Miracle-dz/UniFAR-FTUs huggingface dataset:
Hypervariable DNA fingerprinting in Escherichia coli: minisatellite probe from bacteriophage M13

Extensive restriction-fragment-length polymorphism was revealed in Escherichia coli strains by using a region of the bacteriophage M13 genome as a DNA hybridization probe. This variation was observed across natural strains, in clinical samples, and to a lesser extent in laboratory strains. The sequence in M13 which revealed this fingerprint pattern was a region of the gene III coat protein, which contains two clusters of a 15-base-pair repeat. Oligonucleotides made to a consensus of these repeats also revealed the fingerprint profile. While this consensus sequence has significant homology to the lambda chi site sequence, an oligonucleotide made of the chi sequence did not reveal polymorphic fingerprint patterns in E. coli. The strain variation revealed by the M13 and M13-derived oligonucleotide probes will be useful for bacterial characterization and should find use in studies of bacterial evolution and population dynamics. The findings raise questions about what these repeated sequences are and why they are so variable.
Factors of Income Inequality and Their Influence Mechanisms: A Theoretical Overview

When analysing the factors of income inequality, first as many factors as possible have to be included in order to obtain valid results. The present article systematises the factors of income inequality discussed in the pertinent literature into five groups and summarises the hypotheses about the signs of the influences of the discussed factors on income inequality. But additionally the influences between the factors themselves that form indirect effects on income inequality have to be included. In this article, these influences are discussed and arranged in a system to give an idea about the possible indirect effects on income inequality of all the factors discussed in the article.
PORA and PORB, Two Light-Dependent Protochlorophyllide-Reducing Enzymes of Angiosperm Chlorophyll Biosynthesis.

Chloroplasts are the most abundant organelles in a plant cell. Besides their familiar roles in photosynthesis, chloroplasts also perform important functions during numerous other metabolic processes, such as nitrogen assimilation, amino acid biosynthesis, and tetrapyrrole production. ln particular, a major route of chloroplast anabolism is devoted to the synthesis of chlorophyll (Chl; von Wettstein et al., 1995). As the “pigment of life,” Chl plays a fundamental role in the energy absorption and transduction activities of all photosynthetic organisms (Bogorad, 1967; von Wettstein et al., 1971). In angiosperms, Chl synthesis is dependent on light (Granick, 1950). NADPH:protochlorophyllide oxidoreductase (POR; EC 1.3.1.33) catalyzes the only known light-requiring step of tetrapyrrole biosynthesis, the reduction of protochlorophyllide (Pchlide) to chlorophyllide (Chlide) (Griffiths, 1978; Apel et al., 1980). Both the POR(A) enzyme and its substrate, Pchlide, accumulate to high levels in dark-grown plants. Together with NADPH, they form a ternary complex that instantaneously converts Pchlide to Chlide when illuminated. The operation of PORA hence helps prevent photodynamic damage by large amounts of not immediately photoconvertible Pchlide. The function of PORA is confined to the very early stages of transition from etiolated to light growth (Apel, 1981; Batschauer and Apel, 1984; Mosinger et al., 1985; Forreiter et al., 1990). The amounts of both PORA protein and porA mRNA decrease drastically soon after the beginning of illumination (Mapleston and Griffiths, 1980; Santel and Apel, 1981; Forreiter et al., 1990), due in part to rapid proteolytic turnover of the enzyme protein (Kay and Griffiths, 1983; Hauser et al., 1984). To perform the reduction of Pchlide to Chlide during the final stages of the light-induced greening and to sustain Chl
Swap-aware garbage collection algorithm for NAND flash-based consumer electronics

NAND flash memory is a popular storage device for consumer electronics and it is exploited to be swap space for extending the limited main memory of consumer electronics. Due to the out-of-place update scheme provided by NAND flash memory to solve its erase-before-write hardware constraint, garbage collection should be performed to reclaim garbage in terms of invalid pages and obtain free space in terms of free blocks. The garbage collection, which consists of a series of copy operations and erase operations, is energy-consuming. In order to reduce the energy consumption, a swap-aware garbage collection algorithm for NAND flash-based consumer electronics is proposed in this paper. The proposed algorithm focuses on reducing the garbage collection overhead and improving the endurance of NAND flash memory. Experimental results show that the proposed algorithm is superior to the existing garbage collection algorithms in terms of the number of copy operations, the number of erase operations, the degree of wear-leveling, and energy consumption.
Improvement of fuel economy in Power-Shift Automated Manual Transmission through shift strategy optimization - an experimental study

In this paper, an optimal gear shifting control strategy based on Dynamic Programming (DP) for a vehicle equipped with a Power-Shift Automated Manual Transmission (PS-AMT) is proposed in order to explore the potential fuel savings. Simulation results on the city part of the New European Drive Cycle (NEDC), called ECE cycle, reveal that the relative fuel economy improvement can be reached up to 15.4% by applying DP shifting strategy compared to the case of applying a prescribed gear shift schedule. A forward facing dynamic power train model and control system are designed and developed for the prototype PS-AMT vehicle in order to validate the system modeling and shifting algorithm implementation. The test results of the prototype vehicle on the roller bench show that 11.2% improvement of fuel economy is achieved. It can be concluded that significant potential fuel savings can be obtained by optimal gear shift control and the proposed design method is consistent.
Explicit representation of knowledge acquired from plant historical data using neural network

A causal index, which translates implicit knowledge contained in a neural network into an explicit representation, is proposed. A backpropagation-based learning algorithm which suppresses the nondominant causal relationships to improve association accuracy is developed using the index. The validity of the proposed algorithm is investigated using historical data from a coagulant injection operation in a water-purification plant. Learning of relationships between the operational factor (coagulant injection rate) and influence factors (water qualities and floc image properties) in plant operations is carried out by the proposed algorithm. Improvements in the association ability for unknown conditions and in the reliability of acquired knowledge are realized
An Investigation into the Problematic Use of Facebook

Social networking sites (SNSs) have become new phenomena in social communication and interaction patterns which have profound impact in the way people communicate and connect with one another. The aim of this study is to test the advanced cognitive-behavioral model of generalized problematic Internet use (GPIU) in the context of Face book use. The findings suggested that a preference for online social interaction and use of Face book for mood regulation significantly explained the deficient self-regulation of Face book use. Deficient self-regulation in turn showed great influence on and led to negative outcomes associating with the problematic Face book use. Results indicated the data fit the model well and the variables in the current model accounted for 36 percent of the variance in mood regulation, 35 percent in respondents' deficient self-regulation, and 56 percent of variance explained in the negative outcomes. The findings provided important implications for both researchers and practitioners.
The impact of host's genetic susceptibility on Helicobacter pylori infection in children

Abstract The aim of our study was to investigate the impact of interleukin (IL)-6 190C/T, IL-6 174G/C, IL-6 572G/C, tumor necrosis factor-alpha (TNF-&agr;) 308G/A, and angiotensin-converting enzyme (ACE) I/D gene polymorphisms on Helicobacter pylori (H. pylori) infection in children. A cross-sectional study was performed on 126 children (57 children with H. pylori infection and 69 children without H. pylori infection) aged between 3 and 18 years presenting to a Pediatrics Tertiary Hospital from Romania. Children were assessed clinically, endoscopically, histopathologically, and genetically. In our study, we found that the presence of the CT and CT+TT genotypes of IL-6 190C/T (P < .002 and P = .04), allele G of IL-6 572 G/C polymorphism (P = .01), genotypes GA and AA of TNF-&agr; 308 G/A polymorphism (P = .04, P = .01), and genotype II of ACE I/D polymorphism (P = .02) were associated with H. pylori infection, while the CC genotype of IL-6 174G/C polymorphism was scarcely encountered in children with H. pylori infection [P = . 02, odds ratio (OR) = 0.06; 95% confidence interval (95% CI): 0.003–0.128]. Taking under consideration the 4 variant genotypes (IL-6 572G/C, IL-6 190C/T, TNF-&agr; 308G/A, and ACE I/D), we noticed a 2 times higher incidence of H. pylori infection (OR = 6.34; 95% CI: 2.15–25.8). We may consider that the IL-6 190C/T, IL-6 174G/C, IL-6 572G/C, TNF-&agr; 308G/A, and ACE I/D gene polymorphisms may increase the children's susceptibility for acquiring H. pylori infection; therefore, they may contribute to the pathogenesis of H. pylori gastritis.
Causes and Solutions When Adopting Continuous Delivery-A Systematic Literature

Context: Continuous delivery is a software development discipline in which software is always kept releasable. The literature contains instructions on how to adopt continuous delivery, but the adoption has been challenging in practice. Objective: In this study, a systematic literature review is conducted to survey the faced problems when adopting continuous delivery. In addition, we identify causes for and solutions to the problems. Method: By searching five major bibliographic databases, we identified 293 articles related to continuous delivery. We selected 30 of them for further analysis based on them containing empirical evidence of adoption of continuous delivery, and focus on practice instead of only tooling. We analyzed the selected articles qualitatively and extracted problems, causes and solutions. The problems and solutions were thematically synthesized into seven themes: build design, system design, integration, testing, release, human and organizational and resource. Results: We identified a total of 40 problems, 28 causal relationships and 29 solutions related to adoption of continuous delivery. Testing and integration problems were reported most often, while the most critical reported problems were related to testing and system design. Causally, system design and testing were most connected to other themes. Solutions in the system design, resource and human and organizational themes had the most significant impact on the other themes. The system design and build design themes had the least reported solutions. Conclusions: When adopting continuous delivery, problems related to system design are common, critical and little studied. The found problems, causes and solutions can be used to solve problems when adopting continuous delivery in practice. © 2016 The Authors. Published by Elsevier B.V. This is an open access article under the CC BY license ( http://creativecommons.org/licenses/by/4.0/ ).
UHF-RFID smart gate: Tag action classifier by artificial neural networks

The application of Artificial Neural Networks (ANNs) to discriminate tag actions in UHF-RFID gate is presented in this paper. By exploiting Received Signal Strength Indicator values acquired in a real experimental scenario, a multi-layer perceptron neural network is trained to distinguish among tags incoming, outgoing or passing the RFID gate. A 99% accuracy can be obtained in tag classification by employing only one reader antenna and independently from tag orientation and typology.
Statistical Considerations for Genome-Wide Scans: Design and Application of a Novel Software Package POLYMORPHISM

Objective: Given the cost and complexity of genome-wide scans, optimization of study design is of critical importance. Available algorithms only partially satisfy this need. We designed a software package called ‘POLYMORPHISM’ to meet these needs. Methods: The program is designed to calculate linkage parameters for both ‘single-point’ and ‘two-point’ settings that are applicable also to incompletely informative microsatellite markers. In single-point analysis, the heterozygosity, polymorphism information content (PIC) and linkage information content (LIC) statistics based on marker allele frequencies are provided. In two-point analysis, joint PIC values for two markers, the conditional probability of detecting linkage phase, the frequency of double heterozygotes and the expected number of informative meioses are calculated. Results: Results were obtained using S.A. G.E. /DESPAIR (Design of Linkage Studies Based on Pairs of Relatives) in addition to applying this program to a Centre d’Etude du Polymorphisme pedigree-derived genotyping data set, which estimated critical parameters used in a two-stage genome scan. A single nucleotide polymorphism (SNP)-based one-stage genomic screen strategy is also considered. Conclusions: LIC values are crucial for getting accurate estimates on those parameters that are important for a two-stage genome screening study. Optimization of the cost-effectiveness of an SNP-based genomic screen strategy is possible by modeling a balance between marker information content and marker density.
The feasibility of early hospital discharge with oral antimicrobial therapy in low risk patients with febrile neutropenia following chemotherapy for hematologic malignancies.

BACKGROUND AND OBJECTIVES It is now evident that patients experiencing febrile neutropenia induced by chemotherapy do not constitute a homogeneous group. With increasing accuracy it is now possible to identify low-risk patients for whom less intensive and more convenient treatment may be appropriate. DESIGN AND METHODS In a cohort of such patients with hematologic malignancies, we prospectively validated the usefulness of the risk-index of the Multinational Association of Supportive Care in Cancer (MASCC) in identifying patients at low risk for the development of serious medical complications. Moreover, we studied the feasibility and safety of early discharge of these low-risk patients 24 hours after fever defervescence with subsequent oral antibiotic therapy. RESULTS Of the 279 episodes of febrile neutropenia included, 105 (38%) had a MASCC risk-index score indicating low risk. Serious complications were reported in connection with 111 (63%) high-risk and 16 (15%) low-risk episodes (p<0.0001). The risk-index identified low-risk patients with a specificity, sensitivity and positive predictive value of 87%, 58%, and 84%, respectively. A substantial proportion of the low-risk patients (36%) were considered ineligible for oral therapy, while the remaining 67 (64%) received oral antibiotic treatment following discharge from the hospital 24 hours after defervescence. Upon final evaluation, 64 of the discharged patients (95%) remained afebrile, only three required readmission and there was no mortality in this group. INTERPRETATION AND CONCLUSIONS The MASCC risk-index is a valuable tool for identifying febrile neutropenic patients at low risk for complications. Oral antibiotic treatment following discharge from the hospital 24 hours after defervescence offers a safe and cost-effective alternative to the conventional management of carefully selected low-risk patients.
Comparative pharmacokinetics of cisplatin and three analogues in mice and humans.

Pharmacokinetics of cisplatin, spiroplatin, ethylenediaminemalonatoplatinum(II) (JM-40), and carboplatin was studied in BALB/c x DBA/2 F1 mice receiving 10% lethal doses of 15.5, 6.8, 100, and 165 mg/kg, respectively. Blood samples were collected for up to 5 days after a single i.v. bolus injection. Total platinum in plasma and non-protein-bound free platinum in plasma ultrafiltrate were determined by flameless atomic absorption spectrometry. Parent JM-40 and carboplatin were determined by high performance liquid chromatography. Calculated pharmacokinetic parameters (peak concentrations, half-lives, areas under the curve) were compared with the corresponding values in patients at the maximal tolerated dose. Peak plasma concentrations were 2.4- to 20-fold higher in mice than in humans. Initial and terminal half-lives in mice were up to 6 times shorter than in patients. However, the areas under the plasma concentration versus time curves (AUCs) were found to agree. The ratios of the AUCs of free platinum in patients (AUCp) and mice (AUCm) measured over the first part of the plasma concentration versus time curve were 1.2, 0.3, 1.1, and 0.9 for cisplatin, spiroplatin, JM-40, and carboplatin, respectively. These values changed to 1.3, 0.3, 2.5, and 1.0 when the time interval was extended to free platinum levels just above the detection limit. Ratios of the AUCs of total platinum in patients and mice measured over 5 days were 2.7, 2.6, 4.2, and 1.8, respectively. Using a ratio of 1 for free platinum originating from JM-40, the retrospectively calculated maximal tolerated dose from AUCp at low dosages was 1021 mg/m2 (n = 7; range, 836-1282), compared to 1200 mg/m2 as found in the phase I trial. This suggests that the AUCp/AUCm ratio of free platinum over the first part of the concentration versus time curve can possibly be used to predict the maximal tolerated dose of platinum analogues in humans, during the early stage of phase I studies.
Stabilization of Ca2+-permeable AMPA receptors at perisynaptic sites by GluR1-S845 phosphorylation

AMPA receptor (AMPAR) channel properties and function are regulated by its subunit composition and phosphorylation. Certain types of neural activity can recruit Ca2+-permeable (CP) AMPARs, such as GluR1 homomers, to synapses likely via lateral diffusion from extrasynaptic sites. Here we show that GluR1-S845 phosphorylation can alter the subunit composition of perisynaptic AMPARs by providing stability to GluR1 homomers. Using mice specifically lacking phosphorylation of the GluR1-S845 site (GluR1-S845A mutants), we demonstrate that this site is necessary for maintaining CP-AMPARs. Specifically, in the GluR1-S845A mutants, CP-AMPARs were absent from perisynaptic locations mainly due to lysosomal degradation. This regulation was mimicked by acute desphosphorylation of the GluR1-S845 site in wild-type mice by NMDA application. Furthermore, long-term depression (LTD) was associated with a reduction in perisynaptic CP-AMPAR levels. Our findings suggest that GluR1-S845 is necessary for maintaining CP-AMPARs on the surface, especially at perisynaptic sites, and suggest that the regulation of these receptors is involved in synaptic plasticity.
Non-invasive assessment of ventricular damage in rats with myocardial infarction.

OBJECTIVE The aim was to evaluate whether two dimensional echocardiographic/Doppler (echo/Doppler) techniques could be used to detect left ventricular damage rapidly, accurately, and non-invasively in rats with a myocardial infarction. METHODS Female Wistar rats were initially subjected to either a sham operation or surgery to induce a myocardial infarct by ligating the left main coronary artery. Following a minimum of six weeks to recover from the surgery, all rats were re-anaesthetised and cardiac and stroke indexes were determined at similar heart rates, using echo/Doppler techniques. Postmortem histological assessment of myocardial infarct size was compared with the non-invasive detection of left ventricular wall motion abnormalities, left ventricular dilatation, and the presence of a left ventricular aneurysm found in the living animal. RESULTS Rats with myocardial infarction (n = 8) showed a 33(SEM 4)% reduction (p < 0.01) in cardiac index (due to a 33% reduction in stroke index) when compared to their non-infarcted counterparts (n = 5). In addition, a significant correlation (r = 0.84; n = 25; p < 0.01) was found between the assessment of left ventricular damage via non-invasive echo/Doppler measurements and the histological determination of infarct size. CONCLUSIONS These results support the conclusion that two dimensional echo/Doppler techniques can be used to estimate rapidly and non-invasively the degree of left ventricular damage produced in living rats with myocardial infarction when compared to non-infarcted controls.
Trade Policy and Economic Growth of Turkey in Global Economy: New Empirical Evidences

This paper tries to answer to the questions whether or not trade openness causes economic growth and trade policy changes are good for Turkey as a developing country in global economy before and after 1980. We employ Johansen co-integration and Granger causality tests with error correction modeling based on vector autoregressive. Using WDI data from the pre-1980 and the post-1980, we find that trade openness and economic growth are cointegrated in the second term only. Also the results suggest a lack of long-run causality between our two variables. These findings may imply that trade policy of Turkey should concentrate more on extra complementary economic reforms. JEL Classification—F13, F43, F60, C32. Keywords—Globalization, Trade Policy, Economic Growth, Openness, Co-integration, Turkey.
Susceptibility of Colistin-Resistant, Gram-Negative Bacteria to Antimicrobial Peptides and Ceragenins

ABSTRACT The susceptibility of colistin-resistant clinical isolates of Klebsiella pneumoniae to ceragenins and antimicrobial peptides (AMPs) suggests that there is little to no cross-resistance between colistin and ceragenins/AMPs and that lipid A modifications are found in bacteria with modest changes in susceptibility to ceragenins and with high levels of resistance to colistin. These results suggest that there are differences in the resistance mechanisms to colistin and ceragenins/AMPs.
Asset liability management for individual households

Abstract Personal finance is a challenging topic which can benefit from a scientific approach to individual financial planning. This paper presents an individual asset liability management (iALM) model for life cycle planning which uses the methodology of dynamic stochastic optimisation and incorporates ideas from both classical and behavioural finance. Its implementation is in the form of a decision support tool for use by financial advisers or wealth managers. The investment universe is given by a set of indices for major asset classes and their returns are simulated forward over the lifetime of a household. On the liability side the foreseen cash flows of incomes and outgoings are simulated and punctuated by life events such as illness and death. The household's utility function is constructed for each time period over a range of monetary values in terms of household financial goals and preferences. Taxes and pension savings are treated using the tax shielded saving accounts specific to a national jurisdiction in terms of constraints in the optimisation sub-models. The paper goes on to present an analysis of iALM model recommendations for a representative UK household, together with an evaluation of the sensitivity of the financial plan generated to changes in market environments such as the 2007–9 crisis. The promise of this new technology is to bring modern decision support tools to individual investors in order to facilitate custom designed consumption, savings and investment policies.