gebhart/patrepeval huggingface dataset:
Micronuclei of Tetrahymena contain two types of histone H3. (1979)

Evidence is presented that micronuclei of Tetrahymena thermophila contain significant amounts of two types of histone H3. One is indistinguishable from that found in macronuclei and the other is unique to micronuclei. The micronucleus-specific H3 has a slightly faster mobility than the common H3 in three different gel systems (both of these species were artifactually lost during procedures for histone preparation in previous studies). Both micronuclear H3s appear to contain a single cysteine residue and are present in sucrose gradient-purified nucleosomes. Acid extracts from micronuclei also contain three prominent high molecular weight proteins that also were lost during previous procedures. These proteins are present in extracts from oligomers but are not observed in extracts from mononucleosomes, suggesting that they may be associated with linker regions between nucleosomes.
N<sup>3</sup>ASICs: Designing nanofabrics with fine-grained CMOS integration (2011)

We propose a novel nanofabric approach that mixes unconventional nanomanufacturing with CMOS manufacturing flow and design rules in order to build a reliable nanowire-CMOS fabric called N <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">3</sup> ASIC with no new manufacturing constraints added. Active devices are formed on a dense uniform semiconductor nanowire array and standard area distributed pins/vias; metal interconnects route the signals in 3D. CMOS design rules are followed. Novel nanowire based devices are envisioned and characterized based on 3D physics modeling. Overall N <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">3</sup> ASIC fabric design, associated circuits, interconnection approach, and a layer-by-layer assembly sequence for the fabric are introduced. Key system level metrics such as power, performance, and density for a nanoprocessor design built using N <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">3</sup> ASICs were evaluated and compared against a functionally equivalent CMOS design synthesized with state-of-the-art CAD tools. We show that the N <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">3</sup> ASICs version of the processor is 3X denser and 5X more power efficient for a comparable performance than the 16-nm scaled CMOS version even without any new/unknown-manufacturing requirement added.
Episcleral brachytherapy of uveal melanoma: role of intraoperative echographic confirmation (2016)

Intraoperative echographic confirmation of plaque placement during episcleral brachytherapy for choroidal melanoma reduces the risk of early local recurrence.
Hybrid integrated optical waveguides in glass for enhanced visible photoluminescence of nanoemitters (2016)

Integrated optical devices able to control light&#x2013;matter interactions on the nanoscale have attracted the attention of the scientific community in recent years. However, most of these devices are based on silicon waveguides, limiting their use for telecommunication wavelengths. In this contribution, we propose an integrated device that operates with light in the visible spectrum. The proposed device is a hybrid structure consisting of a high-refractive-index layer placed on top of an ion-exchanged glass waveguide. We demonstrate that this hybrid structure serves as an efficient light coupler for the excitation of nanoemitters. The numerical and experimental results show that the device can enhance the electromagnetic field confinement up to 11 times, allowing a higher photoluminescence signal from nanocrystals placed on its surface. The designed device opens new perspectives in the generation of new optical devices suitable for quantum information or for optical sensing.
Three-Dimensional Target Imaging Based on Vortex Stripmap SAR (2018)

A novel 3D imaging method is proposed based on the vortex electromagnetic waves and the stripmap synthetic aperture radar. First, the imaging model is deduced and the echo characteristics are analyzed. Then, the imaging processing algorithm is proposed to reconstruct the target's profiles, where the 3D echoes are decomposed into two 2D echoes. The azimuthal profile can be obtained by performing fast Fourier transform in the orbital angular momentum domain, and the target information in the y dimension is calculated by the azimuthal distribution, which is as a function of the slow time. The range-Doppler algorithms used in the fast time and slow time domains to achieve the range profile and cross-range profile. Finally, the target's 3D image in the Cartesian coordinate is obtained according to the spatial geometric relationship. This paper can benefit the applications of OAM-carrying waves in radar realms as well as the development of the 3D imaging technique.
Adding Transparent Internetworking to a LAN Application Interface (1987)

The internetworking capability of a network is typically provided transparently by protocols below the network application interface. However, network designs have been implemented in which the internetwork function is limited or absent. This paper describes one way to add transparent internetworking to such systems without affecting the existing network hardware and software. The solution consists of using application-level software and gateways that project a domain structure onto application names in such a way that neither the applications nor the underlying protocols need be aware of internetworking. A research prototype of this internetworking scheme has been implemented in the context of the NETBIOS application interface; the paper discusses its key features and the lessons learned.
Fork Protection and Therapy Resistance in Hereditary Breast Cancer (2017)

The BRCA-Fanconi anemia (FA) pathway preserves the genome and suppresses cancer and is a main determinant of chemotherapeutic efficacy. The hereditary breast cancer genes <i>BRCA1</i> and <i>BRCA2</i> function in DNA double-strand break repair mediating distinct steps of homologous recombination (HR). More recently, independent of DNA repair, functions in the replication stress response have come to light, providing insight as to how the BRCA-FA pathway also balances genome preservation with proliferation. The BRCA-FA proteins associate with the replisome and contribute to the efficiency and recovery of replication following perturbations that slow or arrest DNA replication. Although the full repertoire of functions in the replication stress response remains to be elucidated, the function of <i>BRCA1</i> and <i>BRCA2</i> in protecting stalled replication forks contributes along with HR to the sensitivity of BRCA-associated tumors to chemotherapy. Moreover, chemoresistance evolves from restoration of either HR and/or fork protection. Although mechanisms underlying the restoration of HR have been characterized, it remains less clear how restoration of fork protection is achieved. Here, we outline mechanisms of "rewired" fork protection and chemotherapy resistance in BRCA cancer. We propose that mechanisms are linked to permissive replication that limits fork remodeling and therefore opportunities for fork degradation. Combating this chemoresistance mechanism will require drugs that inactivate replication bypass mechanisms.
Chromodomain Ligand Optimization via Target-Class Directed Combinatorial Repurposing (2016)

Efforts to develop strategies for small-molecule chemical probe discovery against the readers of the methyl-lysine (Kme) post-translational modification have been met with limited success. Targeted disruption of these protein-protein interactions via peptidomimetic inhibitor optimization is a promising alternative to small-molecule hit discovery; however, recognition of identical peptide motifs by multiple Kme reader proteins presents a unique challenge in the development of selective Kme reader chemical probes. These selectivity challenges are exemplified by the Polycomb repressive complex 1 (PRC1) chemical probe, UNC3866, which demonstrates submicromolar off-target affinity toward the non-PRC1 chromodomains CDYL2 and CDYL. Moreover, since peptidomimetics are challenging subjects for structure-activity relationship (SAR) studies, traditional optimization of UNC3866 would prove costly and time-consuming. Herein, we report a broadly applicable strategy for the affinity-based, target-class screening of chromodomains via the repurposing of UNC3866 in an efficient, combinatorial peptide library. A first-generation library yielded UNC4991, a UNC3866 analogue that exhibits a distinct selectivity profile while maintaining submicromolar affinity toward the CDYL chromodomains. Additionally, in vitro pull-down experiments from HeLa nuclear lysates further demonstrate the selectivity and utility of this compound for future elucidation of CDYL protein function.
An Improved Optical Lock-In Detection Method for Contrast-Enhanced Imaging in Living Cells (2010)

Synthetic and genetically encoded optical switch probes and lock-in detection methods provide a means to modulate and isolate fluorescence signals from the optical switch and protein complexes of interest against un-modulated background sources. In this paper we propose an improved method for optical lock-in detection (OLID) fluorescence microscopy that can significantly enhance image contrast of optical switch probes within living cells. In particular, we introduce a method for automatic and optimal determination of the reference waveform, which is consequently used for the correlation analysis and construction of the contrast-enhanced image. The method involves computing the average scope of each pixel in the image over several switching cycles and then selecting the pixel with maximum scope as a reference point. The correlation between the fluorescence emission of each pixel over the switching cycles and the reference waveform is then computed. Finally a new contrast-enhanced image is constructed based on the scope-weighted correlation value. Our results of analysis show that this method and algorithm can remarkably improve contrast enhancement and noise reduction compared to the original method.
Fluorescence enhancement of photoswitchable metal ion sensors (2016)

Spiropyran-based fluorescence sensors are an ideal target for intracellular metal ion sensing, due to their biocompatibility, red emission frequency and photo-controlled reversible analyte binding for continuous signal monitoring. However, increasing the brightness of spiropyran-based sensors would extend their sensing capability for live-cell imaging. In this work we look to enhance the fluorescence of spiropyran-based sensors, by incorporating an additional fluorophore into the sensor design. We report a 5-membered monoazacrown bearing spiropyran with metal ion specificity, modified to incorporate the pyrene fluorophore. The effect of N-indole pyrene modification on the behavior of the spiropyran molecule is explored, with absorbance and fluorescence emission characterization. This first generation sensor provides an insight into fluorescence-enhancement of spiropyran molecules.
High Quality Millimeter Wave Generation via Stimulated Brillouin Scattering (2007)

A new and simple method for the generation and modulation of Millimeter waves is presented. Based on frequency upconversion via Stimulated Brillouin Scattering, it is very flexible in its output frequency and modulation bandwidth.
ChemInform Abstract: Spirocycle Assembly Through Selective Tandem Ring Closing Metathesis Reactions. (1999)

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.
Hiding synchronization delays in a GALS processor microarchitecture (2004)

We analyze an Alpha 21264-like globally-asynchronous, locally-synchronous (GALS) processor organized as multiple clock domain (MCD) microarchitecture and identify the architectural features of the processor that influence the limited performance degradation measured. We show that the out-of-order superscalar execution features of a processor, which allow traditional instruction execution latency to be hidden, are the same features that reduce the performance degradation impact of the synchronization costs of an MCD processor. In the case of our Alpha 21264-like processor, up to 94% of the MCD synchronization delays are hidden and do not impact overall performance. In addition, we show that by adding out-of-order superscalar execution capabilities to a simpler microarchitecture, such as an Intel StrongARM-like processor, as much as 62% of the performance degradation caused by synchronization delays can be eliminated.
Effect of Quercetin on Dexamethasone-Induced C2C12 Skeletal Muscle Cell Injury (2020)

Glucocorticoids are widely used anti-inflammatory drugs in clinical settings. However, they can induce skeletal muscle atrophy by reducing fiber cross-sectional area and myofibrillar protein content. Studies have proven that antioxidants can improve glucocorticoid-induced skeletal muscle atrophy. Quercetin is a potent antioxidant flavonoid widely distributed in fruits and vegetables and has shown protective effects against dexamethasone-induced skeletal muscle atrophy. In this study, we demonstrated that dexamethasone significantly inhibited cell growth and induced cell apoptosis by stimulating hydroxyl free radical production in C2C12 skeletal muscle cells. Our results evidenced that quercetin increased C2C12 skeletal cell viability and exerted antiapoptotic effects on dexamethasone-treated C2C12 cells by regulating mitochondrial membrane potential (ΔΨm) and reducing oxidative species. Quercetin can protect against dexamethasone-induced muscle atrophy by regulating the Bax/Bcl-2 ratio at the protein level and abnormal ΔΨm, which leads to the suppression of apoptosis.
Hypertriglyceridemia and regulation of fibrinolytic activity. (1992)

A relation between elevated triglyceride (TG) levels and alterations of the fibrinolytic system has been recognized in studies of patients with coronary heart disease. In this investigation, the total fibrinolytic activity and the levels of specific components of the fibrinolytic system were evaluated in plasma samples from a highly selected group of patients with type IV hyperlipoproteinemia before and after a dietary treatment aimed at reducing TG levels. The fibrinolytic response of type IV patients was comparable to that of normolipidemic subjects, whereas tissue-type plasminogen activator antigen levels before and after venous occlusion (p less than 0.01) and resting plasminogen activator inhibitor-1 (PAI-1) antigen (p less than 0.01) and activity (p less than 0.01) were significantly higher in hypertriglyceridemic subjects compared with controls. After dietary treatment, a 22% reduction in TG levels was attained in type IV patients, with no appreciable modification of fibrinolytic parameters. The analysis of the single-patient data revealed a tendency toward normalization of PAI-1 levels only in those patients who showed a TG reduction greater than or equal to 20%. Very low density lipoproteins (VLDLs) from both normal and type IV patients concentration-dependently stimulated PAI-1 release by endothelial cells and HepG2 cells, with the effect of VLDL from type IV patients being more pronounced on HepG2 cells. The release of PAI-1 induced by VLDL in competent cells may thus account for the elevated levels of this antifibrinolytic protein that occur in hypertriglyceridemic patients.
Synthesis, Structural Characterization, and Quantitative Basicity Studies of Lithium Zirconimidate Complexes (2008)

Lithium zirconimidate complexes (see structure) were isolated by deprotonation of zirconium methyl amide complexes or by addition of methyllithium across imidozirconium complexes. Quantitative studies on the acidity of these conjugate bases of zirconium amide complexes showed that both the kinetics and thermodynamics of proton exchange are influenced by the ancillary ligands on the zirconium center. Supporting information for this article is available on the WWW under http://www.wiley-vch.de/contents/jc_2002/2008/z801463_s.pdf or from the author. Please note: The publisher is not responsible for the content or functionality of any supporting information supplied by the authors. Any queries (other than missing content) should be directed to the corresponding author for the article.
Mycobacterial phenolic glycolipid synthesis is regulated by cAMP-dependent lysine acylation of FadD22 (2017)

The mycobacterial cell envelope is unique in its chemical composition, and has an important role to play in pathogenesis. Phthiocerol dimycocerosates (PDIMs) and glycosylated phenolphthiocerol dimycocerosates, also known as phenolic glycolipids (PGLs), contribute significantly to the virulence of Mycobacterium tuberculosis. FadD22 is essential for PGL biosynthesis. We have recently shown in vitro that FadD22 is a substrate for lysine acylation by a unique cAMP-dependent, protein lysine acyltransferase found only in mycobacteria. The lysine residue that is acylated is at the active site of FadD22. Therefore, acylation is likely to inhibit FadD22 activity and reduce PGL biosynthesis. Here, we show accumulation of PGLs in a strain of M. bovis BCG deleted for the gene encoding the cAMP-dependent acyltransferase, katbcg, with no change seen in PDIM synthesis. Complementation using KATbcg mutants that are deficient in cAMP-binding or acyltransferase activity shows that PGL accumulation is regulated by cAMP-dependent protein acylation in vivo. Expression of FadD22 and KATbcg mutants in Mycobacterium smegmatis confirmed that FadD22 is a substrate for lysine acylation by KATbcg. We have therefore described a mechanism by which cAMP can regulate mycobacterial virulence as a result of the ability of this second messenger to modulate critical cell wall components that affect the host immune response.
A privacy-preserving solution for compressed storage and selective retrieval of genomic data (2016)

In clinical genomics, the continuous evolution of bioinformatic algorithms and sequencing platforms makes it beneficial to store patients' complete aligned genomic data in addition to variant calls relative to a reference sequence. Due to the large size of human genome sequence data files (varying from 30 GB to 200 GB depending on coverage), two major challenges facing genomics laboratories are the costs of storage and the efficiency of the initial data processing. In addition, privacy of genomic data is becoming an increasingly serious concern, yet no standard data storage solutions exist that enable compression, encryption, and selective retrieval. Here we present a privacy-preserving solution named SECRAM (Selective retrieval on Encrypted and Compressed Reference-oriented Alignment Map) for the secure storage of compressed aligned genomic data. Our solution enables selective retrieval of encrypted data and improves the efficiency of downstream analysis (e.g., variant calling). Compared with BAM, the de facto standard for storing aligned genomic data, SECRAM uses 18% less storage. Compared with CRAM, one of the most compressed nonencrypted formats (using 34% less storage than BAM), SECRAM maintains efficient compression and downstream data processing, while allowing for unprecedented levels of security in genomic data storage. Compared with previous work, the distinguishing features of SECRAM are that (1) it is position-based instead of read-based, and (2) it allows random querying of a subregion from a BAM-like file in an encrypted form. Our method thus offers a space-saving, privacy-preserving, and effective solution for the storage of clinical genomic data.
Red Blood Cell Antioxidant Parameters in Healthy Elderly Subjects Versus Silicosis Patients (1987)

The anti-oxidant phenotype was determined in red blood cell haemolysates of 62 healthy elderly persons (Mean age: 56) and a number of male silicosis patients (Mean age: 65, n = 19). Moreover, analysis of water-soluble fluorescent substances in plasma, recently introduced as a new test for in vivo lipid-peroxidation, was included. Within the control group results were analyzed on the effect of smoking (no effect), use of medication (lowered GSH-content) or gender (no differences apart from haemoglobin content). No simple relationship between any pair of the measured parameters in erythrocytes was present. When comparing the male control persons with the silicosis group a significantly higher red blood cell GSH-level was observed in the latter. Moreover, some factors of the anti-oxidant system are strongly correlated in the diseased, but not in the healthy subjects.
Deep Convolutional Neural Network on iOS Mobile Devices (2016)

Deep Convolutional Neural Network (CNN) draws significant attention in the computer vision community by facilitating machines with more intelligence in understanding visual signals, however, its computation complexity has also increased significantly. To achieve ubiquitous machine intelligence, deep CNN is required to be ported onto local devices rather than cloud-based solution due to low latency consideration. Hence, in this paper, we propose a method to explore the design space for porting deep CNN onto iOS mobile devices, with attempts in maximizing data reusability, which alleviates the high bandwidth burden in the convolution layers of CNN. Furthermore, effective data reuse also makes possible the parallelization of all computing threads without data loading latency. On the other hand, deep CNN is usually over-parametrized with many unused convolution kernels. Based on Algorithm/Architecture Co-Exploration, we introduced a method in pruning redundant kernels in deep CNN with ignorable performance degradation on validation dataset (0.06% loss). This reduces 29% of operations and 34% of storage size on a 16-layer CNN. We used iPhone 6s and iPad Pro for case studies, and ported 8-layer and 16-layer CNNs onto targeted devices. The data reusability strategy improves computation speed up to 1.3x, and redundant kernel removal increases computation speed to 1.43x. As a result, we achieved high computation efficiency and have thus enhanced the capability of machine intelligence on local mobile devices.
Applying a layered control architecture to a free-flying space camera (2002)

Describes a prototype robot for space applications. The robot is the first generation of a free-flying robotic camera that will assist astronauts in constructing and maintaining the space station. The goal of the robot is to provide remote views to astronauts and ground controllers. The robot can autonomously move to locations on an air bearing table, can track targets and can plan paths. The robot contains a large collection of different technologies and this paper concentrates on a layered control architecture that integrates all robot functions.
Augmentin Duo™ in the Treatment of Childhood Blepharokeratoconjunctivitis (2010)

Augmentin Duo 400/57 has not previously been reported in the treatment of BKC in children. In this case series, Augmentin Duo 400/57 proved to be at least as effective as current treatments with systemic erythromycin or doxycycline with the advantage of a twice-daily dosage and a superior side-effect profile.
Algebraic and Slide Attacks on KeeLoq. (2007)

Abstract. KeeLoq is a block cipher used in wireless devices that unlock the doors and alarms in cars manufactured by Chrysler, Daewoo, Fiat,