Miracle-dz/UniFAR-FTUs huggingface dataset:
Characterization of a second MetR-binding site in the metE metR regulatory region of Salmonella typhimurium

Transcription of the metE gene in Salmonella typhimurium and Escherichia coli is positively regulated by the MetR protein, with homocysteine serving as a coactivator. It was shown previously that MetR binds to and protects from DNase I digestion a 24-bp sequence in the metE metR regulatory region from nucleotides -48 to -71 relative to the metE transcription initiation site (designated as site 1). In this study, we show that purified MetR protein also binds to and protects a second 24-bp sequence adjacent to the original site, from nucleotides -24 to -47 relative to the metE transcription initiation site (designated as site 2). Single and multiple base changes were introduced into sites 1 and 2 in a metE-lacZ fusion. Base pair changes in site 1 or site 2 away from the MetR consensus binding sequence resulted in decreased metE-lacZ expression, suggesting that both sites are necessary for expression. DNase I footprint analysis showed that MetR bound at the high-affinity site 1 enhances MetR binding at the low-affinity site 2. A 2-bp change in site 2 toward the MetR consensus binding sequence resulted in high metE-lacZ expression; the increased expression was MetR dependent but homocysteine independent.
On Characterizing Adaptive Events Unique to Modern Humans

Ever since the first draft of the human genome was completed in 2001, there has been increased interest in identifying genetic changes that are uniquely human, which could account for our distinct morphological and cognitive capabilities with respect to other apes. Recently, draft sequences of two extinct hominin genomes, a Neanderthal and Denisovan, have been released. These two genomes provide a much greater resolution to identify human-specific genetic differences than the chimpanzee, our closest extant relative. The Neanderthal genome paper presented a list of regions putatively targeted by positive selection around the time of the human-Neanderthal split. We here seek to characterize the evolutionary history of these candidate regions-examining evidence for selective sweeps in modern human populations as well as for accelerated adaptive evolution across apes. Results indicate that 3 of the top 20 candidate regions show evidence of selection in at least one modern human population (P < 5 × 10(5)). Additionally, four genes within the top 20 regions show accelerated amino acid substitutions across multiple apes (P < 0.01), suggesting importance across deeper evolutionary time. These results highlight the importance of evaluating evolutionary processes across both recent and ancient evolutionary timescales and intriguingly suggest a list of candidate genes that may have been uniquely important around the time of the human-Neanderthal split.
SCHOOL OF ACCOUNTING , FINANCE AND MANAGEMENT A New Institutional Analysis of IFRS Adoption in Egypt : A Case Study of Loosely Coupled Rules and Routines

This paper examines the symbolic use of International Financial Reporting Standards (IFRS) in an Egyptian state-owned company (AQF Co.) that is partially privatised by drawing on new institutional sociology and its extensions. It explains how the ceremonial use of IFRS is shaped by the interplay between institutionalised accounting practices, conflicting institutions, power relations and the use of IT to institutionalizing accounting rules and routines. The research methodology is based on using an intensive case study. Data were collected from multiple sources, including unstructured and semistructured interviews, direct and participative observations, discussions and documentary analysis. The findings revealed that the company faced conflicting institutional demands from outside. The Central Agency for Accountancy required the company to use the Uniform Accounting System (as a state-owned enterprise) and The Egyptian Capital Market Authority required the company to use IFRS (as a partially private sector company registered in the stock exchange). To meet these conflicting institutional demands, the company adopted loosely coupled accounting rules and routines and IT was used to institutionalizing existing Uniform Accounting System and preserving the status quo.
Pediatric Pulmonology

Funding information ATS Research Foundation, Grant/Award Number: Unrestricted Critical Care Grant; NIH, Grant/Award Numbers: K08 HL133459, P01 HL128192 Abstract Background: Bronchopulmonary dysplasia (BPD) with airway hyperreactivity is a long‐ term pulmonary complication of prematurity. The endogenous nonadrenergic, noncholinergic signaling molecule, S‐nitrosoglutathione (GSNO) and its catabolism by GSNO reductase (GSNOR) modulate airway reactivity. Tracheomalacia is a major, underinvestigated complication of BPD. We studied trachealis, left main bronchus (LB), and intrapulmonary bronchiolar (IPB) relaxant responses to GSNO in a murine hyperoxic BPD model. Methods: Wild‐type (WT) or GSNOR knockout (KO) newborn mice were raised in 60% (BPD) or 21% (control) oxygen during the first 3 weeks of life. After room air recovery, adult trachealis, LB, and IPB smooth muscle relaxant responses to GSNO (after methacholine preconstriction) were studied using wire myographs. Studies were repeated after GSNOR inhibitor (GSNORi) pretreatment and in KO mice. Results: GSNO relaxed all airway preparations. GSNO relaxed WT BPD trachealis substantially more than WT controls (P< .05). Pharmacologic or genetic ablation of GSNOR abolished the exaggerated BPD tracheal relaxation to GSNO and also augmented BPD IPB relaxation to GSNO. LB ring contractility was not significantly different between groups or conditions. Additionally, GSNORi treatment induced relaxation of WT IPBs but not trachealis or LB. Conclusion: GSNO dramatically relaxed the trachealis in our BPD model, an effect paradoxically reversed by loss of GSNOR. Conversely, GSNOR inhibition augmented IBP relaxation. These data suggest that GSNOR inhibition could benefit both the BPD trachealis and distal airways, restoring relaxant responses to those of room air controls.
Flexible Cache for Database Management Systems

Cache of a persistent data structure represents an important part, which significantly influence its efficiency. Cache consists from an array of main memory blocks (caled cache nodes) with a constant size. Cache nodes buffer the data structure nodes hence they can be accessed quickly. However, data structure nodes do not usually fully utilize the whole main memory block. Therefore, the constant cache node size the waste of the main memory. In this article, we propose the solution where the cache consists from the cache nodes with a different size. Cache is split into several cache rows. The data structure nodes with the similar size are stored in one cache row. Such a solution has two problems: (1) that the some cache row has to replace the nodes too often during the querying (cache row contention), and (2) that the data structure nodes has to be moved between the cache rows during the insert and the delete operation. In our experimental section we show that the effect of the cache row contention is minimized if we set the cache row size according to the data structure node distribution. We also discuss a solution of the node cache moves problem.
Susceptibility testing of Pseudomonas aeruginosa isolates and clinical response to parenteral antibiotic administration: lack of association in cystic fibrosis.

STUDY OBJECTIVE To determine the relationship between the antibiotic susceptibility of Pseudomonas aeruginosa isolated from the sputum of patients with cystic fibrosis (CF) and the patient's response to parenteral antibiotic administration, we performed a retrospective analysis using data from patients in the placebo arm of a phase 3 trial of tobramycin solution for inhalation. All patients were chronically infected with P aeruginosa. Seventy-seven of the 262 patients receiving placebo experienced a pulmonary exacerbation during the trial for which they received therapy with IV tobramycin and ceftazidime. The susceptibility of the P aeruginosa isolates to ceftazidime and tobramycin was determined at trial enrollment by broth microdilution. DESIGN The clinical response to combination antibiotic therapy was assessed by analyzing differences in spirometry before and after antibiotic administration. The FEV(1) percent predicted at the first visit after the conclusion of antibiotic administration was compared to the FEV(1) percent predicted prior to antibiotic therapy. The results were analyzed both descriptively and by regression analyses. RESULTS The conditions of 54 patients improved, and those of 9 patients worsened, and in 14 patients there was no change in FEV(1) with antibiotic administration. No correlation was observed between the susceptibility of P aeruginosa to tobramycin or ceftazidime and clinical response. Only the three following variables were observed to significantly correlate with FEV(1) after antibiotic treatment on regression analysis: FEV(1) prior to treatment (p < 0.0001); number of days elapsed between the previous FEV(1) measurement and the initiation of IV antibiotic therapy (p < 0.002); and the number of days elapsed between the determination of the minimum inhibitory concentration and the initiation of IV therapy (p < 0.03). No significant trends were observed between the antibiotic susceptibility of P aeruginosa isolates and treatment outcomes. CONCLUSION While lack of statistical significance for a trend between bacterial susceptibilities and the response to parenteral antibiotic administration does not mean that no such trend exists, the precision of the confidence intervals allows us to conclude that even if isolate antibiotic susceptibilities affect outcome, the impact would be small and not clinically relevant.
NBER WORKING PAPER SERIES EXPLAINING THE EFFECTS OF GOVERNMENT SPENDING SHOCKS ON CONSUMPTION AND THE REAL EXCHANGE RATE

Using panel structural VAR analysis and quarterly data from four industrialized countries, we document that an increase in government purchases leads to an expansion in output and private consumption, a deterioration in the trade balance, and a depreciation of the real exchange rate (i.e., a decrease in the domestic CPI relative to the exchange-rate adjusted foreign CPI). We propose an explanation for these observed effects based on the deep habit mechanism. We estimate the key parameters of the deep-habit model employing a limited information approach. The predictions of the estimated deep-habit model fit well the observed responses of output, consumption, the trade balance, and the real exchange rate to an unanticipated government spending shock. In addition, the deep-habit model predicts that in response to an anticipated increase in government spending consumption and wages fail to increase on impact, which is consistent with the empirical evidence stemming from the narrative identification approach. In this way, the deep-habit model reconciles the findings of the SVAR and narrative literatures on the effects of government spending shocks. Morten O. Ravn Department of Economics European University Institute Villa San Paolo Via della Piazzuola 43 50133 Florence Italy morten.ravn@eui.eu Stephanie Schmitt-Grohé Department of Economics Duke University P.O. Box 90097 Durham, NC 27708 and NBER grohe@duke.edu Martín Uribe Department of Economics Duke University Durham, NC 27708-0097 and NBER uribe@duke.edu
Temporal support in the identification of e‐learning efficacy: an example of object classification in the presence of ignorance

Abstract: This study investigates the efficacy of an in‐place e‐learning facility, towards the performance of students on a university module, through the utilization of an information system based on CaRBS (Classification and Ranking Belief Simplex). It attempts to discern the final indifferent and good performance classifications of students based on their activity during the module (online page views). The ongoing assessment of the students every two weeks during the module is modelled with separate classification results reported as the number of two‐week periods builds up. Students who completed the course as well as those who withdrew are considered. The CaRBS system has its emphasis on the visual representation of results (using simplex plots), as well as its operations in the presence of ignorance (using the Dempster–Shafer theory of evidence). In the analysis of the module considered, the activity over certain weeks is consistently shown to be important to discern student performance. This study is of interest to practitioners and theorists, with the results shown offering a benchmark to the type of findings pertinent to expositing e‐learning efficacy.
Dangerous liaisons: the ecology of private interest and common good

Many ecological interactions that are called mutualistic are in fact mixtures of antagonistic and mutualistic aspects. For example, plasmids exploit their bacterial hosts but also protect them against external threats. In this study, we analyse the conditions for the evolution of what we call ‘dangerous liaisons’: interactions combining mutualistic and antagonistic aspects. Starting point of our analysis is a model that was proposed as early as 1934. In this model, partners have to form a complex (either temporary or long lasting) in order to interact. Using this model framework we then set out to define and tease apart private interests of the interacting partners from their common good. This dichotomy provides a unifying perspective to classify ecological interactions. We discuss some examples to illustrate how the outcome of the interaction may depend on densities or on other contextual variables. Finally, we note that having a common good is not a necessary condition for partners to have aligned interests. In a dangerous liaison partners may have interest to cooperate even when this does not bolster the common good.
A Comparative Study of Color Preferences in Japan, China and Indonesia, with Emphasis on the Preference for White

To measure and compare the main color-preference tendencies in Japan, China, and Indonesia, 490 subjects (175 Japanese, 158 Chinese, and 157 Indonesian) were asked to choose from a color chart the three colors they liked most and the three they liked least and to state the reasons for their choices. Analysis of the choices by correspondence analysis showed that each area (country) shows tendencies for unique color preference and that there are statistically significant differences in the frequency of selection of colors of certain hues and tones. However, a high preference for white was common to all areas, along with preferences for some other colors. The successive studies done by the author have shown a common strong preference for white in other Asian areas as well. The reasons given for the choices suggested that associative images based on environmental and cultural aspects may be important influences on color preference.
A reproducible and quantifiable model of choroidal neovascularization induced by VEGF A165 after subretinal adenoviral gene transfer in the rabbit

Purpose To determine the effects of the vascular endothelial growth factor (VEGF)-A165 delivered using a high capacity adenoviral vector (HC Ad.VEGF-A) on vascular growth and pathological changes in the rabbit eye. To combine different detection methods of VEGF-A165 overexpression-induced neovascularization in the rabbit. Methods HC Ad.VEGF-A165 was constructed and injected at 5x106 infectious units (iu) into the subretinal space of rabbit eyes. Two and four weeks postinjection, the development of neovascularization and the expression of HC Ad-transduced VEGF-A165 protein were followed up in vivo by scanning laser ophthalmoscopy, fluorescein and indocyanine green angiographies and ex vivo by electron microscopy and immunohistochemistry Results We observed a choroidal neovascularization (CNV) with leakage in 83% of the rabbit eyes. Our findings present clear indications that there is a significant effect on the endothelial cells of the choriocapillaris after subretinal transduction of the retinal pigment epithelium (RPE) with VEGF-A165 vector. The choroidal endothelial cells were activated, adherent junctions opened, and the fenestration was minimized, while the extracellular matrix localized between the RPE and the endothelium of the choriocapillaris was enlarged toward the lumen of the vessels, inducing a deep invagination of the endothelial cells into the vessel lumen. They also proliferated and formed pathological vessels in the subretinal space. Moreover,there was an increased expression of basic fibroblast growth factor and VEGF-A accompanied by macrophage stimulation, retinal edema, and photoreceptor loss. Conclusions This is the first model of VEGF-induced CNV in the rabbit in which the pathological events following overexpression of VEGF by RPE cells have been described in detail. Many of the features of our experimental CNV resemble those observed clinically in patients having wet age-related macular degeneration.
Content-based ontology matching for GIS datasets

The alignment of separate ontologies by matching related concepts continues to attract great attention within the database and artificial intelligence communities, especially since semantic heterogeneity across data sources remains a widespread and relevant problem. In particular, the Geographic Information System (GIS) domain presents unique forms of semantic heterogeneity that require a variety of matching approaches. Our approach considers content-based techniques for aligning GIS ontologies. We examine the associated instance data of the compared concepts and apply a content-matching strategy to measure similarity based on value types based on N-grams present in the data. We focus special attention on a method applying the concepts of mutual information and N-grams by developing 2 separate variations and testing them over GIS dataset including multi-jurisdictions. In order to align concepts, first we find the appropriate columns. For this, we will exploit mutual information between two columns based on the type distribution of their content. Intuitively, if two columns are semantically same, type distribution should be very similar. We justify the conceptual validity of our ontology alignment technique with a series of experimental results that demonstrate the efficacy and utility of our algorithms on a wide-variety of authentic GIS data.
Mass Spectrometry and Protein Analysis

Mass spectrometry is a central analytical technique for protein research and for the study of biomolecules in general. Driven by the need to identify, characterize, and quantify proteins at ever increasing sensitivity and in ever more complex samples, a wide range of new mass spectrometry–based analytical platforms and experimental strategies have emerged. Here we review recent advances in mass spectrometry instrumentation in the context of current and emerging research strategies in protein science.
Neritoptyx hogansoni new species (Gastropoda, Mollusca) from the Upper Cretaceous Fox Hills Formation on the Dakota Isthmus, western United States

Abstract. In midcontinent North America, the Fox Hills Formation (Upper Cretaceous, upper Maastrichtian) preserves the last marine faunas in the central Western Interior Seaway (WIS). Neritoptyx hogansoni new species, a small littoral snail, exhibited allometric change from smooth to corded ornament and rounded to shouldered shape during growth. Specimens preserve a zig-zag pigment pattern that changes to an axial pattern during growth. Neritoptyx hogansoni new species was preyed on by decapod crustaceans, and spent shells were occupied by pagurid crabs. Dead mollusk shells, particularly those of Crassostrea subtrigonalis (Evans and Shumard, 1857), provided a hard substrate to which they adhered on the Fox Hills tidal flats. This new neritimorph gastropod establishes a paleogeographic and chronostratigraphic proxy for intertidal conditions on the Dakota Isthmus during the lateMaastrichtian. Presence of a neritid extends the marine tropical/temperate boundary in the WIS northward to ∼44° late Maastrichtian paleolatitude. Late Maastrichtian closure of the isthmus subsequently altered marine heat transfer by interrupting northward flow of tropical currents from the Gulf Coast by as much as 1 to 1.5 million years before the Cretaceous ended.
Charge-pump reducing current mismatch in DLLs and PLLs

Conventional CMOS charge-pump circuits have some current mismatch problems. The current mismatch induces a phase offset which deteriorates the performance of PLLs or DLLs. This paper investigates causes of current mismatch of conventional CMOS charge-pump and proposes new charge-pump circuits to reduce the current mismatch. The DLL with proposed charge-pump is simulated in a 0.18 mum CMOS process
Necessary spatial resolution for realistic tactile feeling display

In this paper, we show a hypothesis on the sensing mechanism in the human tactile organ and its resolution. The hypothesis is that human skin cannot resolve any finer pattern than the resolution suggested by the two-point-discrimination test, but that variety created by four kinds of signals from four kinds of mechano-receptors makes it possible to detect fine feature of texture. This means if we control stimulus to four kinds of mechanoreceptors individually, the realistic contact-feeling display will not need higher spatial resolution than suggested by the two-point discrimination threshold. We examine this hypothesis through psychophysical experiments.
Evidence of Selection upon Genomic GC-Content in Bacteria

The genomic GC-content of bacteria varies dramatically, from less than 20% to more than 70%. This variation is generally ascribed to differences in the pattern of mutation between bacteria. Here we test this hypothesis by examining patterns of synonymous polymorphism using datasets from 149 bacterial species. We find a large excess of synonymous GC→AT mutations over AT→GC mutations segregating in all but the most AT-rich bacteria, across a broad range of phylogenetically diverse species. We show that the excess of GC→AT mutations is inconsistent with mutation bias, since it would imply that most GC-rich bacteria are declining in GC-content; such a pattern would be unsustainable. We also show that the patterns are probably not due to translational selection or biased gene conversion, because optimal codons tend to be AT-rich, and the excess of GC→AT SNPs is observed in datasets with no evidence of recombination. We therefore conclude that there is selection to increase synonymous GC-content in many species. Since synonymous GC-content is highly correlated to genomic GC-content, we further conclude that there is selection on genomic base composition in many bacteria.