gebhart/patrepeval huggingface dataset:
Dance of the SNAREs: Assembly and Rearrangements Detected with FRET at Neuronal Synapses (2013)

Soluble N-ethylmaleimide-sensitive fusion protein attachment protein receptors (SNAREs) mediate vesicle fusion with the plasma membrane on activation by calcium binding to synaptotagmin. In the present study, we used fluorescence resonance energy transfer (FRET) and fluorescence lifetime imaging microscopy between fluorescently labeled SNARE proteins expressed in cultured rat hippocampal neurons to detect resting SNARE complexes, their conformational rearrangement on exocytosis, their disassembly before endocytosis of vesicular proteins, and SNARE assembly at newly docked vesicles. Assembled SNAREs are not only present in docked vesicles; unexpected residual "orphan SNARE complexes" also reside in para-active zone regions. Real-time changes in FRET between N-terminally labeled SNAP-25 and VAMP reported a reorientation of the SNARE motif upon exocytosis, SNARE disassembly in the active zone periphery, and SNARE reassembly in newly docked vesicles. With VAMP labeled C-terminally, decreased fluorescence in C-terminally labeled syntaxin (extracellular) reported trans-cis-conformational changes in SNAREs on vesicle fusion. After fusion SNAP-25 and syntaxin disperse along with VAMP, as well as the FRET signal itself, indicating diffusion of intact SNAREs after vesicle fusion but before their peripheral disassembly. Our measurements of spatiotemporal dynamics of SNARE conformational changes and movements refine models of SNARE function. Technical advances required to detect tiny changes in fluorescence in small fractions of labeled proteins in presynaptic boutons on a time scale of seconds permit the detection of rapid intermolecular interactions between small proportions of protein partners in cellular subcompartments.
Strategies for the detection of copy number and other structural variants in the human genome (2006)

Advances in genome scanning technologies are revealing that copy number variants (CNVs) and polymorphisms, ranging from a few kilobases to several megabases in size, are present in genomes at frequencies much greater than previously known. Discoveries of additional forms of genomic variation, including inversions, insertions, deletions and complex rearrangements, are also occurring at an increased rate. Along with CNVs, these sequence alterations are collectively known as structural variants, and their discovery has had an immediate impact on the interpretation of basic research and clinical diagnostic data. This paper discusses different methods, experimental strategies and technologies that are currently available to study copy number variation and other structural variants in the human genome.
Technical Perspective: A simple, elegant approach to non-numeric parallelization (2017)

No abstract available.
ChemInform Abstract: Synthesis of (S)‐Mappicine and Mappicine Ketone via Radical Cascade Reaction of Isonitriles. (1997)

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.
Transverse Modes, Waveguide Dispersion, and 30-ps Recovery in Submicrometer GaAs–AlAs Microresonators (1989)

We have studied room-temperature optical gating of ~5 ps pulses in GaAs/AlAs microresonators with diameters ranging from &lt;0.5 μ m to 1.5 μ m by using a high-refractive-index lens system having a numerical aperture of 1.3. The larger devices show well-defined transverse modes and waveguide dispersion having fair agreement with calculations. The former effect causes decreased modulation of the probe beam. The smallest-diameter devices (&lt;0.5 μ m) show higher modulation, fully recover in &lt;30 ps, and have their peak transmission wavelengths shifted by &gt;500 Å compared to a large ~ 10 μ m region.
Non-blocking steal-half work queues (2002)

The non-blocking work-stealing algorithm of Arora et al. has been gaining popularity as the multiprocessor load balancing technology of choice in both Industry and Academia. At its core is an ingenious scheme for stealing a single item in a non-blocking manner from an array based deque. In recent years, several researchers have argued that stealing more than a single item at a time allows for increased stability, greater overall balance, and improved performance.This paper presents StealHalf, a new generalization of the Arora et al. algorithm, that allows processes, instead of stealing one, to steal up to half of the items in a given queue at a time. The new algorithm preserves the key properties of the Arora et al. algorithm: it is non-blocking, and it minimizes the number of CAS operations that the local process needs to perform. We provide analysis that proves that the new algorithm provides better load distribution: the expected load of any process throughout the execution is less than a constant away from the overall system average.
Graphene induced tunability of the surface plasmon resonance (2012)

Tunability of the surface plasmon resonance wavelength is demonstrated by varying the thickness of Al2O3 spacer layer inserted between the graphene and nanoparticles. By varying the spacer layer thickness from 0.3 to 1.8 nm, the resonance wavelength is shifted from 583 to 566 nm. The shift is due to a change in the electromagnetic field coupling strength between the localized surface plasmons excited in the gold nanoparticles and a single layer graphene film. In contrast, when the graphene film is absent from the system, no noticeable shift in the resonance wavelength is observed upon varying the spacer thickness.
Phase I dose escalation study on DRF 7295: A novel peptide based anticancer drug, in patients with advanced, metastatic adenocarcinomas: Final results (2004)

3094 Background: DRF 7295 is a novel combination of 4 synthetic neuropeptide analogues having antiproliferative, antiangiogenic and proapoptotic properties. It has exhibited potent preclinical activity in adenocarcinoma cell lines Preliminary Ph-I results have been published in ASCO 2003 (abstract no.948). The final results are presented herewith.Methods: 7 recurrent/metastatic adenocarcinoma patients were given escalating doses of DRF 7295 twice daily for one cycle of 21 days starting from 1.3 mg/m2. Single patient cohorts (Modified Fibonacci Method) were used for dose escalation in the absence of any dose limiting toxicities (DLTs). As no DLT was seen even at the highest dose of 11.7 mg/m2, the dose of 9.1 mg/m2 was selected as the cohort expansion dose and 9 patients were further treated at this dose (total=16).Results: There were 11 adverse drug reactions observed. No Grade 3 or 4 toxicities were seen. Most common ADRs included hot flushes (n=5, Grade1), transient fall in blood pressure (n=3, Grade 1) and mild urticaria (n=1, Grade 1), the duration and intensity of these reduced with subsequent doses. Of the 6 pts evaluable for response at the cohort expansion dose of 9.1 mg/m2, 4 had stable disease (67%) at the end of therapy of which 2 maintained their response 1-month post therapy. All responses were observed in metastatic colorectal cancers. Conclusions: DRF 7295, is a well tolerated anticancer drug devoid of toxicities commonly seen with cytotoxic drugs and may have a promising role in disease stabilization in colorectal cancer. Phase-II and combination studies with the drug have been planned. Author Disclosure Employment or Leadership Consultant or Advisory Stock Ownership Honoraria Research Funding Expert Testimony Other Remuneration Dabur Research Foundation Dabur Research Foundation Dabur Research Foundation
Figure S4 from A Four-Chemokine Signature Is Associated with a T-cell–Inflamed Phenotype in Primary and Metastatic Pancreatic Cancer (2023)

&lt;p&gt;Supplementary Figure 4: Immune phenotypes were not impacted by cellularity in primary tumors&lt;/p&gt;
The Treatment Response of Chronically Hepatitis C Virus-Infected Patients Depends on Interferon Concentration but Not on Interferon Gene Expression in Peripheral Blood Mononuclear Cells (2011)

The current treatment of chronic hepatitis C is based on pegylated alpha interferon (PEG-IFN-α) and ribavirin. The aim of this study was to identify biological and clinical variables related to IFN therapy that could predict patient outcome. The study enrolled 47 patients treated with PEG-IFN and ribavirin combined therapy. The interferon concentration was measured in serum by a bioassay. The expression of 93 interferon-regulated genes in peripheral blood mononuclear cells was quantified by real-time quantitative reverse transcription-PCR (RT-PCR) before and after 1 month of treatment. The interferon concentration in the serum was significantly lower in nonresponders than in sustained virological responders. Moreover, a significant correlation was identified between interferon concentration and interferon exposition as well as body weight. The analysis of interferon-inducible genes in peripheral blood mononuclear cells among the genes tested did not permit the prediction of treatment outcome. In conclusion, the better option seems to be to treat patients with weight-adjusted PEG-IFN doses, particularly for patients with high weight who are treated with PEG-IFN-α2a. Although the peripheral blood mononuclear cell samples are the easiest to obtain, the measurement of interferon-inducible genes seems not be the best strategy to predict treatment outcome.
Preliminary Monte Carlo simulations of linear accelerators in Time-of-Flight Compton Scatter imaging for cargo security (2013)

The economic impact of illicit trade is in the trillions of dollars per year, with a proportion of this trade concealed within cargo containers. The interdiction of this trade relies upon efficient and effective external screening of cargo containers, typically using x rays. The present work introduces a technique of x-ray screening that aims to increase the efficiency and effectiveness of x-ray screening. Traditional X-ray screening of cargo containers is performed using high-energy (MV) transmission imaging or low-energy (kV) Compton scatter imaging to provide two-dimensional images. Two-dimensional images can contain complex, overlapping objects and require significant experience and time to interpret. Time-of-Flight information can be used in conjunction with Compton scatter imaging to provide information about the depth of each Compton scatter interaction, leading to three-dimensional images, reducing false positives and image analysis time. The expected Time-of-Flight from photons scattered back from a set of objects is well defined when the photons are produced with a delta-type (infinitely narrow) pulse duration, however, commercially available linear accelerators used for cargo screening typically have pulse widths of the order of 1 μs. In the present work, the possible use of linear accelerators for Time-of-Flight Compton scatter imaging is investigated using a mixture of analytic and Monte Carlo methods. Ideal data are obtained by convolving a number of wide x-ray pulses (up to 5 μs) with the expected Time-of-Flight from a set of objects using a delta-type pulse. Monte Carlo simulations, using Geant4, have been performed to generate x-ray spectra produced by a linear accelerator. The spectra are then used as the input for detailed Monte Carlo simulations of the Time-of-Flight of photons produced by a single linear accelerator pulse scattering back from a set of objects. Both ideal and Monte Carlo data suggest that Time-of-Flight information can be recovered from a wide linear accelerator pulse, provided that the leading and falling edge of the pulse are sharp. In addition, it has been found that using a linear accelerator leads to double the amount of Time-of-Flight information as both the leading and falling edge are utilised (unlike for a delta-type pulse).
Sites et reactivite des sulfures en catalyse d'hydrotraitement : etude theorique ab-initio (1998)

Des simulations ab-initio ont ete menees selon le formalisme de la fonctionnelle de la densite incluant les corrections de gradient afin d'etudier l'origine de l'activite des sulfures de metaux de transition (smt) utilises comme catalyseurs d'hydrodesulfuration (hds). L'etude systematique des proprietes structurales, energetiques et electroniques en volume de plus de trente smt montre l'existence d'une correlation du type volcan reliant l'activite catalytique experimentale d'hds a un parametre energetique unique : l'energie de la liaison soufre-metal (s-m). Les sulfures ioniques-metalliques (ex. Ni 3s 2, co 9s 8) presentent l'energie s-m la plus faible tandis que les sulfures semi-conducteurs iono-covalents (ex. Mos 2) possedent l'energie s-m la plus forte. Les sulfures de cohesion intermediaire sont les plus actifs (rus 2). Ceci suggere la pertinence d'une forme du principe de sabatier. L'etude des etats electroniques des surfaces laterales de la cristallite mos 2 non promue explique par leur caractere accepteur l'activite des sites mo presentant des insaturations de coordinence. Le profil energetique detaille de la reaction d'hds du thiophene montre que l'etape de regeneration du site lacunaire est energetiquement defavorable. Nous calculons la position du metal promoteur (co ou ni) sur les plans de bord de la cristallite et obtenons un excellent accord avec l'exafs. L'introduction de co diminue le taux de sulfuration optimal des surfaces laterales et l'energie de la liaison s-m de surface a proportion de la teneur en co sur la surface (1010). Ni diminue plus fortement que co l'energie s-m sur ce plan. Un profil energetique simplifie de la reaction d'hds du thiophene etabli sur la surface (1010) promue, montre un deplacement de l'etape limitante vers la rupture c-s.
Mechanism of Sodium Ion Storage in Na7[H2PV14O42] Anode for Sodium‐Ion Batteries (2018)

Abstract In this work, the authors explore the sodium salt of the 14‐vanado(V)phosphate, Na 7 [H 2 PV 14 O 42 ], as a potential anode material for sodium‐ion batteries (NIBs). The multi‐electron redox activity of the polyoxovanadate [H 2 PV 14 O 42 ] 7‐ leads to high capacity. This polyanion is synthesized by a simple aqueous solution procedure and isolate as a sodium salt with different numbers of crystal waters, Na 7 [H 2 PV 14 O 42 ]·nH 2 O (n = 15–24). Na 7 [H 2 PV 14 O 42 ] as anode in NIBs exhibits a high and reversible capacity of 322 mA h g −1 at 25 mA g −1 with a high cycling stability (with capacity retention of 87% after 120 cycles). Some of the V 5+ ions in [H 2 PV 14 O 42 ] 7‐ can be reduced to V 3+ after being discharged to 0.01 V versus Na/Na + , resulting in an average oxidation state of V 3.7+ , as based on ex situ X‐ray photoelectron spectroscopy and in situ synchrotron X‐ray absorption near edge structure studies. The crystalline material becomes amorphous during the charge/discharge processes, which can be observed by in situ synchrotron X‐ray diffraction, indicating that functionality does not require crystallinity. The authors propose that the charge storage mechanism of Na 7 [H 2 PV 14 O 42 ] anodes mainly involves redox reactions of V accompanied by insertion/extraction of Na ions in‐between polyoxo‐14‐vanadate ions and adsorption/desorption of Na ions on the surface of the vanadate material.
Toward System on Chip (SoC) Development Using FinFET Technology: Challenges, Solutions, Process Co-Development & Optimization Guidelines (2011)

In this paper, the impact of process/technology co-optimization on System-on-Chip (SoC) performance using detailed 3-D process/device simulations has been studied for nanoscale FinFET devices. We investigated challenges in FinFET device optimization and scaling while using standard ion implantation process for both overlap and underlap designs. Moreover, an implant-free (IF) complementary metal-oxide-semiconductor process is discussed for better scalability with improved performance. FinFETs designed using this IF process shows a ~2× improvement in static random-access memory and digital input/ output performance. Additionally, a modification to the IF process is proposed, which further helps in achieving an improved logic and analog performance for overall SoC development.
FT-Raman Spectroscopy Of Thin Films By Integrated And Fiber Optics Techniques (1989)

Structural studies of thin films containing chromophores have not been possible using Raman spectroscopy with visible excitation due to the presence of fluorescence which results when visible photons are absorbed by the chromophores. To circumvent this problem FT-Raman instrumentation has been developed so that spectra can be obtained with excitation at 1.064 microns, much too low in energy for fluorescence to occur. Integrated optical techniques which have been successfully used to investigate thin films at visible wavelengths has been adapted to the FT-Raman instrumentation with certain modifications. The primary change occurred in the collection optics where the imaging of the laser streak in the film upon the circular entrances aperture of an FTIR yielded a poor S/N spectrum of a thin polymer film. The geometric mismatch of streak image and circular aperture was rectified by the use of a fiber optic image converter. This consisted of a fiber optic bundle which had a linear array of fibers on one end for collection of light from the streak and a circular array of fibers on the other end so as to maximize the amount of light that entered the FTIR. A significant improvement in spectral quality was observed. Feasibility studies of guest/host interactions in thin composite films containing chromophores have been demonstrated and the results for a dye/cellulose acetate film will, in particular, be discussed.
The total synthesis of avermectin A1a. New protocols for the synthesis of novel 2-deoxypyranose systems and their axial glycosides (1987)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTThe total synthesis of avermectin A1a. New protocols for the synthesis of novel 2-deoxypyranose systems and their axial glycosidesSamuel J. Danishefsky, Harold G. Selnick, David M. Armistead, and Francine E. WincottCite this: J. Am. Chem. Soc. 1987, 109, 26, 8119–8120Publication Date (Print):December 1, 1987Publication History Published online1 May 2002Published inissue 1 December 1987https://pubs.acs.org/doi/10.1021/ja00260a046https://doi.org/10.1021/ja00260a046research-articleACS PublicationsRequest reuse permissionsArticle Views463Altmetric-Citations43LEARN 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 optionsGet e-Alertsclose Get e-Alerts
Adenovirus-Mediated Gene Delivery Rescues a Neonatal Lethal Murine Model of mut 0 Methylmalonic Acidemia (2007)

Methylmalonic acidemia (MMA), an autosomal recessive metabolic disorder, is most often caused by mutations in methylmalonyl-CoA mutase (MUT). Severely affected patients typically present with metabolic crisis in the early neonatal period and can perish despite intervention. Survivors follow an unstable course and can require elective liver transplantation to prevent life-threatening metabolic decompensation. Therapeutic alternatives to liver transplantation such as hepatocyte-directed gene and cell therapies lack experimental validation. We have used a murine model of mut0 MMA to assess the efficacy of virus-mediated gene therapy to rescue the neonatal lethality seen in the Mut(-/-) mice. Affected pups and control littermates received either intramuscular or intrahepatic injections of adenovirus carrying the Mut gene expressed under the control of the cytomegalovirus promoter. All of the Mut(-/-) pups injected via the intramuscular route perished within the first 48 hr of birth. However, more than 50% of the Mut(-/-) pups that received intrahepatic injections survived beyond weaning (day 15). The treated mutants expressed methylmalonyl-CoA mutase mRNA and protein, and displayed decreased metabolite levels compared with uninjected Mut(-/-) mice. The results demonstrate that adenovirus-mediated, hepatic methylmalonyl-CoA mutase expression can rescue Mut(-/-) pups from neonatal mortality and provide proof-of-principle evidence for the efficacy of liver-directed gene delivery in methylmalonic acidemia.
Imaging a linearly or circularly polarized scene: micro-components and shrimp (2011)

Polarimetric imaging captures the polarization state of light from all the points of a scene. Snapshot polarimetric imaging collects the Stokes' parameters spatial distribution simultaneously. We will discuss state-of-the-art achievements and some fundamental diffraction limitations in polarimetric imaging with an array of micro-components. We will also look at the natural vision system of the mantis shrimp, with many of these same sensing abilities. The evolved and exquisite vision system possesses a recently-discovered circular polarization capability. This comprehensive polarization vision may enable imaging/communicating advantages in the underwater environment as well as more general turbid environments such as smoke and fog.
Monitoring Fluidization Dynamics for Detection of Changes in Fluidized Bed Composition and Operating Conditions (1999)

In many industrial applications of gas-solids fluidized beds, it is worthwhile to have an on-line monitoring method for detecting changes in the hydrodynamics of the bed (due for example to agglomeration) quickly. In this paper, such a method, based on the short-term predictability of fluidized bed pressure fluctuations, is examined. Its sensitivity is shown by experiments with small step changes in the superficial gas velocity and by experiments with a gradual change in the particle size distribution of the solids in the bed. Furthermore, it is demonstrated that the method is well able to indicate if a stationary hydrodynamic state has been reached after a change in the particle size distribution (a ‘grade change’).
Fundamental equation representing water in the stable, metastable, and unstable states. Final report. [PWR; BWR] (1983)

The goal of this work was to formulate a major fundamental equation for water that would be capable, not only of representing the thermodynamic properties of stable liquid and vapor water with high accuracy, but one that would also represent the superheated liquid and subcooled vapor states. To accomplish this, the conventional nucleation theory had to be modified. A general form of the Keenan-Keyes-Hill-Moore (KKHM) fundamental equation, which has 78 adjustable constants, is used to represent the properties of water in stable and metastable states. A stepwise regression method is then used to fit this equation to available data points that include some experimental measurements for superheated water. The curve fit is restricted to pressures less than 700 bar and temperatures between 273.15 and 673.15K. Sixty-eight terms of the original equation are selected to best fit the data. The resulting equation is consistent with the entries of the International Skeleton Tables in the stable equilibrium regimes, and its isotherms display a single local maximum and minimum in the metastable and unstable regimes.