gebhart/patrepeval huggingface dataset:
SufE Transfers Sulfur from SufS to SufB for Iron-Sulfur Cluster Assembly (2007)

Iron-sulfur (Fe-S) clusters are key metal cofactors of metabolic, regulatory, and stress response proteins in most organisms. The unique properties of these clusters make them susceptible to disruption by iron starvation or oxidative stress. Both iron and sulfur can be perturbed under stress conditions, leading to Fe-S cluster defects. Bacteria and higher plants contain a specialized system for Fe-S cluster biosynthesis under stress, namely the Suf pathway. In Escherichia coli the Suf pathway consists of six proteins with functions that are only partially characterized. Here we describe how the SufS and SufE proteins interact with the SufBCD protein complex to facilitate sulfur liberation from cysteine and donation for Fe-S cluster assembly. It was previously shown that the cysteine desulfurase SufS donates sulfur to the sulfur transfer protein SufE. We have found here that SufE in turn interacts with the SufB protein for sulfur transfer to that protein. The interaction occurs only if SufC is present. Furthermore, SufB can act as a site for Fe-S cluster assembly in the Suf system. This provides the first evidence of a novel site for Fe-S cluster assembly in the SufBCD complex.
Accuracy of statistical image estimates under approximations to Poisson log-likelihood functions (2002)

Emission Computed Tomography (ECT) is widely applied in medical diagnostic imaging. The available set of measurements is, however, often incomplete and corrupted, and the quality of image reconstruction is enhanced by the computation of a statistically optimal estimate. We present here a method for ECT image reconstruction based on a Taylor series quadratic approximation to the usual Poisson log-likelihood function. The quadratic approximation yields simplification in understanding and manipulating models for emission tomographic imagery. We introduce an algorithm similar to global Newton methods which updates the point of expansion a limited number of times and we give quantitative measures of the accuracy of the reconstruction. The results show little difference in quality from those obtained with the Poisson model, thus being greatly improved relative to the conventional filtered back-projection method.
Integrated Cascaded Linear Microcavity Filters (2013)

We experimentally demonstrate cascaded microcavities for enhanced bandwidth and extinction. The cavities are integrated into waveguides by etching three sets of quarter-wavelength trenches, each set forming a reflector. Experiments compare well with transfer matrix predictions.
Barcoded viral tracing of single-cell interactions in central nervous system inflammation (2021)

Cell-cell interactions control the physiology and pathology of the central nervous system (CNS). To study astrocyte cell interactions in vivo, we developed rabies barcode interaction detection followed by sequencing (RABID-seq), which combines barcoded viral tracing and single-cell RNA sequencing (scRNA-seq). Using RABID-seq, we identified axon guidance molecules as candidate mediators of microglia-astrocyte interactions that promote CNS pathology in experimental autoimmune encephalomyelitis (EAE) and, potentially, multiple sclerosis (MS). In vivo cell-specific genetic perturbation EAE studies, in vitro systems, and the analysis of MS scRNA-seq datasets and CNS tissue established that Sema4D and Ephrin-B3 expressed in microglia control astrocyte responses via PlexinB2 and EphB3, respectively. Furthermore, a CNS-penetrant EphB3 inhibitor suppressed astrocyte and microglia proinflammatory responses and ameliorated EAE. In summary, RABID-seq identified microglia-astrocyte interactions and candidate therapeutic targets.
Field-resolved spectroscopy of aqueous biological samples (2020)

Electro-optic sampling (EOS) has established itself as one of the main techniques for coherent THz spectroscopy. In recent years, EOS has been pushed towards recording infrared or even optical waveforms, opening up new possibilities for spectroscopy in these spectral regions. In this contribution, we demonstrate the potential of electric-field-resolved detection via EOS for broadband, mid-infrared molecular vibrational spectroscopy. We show that field-resolved spectroscopy can achieve detection sensitivities orders of magnitude higher than state-of-the art Fourier-transform infrared spectroscopy. This is achieved by high-quantum-efficiency non-linear temporal “piercing” and, therefore, isolation of the molecular signal from the orders-of-magnitude stronger impulsive excitation. Thereby limitations due to detector dynamic range and source excitation noise can be avoided. This promises a new level of molecular sensitivity and molecular coverage for probing complex biological samples.
New architectures for high resolution patterning (2008)

Abstract: The ability of the semiconductor industry to reduce device dimensions below 45 nm is hindered by limitations in both resist material and processing technique. High resolution and sensitivity along with low line edge roughness are key requirements of next generation resist materials. In order to meet the future demands of the semiconductor industry, new resist design strategies are being considered. In the past few years, we have focused on developing small molecule resists capable of high resolution patterning. Despite their small size, these molecules known as molecular glass can be designed to demonstr ate high glass transition temperatures (Tgs) comparable to polymeric resists. Several ring and branched architectures with high Tgs that have attained feature resolution as small as 30nm through Extreme Ultraviolet (EUV) exposure will be discussed. In addition to potential performance advantages, the small size of these resist molecules also allow solvent free processing techniques to be utilized. Our efforts on physical vapor deposition and supercritical CO
A Pilot Study of Diffusion-Weighted MRI in Patients Undergoing Neoadjuvant Chemoradiation for Pancreatic Cancer (2014)

dMRI may be useful to predict response to chemoradiation in pancreatic cancer. In our study, tumors with a low ADC mean value at baseline responded poorly to standard chemoradiation and would be candidates for intensified therapy.
Managing Traffic Growth in Solar Powered Wireless Mesh Networks (2009)

Wireless mesh nodes must often be upgraded so that the network can accommodate evolving user demands. When some of the nodes are operated using a sustainable solar energy source, these upgrades must take into account the cost of updating the node energy resource configurations. This is required so that the new network configuration can properly accommodate the updated energy workloads of the re-provisioned network. In this paper we study this problem in the context of sustainable energy mesh node provisioning costs. We derive a mixed integer linear programming (MILP) formulation which is used to optimize the costs of node resource upgrades. Using this result, a lower bound on the network upgrade cost is obtained. The paper then proposes the use of a genetic algorithm based methodology for determining practical cost-effective mesh node resource upgrading. Various examples are given using networks with random, mesh and tree topologies which show the value of the proposed mechanism. In particular we find that the genetic algorithm approach achieves results which are much better than those from an algorithm which uses local optimization. It also performs well compared to our derived lower bound.
Downstream of Mutant KRAS, the Transcription Regulator YAP Is Essential for Neoplastic Progression to Pancreatic Ductal Adenocarcinoma (2014)

Pancreatic ductal adenocarcinoma (PDAC) is an aggressive cancer with poor survival rates and frequently carries oncogenic KRAS mutation. However, KRAS has thus far not been a viable therapeutic target. We found that the abundance of YAP mRNA, which encodes Yes-associated protein (YAP), a protein regulated by the Hippo pathway during tissue development and homeostasis, was increased in human PDAC tissue compared with that in normal pancreatic epithelia. In genetically engineered Kras(G12D) and Kras(G12D):Trp53(R172H) mouse models, pancreas-specific deletion of Yap halted the progression of early neoplastic lesions to PDAC without affecting normal pancreatic development and endocrine function. Although Yap was dispensable for acinar to ductal metaplasia (ADM), an initial step in the progression to PDAC, Yap was critically required for the proliferation of mutant Kras or Kras:Trp53 neoplastic pancreatic ductal cells in culture and for their growth and progression to invasive PDAC in mice. Yap functioned as a critical transcriptional switch downstream of the oncogenic KRAS-mitogen-activated protein kinase (MAPK) pathway, promoting the expression of genes encoding secretory factors that cumulatively sustained neoplastic proliferation, a tumorigenic stromal response in the tumor microenvironment, and PDAC progression in Kras and Kras:Trp53 mutant pancreas tissue. Together, our findings identified Yap as a critical oncogenic KRAS effector and a promising therapeutic target for PDAC and possibly other types of KRAS-mutant cancers.
Adaptive, efficient, parallel execution of parallel programs (2014)

Future multicore processors will be heterogeneous, be increasingly less reliable, and operate in dynamically changing operating conditions. Such environments will result in a constantly varying pool of hardware resources which can greatly complicate the task of efficiently exposing a program's parallelism onto these resources. Coupled with this uncertainty is the diverse set of efficiency metrics that users may desire. This paper proposes Varuna, a system that dynamically, continuously, rapidly and transparently adapts a program's parallelism to best match the instantaneous capabilities of the hardware resources while satisfying different efficiency metrics. Varuna is applicable to both multithreaded and task-based programs and can be seamlessly inserted between the program and the operating system without needing to change the source code of either. We demonstrate Varuna's effectiveness in diverse execution environments using unaltered C/C++ parallel programs from various benchmark suites. Regardless of the execution environment, Varuna always outperformed the state-of-the-art approaches for the efficiency metrics considered.
Non-referenced genome assembly from epigenomic short-read data (2014)

Current computational methods used to analyze changes in DNA methylation and chromatin modification rely on sequenced genomes. Here we describe a pipeline for the detection of these changes from short-read sequence data that does not require a reference genome. Open source software packages were used for sequence assembly, alignment, and measurement of differential enrichment. The method was evaluated by comparing results with reference-based results showing a strong correlation between chromatin modification and gene expression. We then used our de novo sequence assembly to build the DNA methylation profile for the non-referenced Psammomys obesus genome. The pipeline described uses open source software for fast annotation and visualization of unreferenced genomic regions from short-read data.
Circuit emulation services over Ethernet—Part 2: Prototype and experimental results (2004)

Abstract This paper describes a prototype implementation and experimental results for unstructured circuit emulation service (UCES) of T3 data stream over Ethernet. As explained in Part 1 of this paper, 1 packet‐switched networks such as Ethernet are not designed to transport TDM data and so have no inherent clock distribution and synchronization mechanisms. Thus, to allow the frequency of the source TDM stream to be regenerated at the receiver, the prototype employed the clock synchronization scheme described in Part 1 of this paper. Our experiments showed that the recovered clock conforms to ITU‐T G.824 requirements 2 even for networks that introduce high jitter and packet loss. Copyright © 2004 John Wiley &amp; Sons, Ltd.
Ion Transportation of Electrolytes in a Flow Channel Mapped by an HTS SQUID Scanning System (2014)

In this paper, we propose and develop a device for visualizing the magnetic field produced by ion transportation in electrolyte cells. Using 0.5 mM potassium ferricyanide (K <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">3</sub> [Fe(CN) <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">6</sub> ]) dissolved in 0.5 M sodium sulfate (Na <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sub> SO <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">4</sub> ) as the electrolyte, the magnetic distribution was obtained using high-TC SQUID scanning performed by a planar gradiometer located above the electrolyte cell across the surface. The difference in the ion transportation path in the electrolyte cells is discussed with regard to flow channels fabricated in the electrolyte cells.
Chromophoric fine tuning and the interchromophoric coupling model in ruthenium(II) polypyridyl complexes (1990)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTChromophoric fine tuning and the interchromophoric coupling model in ruthenium(II) polypyridyl complexesR. L. Blakley, M. L. Myrick, R. Pittman, and M. K. De ArmondCite this: J. Phys. Chem. 1990, 94, 12, 4804–4809Publication Date (Print):June 1, 1990Publication History Published online1 May 2002Published inissue 1 June 1990https://pubs.acs.org/doi/10.1021/j100375a012https://doi.org/10.1021/j100375a012research-articleACS PublicationsRequest reuse permissionsArticle Views123Altmetric-Citations8LEARN 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
Paced monophasic and biphasic waveforms alter transmembrane potentials and metabolism of human fibroblasts (2016)

Resting transmembrane potential (TMP) of primary human fibroblast cells was altered in predictable directions by subjecting cell cultures to specific monophasic and biphasic waveforms. Cells electrically stimulated with an anodal pulse resulted in hyperpolarization while a cathodal waveform depolarized the TMP to below that of non-paced control cells. The biphasic waveform, consisting of an anodal pulse followed immediately by an inverse symmetric cathodal pulse, also lessened the TMP similar to that of the cathodal pulse. The effect of short-term pacing on the TMP can last up to 4 h before the potentials equilibrate back to baseline. While subjecting the cells to this electrical field stimulation did not appear to damage the integrity of the cells, the three paced electrical stimulation waves inhibited expansion of the cultures when compared to non-paced control cells. With longer pacing treatments, elongation of the cells and electrotaxis towards the anodal polarity were observed. Pacing the fibroblasts also resulted in modest, yet very statistically significant (and likely underestimated) changes to cellular adenosine-5'-triphosphate (ATP) levels, and cells undergoing anodal and biphasic (anodal/cathodal) stimulation also exhibited altered mitochondrial morphology. These observations indicate an active role of electrical currents, especially with anodal content, in affecting cellular metabolism and function, and help explain accumulating evidence of cellular alterations and clinical outcomes in pacing of the heart and other tissues in general.
Design Guidelines for an Internet-Scaled QoS Framework (2007)

Adding quality of service support to the best-effort Internet is something that has been suggested and researched for a long time now. While individual networks are starting to offer QoS, it remains as elusive as ever for the Internet as a whole. A number of different QoS solutions are being deployed within networks leading to a highly heterogeneous Internet. On the other hand, there are a number of proposed standards that try to solve such great heterogeneity with fully-tailored architectures. The thesis of this paper is that heterogeneity should not be fought; instead, tussles will eventually arise among different approaches and these should be the vector towards evolution and hence must be allowed as part of the design. Each domain should be free to make its own internal choices on how to deliver QoS, while presenting a common interface. The problem then becomes the coordination of the decisions of different domains. The design of such a framework presents several key choices, which will be investigated
That COMP-fusions (1984)

Proceedings of the Tenth Annual Meeting of the Berkeley Linguistics Society (1984), pp. 660-673
Memory Bandwidth Efficient Two-Dimensional Fast Fourier Transform Algorithm and Implementation for Large Problem Sizes (2012)

Prevailing VLSI trends point to a growing gap between the scaling of on-chip processing throughput and off-chip memory bandwidth. An efficient use of memory bandwidth must become a first-class design consideration in order to fully utilize the processing capability of highly concurrent processing platforms like FPGAs. In this paper, we present key aspects of this challenge in developing FPGA-based implementations of two-dimensional fast Fourier transform (2D-FFT) where the large datasets must reside off-chip in DRAM. Our scalable implementations address the memory bandwidth bottleneck through both (1) algorithm design to enable efficient DRAM access patterns and (2) data path design to extract the maximum compute throughput for a given level of memory bandwidth. We present results for double-precision 2D-FFT up to size 2,048-by-2,048. On an Alter a DE4 platform our implementation of the 2,048-by-2,048 2D-FFT can achieve over 19.2 Gflop/s from the 12 GByte/s maximum DRAM bandwidth available. The results also show that our FPGA-based implementations of 2D-FFT are more efficient than 2D-FFT running on state-of-the-art CPUs and GPUs in terms of the bandwidth and power efficiency.
Chiral Glycine Cation Equivalents: N‐Acyliminium Species Derived from Diketopiperazines. (2003)

Abstract For Abstract see ChemInform Abstract in Full Text.
Endocytosis of mannose‐6‐phosphate binding sites by mouse T‐lymphoma cells (1986)

The endocytosis and intracellular transport of mannose-6-phosphate conjugated to bovine serum albumin (Man-6-P:BSA) by mouse T-lymphoma cells were investigated in detail using several methods of analysis, both morphological and biochemical. Man-6-P:BSA was labeled with fluorescein or 125I and used to locate both surface and intracellular Man-6-P binding sites by light or electron microscopy, respectively. Incubation of cells with either fluorescent- or 125I-labeled Man-6-P:BSA at 0 degree C revealed a uniform distribution of the Man-6-P binding sites over the cell surface. Competition experiments indicate that the Man-6-P:BSA binding sites on the cell surface are the same receptors that can recognize lysosomal hydrolases. After as little as 1 min incubation at 37 degrees C, endocytosis of Man-6-P binding sites was clearly observed to occur through regions of the plasma membrane and via vesicles that also bound anticlathrin antibody. After a 5-15-min incubation of cells at 37 degrees C, the internalized ligand was detected first in the cis region of the Golgi apparatus and then in the Golgi stacks using both autoradiography and immunocytochemistry to visualize the ligand. The appearance of Man-6-P:BSA in the Golgi region after 15-30 min was confirmed by subcellular fractionation, which demonstrated an accumulation of Man-6-P:BSA in light membrane fractions that corresponded with the Golgi fractions. After a 30-min incubation at 37 degrees C, the internalized Man-6-P binding sites were localized primarily in lysosomal structures whose membrane but not lumen co-stained for acid phosphatase. These results demonstrate a temporal participation of clathrin-containing coated vesicles during the initial endocytosis of Man-6-P binding sites and that one step in the Man-6-P:BSA transport pathway between plasma membrane and the lysosomal structure can involve a transit through the Golgi stacks.
Enquête nationale de prévalence du virus de l hépatite E dans le réservoir porcin (2011)

National audience
Efficacies of ABT-773, a New Ketolide, against Experimental Bacterial Infections (2001)

ABT-773 is a novel ketolide effective against antibacterial-resistant respiratory tract pathogens. The pharmacokinetic profile of ABT-773 was studied in rats and consisted of a mean peak concentration in plasma of 1.07 microg/ml and an area under the concentration-time curve (AUC) of 12.03 microg. h/ml when the compound was delivered at a dose of 25 mg/kg of body weight. It concentrated in rat lung tissue, with a lung tissue-to-plasma ratio of 29 based on the AUC. In acute systemic infections in mice, ABT-773 showed efficacy against macrolide-susceptible strains of Staphylococcus aureus, Streptococcus pneumoniae, S. pyogenes, and Listeria monocytogenes. Additionally, ABT-773 improved the survival of mice infected with resistant S. pneumoniae containing either the ermB gene, the mefE gene, or altered penicillin binding protein genes. In a rat lung model of infection, ABT-773 demonstrated 50% effective doses lower than those of comparator macrolides when evaluated against the following strains of S. pneumoniae: a macrolide-lincosamide-streptogramin B-susceptible strain, an ermB strain, and an mefE strain. ABT-773 was also effective against Haemophilus influenzae lung infections in rats. Thus, ABT-773 may prove to be a useful new antibacterial agent for the treatment of respiratory tract infections.
CCFA Microbial–Host Interactions Workshop (2007)

This article provides a summary of the proceedings of the CCFA Microbial-Host Interactions Workshop that was held in St. Petersburg, Florida, on March 16-19, 2006. Approximately 75 senior and junior investigators from around the world shared their most current research findings through oral presentations, poster sessions, and active discussion. Because intestinal microbiota are significant contributors in the development of inflammatory bowel diseases (IBD), understanding the body's responses to and interactions with microbes, especially in the colon and distal small intestine, is critical to elucidating the etiology and pathogenesis of IBD and developing effective therapeutic interventions. Major advances have occurred recently in molecular detection of luminal bacterial species, identifying dominant microbial antigens that drive intestinal inflammation, the mechanisms of innate immune and epithelial responses to bacteria, and regulation of inflammation by innate and acquired immune cells.