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Complex organisms have been subjected to intense selective pressure by host-pathogen coevolution to adapt robust immune responses to pathogen sensing. These responses occur by inducing specific genes within the context of large genomes condensed into chromatin. Despite general description of the chromatin changes that occur across inducible genes, little is known of how specific chromatin features, including histone post-translational modifications (PTM), functionally contribute to transcriptional output of responsive genes. We have described two “signaling-to-chromatin” pathways leading to phosphorylation of histone H3 at residues S28 and S31 that are “read out” by chromatin regulatory factors to augment transcription. H3S28 phosphorylation drives early chromatin activation preceding transcription. This modification delineates expansive chromatin architectural domains containing responsive genes. We are pursuing the hypothesis that H3S28 phosphorylation increases chromatin interaction dynamics within the compartment to favor specific enhancer-promoter interactions and concentrate transcription factors. H3.3S31 is co-transcriptionally phosphorylated along the bodies of induced genes, and coordinately stimulates co-activators and ejects repressors to augment transcription. We hypothesize that these stimulation-dependent histone phosphorylations act synergistically as a dedicated histone code selectively employed at stimulation responsive genes in macrophages and B cells, with potential for involvement in diverse cell types. Our data suggest that co-option of these signaling pathways may contribute to lymphomagenesis, and their disruption could represent novel therapeutic strategies.

We present a numerical investigation of effective chipless tags for radio-frequency-identification (RFID) applications. Chipless tags have been introduced recently as alternatives to standard tags with microchips. While they can significantly reduce the overall cost of RFID systems by eliminating microchips and procedures to mount them on tags, chipless tags bring new challenges, especially in terms of identification reliability. We focus on tag structures that consist of resonators and consider alternative scenarios to find out potential misidentification cases. We also present the robustness of resonator-type elements in terms of fabrication errors, as well as array strategies to significantly increase electromagnetic responses of tags at the cost of reduced compactness.

Waste generated by the electrical and electronic devices is huge concern worldwide. With decreasing life cycle of most electronic devices and unavailability of the suitable recycling technologies it is expected to have huge electronic and electrical wastes to be generated in the coming years. The environmental threats caused by the disposal and incineration of electronic waste starting from the atmosphere to the aquatic and terrestrial living system have raised high alerts and concerns on the gases produced (dioxins, furans, polybrominated organic pollutants, and polycyclic aromatic hydrocarbons) by thermal treatments and can cause serious health problems if the flue gas cleaning systems are not developed and implemented. Apart from that there can be also dissolution of heavy metals released to the ground water from the landfill sites. As all these electronic and electrical waste do posses richness in the metal values it would be worth recovering the metal content and protect the environmental from the pollution. Cyanide leaching has been a successful technology worldwide for the recovery of precious metals (especially Au and Ag) from ores/concentrates/waste materials. Nevertheless, cyanide is always preferred over others because of its potential to deliver high recovery with a cheaper cost. Cyanidation process also increases the additional work of effluent treatment prior to disposal. Several non-cyanide leaching processes have been developed considering toxic nature and handling problems of cyanide with non-toxic lixiviants such as thiourea, thiosulphate, aqua regia and iodine. Therefore, several recycling technologies have been developed using cyanide or non-cyanide leaching methods to recover precious and valuable metals.

Thermotoga maritima is a hyperthermophilic anaerobe that utilizes a vast network of ABC transporters to efficiently metabolize a variety of carbon sources to produce hydrogen. For unknown reasons, this organism does not metabolize glucose as readily as it does glucose di- and polysaccharides. The leading hypothesis implicates the thermolability of glucose at the physiological temperatures at which T. maritima lives. After a 25-day laboratory evolution, phenotypes were observed with growth rates up to 1.4 times higher than and glucose utilization rates exceeding 50% those of the wild type. Genome resequencing revealed mutations in evolved cultures related to glucose-responsive ABC transporters. The native glucose ABC transporter, GluEFK, has more abundant transcripts either as a result of gene duplication-amplification or through mutations to the operator sequence regulating this operon. Conversely, BglEFGKL, a transporter of beta-glucosides, is substantially downregulated due to a nonsense mutation to the solute binding protein or due to a deletion of the upstream promoter. Analysis of the ABC2 uptake porter families for carbohydrate and peptide transport revealed that the solute binding protein, often among the transcripts detected at the highest levels, is predominantly downregulated in the evolved cultures, while the membrane-spanning domain and nucleotide binding components are less varied. Similar trends were observed in evolved strains grown on glycerol, a substrate that is not dependent on ABC transporters. Therefore, improved growth on glucose is achieved through mutations favoring GluEFK expression over BglEFGKL, and in lieu of carbon catabolite repression, the ABC transporter network is modulated to achieve improved growth fitness.

In the aviation industry, maintenance and inventory holding costs of spare parts give managers an opportunity to decrease their operational costs. Therefore, highly accurate demand forecasting is an indispensable entity in spare-parts inventory management. In the literature, traditional demand forecasting methods and measures are insufficient due to the variability of demand quantity and the uncertainty of demand occurrence times. When comparing the demand forecasting methods, MAPE and RMSE measures are usually preferred and these methods often give misleading results when inventory cost minimization is considered. In this paper, a cost-based performance measure and a newly generated joint performance measure, GMEIC, are employed to compare the traditional forecasting methods with the methods generated for non-smooth demand. The methodology applied in this paper consists of data classification, parameter tuning, and ordering decisions based on (Q, R) inventory policy and inventory cost evaluations. In order to measure the performances of the employed forecasting methods for non-smooth demand data, 632 different items were selected from the inventory of Turkish Airlines Technic MRO. It was observed that traditional forecasting methods did not perform better than the forecasting methods developed for non-smooth demand data when the inventory costs were taken into account as the performance measure.

Here we present HiC-DC, a principled method to estimate the statistical significance (P values) of chromatin interactions from Hi-C experiments. HiC-DC uses hurdle negative binomial regression account for systematic sources of variation in Hi-C read counts—for example, distance-dependent random polymer ligation and GC content and mappability bias—and model zero inflation and overdispersion. Applied to high-resolution Hi-C data in a lymphoblastoid cell line, HiC-DC detects significant interactions at the sub-topologically associating domain level, identifying potential structural and regulatory interactions supported by CTCF binding sites, DNase accessibility, and/or active histone marks. CTCF-associated interactions are most strongly enriched in the middle genomic distance range (∼700 kb–1.5 Mb), while interactions involving actively marked DNase accessible elements are enriched both at short (1.5 Mb) genomic distances. There is a striking enrichment of longer-range interactions connecting replication-dependent histone genes on chromosome 6, potentially representing the chromatin architecture at the histone locus body., Genome-wide chromosome conformation capture has helped us identify features of genome topology influencing biology but requires careful statistical analysis. Here the authors present HiC-DC, a bioinformatics method that can detect statistically significant regulatory interactions.

Telephone networks first appeared more than a hundred years ago, long beforetransistors were invented. They, therefore, form the oldest large scale networkthat has grown to touch over 7 billion people. Telephony is now merging manycomplex technologies and because numerous services enabled by these technologiescan be monetized, telephony attracts a lot of fraud. In 2015, a telecom fraudassociation study estimated that the loss of revenue due to global telecom fraudwas worth 38 billion US dollars per year. Because of the convergence oftelephony with the Internet, fraud in telephony networks can also have anegative impact on security of online services. However, there is littleacademic work on this topic, in part because of the complexity of such networksand their closed nature. This paper aims to systematically explorefraud in telephony networks. Our taxonomy differentiates the root causes, thevulnerabilities, the exploitation techniques, the fraud types and finally theway fraud benefits fraudsters. We present an overview of eachof these and use CAller NAMe (CNAM) revenue share fraud as aconcrete example to illustrate how our taxonomy helps in better understandingthis fraud and to mitigate it.

International audience; Conversational lures are artificial agents that, when inserted into speech exchanges, are likely to pass for humans. They are therefore distinguished from robots and other embodied agents by their ability to deceive human interactants in a situation. After appearing at the birth of the Artificial Intelligence project in the form of a quasi-experimental test, Alan Turing’s Game of Imitation (also called the Turing test), conversational lures were developed in various directions, like the famous ELIZA program or Lenny, a program intended to put a stop to malicious calls. The category of conversational lures is therefore quite diverse, in terms both of design methods (IT professionals meet enlightened amateurs) and of uses: answering epistemic questions, managing a psychology consultation, or responding to unsolicited telemarketing calls. In this article, we show the advantages of adopting a configurational approach to study three types of conversational lures and the different linguistic contexts in which they operate, and to understand how they slip into the intelligible texture of interactions, for various practical purposes.; Les leurres conversationnels sont des agents artificiels qui, une fois insérés au sein d’échanges langagiers, sont susceptibles de passer pour des humains. Ils se distinguent donc des robots et autres agents incarnés par leur capacité à leurrer des interactants humains en situation. Apparus à la naissance du projet de l’Intelligence Artificielle dans le Jeu de l’Imitation d’Alan Turing (appelé aussi test de Turing), les leurres conversationnels ont été ensuite développés dans des directions différentes, dont nous proposons une première généalogie. Les modalités de la conception des leurres (des professionnels de l’informatique y croisent des amateurs éclairés) diffèrent, de même que leurs usages : répondre à des interrogations épistémiques, gérer une consultation de psychologie non directive, répondre à des appels non sollicités de télémarketing. Dans cet article, nous montrons l’intérêt d’adopter une approche configurationnelle pour étudier les trois principaux types de leurres conversationnels, les différents contextes langagiers au sein desquels ils interviennent et comment ils parviennent à se glisser dans la texture intelligible des interactions, en vue de réaliser différentes fins pratiques.

Densities and speeds of sound for LiCl in 1-butyl-3-methylimidazolium tetrafluoroborate (bmimBF(4)) and in water were accurately measured as a function of concentration at five temperatures from 288.15 K to 308.15 K. Apparent molar volumes and isentropic compressions were calculated from the measured density and speed of sound data. Infinite dilution values of these derived thermodynamic properties were obtained by a suitable extrapolation procedure. The temperature dependence of apparent molar volumes at infinite dilution was also examined. The results were discussed in terms of interactions between LiCl and bmimBF4 in comparison with those between LiCI and water. (C) 2017 Elsevier Ltd.

BACKGROUND: Effect of pH on recombinant human growth hormone (rhGH) production by Pichia pastoris hGH-Mut+ was investigated at pH = 4.2, 5.0, 5.5, and 6.0. RESULTS: The highest cell concentration was obtained at pH = 6.0 with 53 g L−1, while the highest rhGH concentration was attained at pH = 5.0 as 0.27 g L−1. Total protease secretion increased with increase in pH and with the cultivation time. Oxygen uptake rate increased with increasing pH up to pH = 6.0, having the maximum value, 37 mmol m−3 s−1, at pH = 5.5. KLa values were similar at all the conditions, having a maximum value of 0.14 s−1 at pH = 5.0. Taking the final rhGH concentration into account, the most favourable pH was 5.0; where AOX1 expression level showed a similar trend to AOX activity profiles, having the highest value of 9.4 × 1010 copy mg−1 CDW at t = 15 h; in parallel to AOX1 expression profile, hGH expression level increased until t = 15 h, with the highest value of 4.0 × 1010 copy mg−1 CDW, where a sharp increase in rhGH concentration was obtained. The expression levels of pep4, prb1 and prc1 genes, responsible from the production of proteinase A, proteinase B and, carboxypeptidase Y, were parallel to each other. CONCLUSION: Since it was shown that pH is a crucial operating parameter in fermentation processes using P. pastoris, keeping pH constant at its determined optimum value, pH = 5.0, during the bioprocess is vital in terms of recombinant protein production. Copyright © 2010 Society of Chemical Industry

BACKGROUND: The influence of methanol feed rate on recombinant human growth hormone (rhGH) production by Pichia pastoris hGH-Mut+ in medium containing sorbitol was investigated at three different specific growth rates (µ), namely, 0.02 (MS-0.02), 0.03 (MS-0.03), and 0.04 (MS-0.04). RESULTS: Increasing methanol feed rate above MS-0.03 did not affect sorbitol consumption, showing that µ = 0.03 h−1 is a threshold limiting value, above which sorbitol utilization became independent of methanol feed rate. Moreover, when sorbitol was consumed, no further cell growth was observed. Increase in methanol feed rate triggered cell synthesis and the highest cell concentration was obtained at MS-0.04 as 48 g L−1 (t = 18 h); whereas, the highest rhGH production, 270 mg L−1, was obtained at MS-0.03 as a consequence of lower extracellular protease production and higher AOX activity (41 U g−1 CDW). Oxygen uptake rate increased with increasing µ, having the maximum value, 76.6 mmol m−3 s−1, at MS-0.04. KLa had a tendency to increase with µ, having a maximum value of 0.15 s−1 at MS-0.04 (t = 15 h). CONCLUSION: By considering rhGH concentration and oxygen transfer characteristics, the bioprocess can be improved by a two-stage feeding strategy, operating at MS-0.04 at the beginning of fermentation, and thereafter shifting to MS-0.03. Copyright © 2009 Society of Chemical Industry

Bu araştırmanın amacı kayıp veri sorununun çözümünde kullanılan farklı yöntemlerin etkililiğini ölçeklerin geçerliği ve güvenirliği bağlamında karşılaştırmaktır. Bu amaçla, PISA 2012 Türkiye örneklemi ve "Matematik Çalışma Etiği" ölçeğinden yararlanılmıştır. Analizler için Türkiye örnekleminden rastgele 200 kişilik tam veri seti çekilmiştir. Tam veri setinden, tamamıyla rassal olarak kayıp (TROK) mekanizması altında, farklı oranlarda veri silme ve bu verileri farklı kayıp veri yöntemleriyle yeni tam veri setlerine dönüştürme işlemlerinden sonra geçerlik ve güvenirliğe ilişkin analizler gerçekleştirilmiştir. Kayıp veri içeren setlerin yeni tam veri setlerine dönüştürülmesinde seri ortalaması, yakın noktaların ortalaması, yakın noktaların medyanı, doğrusal değer kestirimi, noktanın doğrusal eğimi, liste bazında silme, beklenti maksimizasyonu, regresyon ataması ve çoklu atama kayıp veri yöntemleri kullanılmıştır. Yeni tam veri setlerinden geçerlik ve güvenirliğe ilişkin elde edilen değerleri karşılaştırarak yorumlamada tam veri setinden elde edilen değerler referans değerler olarak kullanılmıştır. Araştırma sonuçlarına göre liste bazında silme yöntemi için elde edilen değerler, genel olarak tam veri setinden elde edilen değerlere en az benzerlik gösteren değerler olmuştur. Yaklaşık değer atama yöntemleri için elde edilen değerler kayıp veri oranının düşük olduğu durumlarda genel olarak tam veri setinden elde edilen değerlere yakın veya aynı değerleri verirken, tüm kayıp veri oranları için tam veri setinden elde edilen değerlere en yakın değer veren yöntemler çoklu atama, beklenti maksimizasyonu ve regresyon ataması yöntemleri olmuştur. The purpose of this research is to compare the effectiveness of various methods used in solving missing data problems in the context of validity and reliability of the scales. For this purpose PISA 2012 Turkey sample and "Math Work Ethics" scale was used. For the analysis, complete data set of 200 persons were chosen from the Turkey sample at random. After the process of data deletion at different rates from complete data set and transforming them into new complete data sets, under missing completely at random (MCAR) mechanism, analysis of validity and reliability were realized. During the phase of transforming missing data set into new complete data sets, series mean, mean of nearby points, median of nearby points, linear interpolation, linear trend at point, listwise deletion, expectation maximization, regression imputation and multiple imputation methods were used. The values obtained from the complete data set were used as reference values in interpreting the values by comparing the values of validity and reliability at the new complete data sets. The research results reveal that the values obtained for the listwise deletion at different rates of missing data are the values with the least similarity to the ones generally obtained from the complete data set. While the values obtained for the approximate value imputation methods resulted in proximal or same values as the ones generally obtained from the complete data set in cases where the missing data rate is low multiple imputation, expectation maximization and regression imputation methods resulted in close proximal values at all missing data rates as the ones obtained from the complete data set.

Background The metabolic capabilities of acetogens to ferment a wide range of sugars, to grow autotrophically on H2/CO2, and more importantly on synthesis gas (H2/CO/CO2) make them very attractive candidates as production hosts for biofuels and biocommodities. Acetogenic metabolism is considered one of the earliest modes of bacterial metabolism. A thorough understanding of various factors governing the metabolism, in particular energy conservation mechanisms, is critical for metabolic engineering of acetogens for targeted production of desired chemicals. Results Here, we present the genome-scale metabolic network of Clostridium ljungdahlii, the first such model for an acetogen. This genome-scale model (iHN637) consisting of 637 genes, 785 reactions, and 698 metabolites captures all the major central metabolic and biosynthetic pathways, in particular pathways involved in carbon fixation and energy conservation. A combination of metabolic modeling, with physiological and transcriptomic data provided insights into autotrophic metabolism as well as aided the characterization of a nitrate reduction pathway in C. ljungdahlii. Analysis of the iHN637 metabolic model revealed that flavin based electron bifurcation played a key role in energy conservation during autotrophic growth and helped identify genes for some of the critical steps in this mechanism. Conclusions iHN637 represents a predictive model that recapitulates experimental data, and provides valuable insights into the metabolic response of C. ljungdahlii to genetic perturbations under various growth conditions. Thus, the model will be instrumental in guiding metabolic engineering of C. ljungdahlii for the industrial production of biocommodities and biofuels.

The influence of methanol feeding rate on intracellular reaction network of recombinant human growth hormone (rhGH) producing Pichia pastoris was investigated at three different specific growth rates, namely, 0.02 (MS-0.02), 0.03 (MS-0.03), and 0.04 h(-1) (MS-0.04) where Period-I (33 ≤ t42 h) includes the early exponential growth phase; Period-II (42 ≤ t48 h) is the exponential growth phase where the specific cell growth rate decreases; Period-III (48 ≤ t ≤51 h) is the exponential growth phase where rhGH concentration was the highest; and Period-IV (t51 h) is the diminution phase for rhGH and cell synthesis. In Period-I, almost all of the formaldehyde entered the assimilatory pathway, at MS-0.02 and MS-0.03, whereas, at MS-0.04 high methanol feeding rate resulted in an adaptation problem. In Period-III, only at MS-0.02 co-carbon source sorbitol uptake-flux was active showing that sorbitol uptake does not affected from the predetermined feeding rate of methanol at μ(0)0.02 h(-1). The biomass synthesis flux value was the highest in Period-I, -II and -III, respectively at MS-0.03MS-0.04, MS-0.04 and MS-0.02; whereas, rhGH flux was the highest in Period-I, -II, and -III, respectively at MS-0.03, MS-0.02 and MS-0.03. Based on the fluxes, Period-I should start with MS-0.03 methanol feeding rate and starting from the middle of Period-II methanol feeding rate should be shifted to MS-0.02.

Printed circuit board (PCB) is the essential part of electronic devices and has an important source of base and precious metals with high economic potential. In this study, selective leaching of gold from PCB was performed in an iodine-hydrogen peroxide (I-2-H2O2) solution system. The effects of different parameters such as iodine concentrations, H2O2 concentrations and solids-% on the gold leaching dynamics were investigated. The results show that increasing solids-% has a negative influence on the gold leaching. However, gold recovery from the e-wastes in a solution containing 3% iodine, 1% H2O2 with solids-% of 15% resulted with 100% recovery among all leaching tests.

Beginning in the 1960’s, Denmark recruited Turkish guest workers. Today, the Turkish minority is Denmark’s largest minority group from non-western countries. This article examines the social challenges of the Turkish minority in Denmark from 1970 to 2021, and their integration during this period. This study uses several methods to obtain insight into the integration process of Turkish immigrants over three generations in Denmark and the challenges they faced and continue to face. In addition to the source criticism and a comprehensive literature review, this study uses qualitative and quantitative methods to understand Turkish immigrants’ immigration processes. Qualitative and quantitative analysis in the field of Danish historical research, specifically the area concerning the Turkish minority are not adequately covered by the existing literature. This study finds that all three generations of the Turkish minority in Denmark experienced social challenges in several areas that are related to each other, and these social challenges have an effect on their integration status. Some social challenges have decreased over generations but specifically discrimination and racism have not.