bluuebunny/crossref_metadata_2025 huggingface dataset:
A physical map of the Salmonella typhimurium LT2 genome made by using XbaI analysis
Authors: Liu S L , Sanderson K E
Published: November 2016

XbaI digestion and pulsed-field gel electrophoresis of the genome of Salmonella typhimurium LT2 yields 24 fragments: 23 fragments (total size, 4,807 kb) are from the chromosome, and one fragment (90 kb) is from the virulence plasmid pSLT. Some of the 23 fragments from the chromosome were located on the linkage map by the use of cloned genes as probes and by analysis of strains which gain an XbaI site from the insertion of Tn10. Twenty-one of the fragments were arranged as a circular physical map by the use of linking probes from a set of 41 lysogens in which Mud-P22 was stably inserted at different sites of the chromosome; fragment W (6.6 kb) and fragment X (6.4 kb) were not located on the physical map. XbaI digestion of strains with Tn10 insertions allowed the physical locations of specific genes along the chromosome to be determined on the basis of analysis of new-fragment sizes. There is good agreement between the order of genes on the linkage map, which is based primarily on P22 joint transduction and F-mediated conjugation, and the physical map, but there are frequently differences in the length of the interval from the two methods. These analyses allowed the measurement of the amount of DNA packaged in phage P22 heads by Mud-P22 lysogens following induction; this varies from ca. 100 kb (2 min) to 240 kb (5 min) in different parts of the chromosome.
Cloning, sequencing, and transcriptional regulation of the Vibrio cholerae fur gene
Authors: Litwin C M , Boyko S A , Calderwood S B
Published: November 2016

Many genes involved in the transport of iron by bacteria as well as in pathogenesis are regulated by the environmental concentration of iron, with increased expression under low-iron conditions. In Escherichia coli, transcriptional regulation by iron depends on the fur gene. A virulence gene in Vibrio cholerae (irgA) is also transcriptionally regulated by iron, and the promoter of irgA contains a dyad repeat homologous to Fur binding sites in E. coli. Southern hybridization of V. cholerae chromosomal DNA, using an internal fragment of E. coli fur as a probe, showed a single hybridizing sequence under conditions of low stringency. We derived a restriction map in the vicinity of this hybridizing sequence; overlapping PstI and HindIII fragments were identified at the center of this map. The cloned PstI fragment failed to complement an E. coli fur mutant; sequence analysis revealed an open reading frame that began just downstream of the PstI site, suggesting that the clone was not functional because it lacked its promoter. The overlapping HindIII fragment contained the intact V. cholerae fur gene with its promoter and complemented an E. coli fur mutant. DNA sequencing of the HindIII fragment demonstrated a single open reading frame of 150 amino acids that was 76% homologous to E. coli Fur. Primer extension analysis localized two promoters for the V. cholerae fur gene; no significant homology to an E. coli Fur binding site was identified for either promoter. Northern blot analysis showed that the two fur transcripts were not strongly regulated by iron. These studies identify a gene in V. cholerae homologous in both function and sequence to the fur gene of E. coli, and we have designated this gene the fur gene of V. cholerae.
Phylogeny of 54 representative strains of species in the family Pasteurellaceae as determined by comparison of 16S rRNA sequences
Authors: Dewhirst F E , Paster B J , Olsen I , Fraser G J
Published: November 2016

Virtually complete 16S rRNA sequences were determined for 54 representative strains of species in the family Pasteurellaceae. Of these strains, 15 were Pasteurella, 16 were Actinobacillus, and 23 were Haemophilus. A phylogenetic tree was constructed based on sequence similarity, using the Neighbor-Joining method. Fifty-three of the strains fell within four large clusters. The first cluster included the type strains of Haemophilus influenzae, H. aegyptius, H. aphrophilus, H. haemolyticus, H. paraphrophilus, H. segnis, and Actinobacillus actinomycetemcomitans. This cluster also contained A. actinomycetemcomitans FDC Y4, ATCC 29522, ATCC 29523, and ATCC 29524 and H. aphrophilus NCTC 7901. The second cluster included the type strains of A. seminis and Pasteurella aerogenes and H. somnus OVCG 43826. The third cluster was composed of the type strains of Pasteurella multocida, P. anatis, P. avium, P. canis, P. dagmatis, P. gallinarum, P. langaa, P. stomatis, P. volantium, H. haemoglobinophilus, H. parasuis, H. paracuniculus, H. paragallinarum, and A. capsulatus. This cluster also contained Pasteurella species A CCUG 18782, Pasteurella species B CCUG 19974, Haemophilus taxon C CAPM 5111, H. parasuis type 5 Nagasaki, P. volantium (H. parainfluenzae) NCTC 4101, and P. trehalosi NCTC 10624. The fourth cluster included the type strains of Actinobacillus lignieresii, A. equuli, A. pleuropneumoniae, A. suis, A. ureae, H. parahaemolyticus, H. parainfluenzae, H. paraphrohaemolyticus, H. ducreyi, and P. haemolytica. This cluster also contained Actinobacillus species strain CCUG 19799 (Bisgaard taxon 11), A. suis ATCC 15557, H. ducreyi ATCC 27722 and HD 35000, Haemophilus minor group strain 202, and H. parainfluenzae ATCC 29242. The type strain of P. pneumotropica branched alone to form a fifth group. The branching of the Pasteurellaceae family tree was quite complex. The four major clusters contained multiple subclusters. The clusters contained both rapidly and slowly evolving strains (indicated by differing numbers of base changes incorporated into the 16S rRNA sequence relative to outgroup organisms). While the results presented a clear picture of the phylogenetic relationships, the complexity of the branching will make division of the family into genera a difficult and somewhat subjective task. We do not suggest any taxonomic changes at this time.
Membrane localization and topology of a viral assembly protein
Authors: Guy-Caffey J K , Rapoza M P , Jolley K A , Webster R E
Published: November 2016

The gene I protein (pI) of the filamentous bacteriophage f1 is required for the assembly of this virus. Antibodies specific to either the amino or carboxyl terminus of this protein were used to determine the location and topology of the gene I protein in f1-infected bacteria. pI is anchored in the inner membrane of Escherichia coli cells via a 20-amino-acid hydrophobic stretch, with its carboxyl-terminal 75 residues located in the periplasm and its amino-terminal 253 amino acids residing in the cytoplasm. By using the carboxyl-terminal pI antibody, a smaller protein, pI*, is also detected in f1-infected cells at a ratio of one to two molecules per molecule of pI. Analysis of proteins produced from a gene I amber mutant plasmid or bacteriophage suggests that pI* is most likely the result of an in-frame internal translational initiation event at methionine 241 of the 348-amino-acid pI. pI* is shown to be an integral inner membrane protein inserted in the same orientation as pI. The relation of the cellular locations of pI and pI* to some of the proposed functions of pI is discussed.
The Tn10-encoded tetracycline resistance mRNA contains a translational silencer in the 5' nontranslated region
Authors: Flache P , Baumeister R , Hillen W
Published: November 2016

We performed a mutational analysis of the left half of Tn10-encoded tet operator O2, located in the 5' nontranslated region of the mRNA for the resistance protein TetA, and determined the importance of that region for translation efficiency and mRNA stability. Transcriptional fusions of 17 mutants to lacZ expressed the same amounts of beta-galactosidase, while translational fusions varied 35-fold in expression efficiency. The mRNA half-lives varied 24-fold, with 9.6 min for the most highly expressed mRNA and 0.4 min for the least efficiently expressed mRNA. Toeprint experiments were performed to distinguish whether these mutations define a determinant of mRNA stability or influence translation initiation. The highly expressed mRNA was 24-fold more efficient in forming the initiation complex in vitro than the low-expression mutant. It was concluded that this sequence, albeit located upstream of the ribosome-binding sequence, is an important determinant for efficient initiation of translation. Secondary-structure calculations of the mRNAs revealed no correlation of the potential to form double strands masking the ribosome-binding sequence with expression efficiency.
Dissection of IncP conjugative plasmid transfer: definition of the transfer region Tra2 by mobilization of the Tra1 region in trans
Authors: Lessl M , Balzer D , Lurz R , Waters V L , Guiney D G , Lanka E
Published: November 2016

We constructed a transfer system consisting of two compatible multicopy plasmids carrying the transfer regions Tra1 and Tra2 of the broad-host-range IncP plasmid RP4. In this system, the plasmid containing the Tra1 region with the origin of transfer (oriT) was transferred, whereas additional functions essential for the conjugative process were provided from the Tra2 plasmid in trans. The Tra2 region, as determined for matings between Escherichia coli cells, maps between coordinates 18.03 and 29.26 kb of the RP4 standard map. The section of Tra2 required for mobilization of the plasmid RSF1010 (IncQ) and the propagation of bacteriophages Pf3 and PRD1 appears to be the same as that needed for RP4 transfer. Tra2 regions of RP4 (IncP alpha) and R751 (IncP beta) are interchangeable, facilitating mobilization of the plasmid carrying the RP4 Tra1 region. The transfer frequencies of both systems are similar. Transcription of Tra2 proceeds clockwise relative to the standard map of RP4 and is probably initiated at a promoter region located upstream of trbB (kilB). From this promoter region the trfA operon and the Tra2 operon are likely to be transcribed divergently. A second potential promoter has been located immediately upstream of trbB (kilB). Plasmids encoding the functional Tra2 region can only be maintained stably in host cells in the presence of the RP4 regulation region carrying the korA-korB operon or part of it. This indicates the involvement of RP4 key regulatory functions that apparently are active not only in the control of replication but also in conjugation.
Evidence for two phosphonate degradative pathways in Enterobacter aerogenes
Authors: Lee K S , Metcalf W W , Wanner B L
Published: November 2016

We screened mini-Mu plasmid libraries from Enterobacter aerogenes IFO 12010 for plasmids that complement Escherichia coli phn mutants that cannot use phosphonates (Pn) as the sole source of phosphorus (P). We isolated two kinds of plasmids that, unexpectedly, encode genes for different metabolic pathways. One kind complements E. coli mutants with both Pn transport and Pn catalysis genes deleted; these plasmids allow degradation of the 2-carbon-substituted Pn alpha-aminoethylphosphonate but not of unsubstituted alkyl Pn. This substrate specificity is characteristic of a phosphonatase pathway, which is absent in E. coli. The other kind complements E. coli mutants with Pn catalysis genes deleted but not those with both transport and catalysis genes deleted; these plasmids allow degradation of both substituted and unsubstituted Pn. Such a broad substrate specificity is characteristic of a carbon-phosphorus (C-P) lyase pathway, which is common in gram-negative bacteria, including E. coli. Further proof that the two kinds of plasmids encode genes for different pathways was demonstrated by the lack of DNA homology between the plasmids. In particular, the phosphonatase clone from E. aerogenes failed to hybridize to the E. coli phnCDEFGHIJKLMNOP gene cluster for Pn uptake and degradation, while the E. aerogenes C-P lyase clone hybridized strongly to the E. coli phnGHIJKLM genes encoding C-P lyase but not to the E. coli phnCDE genes encoding Pn transport. Specific hybridization by the E. aerogenes C-P lyase plasmid to the E. coli phnF, phnN, phnO, and phnP genes was not determined. Furthermore, we showed that one or more genes encoding the apparent E. aerogenes phosphonatase pathway, like the E. coli phnC-to-phnP gene cluster, is under phosphate regulon control in E. coli. This highlights the importance of Pn in bacterial P assimilation in nature.
Export of the outer membrane lipoprotein is defective in secD, secE, and secF mutants of Escherichia coli
Authors: Sugai M , Wu H C
Published: November 2016

The export of major outer membrane lipoprotein has been found to be affected in secD, secE, and secF mutants of Escherichia coli, which are defective in protein export in general. After a shift to the nonpermissive temperature, the kinetics of accumulation of prolipoprotein and pre-OmpA protein was indistinguishable from that of pre-OmpA protein accumulation in the secD and secF mutants but different in the secE mutant. The prolipoprotein accumulated in the secD, secE, and secF mutants at the nonpermissive temperature was not modified with glyceride. We conclude from these results and those of previous studies that the export of lipoprotein requires all common sec gene products except the SecB protein, i.e., the SecA, SecD, SecE, SecF, and SecY proteins.
Genes encoding the phycobilisome rod substructure are clustered on the Anabaena chromosome: characterization of the phycoerythrocyanin operon
Authors: Swanson R V , de Lorimier R , Glazer A N
Published: November 2016

The phycoerythrocyanin (pec) operon, cloned from Anabaena sp. strain PCC 7120, encodes four genes, pecBACE, located upstream of the C-phycocyanin (cpc) operon. This pec-cpc cluster includes all the genes for the structural components of the phycobilisome rod. Oligonucleotide probes based on the amino-terminal sequence of the phycoerythrocyanin beta subunit were used to clone an 8.0-kbp EcoRI fragment which was determined, by sequencing, to partially overlap the previously cloned cpc operon. A 5.0-kbp EcoRI-ClaI fragment corresponding to the region upstream of the cpc operon was subsequently subcloned and sequenced. Five open reading frames whose polarity of transcription is parallel to that of the cpc genes were identified. pecB and pecA encode the beta and alpha subunits of phycoerythrocyanin, respectively. pecC encodes the phycoerythrocyanin-associated linker polypeptide LR34.5,PEC. The identities of these genes are confirmed by agreement with amino-terminal sequences determined from purified phycobilisome components. A gene homologous to cpcE, found downstream of pecC, has been designated pecE. The cpcE gene product is involved in the attachment of the phycocyanobilin chromophore to the alpha subunit of phycocyanin. Three transcripts were observed by Northern (RNA) analyses. The most abundant of these transcripts, 1.35 kbp, corresponds to the beta and alpha subunit genes, whereas the less-abundant transcripts, 2.3 and 3.1 kbp, correspond to pecBAC and pecBACE, respectively. Phycoerythrocyanin is strongly induced in cells cultured under low light. In parallel, all three transcripts were present at much higher levels in cells cultured under low light.
The role of buoyancy reversal in turbidite deposition and submarine fan geometry
Authors: Steel Elisabeth , Buttles James , Simms Alexander R. , Mohrig David , Meiburg Eckart
Published: November 2016

Although recent work has shown that changing interstitial fluid density within turbidity currents is a frequently overlooked factor affecting the texture and internal architecture of turbidites, little is known about its influence on submarine fan morphology. Here we present the results of three-dimensional flume experiments of turbidity currents that clearly demonstrate the role of low-density interstitial fluid, in combination with sediment concentration and basin gradient, on submarine fan geometry. The experiments show that turbidity currents with reversing buoyancy, and their resulting deposits, are narrower than those that remain ground hugging. Furthermore, wider deposits result from increases in sediment concentration and/or basin-floor gradient. We also propose that Taylor-Görtler vortices associated with currents traveling over a break in slope may lead to the deposition of wider lobes compared with those traveling over a constant gradient.
Rates of glaucomatous visual field change after trabeculectomy
Authors: Baril C , Vianna J R , Shuba L M , Rafuse P E , Chauhan B C , Nicolela M T
Published: November 2016

Background

Trabeculectomy is frequently performed in patients with glaucoma who are deteriorating, although its effects on rates of visual field (VF) progression are not fully understood. We studied the rate of VF progression post trabeculectomy comparing with medically treated patients matched for VF loss.

Methods

Medical records of patients who underwent trabeculectomy alone or combined with cataract extraction were reviewed. Patients with 5 or more 24–2 VF examinations post trabeculectomy were selected. The rate of mean deviation (MD) change after surgery was calculated for each patient. These patients were pairwise matched based on baseline MD with patients with glaucoma who were treated medically and had at least 5 VF tests.

Results

180 surgical patients were identified and matched with 180 medically treated patients (baseline MD of −8.72 (5.24) dB and −8.71 (5.22) dB, respectively). Surgically and medically treated patients were followed for 7.4 (2.9) and 6.8 (3.1) years respectively. The MD slopes were −0.22 (0.55) dB/year and −0.08 (1.10) dB/year in the surgically and medically treated patients, respectively, and not statistically different (p=0.13, 95% CI −0.31 to 0.04). More patients in the surgical group had fast progression (rates worse than −1 dB/year) than in the medical group (17 and 7 patients, respectively, p=0.05).

Conclusions

Our findings suggest that most patients who undergo trabeculectomy demonstrate relatively slow rates of VF progression postoperatively, similar to patients treated medically, although some patients can continue to progress despite adequate surgical control of intraocular pressure.
Primary biliary cholangitis: new treatments for an old disease
Authors: Trivedi Hirsh D , Lizaola Blanca , Tapper Elliot B , Bonder Alan
Published: November 2016

Primary biliary cholangitis (PBC) is an immunological condition that causes a significant health disturbance and dramatically reduces the quality of life for those affected with the disease. It is a potentially fatal disease that can lead to multiple hepatic and extrahepatic complications. Having adequate therapeutic interventions that can improve the course of the disease is imperative in reducing the associated morbidity and mortality. Ursodeoxycholic acid (UDCA) is the gold standard therapy. However, it has been associated with suboptimal response rates in a significant proportion of patients. Despite UDCA, approximately 35%–40% of individuals with PBC still experience a progression of the disease, leading to liver failure and requiring liver transplantation. Recent studies of new pharmacological approaches have shown beneficial outcomes. Some of these agents can now be applied to a clinical scenario. In this review article, we will outline the new and emerging treatments for PBC.
A standardized neurointerventional thrombectomy protocol leads to faster recanalization times
Authors: Frei Donald , McGraw Constance , McCarthy Kathryn , Whaley Michelle , Bellon Richard J , Loy David , Wagner Jeff , Orlando Alessandro , Bar-Or David
Published: November 2016

Background and purpose

Intra-arterial therapy (IAT) is most effective when performed rapidly after ischemic stroke onset. However, there are limited performance benchmarks in IAT and there is a scarcity of information on how to structure an effective IAT protocol and its impact on time to treatment. The objective of our study was to detail a standardized IAT protocol, and to assess its influence on time to treatment in ischemic stroke.

Methods

This was a retrospective observational study over 4 years at a comprehensive stroke center. A standardized IAT protocol was implemented in June 2013 that included pre-notifying the stroke team before hospital arrival, defining clinician roles, processing tasks in parallel, and standardizing IAT procedures. Three time metrics were examined and reported as median (IQR) minutes: arrival to CT imaging, CT to groin puncture, and puncture to recanalization. We compared these metrics in patients admitted before implementation (January 2012–May 2013) to patients admitted after (June 2013–December 2015) using Wilcoxon Mann–Whitney tests.

Results

380 patients were included. After the protocol was implemented, there were significant reductions in time from arrival to CT (17 (14–21) vs 13 (11–19) min, p<0.001), CT to puncture (46 (30–82) vs 31 (23–54) min, p<0.001), and puncture to recanalization (65 (33–90) vs 37 (22–65) min, p<0.001). 60% of time was saved during puncture to recanalization. Significant reductions in time were observed during both normal working hours and off-hours.

Conclusions

Implementation of a standardized protocol resulted in a significant reduction in time to recanalization for patients with an ischemic stroke. A standardized IAT protocol decreases time to recanalization when team roles are clearly defined, tasks are processed in parallel, and procedures are standardized.
Efficacy of endovascular treatment and feasibility of stent-assisted coiling in the presence of severe and symptomatic vasospasm
Authors: Andic Cagatay , Kardes Ozgur , Durdag Emre , Gedikoglu Murat , Akin Sule
Published: November 2016

Background and purpose

In patients with aneurysmal subarachnoid hemorrhage, deciding the optimal treatment strategy is challenging in the presence of severe and symptomatic vasospasm and the existing literature is limited. The purpose of this study was to evaluate the safety and effectiveness of endovascular treatment of intracranial aneurysms and the feasibility of stent-assisted coiling during severe and symptomatic vasospasm.

Materials and methods

Fifteen consecutive patients with 18 aneurysms who underwent endovascular treatment during severe and symptomatic vasospasm were included in the study. Patient and aneurysm characteristics, treatment technique, and clinical and angiographic outcomes were retrospectively evaluated.

Results

Aneurysms were treated by the following techniques: single catheter coiling in 9, stent-assisted coiling in 8 (3 aneurysms with Y-configuration double stents), and balloon-assisted coiling in 1. All patients showed angiographic improvement of vasospasm after treatment including a noticeable dilation of the spastic parent arteries following deployment of the stents. According to the immediate post-treatment angiography results, 14 aneurysms (77.8%) had class I occlusion and 4 (22.2%) had class II occlusion. Three patients died during the course of subarachnoid hemorrhage. Mortality was related to the poor grade (Hunt and Hess grade V) and cardiovascular complications in two and refractory vasospasm one patient. The remaining patients had favorable clinical outcomes at follow-up (modified Rankin Scale 0–2).

Conclusions

Endovascular treatment of intracranial aneurysms during severe and symptomatic vasospasm is safe and effective. Stent-assisted coiling in the presence of severe vasospasm is also feasible in wide-necked aneurysms with the additional benefits of mechanical vasodilation.
Comparison of the use of LigaSure versus a standard technique for tonsillectomy in dogs
Authors: Belch A. , Matiasovic M. , Rasotto R. , Demetriou J.
Published: November 2016

The principal aim of this study was to document the effectiveness of tonsillectomy in dogs using a vessel‐sealing device compared with a standard technique with tonsillectomy forceps. A secondary aim of the study was to document histopathological changes of the excised tonsillar tissue in dogs with brachycephalic obstructive airway syndrome. 20 dogs were studied. The time taken to remove a tonsil using LigaSure was a mean of 44.8 seconds (sd 15 seconds, 95 per cent CI 40 to 57 seconds) and with the standard technique a mean of 305.9 seconds (sd 67 seconds, 95 per cent CI 272 to 349 seconds). Significantly less haemorrhage occurred using LigaSure compared with the standard technique. Histopathology of the tonsils was characterised by multifocal neutrophilic and lymphocytic inflammation, and 1–2 mm of heat‐induced coagulation necrosis at the cut edge of LigaSure tonsils. This study shows that LigaSure is significantly faster and resulted in less bleeding than the standard technique.
The LHC searches for heavy neutral Higgs bosons by jet substructure analysis
Authors: Chen Ning
Published: November 2016

The two-Higgs-doublet model contains extra Higgs bosons with mass ranges spanning from several hundred GeV to about 1 TeV. We study the possible experimental searches for the neutral Higgs bosons of [Formula: see text] and [Formula: see text] at the future high-luminosity LHC runs. Besides of the conventional search modes that are inspired by the supersymmetric models, we discuss two search modes which were not quite addressed previously. They are the decay modes of [Formula: see text] and [Formula: see text]. Thanks to the technique of tagging boosted objects of SM-like Higgs bosons and top quarks, we show the improved mass reaches for heavy neutral Higgs bosons with masses up to [Formula: see text]. The modes proposed here are complementary to the conventional experimental searches motivated by the MSSM.
2-state asymmetries: Matter–antimatter and other effects
Authors: Sidharth B. G. , Das Abhishek
Published: November 2016

This paper is based on the framework of a two-dimensional universe considering it to be a lattice structure. The Ising model has been used to show that there is a spontaneous phase transition from the Planck scale to the Compton scale. Also, a mean field theoretic approach has been considered to delve into the statistical properties of such a lattice-structured universe.
Analyzing the Cross-Correlation Between Onshore and Offshore RMB Exchange Rates Based on Multifractal Detrended Cross-Correlation Analysis (MF-DCCA)
Authors: Xie Chi , Zhou Yingying , Wang Gangjin , Yan Xinguo
Published: November 2016

We use the multifractal detrended cross-correlation analysis (MF-DCCA) method to explore the multifractal behavior of the cross-correlation between exchange rates of onshore RMB (CNY) and offshore RMB (CNH) against US dollar (USD). The empirical data are daily prices of CNY/USD and CNH/USD from May 1, 2012 to February 29, 2016. The results demonstrate that: (i) the cross-correlation between CNY/USD and CNH/USD is persistent and its fluctuation is smaller when the order of fluctuation function is negative than that when the order is positive; (ii) the multifractal behavior of the cross-correlation between CNY/USD and CNH/USD is significant during the sample period; (iii) the dynamic Hurst exponents obtained by the rolling windows analysis show that the cross-correlation is stable when the global economic situation is good and volatile in bad situation; and (iv) the non-normal distribution of original data has a greater effect on the multifractality of the cross-correlation between CNY/USD and CNH/USD than the temporary correlation.
Laboratory experiments on bentonite pellet saturation
Authors: Trpkošová Dagmar , Večerník Petr , Gondolli Jenny , Havlová Václava , Svoboda Jiří , Hanusová Irena
Published: November 2016

The aim of the DOPAS project is to address the design basis, reference designs and strategies for the plugs and seals to be used in geological disposal facilities. The Czech ‘Experimental Pressure and Sealing Plug’ (EPSP) experiment has the following objectives: to develop, monitor and verify the functionality of an
in situ
experimental plug, and to determine and describe in detail the materials to be used with respect to experimental plug construction. The functionality of the experimental plug will be verified by means of conducting pressure tests after the construction phase of EPSP. The internal bentonite section of the EPSP will be constructed from bentonite pellets with a dry density of 1850 kg m
−3
; the pellets will disintegrate following saturation and swelling to form a homogeneous material with a dry density of around 1400 kg m
−3
. This process leads to the question of the pore space of the bentonite material: that is, whether it will be possible to employ a numerical model for homogeneous compacted bentonite powder porosity instead of that of the double pore/void space of the bentonite pellets used in the experiment. For this reason, a laboratory physical model (PHM – physical hydraulic model) was incorporated into the DOPAS project for the purpose of describing the saturation and disintegration of the bentonite pellets. The aim of this paper is to describe the results of the space distribution of relative humidity in a sample consisting of bentonite pellets with a view to subsequent numerical modelling and to extend the current knowledge concerning the behaviour of the bentonite pellets used in the EPSP experiment. The results show that following water saturation and the swelling of the bentonite the pellets form a homogeneous mass in the same way as does the compacted bentonite powder. After a period of 160 days, the pellets attained 100% relative humidity at a distance of 12.5 cm and swelling pressure recorded at the end of the model was seen to slowly increase over this time period.
System-Level Design to Detect Fault Injection Attacks on Embedded Real-Time Applications
Authors: Jiang Wei , Wen Liang , Jiang Ke , Zhang Xia , Pan Xiong , Zhou Keran
Published: November 2016

Fault injection attack has been a serious threat to security-critical embedded systems for a long time, yet existing research ignores addressing of the problem from a system-level perspective. This article presents an approach to the synthesis of secure real-time applications mapped on distributed embedded systems, which focuses on preventing fault injection attacks of the security protection on processing units. We utilize symmetric cryptographic service to protect confidentiality and deploy fault detection within a confidential algorithm to resist fault injection attacks. Several fault detection schemes are identified, and their fault coverage rates and time overheads are derived and measured. Our synthesis approach makes efforts to determine the best fault detection schemes for the encryption/decryption of messages such that the overall security strength of detecting a fault injection attack is maximized and the deadline constraint of the real-time applications is guaranteed. Due to the complexity of the problem, we propose an efficient algorithm based on the fruit fly optimization algorithm, and we compare it to the simulated annealing approach. Extensive experiments and a real-life application evaluation demonstrate the superiority of our approach.
Electro-Photonic NoC Designs for Kilocore Systems
Authors: Abellán José L. , Chen Chao , Joshi Ajay
Published: November 2016

The increasing core count in manycore systems requires a corresponding large Network-on-chip (NoC) bandwidth to support the overlying applications. However, it is not possible to provide this large bandwidth in an energy-efficient manner using electrical link technology. To overcome this issue, photonic link technology has been proposed as a replacement. This work explores the limits and opportunities for using photonic links to design the NoC architecture for a future Kilocore system. Three different NoC designs are explored: ElecNoC, an electrical concentrated two-dimensional- (2D) mesh NoC; HybNoC, an electrical concentrated 2D mesh with a photonic multi-crossbar NoC; and PhotoNoC, a photonic multi-bus NoC. We consider both private and shared cache architectures and, to leverage the large bandwidth density of photonic links, we investigate the use of prefetching and aggressive non-blocking caches. Our analysis using contemporary Big Data workloads shows that the non-blocking caches with a shared LLC can best leverage the large bandwidth of the photonic links in the Kilocore system. Moreover, compared to ElecNoC-based and HybNoC-based Kilocore systems, a PhotoNoC-based Kilocore system achieves up to 2.5× and 1.5× better performance, respectively, and can support up to 2.1× and 1.1× higher bandwidth, respectively, while dissipating comparable power in the overall system.
A Supervised Learning Model for High-Dimensional and Large-Scale Data
Authors: Peng Chong , Cheng Jie , Cheng Qiang
Published: November 2016

We introduce a new supervised learning model using a discriminative regression approach. This new model estimates a regression vector to represent the similarity between a test example and training examples while seamlessly integrating the class information in the similarity estimation. This distinguishes our model from usual regression models and locally linear embedding approaches, rendering our method suitable for supervised learning problems in high-dimensional settings. Our model is easily extensible to account for nonlinear relationship and applicable to general data, including both high- and low-dimensional data. The objective function of the model is convex, for which two optimization algorithms are provided. These two optimization approaches induce two scalable solvers that are of mathematically provable, linear time complexity. Experimental results verify the effectiveness of the proposed method on various kinds of data. For example, our method shows comparable performance on low-dimensional data and superior performance on high-dimensional data to several widely used classifiers; also, the linear solvers obtain promising performance on large-scale classification.
Two-Variable Logic with Counting and Trees
Authors: Charatonik Witold , Witkowski Piotr
Published: November 2016

We consider the two-variable logic with counting quantifiers (C
2
) interpreted over finite structures that contain two forests of ranked trees. This logic is strictly more expressive than standard C
2
and it is no longer a fragment of first-order logic. In particular, it can express that a structure is a ranked tree, a cycle, or a connected graph of bounded degree. It is also strictly more expressive than first-order logic with two variables and two successor relations of two finite linear orders. We present a decision procedure for the satisfiability problem for this logic. The procedure runs in NE
xp
T
ime
, which is optimal since the satisfiability problem for plain C
2
is NE
xp
T
ime
-complete.
Quality assessment of wikipedia articles: a deep learning approach by Quang Vinh Dang and Claudia-Lavinia Ignat with Martin Vesely as coordinator
Authors: Dang Quang Vinh , Ignat Claudia-Lavinia
Published: November 2016

Wikipedia is indeed a very important knowledge sharing platform. However, since its start in 2001, the quality of Wikipedia is questioned because its content is created potentially by everyone who can access the Internet. Currently, the quality of Wikipedia articles is assessed by human judgement. The method is not scalable up to huge size and fast changing speed of Wikipedia today. An automatic quality classifier for Wikipedia articles is required to support user to choose high quality articles for reading and to notify authors for improving their products. While other existing approaches are based on manually predefined specific feature set, we present our approach of using deep learning to automatically represent Wikipedia articles for quality classification.
Deep Learning at Scale and at Ease
Authors: Wang Wei , Chen Gang , Chen Haibo , Dinh Tien Tuan Anh , Gao Jinyang , Ooi Beng Chin , Tan Kian-Lee , Wang Sheng , Zhang Meihui
Published: November 2016

Recently, deep learning techniques have enjoyed success in various multimedia applications, such as image classification and multimodal data analysis. Large deep learning models are developed for learning rich representations of complex data. There are two challenges to overcome before deep learning can be widely adopted in multimedia and other applications. One is usability, namely the implementation of different models and training algorithms must be done by nonexperts without much effort, especially when the model is large and complex. The other is scalability, namely the deep learning system must be able to provision for a huge demand of computing resources for training large models with massive datasets. To address these two challenges, in this article we design a distributed deep learning platform called
SINGA
, which has an intuitive programming model based on the common layer abstraction of deep learning models. Good scalability is achieved through flexible distributed training architecture and specific optimization techniques. SINGA runs on both GPUs and CPUs, and we show that it outperforms many other state-of-the-art deep learning systems. Our experience with developing and training deep learning models for real-life multimedia applications in SINGA shows that the platform is both usable and scalable.
Support for the logical execution time model on a time-predictable multicore processor
Authors: Kluge Florian , Schoeberl Martin , Ungerer Theo
Published: November 2016

The
logical execution time
(LET) model increases the compositionality of real-time task sets. Removal or addition of tasks does not influence the communication behavior of other tasks. In this work, we extend a multicore operating system running on a time-predictable multicore processor to support the LET model. For communication between tasks we use message passing on a time-predictable network-on-chip to avoid the bottleneck of shared memory. We report our experiences and present results on the costs in terms of memory and execution time.
On the quality of semantic interest profiles for onine social network consumers
Authors: Besel Christoph , Schlötterer Jörg , Granitzer Michael
Published: November 2016

Social media based recommendation systems infer user' interests and preferences from their social network activity in order to provide personalised recommendations. Typically, the user profiles are generated by analysing the users' posts or tweets. However, there might be a significant difference between what a user
produces
and what she
consumes.
We propose an approach for inferring user interests from followees (the accounts the user follows) rather than tweets. This is done by extracting named entities from a user's followees using the English Wikipedia as knowledge base and regarding them as interests. Afterwards, a spreading activation algorithm is performed on a Wikipedia category taxonomy to aggregate the various interests to a more abstract and broader interest profile. We evaluate the coverage of followee lists in terms of named entities and show that they provide sufficient input to infer comprehensive semantic interest profiles. Further, we compare the profiles created with the followee-based approach against tweet-based profiles. With over 7 out of 10 items being relevant to the users in our evaluation, we show that the followee-based approach can compete with the state of the art and performs even better in predicting the user's interests than their human friends do.
Sonata
Authors: Aichinger Erhard , Yatchak Rika
Published: November 2016

A nearringNis an algebra that does not satisfy the ring axioms, but nevertheless satisfies a one-sided distributivity law. SONATA is a GAP package designed as a research tool for nearrings. Users are able to define and work with finite nearrings in order to generate and test conjectures.
p53: Multiple Facets of a Rubik's Cube
Authors: Zhang Yun , Lozano Guillermina
Published: November 2016

The p53 tumor suppressor has been studied for decades, and still there are many questions left unanswered. In this review, we first describe the current understanding of the wild-type p53 functions that determine cell survival or death, and regulation of the protein, with a particular focus on the negative regulators, the murine double minute family of proteins. We also summarize tissue-, stress-, and age-specific p53 activities and the potential underlying mechanisms. Among all p53 gene alterations identified in human cancers, p53 missense mutations predominate, suggesting an inherent biological advantage. Numerous gain-of-function activities of mutant p53 in different model systems and contexts have been identified. The emerging theme is that mutant p53, which retains a potent transcriptional activation domain, also retains the ability to modify gene transcription, albeit indirectly. Lastly, because mutant p53 stability is necessary for its gain of function, we summarize the mechanisms through which mutant p53 is specifically stabilized. A deeper understanding of the multiple pathways that impinge upon wild-type and mutant p53 activities and how these, in turn, regulate cell behavior will help identify vulnerabilities and therapeutic opportunities.
MicroRNAs and the Evolution of Insect Metamorphosis
Authors: Belles Xavier
Published: November 2016

MicroRNAs (miRNAs) are involved in the regulation of a number of processes associated with metamorphosis, either in the less modified hemimetabolan mode or in the more modified holometabolan mode. The miR-100/let-7/miR-125 cluster has been studied extensively, especially in relation to wing morphogenesis in both hemimetabolan and holometabolan species. Other miRNAs also participate in wing morphogenesis, as well as in programmed cell and tissue death, neuromaturation, neuromuscular junction formation, and neuron cell fate determination, typically during the pupal stage of holometabolan species. A special case is the control of miR-2 over Kr-h1 transcripts, which determines adult morphogenesis in the hemimetabolan metamorphosis. This is an elegant example of how a single miRNA can control an entire process by acting on a crucial mediator; however, this is a quite exceptional mechanism that was apparently lost during the transition from hemimetaboly to holometaboly.
Ebola: Anatomy of an Epidemic
Authors: Lo Terrence Q. , Marston Barbara J. , Dahl Benjamin A. , De Cock Kevin M.
Published: November 2016

As of the end of March 2016, the West Africa epidemic of Ebola virus disease (Ebola) had resulted in a total of 28,646 cases, 11,323 of them fatal, reported to the World Health Organization. Guinea, Liberia, and Sierra Leone were most heavily affected, but Ebola cases were exported to several other African and European countries as well as the United States, with limited further transmission, including to healthcare workers. We review the descriptive epidemiology of the outbreak, novel aspects and insights concerning the unprecedented response, scientific observations, and public health implications. The large number of Ebola survivors has highlighted the frequency of persistent symptoms and the possibility of virus persistence in sanctuary sites, sometimes leading to delayed transmission. Although transmission appears to have ceased in 2016, the West Africa Ebola epidemic has profoundly influenced discussions and practice concerning global health security.
Next-Generation Sequencing and Result Interpretation in Clinical Oncology: Challenges of Personalized Cancer Therapy
Authors: Khotskaya Yekaterina B. , Mills Gordon B. , Mills Shaw Kenna R.
Published: November 2016

The tools of next-generation sequencing (NGS) technology, such as targeted sequencing of candidate cancer genes and whole-exome and -genome sequencing, coupled with encouraging clinical results based on the use of targeted therapeutics and biomarker-guided clinical trials, are fueling further technological advancements of NGS technology. However, NGS data interpretation is associated with challenges that must be overcome to promote the techniques' effective integration into clinical oncology practice. Specifically, sequencing of a patient's tumor often yields 30–65 somatic variants, but most of these variants are “passenger” mutations that are phenotypically neutral and thus not targetable. Therefore, NGS data must be interpreted by multidisciplinary decision-support teams to determine mutation actionability and identify potential “drivers,” so that the treating physician can prioritize what clinical decisions can be pursued in order to provide cancer therapy that is personalized to the patient and his or her unique genome.
GPER (GPR30): A Nongenomic Receptor (GPCR) for Steroid Hormones with Implications for Cardiovascular Disease and Cancer
Authors: Feldman Ross D. , Limbird Lee E.
Published: November 2016

Although the rapid effects of steroids, such as estrogen and aldosterone, were postulated originally to be nongenomic, it is now appreciated that activation of such signaling pathways via a steroid-acting G protein–coupled receptor, the G protein estrogen receptor (GPER), has important transcription-dependent outcomes in the regulation of cell growth and programmed cell death secondary to GPER-regulated second-messenger pathways. GPER is expressed ubiquitously and has diverse biological effects, including regulation of endocrine, immune, neuronal, and cardiovascular functions. Perhaps the most biologically important consequences of GPER activation are the regulation of cell growth, migration, and apoptotic cell death. These cell growth regulatory effects, important in cancer biology, are also relevant in the regulation of cardiac and vascular hypertrophy and in the response to ischemia. This review provides a summary of relevant findings of the impact of GPER regulation by either estradiol or aldosterone in in vitro model systems and extends those findings to in vivo studies of direct clinical relevance for development of GPER-directed agents for treatment of cancer and cardiovascular diseases associated with cellular proliferation.
Receptor-Mediated Endocytosis in the Proximal Tubule
Authors: Eshbach Megan L. , Weisz Ora A.
Published: November 2016

Cells lining the proximal tubule (PT) of the kidney are highly specialized for apical endocytosis of filtered proteins and small bioactive molecules from the glomerular ultrafiltrate to maintain essentially protein-free urine. Compromise of this pathway results in low molecular weight (LMW) proteinuria that can progress to end-stage kidney disease. This review describes our current understanding of the endocytic pathway and the multiligand receptors that mediate LMW protein uptake in PT cells, how these are regulated in response to physiologic cues, and the molecular basis of inherited diseases characterized by LMW proteinuria.
Structure Learning in Graphical Modeling
Authors: Drton Mathias , Maathuis Marloes H.
Published: November 2016

A graphical model is a statistical model that is associated with a graph whose nodes correspond to variables of interest. The edges of the graph reflect allowed conditional dependencies among the variables. Graphical models have computationally convenient factorization properties and have long been a valuable tool for tractable modeling of multivariate distributions. More recently, applications such as reconstructing gene regulatory networks from gene expression data have driven major advances in structure learning, that is, estimating the graph underlying a model. We review some of these advances and discuss methods such as the graphical lasso and neighborhood selection for undirected graphical models (or Markov random fields) and the PC algorithm and score-based search methods for directed graphical models (or Bayesian networks). We further review extensions that account for effects of latent variables and heterogeneous data sources.