gebhart/patrepeval huggingface dataset:
The Latest Techniques in Genetic Engineering (1982)

Journal Article The Latest Techniques in Genetic Engineering Get access Genetic Engineering, Principles and Methods. Volume 3, edited by Setlow Jane K. Hollaender Alexander. Plenum Press, New York, 1981, 346 p., illus., $39.50 (79-644807). Luther S. Williams Luther S. Williams Department of Biology, Washington University, St. Louis, MO 63130 Search for other works by this author on: Oxford Academic Google Scholar BioScience, Volume 32, Issue 7, July/August 1982, Page 625, https://doi.org/10.2307/1308618 Published: 01 August 1982
Effect of fully automated closed‐loop insulin delivery using faster aspart versus standard aspart on gluco‐regulatory hormones in type 2 diabetes (2020)

We retrospectively assessed gluco-regulatory hormones over 10 h (including two meals) of fully automated closed-loop insulin delivery using faster (FA) versus standard insulin aspart (IAsp) in adults with type 2 diabetes [n = 15, age 59 ± 10 years, body mass index 34.5 ± 9.1 kg/m<sup>2</sup> , glycated haemoglobin 7.7 ± 1.2% (60 ± 13 mmol/mol)]. Plasma concentration of human insulin, IAsp, C-peptide, glucagon, glucagon-like peptide 1, glucose-dependent insulinotropic peptide and peptide tyrosine tyrosine were measured every 15-30 min. Endogenous insulin secretion was calculated using C-peptide deconvolution and exposures to hormones were compared using their mean plasma concentrations. Ten-hour exposure of IAsp was higher with FA versus IAsp (P = .037) in line with the 10% higher insulin requirements to achieve similar glucose control. No significant difference was found for total insulin exposure and endogenous insulin secretion. Similarly, other gluco-regulatory hormones did not significantly differ. In conclusion, the faster pharmacokinetic profile and slightly higher aspart exposure of FA versus IAsp remained without significant effects on endogenous insulin secretion or other gluco-regulatory hormones. Further studies are warranted to explore the metabolic and endocrine effects of novel insulins with accelerated pharmacokinetic properties.
Design of Wide Angle and Large Aperture Optical System with Inner Focus for Compact System Camera Applications (2019)

Conventionally, a bright, very wide-angle optical system is designed as a floating type optical system that moves two or more lens groups composed of multiple lens in order to focus accurately. These have been widely used as phase detection auto focus (AF) methods within conventional digital single-lens reflex (DSLR) cameras. However, a phase detection AF optical system cannot be used when recording motion pictures. In contrast, a compact system camera (CSC) performs AF by the contrast method, where a stepper motor is used as the driving source for moving the optical lens. Nonetheless, to ensure that the focusing lens is lighter, these stepper motors should not have high torque and AF must be possible by moving only one lens. Yet, when focusing is performed with only one lens, aberration change due to focusing lens movement is magnified. Therefore, a very wide-angle optical system comprised of a half-angle of view more than 40 degrees and F of 1/4 has not been developed. Here, a very wide-angle optical system was designed with high resolving power that enables high speed AF, even in contrast mode, by moving only one lens while minimizing aberration change.
Two P domain potassium channels in GtoPdb v.2021.2 (2021)

The 4TM family of K channels mediate many of the background potassium currents observed in native cells. They are open across the physiological voltage-range and are regulated by a wide array of neurotransmitters and biochemical mediators. The pore-forming α-subunit contains two pore loop (P) domains and two subunits assemble to form one ion conduction pathway lined by four P domains. It is important to note that single channels do not have two pores but that each subunit has two P domains in its primary sequence; hence the name two P domain, or K2P channels (and not two-pore channels). Some of the K2P subunits can form heterodimers across subfamilies (e.g. K2P3.1 with K2P9.1). The nomenclature of 4TM K channels in the literature is still a mixture of IUPHAR and common names. The suggested division into subfamilies, described in the More detailed introduction, is based on similarities in both structural and functional properties within subfamilies and this explains the "common abbreviation" nomenclature in the tables below.
Construction of cDNA Libraries in Vaccinia Virus (2004)

Poxvirus expression vectors have gained widespread use for expression of foreign proteins and as delivery vehicles for vaccine antigens. We have developed a novel method using the poxvirus as a library vector for functional selection of specific cDNA. Poxviruses have several unique and useful properties as a library vector. Most importantly, because poxviruses are packaged into fully infectious particles in the cell cytoplasm, specific recombinants can be readily recovered even from a very small number of selected cells. Moreover, in contrast to libraries constructed in retrovirus or plasmid-based vectors, recombinant vaccinia virus can be efficiently recovered even from cells that have been induced to undergo apoptosis or cessation of cell growth. In the past, the major obstacle in this application to poxviruses has been the low frequency with which recombinants can be generated. The most commonly used method to construct recombinant poxvirus is homologous recombination. The frequency of recombinants derived in this manner is of the order of 0.1%, sufficient to recover a recombinant of a purified DNA clone in a transfer plasmid, but far too low to permit construction of a representative cDNA library. We have developed a method that generates nearly 100% recombinant vaccinia viruses at good titer. We have termed this method trimolecular recombination. cDNA libraries of as many as 107 or more independent viral recombinants can be constructed by trimolecular recombination. For the first time, large, diverse, and representative cDNA libraries can be screened in a vaccinia virus-based expression vector.
YY1 Is Regulated by O-LinkedN-Acetylglucosaminylation (O-GlcNAcylation) (2003)

YY1 is a zinc finger DNA-binding transcription factor that influences expression of a wide variety of cellular and viral genes. YY1 is essential for the development of mammalian embryos. It regulates the expression of genes with important functions in DNA replication, protein synthesis, and cellular response to external stimuli during cell growth and differentiation. How YY1 accomplishes such a variety of functions is unknown. Here, we show that a subset of the nuclear YY1 appears to be O-GlcNAcylated regardless of the differentiation status of the cells. We found that glucose strongly stimulates O-linked N-acetylglucosaminylation (O-GlcNAcylation) on YY1. Glycosylated YY1 no longer binds the retinoblastoma protein (Rb). Upon dissociation from Rb, the glycosylated YY1 is free to bind DNA. The ability of the O-glycosylation on YY1 to disrupt the complex with Rb leads us to propose that O-glycosylation might have a profound effect on cell cycle transitions that regulate the YY1-Rb heterodimerization and promote the activity of YY1. Our observations provide strong evidence that YY1-regulated transcription is very likely connected to the pathway of glucose metabolism that culminates in the O-GlcNAcylation on YY1, changing its function in transcription.
Evaluation of the pharmacokinetics of posaconazole and rifabutin following co-administration to healthy men (2007)

Based on the reduced exposure to posaconazole observed in the limited number of subjects in this study and the increased risk for adverse events associated with elevated rifabutin concentrations, concomitant use of rifabutin and posaconazole should be avoided unless the benefit outweighs the risk.
Supplementary Table 3 from Biased Expression of the FOXP3Δ3 Isoform in Aggressive Bladder Cancer Mediates Differentiation and Cisplatin Chemotherapy Resistance (2023)

&lt;p&gt;Table 3 lists is an Excel file listing genes shared between p-53-like gene and subtype II, SW780Foxop3del3 and p53-like and HT1376Foxp3del3 and p53-like.&lt;/p&gt;
Oxazolidine Formation, or Loss of Acid, from Attempted Fluorination of Amide Side‐Chain in 2‐Nitroimidazoles (2018)

Reaction of Etanidazole (a 2‐nitroimidazole derivative with an amide side‐chain containing a hydroxyethyl group) with triflic anhydride gives, depending on conditions, a trifluoromethyl(sulfonyl)oxazolidine via a cyclization reaction, or a fluorine‐free formate derivative; reaction with tosyl chloride gives only a chloroethyl derivative. An attempt to replace a Br‐atom in a related propyl‐containing amide side‐chain by a F‐atom forms instead a propylene derivative via loss of HBr. The studies stem from interest in use of 2‐nitroimidazoles with fluorine‐containing amide side‐chains as hypoxia markers.
Control of Boost type Converter at Discontinuous Conduction Mode by Controlling the Product of Inductor Voltage-Second (2006)

Battery-operated system such as cell-phone, digital camera becomes more and more popular. In this application, a boost-type converter is usually required to convert low battery voltage to high voltage application. In this paper, a variable frequency control of boost converter is discussed. The prototype circuit is built to prove the concept. The extension of this approach in power factor-correction application is discussed
A mitotic CDK5-PP4 phospho-signaling cascade primes 53BP1 for DNA repair in G1 (2019)

Mitotic cells attenuate the DNA damage response (DDR) by phosphorylating 53BP1, a critical DDR mediator, to prevent its localization to damaged chromatin. Timely dephosphorylation of 53BP1 is critical for genome integrity, as premature recruitment of 53BP1 to DNA lesions impairs mitotic fidelity. Protein phosphatase 4 (PP4) dephosphorylates 53BP1 in late mitosis to allow its recruitment to DNA lesions in G1. How cells appropriately dephosphorylate 53BP1, thereby restoring DDR, is unclear. Here, we elucidate the underlying mechanism of kinetic control of 53BP1 dephosphorylation in mitosis. We demonstrate that CDK5, a kinase primarily functional in post-mitotic neurons, is active in late mitotic phases in non-neuronal cells and directly phosphorylates PP4R3β, the PP4 regulatory subunit that recognizes 53BP1. Specific inhibition of CDK5 in mitosis abrogates PP4R3β phosphorylation and abolishes its recognition and dephosphorylation of 53BP1, ultimately preventing the localization of 53BP1 to damaged chromatin. Our results establish CDK5 as a regulator of 53BP1 recruitment.
Regulation of T-Cell Chemotaxis by Programmed Death-Ligand 1 (PD-L1) in Dry Eye–Associated Corneal Inflammation (2010)

PURPOSE. Given that dry eye disease (DED) is associated with T cell-mediated inflammation of the ocular surface and that PD-L1 is an important negative or inhibitory regulator of immune responses constitutively expressed at high levels by corneal epithelial cells, the authors studied the expression and function of PD-L1 in DED. METHODS. Dry eye was induced in untreated wild-type mice, PD-L1(-/-) mice, and wild-type mice treated with anti-PD-L1 antibody by exposing these mice to a desiccating environment in the controlled environment chamber modified with subcutaneous administration of scopolamine. Real-time PCR was used to quantify the expression of chemokine gene transcript levels of multiple CC and CXC chemokine ligands and receptors. Epifluorescence microscopy was used to evaluate corneal infiltration of CD3(+) T cells after immunohistochemical staining. RESULTS. The increased expression of specific chemokine ligands and receptors in PD-L1(-/-) corneas of normal mice is associated with significant increases in T-cell homing into these corneas. Similar, and more enhanced, increases in T-cell infiltration were observed in PD-L1(-/-) DED mice or DED mice treated with anti-PD-L1 antibody compared with controls. In addition, the authors found significantly decreased expression of PD-L1 by corneal epithelial cells in DED and significantly increased corneal fluorescein staining score with PD-L1 functional blockade using anti-PD-L1 antibody. CONCLUSIONS. Downregulation of corneal epithelial PD-L1 amplifies dry eye-associated corneal inflammation and epitheliopathy by increasing the expression of chemokine ligands and receptors that promote T-cell homing to the ocular surface.
Biochemical and Structural Characterisation of Dehalogenases from Marine Bacteria (2011)

An L-haloacid dehalohenase from the psychrophilic marine bacteria Psychromonas ingrahamii has been cloned, over-expressed in a bacterial expression system and biochemically characterised. The enzyme is stable at temperatures of up to 60ºC for 90 min and shows highest activity towards substrates with short carbon chains (≤C3). The enzyme is stable in up to 30% ethanol, methanol and DMSO when incubated for 1 h. The Km for the enzyme is 1.36 mM. The genome of AQP5750 from the Aquapharm Biodiscovery Ltd Microbial library was sequenced. An L-haloacid dehalohenase and a haloalkane dehalogenase gene were identified within the genome. The AQP5750 L-haloacid dehalohenase has been cloned, over-expressed in a bacterial expression system, biochemically characterised, crystallized and the native and crystal complex structure with chloropropionic acid (MCP) determined. The L-haloacid dehalohenase from AQP5750 shows highest activity at 55ºC towards brominated substrates with short carbon chains (≤C3). The enzyme shows increased activity of 150% in 40% DMSO and 123% in 30% methanol. The L-haloacid dehalohenase crystal complex structure with covalently bound MCP confirmed Asp 18 as the main catalytic residue. Residues His 183, Asp 186 and Glu 21 in the active site are proposed to be involved in activation of the catalytic water which attacks the ester intermediate in the second part of the SN2 dehalogenase mechanism. The AQP5750 haloalkane dehalogenase has been cloned, over-expressed in a bacterial expression system, crystallized and the native and complex structure with 1-hexanol has been determined. Substrate specificity experiments showed that the haloalkane dehalogenase from AQP5750 does not show high activity towards substrates used by other haloalkane dehalogenases with high amino acid sequence identity. The large active site cavity and the presence of Ser 176 and Arg 136 in the hydrophobic binding pocket may alter the binding of substrates tested which could account for the low activity observed.
Micro/nanoscale modeling of anisotropic mechanical properties of polymer/layered-silicate nanocomposites (2002)

Thesis (S.M.)--Massachusetts Institute of Technology, Dept. of Mechanical Engineering, 2002.
Efficient Architectures for Retrieving Mixed Data with Rest Architecture Style and HTML5 Support (2013)

This Thesis is brought to you for free and open access by TopSCHOLAR®. It has been accepted for inclusion in Masters Theses &amp;amp; Specialist Projects by an authorized administrator of TopSCHOLAR®. For more information, please contact connie.foster@wku.edu.
The Genome of the Western Clawed Frog Xenopus tropicalis (2010)

Frog Genome The African clawed frog Xenopus tropicalis is the first amphibian to have its genome sequenced. Hellsten et al. (p. 633 , see the cover) present an analysis of a draft assembly of the genome. The genome of the frog, which is an important model system for developmental biology, encodes over 20,000 protein-coding genes, of which more than 1700 genes have identified human disease associations. Detailed comparison of the content of protein-coding genes with other tetrapods—human and chicken—reveals extensive shared synteny, occasionally spanning entire chromosomes.
Hydroacylation. Synthesis of ketones from olefins using metal hydride reagents (1974)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTHydroacylation. Synthesis of ketones from olefins using metal hydride reagentsJeffrey Schwartz and John B. CannonCite this: J. Am. Chem. Soc. 1974, 96, 14, 4721–4723Publication Date (Print):July 1, 1974Publication History Published online1 May 2002Published inissue 1 July 1974https://doi.org/10.1021/ja00821a085Request reuse permissionsArticle Views338Altmetric-Citations40LEARN 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 InReddit PDF (356 KB) Get e-Alertsclose Get e-Alerts
Phage-Encoded LuxR-Type Receptors Responsive to Host-Produced Bacterial Quorum-Sensing Autoinducers (2019)

Abstract Quorum sensing (QS) is a process of cell-to-cell communication that bacteria use to orchestrate collective behaviors. QS relies on the cell-density-dependent production, accumulation, and receptor-mediated detection of extracellular signaling molecules called autoinducers (AIs). Gram-negative bacteria commonly use N -acyl homoserine lactones (AHLs) as their AIs and they are detected by LuxR-type receptors. Often, LuxR-type receptors are insoluble when not bound to a cognate AI. In this report, we show that LuxR-type receptors are encoded on phage genomes and, in the cases we tested, the phage LuxR-type receptors bind to and are solubilized specifically by the AHL AI produced by the host bacterium. We do not yet know the viral activities that are controlled by these phage QS receptors, however, our observations, coupled with recent reports, suggest that their occurrence is more widespread than previously appreciated. Using receptor-mediated detection of QS AIs could enable phages to garner information concerning the population density status of their bacterial hosts. We speculate that such information can be exploited by phages to optimize the timing of execution of particular steps in viral infection. Importance Bacteria communicate with chemical signal molecules to regulate group behaviors in a process called quorum sensing (QS). In this report, we find that genes encoding receptors for Gram-negative bacterial QS communication molecules are present on genomes of viruses that infect these bacteria. These viruses are called phages. We show that two phage-encoded receptors, like their bacterial counterparts, bind to the communication molecule produced by the host bacterium, suggesting that phages can “listen in” on their bacterial hosts. Interfering with bacterial QS and using phages to kill pathogenic bacteria represent attractive possibilities for development of new antimicrobials to combat pathogens that are resistant to traditional antibiotics. Our findings of interactions between phages and QS bacteria need consideration as new antimicrobial therapies are developed.
Comparison of atherosclerotic inflammation and calcification in subjects with end stage renal disease (ESRD) on hemodialysis to normal controls utilizing 18F-FDG PET/CT. (2019)

SUV measurements representing the atherosclerotic inflammatory changes and macroscopic atherosclerotic calcifications appear to be accelerated in subjects with ESRD on hemodialysis compared to normal controls. Fluorine-18 FDG PET/CT is a valuable diagnostic tool for verifying and quantifying accelerated atherosclerosis secondary to ESRD.
Hardware architecture for real-time EEG-based functional brain connectivity parameter extraction (2020)

<i>Objective</i>. Design a novel architecture for real-time quantitative characterization of functional brain connectivity (FC) networks derived from wearable electroencephalogram (EEG).<i>Approach</i>. We performed an algorithm to architecture mapping for the calculation of phase lag index to form the functional connectivity networks and the extraction of a set of graph-theoretic parameters to quantitatively characterize these networks. This mapping was optimized using approximations in the mathematical definitions of the algorithms which reduce its computational complexity and produce a more hardware amenable implementation.<i>Main results</i>. The architecture was developed for a 19-channel EEG system. The system can calculate all the functional connectivity parameters in a total time of 131 <i>µ</i>s, utilizes 71% of the total logic resources in the FPGA, and shows 51.84 mW dynamic power consumption at 22.16 MHz operation frequency when implemented in a Stratix IV EP4SGX230K FPGA. Our analysis also showed that the system occupies an area equivalent to approximately 937 K 2-input NAND gates, with an estimated power consumption of 39.3 mW at 0.9 V supply using a 90 nm CMOS application specific integrated circuit technology.<i>Significance</i>. The proposed architecture can calculate the FC and extract the graph-theoretic parameters in real-time with low power consumption. This characteristic makes the architecture ideal for applications such as a wearable closed-loop neurofeedback systems, where constant monitoring of the brain activity and fast processing of EEG is necessary to control the appropriate feedback.
An RLL-Constrained LDPC Coded Recording System Using Deliberate Flipping and Flipped-Bit Detection (2012)

In this paper, a low-density parity-check (LDPC) coded recording system is investigated, for which the run-length-limited (RLL) constraint is satisfied by deliberate flipping at the write side and by estimating the flipped bits at the read side. Two approaches are proposed for enhancing the error performance of such a system. The first approach is to alleviate the negative effect of incorrect estimation of the flipped bits by adjusting the soft information. The second approach is to increase the likelihood of the correct detection of flipped bits by designing a flipped-bit detection algorithm that utilizes both the RLL constraint and the parity-check constraint of the LDPC code. These two approaches can be combined to obtain significant improvement in performance over previously proposed methods.