Miracle-dz/UniFAR-FTUs huggingface dataset:
The phn Genes of Burkholderiasp. Strain RP007 Constitute a Divergent Gene Cluster for Polycyclic Aromatic Hydrocarbon Catabolism

ABSTRACT Cloning and molecular ecological studies have underestimated the diversity of polycyclic aromatic hydrocarbon (PAH) catabolic genes by emphasizing classical nah-like (nah,ndo, pah, and dox) sequences. Here we report the description of a divergent set of PAH catabolic genes, the phn genes, which although isofunctional to the classical nah-like genes, show very low homology. Thisphn locus, which contains nine open reading frames (ORFs), was isolated on an 11.5-kb HindIII fragment from phenanthrene-degrading Burkholderia sp. strain RP007. The phn genes are significantly different in sequence and gene order from previously characterized genes for PAH degradation. They are transcribed by RP007 when grown at the expense of either naphthalene or phenanthrene, while in Escherichia coli the recombinant phn enzymes have been shown to be capable of oxidizing both naphthalene and phenanthrene to predicted metabolites. The locus encodes iron sulfur protein α and β subunits of a PAH initial dioxygenase but lacks the ferredoxin and reductase components. The dihydrodiol dehydrogenase of the RP007 pathway, PhnB, shows greater similarity to analogous dehydrogenases from described biphenyl pathways than to those characterized from naphthalene/phenanthrene pathways. An unusual extradiol dioxygenase, PhnC, shows no similarity to other extradiol dioxygenases for naphthalene or biphenyl oxidation but is the first member of the recently proposed class III extradiol dioxygenases that is specific for polycyclic arene diols. Upstream of the phn catabolic genes are two putative regulatory genes, phnR andphnS. Sequence homology suggests that phnS is a LysR-type transcriptional activator and that phnR, which is divergently transcribed with respect to phnSFECDAcAdB, is a member of the ς54-dependent family of positive transcriptional regulators. Reverse transcriptase PCR experiments suggest that this gene cluster is coordinately expressed and is under regulatory control which may involve PhnR and PhnS.
Maximally Inflected Real Rational Curves

We introduce and begin the topological study of real rational plane curves, all of whose inflection points are real. The existence of such curves is a corollary of results in the real Schubert calculus, and their study has consequences for the important Shapiro and Shapiro conjecture in the real Schubert calculus. We establish restrictions on the number of real nodes of such curves and construct curves realizing the extreme numbers of real nodes. These constructions imply the existence of real solutions to some problems in the Schubert calculus. We conclude with a discussion of maximally inflected curves of low degree.
Omitting types in fuzzy logic with evaluated syntax

This paper is a contribution to the development of model theory of fuzzy logic in narrow sense. We consider a formal system EvŁ of fuzzy logic that has evaluated syntax, i. e. axioms need not be fully convincing and so, they form a fuzzy set only. Consequently, formulas are provable in some general degree. A generalization of Gödel's completeness theorem does hold in EvŁ. The truth values form an MV‐algebra that is either finite or Łukasiewicz algebra on [0, 1].
Insulin sensitivity differs among ethnic groups with a compensatory response in beta-cell function.

OBJECTIVE A drastic difference is evident in the prevalence of type 2 diabetes among ethnic groups. We examined the role of beta-cell function and insulin sensitivity in this disparity among 4 ethnic groups. RESEARCH DESIGN AND METHODS beta-Cell function and insulin sensitivity were assessed in 77 healthy glucose-tolerant subjects using a hyperglycemic clamp (18 Asian-Americans, 9 African-Americans, 34 Caucasians, and 16 Mexican-Americans). RESULTS A wide range of variation was evident in clinical features of the studied subjects. Insulin sensitivity index and the second-phase insulin response differed among the 4 groups (P = 0.0023 and P = 0.0082, respectively), whereas the first-phase insulin response was marginally different (P = 0.1090). Stepwise regression analysis revealed that ethnicity was an independent determinant for the insulin sensitivity index (P = 0.0014) after adjusting for sex, age, diastolic blood pressure, waist-to-hip ratio, and BMI. Also, a compensatory response of beta-cell function was observed among the ethnic groups. CONCLUSIONS In this study, we observed a drastic difference in insulin sensitivity among the different ethnic groups and observed that their beta-cell function compensates for the prevailing insulin sensitivity. The difference in the prevalence of abnormal glucose tolerance in different ethnic groups could be a result of differences in insulin sensitivity
Rationale-Based, De Novo Design of Dehydrophenylalanine-Containing Antibiotic Peptides and Systematic Modification in Sequence for Enhanced Potency

ABSTRACT Increased microbial drug resistance has generated a global requirement for new anti-infective agents. As part of an effort to develop new, low-molecular-mass peptide antibiotics, we used a rationale-based minimalist approach to design short, nonhemolytic, potent, and broad-spectrum antibiotic peptides with increased serum stability. These peptides were designed to attain an amphipathic structure in helical conformations. VS1 was used as the lead compound, and its properties were compared with three series of derivates obtained by (i) N-terminal amino acid addition, (ii) systematic Trp substitution, and (iii) peptide dendrimerization. The Trp substitution approach underlined the optimized sequence of VS2 in terms of potency, faster membrane permeation, and cost-effectiveness. VS2 (a variant of VS1 with two Trp substitutions) was found to exhibit good antimicrobial activity against both the Gram-negative Escherichia coli and the Gram-positive bacterium Staphylococcus aureus. It was also found to have noncytolytic activity and the ability to permeate and depolarize the bacterial membrane. Lysis of the bacterial cell wall and inner membrane by the peptide was confirmed by transmission electron microscopy. A combination of small size, the presence of unnatural amino acids, high antimicrobial activity, insignificant hemolysis, and proteolytic resistance provides fundamental information for the de novo design of an antimicrobial peptide useful for the management of infectious disease.
Quality Estimation of Local Contents Based on PageRank Values of Web Pages

Recently, it is getting more frequent to search not Web contents but local contents, e.g., by Google Desktop Search. Google succeeded in the Web search because of its PageRank algorithm for the ranking of the search results. PageRank estimates the quality of Web pages based on their popularity, which in turn is estimated by the number and the quality of pages referring to them through hyperlinks. This algorithm, however, is not applicable when we search local contents without link structure, such as text data. In this research, we propose a method to estimate the quality of local contents without link structure by using the PageRank values of Web contents similar to them. Based on this estimation, we can rank the desktop search results. Furthermore, this method enables us to search contents across different resources such as Web contents and local contents. In this paper, we applied this method to Web contents, calculated the scores that estimate their quality, and we compare them with their page quality scores by PageRank.
A method to improve a resolution of digital PWM generator for DC-DC converter control

In recent years, digitization of all control parts in switching power supplies including PWM generators is progressing for demands such as intelligent performances and common use of hardware, etc. Then, a problem is in the resolution of digital PWM generators for improving control performances. Since the digital PWM generator is constituted using a counter, a carrier wave turns into a stairs wave, and step amplitudes is decided with a clock cycle. When the clock cycle is fixed, the resolution becomes low as the switching frequency becomes high. Consequently, the accuracy of output voltage becomes bad. In this paper, a method for remarkably improving the resolution of the digital PWM generator using the pulse composite technique is proposed. The method is realizable by some parts and easy computation, and is applied to the digital PWM generator built-in DSP. The usefulness and practicality are verified by experiments
Rethinking Customer Solutions: From Product Bundles to Relational Processes

This study draws on depth interviews with 49 managers in customer firms and 55 managers in supplier firms and on discussions with 21 managers in two focus groups to propose a new way of thinking about customer solutions. Extant literature and suppliers interviewed for this study view a solution as a customized and integrated combination of goods and services for meeting a customer's business needs. In contrast, customers view a solution as a set of customer–supplier relational processes comprising (1) customer requirements definition, (2) customization and integration of goods and/or services and (3) their deployment, and (4) postdeployment customer support, all of which are aimed at meeting customers' business needs. The relational process view can help suppliers deliver more effective solutions at profitable prices. In addition, field research suggests that the effectiveness of a solution depends not only on supplier variables but also on several customer variables. Supplier variables include contingent hierarchy, documentation emphasis, incentive externality, customer interactor stability, and process articulation. Customer variables include adaptiveness to supplier offerings and political and operational counseling that a customer provides to a supplier. Several of these variables underscore the importance of suppliers developing social capital with customers. The authors discuss implications for solution suppliers and identify areas for further research.
Federal Reserve Bank of Dallas Globalization and Monetary Policy Institute Global Slack and Domestic Inflation Rates: a Structural Investigation for G-7 Countries

Recent papers have argued that one implication of globalization is that domestic inflation rates may have now become more a function of " global " , rather than domestic, economic conditions, as postulated by closed-economy Phillips curves. This paper aims to assess the empirical importance of global output in determining domestic inflation rates by estimating a structural model for a sample of G-7 economies. The model can capture the potential effects of global output fluctuations on both the aggregate supply and the aggregate demand relations in the economy and it is estimated using full-information Bayesian methods. The empirical results reveal a significant effect of global output on aggregate demand in most countries. Through this channel, global economic conditions can indirectly affect inflation. The results, instead, do not seem to provide evidence in favor of altering domestic Phillips curves to include global slack as an additional driving variable for inflation. The views in this paper are those of the author and do not necessarily reflect the views of the Federal Reserve Bank of Dallas or the Federal Reserve System.
Temperate phages both mediate and drive adaptive evolution in pathogen biofilms

Significance During chronic infection, bacterial pathogens undergo rapid evolutionary adaptation and extensive genetic diversification affecting patient symptoms and treatment outcomes. Temperate phages are common in pathogen genomes, and phage particles can reach high abundance in human infections, but their role in pathogen evolution is unclear. Using experimental evolution and population genomics, we show that temperate phages found in human infections accelerated pathogen evolution by increasing the supply of beneficial mutations and imposing strong selection on bacterial populations. Notably, phages accelerated the loss of clinically important virulence-related bacterial traits, including motility and quorum sensing. Temperate phages are likely therefore to facilitate rapid evolution of bacterial pathogens and contribute to their adaptation to the host environment and clinical treatments. Temperate phages drive genomic diversification in bacterial pathogens. Phage-derived sequences are more common in pathogenic than nonpathogenic taxa and are associated with changes in pathogen virulence. High abundance and mobilization of temperate phages within hosts suggests that temperate phages could promote within-host evolution of bacterial pathogens. However, their role in pathogen evolution has not been experimentally tested. We experimentally evolved replicate populations of Pseudomonas aeruginosa with or without a community of three temperate phages active in cystic fibrosis (CF) lung infections, including the transposable phage, ɸ4, which is closely related to phage D3112. Populations grew as free-floating biofilms in artificial sputum medium, mimicking sputum of CF lungs where P. aeruginosa is an important pathogen and undergoes evolutionary adaptation and diversification during chronic infection. Although bacterial populations adapted to the biofilm environment in both treatments, population genomic analysis revealed that phages altered both the trajectory and mode of evolution. Populations evolving with phages exhibited a greater degree of parallel evolution and faster selective sweeps than populations without phages. Phage ɸ4 integrated randomly into the bacterial chromosome, but integrations into motility-associated genes and regulators of quorum sensing systems essential for virulence were selected in parallel, strongly suggesting that these insertional inactivation mutations were adaptive. Temperate phages, and in particular transposable phages, are therefore likely to facilitate adaptive evolution of bacterial pathogens within hosts.
Augmented Board Games – Enhancing board games with electronics

This paper examines Augmented Board Games, the result of using computational power to extend functionality and gameplay in board games. Experimental interaction design has been used as the primary research method, through the use of numerous models and design tools, including social and functional roles, game design patterns, and task analysis. The paper is concluded with descriptions of concepts and prototypes as well as novel game design possibilities within the design space of augmented board games.
Delimited smoothing technique over pruned and not pruned syntactic language models; perplexity and WER

Continuous Speech Recognition (CSR) systems require a Language Model (LM) to represent the syntactic constraints of the language. A sub-class of the regular languages, the k Testable in the Strict Sense (k-TSS) languages, has been used to generate LMs. Then, a smoothing technique needs to be applied to also consider events not represented in the training corpus. In this work, a new syntactic backing off smoothing approach, the Delimited discounting, was applied to several pruned and no pruned k-TSS LMs. Delimited discounting deals with the Turing discounting problems while keeping the Katz’ smoothing schema. The experimental evaluation was carried out over a Spanish speech application task, showing that an increase of the test set perplexity of a LM does not always mean a degradation in the model performance when integrated in a CSR system. Besides, there is a strong dependence between the amount of probability reserved by the smoothing technique to be assigned to unseen events and the value of the balance parameter applied to the LM probabilities in the Bayes s rule needed to get the best system performance.
Extended Haplotypes in the Growth Hormone Releasing Hormone Receptor Gene (GHRHR) Are Associated with Normal Variation in Height

Mutations in the gene for growth hormone releasing hormone receptor (GHRHR) cause isolated growth hormone deficiency (IGHD) but this gene has not been found to affect normal variation in height. We performed a whole genome linkage analysis for height in a population from northern Sweden and identified a region on chromosome 7 with a lod-score of 4.7. The GHRHR gene is located in this region and typing of tagSNPs identified a haplotype that is associated with height (p = 0.00077) in the original study population. Analysis of a sample from an independent population from the most northern part of Sweden also showed an association with height (p = 0.0039) but with another haplotype in the GHRHR gene. Both haplotypes span the 3′ part of the GHRHR gene, including the region in which most of the mutations in IGHD have been located. The effect size of these haplotypes are larger than that of any gene previously associated with height, which indicates that GHRHR might be one of the most important genes so far identified affecting normal variation in human height.
Effect of microclimate alteration on milk production and composition in Murrah buffaloes

Aim: The aim of this study was to assess the effect of microclimate alteration on temperature-humidity index (THI), milk yield, and milk composition of Murrah buffaloes during summer for a period of 90-day from March to May-2014 at Buffalo Research Station, Venkataramannagudem, Andhra Pradesh, India. Materials and Methods: A total of 40 lactating Murrah buffaloes were selected having similar body weight, parity, and milk yield. They were divided into four groups of 10 each. Three groups of buffaloes were provided with microclimate alteration using supplemental cooling like foggers, fans and foggers plus fans, and the fourth group (control) was without any cooling system. The daily THI was measured using dry and wet bulb thermometer. The physiological responses viz. rectal temperature, respiration rate, and pulse rate were measured by a clinical thermometer, measuring the flank movements a minute and observing the pulsation of the middle coccygeal artery at the base of tail with the help of finger. Milk samples were analyzed for chemical composition viz., fat, solids-not-fat (SNF), total solids (TS), specific gravity. Results: In the present study, significant (p<0.001) decrease in the average THI values were observed in experimental Murrah buffalo houses of GroupII (foggers), GroupIII (fans), and GroupIV (foggers and fans) compared to GroupI (control). Significant (p<0.001) decrease in average rectal temperature (°F), respiration rate (breaths/min) and pulse rate (beats/min) values were recorded in Murrah buffaloes of Groups II, III and IV compared to Group I. Significant (p<0.001) increase in the average milk yield (kg/day) was recorded in Murrah buffaloes of Groups II, III, and IV compared with Group I. Significant (p<0.001) increase in the average milk fat, SNF, and TS percent were recorded in Murrah buffalo Groups of II, III, and IV compared with Group I. Conclusion: Microclimate alteration by the provision of foggers and air circulators in the buffalo houses increased feed intake in buffaloes resulting increased milk production, fat and SNF yield which was due to decreased heat stress in buffaloes.
Examining the Lived Experiences of Nontraditional Students in a Teacher Education Program

The purpose of this phenomenological study was to examine the lived experiences of five nontraditional students who graduated from the Elementary Education Program at George Fox University (a degree-completion program targeting adult learners). Each of the participants simultaneously completed a Bachelor of Science Degree and obtained a teaching license during their program. The researcher sought to hear participants’ stories and how they gave meaning to experiences while completing the alternative teaching licensing program. Participants’ status as nontraditional included their age of 23 and older, working part-time, and attending classes in a hybrid part-time format. Participants shared unique stories fraught with challenges, yet all persevered to program completion and are currently teaching. In an analysis of the data, three major themes surfaced including, Participants identified multiple educational experiences both before and during their alternative teacher education program that made them self-identify as nontraditional, Participants entered the program with determination, believing that not finishing was not an option, and Participants entered the program knowing they wanted to be teachers; they wanted a clear path to completion. The implications of this work suggest a further examination of the role of grit regarding nontraditional student performance, a call to universities to include structures that support nontraditional student success, and an understanding of how the identity of nontraditional can impact student success at the university level.
Gravity Affects the Vertical Curvature in Human Grasping Movements

ABSTRACT When humans make grasping movements their digits’ paths are curved vertically. In a previous study the authors found that this curvature is largely caused by the local constraints at the start and end of the movement. Here the authors examined the contribution of gravity to the part of the curvature that was not explained by the local constraints. Subjects had to grasp a tealight (small cylinder) while sitting on a chair. The authors could rotate the whole setup, including the subject, relative to gravity, whereby the positions of the starting point and of the tealight relative to the subject did not change. They found differences between the paths that are consistent with a direct effect of gravity pulling the arm downward.
Identifying geographic hot spots of reassortment in a multipartite plant virus

Reassortment between different species or strains plays a key role in the evolution of multipartite plant viruses and can have important epidemiological implications. Identifying geographic locations where reassortant lineages are most likely to emerge could be a valuable strategy for informing disease management and surveillance efforts. We developed a predictive framework to identify potential geographic hot spots of reassortment based upon spatially explicit analyses of genome constellation diversity. To demonstrate the utility of this approach, we examined spatial variation in the potential for reassortment among Cardamom bushy dwarf virus (CBDV; Nanoviridae, Babuvirus) isolates in Northeast India. Using sequence data corresponding to six discrete genome components for 163 CBDV isolates, a quantitative measure of genome constellation diversity was obtained for locations across the sampling region. Two key areas were identified where viruses with highly distinct genome constellations cocirculate, and these locations were designated as possible geographic hot spots of reassortment, where novel reassortant lineages could emerge. Our study demonstrates that the potential for reassortment can be spatially dependent in multipartite plant viruses and highlights the use of evolutionary analyses to identify locations which could be actively managed to facilitate the prevention of outbreaks involving novel reassortant strains.
Toward High-Performance and Scalable Network Functions Virtualization

Network functions virtualization (NFV) promises to bring significant flexibility and cost savings to networking. These improvements are predicated on being able to run many virtualized network elements on a server, which leads to a fundamental question on how scalable an NFV platform can be. With this in mind, the authors build an experimental platform with commonly used NFV technologies. They evaluate the NFVs performance and scalability and, based on their demonstrated improvements, discuss best practices for achieving optimum NFV performance on commodity hardware. They also reveal the limitations on NFV scalability and propose a new architecture to address them.