gebhart/patrepeval huggingface dataset:
Isogenic mutants of the cag pathogenicity island of Helicobacter pylori in the mouse model of infection: effects on colonization efficiency (2002)

Strains of Helicobacter pylori that contain the cag pathogenicity island (cag PAI) are associated with increased virulence and severe clinical outcomes. To evaluate the role of the cag island in infection, isogenic null mutations were generated in two clinical isolates (SS1 and Iris1) with distinct genetic backgrounds. When tested for their ability to establish infection in the stomach of CD1/SPF mice, at the early phase of infection, strains in which cagE, ORF528, ORF527 or ORF525 were inactivated showed a reduced capacity to initiate colonization compared to the wild-type strain. Strains with a mutation in the ORF524 gene were more efficient than the other mutants, but still less efficient than the wild-type strain. Mutation in the effector protein, CagA, which is injected into host cells and tyrosine-phosphorylated, did not change the colonization efficiency. In conclusion, all cag genes analysed, with the exception of the effector protein, CagA, influenced the early phase of colonization in the mouse model of infection. These results suggest that the structure of the H. pylori secretion apparatus itself is involved in this process.
Comparative Effects of Monatepil a Novel Calcium Antagonist With a1-Adrenergic-Blocking Activity, and Nitrendipine on Lipoprotein and Carbohydrate Metabolism in Patients With Hypertension (1994)

The effects of monatepil, a new calcium antagonist with α1-blocking activity, and nitrendipine on lipoprotein and carbohydrate metabolism in 86 patients with mild-to-moderate hypertension were examined in a randomized, open-label, multicenter (32 hospitals) study. Thirty-nine patients treated with monatepil and 33 patients treated with nitrendipine completed the 12-week study. Monatepil and nitrendipine each significantly decreased both systolic and diastolic blood pressure. Changes in heart rate were not seen in either group. Monatepil administration significantly decreased total cholesterol, low density lipoprotein (LDL) cholesterol, the LDL cholesterol to high density lipoprotein (HDL) cholesterol ratio, apolipoprotein (Apo) B levels, and HbAlc levels, whereas no changes in these measurements were observed in nitrendipine-treated patients. Monatepil also significantly decreased lipoprotein(a) levels, but there were no significant changes in HDL cholesterol, Apo-AI, or Apo-E levels. After nitrendipine treatment, the C peptide concentration decreased significantly, although no significant changes were observed in fasting blood glucose or immunoreactive insulin levels. On the basis of these results, it can be concluded that monatepil belongs to a new class of antihypertensive calcium antagonist with favorable carbohydrate metabolism and lipid-lowering activity, although the clinical importance of these findings has not been established. Am J Hypertens 1994;7:161S–166S
Pulsed Reduced Dose Rate Radiotherapy in Conjunction With Bevacizumab or Bevacizumab Alone in Recurrent High-grade Glioma: Survival Outcomes (2020)

This retrospective analysis suggests that treatment with pRDR in addition to bevacizumab could significantly prolong PFS and overall survival compared with bevacizumab alone for recurrent high-grade glioma.
Advancements in indirect Time of Flight image sensors in front side illuminated CMOS (2021)

We will present major advances in Time of Flight (ToF) image sensors for consumer applications. Several innovative elements integrated into a 130nm front side illumination CMOS node reveal superior sensor performance so far only attributed to much more complex backside illumination technologies. The gate controlled pixels comprising deep trenches, buried mirrors and integrated prisms, reveal high quantum efficiency and modulation transfer function (MTF) close to the physical pixel size. In-pixel common mode suppression prevents saturation even under backlight conditions. The comprehensive System on Chip integrates high speed ADCs, a flexible phase shifter, as well as current monitoring for laser safety.
DISCS: Secure content distribution in IP using information centric networking (2017)

Edge caching is one of the main features provided by fog storage service. However, according to recent studies, currently more than 60% of Internet traffic goes over HTTPS. In the presence of HTTPS, caching solutions become useless, as the application payload is encrypted by the transport layer security protocol i.e. SSL (Secure Socket Layer). This paper addresses this issue and proposes an alternate approach of content caching. Our approach leverages ICN (Information Centric Networking) protocol by naming encrypted content objects. To cache encrypted content objects we first propose DCAR (Dual-mode Content Aware Router), an edge router that incorporates caches and understands both IP and ICN flows. Next we present the details of DISCS (DCAR based Information centric Secure Content Sharing) architecture that leverages DCAR and enables secure content distribution. Finally we provide the details of realizing such a system and evaluate its performance on a proof-of-concept prototype.
Imidazoquinoxaline Src-Family Kinase p56Lck Inhibitors:  SAR, QSAR, and the Discovery of (S)-N-(2-Chloro-6-methylphenyl)-2-(3-methyl-1-piperazinyl)imidazo- [1,5-a]pyrido[3,2-e]pyrazin-6-amine (BMS-279700) as a Potent and Orally Active Inhibitor with Excellent in Vivo Antiinflammatory Activity (2004)

A series of novel anilino 5-azaimidazoquinoxaline analogues possessing potent in vitro activity against p56Lck and T cell proliferation have been discovered. Subsequent SAR studies led to the identification of compound 4 (BMS-279700) as an orally active lead candidate that blocks the production of proinflammatory cytokines (IL-2 and TNFalpha) in vivo. In addition, an expanded set of imidazoquinoxalines provided several descriptive QSAR models highlighting the influence of significant steric and electronic features. The H-bonding (Met319) contribution to observed binding affinities within a tightly congeneric series was found to be significant.
A general and facile synthesis of 1,3-diaryl-4-pyrazoleacetic acid esters (2005)

A general synthesis of 1,3-diaryl-4-pyrazoleacetic acid esters has been realized via the condensation of a γ-carboxy ester hydrazone with the Vilsmeier reagent.
The Effect of Caffeine on Digital Haemodynamics (1994)

Caffeine has been shown to increase mean blood pressure, but studies documenting the effect of caffeine on digits are lacking. We evaluated the effect of caffeine on digital blood pressure and pulse volume in normal volunteers. In the first part of the study, 24 subjects were given water containing either 200 mg of caffeine or placebo. Bilateral brachial and middle finger digital pressures were measured at room temperature before ingestion and at 30 and 60 minutes after ingestion. In the second part of the study, pulse volume recordings (PVRs) were obtained in 24 subjects at the level of the distal phalanx of the middle finger of one hand immediately prior to beverage ingestion and at 10 minute intervals for 90 minutes. Differences in mean digital systolic pressure, digital/brachial index, or PVR amplitude between the control and caffeine groups were not statistically significant. The administration of caffeine was found not to alter the haemodynamics of digital blood flow or digital pressure in this population.
A Consistency Checking Optimization Algorithm for Memory-Intensive Transactions ; CU-CS-1049-08 (2008)

Transactional memory (TM), a recent parallel programming concept, aims to simplify parallel programming while simultaneously maintaining performance benefits found in concurrent applications.Consistency checking, the manner in which memory conflicts are identified in transactional memory, is a critical aspect to TM system performance.We present a theoretical, analytical and empirical view of our novel consistency checking algorithm which is optimized for spatially wide transactional workloads.Initial tests show our algorithm yields super linear performance improvements over other alternatives as transaction size grows, resulting in performance gains between 5x -250x for experimental benchmarks.
Predicting Antimicrobial Activity of Conjugated Oligoelectrolyte Molecules via Machine Learning (2021)

New antibiotics are needed to battle growing antibiotic resistance, but the development process from hit, to lead, and ultimately to a useful drug takes decades. Although progress in molecular property prediction using machine-learning methods has opened up new pathways for aiding the antibiotics development process, many existing solutions rely on large data sets and finding structural similarities to existing antibiotics. Challenges remain in modeling unconventional antibiotic classes that are drawing increasing research attention. In response, we developed an antimicrobial activity prediction model for conjugated oligoelectrolyte molecules, a new class of antibiotics that lacks extensive prior structure-activity relationship studies. Our approach enables us to predict the minimum inhibitory concentration for <i>E. coli</i> K12, with 21 molecular descriptors selected by recursive elimination from a set of 5305 descriptors. This predictive model achieves an <i>R</i><sup>2</sup> of 0.65 with no prior knowledge of the underlying mechanism. We find the molecular representation optimum for the domain is the key to good predictions of antimicrobial activity. In the case of conjugated oligoelectrolytes, a representation reflecting the three-dimensional shape of the molecules is most critical. Although it is demonstrated with a specific example of conjugated oligoelectrolytes, our proposed approach for creating the predictive model can be readily adapted to other novel antibiotic candidate domains.
Studies on the Bacteriophage MS2 (1969)

Undegraded, uniformly 32 P‐labelled replicative form and replicative intermediate were prepared and fractionated according to sedimentation rate. For each fraction the amount of 5′‐terminal residues, which after alkaline hydrolysis are released as 5′‐triphosphoryl, 3′(2′)‐phosphoryl nucleosides (nucleoside tetraphosphates), was quantitatively determined. The replicative form contained O, and the replicative intermediate 2.5 nascent chains, if the assumption is made that the latter are on the average half completed. The number of nascent chains apparently increases with increasing sedimentation constant of the replicative intermediate molecules. The nucleoside tetraphosphate, released from each fraction, was identified as exclusively pppGp. This is interpreted as evidence for a 5′ to 3′ polarity in the synthesis of viral RNA, i.e. a growing 3′OH end. The replicative form and replicative intermediate were also prepared from cells, in which the 32 P‐label was chased for 5 min before harvest. The amount of nucleoside tetraphosphate released agreed with a single end group per complete chain. Presumably 50 to 100% of the residual labelled terminal was derived from the complementary strand, and again only pppGp was found. It follows that the 3′‐terminal adenosine residue of the viral RNA is presumably not part of the genetic information transferred during replication.
Reflectivity and Bandwidth Modulation of Fiber Bragg Gratings in a Suspended Core Fiber by Tunable Acoustic Waves (2014)

The acousto-optic modulation of fiber Bragg gratings in a four-hole suspended core fiber is experimentally demonstrated. Strong modulations with a reflectivity amplitude decrease by up to 67% and a 57% bandwidth increase in the Bragg resonance are obtained for gratings of 0.26- and 1-nm 3-dB bandwidths, respectively. The reduction of the required acoustic power for achieving the acousto-optic modulation compared to conventional solid-core single-mode fibers points to more efficient modulator devices in suspended core fibers.
Molecular Cytogenetic Characterization of the Sequential Development of Multidrug Resistance in Two Panels of Colchicine-Resistant Cell Lines (2020)

Cytogenetic analysis of both colchicine-resistant (CLC) panels reveals an increase in the complexity of the karyotype with increasing CLC. Gene amplification was observed at higher levels of CLC associated with recognizable abnormally banding regions or double minute chromosomes. Investigators have described and characterized distinctive chromosomal structures formed early in the amplification of several different amplified genes. The finding of the large extended regions of DNA at the site of the single copy gene in early steps in the process of CLC drug selection appears to be entirely analogous to the examples visualized in early steps of CAD and dihydrofolate reductase amplification. The PGY cDNA probe was tritium-labeled by nick translation to a specific activity of approximately 10 counts per minute per microgram of probe DNA. At the earliest steps of selection in both independent panels, unusual chromosomal structures characteristic of newly amplified PGY DNA were observed linked to the long arm chromosome 1, presumably by a process of interstitial duplication.
Nonrigid registration based on projected joint entropy combined with gradient similarity (2010)

Our study proposes a nonrigid image registration method between different color channels in a color image sequence. It minimizes the entropy in a dominant subspace of the joint distribution of two or more images. The proposed algorithm is based on the observation that the displacement between color channels affects only the dominant subspace in the joint distribution of pixel values. We also propose the use of gradient direction to give extra robustness to our similarity function. Experiments estimating motion parameters for B-spline nonrigid deformation models demonstrate the effectiveness of the proposed registration technique.
Low-Cost, Dendrite-Blocking Polymer-Sb2O3Separators for Lithium and Sodium Batteries (2014)

We describe here preparation and performance of an ultra-flexible and low-cost Sb2O3/polymer composite membrane separator for Na-ion or Li-ion batteries operating with metallic Na or Li anodes. The separator has a large electrolyte window, excellent thermal and mechanical stabilities when infused with EC/DEC/AClO4 (1M) electrolyte (A = Li or Na), excellent wettability and acceptable ionic conductivity to 1C rate. The ability of the separator to block anode dendrites from crossing it is demonstrated in symmetric alkali-metal cells and in the performances of Na-ion and Li-ion cells with/without loading with Sb2O3.
ChemInform Abstract: Resonance Raman and Surface‐ and Tip‐Enhanced Raman Spectroscopy Methods to Study Solid Catalysts and Heterogeneous Catalytic Reactions (2011)

Abstract Review: 300 refs.
Induced Current Thermal Imaging in Breast Cancer Detection (2021)

Infrared thermal imaging method has started to be used in routine controls due to the disadvantages (uses ionizing energy, applies pressure) of mammography, which is frequently used in the diagnosis of breast cancer. With passive thermography, infrared radiation emitted naturally from the body surface is detected by a thermal camera and the surface temperature distribution is displayed. Using a passive thermal imaging system with 30 mK thermal sensitivity, 10 mm tumor can be detected at a depth of 12 mm. The performance of passive thermography is limited for small and deep tumors. In the active thermography method, it is aimed to detect deeper tumors by using an external heat source. In the active thermography method, deeper tumors are detected using external heat sources. In this study, the currents induced by time varying magnetic fields (27.12 MHz) were used as the external heat source. In the simulation study, breast and cancerous tissue were modeled in three dimensions and the bioheat equation for active and passive modes was solved by using realistic values of the tissues. As a result of the simulation studies, it was observed that a 10 mm malignant tumor could be detected up to a depth of 20 mm. It was shown that this method can be used with multiple frequencies as the temperature distributions obtained from the surface for different frequency values are different from each other.
Abstract 1706: A non-canonical MiT/TFE-dependent NRF2 program is a druggable vulnerability in multiple cancer types (2023)

Abstract The transcription factor NRF2 is a master regulator of cellular responses to oxidative stress, contributing to the pathogenesis of autoimmunity, metabolic disorders, and neurodegeneration. Somatic alterations in the NRF2 pathway also contribute to the growth and metastasis of many cancer types including ~30% of lung cancers. Still, the activation of NRF2 has frequently been observed in the absence of known genomic alterations, indicating that other pathways may drive its dysregulation. Further, approaches to target NRF2 pharmacologically have remained elusive. Here, we conducted a screen that identified a small molecule, ML329, exhibiting selective cytotoxicity in cells exhibiting NRF2 dependency and synthetic lethality to NRF2 pathway mutations across 489 cell lines. Surprisingly, we find that melanomas—which rarely have somatic mutations in the NRF2 pathway—were commonly sensitive to ML329. Melanomas were seen to exhibit NRF2-dependent metabolomic and transcriptional programs through the transcriptional activation of the adaptor protein p62/SQSTM1 by the melanocyte master regulator and oncoprotein MITF. This pathway was found to be conserved among all cancers characterized by genomic alterations of the MiT family (MITF, TFEB and TFE3) including subsets of renal cell carcinomas, pediatric sarcomas, and uveal and cutaneous melanomas. Our data identify a previously unrecognized, non-canonical mechanism of NRF2 activation by the MiT family, clarifying the regulation of NRF2 in pathologic and physiologic contexts. Pharmacologic inhibition of NRF2 could be valuable in the treatment of conditions with MITF family dysregulation. Citation Format: Xinbo Luo, Bart Lutterbach, Priya Pancholi, Yeon Sook Choi, Xiao Liu, Phillip Munson, Saqib Faisal, David A. Whipple, Robert A. Smith, Warren S. Weiner, David K. Johnson, Myriam Boukhali, Nicole S. Persky, Matthew G. Rees, Shunsuke Kitajima, David Barbie, Anuradha Roy, Michael Baltezor, Lian Rajewski, William McGuinness, John Haslam, Ananthan Sadagopan, Charles H. Yoon, Cory M. Johannessen, Christine G. Lian, Jason L. Hornick, Srinivas R. Viswanathan, David Liu, Vicki Nienaber, Wilhelm Haas, Frank J. Schoenen, David E. Fisher, Rizwan Haq. A non-canonical MiT/TFE-dependent NRF2 program is a druggable vulnerability in multiple cancer types [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 1706.
Nanoscale Signature of Surface Charge Density of Off-Resonance Excited Metal Nanoparticles (2010)

International audience
Complex III Inhibiting Strobilurin Esters, Amides, and Carbamates as Broad-Spectrum Fungicides (2016)

Almost all commercialized strobilurin fungicides belong to the subclasses of methoxyacrylates, such as azoxystrobin; methoxyiminoacetates, such as kresoxim-methyl; methoxyiminoacetamides, such as orysastrobin; methoxyacetamides, such as mandestrobin; methoxycarbamates, such as pyraclostrobin; and benzylcarbamates, such as pyribencarb. The strobilurins are inhibitors of the fungal respiration by blocking complex III of the mitochondrial respiratory chain. This mode of action enables them to be broad-spectrum fungicides for the control of all four major classes of phytopathogenic fungi: Ascomycetes; Basidiomycetes; Deuteromycetes; and Oomycetes. The fungicidal efficacy of the strobilurins results from their ability to inhibit the mitochondrial respiration by binding to the ubiquinol-oxidation center (Qo site) of cytochrome b. Cytochrome b is part of the cytochrome bc 1 complex, located in the inner mitochondrial membrane of fungi and other eukaryotes. The characteristic feature of all strobilurins with excellent fungicidal activity is an (E)-methyl ß-methoxyacrylate pharmacophore.
Analysis of Pole-Ascending–Descending Action by Insects Subjected to High Voltage Electric Fields (2020)

The present study was conducted to establish an electrostatic-based experimental system to enable new investigations of insect behavior. The instrument consists of an insulated conducting copper ring (ICR) linked to a direct current voltage generator to supply a negative charge to an ICR and a grounded aluminum pole (AP) passed vertically through the center of the horizontal ICR. An electric field was formed between the ICR and the AP. Rice weevil (<i>Sitophilus oryzae</i>) was selected as a model insect due to its habit of climbing erect poles. The electric field produced a force that could be imposed on the insect. In fact, the negative electricity (free electrons) was forced out of the insect to polarize its body positively. Eventually, the insect was attracted to the oppositely charged ICR. The force became weaker on the lower regions of the pole; the insects sensed the weaker force with their antennae, quickly stopped climbing, and retraced their steps. These behaviors led to a pole-ascending-descending action by the insect, which was highly reproducible and precisely corresponded to the changed expansion of the electric field. Other pole-climbing insects including the cigarette beetle (<i>Lasioderma serricorne</i>), which was shown to adopt the same behavior.
A 3.75-kW High-Power-Transfer-Density Capacitive Wireless Charging System for EVs Utilizing Toro idal-Interleaved-Foil Coupled Inductors (2020)

This paper presents a multi-kilowatt-scale high-power-transfer-density high-efficiency capacitive wireless power transfer (WPT) system suitable for electric vehicle (EV) charging. The system's high performance is enabled by innovative toroidal-interleaved-foil (TIF) coupled-inductor based matching networks. These matching networks also leverage the charging environment's parasitic capacitances to provide gain and reactive compensation. This new coupled inductor design is optimized to minimize losses while achieving a sufficiently high self-resonance frequency. TIF coupled inductors optimized for a 3.75-kW capacitive WPT system achieve a quality factor of 2055 and self-resonance frequency of 22.3 MHz. A 13.56-MHz 12-cm air-gap 22-cm diameter coupling-plate prototype capacitive WPT system using TIF coupled inductors is designed, built and tested. This system achieves record-breaking performance for a capacitive EV charging system, transferring 3.75 kW at an efficiency of 94.7%, corresponding to a power transfer density of 49.4 kW/m <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sup> .
100-MHz serial access architecture for 4-Mb field memory (1991)

A 4-Mb field memory with a 100-MHz serial access rate has been developed. A new architecture that significantly improves serial I/O operation speed, reduces layout area, and offers simple control is proposed. To accomplish this task, a new architectural data shifter and high-speed redundancy circuit have been developed. The field memory has a 568-line*960 pixel*8-b (4,362,240 b) memory cell array designed for high-definition television (HDTV) screens. A 1.0 mu m CMOS process technology is used to produce a die size of 12.94 mm*25.9 mm. The write-read cycle time is 9 ns, the access time is 8 ns, and the active current is 170 mA at a 50-MHz cycle rate with a standby current of about 3 mA.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>