Miracle-dz/UniFAR-FTUs huggingface dataset:
COMPARATIVE METHODS FOR THE ANALYSIS OF CONTINUOUS VARIABLES: GEOMETRIC INTERPRETATIONS

Abstract This study is concerned with statistical methods used for the analysis of comparative data (in which observations are not expected to be independent because they are sampled across phylogenetically related species). The phylogenetically independent contrasts (PIC), phylogenetic generalized least-squares (PGLS), and phylogenetic autocorrelation (PA) methods are compared. Although the independent contrasts are not orthogonal, they are independent if the data conform to the Brownian motion model of evolution on which they are based. It is shown that uncentered correlations and regressions through the origin using the PIC method are identical to those obtained using PGLS with an intercept included in the model. The PIC method is a special case of PGLS. Corrected standard errors are given for estimates of the ancestral states based on the PGLS approach. The treatment of trees with hard polytomies is discussed and is shown to be an algorithmic rather than a statistical problem. Some of the relationships among the methods are shown graphically using the multivariate space in which variables are represented as vectors with respect to OTUs used as coordinate axes. The maximum-likelihood estimate of the autoregressive parameter, ρ, has not been computed correctly in previous studies (an appendix with MATLAB code provides a corrected algorithm). The importance of the eigenvalues and eigenvectors of the connection matrix, W, for the distribution of ρ is discussed. The PA method is shown to have several problems that limit its usefulness in comparative studies. Although the PA method is a generalized least-squares procedure, it cannot be made equivalent to the PGLS method using a phylogenetic model. Corresponding Editor: T. Garland Jr.
Organizational Heterogeneity of the Human Genome: Significant Variation of Recombination Rate of 100 kbp Sequences within GC Ranges

The association of nucleotide composition of genome sequences with their functional characteristics is widely known, among the most studied characteristics correlated with GC content are gene density and expression and recombination rate. Previously, we found that similar in nucleotide composition genomic regions may exhibit considerable differences in sequence organization and hypothesized that organizationally different regions may also exhibit functional and evolutionary heterogeneity. Here we examine this hypothesis by classifying 100 kbp segments of human genome into 14 compositionally homogeneous groups according to their GC content and differentiating the segments within each group by organization patterns (OP) using oligonucleotide (k-mer) counting, referred to as Compositional Spectra (CS) Analysis. We identified 141 groups of segments different in their CS organization and found that obtained compositionally similar OP groups (OPG) differ significantly in their recombination rate. This conclusion was robust with respect to the selected window size (confirmed by independent analysis for 50 kb and 200 kb segments). We further performed a test of contribution of specific k-mers in clustering of 100 kbp segments to OPGs with contrast levels of recombination rates. Eight k-mers, which demonstrated highest importance for such clustering, allowed correct classification at least 76% of segments in all 14 OPG pairs. Moreover, these k-mers proved similar with five previously described patterns related to recombination hotspots including the most known 13 bp recombination motif CCNCCNTNNCCNC.
A simple real-time assay for in vitro translation

A high-throughput assay for real-time measurement of translation rates in cell-free protein synthesis (SNAP assay) is described. The SNAP assay enables quantitative, real-time measurement of overall translation rates in vitro via the synthesis of O6-alkylguanine DNA O6-alkyltransferase (SNAP). SNAP production is continuously detected by fluorescence produced by the reaction of SNAP with a range of quenched fluorogenic substrates. The capabilities of the assay are exemplified by measurements of the activities of Escherichia coli MRE600 ribosomes and fluorescently labeled E. coli mutant ribosomes in the PURExpress translation system and by determination of the 50% inhibitory concentrations (IC50) of three common macrolide antibiotics.
Proton mobility in protonated peptides: a joint molecular orbital and RRKM study.

The mobile proton model was critically evaluated by using purely theoretical models which include quantum mechanical calculations to determine stationary points on the potential energy surface (PES) of a model compound, and Rice-Ramsperger-Kassel-Marcus (RRKM) calculations to determine the rate constants of various processes (conformational changes, proton transfer reactions) which occur during mass analysis of protonated peptides. Extensive mapping of the PES of protonated N-formylglycinamide resulted in various minima which were stabilized by one or more of the following types of interaction: internal hydrogen bond, charge transfer interaction, charge delocalization, and ring formation. The relative energies of most of the investigated minima are less then 20 kcal mol(-1) compared with the most stable species. More importantly, the relative energies of the transition structures connecting these minima are fairly low, allowing facile transitions among the energetically low-lying species. It is demonstrated that a path can be found leading from the energetically most stable species, protonated on an amide oxygen, to the structure from which the energetically most favorable fragmentation occurs. It is also shown that the added proton can sample all protonation sites prior to fragmentation. The RRKM calculations applied the results of ab initio computations (structures, energetics, vibrational frequencies) to the reactions (internal rotations, proton transfers) occurring in protonated N-formylglycinamide, and clearly lend additional evidence to the mobile proton model. Based on the results of the PES search on protonated N-formylglycinamide, we also comment on the mechanism proposed by Arnot et al. (Arnot D, Kottmeier D, Yates N, Shabanowitz J, Hunt D F. 42(nd) ASMS Conference on Mass Spectrometry, 1994; 470) and Reid et al. (Reid G E, Simpson R J, O'Hair R A J. J. Am. Soc. Mass Spectrom. 1998; 9:945) for the formation of b(2)(+) ions. According to the high level ab initio results, the mechanism relying on amide oxygen protonated species seems to be less feasible than the one which involves N-protonated species.
Policy implementation in the era of accelerating projectification: Synthesizing Matland’s conflict–ambiguity model and research on temporary organizations

It has become increasingly common to use the project as a form of organization when implementing public policies. Previous research has identified political, administrative and organizational motives behind this trend towards more project-based organizations within the public administration. The problem is that project-based organization carries inherent problems and special challenges when these projects are supposed to be implemented in permanent agencies and organizations. The purpose of this paper is to identify problems and challenges that public administrations face when ‘the project organization’ is used as a structural form of organization in implementing different kinds of public policies. The article takes its starting point in the policy implementation research and especially in Matland’s conflict-ambiguity model. This research tradition is complemented by a review of research on temporary organizations, which draws attention to some inherent and significant characteristics of project organizations, that is the concepts of entity, relationship and time. Our analysis shows that the use of project organization puts special demands on the players involved, and if these are not taken into account, there is a high risk that projects designed to bring about social change will not produce the effects that policymakers and citizens expect.
The Impact of Tax Rebates on Export Performance: China's Textile Exports to the USA

The paper evaluates the effectiveness of China increasing its tax rebate on textile exports to the USA. Using the difference-in-differences technique and employing The Harmonized System six-digit data, it is found that the tax rebate policy boosted the growth of textile exports to the USA. Approximately 6 to 25 per cent of the growth can be attributed to this policy. The difference-in-differences technique appears useful in evaluating such policies and opens the door to studies measuring the impact of polices. The effectiveness of the export tax rebate policy should be a lesson for policymakers facing slumps in their exports in economic downturns and perhaps become part of the standard trade policy arsenal.
Vitamin B12 deficiency and hyperhomocysteinemia in rural and urban Indians.

BACKGROUND Low vitamin B12 concentration in South Asian Indians is common, but the exact prevalence is not known. AIM To investigate prevalence and associations of low vitamin B12 concentration and hyperhomocysteinemia in rural and urban Indian men living in and around Pune, Maharashtra. METHOD We studied 441 middle-aged men (149 rural, 142 slum and 150 urban middle-class residents, mean age 39 y). Data on lifestyle, socio-economic status, nutrition and medical history were obtained. Circulating concentrations of vitamin B12, folate, ferritin, total homocysteine (tHcy), and haematological indices, and cardiovascular risk variables were measured. RESULTS Median plasma B12 concentration was low (110 pmol/L): Overall, 67% of men had low vitamin B12 concentration (<150 pmol/L) and 58% had hyperhomocysteinemia (>15 micromol/L). Of the urban middle class, 81% had low vitamin B12 concentration and 79% had hyperhomocysteinemia. Low vitamin B12 concentration contributed 28% to the risk of hyperhomocysteinemia (population attributable risk) while low red cell folate contributed 2%. Vegetarians had 4.4 times (95% CI 2.1, 9.4) higher risk of low vitamin B12 concentrations and 3.0 times (95% CI 1.4, 6.5) higher risk of hyperhomocysteinemia compared to those who ate non-vegetarian foods frequently. Urban middle-class residence was an additional independent risk factor of hyperhomocysteinemia (odds ratio 7.6 (95% CI 2.5, 22.6), compared to rural men). Low vitamin B12 concentration was related to lower blood haemoglobin concentration and higher mean corpuscular volume, but macrocytic anemia was rare. CONCLUSION Low vitamin B12 concentration and hyperhomocysteinemia are common in Indian men, particularly in vegetarians and urban middle class residents. Further studies are needed to confirm these findings in other parts of India.
The clonal root system of balsam poplar in upland sites of Quebec and Alberta

Abstract Balsam poplar seeds are short‐lived and require moist seedbeds soon after they are released to germinate. In addition to sexual reproduction, balsam poplar stands can regenerate clonally by root suckering. The origin of stands will in turn affect their genetic structure and root system architecture, which are poorly understood for upland forest stands. Three stands were hydraulically excavated in Quebec (moist) and Alberta (dry) to determine the origin of trees and to characterize root systems with respect to presence of parental roots and root grafts connections. Clones were identified using single‐nucleotide polymorphism (SNPs), and all stems, roots and root grafts were aged using dendrochronology techniques. All 82 excavated trees were of sucker origin, and four of the six stands contained a single clone. Parental root connections were found between 22% and 25% of excavated trees, and 53% and 48% of trees were linked with a root graft between the same or different clones, in Alberta and Quebec, respectively. Mean distance between trees connected by parental root was significantly lower than the distance between unconnected trees (0.47 ± 0.25 m vs. 3.14 ± 0.15 m and 1.55 ± 0.27 m vs. 4.25 ± 0.13 m) in Alberta and in Quebec, respectively. The excavations also revealed many dead stumps with live roots, maintained through root connections with live trees. This research highlights that balsam poplar growing in upland stands is a clonal species that can maintain relatively high genotypic diversity, with frequent root connections between trees at maturity. Maintaining an extensive root system through root connections increases the chances of a clone surviving when the above ground tree is dead and may also enhance the resilience of balsam poplar stands after disturbance.
Estimation of Plasma IC50 of Donepezil for Cerebral Acetylcholinesterase Inhibition in Patients With Alzheimer Disease Using Positron Emission Tomography

Objectives:Estimate the value of in vivo plasma IC50 of donepezil, the concentration of donepezil in plasma that inhibits brain acetylcholinesterase (AChE) activity by 50% at the steady-state conditions of donepezil between the plasma and the brain. Methods:N-[11C] methylpiperidin-4-yl acetate ([11C]MP4A) positron emission tomography was performed in 16 patients with probable Alzheimer disease (AD) before and during the treatment of donepezil (5 mg/day) with a mean interval of 5.3 months. The plasma IC50 value of donepezil was estimated from plasma donepezil concentrations and cerebral cortical mean AChE inhibition rates measured by positron emission tomography, using one-parameter model. Results:Donepezil reduced AChE activity uniformly in the cerebral cortex compared with the baseline in each AD patient, and the mean reduction rate in the cerebral cortex was 34.6%. The donepezil concentrations in the plasma ranged from 18.5 to 43.9 ng/mL with a mean of 28.9 ± 7.3 ng/mL. The plasma IC50 value was estimated to be 53.6 ± 4.0 ng/mL. Conclusions:Once the plasma IC50 of donepezil is determined, the brain AChE inhibition rate could be estimated from the plasma concentration of donepezil in each subject based on the plasma IC50. Now that the mean donepezil concentrations in the plasma, when the patients took 5 mg/day, remained 28.9 ng/mL, approximately half of the plasma IC50, higher dose of donepezil might provide further benefits for patients with AD. This technique can be also applied to measure the in vivo plasma IC50 of other cholinesterase inhibitors such as rivastigmine and galantamine.
Industrial Electricity Usage and Stock Returns

The growth rate of industrial electricity usage predicts future stock returns up to 1 year with an R 2 of 9%. High industrial electricity usage today predicts low stock returns in the future, consistent with a countercyclical risk premium. Industrial electricity usage tracks the output of the most cyclical sectors. Our findings bridge a gap between the asset pricing literature and the business cycle literature, which uses industrial electricity usage to gauge production and output in real time. Industrial electricity growth compares favorably with traditional financial variables, and it outperforms Cooper and Priestley’s output gap measure in real time.
PICTURING ORGANIZATIONAL READINESS FOR CHANGE WITH SYSTEMS MODEL OF CHANGE

The study draws the attention towards organizational change and its relevance to organization readiness of change. We have tested the compatibility of organizational readiness with The Systems Model of Change. Structured questionnaires have been used for data collection from 150 managers who ranges from front line to middle managers. The study provides the empirical evidence that organizational readiness have an effect on Organizational Arrangements, Methods & Social Factors and organizational readiness does not have an effect on Organizational Goals and People but, overall, organizational readiness have an effect on The Systems Model of Change. The implications of the study on managers and, in particularly, human resources managers are also discussed.
Water flow in carbon-based nanoporous membranes impacted by interactions between hydrated ions and aromatic rings

Carbon-based nanoporous membranes, such as carbon nanotubes (CNTs), graphene/graphene oxide and graphyne, have shown great potential in water desalination and purification, gas and ion separation, biosensors, and lithium-based batteries, etc. A deep understanding of the interaction between hydrated ions in an aqueous solution and the graphitic surface in systems composed of water, ions and a graphitic surface is essential for applications with carbon-based nanoporous membrane platforms. In this review, we describe the recent progress of the interaction between hydrated ions and aromatic ring structures on the carbon-based surface and its applications in the water flow in a carbon nanotube. We expect that these works can be extended to the understanding of water flow in other nanoporous membranes, such as nanoporous graphene, graphyne and stacked sheets of graphene oxide.
Sentiment Analysis on Twitter Using Streaming API

In general, opinion mining has been used to know about what people think and feel about their products and services in social media platforms. Millions of users share opinions on different aspects of life every day. Spurred by that growth, companies and media organizations are increasingly seeking way to mine information. It requires efficient techniques to collect a large amount of social media data and extract meaningful information from them. This paper aims to provide an interactive automatic system which predicts the sentiment of the review/tweets of the people posted in social media using hadoop, which can process the huge amount of data. Till now, there are few different problems predominating in this research community, namely, sentiment classification, feature based classification and handling negations. A precise method is used for predicting sentiment polarity, which helps to improve marketing strategies. This paper deals with the challenges that appear in the process of Sentiment Analysis, real time tweets areconsidered as they are rich sources of data for opinion mining and sentiment analysis. This paper focus on Sentiment analysis, Feature based Sentiment classification and Opinion Summarization. The main objective of this paper is to perform real time sentimental analysis on the tweets that are extracted from the twitter and provide time based analytics to the user.
AtnMat2, a nuclear-encoded maturase required for splicing of group-II introns in Arabidopsis mitochondria.

Mitochondria (mt) in plants house about 20 group-II introns, which lie within protein-coding genes required in both organellar genome expression and respiration activities. While in nonplant systems the splicing of group-II introns is mediated by proteins encoded within the introns themselves (known as "maturases"), only a single maturase ORF (matR) has retained in the mitochondrial genomes in plants; however, its putative role(s) in the splicing of organellar introns is yet to be established. Clues to other proteins are scarce, but these are likely encoded within the nucleus as there are no obvious candidates among the remaining ORFs within the mtDNA. Intriguingly, higher plants genomes contain four maturase-related genes, which exist in the nucleus as self-standing ORFs, out of the context of their evolutionary-related group-II introns "hosts. " These are all predicted to reside within mitochondria and may therefore act "in-trans" in the splicing of organellar-encoded introns. Here, we analyzed the intracellular locations of the four nuclear-encoded maturases in Arabidopsis and established the roles of one of these genes, At5g46920 (AtnMat2), in the splicing of several mitochondrial introns, including the single intron within cox2, nad1 intron2, and nad7 intron2.
Qualified Foreign Institutional Investor Shareholdings and Corporate Operating Performance

Résumé:Dans cet article, les auteurs utilisent la profitabilité, la qualité des actifs, le risque d'endettement et la croissance des ventes comme indices de mesure du rendement d'exploitation des entreprises. Grâce à des données recueillies au moyen d'un panel de 630 entreprises et couvrant la période 2008-2014, donc après la réforme chinoise en matière d'actions scindées, les auteurs construisent un modèle d'entité à effets fixes pour analyser l'effet des participations des investisseurs institutionnels étrangers qualifiés (IIEQ) sur le rendement d'exploitation des entreprises transnationales non financières chinoises. Les résultats montrent que le ratio de participations des IIEQ et les participations du système de poids et contrepoids des IIEQ sont positivement correlés de façon significative avec le rendement des capitaux propres et le ratio de rotation de l'actif total, mais qu'ils ne sont pas significativement corrélés avec le ratio actif/passif et le taux de croissance des ventes. Ces résultats suggèrent donc que, plus le ratio de participation des IIEQ est élevé, plus l'enthousiasme des IIEQ pour la participation à la gouvernance d'entreprise l'est également, et que meilleur est alors le rendement global d'exploitation. Ces résultats fournissent également des éléments importants pour inciter les entreprises transnationales chinoises à avoir recours aux IIEQ pour améliorer leur structure de gouvernance et leur rendement d'exploitation.In this article, profitability, asset quality, debt risk, and sales growth are used as measurement indices of corporate operating performance. On the basis of panel data of 630 companies for 2008–2014, which is after the completion of China's split-share structure reform, an entity fixed-effects model is used to study the effect of qualified foreign institutional investor (QFII) shareholdings on the operating performance of Chinese non-financial transnational corporations. The results show that the QFII shareholdings ratio and shareholdings checks and balances degree are significantly positively correlated with return on equity and total assets turnover, but they have no significant correlation with asset liability ratio and sales growth rate. The evidence therefore suggests that the higher the QFII shareholdings ratio is, the higher the enthusiasm is for QFII shares participating in corporate governance, and the better the general corporate operating performance. The findings provide an important reference for Chinese transnational corporations to introduce QFII shares to improve governance structure and corporate operating performance.