bluuebunny/crossref_metadata_2025 huggingface dataset:
Regulation of the pAD1-encoded sex pheromone response in Enterococcus faecalis: nucleotide sequence analysis of traA
Authors: Pontius L T , Clewell D B
Published: November 2016

The Enterococcus faecalis plasmid pAD1 conjugatively transfers in response to a sex pheromone, cAD1, excreted by potential recipient cells. A key determinant responsible for regulation of pAD1 transfer is traA, which encodes a negative regulator also believed to function in signal sensing. In this study, we analyzed the nucleotide sequence and transcription of traA. A protein of 319 amino acids with a molecular weight of 37,856 was inferred and found to exhibit limited homology with several DNA-binding proteins. Analysis of Tn917-lac insertions resulting in transcriptional lacZ fusions within the 3' end of the traA transcript showed that it overlaps slightly with a convergently-transcribed C-region transcript. Insertional mutations affecting TraA repressor function and signal sensing functions were localized.
Replacement of the aliphatic chains of Clostridium acetobutylicum by exogenous fatty acids: regulation of phospholipid and glycolipid composition
Authors: Johnston N C , Goldfine H
Published: November 2016

The membrane lipid aliphatic chains of Clostridium acetobutylicum ATCC 4259 have been extensively modified by growth in biotin-free medium containing vitamin-free casein hydrolysate supplemented with either elaidic acid, oleic acid, or mixtures of palmitic and oleic acids. Growth with elaidic acid resulted in polar lipids containing 88.6% 18:1 acyl chains and 94.5% 18:1 ether-linked chains. Growth with oleic acid resulted in comparable levels of enrichment of the lipids with 18:1 chains and C19 chains containing cyclopropane rings. When cells were grown with mixtures of palmitic and oleic acids, the ether-linked chains of the plasmalogens were greater than or equal to 64% 18:1 plus C19 chains containing cyclopropane rings at all ratios of oleic to palmitic acid in the medium. The acyl chains reflected the palmitic acid content of the medium more closely. Marked changes were observed in both phospholipid and glycosyldiglyceride compositions as the lipid acyl and ether-linked chains became more enriched with unsaturated and cyclopropane chains. The ratio of the glycerol acetal of plasmenylethanolamine to phosphatidylethanolamine increased, the ratio of cardiolipin to phosphatidylglycerol decreased, and the ratio of diglycosyldiglyceride to monoglycosyldiglyceride increased. However, the monoglycosyldiglyceride/diglycosyldiglyceride ratio was lower for cells grown on 100% oleic acid than for cells grown on 60 or 80% oleic acid. In the membranes of cells grown on 100% oleic acid, the ratio of glycolipids to phospholipids was lower than that found in cells grown on 60% oleic acid. These results indicate that C. acetobutylicum regulates its polar lipid composition in a complex manner involving phospholipids and glycosyldiglycerides. These changes can affect the equilibria between those lipids that form bilayers and those lipids that tend to form nonlamellar phases when enriched with unsaturated aliphatic chains. Phosphoglycolipids of unknown structure were also observed in cells grown either with biotin or with fatty acids. The content of the most abundant phosphoglycolipid also varied with the degree of unsaturation of the cellular lipids.
Expression, secretion, and processing of staphylococcal nuclease by Corynebacterium glutamicum
Authors: Liebl W , Sinskey A J , Schleifer K H
Published: November 2016

The gene for staphylococcal nuclease (SNase), an extracellular enzyme of Staphylococcus aureus, was introduced into Corynebacterium glutamicum. The heterologous gene was expressed in this host organism, and SNase was efficiently exported to the culture medium. Amino-terminal sequencing of SNase secreted by C. glutamicum revealed that the signal peptide was apparently cleaved off at precisely the same position as in the original host, S. aureus. As with S. aureus, a second smaller form of SNase (A form), whose appearance is presumably the result of a secondary processing step, was found in the culture medium of the recombinant C. glutamicum strain. The A form was one residue shorter than the mature nuclease A produced by S. aureus. Variation of the sodium chloride concentration in the growth medium had a marked influence on the location and the processing of SNase by C. glutamicum. In a complex growth medium containing 4% sodium chloride, SNase was exclusively located in the supernatant, but a significant amount of the enzyme remained cell associated if the strain was grown in a low-salt medium. Also, high salt concentrations seemed to inhibit processing of the high-molecular-weight form of SNase (B form) to the smaller A form. Similarities and differences in the export and modes of processing of SNase by three different, nonrelated gram-positive host organisms are discussed. Finally, a versatile Escherichia coli-C. glutamicum tac-lacIq expression shuttle vector was constructed. With this vector, it was possible to achieve isopropyl-beta-D-galactopyranoside (IPTG)-inducible overexpression and secretion of SNase in C. glutamicum, whereby the expression level was dependent on the concentration of the inducer.
Structures of chaperonins from an intracellular symbiont and their functional expression in Escherichia coli groE mutants
Authors: Ohtaka C , Nakamura H , Ishikawa H
Published: November 2016

An intracellular symbiont harbored by the aphid bacteriocyte, a specialized fat body cell, synthesizes in vivo substantially only one protein, symbionin, which is a member of the chaperonin-60 family of molecular chaperones. Nucleotide sequence determination of the symbionin region of the endosymbiont genome revealed that it contains the two-cistron operon sym. Just like the Escherichia coli groE operon, the sym operon was dually led by a heat shock and an ordinary promoter sequence. According to the nucleotide sequence, symbionin was 85.5% identical to GroEL of E. coli at the amino acid sequence level. SymS, another protein encoded in the sym operon, which is a member of chaperonin-10, was 79.6% identical to GroES. Complementation experiments with E. coli groE mutants showed that the chaperonin-10 and chaperonin-60 genes from the endosymbiont are expressed in E. coli and that they can function as molecular chaperones together with endogenous GroEL and GroES, respectively.
Expression of Erwinia amylovora hrp genes in response to environmental stimuli
Authors: Wei Z M , Sneath B J , Beer S V
Published: November 2016

Seven hrp loci that are essential for the hypersensitive reaction elicited by Erwinia amylovora were transcriptionally fused with a derivative of transposon Tn5, containing the promoterless Escherichia coli beta-glucuronidase reporter gene. The seven hrp fusions were used to monitor expression of the hrp loci in vitro and in planta. No significant expression was detected in rich medium for any of the fusions. However, five of them were expressed highly in planta and in inducing medium that contains mannitol, salts, and 5 mM (NH4)2SO4. Expression of these five hrp loci is regulated by ammonium, nicotinic acid, complex-nitrogen sources, certain carbon sources, temperature, and pH. Under well-defined conditions, i.e., in inducing medium, no specific plant components were required for transcriptional activation of the hrp loci. The high levels of expression detected in vitro were comparable to those determined during the development of the hypersensitive reaction in tobacco. Differential levels of expression of the hrp loci occurred in host and nonhost plants. In pear, a host plant, expression of the hrp loci was delayed and greatly reduced compared with expression in tobacco leaves, a nonhost.
Effects of nitrate and nitrite on dissimilatory iron reduction by Shewanella putrefaciens 200
Authors: DiChristina T J
Published: November 2016

The inhibitory effects of nitrate (NO3-) and nitrite (NO2-) on dissimilatory iron (FE3+) reduction were examined in a series of electron acceptor competition experiments using Shewanella putrefaciens 200 as a model iron-reducing microorganism. S. putrefaciens 200 was found to express low-rate nitrate reductase, nitrite reductase, and ferrireductase activity after growth under highly aerobic conditions and greatly elevated rates of each reductase activity after growth under microaerobic conditions. The effects of NO3- and NO2- on the Fe3+ reduction activity of both aerobically and microaerobically grown cells appeared to follow a consistent pattern; in the presence of Fe3+ and either NO3- or NO2-, dissimilatory Fe3+ and nitrogen oxide reduction occurred simultaneously. Nitrogen oxide reduction was not affected by the presence of Fe3+, suggesting that S. putrefaciens 200 expressed a set of at least three physiologically distinct terminal reductases that served as electron donors to NO3-, NO2-, and Fe3+. However, Fe3+ reduction was partially inhibited by the presence of either NO3- or NO2-. An in situ ferrozine assay was used to distinguish the biological and chemical components of the observed inhibitory effects. Rate data indicated that neither NO3- nor NO2- acted as a chemical oxidant of bacterially produced Fe2+. In addition, the decrease in Fe3+ reduction activity observed in the presence of both NO3- and NO2- was identical to the decrease observed in the presence of NO2- alone. These results suggest that bacterially produced NO2- is responsible for inhibiting electron transport to Fe3+.
Mutations of the phage lambda nutL region that prevent the action of Nun, a site-specific transcription termination factor
Authors: Baron J , Weisberg R A
Published: November 2016

Phage HK022 encodes a protein, Nun, that promotes transcription termination within the pL and pR operons of its relative, phage lambda. The lambda sequences required for termination had previously been shown to overlap the nut sites, which are essential for transcription antitermination during normal lambda growth. To further specify the Nun target and to determine its relation to the nut sites, we constructed deletion and base substitution mutations of the lambda nutL region and measured Nun-dependent reduction of the expression of a downstream reporter gene. The shortest construct that retained full Nun responsiveness was a 42-bp segment that included both boxA and boxB, sequences that have been implicated in lambda antitermination. Deletion of boxA reduced Nun termination, and deletion of both sequences eliminated Nun termination. Base substitutions in boxA and the proximal portion of boxB impaired Nun termination, while base substitutions between boxA and boxB, in the distal portion of boxB, and immediately downstream from boxB had no appreciable effect. The termination defect of all of the base substitution mutations was relieved by increasing the level of Nun protein; in contrast, the deletions and a multiple-base substitution did not regain full Nun responsiveness at elevated Nun concentrations. We also asked if these mutant nut regions retained their ability to interact with N, the lambda-encoded antitermination protein. A qualitative assay showed that mutations within boxA or boxB reduced interaction, while mutations outside boxA and boxB did not. These data show that (i) the recognition sites for N and Nun overlap to a very considerable extent but are probably not identical and (ii) a high concentration of Nun promotes its interaction with mutant nut sites, a behavior also reported to be characteristic of N.
Localization of diphtheria toxin nuclease activity to fragment A
Authors: Lessnick S L , Lyczak J B , Bruce C , Lewis D G , Kim P S , Stolowitz M L , Hood L , Wisnieski B J
Published: November 2016

We describe a series of experiments that aimed to establish whether nuclease activity is actually associated with diphtheria toxin (DTx) and its A subunit (DTA), as we originally reported (M. P. Chang, R. L. Baldwin, C. Bruce, and B. J. Wisnieski, Science 246:1165-1168, 1989). Here we show that (i) trypsinization of DTx does indeed produce nucleolytically active DTA, (ii) reduction of electroeluted, unreduced, cleaved DTx (58 kDa) yields nuclease-active DTA (24 kDa), and (iii) fractionation of DTx and DTA by anion-exchange chromatography leads to coelution of nuclease activity with both forms of the toxin, even though each form elutes at a distinct salt concentration. In addition, we show that Escherichia coli-derived DTA also expresses nuclease activity. These studies confirm our initial assertion that the nuclease activity observed in DTx preparations is intrinsic to the DTA portion of DTx.
Differential depolymerization mechanisms of pectate lyases secreted by Erwinia chrysanthemi EC16
Authors: Preston J F , Rice J D , Ingram L O , Keen N T
Published: November 2016

The four pectate lyases (EC 4.2.2.2) secreted by Erwinia chrysanthemi EC16 have been individually produced as recombinant enzymes in Escherichia coli. Oligogalacturonates formed from polygalacturonic acid during reactions catalyzed by each enzyme have been determined by high-performance liquid chromatography analysis. PLa catalyzes the formation of a series of oligomers ranging from dimer to dodecamer through a random endolytic depolarization mechanism. PLb and PLc are trimer- and tetramer-generating enzymes with an identical combination of endolytic and exolytic mechanisms. PLe catalyzes a nonrandom endolytic depolymerization with the formation of dimer as the predominant product. The pectate lyases secreted by E. chrysanthemi EC16 represent a battery of enzymes with three distinct approaches to the depolymerization of plant cell walls.
Heterologous expression and secretion of a Streptomyces scabies esterase in Streptomyces lividans and Escherichia coli
Authors: Hale V , McGrew M , Carlson B , Schottel J L
Published: November 2016

The esterase gene from Streptomyces scabies FL1 was cloned and expressed in Streptomyces lividans on plasmids pIJ486 and pIJ702. In S. lividans, the esterase gene was expressed during later stages of growth and was regulated by zinc, as is seen with S. scabies. The 36-kDa secreted form of the esterase was purified from S. lividans. N-terminal amino acid sequencing indicated that the processing site utilized in S. lividans for the removal of the signal sequence was the same as that recognized for processing in S. scabies. Western blots (immunoblots) revealed the presence of a 40-kDa precursor form of the esterase in cytoplasmic extracts. A 23-amino-acid deletion was introduced into the putative signal sequence for the esterase. When this deleted form of the esterase was expressed in S. lividans, a cytoplasmic 38-kDa precursor protein was produced but no secreted esterase was detected, suggesting the importance of the deleted sequence for efficient processing and secretion. The esterase gene was also cloned into the pUC119 plasmid in Escherichia coli. By using the lac promoter sequence, the esterase gene was expressed, and the majority of the esterase was localized to the periplasmic space.
Activities of two dissimilar thioredoxins from the cyanobacterium Anabaena sp. strain PCC 7120
Authors: Gleason F K
Published: November 2016

Thioredoxin is a small redox protein that functions as a reducing agent and modulator of enzyme activity. A gene for an unusual thioredoxin was previously isolated from the cyanobacterium Anabaena sp. strain PCC 7120 and cloned and expressed in Escherichia coli. However, the protein could not be detected in Anabaena cells (J. Alam, S. Curtis, F. K. Gleason, M. Gerami-Nejad, and J. A. Fuchs, J. Bacteriol. 171:162-171, 1989). Polyclonal antibodies to the atypical thioredoxin were prepared, and the protein was detected by Western immunoblotting. It occurs at very low levels in extracts of Anabaena sp. and other cyanobacteria. No antibody cross-reaction was observed in extracts of eukaryotic algae, plants, or eubacteria. The anti-Anabaena thioredoxin antibodies did react with another unusual thioredoxin-glutaredoxin produced by bacteriophage T4. Like the T4 protein and other glutaredoxins, the unusual cyanobacterial thioredoxin can be reduced by glutathione. The Anabaena protein can also activate enzymes of carbon metabolism and has some functional similarity to spinach chloroplast thioredoxin f. However, it shows only 23% amino acid sequence identity to the spinach chloroplast protein and appears to be distantly related to other thioredoxins. The data indicate that cyanobacteria, like plant chloroplasts, have two dissimilar thioredoxins. One is related to the more common protein found in other prokaryotes, and the other is an unusual thioredoxin that can be reduced by glutathione and may function in glucose catabolism.
Fluidized-sediment pipes in Gale crater, Mars, and possible Earth analogs
Authors: Rubin David M. , Fairén A.G. , Martínez-Frías J. , Frydenvang J. , Gasnault O. , Gelfenbaum G. , Goetz W. , Grotzinger J.P. , Le Mouélic S. , Mangold N. , Newsom H. , Oehler D.Z. , Rapin W. , Schieber J. , Wiens R.C.
Published: November 2016

Since landing in Gale crater, the Mars Science Laboratory rover Curiosity has traversed fluvial, lacustrine, and eolian sedimentary rocks that were deposited within the crater ∼3.6 to 3.2 b.y. ago. Here we describe structures interpreted to be pipes formed by vertical movement of fluidized sediment. Like many pipes on Earth, those in Gale crater are more resistant to erosion than the host rock; they form near other pipes, dikes, or deformed sediment; and some contain internal concentric or eccentric layering. These structures provide new evidence of the importance of subsurface aqueous processes in shaping the near-surface geology of Mars.
Barriers and facilitators to physical activity in people with hip or knee osteoarthritis: protocol for a systematic review of qualitative evidence
Authors: Kanavaki Archontissa M , Rushton Alison , Klocke Rainer , Abhishek Abhishek , Duda Joan L
Published: November 2016

Introduction

This protocol aims to describe the objective and methods to be followed in a systematic review of qualitative studies on barriers and facilitators to physical activity (PA) in people with hip or knee osteoarthritis (OA).

Methods and analysis

MEDLINE, EMBASE, PhychINFO, Web of Science, CINAHL, SPORTDiscus, Scopus and grey literature sources will be electronically searched. Hand search of qualitative research-centred journals, reference screening of relevant reviews and inquiries to researchers active in the field will complement the search. Studies will be selected if they apply qualitative or mixed-methods designs to directly explore factors that correspond to engagement in PA/exercise or, the perceptions regarding PA/exercise in people with hip or knee OA. The Critical Appraisal Skills Programme Qualitative Checklist and the evaluative criteria of credibility, transferability, dependability and confirmability will be applied for the study appraisal. 2 independent reviewers will perform the search, study selection and study appraisal. Thematic synthesis will be used for synthesising the findings of the primary studies and the process and product of the synthesis will be checked by a second researcher. ConQual approach will be used for assessing the confidence in the qualitative findings.

Ethics and dissemination

This systematic review will inform our understanding of the PA determinants and how to optimise behaviour change in people living with hip or knee OA. The review findings will be reported in a peer-reviewed journal and presented at national or international conferences. The study raises no ethical issues.

Trial registration number

CRD42016030024.
Association between obesity indices and type 2 diabetes mellitus among middle-aged and elderly people in Jinan, China: a cross-sectional study
Authors: Wang Shukang , Ma Wei , Yuan Zhongshang , Wang Shu-mei , Yi Xiangren , Jia Hongying , Xue Fuzhong
Published: November 2016

Background

The relationship between obesity and type 2 diabetes mellitus (T2DM) varies with geographical area and race.

Objectives

To investigate the prevalence of T2DM and the proportion of subjects with undiagnosed T2DM. In addition, to compare the associations between different obesity indices and T2DM for middle-aged and elderly people from six communities in Jinan, China.

Setting

A cross-sectional study was designed and the study subjects were chosen from blocks which were randomly selected in the 6 communities of Jinan, China in 2011–2012.

Participants

A total of 3277 residents aged ≥50 years were eligible for this study, but 1563 people were excluded because they did not provide anthropometric data such as height, weight, waist circumference (WC), hip circumference, systolic blood pressure, diastolic blood pressure, fasting plasma glucose, triglyceride (TG), total cholesterol (TC) or information about their current medication use. Hence, 1714 participants were included in the final data analysis.

Results

The prevalence of T2DM among people aged ≥50 years was 16.6% (19.3% for men and 15.3% for women) and the proportion of patients with undiagnosed T2DM was 32.7%. Compared with the lowest levels of body mass index (BMI), WC, waist-to-hip ratio or waist-to-stature ratio (WSR), the ORs and 95% CIs of the highest levels for men, after adjusting for age, smoking, alcohol drinking, regular exercise, hypertension, TG and TC, were 1.607 (0.804 to 3.210), 2.189 (1.118 to 4.285), 1.873 (0.968 to 3.623) and 2.572 (1.301 to 5.083), respectively, and for women, 2.764 (1.622 to 4.712), 2.407 (1.455 to 3.985), 2.500 (1.484 to 4.211) and 2.452 (1.447 to 4.155), respectively.

Conclusions

Among adults aged ≥50 years in Jinan, China, the best indicator of the relationship between obesity and T2DM is WSR for men and BMI for women, respectively.
Plants, fungi, and freeloaders: examining temporal changes in the “taxonomic richness” of endophytic fungi in the dwarf mistletoe Arceuthobium americanum over its growing season
Authors: Hampel Lucas D. , Cheeptham Naowarat , Flood Nancy J. , Ross Friedman Cynthia
Published: November 2016

Arceuthobium americanum Nutt. ex Engelm. (lodgepole pine dwarf mistletoe) is a dioecious plant parasitizing conifers in North America. Here, we documented changes in the “taxonomic richness” of culturable endophytic fungi in male and female A. americanum over the growing season. Endophytic fungi were isolated from vegetative stems of surface-sterilized aerial shoots from male and female A. americanum collected weekly from April to September. Isolated fungi were characterized macroscopically, generating a database of 48 morphologically unique forms that likely represented individual taxa. A random sample of endophytic fungi was sequenced to determine identity based on ITS rDNA. Richness increased throughout the growing season similarly in the stems of both sexes, suggesting that increased developmental age or time in the environment facilitates an increase in endophyte richness: male and female endophyte communities were 91% similar based on Sorensen’s coefficient. Sequenced endophytes came from many diverse taxa, including Serpula, Alternaria, and Tremella, which may function as mutualistic symbionts within the mistletoe. An increase in fungal richness throughout the growing season has been observed in all flowering plants examined to date, although our observation is the first for the genus and for parasitic plants in general, and has also contributed to knowledge of fungal diversity in dioecious plants.
Beam–beam effects of single ring and partial double ring scheme in CEPC
Authors: Zhang Yuan
Published: November 2016

After the Higgs discovery, it is believed that a circular [Formula: see text] collider could serve as a Higgs factory. The high energy physics community in China launched a study of a 50–100 km ring collider. A preliminary conceptual design report (Pre-CDR) has been published in early 2015. This report is based on a 54-km ring design. Some progress on beam–beam effect study after Pre-CDR is shown in the paper. We estimate the beamstrahlung lifetime using a pure strong–strong code as a comparison with the result obtained using a quasi-strong–strong method. The effect of parasitic crossing in the pretzel scheme is also estimated for the very first time. The feasibility of the main parameters for partial double ring scheme are evaluated from the point view of beam–beam interaction.
Hybrid driven three-terminal thermoelectric refrigerators based on resonant tunneling quantum dots
Authors: Shi Zhicheng , Qin Weifeng , He Jizhou
Published: November 2016

In this paper, we propose a pair of symmetric three-terminal refrigerator models with a hot cavity connected to two colder reservoirs via ideal tunneling quantum dots. The cooling of the refrigerators is achieved by investing thermal power from a hot reservoir and electric power from an applied voltage. Based on the model proposed, we numerically analyze the performance of the refrigerators with different half width of energy levels, and particularly discuss the coefficient of performance for zero applied voltage in the limit of a small half level width. Finally, we optimize with half width of energy levels and get the optimal region of the refrigerators.
Multi-Edged Wide-Band Rectangular Microstrip Fractal Antenna Array for C- and X-Band Wireless Applications
Authors: Khinda Jaspal Singh , Tripathy Malay Ranjan , Gambhir Deepak
Published: November 2016

A low-cost multi-edged rectangular microstrip fractal antenna (RMFA) yielding a huge bandwidth of 8.62[Formula: see text]GHz has been proposed in this paper. The proposed fractal antenna design constitutes a radiation patch, fed with 50[Formula: see text][Formula: see text] microstrip line and a partial ground plane. The partial ground plane is the combination of shapes of rectangle and three-point arc. The proposed antenna is simulated as well as fabricated. The simulated results using electromagnetic solver software and measured with vector network analyzer bench MS46322A are presented and compared. The various parameters such as return loss, voltage standing wave ratio (VSWR), antenna impedance, gain, directivity, group delay and phase of [Formula: see text], radiation efficiency and patterns are presented here. The depth of return loss is improved for a wide range of frequencies. The proposed fractal antenna is further extended to linear array to improve the gain and impedance bandwidth. The simulated and measured results prove the superiority of the proposed antenna.
Improvement of nonlinear optical properties of phthalocyanine bearing diethyleneglycole chains: Influence of symmetry lowering vs. heavy atom effect
Authors: Britton Jonathan , Martynov Alexander G. , Oluwole David O. , Gorbunova Yulia G. , Tsivadze Aslan Yu. , Nyokong Tebello
Published: November 2016

This paper reports the successful synthesis of the low symmetry phthalocyanines: metal-free 2,3-bis[2′-(2′′-hydroxyethoxy)ethoxy]-9,10,16,17,23,24-hexa-[Formula: see text]-butoxyphthalocyanine 1H[Formula: see text] and its zinc complex 1Zn along with their nonlinear optical (NLO) behavior in solution and in thin films. 1H NMR investigations evidenced of higher dissymmetry of electronic density in 1H[Formula: see text] in comparison with 1Zn. This dissymmetry is responsible for unusually higher values of Im[[Formula: see text]]/[Formula: see text], [Formula: see text], and [Formula: see text] for 1H[Formula: see text]in contrast to 1Zn, where the notable effect of heavy-metal enhancement of ISC was expected. Both compounds showed Im[[Formula: see text]]/[Formula: see text] values of the order of 10[Formula: see text] in chloroform which are higher in comparison to the symmetrical octabutoxyphthalocyanine H2[(BuO)8Pc]. NLO properties of 1H[Formula: see text] were improved via its incorporation into polycarbonate polymeric matrix together with CdSe@CdS-TOPO quantum dots. In such composite the value of Im[[Formula: see text]]/[Formula: see text] was almost three times higher in comparison with 1H[Formula: see text] solution in chloroform. The obtained composites are expected to be perspective components of optical materials, capable of protection against strong light irradiation.
RAROC in portfolio optimization
Authors: Xidonas Panagiotis , Kountzakis Christos E. , Hassapis Christis , Staikouras Christos
Published: November 2016

In this paper, we provide the implications of using the performance ratio being defined by the expected shortfall-well known as RAROC-in static portfolio optimization, by giving the proof of the relevant results. We also use RAROC as a primary function in the AUGMECON algorithm, providing the main scheme of such an application on data from Athens Stock Exchange. The use of RAROC in AUGMECON as a primary function is also faced as an optimization problem under a general nonconvex optimization framework.
Asymmetric Underlapped FinFETs for Near- and Super-Threshold Logic at Sub-10nm Technology Nodes
Authors: Goud A. Arun , Venkatesan Rangharajan , Raghunathan Anand , Roy Kaushik
Published: November 2016

Extending double-gate FinFET scaling to sub-10nm technology regime requires device-engineering techniques for countering the rise of direct source to drain tunneling (DSDT), edge direct tunneling (EDT) and short channel effects (SCE) that degrade FinFET I-V characteristics. Symmetric underlap is effective for eliminating EDT, diminishing DSDT, and lowering the fringe component of gate capacitance. However, excessive symmetric underlap also lowers the on-current, which is mainly due to thermionic emission. In this work, it is demonstrated that at sub-10nm node, asymmetric underlapped FinFETs with slightly longer underlap toward drain side than source side are superior to symmetric underlapped FinFETs due to further improvement in I
on
/I
off
and reduction in gate-to-drain capacitance. Using quantum mechanical device simulations, FinFETs with various degrees of underlap have been analyzed for improvement in I-V characteristics. A FinFET model for circuit simulations has been constructed that captures the major sub-10nm leakage components, namely, thermionic emission, DSDT, EDT, direct gate oxide tunneling and its associated components. By simulating a 10-stage NAND circuit and a LEON3 processor with interconnect parasitics using these devices, it is shown that asymmetric underlap instead of symmetric underlap in sub-10nm FinFETs can offer lower energy consumption with improved performance for near-threshold logic and higher energy-efficiency for super-threshold logic operation.
How Hard Is Positive Quantification?
Authors: Schubert Aleksy , Urzyczyn Paweł , Walukiewicz-Chrząszcz Daria
Published: November 2016

We show that the constructive predicate logic with positive (covariant) quantification is hard for doubly exponential universal time, that is, for the class
co-
2-N
exptime
. Our approach is to represent proof-search as computation of an alternating automaton. The memory of the automaton is structured in a way that strictly corresponds to scopes of the binders used in the constructed proof. This provides an application of automata-theoretic techniques in proof theory.
Hypertext 2016 in Halifax
Authors: Gkantouna Vassiliki , Rubart Jessica
Published: November 2016

The 27
th
ACM Conference on Hypertext and Social Media was held in Halifax, Canada, from July 10 to 13 hosted at the campus of the Dalhousie University. The General Chairs were Professor Dr. Jamie Blustein and Dr. Eelco Herder, Complemented by the Program Charis Professors Dr. Helen Ashman and Dr. Jessica Rubart. The conference provided one day of workshops and three main conference days. Apart from the regular research tracks, HT'16 also featured an intersting creative track. HT'16 was collocated with UMAP 2016, the 24
th
international conference on User Modeling, Adaptation and Personalization. This newsletter article briefly describes the conference and also the venue, based on the authors' personal perspectives.
Upcoming SIGWEB supported conferences
Authors: Samuel Hamman
Published: November 2016

The Special Interest Group on Hypertext and the Web, SIGWEB was created in 1989 to support the community participating in the annual ACM Hypertext Conference. Now in its third decade, SIGWEB has grown considerably and now sponsors seven annual conferences of different size and covering a wide range of topics. SIGWEB supports several specialized conferences, short courses, and workshops, as well as the Annual Hypertext Conference. SIGWEB sponsored conferences focus on timely topics in applied and computational hypertext and Web disciplines and provide a place for members and the entire applied Hypermedia and Web community to exchange ideas and to meet with and expand their network of colleagues. In this article, we provide a brief overview of SIGWEB sponsored conferences, in addition to events that are in cooperation with SEGWEB. overview of SIGWEB sponsored conferences, in addition to events that are in cooperation with SIGWEB.
A lazy DVS approach for dynamic real time system
Authors: Agrawal Smriti
Published: November 2016

This paperpresents a LazyDVS scheduling algorithm that offers higher acceptance ratio (number of tasks able to meet their deadline is to number of tasks appearing) with equivalent orlesser energy consumption for battery powered dynamic real time system. It is modeled for aperiodic workload by utilizing the concept of late start and dynamic voltage scaling. In this paper, with a motivational example we show that existing approaches have poor energy and aperiodic workload management, thus, are not suitable for scheduling aperiodic workload on limited source of energy. Based on this motivation we propose a Lazy DVS scheduling algorithm that tradeoffs between timing constraint and the available energy to provide better acceptance ratio with lower energy. The extensive examples and simulation results illustrate that our approach can effectively improve the acceptance ratio while consuming lower energy.
Routing optimization of AVB streams in TSN networks
Authors: Laursen Sune Mølgaard , Pop Paul , Steiner Wilfried
Published: November 2016

In this paper we are interested in safety-critical real-time applications implemented on distributed architectures using the Time-Sensitive Networking (TSN) standard. The ongoing standardization of TSN is an IEEE effort to bring deterministic real-time capabilities into the
IEEE 802.1
Ethernet standard supporting safety-critical systems and guaranteed Quality-of-Service. TSN will support Time-Triggered (TT) communication based on schedule tables, Audio-Video-Bridging (AVB) streams with bounded end-to-end latency as well as Best-Effort messages. We consider that we know the topology of the network as well as the routes and schedules of the TT streams. We are interested to determine the routing of the AVB streams such that all frames are schedulable and their worst-case end-to-end delay is minimized. We have proposed a search-space reduction technique and a Greedy Randomized Adaptive Search Procedure (GRASP)-based heuristic for this routing optimization problem. The proposed approaches has been evaluated using several test cases.
The growth of computing education doctoral research
Authors: Robins Anthony , Shapiro R. Benjamin
Published: November 2016

Computer Science has been experiencing rapid growth in undergraduate and K-12 participation. This growth underscores the need for an improved understanding of the teaching and learning of computing topics, or in other words for progress in Computer Science Education (CSEd) and Computing Education Research (CER).
Member spotlight
Authors: Doyle Maureen
Published: November 2016

In this feature of the Bulletin, we highlight members of the SIGCSE community. In this issue, Bulletin co-editor Maureen Doyle interviewed David Kauchak, outgoing SIGCSE Bulletin co-chair.
Using mobile message to improve student participation in blended courses
Authors: Marçal Edgar , Andrade Rossana , Melo Rosemeiry , Viana Windson , Junqueira Eduardo
Published: November 2016

Studies have shown the benefits of mobile messages in education. They assist to fix the classroom lectures, help to remind study activities, and also allow the exchange of education messages among classmates. Researchers argue that more studies must be conducted to assess the extension of these benefits, and to better identify in which context mobile messaging is the best approach to be applied. In this sense, our study examined a post-graduate class consisting of 474 learners in which Short Message Service was used. The main goal was to find out if this technology would improve student participation in the course. Two groups of learners were created, control and experimental, in order to analyze the activities' fulfillment rate and the response time. The result from the data analysis showed that students who received mobile messaging outperformed significantly students from the control group. The experimental group had better results both in completion rate and response time. They were almost 20% more effective at completing their assigned activity and up to 78 hours faster than students from the control group. In addition, a questionnaire was implemented in order to evaluate participants' satisfaction with the use of SMS. Result found that most part of the students were satisfied and enjoyed the use of the mobile messages.
The Type I Interferonopathies
Authors: Lee-Kirsch Min Ae
Published: November 2016

Type I interferons (IFNs) play a central role in the immune defense against viral infections. Type I IFN activation is induced by pattern-recognition receptors of the innate immune system that sense pathogen-derived nucleic acids. Cellular responses to type I IFN signaling are orchestrated by a complex network of regulatory pathways that involve both the innate and adaptive immune system. The genetic and molecular dissection of rare Mendelian disorders associated with constitutive overproduction of type I IFN has provided unique insight into cell-intrinsic disease mechanisms that initiate and sustain autoinflammation and autoimmunity and that are caused by disturbances in the intracellular nucleic acid metabolism or in cytosolic nucleic acid–sensing pathways. Collectively, these findings have greatly advanced our understanding of mechanisms that protect the organism against inappropriate immune activation triggered by self nucleic acids while maintaining a prompt and efficient immune response to foreign nucleic acids derived from invading pathogens.
Biosimilars: The US Regulatory Framework
Authors: Christl Leah A. , Woodcock Janet , Kozlowski Steven
Published: November 2016

With the passage of the Biologics Price Competition and Innovation Act of 2009, the US Food and Drug Administration established an abbreviated pathway for developing and licensing biosimilar and interchangeable biological products. The regulatory framework and the technical requirements of the US biosimilars program involve a stepwise approach that relies heavily on analytical methods to demonstrate through a “totality of the evidence” that a proposed product is biosimilar to its reference product. By integrating analytical, pharmacological, and clinical data, each of which has limitations, a high level of confidence can be reached regarding clinical performance. Although questions and concerns about the biosimilars pathway remain and may slow uptake, a robust scientific program has been put in place. With three biosimilars already licensed and numerous development programs under way, clinicians can expect to see many new biosimilars come onto the US market in the coming decade. [Note added in proof: Since the writing of this article, a fourth biosimilar has been approved.]
Harnessing Big Data for Systems Pharmacology
Authors: Xie Lei , Draizen Eli J. , Bourne Philip E.
Published: November 2016

Systems pharmacology aims to holistically understand mechanisms of drug actions to support drug discovery and clinical practice. Systems pharmacology modeling (SPM) is data driven. It integrates an exponentially growing amount of data at multiple scales (genetic, molecular, cellular, organismal, and environmental). The goal of SPM is to develop mechanistic or predictive multiscale models that are interpretable and actionable. The current explosions in genomics and other omics data, as well as the tremendous advances in big data technologies, have already enabled biologists to generate novel hypotheses and gain new knowledge through computational models of genome-wide, heterogeneous, and dynamic data sets. More work is needed to interpret and predict a drug response phenotype, which is dependent on many known and unknown factors. To gain a comprehensive understanding of drug actions, SPM requires close collaborations between domain experts from diverse fields and integration of heterogeneous models from biophysics, mathematics, statistics, machine learning, and semantic webs. This creates challenges in model management, model integration, model translation, and knowledge integration. In this review, we discuss several emergent issues in SPM and potential solutions using big data technology and analytics. The concurrent development of high-throughput techniques, cloud computing, data science, and the semantic web will likely allow SPM to be findable, accessible, interoperable, reusable, reliable, interpretable, and actionable.
NNMT Silencing Activates Tumor Suppressor PP2A, Inactivates Oncogenic STKs, and Inhibits Tumor Forming Ability
Authors: Palanichamy Kamalakannan , Kanji Suman , Gordon Nicolaus , Thirumoorthy Krishnan , Jacob John R. , Litzenberg Kevin T. , Patel Disha , Chakravarti Arnab
Published: November 2016

Purpose: To identify potential molecular hubs that regulate oncogenic kinases and target them to improve treatment outcomes for glioblastoma patients.

Experimental Design: Data mining of The Cancer Genome Atlas datasets identified nicotinamide-N-methyl transferase (NNMT) as a prognostic marker for glioblastoma, an enzyme linked to the reorganization of the methylome. We tested our hypothesis that NNMT plays a crucial role by modulating protein methylation, leading to inactivation of tumor suppressors and activation of oncogenes. Further experiments were performed to understand the underlying biochemical mechanisms using glioblastoma patient samples, established, primary, and isogenic cells.

Results: We demonstrate that NNMT outcompetes leucine carboxyl methyl transferase 1 (LCMT1) for methyl transfer from principal methyl donor SAM in biological systems. Inhibiting NNMT increased the availability of methyl groups for LCMT1 to methylate PP2A, resulting in the inhibition of oncogenic serine/threonine kinases (STK). Further, NNMT inhibition retained the radiosensitizer nicotinamide and enhanced radiation sensitivity. We have provided the biochemical rationale of how NNMT plays a vital role in inhibiting tumor suppressor PP2A while concomitantly activating STKs.

Conclusions: We report the intricate novel mechanism in which NNMT inhibits tumor suppressor PP2A by reorganizing the methylome both at epigenome and proteome levels and concomitantly activating prosurvival STKs. In glioblastoma tumors with NNMT expression, activation of PP2A can be accomplished by FDA approved perphenazine (PPZ), which is currently used to treat mood disorders such as schizophrenia, bipolar disorder, etc. This study forms a foundation for further glioblastoma clinical trials using PPZ with standard of care treatment. Clin Cancer Res; 23(9); 2325–34. ©2016 AACR.
The Triad of Sleep Apnea, Hypertension, and Chronic Kidney Disease: A Spectrum of Common Pathology
Authors: Aziz Fahad , Chaudhary Kunal
Published: November 2016

Obstructive sleep apnea (OSA), hypertension, and chronic kidney disease (CKD) are different entities and are generally managed individually most of the time. However, CKD, OSA, and hypertension share many common risk factors and it is not uncommon to see this complex triad together. In fact, they share similar pathophysiology and have been interlinked with each other. The common pathophysiology includes chronic volume overload, hyperaldosteronism, increased sympathetic activity, endothelial dysfunction, and increased inflammatory markers. The combination of this triad has significant negative impact on the cardiovascular health, and increases the mortality and morbidity in this complicated group of patients. On one hand, progression of CKD can lead to the worsening of OSA and hypertension; similarly, worsening sleep apnea can make the hypertension difficult to treat and enhance the progression of CKD. This review article highlights the bidirectional interlink among these apparently different disease processes which share common pathophysiological mechanisms and emphasizes the importance of treating them collectively to improve outcomes.
Individual growth estimation of Ucides occidentalis (Brachyura, Ocypodidae) in the Gulf of Guayaquil, Ecuador by indirect methods and multi-model selection
Authors: Zambrano René , Aragón-Noriega E. Alberto , Galindo-Cortes Gabriela , Jiménez-Badillo Lourdes , Peralta Manuel
Published: November 2016

Ucides occidentalis(Ortmann, 1897) is a commercial crab in the Ecuadorian continental coast, however, little knowledge is available about its biology. A very important aspect for stock assessment and fisheries management is the species’ individual growth. In this paperU. occidentalisgrowth in males and females was determined by indirect methods and the multi-model approach. By Kernel density estimators size frequency distributions were built, separating their Gaussian components by the Bhattacharya’s method. Using modal progression, the cohorts were identified, and one was selected to apply asymptotic, non-asymptotic, and Schnute’s versatile growth models. The best fit model was selected using the Akaike and Bayesian weights. Case 1 of Schnute was the winner model in both sexes, asymptotic in males with cephalothorax width (CW), and , but it was non-asymptotic for females with an inflexion point in 2.49 years that corresponded to 73.72 mm CW. The type of individual growth of this species varies between sexes, which may be linked to reproductive issues; however, we should consider the data source and their impact on the interpretations that we can draw about individual growth. Therefore, for future studies, using other sources of information such as commercial catches or capture-recapture to validate the results presented, is recommended.
Composition and spatio-temporal variation in the density of the Brachyura (Decapoda, Pleocyemata) in the rocky substrates of an Amazonian estuary
Authors: Nóbrega Priscila S. V. , Martinelli-Lemos Jussara M.
Published: November 2016

The present study investigated the composition, spatio-temporal distribution, and the influence of temperature and salinity on the density of brachyurans associated with rocky substrates in an estuary of the Brazilian Amazonian coast. Specimens were collected monthly at four sites representing the two margins (profiles), zones (inner and outer estuary) and the lower and upper mediolittoral portions at each site of the Marapanim estuary. A total of 14 species were collected and multivariate analyses revealed that the species composition varied systematically between zones, margins, mediolittoral sectors and seasons, with the more saline zone, the most eroded margin, the lower mediolittoral, and the rainy season all being characterized by higher densities and a more homogeneous distribution of species. In general, high densities of brachyurans, but low species richness, and marked dominance characterized the sites. Salinity proved to play an important role in the structuring of the community.