gebhart/patrepeval huggingface dataset:
Species-specific microhelix aminoacylation by a eukaryotic pathogen tRNA synthetase dependent on a single base pair (1995)

We report here that tyrosyl-tRNA synthetase from the eukaryotic pathogen Pneumocystis carinii is a 370 amino acid polypeptide with characteristic elements of a class I aminoacyl-tRNA synthetase and aligns with the prokaryotic tyrosyl-tRNA synthetases in the class-defining active site region, including the tRNA acceptor helix-binding region. The expressed enzyme is a dimer that aminoacylates yeast tRNA but not Escherichia coli tRNA(Tyr). Like most tRNAs, prokaryotic tyrosine tRNAs have a G1.C72 base pair at the ends of their respective acceptor helices. However, the eukaryote cytoplasmic tyrosine tRNAs have an uncommon C1.G72 base pair. We show that P. carinii tyrosyl-tRNA synthetase charges a seven base pair hairpin microhelix (microhelixTyr) whose sequence is derived from the acceptor stem of yeast cytoplasmic tRNATyr. In contrast, the enzyme does not charge E. coli microhelixTyr. Changing the C1.G72 of yeast microhelixTyr to G1.C72 abolishes charging by the P. carinii tyrosyl-tRNA synthetase. Conversely, we found that E. coli tyrosyl-tRNA synthetase can charge an E. coli microhelixTyr and that charging is sensitive to having a G1.C72 rather than a C1.G72 base pair. The results demonstrate that the common structural framework of homologous tRNA synthetases has the capacity to coadapt to a transversion in a critical acceptor helix base pair and that this coadaptation can account for species-selective microhelix aminoacylation. We propose that species-selective acceptor helix recognition can be used as a conceptual basis for species-specific inhibitors of tRNA synthetases.
Extent of Corporate Triple Bottom Line Reporting In Case of Indian Listed Power Companies (2014)

Corporate social reporting discloses social and environmental information relating to an organisation’s interaction with its community, shareholders, physical and social environment to outsiders through corporate annual reports. Triple Bottom Line Reporting (subsequently refer to as TBLR) goes beyond the traditional way of reporting mechanism and encourages businesses to give closer attention to the whole impact of their commercial activities, over and above their financial performance. The Corporate Triple Bottom Line Reporting is based on three pillars - (i) environmental, (ii) social, (iii) economic causes. In this study, Corporate Triple Bottom Line (CTBL) disclosure items are handpicked from the annual reports/corporate social responsibility reports/sustainability reports of the sample units after a thorough examination of the contents of annual reports/corporate social responsibility reports/sustainability reports. The level of Triple Bottom Line reporting in India is in its infancy and still evolving. The three dimensions for TBL Reporting in India are people, planet and profit, which lead to sustainable development. We have considered listed companies of Bombay Stock Exchange (BSE) comprising BSE 500 index as our population. Considering time and resource constraints, it was decided to restrict the survey only power generating companies (15 units) among those 500 units. Accordingly, annual reports/corporate social responsibility reports/sustainability reports for these 15 numbers of listed power companies were planned to be reviewed. For measuring the extent of corporate triple bottom line reporting in annual reports/corporate social responsibility reports/sustainability reports of the companies, we have constructed a weighted disclosure index based on the previous empirical studies. The study evaluated the combined corporate triple bottom line disclosure score value of the sample companies based on performance with respect to 3 primary indicators – environment, social and economic. The maximum score of corporate triple bottom line disclosure is high enough i.e. 77.3% and the minimum score of corporate triple bottom line disclosure is very low i.e. 22.6%.
Serotonin 5-HT2a and 5-HT2c Receptors Stimulate Amyloid Precursor Protein Ectodomain Secretion (1996)

Alzheimer's disease amyloid consists of amyloid beta-peptides (Abeta) derived from the larger precursor amyloid precursor protein (APP). Non-amyloidogenic APP processing involves regulated cleavage within the Abeta domain followed by secretion of the ectodomain (APPs). APPs secretion can be stimulated by muscarinic acetylcholine receptors coupled to phospholipases and kinases. To determine whether other receptor classes can regulate APP processing, we examined the relation between serotonin receptors and APPs secretion. Serotonin increased APPs release 3-4-fold in 3T3 cells stably overexpressing 5-HT2aR or 5-HT2cR. The increase was dose-dependent and was blocked by serotoninergic antagonists. Phorbol esters also increased APPs secretion, but neither kinase inhibitors nor down-regulation of PKC blocked the serotonin-induced increase in APPs secretion. Thus PKC is not necessary to stimulate APPs secretion. Phospholipase A2 (PLA2) inhibitors blocked the 5-HT2aR-mediated increase in APPs secretion, suggesting a role of PLA2 in coupling 5-HT2aR to APP processing. In contrast, coupling of 5-HT2cR to APPs secretion involved both PKC and PLA2. Serotonin also stimulated the release of the APLP2 ectodomain, suggesting that additional members of the APP multigene family are processed via similar regulated pathways. Inasmuch as generation of APPs precludes the formation of amyloidogenic derivatives, serotonin receptors provide a novel pharmacological target to reduce these derivatives in Alzheimer's disease.
The Porcine Reproductive and Respiratory Syndrome Virus nsp2 Cysteine Protease Domain Possesses bothtrans- andcis-Cleavage Activities (2009)

The N terminus of the replicase nonstructural protein 2 (nsp2) of porcine reproductive and respiratory syndrome virus (PRRSV) contains a putative cysteine protease domain (PL2). Previously, we demonstrated that deletion of either the PL2 core domain (amino acids [aa] 47 to 180) or the immediate downstream region (aa 181 to 323) is lethal to the virus. In this study, the PL2 domain was found to encode an active enzyme that mediates efficient processing of nsp2-3 in CHO cells. The PL2 protease possessed both trans- and cis-cleavage activities, which were distinguished by individual point mutations in the protease domain. The minimal size required to maintain these two enzymatic activities included nsp2 aa 47 to 240 (Tyr(47) to Cys(240)) and aa 47 to 323 (Tyr(47) to Leu(323)), respectively. Introduction of targeted amino acid mutations in the protease domain confirmed the importance of the putative Cys(55)- His(124) catalytic motif for nsp2/3 proteolysis in vitro, as were three additional conserved cysteine residues (Cys(111), Cys(142), and Cys(147)). The conserved aspartic acids (e.g., Asp(89)) were essential for the PL2 protease trans-cleavage activity. Reverse genetics revealed that the PL2 trans-cleavage activity played an important role in the PRRSV replication cycle in that mutations that impaired the PL2 protease trans function, but not the cis activity, were detrimental to viral viability. Lastly, the potential nsp2/3 cleavage site was probed. Mutations with the largest impact on in vitro cleavage were at or near the G(1196)|G(1197) dipeptide.
Fructan as a New Carbohydrate Sink in Transgenic Potato Plants (1994)

Ingrid M. van der Meer, Michel J. M. Ebskamp, Richard G. F. Visser, Peter J. Weisbeek, Sjef C. M. Smeekens, Fructan as a New Carbohydrate Sink in Transgenic Potato Plants, The Plant Cell, Vol. 6, No. 4 (Apr., 1994), pp. 561-570
Editorial Commentary: For Nosocomial Vancomycin‐Resistant Enterococcal Infections: The Ounce of Prevention or the Pound of Cure? (2004)

ICU patients. This is a significant problem, because VRE infections appear to be more deadly and more costly than do infections caused by vancomycin-susceptible strains [3‐5]. Second, many epidemiologic studies have shown better control of VRE using active surveillance cultures and contact
Oxidative stress in Parkinson's disease (1995)

Oxidative damage and mitochondrial dysfunction are now considered to be important events in the cause of dopaminergic cell death in Parkinson's disease (PD). It is not known whether these biochemical abnormalities represent primary causes of PD or whether they are the end result of a series or reactions precipitated by environmental and genetic factors. Both oxidative damage and complex I deficiency are linked in a reciprocal manner and can potentially produce a toxic cellular environment capable of attacking a variety of biomolecules as well as inhibiting energy production. Defining the roles that these two biochemical defects play in nigral neuronal loss will provide important insights into the aetiology of PD.
Interactive evolutionary image processing for face beautification using smaller population size (2012)

A method to improve image processing with interactive evolutionary computing (IEC) is proposed in order to get a satisfactory output image with smaller population size. IEC is a powerful method for designing a system on the basis of human subjective criteria. Image processing with IEC is effective to process images considering human subjective criteria and taste, however, it requires a large PC system to show enough number of candidate output images on a large display; this feature makes this method difficult to be realized on a small mobile device. Here, the number of the candidates corresponds to the population size in the genetic algorithm (GA) in IEC. If the number of candidate output images is restricted, IE image processing takes more iteration time to get satisfactory result from small number of candidates. In order to solve this problem, a method to improve IEC is proposed so that the initial population is designed effectively by clustering past optimized parameters, and the generation change is modified by considering the significance of the first choice. This method is applied to human face image beautifying system, and the experimental results show that users can get more satisfactory result with smaller number of iterations.
Serum uric acid is an independent predictor of all‐cause mortality in patients at high risk of cardiovascular disease: A preventive cardiology information system (PreCIS) database cohort study (2008)

Serum uric acid levels are an independent predictor of death in patients at high risk of cardiovascular disease. Further studies are warranted to evaluate its prognostic implications and potential utility in the monitoring of therapy.
Editors' Introduction (1970)

The people of the Soviet Union encompass more than one hundred national groups. While those of broadly Slavic origin (Russian, Ukrainian, and Belorussian) formed 76 percent of the population of the USSR according to the 1959 census, the Russians alone were only 55 percent; when the results of the January 1970 census are published, the percentage of Russians in the USSR population may be significantly lower. Many national groups, especially those in Soviet Central Asia, are increasing in number much more quickly than are the Russians.
Low Molecular Weight Heparins: Structural Differentiation by Bidimensional Nuclear Magnetic Resonance Spectroscopy (2007)

Individual low molecular weight heparins (LMWHs) exhibit distinct pharmacological and biochemical profiles because of manufacturing differences. Correlation of biological properties with particular structural motifs is a major challenge in the design of new LMWHs as well as in the development of generic versions of proprietary LMWHs. Two-dimensional nuclear magnetic resonance (NMR) spectroscopy permits identification and quantification of structural peculiarities of LMWH preparations. In this article, heteronuclear single quantum coherence spectroscopy, previously used to determine variously substituted monosaccharide components of heparan sulfate (HS) and HS-like glycosaminoglycan mimics, has been applied to the structural characterization of three commercially available LMWHs (enoxaparin, dalteparin, and tinzaparin). Relevant residues belonging to the parent heparin, as well as minor residues generated by each depolymerization procedure, have been characterized and quantified. The use of a high-sensitivity NMR spectrometer (600 MHz equipped with cryoprobe) allowed the accurate quantification of residues with sensitivity better than 1 to 2%.
Experimental cerebral "no-reflow phenomenon". (1982)

The authors describe an experimental model of transient (15 min). unilateral, cerebral ischemia followed by 60 min of reperfusion in anesthetized rats. Zones of non perfusion are recorded and referred to as the "no-reflow phenomenon". The authors believe that vascular changes which interfere with postischemic reperfusion are due to ischemia-induced swelling of perivascular glia. The effects of the intracarotid injection of dexamethasone, furosemide and escina are evaluated in the attempt to show the importance of brain edema in ischemic cerebral damage.
Sensor array calibration in the presence of mutualcoupling and unknown sensor gains and phases (1994)

The Letter presents a calibration algorithm for arrays whose spatial responses are perturbed by mutual coupling and unknown sensor gains and phases. Unlike the algorithm proposed by Pierre and Kaveh, the algorithm that we propose does not require the length of the true steering vector to be known explicitly.
Effects of the Nei-Guan Acupressure by Wrist Band on Postoperative Nausea and Vomiting after Middle Ear Surgery (2008)

Acupressure on the P6 point using a wrist band is effective to alleviate nausea for middle ear surgery patients.
A Non–Contacting Torque Sensor for the Internal Combustion Engine (1981)

&lt;div class="htmlview paragraph"&gt;This paper discusses an inexpensive, non-contacting sensor for the measurement of the quasi-average torque of an internal combustion engine. The quantity which is actually measured by this sensor is a low-pass filter transformation of instantaneous developed torque having a bandwidth of about 9Hz. This method of torque measurement uses an inexpensive sensor which directly measures instantaneous crankshaft angular velocity. Electronic signal processing generates a signal which is proportional to instantaneous crankshaft angular acceleration.&lt;/div&gt; &lt;div class="htmlview paragraph"&gt;The relationship between engine developed torque and various transformations of this acceleration have been experimentally studied. This paper shows that certain of these transformations are highly correlated with the desired torque signal under transient as well as steady state operation. Transient operations which have been studied include changes in throttle position.&lt;/div&gt; &lt;div class="htmlview paragraph"&gt;The paper explains the sensor concept in terms of specific mathematical models for the torque and engine dynamics.&lt;/div&gt;
Brief Ultrasonication Improves Detection of Biofilm-formative Bacteria Around a Metal Implant (2006)

Biofilms are complex microenvironments produced by microorganisms on surfaces. Ultrasonication disrupts biofilms and may make the microorganism or its DNA available for detection. We determined whether ultrasonication could affect our ability to detect bacteria adherent to a metal substrate. A biofilm-formative Staphylococcus aureus strain was used for an in vitro implant infection model (biofilm-formative condition). We used quantitative culture and real time-polymerase chain reaction to determine the influence of different durations of ultrasound on bacterial adherence and viability. Sonication for 1 minute increased the yield of bacteria. Sonication longer than 5 minutes led to fewer bacterial colonies by conventional culture but not by polymerase chain reaction. This suggests short periods of sonication help release bacteria from the metal substrate by disrupting the biofilm, but longer periods of sonication lyse bacteria prohibiting their detection in microbiologic cultures. A relatively short duration of sonication may be desirable for maximizing detection of biofilm-formative bacteria around implants by culture or polymerase chain reaction.
Fragment Deconstruction of Small, Potent Factor Xa Inhibitors: Exploring the Superadditivity Energetics of Fragment Linking in Protein–Ligand Complexes (2011)

More than just the sum of its parts: The superadditivity effect of fragment linking on ΔG was quantified by deconstructing two fXa inhibitors with congeneric fragments, but different linkers. By connecting both fragments with a single bond, a high linker contribution ΔGlink of −14.0 kJ mol−1 results, which corresponds to an improvement in affinity by around 2.5 orders of magnitude relative to the sum of fragment ΔG values (see picture). Detailed facts of importance to specialist readers are published as ”Supporting Information”. Such documents are peer-reviewed, but not copy-edited or typeset. They are made available as submitted by the authors. Please note: The publisher is not responsible for the content or functionality of any supporting information supplied by the authors. Any queries (other than missing content) should be directed to the corresponding author for the article.
Determination of Macromolecular Structures from Anomalous Diffraction of Synchrotron Radiation (1991)

Resonance between beams of x-ray waves and electronic transitions from bound atomic orbitals leads to a phenomenon known as anomalous scattering. This effect can be exploited in x-ray crystallographic studies on biological macromolecules by making diffraction measurements at selected wavelengths associated with a particular resonant transition. In this manner the problem of determining the three-dimensional structure of thousands of atoms is reduced to that of initially solving for a few anomalous scattering centers that can then be used as a reference for developing the entire structure. This method of multiwavelength anomalous diffraction has now been applied in a number of structure determinations. Optimal experiments require appropriate synchrotron instrumentation, careful experimental design, and sophisticated analytical procedures. There are rich opportunities for future applications.
The ArabidopsisSomatic Embryogenesis Receptor Kinase 1Gene Is Expressed in Developing Ovules and Embryos and Enhances Embryogenic Competence in Culture (2001)

We report here the isolation of the Arabidopsis SOMATIC EMBRYOGENESIS RECEPTOR-LIKE KINASE 1 (AtSERK1) gene and we demonstrate its role during establishment of somatic embryogenesis in culture. The AtSERK1 gene is highly expressed during embryogenic cell formation in culture and during early embryogenesis. The AtSERK1 gene is first expressed in planta during megasporogenesis in the nucellus [corrected] of developing ovules, in the functional megaspore, and in all cells of the embryo sac up to fertilization. After fertilization, AtSERK1 expression is seen in all cells of the developing embryo until the heart stage. After this stage, AtSERK1 expression is no longer detectable in the embryo or in any part of the developing seed. Low expression is detected in adult vascular tissue. Ectopic expression of the full-length AtSERK1 cDNA under the control of the cauliflower mosaic virus 35S promoter did not result in any altered plant phenotype. However, seedlings that overexpressed the AtSERK1 mRNA exhibited a 3- to 4-fold increase in efficiency for initiation of somatic embryogenesis. Thus, an increased AtSERK1 level is sufficient to confer embryogenic competence in culture.
A Concerted Structural Transition in the Plasminogen Activator Inhibitor-1 Mechanism of Inhibition (2002)

The inhibition mechanism of serpins requires a change in structure to entrap the target proteinase as a stable acyl-enzyme complex. Although it has generally been assumed that reactive center loop insertion and associated conformational change proceeds in a concerted manner, this has not been demonstrated directly. Through the substitution of tryptophan with 7-azatryptophan and an analysis of transient reaction kinetics, we have described the formation of an inhibited serpin-proteinase complex as a single concerted transition of the serpin structure. Replacement of the four tryptophans of plasminogen activator inhibitor type-1 (PAI-1) with the spectrally unique analogue 7-azatryptophan permitted observations of conformational changes in the serpin but not those of the proteinase. Formation of covalent acyl-enzyme complexes, but not noncovalent Michaelis complexes, with tissue-type plasminogen activator (t-PA) or urokinase (u-PA) resulted in rapid decreases of fluorescence coinciding with insertion of the reactive center loop and expansion of beta-sheet A. Insertion of an octapeptide consisting of the P14-P7 residues of the reactive center loop into beta-sheet A produced the same conformational change in serpin structure measured by 7-azatryptophan fluorescence, suggesting that introduction of the proximal loop residues induces the structural rearrangement of the serpin molecule. The atom specific modification of the tryptophan indole rings through analogue substitution produced a proteinase specific effect on function. The reduced inhibitory activity of PAI-1 against t-PA but not u-PA suggested that the mechanism of loop insertion is sensitive to the intramolecular interactions of one or more tryptophan residues.
Intracellular Amyloid-β1–42, but Not Extracellular Soluble Amyloid-β Peptides, Induces Neuronal Apoptosis (2002)

Alzheimer disease (AD), the most frequent cause of dementia, is characterized by an important neuronal loss. A typical histological hallmark of AD is the extracellular deposition of beta-amyloid peptide (A beta), which is produced by the cleavage of the amyloid precursor protein (APP). Most of the gene mutations that segregate with the inherited forms of AD result in increasing the ratio of A beta 42/A beta 40 production. A beta 42 also accumulates in neurons of AD patients. Altogether, these data strongly suggest that the neuronal production of A beta 42 is a critical event in AD, but the intraneuronal A beta 42 toxicity has never been demonstrated. Here, we report that the long term expression of human APP in rat cortical neurons induces apoptosis. Although APP processing leads to production of extracellular A beta 1-40 and soluble APP, these extracellular derivatives do not induce neuronal death. On the contrary, neurons undergo apoptosis as soon as they accumulate intracellular A beta 1-42 following the expression of full-length APP or a C-terminal deleted APP isoform. The inhibition of intraneuronal A beta 1-42 production by a functional gamma-secretase inhibitor increases neuronal survival. Therefore, the accumulation of intraneuronal A beta 1-42 is the key event in the neurodegenerative process that we observed.
Quantitative <I>In Situ</I> Hybridization of Tissue Microarrays (2006)

Tissue microarrays enable the rapid histological localization of gene expression in hundreds of archival samples by in situ hybridization. However, the scoring of tissue microarray data may be influenced by intra- and inter-observer variations, and categorizing continuous variables risks discarding potentially meaningful information. Quantitation imposes a greater degree of objectivity, is more reproducible than subjective discriminations, and facilitates the communication and clarity of definitions. Phosphorimaging has been successfully used to quantitate the hybridization signal intensity from arrayed tissues. The process is rapid and has a wide dynamic range, surpassing the densitometric analysis of autoradiograms. This paper presents a detailed method for quantitative isotopic in situ hybridization on formalin-fixed paraffin-embedded tissue microarrays. In addition, the method includes a protocol for the development of synthetic agarose cores to control for the specificity and sensitivity of hybridization.