gebhart/patrepeval huggingface dataset:
Actin binding domain of Rng2 sparsely bound on F-actin strongly inhibits actin movement on myosin II (2020)

Abstract Substoichiometric binding of certain actin-binding proteins induces conformational changes in a disproportionally large number of actin protomers in actin filaments. Here, we report a case in which such conformational changes in actin filaments have profound functional consequences. Rng2 is an IQGAP protein implicated in the assembly and contraction of contractile rings in Schizosaccharomyces pombe . We found that the calponin-homology actin-binding domain of Rng2 (Rng2CHD) strongly inhibits the motility of actin filaments on myosin II in vitro. On skeletal muscle myosin II-coated surfaces, Rng2CHD halved the sliding speed of actin filaments at a binding ratio of 1.3% (=1/77), and virtually stopped movement at a binding ratio of 11% (=1/9). Rng2CHD also inhibited actin movements on Dictyostelium myosin II, but in this case by inducing the detachment of actin filaments from myosin II-coated surfaces. Rng2CHD induced cooperative structural changes of actin filaments accompanied by shortening of the filament helical pitch, and reduced the affinity between actin filaments and subfragment 1 (S1) of muscle myosin II in the presence of ADP. Intriguingly, actin-activated ATPase of S1 was hardly inhibited by Rng2CHD. We suggest that sparsely bound Rng2CHD induces global structural changes of actin filaments and interferes with the force generation by actin-myosin II.
Determination of the Spacing Between Hydrogen-Intercalated Quasi-Free-Standing Monolayer Graphene and 6H-SiC(0001) Using Total-Reflection High-Energy Positron Diffraction (2023)

We have investigated the structure of hydrogen-intercalated quasi-free-standing monolayer graphene (QFMLG) grown on 6H-SiC(0001) by employing total-reflection high-energy positron diffraction (TRHEPD). At least nine diffraction spots of the zeroth order Laue zone were resolved along &lt;11-20&gt; and three along &lt;1-100&gt;, which are assigned to graphene, SiC and higher order spots from multiple diffraction on both lattices. We further performed rocking curve analysis based on the full dynamical diffraction theory to precisely determine the spacing between QFMLG and the SiC substrate. Our study yields a spacing of d = 4.18(6)Å that is in excellent agreement with the results from density-functional theory (DFT) calculations published previously.
Mechanism for the Isotype Dependence of Antibody-Mediated Toxicity in Cryptococcus neoformans-Infected Mice (2000)

Ab-based therapies have undergone a renaissance in recent years, but infusion-related reactions are a significant clinical problem. Administration of certain mAbs to Swiss Webster mice infected with Cryptococcus neoformans can result in acute lethal toxicity (ALT) characterized by cardiovascular collapse. The ability of a mAb to produce ALT is isotype dependent and occurs with IgG1 but not IgG3. To investigate this phenomenon, we measured spleen and liver cytokine responses and platelet-activating factor (PAF) content in mice given C. neoformans glucuronoxylomannan (GXM) followed by specific Ab of IgG1 or IgG3 isotype. We found no evidence to suggest that the differences in IgG1 and IgG3 toxicity were due to differences in chemokine or cytokine response. In contrast, liver and spleen tissue PAF content was significantly greater in mice IgG1. Furthermore, our results show differences in the response to IgG1- and IgG3-GXM complexes regarding: 1) macrophage-inflammatory protein-1alpha and monocyte chemoattractant protein-1 regulation, 2) splenic and hepatic PAF content, and 3) hepatic PAF content in infected mice. IgG1-associated ALT appears to be the result of greater production of PAF in response to IgG1-GXM complex formation. The results are consistent with the view that IgG1 and IgG3 interact with different Fc receptors. Our findings strongly suggest that the mechanism for Ab-mediated ALT is different from the cytokine release syndrome described after administration of other therapeutic mAbs.
Comparative Analyses Between Lolium/Festuca Introgression Lines and Rice Reveal the Major Fraction of Functionally Annotated Gene Models Is Located in Recombination-Poor/Very Recombination-Poor Regions of the Genome (2007)

Publication of the rice genome sequence has allowed an in-depth analysis of genome organization in a model monocot plant species. This has provided a powerful tool for genome analysis in large-genome unsequenced agriculturally important monocot species such as wheat, barley, rye, Lolium, etc. Previous data have indicated that the majority of genes in large-genome monocots are located toward the ends of chromosomes in gene-rich regions that undergo high frequencies of recombination. Here we demonstrate that a substantial component of the coding sequences in monocots is localized proximally in regions of very low and even negligible recombination frequencies. The implications of our findings are that during domestication of monocot plant species selection has concentrated on genes located in the terminal regions of chromosomes within areas of high recombination frequency. Thus a large proportion of the genetic variation available for selection of superior plant genotypes has not been exploited. In addition our findings raise the possibility of the evolutionary development of large supergene complexes that confer a selective advantage to the individual.
Increased Efficacy of Delayed-Release mesalamine 4.8 g/D (800 mg Tablet) Compared to 2.4 g/D (400 mg Tablet) for Treatment of Moderately Active Ulcerative Colitis in Patients with a History of More Difficult to Treat Disease (2008)

Purpose: To determine the efficacy of and identify patients more likely to respond to higher dose (4.8 g/d, using an investigational 800 mg tablet) mesalamine for the treatment of moderately active ulcerative colitis (UC) according to prior medical therapies. Methods: Data from 3 Phase III, multi-center, randomized, double-blind, 6-week active-controlled studies of similar design (ASCEND I, II, & III) were combined and analyzed. Efficacy of delayed-release mesalamine 4.8 g/d (800 mg tablet) was compared with 2.4 g/d (marketed Asacol® 400 mg tablet) in patients with moderately active UC (Physician's Global Assessment [PGA] = 2). The primary endpoint was treatment success defined as improvement from baseline in PGA (based on clinical assessments of rectal bleeding (RB), stool frequency (SF) and sigmoidoscopy) with no worsening in any individual clinical assessment. [Note that patient functional assessment was also considered in ASCEND I & II and that sigmoidoscopy results were assessed differently in ASCEND III as compared with ASCEND I & II]. Hallmark symptoms of UC, RB and SF, were evaluated identically in all three studies. Improvement in RB and SF was defined as a decrease from baseline of at least 1 point based on a 4 point scale (0–3). Clinical remission was defined as resolution of both RB and SF. Results: A total of 1220 patients with moderately active UC were randomized and dosed. At 6 weeks, treatment success occurred in 69% and 62% of patients receiving 4.8 g/d vs 2.4 g/d, respectively, P= 0.006. Similarly, at 6 weeks, more patients receiving 4.8 g/d vs 2.4 g/d had RB improvement (83% vs 79%, P= 0.04), SF improvement (78% vs 73%, P= 0.07) and clinical remission (43% vs 37%, P= 0.06). A therapeutic advantage of 4.8 g/d was seen in patients with previous use of UC medications as evidenced in the Table below.TableConclusion: Delayed-release mesalamine at 4.8 g/d (investigational 800 mg tablet) demonstrated efficacy for the treatment of moderately active UC, with evidence of a therapeutic advantage in patients with a history of more difficult to treat disease (e.g., previous use of oral 5-ASAs, rectal therapies, steroids, or multiple medications).
Small Molecule Coagulation Cascade Inhibitors in the Clinic (2005)

Venous thromboembolic disease, including deep vein thrombosis and pulmonary embolism, is a cause of significant mortality and morbidity. For several decades, anticoagulant options for the treatment and prevention of thrombosis have been limited mainly to agents such as unfractionated heparin and oral vitamin K antagonists such as warfarin. Although these therapies have proven benefits, they also have important limitations that result in their underuse in routine clinical practice. A variety of novel anticoagulants with improved pharmacologic and clinical profiles are in development, offering benefits over traditional therapies. Specifically, progress has been made in the development of small molecule Factor Xa inhibitors and thrombin inhibitors. The most advanced drugs reviewed include DPC-423, DPC-602, razaxaban, GSK's 813893, Portola's Xa inhibitors (formerly Millennium), otamixaban, DU-176b, KFA-1982, BAY-59-7939, DX-9065a, YM-150, LY-517717, Exanta, 3DP's thrombin inhibitors, SSR-182289, LB-30057, LB-30870, BIBR-1048 and Merck's thrombin inhibitors. With their potentially consistent and predictable pharmacological profile, oral formulation, and decreased need for coagulation monitoring, these new agents will likely increase the use and duration of anticoagulation treatment in thromboembolic disorders and reduce the burden associated with long-term management.
Object-Distribution Analysis for Program Decomposition and Re-Clustering (2005)

The next-generation of embedded systems confronts the designer with multi-processor systems both for performance and energy reasons. Exploiting task-level parallelism in combination with loop-level parallelism is becoming crucial. The challenge is to build compiler tools for the exploration of these types of parallelism. To achieve this goal, we have designed a transformation framework for analysis and extraction of the potential parallelism in sequential object-oriented programs. We present an inter-procedural, compositional, context and flow-sensitive algorithm for analysis of object distribution in sequential object-oriented programs. Our technique consists of three main phases: compositional inter-procedural object-distribution analysis, construction of minimal hierarchical object-distribution graph, and graph rendering using constrained force-directed layout. Integration of these algorithms allows us to reduce number of prospective program decompositions with respect to program flow and object-distribution properties. The visualisation environment further extends usability of our tools for employment of semi-automated as well as fully-automated heuristics with further constraints on definition of the final task boundaries. We demonstrate the usability of our approach on a number of realistic Java applications.
A 64-b microprocessor with multimedia support (1995)

A 167 MHz 64 b VLSI CPU chip is described. The chip executes a 333-MFLOPS (peak) with an estimated system performance of 270SPECint92/380SPECfp92 (@167 MHz, 2 MB E-cache). The 17.7/spl times/17.8 mm die is fabricated with a 0.5 micron CMOS technology with four metal layers and contains 5.2 M transistors. The superscalar processor is capable of sustaining an execution rate of four instructions per cycle even in the presence of conditional branches and cache misses. Four fully pipelined 8/spl times/16 b multipliers and four single-cycle latency 16 b adders combine to speed up image processing, 2-D, 3-D graphics, video compression/decompression by up to an order of magnitude. High clock speed was obtained by the use of delayed reset logic, a new register file design; and novel comparators. Strict design methodology allowed fully functional first silicon which met all speed targets. The power dissipation of the chip is 28 W.
A magnetic circular dichroism study of the 3p Rydberg states of acetone (1985)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTA magnetic circular dichroism study of the 3p Rydberg states of acetoneAharon GedankenCite this: J. Phys. Chem. 1985, 89, 18, 3781–3782Publication Date (Print):August 1, 1985Publication History Published online1 May 2002Published inissue 1 August 1985https://pubs.acs.org/doi/10.1021/j100264a004https://doi.org/10.1021/j100264a004research-articleACS PublicationsRequest reuse permissionsArticle Views36Altmetric-Citations7LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InRedditEmail Other access options Get e-Alerts
SOLID-PHASE SYNTHESIS OF OLIGODEOXYNUCLEOTIDES CONTAINING 3′-S-PHOSPHOROTHIOLATE LINKAGES (2001)

For the first time a fully automated procedure has been developed for the incorporation of a 3'-S-phosphorothiolate linkage into DNA, using phosphorothioamidite monomers. Coupling yields with either of the activators 5-ethylthiotetrazole or 4,5-dicyanoimidazole were in the range of 80-90%. Coupling yields were equally good when performed on either a 0.2 or 1 mumole reaction column, thus facilitating large scale synthesis.
Breath‐hold 3D steady‐state free precession coronary MRA compared with conventional X‐ray coronary angiography (2006)

Breath-hold SSFP coronary MRA has good specificity but inconclusive sensitivity in diagnosing significant coronary stenoses, and provides important image features for depicting coronary lesions.
Fenofibrate: A New Treatment for Diabetic Retinopathy. Molecular Mechanisms and Future Perspectives (2013)

Despite improving standards of care, people with diabetes remain at risk of development and progression of diabetic retinopathy (DR) and visual impairment. Identifying novel therapeutic approaches, preferably targeting more than one pathogenic pathway in DR, and at an earlier stage of disease, is attractive. There is now consistent evidence from two major trials, the Fenofibrate Intervention and Event Lowering in Diabetes (FIELD) study and the Action to Control Cardiovascular Risk in Diabetes Eye (ACCORD-Eye) study, totalling 11,388 people with type 2 diabetes (5,701 treated with fenofibrate) that fenofibrate reduces the risk of development and progression of DR. Therefore, fenofibrate may be considered a preventive strategy for patients without DR or early intervention strategy for those with mild DR. A number of putative therapeutic mechanisms for fenofibrate, both dependent and independent of lipids, have been proposed. A deeper understanding of the mode of action of fenofibrate will further help to define how best to use fenofibrate clinically as an adjunct to current management of DR.
Fenbendazole Attenuates Bleomycin-Induced Pulmonary Fibrosis in Mice via Suppression of Fibroblast-to-Myofibroblast Differentiation (2022)

Idiopathic pulmonary fibrosis (IPF) is a chronic, progressive, and fatal interstitial lung disease with unknown etiology. Despite substantial progress in understanding the pathogenesis of pulmonary fibrosis and drug development, there is still no cure for this devastating disease. Fenbendazole (FBZ) is a benzimidazole compound that is widely used as an anthelmintic agent and recent studies have expanded the scope of its pharmacological effects and application prospect. This study demonstrated that FBZ treatment blunted bleomycin-induced lung fibrosis in mice. In vitro studies showed that FBZ inhibited the proliferation and migration of human embryo lung fibroblasts. Further studies showed that FBZ significantly inhibited glucose consumption, moderated glycolytic metabolism in fibroblasts, thus activated adenosine monophosphate-activated protein kinase (AMPK), and reduced the activation of the mammalian target of rapamycin (mTOR) pathway, thereby inhibiting transforming growth factor-β (TGF-β1)-induced fibroblast-to-myofibroblast differentiation and collagen synthesis. In summary, our data suggested that FBZ has potential as a novel treatment for pulmonary fibrosis.
Cellular Network Planning under Variable QoS Requirements Using Voronoi Algorithm (2020)

We study the optimization of base station (BS) localization in cellular networks with non-uniform service demand distribution taking into account a variety of server-side and user-side requirements. To this end, we propose a power Voronoi algorithm (PVA) to obtain uniform traffic volume shares per cell while simultaneously meeting the user-side and server-side requirements of the heterogeneous devices. We describe a numerical method to solve the optimization problem by updating the weights associated to different cells in the PVA. Then, we take into account minimum signal to interference plus noise ratio at all devices as a user-side requirement. It is observed that BSs are concentrated in the areas with condensed demand and high SINR requirements. To show the advantages of the proposed method, the results are compared for different SINR requirement distributions giving insight on the performance of the algorithm.
The Association of Circulating L-Carnitine, γ-Butyrobetaine and Trimethylamine N-Oxide Levels with Gastric Cancer (2023)

Our study aimed to evaluate the association between gastric cancer (GC) and higher concentrations of the metabolites L-carnitine, γ-butyrobetaine (GBB) and gut microbiota-mediated trimethylamine N-oxide (TMAO) in the circulation. There is evidence suggesting that higher levels of TMAO and its precursors in blood can be indicative of either a higher risk of malignancy or indeed its presence; however, GC has not been studied in this regard until now. Our study included 83 controls without high-risk stomach lesions and 105 GC cases. Blood serum L-carnitine, GBB and TMAO levels were measured by ultra-high-performance liquid chromatography-mass spectrometry (UPLC/MS/MS). Although there were no significant differences between female control and GC groups, we found a significant difference in circulating levels of metabolites between the male control group and the male GC group, with median levels of L-carnitine reaching 30.22 (25.78-37.57) nmol/mL vs. 37.38 (32.73-42.61) nmol/mL (<i>p</i> < 0.001), GBB-0.79 (0.73-0.97) nmol/mL vs. 0.97 (0.78-1.16) nmol/mL (<i>p</i> < 0.05) and TMAO-2.49 (2.00-2.97) nmol/mL vs. 3.12 (2.08-5.83) nmol/mL (<i>p</i> < 0.05). Thus, our study demonstrated the association between higher blood levels of L-carnitine, GBB, TMAO and GC in males, but not in females. Furthermore, correlations of any two investigated metabolites were stronger in the GC groups of both genders in comparison to the control groups. Our findings reveal the potential role of L-carnitine, GBB and TMAO in GC and suggest metabolic differences between genders. In addition, the logistic regression analysis revealed that the only significant factor in terms of predicting whether the patient belonged to the control or to the GC group was the blood level of L-carnitine in males only. Hence, carnitine might be important as a biomarker or a risk factor for GC, especially in males.
Integration of Organic Light Emitting Diodes and Organic Photodetectors for Lab-on-a-Chip Bio-Detection Systems (2014)

The rapid development of microfluidics and lab-on-a-chip (LoC) technologies have allowed for the efficient separation and manipulation of various biomaterials, including many diagnostically relevant species. Organic electronics have similarly enjoyed a great deal of research, resulting in tiny, highly efficient, wavelength-selective organic light-emitting diodes (OLEDs) and organic photodetectors (OPDs). We consider the blend of these technologies for rapid detection and diagnosis of biological species. In the ideal system, optically active or fluorescently labelled biological species can be probed via light emission from OLEDs, and their subsequent light emission can be detected with OPDs. The relatively low cost and simple fabrication of the organic electronic devices suggests the possibility of disposable test arrays. Further, with full integration, the finalized system can be miniaturized and made simple to use. In this review, we consider the design constraints of OLEDs and OPDs required to achieve fully organic electronic optical bio-detection systems. Current approaches to integrated LoC optical sensing are first discussed. Fully realized OLED- and OPD-specific photoluminescence detection systems from literature are then examined, with a specific focus on their ultimate limits of detection. The review highlights the enormous potential in OLEDs and OPDs for integrated optical sensing, and notes the key avenues of research for cheap and powerful LoC bio-detection systems.
Exploiting & Refining Depth Distributions with Triangulation Light Curtains (2021)

Active sensing through the use of Adaptive Depth Sensors is a nascent field, with potential in areas such as Advanced driver-assistance systems (ADAS). They do however require dynamically driving a laser / light-source to a specific location to capture information, with one such class of sensor being the Triangulation Light Curtains (LC). In this work, we introduce a novel approach that exploits prior depth distributions from RGB cameras to drive a Light Curtain’s laser line to regions of uncertainty to get new measurements. These measurements are utilized such that depth uncertainty is reduced and errors get corrected recursively. We show real-world experiments that validate our approach in outdoor and driving settings, and demonstrate qualitative and quantitative improvements in depth RMSE when RGB cameras are used in tandem with a Light Curtain.
Modeling full-length VBR video using Markov-renewal-modulated TES models (1998)

This paper describes a general methodology for constructing accurate source models of long sequences (full-length movies) of full-motion compressed VBR (variable bit rate) video, directly from empirical data sets of observed bit rate (frame size) records. The main idea is to first cluster scenes into classes and use TES (transform-expand-sample) processes to carefully model their duration and bit rate processes, and then modulate these scene class models by a Markov-renewal process that governs scene transitions. The resulting model is a Markov-renewal-modulated TES (MRMT) process. The fidelity criteria imposed are relatively stringent in that they call for the simultaneous capture of empirical histograms and autocorrelation functions, as well as the qualitative appearance of the empirical data, including burstiness. To illustrate the methodology, the paper provides a detailed description of the modeling procedure, using a JPEG-like coding trace of the "Star Wars" movie as a working example. The resulting MRMT model was validated by comparing its simulation-based statistics to their empirical counterparts, and by a performance study of the corresponding loss rates for various buffer sizes. The results support the efficacy of the modeling methodology and suggest that suites of realistic and compact source models can be developed for other types of movies under a variety of coding schemes. These may be used to drive realistic Monte Carlo simulations of broadband telecommunications networks.