver separately or cooperatively. Moreover, the existing IM schemes rely mainly on the use of channel state information (CSI). However, in some communication scenarios, the option to adjust the interferer is not available, and, in the case of downlink transmission, it is always difficult or even impossible for the interfered receiver to acquire necessary information for IM. Based on the above observations, we first propose a novel IM technique, called interference steering (IS). By making use of both CSI with respect to and data carried in the interfering signal, IS generates a signal to modify the spatial feature of the original interference, so that the steered interference at the interfered receiver is orthogonal to its intended signal. We then apply IS to a wireless local area network (WLAN)-based IoT in which the same frequency band is reused by adjacent basic service sets (BSSs) with overlapping areas. With IS, multiple nearby access points (APs) could simultaneously transmit data on the same channel to their mobile stations (STAs), thus enhancing spectrum reuse. Our in-depth simulation results show that IS significantly improves network SE over existing IM schemes.
Analysis of 80-MeV Carbon and 80-MeV Nitrogen Ion Irradiation Effects on N-Channel MOSFETs (2019)

N-channel depletion MOSFETs were irradiated with 80 MeV Carbon (C <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">6+</sup> ) and 80 MeV Nitrogen (N <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">6+</sup> ) ions in the dose range from 100 krad (Si) to 30 Mrad (Si). The electrical characteristics of MOSFET such as threshold voltage (V <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">th</sub> ), density of interface trapped charges (AN <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">it</sub> ), density of oxide trapped charges (AN <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">ot</sub> ), transconductance (g <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">m</sub> ), mobility (μ), leakage current (I <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">L</sub> ) and drain saturation current (IDSat) were studied as a function of dose. A considerable increase in AN <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">it</sub> and AN <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">ot</sub> and decrease in V <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">th</sub> , g <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">m</sub> , μ, and ID Sat was observed after irradiation. The μ was correlated with AN <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">it</sub> and it is found that the contribution of AN <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">ot</sub> in degrading the mobility of charge carriers is negligible.The ion irradiated results were compared with Co-60 gamma irradiated results and found that the degradation is more for Co-60 gamma irradiated devices at lower doses, whereas at higher doses, the degradation is more for heavy ion irradiated devices.
Abstract B32: Inhibiting DNA methylation causes an interferon response in cancer via dsRNA including endogenous retroviruses (2016)

Abstract DNA methyltransferase inhibitors (DNMTis) upregulate immune attraction, including the interferon response, in solid tumors. We now define viral defense signaling as one mechanism for this. In epithelial ovarian cancer cells DNMTis upregulate viral defense by cytosolic sensing of double-stranded RNA (dsRNA), triggering a Type I Interferon response, upregulation of downstream interferon response genes, and increased apoptosis. Knockdown of the dsRNA sensors TLR3 and MAVS and inhibition of the interferon alpha/beta receptor blunt the DNMTi induced dsRNA response. DNMTis cause apoptosis of cancer cells, which is partially rescued by inhibiting the interferon alpha/beta receptor. We observe upregulation and demethylation of hypermethylated endogenous retroviruses (ERVs) and overexpression of individual ERVs whose sense and anti-sense transcripts may be key candidates for triggering the above signaling. Overexpression of ERVs alone is sufficient to trigger an interferon response in the absence of DNMTis. Basal levels of ERV and viral defense gene expression significantly correlate in primary OC and basal expression of the viral defense signature separates primary TCGA samples for multiple tumor types into low versus high expression groups. In melanoma patients treated with an immune checkpoint therapy, high viral defense signature expression in tumors significantly associates with durable clinical response and DNMTi treatment sensitizes to anti-CTLA4 therapy in a pre-clinical melanoma model. We thus define a major mechanism for how DNMTis may induce cancer cells to increase immune attraction and possibly sensitize patients to immunotherapy. Experiments determining which Aza-upregulated molecules on tumor cells are necessary for attraction and activation of host immune cells are ongoing. Citation Format: Katherine B. Chiappinelli, Pamela L. Strissel, Alexis Desrichard, Huili Li, Christine Henke, Benjamin Akman, Alexander Hein, Neal S. Rote, Leslie M. Cope, Alexandra Snyder, Vladimir Makarov, Sadna Budhu, Jedd Wolchok, Cynthia A. Zahnow, Taha Mergoub, Timothy A. Chan, Reiner Strick, Stephen B. Baylin. Inhibiting DNA methylation causes an interferon response in cancer via dsRNA including endogenous retroviruses. [abstract]. In: Proceedings of the AACR Special Conference on Chromatin and Epigenetics in Cancer; Sep 24-27, 2015; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2016;76(2 Suppl):Abstract nr B32.
Targeted learning with daily EHR data (2019)

Electronic health records (EHR) data provide a cost- and time-effective opportunity to conduct cohort studies of the effects of multiple time-point interventions in the diverse patient population found in real-world clinical settings. Because the computational cost of analyzing EHR data at daily (or more granular) scale can be quite high, a pragmatic approach has been to partition the follow-up into coarser intervals of pre-specified length (eg, quarterly or monthly intervals). The feasibility and practical impact of analyzing EHR data at a granular scale has not been previously evaluated. We start filling these gaps by leveraging large-scale EHR data from a diabetes study to develop a scalable targeted learning approach that allows analyses with small intervals. We then study the practical effects of selecting different coarsening intervals on inferences by reanalyzing data from the same large-scale pool of patients. Specifically, we map daily EHR data into four analytic datasets using 90-, 30-, 15-, and 5-day intervals. We apply a semiparametric and doubly robust estimation approach, the longitudinal Targeted Minimum Loss-Based Estimation (TMLE), to estimate the causal effects of four dynamic treatment rules with each dataset, and compare the resulting inferences. To overcome the computational challenges presented by the size of these data, we propose a novel TMLE implementation, the "long-format TMLE," and rely on the latest advances in scalable data-adaptive machine-learning software, xgboost and h2o, for estimation of the TMLE nuisance parameters.
Phosphatidylinositol 3‐kinase activity is required for the expression of glial fibrillary acidic protein upon cAMP‐dependent induction of differentiation in rat C6 glioma (2001)

Glial fibrillary acidic protein (GFAP) is an intermediate filament (IF) protein expressed upon maturation of astrocytes and upregulated during reactive astrogliosis. Its expression is modulated by several growth factors and hormones. Although an upregulation of intracellular cAMP is required for the induction of GFAP expression in astrocytes, little information is available on other downstream factors of the signal transduction pathways involved in the regulation of its expression. In this communication, we identified phosphatidylinositol 3-kinase (PI 3-K) as a necessary enzyme for GFAP expression in rat C6 glioma cells. Use of the specific PI 3-K inhibitors wortmannin and LY294002 and transfection of C6 cells with a dominant negative PI 3-K construct, resulting in a decrease of the enzymatic activity of PI 3-K, inhibited the cAMP-dependent expression of GFAP. Furthermore, confocal laser scanning microscopy demonstrated that inhibition of the PI 3-K activity by LY294002 or wortmannin concomitant with induction of differentiation changes the cellular distribution leading to a pericentrosomal localization of GFAP and an altered cell shape lacking process formation. We conclude that the expression and cellular distribution of GFAP is mediated through a PI 3-K-dependent mechanism.
Modulating Angiogenesis (2004)

The present study explains, for the first time, the ambiguity about the effects of ginseng in vascular pathophysiology based on the existence of opposing active principles in the extract. We also unraveled a speciogeographic variation impinging on the compositional fingerprint that may modulate the final phenotype. This emphasizes the need for regulations standardizing herbal therapy, currently under the Dietary Supplement and Health Education Act. Furthermore, we propose that Rg1 could be a prototype for a novel group of nonpeptide molecules that can induce therapeutic angiogenesis, such as in wound healing.