gebhart/patrepeval huggingface dataset:
Structural features of the large subunit rRNA expressed in Plasmodium falciparum sporozoites that distinguish it from the asexually expressed subunit rRNA. (1996)

The developmentally regulated transcription of at least two distinct sets of nuclear-encoded ribosomal RNAs is detected in Plasmodium species. The identification of functional differences between the two sets of rRNAs is of interest. To facilitate the search for such differences, we have identified the 5.8S and 28S rRNAs from Plasmodium falciparum that are expressed in the sporozoite stage (S gene) of the parasites' life cycle in the mosquito host and compare them to transcripts expressed in the red blood cells (A gene) of the vertebrate host. This completes the first set of A- and S-type nuclear-encoded rRNA genes for a Plasmodium species. Analysis of the predicted secondary structures of the two units reveals the majority of differences between the A- and S-type genes occur in regions previously known to be variable. However, the predicted secondary structure of both 28S rRNAs indicates 11 positions within conserved areas that are not typical of eucaryotic rRNAs. Although the A-type gene resembles almost all eucaryotes, being atypical in only 4 of the 11 positions, the S gene is variant in 8 of the 11 positions. In three of these positions, the S-type gene resembles the consensus nucleotides for the 23S rRNA from Eubacteria and/or Archaea. A few differences occur in regions associated with ribosome function, in particular the GTPase site where the S-type differs in a base pair and loop from all known sequences. Further, the identification of compensatory changes at conserved points of interactions between the 5.8S-28S rRNAs indicates that transcripts from A- and S-units should not be interchangeable.
Micro-Coaxial Fed 18 to 110 GHz Planar Log-Periodic Antennas With RF Transitions (2014)

Design, fabrication, measurement setup, and performance of a surface micromachined 18 to 110 GHz planar log-periodic antenna are discussed. The antenna design features a monolithically integrated five-step rectangular-coaxial line impedance transformer used to match the antenna's nominal impedance of 160 Ω to the 50 Ω system impedance. Three measurement transitions are developed to characterize the impedance and far-field performance of the antenna over the full operational bandwidth. Measured data are compared to simulations to assess technology maturation and the performance of the fabricated devices. Realized gain above 3 dBi with stable co-polarized patterns and VSWR under 2:1 are measured for the majority of the operational bandwidth.
Evidence for a strong sulfur-aromatic interaction derived from crystallographic data (2000)

We have uncovered new evidence for a significant interaction between divalent sulfur atoms and aromatic rings. Our study involves a statistical analysis of interatomic distances and other geometric descriptors derived from entries in the Cambridge Crystallographic Database (F. H. Allen and O. Kennard, Chem. Design Auto. News, 1993, Vol. 8, pp. 1 and 31-37). A set of descriptors was defined sufficient in number and type so as to elucidate completely the preferred geometry of interaction between six-membered aromatic carbon rings and divalent sulfurs for all crystal structures of nonmetal-bearing organic compounds present in the database. In order to test statistical significance, analogous probability distributions for the interaction of the moiety X-CH(2)-X with aromatic rings were computed, and taken a priori to correspond to the null hypothesis of no significant interaction. Tests of significance were carried our pairwise between probability distributions of sulfur-aromatic interaction descriptors and their CH(2)-aromatic analogues using the Smirnov-Kolmogorov nonparametric test (W. W. Daniel, Applied Nonparametric Statistics, Houghton-Mifflin: Boston, New York, 1978, pp. 276-286), and in all cases significance at the 99% confidence level or better was observed. Local maxima of the probability distributions were used to define a preferred geometry of interaction between the divalent sulfur moiety and the aromatic ring. Molecular mechanics studies were performed in an effort to better understand the physical basis of the interaction. This study confirms observations based on statistics of interaction of amino acids in protein crystal structures (R. S. Morgan, C. E. Tatsch, R. H. Gushard, J. M. McAdon, and P. K. Warme, International Journal of Peptide Protein Research, 1978, Vol. 11, pp. 209-217; R. S. Morgan and J. M. McAdon, International Journal of Peptide Protein Research, 1980, Vol. 15, pp. 177-180; K. S. C. Reid, P. F. Lindley, and J. M. Thornton, FEBS Letters, 1985, Vol. 190, pp. 209-213), as well as studies involving molecular mechanics (G. Nemethy and H. A. Scheraga, Biochemistry and Biophysics Research Communications, 1981, Vol. 98, pp. 482-487) and quantum chemical calculations (B. V. Cheney, M. W. Schulz, and J. Cheney, Biochimica Biophysica Acta, 1989, Vol. 996, pp.116-124; J. Pranata, Bioorganic Chemistry, 1997, Vol. 25, pp. 213-219)-all of which point to the possible importance of the sulfur-aromatic interaction. However, the preferred geometry of the interaction, as determined from our analysis of the small-molecule crystal data, differs significantly from that found by other approaches.
MCLUST Version 3 for R: Normal Mixture Modeling and Model-Based Clustering † (2007)

MCLUST is a contributed R package for normal mixture modeling and model-based clustering. It provides functions for parameter estimation via the EM algorithm for normal mixture models with a variety of covariance structures, and functions for simulation from these models. Also included are functions that combine model-based hierarchical clustering, EM for mixture estimation and the Bayesian Information Criterion (BIC) in comprehensive strategies for clustering, density estimation and discriminant analysis. There is additional functionality for displaying and visualizing the models along with clustering and classification results. A number of features of the software have been changed in this version, and the functionality has been expanded to include regularization for normal mixture models via a Bayesian prior. MCLUST is licensed by the University of Washington and distributed through
Optical cross connects for optical networking (2002)

As the transmission line rate supported by optical fibers increased from 45 Mb/s to 2.5 Gb/s during the 1980s, interexchange carrier networks introduced various digital cross connects to provision, groom, and restore DS0 (64-kb/s), DS1 (1.5-Mb/s), and DS3 (45-Mb/s) traffic. With the recent release of its WaveStar™ Optical Line System (OLS) 400G, Lucent Technologies has increased the fiber transmission capacity more than one-hundred-fold using dense wavelength division multiplexed (DWDM) 2.5- and 10-Gb/s signals. To meet the challenge of managing the bandwidth within emerging “terabit offices” enabled by DWDM, Lucent and other vendors are aggressively pursuing research and development of optical cross connects capable of directing traffic on a per-wavelength basis. In this paper we explore the role of an optical cross connect (OXC) in evolving wavelength division multiplexed (WDM) optical networks. We also examine various OXC architectures and address the technological challenges and practical tradeoffs that affect their port count (size), functionality, and cost.
Synthetic Hydrogels for Biomedical Applications (1976)

It is the intention of this paper to review the literature concerning the preparation, properties, and biomedical applications of synthetic hydrogel materials. As the literature on this subject is now voluminous and rapidly expanding (e.g. this symposium) it is difficult to produce a completely comprehensive review of the subject. However, a large number of articles will be examined which should give a useful overview of research interests and directions in this growing, multidisciplinary field. This review will be organized as follows: The introduction will discuss general aspects of synthetic hydrogels and point out similarities between the various distinctly different chemical structures which fit into this category. A short section is included within the introduction on problems related to the measurement and description of the biocompatibility of materials. The following six classes of hydrogel materials will then each be treated individually: poly(hydroxyalkyl methacrylates); poly(acrylamide), poly(methacrylamide) and derivatives; poly(N-vinyl-2-pyrrolidone); anionic and cationic
Influence of Temperature during Transportation on Cell-Free DNA Analysis (2012)

BCT tubes are suitable for shipping whole blood prior to processing with respect to cf-DNA levels. However, care should be taken to ensure that samples are not exposed to extreme temperatures during shipment. This finding will benefit the development and clinical application of noninvasive methods of fetal diagnosis that utilize cf-DNA.
Metal ion binding by amino acids. Preparation and crystal structures of magnesium, strontium, and barium L‐glutamate hydrates (1989)

Abstract Crystalline magnesium, strontium, and barium L ‐glutamate complexes containing the dianion L ‐Glu 2− have been prepared as the tetrahydrate (Mg) and hexahydrates (Sr, Ba), respectively. Their aqueous solutions have pH values of 10.45, 11.05, and 10.93, respectively. The solid state structures of the Mg and Sr complexes have been determined by single crystal X‐ray methods, and the structure of the Ba analogue inferred through its isomorphism with the Sr analogue. The crystals are orthorhombic, space group P 2 1 2 1 2 1 . The magnesium atoms were found to be hexacoordinated with the L ‐glutamate functioning as a chelating N,O α ‐donor. Four water molecules complete the first coordination sphere. The γ‐carboxylate group is only engaged in hydrogen bonding. Strontium and barium are nine‐coordinated. The α‐carboxylate group of the L ‐Glu 2− ligand is O , O ‐chelating to one metal and forming oxygen bridges to two further metal atoms. The γ‐carboxylate group is also chelating a neighbouring strontium atom, but the nitrogen function is not engaged in metal coordination. By MOM bridging double strings of metal‐oxygen chains are formed, which are interlinked by the amino acids to give a layered structure. Three water molecules are also part of the first coordination sphere of each metal, while three others are interlayer hydrogen‐bonded components. The amino groups are also involved in this hydrogen bonding.
Cisplatin Induces a Mitochondrial-ROS Response That Contributes to Cytotoxicity Depending on Mitochondrial Redox Status and Bioenergetic Functions (2013)

Cisplatin is one of the most effective and widely used anticancer agents for the treatment of several types of tumors. The cytotoxic effect of cisplatin is thought to be mediated primarily by the generation of nuclear DNA adducts, which, if not repaired, cause cell death as a consequence of DNA replication and transcription blockage. However, the ability of cisplatin to induce nuclear DNA (nDNA) damage per se is not sufficient to explain its high degree of effectiveness nor the toxic effects exerted on normal, post-mitotic tissues. Oxidative damage has been observed in vivo following exposure to cisplatin in several tissues, suggesting a role for oxidative stress in the pathogenesis of cisplatin-induced dose-limiting toxicities. However, the mechanism of cisplatin-induced generation of ROS and their contribution to cisplatin cytotoxicity in normal and cancer cells is still poorly understood. By employing a panel of normal and cancer cell lines and the budding yeast Saccharomyces cerevisiae as model system, we show that exposure to cisplatin induces a mitochondrial-dependent ROS response that significantly enhances the cytotoxic effect caused by nDNA damage. ROS generation is independent of the amount of cisplatin-induced nDNA damage and occurs in mitochondria as a consequence of protein synthesis impairment. The contribution of cisplatin-induced mitochondrial dysfunction in determining its cytotoxic effect varies among cells and depends on mitochondrial redox status, mitochondrial DNA integrity and bioenergetic function. Thus, by manipulating these cellular parameters, we were able to enhance cisplatin cytotoxicity in cancer cells. This study provides a new mechanistic insight into cisplatin-induced cell killing and may lead to the design of novel therapeutic strategies to improve anticancer drug efficacy.
A wavelength routing approach to optical communications networks (2003)

A class of wavelength-routing optical networks is described on the basis of the interconnection of wavelength multiplexed channels. Unlike previously described optical network structures, these networks allow the reuse of wavelengths in different transmission sections and this leads to fewer wavelengths being needed. A choice of structures using a common set of components leads to the opportunity to design a network according to the geographical distribution of the switching nodes. The structures provide for a set of point-to-point interconnections and, with modest numbers of wavelengths, full interconnection between the optoelectronic nodes is possible at the optical level. In bypassing intermediate electronic stages the networks appear to offer good reliability characteristics. Providing the components in an initial network are designed to utilize bandwidth efficiently, the networks could be upgraded to incorporate more channels, optical switching, and other forms of optical processing at the optical nodes.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Suppression of Transgene Silencing by Matrix Attachment Regions in Maize (2002)

Matrix attachment regions (MARs) are DNA sequences that bind an internal nuclear network of nonhistone proteins called the nuclear matrix. Thus, they may define discrete gene-containing chromatin loops in vivo. We have studied the effects of flanking transgenes with MARs on transgene expression levels in maize callus and in transformed maize plants. Three MAR elements, two from maize (Adh1 5' MAR and Mha1 5' MAR) and one from yeast (ARS1), had very different effects on transgene expression that bore no relation to their affinity for the nuclear matrix in vitro. In callus, two of the MAR elements (Adh1 5' MAR and ARS1) reduced transgene silencing but had no effect on the variability of expression. In transgenic plants, Adh1 5' MAR had the effect of localizing beta-glucuronidase expression to lateral root initiation sites. A possible model accounting for the function of Adh1 5' MAR is discussed.
Self-Powered Electrostatic Filter with Enhanced Photocatalytic Degradation of Formaldehyde Based on Built-in Triboelectric Nanogenerators (2017)

Recently, atmospheric pollution caused by particulate matter or volatile organic compounds (VOCs) has become a serious issue to threaten human health. Consequently, it is highly desirable to develop an efficient purifying technique with simple structure and low cost. In this study, by combining a triboelectric nanogenerator (TENG) and a photocatalysis technique, we demonstrated a concept of a self-powered filtering method for removing pollutants from indoor atmosphere. The photocatalyst P25 or Pt/P25 was embedded on the surface of polymer-coated stainless steel wires, and such steel wires were woven into a filtering network. A strong electric field can be induced on this filtering network by TENG, while both electrostatic adsorption effect and TENG-enhanced photocatalytic effect can be achieved. Rhodamine B (RhB) steam was selected as the pollutant for demonstration. The absorbed RhB on the filter network with TENG in 1 min was almost the same amount of absorption achieved in 15 min without using TENG. Meanwhile, the degradation of RhB was increased over 50% under the drive of TENG. Furthermore, such a device was applied for the degradation of formaldehyde, where degradation efficiency was doubled under the drive of TENG. This work extended the application for the TENG in self-powered electrochemistry, design and concept of which can be possibly applied in the field of haze governance, indoor air cleaning, and photocatalytic pollution removal for environmental protection.
Berkeleyones and Related Meroterpenes from a Deep Water Acid Mine Waste Fungus That Inhibit the Production of Interleukin 1-β from Induced Inflammasomes (2011)

The Berkeley Pit, an acid mine waste lake, is a source of extremophilic microorganisms that produce interesting bioactive compounds. We have previously reported the isolation of berkeleydione (1), berkeleytrione (2), the berkeleyacetals, and the berkeleyamides from the Pit Lake fungus Penicillium rubrum. In this paper we report the isolation and characterization of berkeleyones A-C (4, 5, and 7) as well as previously described preaustinoid A (3) and A1(6) from this same fungus. These compounds were evaluated as inhibitors of the signaling enzyme caspase-1 and as potential inhibitors of interleukin 1-β production by inflammasomes in induced THP-1 cell line assays.
On the imbalance of international communications: an analysis, a review, and some solutions (1985)

International communication today is typified by the southern flow of information, from the northern hemisphere to the southern hemisphere, dominated by the developed nations in information gathering and dissemination, and Intensified by technological advances in communication in the last two decades. The Incessant cries of imperialism, cultural domination, and invasion echoing from Africa, Asia, the Middle East, and Latin America have precipitated a rigid control of communication in many developing countries. The imbalance of communication flow, castigated, and denounced by every developing country, is considered to be the source of all evils, ranging from the failure of politico-economical policies and erosion of social norms and values to street crimes and prostitution; nevertheless, the verdict is still not yet in. This study attempts to illustrate the fundamental problems, to explore the consequences of communication imbalance, and to examine communication dysfunctions In order to provide a set of solutions specifically addressed to the elimination or the reduction of the detrimental effects of communication dysfunctions. In the meantime, evidence is provided to substantiate the contention that communication imbalance can be eventually corrected, not by control but by allowing the free flow of all types of communications. Japan is a typical example: she absorbed the best and discarded the disharmonious features of Chinese and Western civilizations. Further attempts are also made to examine the inherent, natural immunity of cultures against alien concepts and practices. The conclusion is aimed at the battle cries of i?½cultural imperialism: much ado about nothing.
Four polymorphic variations in the PEDF gene identified during the mutation screening of patients with Leber congenital amaurosis. (1999)

We report the discovery of four new polymorphic alterations in the PEDF gene in LCA patients and exclude by RFLP analysis the PEDF gene as a common cause of Leber congenital amaurosis. These single nucleotide polymorphisms will aid in future linkage analysis of complex multifactorial diseases involving retinal and RPE dysfunctions.
The RIG-I-like Receptor LGP2 Recognizes the Termini of Double-stranded RNA (2009)

The RIG-I-like receptors (RLRs), RIG-I and MDA5, recognize single-stranded RNA with 5' triphosphates and double-stranded RNA (dsRNA) to initiate innate antiviral immune responses. LGP2, a homolog of RIG-I and MDA5 that lacks signaling capability, regulates the signaling of the RLRs. To establish the structural basis of dsRNA recognition by the RLRs, we have determined the 2.0-A resolution crystal structure of human LGP2 C-terminal domain bound to an 8-bp dsRNA. Two LGP2 C-terminal domain molecules bind to the termini of dsRNA with minimal contacts between the protein molecules. Gel filtration chromatography and analytical ultracentrifugation demonstrated that LGP2 binds blunt-ended dsRNA of different lengths, forming complexes with 2:1 stoichiometry. dsRNA with protruding termini bind LGP2 and RIG-I weakly and do not stimulate the activation of RIG-I efficiently in cells. Surprisingly, full-length LGP2 containing mutations that abolish dsRNA binding retained the ability to inhibit RIG-I signaling.
Endogenous reverse transcription of human immunodeficiency virus type 1 in physiological microenviroments: an important stage for viral infection of nondividing cells (1996)

Endogenous reverse transcription (ERT) of retroviruses has long been considered a somewhat artificial process which only mimics reverse transcription occurring in target cells, as detergents or amphipathic peptides have classically been used to make the envelopes of retroviruses in these reaction systems permeable. Recently, several studies suggested that ERT of human immunodeficiency virus type 1 (HIV-1) might occur without detergent treatment. However, this phenomenon could be due to damage of the retroviral envelope during the process of virion purification or freezing and thawing. In this report, intravirion HIV-1 ERT, without detergent-induced permeabilization, is demonstrated to occur in the natural microenvironments of HIV-1 virions and is not caused by artificial processes. Therefore, this stage of the viral life cycle was termed natural ERT (NERT). The efficiency of NERT in HIV-1 virions was markedly augmented by several physiological substances in the extracellular milieu, such as polyamines and deoxyribonucleoside triphosphates. In addition, HIV-1 virions in seminal plasma samples harbored dramatically higher levels of full-length or nearly full-length reverse transcripts than virions isolated from peripheral blood plasma samples of HIV-1-seropositive men. When HIV-1 virions were incubated with seminal plasma samples, infectivity in initially nondividing cells was also significantly enhanced. Thus, we suggest that HIV-1 virions are actively altered by the extracellular microenvironment and that NERT may play an important role in viral infection of nondividing cells.
Service Templates and Service: Schemes (1999)

The URL scheme name is used to define (called URLs in this document) that are primarily intended to be used by the Service Location Protocol in order to distribute service access information. These schemes provide an extensible framework for client-based network software to obtain configuration information required to make use of network services. When registering a service: URL, the URL is accompanied by a set of well-defined attributes which define the service. These attributes convey configuration information to client software, or service characteristics meaningful to end users.
Cyclosporine Treatment of Glomerular Diseases (1999)

Cyclosporine-A is primary therapy for organ transplantation. Its immunosuppressive effect might suggest a therapeutic role in autoimmune diseases, including several idiopathic and secondary glomerular conditions. Various forms of idiopathic nephrotic syndrome, including focal segmental glomerulosclerosis (FSGS), minimal change disease (MCD), and membranous nephropathy (MN), may respond well to cyclosporine in selected patients. However, frequent relapse limits its use to those who have failed to respond to, or were intolerant of, steroids or cytotoxics. Cyclosporine's efficacy in other glomerulopathies, such as IgA nephropathy (IgAN) and membranoproliferative glomerulonephritis (MPGN) remains poorly studied and, given the risk of nephrotoxicity, cannot be recommended for treatment of these entities until further data are available. Cyclosporine demonstrates some efficacy in treating proliferative lupus nephritis and, based on pilot study data, membranous lupus as well. Again, given relapse rates and potential nephrotoxicity, it should be used only in combination with azathioprine and steroids, assuming cytotoxic therapy has failed. Finally, cyclosporine toxicity is briefly reviewed.