gebhart/patrepeval huggingface dataset:
Molecular Analysis of the <i>pmo</i> (Particulate Methane Monooxygenase) Operons from Two Type II Methanotrophs (2000)

ABSTRACT The particulate methane monooxygenase gene clusters, pmoCAB , from two representative type II methanotrophs of the α- Proteobacteria , Methylosinus trichosporium OB3b and Methylocystis sp. strain M, have been cloned and sequenced. Primer extension experiments revealed that the pmo cluster is probably transcribed from a single transcriptional start site located 300 bp upstream of the start of the first gene, pmoC , for Methylocystis sp. strain M. Immediately upstream of the putative start site, consensus sequences for ς 70 promoters were identified, suggesting that these pmo genes are recognized by ς 70 and negatively regulated under low-copper conditions. The pmo genes were cloned in several overlapping fragments, since parts of these genes appeared to be toxic to the Escherichia coli host. Methanotrophs contain two virtually identical copies of pmo genes, and it was necessary to use Southern blotting and probing with pmo gene fragments in order to differentiate between the two pmoCAB clusters in both methanotrophs. The complete DNA sequence of one copy of pmo genes from each organism is reported here. The gene sequences are 84% similar to each other and 75% similar to that of a type I methanotroph of the γ- Proteobacteria , Methylococcus capsulatus Bath. The derived proteins PmoC and PmoA are predicted to be highly hydrophobic and consist mainly of transmembrane-spanning regions, whereas PmoB has only two putative transmembrane-spanning helices. Hybridization experiments showed that there are two copies of pmoC in both M. trichosporium OB3b and Methylocystis sp. strain M, and not three copies as found in M. capsulatus Bath.
Electric Current-Induced Detachment of <i>Staphylococcus epidermidis</i> Biofilms from Surgical Stainless Steel (2004)

Biomaterial-centered infections of orthopedic percutaneous implants are serious complications which can ultimately lead to osteomyelitis, with devastating effects on bone and surrounding tissues, especially since the biofilm mode of growth offers protection against antibiotics and since removal frequently is the only ultimate solution. Recently, it was demonstrated that as a possible pathway to prevent infections of percutaneous stainless steel implants, electric currents of 60 to 100 microA were effective at stimulating the detachment of initially adhering staphylococci from surgical stainless steel. However, initially adhering bacteria are known to adhere more reversibly than bacteria growing in the later stages of biofilm formation. Hence, the aim of this study was to examine whether a growing Staphylococcus epidermidis biofilm can be stimulated to detach from surgical stainless steel by the use of electric currents. In separate experiments, four currents, i.e., 60 and 100 microA of direct current (DC) and 60 and 100 microA of block current (50% duty cycle, 1 Hz), were applied for 360 min to stimulate the detachment of an S. epidermidis biofilm that had grown for 200 min. A 100-microA DC yielded 78% detachment, whereas a 100-microA block current under the same experimental conditions yielded only 31% detachment. The same trend was found for 60 microA, with 37% detachment for a DC and 24% for a block current. Bacteria remaining on the surface after the current application were less viable than they were prior to the current application, as demonstrated by confocal laser scanning microscopy. In conclusion, these results suggest that DCs are preferred for curing infections.
Immune-Mediated Protection and Pathogenesis of Chikungunya Virus (2016)

Chikungunya virus (CHIKV) is a re-emerging alphavirus that causes debilitating acute and chronic arthritis. Infection by CHIKV induces a robust immune response that is characterized by production of type I IFNs, recruitment of innate and adaptive immune cells, and development of neutralizing Abs. Despite this response, chronic arthritis can develop in some individuals, which may be due to a failure to eliminate viral RNA and Ag and/or persistent immune responses that cause chronic joint inflammation. In this review, based primarily on advances from recent studies in mice, we discuss the innate and adaptive immune factors that control CHIKV dissemination and clearance or contribute to pathogenesis.
Distribution of [2-14C]merbarone in mice by autoradiography of whole-body cryosections. (1987)

The distribution of radiolabel in male mice was studied by autoradiography of whole-body cryosections at intervals during 24 h after i.v. injection (46.6 mg/kg) and during 4 h after oral administration (140 mg/kg) of [2-14C]merbarone. Following injection, radioactivity levels in the blood and highly vascular tissues declined to 8 h at which time only low levels were present in the systemic circulation. Only very low levels were seen in the brain and spinal cord at 0.5-3 min after dosing and levels were barely above background in autoradiograms obtained at 0.5-1 h. Radiolabel was concentrated in those regions which lack an effective blood-brain barrier particularly within the choroid plexuses. Radioactivity was rapidly taken up by the liver and kidneys and as the blood and body radioactivity levels decreased, these organs remained densely labeled. Significant biliary excretion had occurred by 30 min and the autoradiograms to 24 h showed radiolabeled compounds in the intestinal lumen. Between 1 and 8 h, the liver exhibited a stippled appearance as a result of labeling around branches of the portal vein due to enterohepatic recycling. The stippling was substantially diminished at 16 h. High levels of radioactivity were present in the kidney at 0.5-3 min after injection with both the kidney cortex and medulla initially densely labeled. At 4 h and thereafter, the radioactivity levels in the kidney were lower with most of the labeled compounds in the medulla. Accumulation in the liver and kidney was very low at 16-24 h after dosing and most of the merbarone dose had cleared from the body. Rapid absorption of merbarone occurred after oral administration with radiolabel first observed in the liver and kidney at 3-6 min after dosing. Peak levels in these organs and systemically were seen between 0.5 and 2 h. At 4 h, the radioactivity had largely cleared from the systemic circulation. The liver exhibited a stippled appearance soon after oral dosing similar to that observed following i.v. dosing affording evidence for enterohepatic recycling after i.v. administration. The relatively low systemic levels observed after oral dosing suggests that the liver binds much of the absorbed drug and its metabolites limiting the levels which reach the systemic circulation.
For COPD a Combination of Ipratropium Bromide and Albuterol Sulfate Is More Effective Than Albuterol Base (1999)

We conclude that a combination of ipratropium bromide and albuterol sulfate is more effective at improving pulmonary function than albuterol base alone, with no potentiation of adverse effects.
[2,3]-Wittig rearrangement of unsymmetrical bis-allylic ethers. Facile method for regio- and stereoselective synthesis of 1,5-dien-3-ols (1981)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXT[2,3]-Wittig rearrangement of unsymmetrical bis-allylic ethers. Facile method for regio- and stereoselective synthesis of 1,5-dien-3-olsT. Nakai, K. Mikami, S. Taya, and Y. FujitaCite this: J. Am. Chem. Soc. 1981, 103, 21, 6492–6494Publication Date (Print):October 1, 1981Publication History Published online1 May 2002Published inissue 1 October 1981https://pubs.acs.org/doi/10.1021/ja00411a038https://doi.org/10.1021/ja00411a038research-articleACS PublicationsRequest reuse permissionsArticle Views550Altmetric-Citations68LEARN 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-AlertscloseSupporting Info (1)»Supporting Information Supporting Information Get e-Alerts
Characterization of the 5′-Flanking Region of the Human Preprogalanin Gene (1995)

Expression of the human galanin gene was analysed using a 3.5-kb DNA fragment comprising the 5′-flanking sequence of the gene. This sequence contains a TATA box (ATATATA) preceded by numerous potential binding sites for transcription factors such as SP1, AP2, and NFκB. Three half-palindromic estrogen response elements (EREs, GGTCA) are also found at positions −1,162, −361, and −122 bp relative to the transcription start site. To localize functionally important portions of the promoter region, several shorter fragments of the galanin 5′-flanking region were placed upstream from the chloramphenicol acetyltransferase (CAT) reporter gene. In transient transfection assays, all constructs demonstrated substantial transcriptional activity in both rat glioma/mouse neuroblastoma hybrid cells (NG108-15) and Chinese hamster ovary (CHO-K1) cells. Comparison of the basal expression levels of the different constructs suggests the presence of a negative modulator between positions −1,891 and −207. When cotransfected into NG108-15 cells with the human estrogen receptor cDNA, estrogen did not induce transcription of the human galanin gene at physiological levels of estrogen receptor, although transcription was induced up to 30-fold in the presence of high levels of receptor.
A review of synthesis techniques for Petri nets with applications to automated manufacturing systems (1993)

Research results in both bottom-up and top-down synthesis techniques for Petri net modeling are reviewed. These methods can be adopted for representing parallel and distributed application environments such as automated manufacturing systems. Bottom-up techniques, consisting of the merging of places and sharing of simple elementary paths, have the advantage of ease of system description since the modeled subsystems usually have real-life correspondences. Nevertheless, with current bottom-up techniques, the synthesized system may not exhibit the same control properties as the subsystems. Top-down methods, including refinement of transitions and refinement of places, have the advantage of viewing the system globally, which may generate more structured designs. However, it is difficult to apply these methods to the environments with highly shared resources. Examples in the context of automated manufacturing systems are given to demonstrate application of these techniques. Petri net reduction techniques and their relationship to synthesis methods are discussed.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
Clustered objects (2005)

In this dissertation we establish that the use of distribution in the implementation of a shared memory multi-processor operating system is both feasible and able to substantially improve performance of core operating system services. Specifically we apply distribution in the form of replication and partitioning in the construction of K42, a shared memory multi-processor operating system. Clustered Objects, a software construction for the systematic and selective application of distribution to objects of K42's object oriented system layer, is presented. A study of the virtual memory services of K42 is conducted in which distribution is applied to key virtual memory objects to enable performance improvements. The distributed versions of these objects substantially improve scalability, and specifically improve throughput of a standard multiuser benchmark by 68% on a 24 way multi-processor. Additionally, a methodology for the dynamic hot-swapping of Clustered Object instances is presented as a means for enabling dynamic adaptation. Motivated by the desire to hot-swap between centralized and distributed implementations of Clustered Objects, the methodology presented is correct, efficient and integrated with the Clustered Object support.
An Interactive Visualization Environment for Data Exploration (2018)

Exploratory data analysis is a process of sifting through data in search of interesting information or patterns. Analysts' current tools for exploring data include database management systems, statistical analysis packages, data mining tools, visualization tools, and report generators. Since the exploration process seeks the unexpected in a data-driven manner, it is crucial that these tools are seamlessly integrated so analysts can flexibly select and compose tools to use at each stage of analysis. Few systems have integrated all these capabilities either architecturally or at the user interface level. Visage's information-centric approach allows coordination among multiple application user interfaces. It uses an architecture that keeps track of the mapping of visual objects to information in shared databases. One result is the ability to perform direct manipulation operations such as drag-and-drop transfer of data among applications. This paper describes Visage's Visual Query Language and visualization tools, and illustrates their application to several stages of the exploration process: creating the target dataset, data cleaning and preprocessing, data reduction and projection, and visualization of the reduced data. Unlike previous integrated KDD systems' interfaces, direct manipulation is used pervasively, and the visualizations are more diverse and can be customized automatically as needed. Coordination among all interface objects simplifies iterative modification of decisions at any stage.
FedFace: Collaborative Learning of Face Recognition Model (2021)

DNN-based face recognition models require large centrally aggregated face datasets for training. However, due to the growing data privacy concerns and legal restrictions, accessing and sharing face datasets has become exceedingly difficult. We propose FedFace, a federated learning (FL) framework for collaborative learning of face recognition models in a privacy aware manner. FedFace utilizes the face images available on multiple clients to learn an accurate and generalizable face recognition model where the face images stored at each client are neither shared with other clients nor the central host and each client is a mobile device containing face images pertaining to only the owner of the device (one identity per client). Our experiments show the effectiveness of FedFace in enhancing the verification performance of pre-trained face recognition system on standard face verification benchmarks namely LFW, IJB-A and IJB-C.
Ties among Adult Siblings (1992)

We use a National Survey of Families and Households sample of 7,730 adults with siblings to test a model of perceived and actual social support among adult siblings. Despite low levels of actual exchange, nearly 30% of the sample would call on a sibling first in an emergency. Social support among siblings was higher for those with living sisters and for those without adult children, but African Americans and respondents with lower education and family income levels were less likely to be involved in actual exchange with siblings. Although weak support from siblings may simply represent a contraction of the support network to the “inner circle” of parents and children, these findings suggest caution in assuming that disadvantaged groups can rely on stronger extended family networks.
Class D Audio Amplifier with Trim-able Ramp Generator Design Theory and Design implementation for portable applications (2011)

This paper presents a single chip class D amplifier with two selectable gains 6dB & 9dB, 1.4 W output power and 86% efficiency with an 8 ohm load. This chip uses a frequencies trim-able ramp generator. Input Clock Frequency Range with 250kHz – 550kHz and 8 bits trim, 4 bits (LSB) to trim the ramp amplitude to vdd/5 peak-to-peak, 4 bits (MSB) to adjust the ramp continuity, the trimming procedures consists on putting a zero input signal, and adjust the trim code such as to get a 50% duty cycle Pulse Wide Modulation output signal, Reduction of inter- modulation in case of mixing of Audio and Voice. It operates with a 2.5 V to 5.5V supply voltage, 0.5 um, double-poly, triple-metal BiCMOS process. It has an area of 1.5 x 1.2 mm2 and it achieves a THD as low as 0.04%, with a flat band response between 20 Hz and 20 kHz.
Electrochemical Preparation of CdSe Nanowire Arrays (2000)

We have successfully prepared CdSe nanowire arrays by direct-current electrodeposition in porous anodic aluminum oxide templates from a dimethyl sulfoxide solution containing CdCl2 and elemental Se. Electron microscopy results show that the length, diameter, and direction of growth of the nanowires are quite uniform. X-ray energy dispersion analysis indicates that the atomic composition of Cd and Se is very close to a 1:1 stoichiometry. Furthermore, X-ray diffraction and high-resolution electron microscope investigations demonstrate that the CdSe nanowires are a uniform hexagonal CdSe crystal.
Wide spectrum detection of precarcinogens in short-term bioassays by simultaneous superinduction of multiple forms of cytochrome P450 isoenzymes (1991)

The use of Aroclor 1254 to induce S9 liver fractions is a standard method for conducting short-term genotoxicity assays. An alternative induction procedure, using beta-naphthoflavone (beta-NF), as a safe (non-carcinogenic) substitute for polychlorinated biphenyls, combined with sodium phenobarbital (PB), was found to be equally effective. The aim of this work is to realize a novel schedule of induction for the preparation of metabolizing systems containing a wider spectrum of induced cytochrome P450s. Five inducers of different 'classes' such as PB (class IIB P450s), beta-NF (IA), isosafrol (IA2), ethanol (IIE1) and pregnenolone 16 alpha-carbonitrile (IIIA) were injected daily both separately (to achieve maximal monooxygenase induction) in male and female mice. Induction was monitored using specific P450-linked activities. In the optimal schedule for complete induction, the various monooxygenases were greater (2- to 4-fold) than those achieved by the classical schedule. More than a 14-fold increase of total P450 and 3.3-fold increase of NADPH-cytochrome (P450) c-reductase activity, over those uninduced, account for the above increase. For example, there was a marked increase in the deethylation of ethoxyresorufin (37-fold) compared to the uninduced mice that was considerably higher than classical induction (8-fold over uninduced). On the contrary, phase II reactions i.e. epoxide hydrolase, glutathione S-transferase, glutathione S-epoxide transferase and UDP-glucuronosyl transferase, examined to compare the phase I/phase II ratios in the traditional and proposed procedures, were increased to a lesser extent (2-fold over uninduced). No significant sex differences were seen. Five precarcinogens specifically metabolized by each of the induced P450s elicited a higher mutagenicity response in the presence of superinduced fractions with respect to the classical one, when tested on Salmonella typhimurium (cyclophosphamide, benzo[alpha]pyrene, 2-naphthylamine and dimethylnitrosamine) or Saccharomyces cerevisiae D7 strain (diethylstilbestrol). These novel metabolizing biosystems, with an enhanced spectrum of induced P450s and oxidative/post-oxidative reaction rates, are recommended for detecting unknown xenobiotics in genotoxicity studies.
Cost-Effective Integration of Efficient Low-Lift Base Load Cooling Equipment (2008)

The long-term goal of DOE’s Commercial Buildings Integration subprogram is to develop cost-effective technologies and building practices that will enable the design and construction of net Zero Energy Buildings — commercial buildings that produce as much energy as they use on an annual basis — by 2025. To support this long-term goal, DOE further called for — as part of its FY07 Statement of Needs — the development by 2010 of “five cost-effective design technology option sets using highly efficient component technologies, integrated controls, improved construction practices, streamlined commissioning, maintenance and operating procedures that will make new and existing commercial buildings durable, healthy and safe for occupants.” In response, PNNL proposed and DOE funded a scoping study investigation of one such technology option set, low-lift cooling, that offers potentially exemplary HVAC energy performance relative to ASHRAE Standard 90.1-2004. The primary purpose of the scoping study was to estimate the national technical energy savings potential of this TOS.
Grx5 Glutaredoxin Plays a Central Role in Protection against Protein Oxidative Damage in <i>Saccharomyces cerevisiae</i> (1999)

Glutaredoxins are members of a superfamily of thiol disulfide oxidoreductases involved in maintaining the redox state of target proteins. In Saccharomyces cerevisiae, two glutaredoxins (Grx1 and Grx2) containing a cysteine pair at the active site had been characterized as protecting yeast cells against oxidative damage. In this work, another subfamily of yeast glutaredoxins (Grx3, Grx4, and Grx5) that differs from the first in containing a single cysteine residue at the putative active site is described. This trait is also characteristic for a number of glutaredoxins from bacteria to humans, with which the Grx3/4/5 group has extensive homology over two regions. Mutants lacking Grx5 are partially deficient in growth in rich and minimal media and also highly sensitive to oxidative damage caused by menadione and hydrogen peroxide. A significant increase in total protein carbonyl content is constitutively observed in grx5 cells, and a number of specific proteins, including transketolase, appear to be highly oxidized in this mutant. The synthetic lethality of the grx5 and grx2 mutations on one hand and of grx5 with the grx3 grx4 combination on the other points to a complex functional relationship among yeast glutaredoxins, with Grx5 playing a specially important role in protection against oxidative stress both during ordinary growth conditions and after externally induced damage. Grx5-deficient mutants are also sensitive to osmotic stress, which indicates a relationship between the two types of stress in yeast cells.
A 10-GHz SiGe BiCMOS phase-locked-loop frequency synthesizer (2002)

A SiGe BiCMOS phase-locked-loop (ILL) circuit is presented. A maximum operational frequency of 10 GHz and a current consumption of 7.6 mA, i.e., 17 mW, is demonstrated. For a 9-mW low-power version, a maximum frequency of 4.7 GHz is determined. In a GSM direct conversion application, an in-band phase noise of -79 dBc/Hz at 2 kHz and a spurious suppression of -75 dBc at 400 kHz was measured at 3.4 GHz, which corresponds to a PLL phase noise floor of -214 dBc/Hz. For low-power applications, the PLL can be operated at supply voltages as low as 2.2 V and at RF input powers as low as -20 dBm while having a large output voltage range of 0.2 V to (V/sub cc/-0.3 V). This demonstrates the speed and power advantage of the SiGe BiCMOS over Si BiCMOS and CMOS technologies for wireless communications.