gebhart/patrepeval huggingface dataset:
Evolution of the C4 photosynthetic mechanism: are there really three C4 acid decarboxylation types? (2011)

Some of the most productive plants on the planet use a variant of photosynthesis known as the C(4) pathway. This photosynthetic mechanism uses a biochemical pump to concentrate CO(2) to levels up to 10-fold atmospheric in specialized cells of the leaf where Rubisco, the primary enzyme of C(3) photosynthesis, is located. The basic biochemical pathways underlying this process, discovered more than 40 years ago, have been extensively studied and, based on these pathways, C(4) plants have been subdivided into two broad groups according to the species of C(4) acid produced in the mesophyll cells and into three groups according to the enzyme used to decarboxylate C(4) acids in the bundle sheath to release CO(2). Recent molecular, biochemical, and physiological data indicate that these three decarboxylation types may not be rigidly genetically determined, that the possibility of flexibility between the pathways exists and that this may potentially be both developmentally and environmentally controlled. This evidence is synthesized here and the implications for C(4) engineering discussed.
Detection of <i>Brugia</i> Parasite DNA in Human Blood by Real-Time PCR (2006)

Brugian filariasis (caused by the nematodes Brugia malayi and B. timori) is an important cause of disability in Southeast Asia. Improved diagnostic tests are needed for filariasis elimination programs (to identify areas of endemicity and to monitor progress) and for diagnosis of the disease in infected individuals. We have developed and evaluated two real-time PCR assays for detecting Brugia DNA in human blood and compared the results of these assays to those of "gold standard" assays. One assay uses a TaqMan probe (TaqM) to amplifiy a 320-bp "HhaI repeat" DNA sequence. The other assay uses a minor groove binding probe (MGB) and modified nucleotides in primers (Eclipse MGB) to amplify a 120-bp fragment of the HhaI repeat. This assay detects 22 copies of the target sequence, and it is more sensitive than the TaqM assay. Both assays were evaluated with human blood samples from two different areas of endemicity. The MGB assay was as sensitive as membrane filtration and microscopy for the detection of B. malayi infection in 57 blood samples recovered at night from patients in Sulawesi, Indonesia. The MGB assay also detected parasite DNA in 17 of 31 (55%) of microfilaria-negative day blood samples from these subjects. This test was more sensitive than the conventional and the TaqM PCRs (and was almost as sensitive as night blood membrane filtration) for the detection of infection in 52 blood samples recovered at night from individuals in an area of B. timori endemicity on Alor Island, Indonesia, where microfilaria-positive individuals had low densities after mass treatment. Thus, the Eclipse MGB real-time PCR assay is a sensitive means of detecting Brugia parasite DNA in human blood.
Reliability of a bioluminescence ATP assay for detection of bacteria (1992)

The reliability of bioluminescence assays which employ the luciferin-luciferase ATP-dependent reaction to evaluate bacterial counts was studied, both in vitro and on urine specimens. Bioluminescence and cultural results for the most common urinary tract pathogens were analyzed. Furthermore, the influence of the culture medium, of the assaying method, and of the phase of growth on bioluminescence readings was studied. Results show that Proteus, Providencia, and Morganella strains are not correctly detected, neither in vitro nor in urine samples, by the standard assaying method. The analysis of assaying parameters demonstrated that some modifications to the extraction procedure of bacterial ATP could improve the reliability of this technique.
Aromatase Cytochrome P450 and Extragonadal Estrogen Play a Role in Ischemic Neuroprotection (2003)

Female animals are protected from many forms of neurological injury and degeneration relative to their male counterparts, in part attributable to their native estrogens. We hypothesized that estradiol aromatized from precursor androgens via the cytochrome P450 aromatase contributes to ischemic neuroprotection in the female. Female homozygous aromatase knock-out (ArKO) mice and randomly cycling, wild-type (WT) female littermates were treated with reversible middle cerebral artery occlusion (90 min; 22 hr reperfusion). Total and regional ischemic damage was greater in female ArKOs (total, 33.5 +/- 4.8%; cortical, 47.4 +/- 5.7%; striatal, 44.8 +/- 7.8%) compared with WT (total, 14.2 +/- 5%; cortical, 14.2 +/- 4.5%; striatal, 17.5 +/- 8%). Baseline blood pressure and intra-ischemic cortical perfusion were comparable in knock-outs and WT, suggesting that vascular factors do not explain ArKO ischemic sensitivity. Injury was smaller in ovariectomized WT than in ArKO, emphasizing that extragonadal local estradiol plays a critical role in females. Similar increases in cortical and striatal damage were observed in female WT mice chronically treated with the aromatase inhibitor fadrozole compared with vehicle-treated control mice. Restoration of plasma 17beta-estradiol to physiological levels completely reversed the ArKO female's susceptibility to injury. These findings indicate that the biosynthetic enzyme P450 aromatase is key to endogenous neuroprotection in females and suggest that enhancing local, nongonadal estrogen formation could have therapeutic implications is ischemic neuropathology.
Effect of nonidealities on the performance of the 3-phase current source PWM converter (2002)

Usually, IGBTs in a current source converter are controlled by using a high switching frequency. This means that the filtered DC-link current and supply currents should not,include significant low order current harmonics. However, nonidealities like the switch overlap-time, the supply voltage unbalance or low order voltage harmonics in the supply voltages produce low order current harmonics into the DC-link and the supply currents. Especially, a 2nd, 6th and 12th harmonic appear in the DC-link current and a 3rd, 5th and 7th harmonic in the supply phase currents. These low order current harmonics are hardly attenuated by the filters which are tuned for the high order harmonics appearing around the switching frequency or it's multiples. Thus, the low order current harmonics, for example, can be a source of resonance problems in a converter current control loops. The purpose of this paper is to show the amplitude levels of the low order current harmonics resulting from the nonidealities in the current source converter bridge. This will further help to understand the nonideal behavior of the converter.
PAC duo system power estimation at ESL (2010)

In this work, we develop an electronic system-level (ESL) power estimation framework which uses the specified power model interface. Using the proposed power model interface we can easily integrate the various power models in ESL virtual platform. Designers can choose either the coarse-grained or fine-grained power models according to the trade-off between accuracy and computing cost. The experimental results show the proposed method can accurate estimate the system power trend immediately compared with traditional method. We also demonstrated the capability of system power and performance analysis in both hardware-view and software-view by using our approach at ESL. Meanwhile, it can be used for high level architecture exploration directly.
o-Phenylene Silicon Derivatives. Dihydrosilanthrene and Related Compounds<sup>1</sup> (1960)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTo-Phenylene Silicon Derivatives. Dihydrosilanthrene and Related Compounds1Henry Gilman and Ernest A. ZuechCite this: J. Am. Chem. Soc. 1960, 82, 14, 3605–3608Publication Date (Print):July 1, 1960Publication History Published online1 May 2002Published inissue 1 July 1960https://pubs.acs.org/doi/10.1021/ja01499a032https://doi.org/10.1021/ja01499a032research-articleACS PublicationsRequest reuse permissionsArticle Views163Altmetric-Citations11LEARN 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
The C3-activator system: an alternate pathway of complement activation. (1971)

Evidence has accumulated indicating the existence of a second complement activation mechanism which is functionally analogous to C1, C2, and C4. The noncomplement protein C3PA, previously recognized through its ability to form a complex enzyme with a protein from cobra venom, appears to be the precursor of the C4,2 analogue. It is a thermolabile beta-globulin with a molecular weight of 80,000. When serum is treated with naturally occurring plant or bacterial polysaccharides, the C3PA is cleaved into at least two fragments, one having the electrophoretic mobility of a gamma-globulin and a molecular weight of 60,000, and the other being an acidic peptide with a molecular weight of 20,000. The larger fragment has the ability to cleave C3 into C3a and C3b and is therefore called C3 activator. It arises from the action of an as yet unidentified serum enzyme upon the C3PA, which is tentatively called C3PA convertase. In addition to endotoxins, yeast cell walls, inulin, and agar, aggregates of immunoglobulins were found to be activating substances, including human IgA, guinea pig gamma1, and duck antibody. Serum depleted of C3PA had reduced E. coli bactericidal and increased hemolytic activity. The relationship of the C3-activator system to experimental and clinical observations has been discussed.
MagiTact (2010)

In this work, we present a new technique for efficient use of 3D space around a mobile device for interaction with the device. Around Device Interaction (ADI) enables extending interaction space of small mobile and tangible devices beyond their physical boundary. Our proposed method is based on using compass (magnetic field) sensor integrated in mobile devices (e.g. iPhone 3GS, G1 Android). In this method, a properly shaped permanent magnet (e.g. in the shape of a rod, pen or a ring) is used for interaction. The user makes coarse gestures in the 3D space around the device using the magnet. Movement of the magnet affects the magnetic field sensed by the compass sensor integrated in the device. The temporal pattern of the gesture is then used as a basis for sending different interaction commands to the mobile device. Zooming, turning pages, accepting/rejecting calls, clicking items, controlling a music player, and game interaction are some example use cases. The proposed method does not impose changes in hardware specifications of the mobile device, and unlike optical methods is not limited by occlusion problems.
Properties of poly(3-hydroxybutyrate) depolymerase from a marine bacterium, Alcaligenes faecalis AE122 (1995)

Alcaligenes faecalis AE122 that used poly(3-hydroxybutyrate) (PHB) as a sole source of carbon was newly isolated from a coastal seawater sample. The strain required seawater for growth on PHB as well as in a nutrient broth, in which seawater could be replaced by an appropriate concentration of NaCl. PHB depolymerase was purified to homogeneity from the culture supernatant of A. faecalis AE122 by sodium dodecyl sulfate-polyacrylamide gel electrophoresis. The enzyme consisted of a monomer subunit with a molecular mass of 95.5 kDa. The N-terminal amino acid sequence was GAWQNNLAGGFNKV. The dimeric and trimeric esters of 3-hydroxybutyrate were the main hydrolysis products of the purified enzyme. The enzyme was most active at pH 9.0 and 55 degrees C and was inhibited by phenylmethylsulfonyl fluoride. Several cations in seawater greatly enhanced the enzyme activity.
In Vitro Development of Resistance to Ofloxacin and Doxycycline in <b> <i>Bacillus anthracis</i> Sterne </b> (2000)

Anthrax is an infection caused by Bacillus anthracis . It occurs endemically and could also be used for biological warfare with devastating effects ([3][1]). The worldwide increase in the development of drug resistance in bacteria is a major concern. This phenomenon can develop after in vitro
A Heads-Up Display for Diabetic Limb Salvage Surgery (2014)

Although the use of augmented reality has been well described over the past several years, available devices suffer from high cost, an uncomfortable form factor, suboptimal battery life, and lack an app-based developer ecosystem. This article describes the potential use of a novel, consumer-based, wearable device to assist surgeons in real time during limb preservation surgery and clinical consultation. Using routine intraoperative, clinical, and educational case examples, we describe the use of a wearable augmented reality device (Google Glass; Google, Mountain View, CA). The device facilitated hands-free, rapid communication, documentation, and consultation. An eyeglass-mounted screen form factor has the potential to improve communication, safety, and efficiency of intraoperative and clinical care. We believe this represents a natural progression toward union of medical devices with consumer technology.
A descriptive report of the selenium distribution in tissues from pigs with mulberry heart disease (MHD) (2019)

Based on the present work, the current common practice regarding tissue analyses in MHD cases could be refined to include other organs than liver and heart. The evident differences in mean Se concentrations in 9 out of 10 samples from the muscular system, could make such samples relevant for complementary measurements of Se concentrations to help confirm the MHD diagnosis. We find it interesting that although our limited number of sampled pigs are different in terms of genetics, size and feeding regimes, the variation of Se concentrations in a given organ was low between MHD cases. Since this report includes a limited number of MHD cases and controls, our results should be corroborated by a controlled, larger study.
Petroleum Refinery Process Economics (1993)

Designed to present the reader with an organized look at the yield data for refinery processes and how to use this information in performing process economic studies of various types.
Effects of hydrostatic pressure on phase and group modal birefringence in microstructured holey fibers (2004)

We calculated the sensitivity of phase (dB/dp) and group (dG/dp) modal birefringence to hydrostatic pressure versus wavelength in two birefringent holey fibers of different construction, where B is the phase modal birefringence, G is the group modal birefringence, and p is the pressure applied to the fiber. The contributions of the geometrical effects that were related only to deformation of the holey structure and the stress-related contribution to the overall pressure sensitivities were analyzed separately. Our results show that these two factors decrease the phase modal birefringence in both structures, which results in negative signs of dB/dp and dG/dp. Furthermore, we demonstrate that the geometrical effects are much weaker than the stress-related effects and contribute only a few percent to the overall pressure sensitivity.
Novel strategy for a high-yielding mAb-producing CHO strain (overexpression of non-coding RNA enhanced proliferation and improved mAb yield) (2013)

Background Innovation in mAb production is driven by strategies to increase yield. A host cell line constructed to overexpress TAUT (taurine transporter) produced a higher proportion of high-mAb-titer strains [1]. From these we selected a single TAUT/mAb strain that remained viable for as long as 1 month. Its improved viability is attributed to improved metabolic properties. It was also more productive (>100 pg/cell/day) and yielded more mAb (up to 8.1 g/L/31 days) than the parent cell line [2]. These results suggested that this host cell engineering strategy has great potential for the improvement of mAb-producing CHO cells.
Surface modification of poly(dimethylsiloxane) microfluidic devices and its application in simultaneous analysis of uric acid and ascorbic acid in human urine (2008)

A novel and simple method based on layer-by-layer (LBL) technique has been developed for the modification of the channel in PDMS electrophoresis microchip to create a hydrophilic surface with a stable EOF. The functional surface was obtained by sequentially immobilizing chitosan and deoxyribonucleic acid (DNA) onto the microfluidic channel surface using the LBL assembly technique. Compared to the native PDMS microchips, the contact angle of the chitosan-DNA modified PDMS microchips decreased and the EOF increased. Experimental conditions were optimized in detail. The chitosan-DNA modified PDMS microchips exhibited good reproducibility and long-term stability. Separation of uric acid (UA) and ascorbic acid (AA) performed on the modified PDMS microchip generated 43,450 and 46,790 N/m theoretical plates compared with 4048 and 19,847 N/m with the native PDMS microchip. In addition, this method has been successfully applied to real human urine samples, without SPE, with recoveries of 97-105% for UA and AA.
An Entropy-Based Distributed DDoS Detection Mechanism in Software-Defined Networking (2015)

Software-Defined Networking (SDN) and OpenFlow (OF) protocol have brought a promising architecture for the future networks. However, the centralized control and programmable characteristics also bring a lot of security challenges. Distributed denial-of-service (DDoS) attack is still a security threat to SDN. To detect the DDoS attack in SDN, many researches collect the flow tables from the switch and do the anomaly detection in the controller. But in the large scale network, the collecting process burdens the communication overload between the switches and the controller. Sampling technology may relieve this overload, but it brings a new tradeoff between sampling rate and detection accuracy. In this paper, we first extend a copy of the packet number counter of the flow entry in the OpenFlow table. Based on the flow-based nature of SDN, we design a flow statistics process in the switch. Then, we propose an entropy-based lightweight DDoS flooding attack detection model running in the OF edge switch. This achieves a distributed anomaly detection in SDN and reduces the flow collection overload to the controller. We also give the detailed algorithm which has a small calculation overload and can be easily implemented in SDN software or programmable switch, such as Open vSwitch and NetFPGA. The experimental results show that our detection mechanism can detect the attack quickly and achieve a high detection accuracy with a low false positive rate.
Steric Hindrance Mutagenesis in the Conserved Extracellular Vestibule Impedes Allosteric Binding of Antidepressants to the Serotonin Transporter (2012)

The serotonin transporter (SERT) controls synaptic serotonin levels and is the primary target for antidepressants, including selective serotonin reuptake inhibitors (e.g. (S)-citalopram) and tricyclic antidepressants (e.g. clomipramine). In addition to a high affinity binding site, SERT possesses a low affinity allosteric site for antidepressants. Binding to the allosteric site impedes dissociation of antidepressants from the high affinity site, which may enhance antidepressant efficacy. Here we employ an induced fit docking/molecular dynamics protocol to identify the residues that may be involved in the allosteric binding in the extracellular vestibule located above the central substrate binding (S1) site. Indeed, mutagenesis of selected residues in the vestibule reduces the allosteric potency of (S)-citalopram and clomipramine. The identified site is further supported by the inhibitory effects of Zn(2+) binding in an engineered site and the covalent attachment of benzocaine-methanethiosulfonate to a cysteine introduced in the extracellular vestibule. The data provide a mechanistic explanation for the allosteric action of antidepressants at SERT and suggest that the role of the vestibule is evolutionarily conserved among neurotransmitter:sodium symporter proteins as a binding pocket for small molecule ligands.
Interactions of Ni Nanoparticles with Reducible CeO<sub>2</sub>(111) Thin Films (2012)

The interaction between Ni and ceria was investigated under ultrahigh vacuum conditions using model Ni/ceria systems consisting of Ni nanoparticles vapor-deposited on well-ordered CeOx(111) (1.5 < x < 2) thin films grown on Ru(0001). As indicated by X-ray photoelectron spectroscopy studies, metallic Ni is the only species present on the reduced ceria. Ni0 is the predominate species observed upon deposition of a submonolayer of Ni on CeO2 at 300 K. However, a small amount of Ni is oxidized to Ni2+. A decreased ratio of Ni2+ to Ni0 was observed with further increase of Ni coverage. Oxidation of Ni on CeO2 can be facilitated by annealing as well as by depositing Ni at 500 K. Scanning tunneling microscopy studies show that Ni forms two-dimensional particles on ceria at room temperature, which suggests a strong Ni–ceria interaction. Upon deposition at 500 K, metallic Ni particles as well as NiO particles can be formed on the reduced and oxidized ceria, respectively. NiO particles exhibit a flatter particle shape than that of Ni particles. Our results can be explained by thermodynamics as well as by previous computational studies.
Biomimetic design of chelating interfaces (2014)

ABSTRACT Siderophores are naturally occurring small molecules with metal binding constants greater than many synthetic chelators. Herein, we report a two‐step process to graft a siderophore‐mimetic metal chelating polymer from a polypropylene (PP) surface. Poly(methyl acrylate) was first grafted from the PP surface by photoinitiated graft polymerization, followed by the conversion into poly(hydroxamic acid) (PHA) to obtain PP‐ g ‐PHA films. ATR/FTIR, contact angle, SEM, and AFM were performed to characterize surface properties of films. Iron binding kinetics and the influence of pH (3.0–5.0) on the chelating ability of films were determined. PP‐ g ‐PHA exhibited significant iron chelating activity (∼80 nmol/cm 2 ) with an equilibration time of 24 h. The materials retained 50% chelating ability at pH 3.0 compared with pH 5.0, almost double the retention of previously reported polycarboxylate chelating interfaces. By using siderophore‐mimetic surface chemistry, such effective metal chelating interfaces can extend the applications of metal chelating polymers in environmental remediation, water purification, and active packaging areas. © 2014 Wiley Periodicals, Inc. J. Appl. Polym. Sci. 2015 , 132 , 41231.