bluuebunny/crossref_metadata_2025 huggingface dataset:
Rafting spiders or drifting islands? Origins and diversification of the endemic trap‐door spiders from the Balearic Islands, Western Mediterranean
Authors: Mora Elisa , Paspati Angeliki , Decae Arthur E. , Arnedo Miquel A.
Published: October 2016

Aim

To unravel the origins and to infer the processes of diversification in the low‐vagility nemesiid trap‐door spiders of the Balearic Islands. The specific goals were: (1) to determine whether nemesiid spiders colonized the islands by oversea dispersal, or whether they are the result of the fragmentation of a once continuous distribution by continental drift, and (2) to test whether the Balearic lineages have undergone local diversification processes.

Locations

Balearic Islands, Iberian Peninsula, Western Mediterranean.

Methods

Multilocus molecular phylogenetic inference using parsimony and model‐based methods, and divergence time estimation with relaxed clocks and informed substitution rate priors, and biogeographical ancestral reconstruction inferred in a Bayesian framework.

Results

Phylogenetic analyses revealed the monophyly of the generaIberesiaandNemesia. Four independent clades were recovered for the Balearic fauna. One of the clades included a formerly unknown species from Minorca. The Balearic clades split from their continental relatives in the early Tortonian, except forIberesia brauni, which dates to the Messinian‐Zanclean. The biogeographical reconstruction indicated that the Balearic fauna probably originated in the Betic region of the Iberian Peninsula.

Main conclusions

The presence ofNemesiaon the Balearic Islands was explained by fragmentation of an ancestral distribution range that included the Betic region and the islands in the Early Tortonian. The arrival ofIberesiato the islands, however, was the result of a secondary range expansion that was facilitated by the emergence of land bridges with the continent during the Messinian salinity crisis (MSC). Similarly, the drops in the sea level that occurred during theMSCand subsequently in the Quaternary glacial cycles established land passages between Majorca and Minorca.
Food fussiness and food neophobia share a common etiology in early childhood
Authors: Smith Andrea D. , Herle Moritz , Fildes Alison , Cooke Lucy , Steinsbekk Silje , Llewellyn Clare H.
Published: October 2016

Background

‘Food fussiness’ (FF) is the tendency to be highly selective about which foods one is willing to eat, and emerges in early childhood; ‘food neophobia’ (FN) is a closely related characteristic but specifically refers to rejection of unfamiliar food. These behaviors are associated, but the extent to which their etiological architecture overlaps is unknown. The objective of this study was to quantify the relative contribution of genetic and environmental influences to variation inFFandFNin early childhood; and to establish the extent to which they share common genetic and environmental influences.

Method

Participants were 1,921 families with 16‐month‐old twins from the Gemini birth cohort. Parents completed the Child Eating Behaviour Questionnaire which included threeFFitems and fourFNitems. Bivariate quantitative genetic modeling was used to quantify: (a) genetic and environmental contributions to variation inFFandFN; and (b) the extent to which genetic or environmental influences onFFandFNare shared across the traits.

Results

Food fussiness andFNwere strongly correlated (r = .72,p < .001). Proportions of variation inFFwere equally explained by genetic (.46; 95%CI: 0.41–0.52) and shared environmental influences (.46; 95%CI: 0.41–0.51). Shared environmental effects accounted for a significantly lower proportion of variation inFN(.22; 95%CI: 0.14–0.30), but genetic influences were not significantly different from those onFF(.58, 95%CI: 0.50–0.67).FFandFNlargely shared a common etiology, indicated by high genetic (.73; 95%CI: 0.67–0.78) and shared environmental correlations (.78; 95%CI: 0.69–0.86) across the two traits.

Conclusions

Food fussiness andFNboth show considerable heritability at 16 months but shared environmental factors, for example the home environment, influenced more interindividual differences in the expression ofFFthan inFN.FFandFNlargely share a common etiology.
Anal‐fin ray morphology indicates sexual maturity in Brevimyrus niger (Teleostei, Mormyridae)
Authors: Stell S. K. , Moller P.
Published: October 2016

This osteological survey of 249 specimens of Brevimyrus niger ranging in size from 44 to 137 mm standard length (LS) demonstrated that developmental changes in anal‐fin morphology can serve as a predictor of sexual maturity in this species. Anal‐fin ray bases begin to expand when fish reach c. 90 mm LS at which size and above there were roughly equal numbers of individuals observed with expanded and unmodified anal‐fin bases, reflecting a 1:1 sex ratio.
Assembling and auditing a comprehensive DNA barcode reference library for European marine fishes
Authors: Oliveira L. M. , Knebelsberger T. , Landi M. , Soares P. , Raupach M. J. , Costa F. O.
Published: October 2016

A large‐scale comprehensive reference library of DNA barcodes for European marine fishes was assembled, allowing the evaluation of taxonomic uncertainties and species genetic diversity that were otherwise hidden in geographically restricted studies. A total of 4118 DNA barcodes were assigned to 358 species generating 366 Barcode Index Numbers (BIN). Initial examination revealed as much as 141 BIN discordances (more than one species in each BIN). After implementing an auditing and five‐grade (A–E) annotation protocol, the number of discordant species BINs was reduced to 44 (13% grade E), while concordant species BINs amounted to 271 (78% grades A and B) and 14 other had insufficient data (grade D). Fifteen species displayed comparatively high intraspecific divergences ranging from 2·6 to 18·5% (grade C), which is biologically paramount information to be considered in fish species monitoring and stock assessment. On balance, this compilation contributed to the detection of 59 European fish species probably in need of taxonomic clarification or re‐evaluation. The generalized implementation of an auditing and annotation protocol for reference libraries of DNA barcodes is recommended.
Defective synthesis and release of astrocytic thrombospondin‐1 mediates the neuronal TDP‐43 proteinopathy, resulting in defects in neuronal integrity associated with chronic traumatic encephalopathy: in vitro studies
Authors: Jayakumar Arumugam Radhakrishnan , Tong Xiao Y. , Shamaladevi Nagarajarao , Barcelona Stephanie , Gaidosh Gabriel , Agarwal Apeksha , Norenberg Michael D.
Published: October 2016

Transactivating DNA‐binding protein‐43 (TDP‐43) inclusions and the accumulation of phosphorylated and ubiquitinated tau proteins (p‐tau) have been identified in postmortem brain specimens from patients with chronic traumatic encephalopathy (CTE). To examine whether these proteins contribute to the development of CTE, we utilized an in vitro trauma system known to reproduce many of the findings observed in humans and experimental animals with traumatic brain injury. Accordingly, we examined the role of TDP‐43 and Tau in an in vitro model of trauma, and determined whether these proteins contribute to the defective neuronal integrity associated with CNS trauma. Single or multiple episodes of trauma to cultured neurons resulted in a time‐dependent increase in cytosolic levels of phosphorylated TDP‐43 (p‐TDP‐43). Trauma to cultured neurons also caused an increase in levels of casein kinase 1 epsilon (CK1ε), and ubiquitinated p‐TDP‐43, along with a decrease in importin‐β (all factors known to mediate the “TDP‐43 proteinopathy”). Defective neuronal integrity, as evidenced by a reduction in levels of the NR1 subunit of the NMDA receptor, and in PSD95, along with increased levels of phosphorylated tau were also observed. Additionally, increased levels of intra‐ and extracellular thrombospondin‐1 (TSP‐1) (a factor known to regulate neuronal integrity) were observed in cultured astrocytes at early stages of trauma, while at later stages decreased levels were identified. The addition of recombinant TSP‐1, conditioned media from cultured astrocytes at early stages of trauma, or the CK1ε inhibitor PF4800567 hydrochloride to traumatized cultured neurons reduced levels of p‐TDP‐43, and reversed the trauma‐induced decline in NR1 subunit of the NMDA receptor and PSD95 levels. These findings suggest that a trauma‐induced increase in TDP‐43 phosphorylation contributes to defective neuronal integrity, and that increasing TSP‐1 levels may represent a useful therapeutic approach for the prevention of the neuronal TDP‐43 proteinopathy associated with CTE.

image

Read the Editorial Highlight for this article on page 531.
Enter the dragon!
Authors: Britton Philip N , Cheng Gang
Published: October 2016

See Answer
Effect of intravenous and intracoronary melatonin as an adjunct to primary percutaneous coronary intervention for acute ST‐elevation myocardial infarction: Results of the Melatonin Adjunct in the acute myocaRdial Infarction treated with Angioplasty trial
Authors: Dominguez‐Rodriguez Alberto , Abreu‐Gonzalez Pedro , de la Torre‐Hernandez Jose M. , Gonzalez‐Gonzalez Julia , Garcia‐Camarero Tamara , Consuegra‐Sanchez Luciano , Garcia‐Saiz Maria del Mar , Aldea‐Perona Ana , Virgos‐Aller Tirso , Azpeitia Agueda , Reiter Russel J. ,   the MARIA Investigators
Published: October 2016

The MARIA randomized trial evaluated the efficacy and safety of melatonin for the reduction of reperfusion injury in patients undergoing revascularization for ST‐elevation myocardial infarction (STEMI). This was a prespecified interim analysis. A total of 146 patients presenting with STEMI within 6 hours of chest pain onset were randomized to receive intravenous and intracoronary melatonin (n=73) or placebo (n=73) during primary percutaneous coronary intervention (PPCI). Primary endpoint was myocardial infarct size as assessed by magnetic resonance imaging (MRI) at 6 ± 2 days. Secondary endpoints were changes in left ventricular volumes and ejection fraction (LVEF) at 130 ± 10 days post‐PPCI and adverse events during the first year. No significant differences in baseline characteristics were observed between groups. MRI was performed in 108 patients (86.4%). Myocardial infarct size by MRI evaluated 6 ± 2 days post‐PPCI, did not differ between melatonin and placebo groups (P=.63). Infarct size assessed by MRI at 130 ± 10 days post‐PPCI, performed in 91 patients (72.8%), did not show statistically significant differences between groups (P=.27). The recovery of LVEF from 6 ± 2 to 130 ± 10 days post‐PPCI was greater in the placebo group (60.0 ± 10.4% vs 53.1 ± 12.5%, P=.008). Both left ventricular end‐diastolic and end‐systolic volumes were lower in the placebo group (P=.01). The incidence of adverse events at 1 year was comparable in both groups (P=.150). Thus, in a nonrestricted STEMI population, intravenous and intracoronary melatonin was not associated with a reduction in infarct size and has an unfavourable effect on the ventricular volumes and LVEF evolution. Likewise, there is lack of toxicity of melatonin with the doses used.
Comparison of bacterial cultures of the larynx between dogs with laryngeal paralysis and normal dogs
Authors: Ganjei J. , Langenbach A. , Watrous G. , Hodgson J.
Published: October 2016

Objective

To document the most common types of bacteria isolated from the canine larynx and to compare isolates, degree of growth and susceptibility patterns between dogs with laryngeal paralysis and dogs with normal laryngeal function.

Methods

Laryngeal swabs were collected from each patient and submitted for bacterial culture and susceptibility testing. Dogs with laryngeal paralysis (n=23) underwent a unilateral arytenoid lateralisation and control dogs (n=24) underwent an elective orthopaedic procedure. Results of the cultures were compared between groups.

Results

Bacterial organisms isolated from the larynx were similar to those normally found in the oropharynx, trachea and lungs. The most common bacteria isolated from the larynges of all dogs wereEscherichia coli,Klebsiellaspecies andPasteurellaspecies. Pure colonies were more commonly seen in dogs with laryngeal paralysis while mixed colonies were more commonly seen in control dogs. Antimicrobial resistance was similar between study and control dogs.

Clinical Significance

The laryngeal flora appears to contain bacteria that are commonly isolated from the oropharynx, trachea and lungs. Differences in antimicrobial susceptibility were not identified between study and control dogs.
Wandering and web spiders feeding on the nectar from extrafloral nectaries in neotropical savanna
Authors: Nahas L. , Gonzaga M. O. , Del‐Claro K.
Published: October 2016

Despite their essentially carnivorous habits, spiders can supplement their diets with other food sources, such as extrafloral nectar. The extrafloral nectar can constitute an excellent complementary energy source for spiders because it is rich in mono and disaccharides besides other compounds. We investigate the presence of fructose and its concentration in the bodies of wandering and web weaver spiders collected on extrafloral nectary‐bearing plants from a neotropical savanna area by means of cold anthrone test. The tested spiders belonged to seven families: Anyphaenidae, Araneidae, Oxyopidae, Pisauridae, Salticidae, Theridiidae and Thomisidae. A total of 265 (88.04%) of all tested individuals were fructose intake positive. In general, there was no difference in the percentage of positive spiders between wandering and web weaver spider species or between adult and immature individuals. Results found in this study corroborate those from other studies that suggest that nectar feeding is a common activity among spiders and it includes a new family (Theridiidae) in the nectivory spiders list.
Structural basis for the transcriptional repressor NicR2 in nicotine degradation from Pseudomonas
Authors: Zhang Kunzhi , Wu Geng , Tang Hongzhi , Hu Chuanming , Shi Ting , Xu Ping
Published: October 2016

Nicotine is an environmental toxicant in tobacco wastes, imposing severe hazards for the health of human and other mammalians. NicR2, a TetR‐like repressor from Pseudomonas putida S16, plays a critical role in regulating nicotine degradation. Here, we determined the crystal structures of NicR2 and its complex with the inducer 6‐hydroxy‐3‐succinoyl‐pyridine (HSP). The N‐terminal domain of NicR2 contains a conserved helix‐turn‐helix (HTH) DNA‐binding motif, while the C‐terminal domain contains a cleft for its selective recognition for HSP. Residues R91, Y114 and Q118 of NicR2 form hydrogen bonds with HSP, their indispensable roles in NicR2's recognition with HSP were confirmed by structure‐based mutagenesis combined with isothermal titration calorimetry analysis. Based on sequence alignment and structure comparison, Tyr67, Tyr68 and Lys72 of HTH motif were corroborated to take the major responsibility for DNA‐binding using site‐directed mutants. The 30‐residue N‐terminal extension of NicR2, especially residues 21–30 in the TFR arm, is required for the association with the operator DNA. Finally, we proposed that either NicR2 or the DNA would undergo a conformational change upon their association. Altogether, our structural and biochemical investigations unravel how NicR2 selectively recognizes HSP and DNA, and provide new insights into the TetR family of repressors.
Towards unified hypotheses of the impact of polyploidy on ecological niches
Authors: Parisod Christian , Broennimann Olivier
Published: October 2016

This article is a commentary on Marchant et al., 212: 708–718.
A countermeasure development pipeline
Authors: MacRae Calum A. , Boss Gerry , Brenner Matthew , Gerszten Robert E. , Mahon Sari , Peterson Randall T.
Published: October 2016

We have developed an integrated pipeline for countermeasure discovery that, under the auspices of the National Institutes of Health Countermeasures Against Chemical Threats network, is one of the few efforts within academia that by design spans the spectrum from discovery to phase I. The successful implementation of this approach for cyanide would enable efficient proof‐of‐concept studies that would lay the foundation for a generalizable strategy for parallel mechanistic studies and accelerated countermeasure development in the face of new and emerging chemical threats.
An (E,E)‐α‐farnesene synthase gene of soybean has a role in defence against nematodes and is involved in synthesizing insect‐induced volatiles
Authors: Lin Jingyu , Wang Dan , Chen Xinlu , Köllner Tobias G. , Mazarei Mitra , Guo Hong , Pantalone Vincent R. , Arelli Prakash , Stewart Charles Neal , Wang Ningning , Chen Feng
Published: October 2016

Plant terpene synthase genes (TPSs) have roles in diverse biological processes. Here, we report the functional characterization of one member of the soybean TPS gene family, which was designated GmAFS. Recombinant GmAFS produced in Escherichia coli catalysed the formation of a sesquiterpene (E,E)‐α‐farnesene. GmAFS is closely related to (E,E)‐α‐farnesene synthase gene from apple, both phylogenetically and structurally. GmAFS was further investigated for its biological role in defence against nematodes and insects. Soybean cyst nematode (SCN) is the most important pathogen of soybean. The expression of GmAFS in a SCN‐resistant soybean was significantly induced by SCN infection compared with the control, whereas its expression in a SCN‐susceptible soybean was not changed by SCN infection. Transgenic hairy roots overexpressing GmAFS under the control of the CaMV 35S promoter were generated in an SCN‐susceptible soybean line. The transgenic lines showed significantly higher resistance to SCN, which indicates that GmAFS contributes to the resistance of soybean to SCN. In soybean leaves, the expression of GmAFS was found to be induced by Tetranychus urticae (two‐spotted spider mites). Exogenous application of methyl jasmonate to soybean plants also induced the expression of GmAFS in leaves. Using headspace collection combined with gas chromatography–mass spectrometry analysis, soybean plants that were infested with T. urticae were shown to emit a mixture of volatiles with (E,E)‐α‐farnesene as one of the most abundant constituents. In summary, this study showed that GmAFS has defence roles in both below‐ground and above‐ground organs of soybean against nematodes and insects, respectively.
Golden bananas in the field: elevated fruit pro‐vitamin A from the expression of a single banana transgene
Authors: Paul Jean‐Yves , Khanna Harjeet , Kleidon Jennifer , Hoang Phuong , Geijskes Jason , Daniells Jeff , Zaplin Ella , Rosenberg Yvonne , James Anthony , Mlalazi Bulukani , Deo Pradeep , Arinaitwe Geofrey , Namanya Priver , Becker Douglas , Tindamanyire James , Tushemereirwe Wilberforce , Harding Robert , Dale James
Published: October 2016

Vitamin A deficiency remains one of the world's major public health problems despite food fortification and supplements strategies. Biofortification of staple crops with enhanced levels of pro‐vitamin A (PVA) offers a sustainable alternative strategy to both food fortification and supplementation. As a proof of concept, PVA‐biofortified transgenic Cavendish bananas were generated and field trialed in Australia with the aim of achieving a target level of 20 μg/g of dry weight (dw) β‐carotene equivalent (β‐CE) in the fruit. Expression of a Fe'i banana‐derived phytoene synthase 2a (MtPsy2a) gene resulted in the generation of lines with PVA levels exceeding the target level with one line reaching 55 μg/g dw β‐CE. Expression of the maize phytoene synthase 1 (ZmPsy1) gene, used to develop ‘Golden Rice 2’, also resulted in increased fruit PVA levels although many lines displayed undesirable phenotypes. Constitutive expression of either transgene with the maize polyubiquitin promoter increased PVA accumulation from the earliest stage of fruit development. In contrast, PVA accumulation was restricted to the late stages of fruit development when either the banana 1‐aminocyclopropane‐1‐carboxylate oxidase or the expansin 1 promoters were used to drive the same transgenes. Wild‐type plants with the longest fruit development time had also the highest fruit PVA concentrations. The results from this study suggest that early activation of the rate‐limiting enzyme in the carotenoid biosynthetic pathway and extended fruit maturation time are essential factors to achieve optimal PVA concentrations in banana fruit.
Identification of a novel HLA‐B*15 allele, HLA‐B*15:374, in a Chinese individual
Authors: Zou H.‐Y. , Jin S.‐Z. , Zhou D. , Wang D.‐M.
Published: October 2016

HLA‐B*15:374 has one nucleotide change from HLA‐B*15:02:01 at nucleotide 553 bp where G → A in exon 3.
Gender and the ownership of English in South Africa
Authors: PARMEGIANI ANDREA
Published: October 2016

This paper explores the role gender plays in the ownership of English as an additional language in South Africa. The question of who is a ‘legitimate’ owner of the dominant language is crucial for democratic transformation, as it is related to the allocation of opportunities for socio‐economic empowerment. After deconstructing the notion that only native speakers can be considered legitimate owners, I will present an empirical study which explores how a group of black South African university students are taking ownership of English as part of their process of self‐empowerment, and how this process is implicated in the re(construction) of gender identities.
Surface oxidation of the topological insulator Bi2Se3
Authors: Green Avery J. , Dey Sonal , An Yong Q. , O'Brien Brendan , O'Mullane Samuel , Thiel Bradley , Diebold Alain C.
Published: October 2016

An understanding of the aging and oxidation of the (0001) surface of Bi2Se3 is critical to a comprehensive physical picture of its topologically protected surface states. Here, the authors contribute new experimental observations about the aging and oxidation process. The authors find that surface aging in ambient conditions occurs in two major steps. Within 2 h of exfoliation, a series of ∼3.2 Å high islands are observed by atomic force microscopy over approximately 10% of the surface. Subsequently, patch growth stops, and oxidation begins after the 2 h and continues until one quintuple layer has been oxidized. X-ray photoelectron spectroscopy shows no sign of oxidation before ∼120 min of exposure to air, and the oxygen 1 s peak, as well as oxidized Se 3d and Bi 4d peaks, are clearly present after ∼190 min of ambient exposure. Variable angle spectroscopic ellipsometry indicates that the oxidation of a full quintuple layer occurs on the time scale of days. These results are in good agreement with the time dependent changes observed in the surface crystal structure by second harmonic generation. In addition to providing the ability to nondestructively measure oxide on the surface of Bi2Se3 crystals, ellipsometry can be used to identify the thickness of Bi2Se3 flakes. With these methods, the authors have constructed a consistent, experimentally based model of aging process at the surface of Bi2Se3.
The visible signal responsible for proton therapy dosimetry using bare optical fibers is not Čerenkov radiation
Authors: Darafsheh Arash , Taleei Reza , Kassaee Alireza , Finlay Jarod C.
Published: October 2016

Purpose

Proton beam dosimetry using bare plastic optical fibers has emerged as a simple approach to proton beam dosimetry. The source of the signal in this method has been attributed to Čerenkov radiation. The aim of this work was a phenomenological study of the nature of the visible light responsible for the signal in bare fiber optic dosimetry of proton therapy beams.

Methods

Plastic fiber optic probes embedded in solid water phantoms were irradiated with proton beams of energies 100, 180, and 225 MeV produced by a proton therapy cyclotron. Luminescence spectroscopy was performed by a CCD‐coupled spectrometer. The spectra were acquired at various depths in phantom to measure the percentage depth dose (PDD) for each beam energy. For comparison, the PDD curves were acquired using a standard multilayer ion chamber device. In order to further analyze the contribution of the Čerenkov radiation in the spectra, Monte Carlo simulation was performed using fluka Monte Carlo code to stochastically simulate radiation transport, ionizing radiation dose deposition, and optical emission of Čerenkov radiation.

Results

The measured depth doses using the bare fiber are in agreement with measurements performed by the multilayer ion chamber device, indicating the feasibility of using bare fiber probes for proton beam dosimetry. The spectroscopic study of proton‐irradiated fibers showed a continuous spectrum with a shape different from that of Čerenkov radiation. The Monte Carlo simulations confirmed that the amount of the generated Čerenkov light does not follow the radiation absorbed dose in a medium.

Conclusions

The source of the optical signal responsible for the proton dose measurement using bare optical fibers is not Čerenkov radiation. It is fluorescence of the plastic material of the fiber.
The effects of click and masker spectrum on the auditory brainstem response of bottlenose dolphins (Tursiops truncatus)
Authors: Mulsow Jason , Finneran James J. , Houser Dorian S. , Burkard Robert F.
Published: October 2016

Two experiments were performed that investigated the effects of (1) click level and (2) continuous broadband noise on the binaural auditory brainstem response (ABR) of normal-hearing and hearing-impaired bottlenose dolphins (Tursiops truncatus). In addition to spectrally uncompensated clicks and noise, stimuli were digitally compensated to achieve “white” spectra (flat spectral density level) or “pink” spectra (spectral density level rolling off at −3 dB/octave). For experiment 1, in all spectral conditions, ABR peak latencies increased and peak amplitudes decreased with decreasing click level, but interwave intervals changed little. Latency-intensity function (LIF) slopes ranged from −3 to −11 μs/dB. The LIF slopes of ABR peaks evoked by uncompensated clicks were steeper in dolphins with hearing loss. Click level was held constant during experiment 2, and the effect of bilaterally delivered broadband masking noise on the ABR was investigated. Clicks and noise were filtered to create a pink click/noise condition and a white click/noise condition. With increasing levels of masking noise, peak latencies increased (although only P1-P4 white reached significance), peak amplitudes decreased, and interpeak intervals increased (although not significantly). These effects are compared to results reported for terrestrial mammals, and implications for auditory health assessment and biosonar function are discussed.
Mechanics of human voice production and control
Authors: Zhang Zhaoyan
Published: October 2016

As the primary means of communication, voice plays an important role in daily life. Voice also conveys personal information such as social status, personal traits, and the emotional state of the speaker. Mechanically, voice production involves complex fluid-structure interaction within the glottis and its control by laryngeal muscle activation. An important goal of voice research is to establish a causal theory linking voice physiology and biomechanics to how speakers use and control voice to communicate meaning and personal information. Establishing such a causal theory has important implications for clinical voice management, voice training, and many speech technology applications. This paper provides a review of voice physiology and biomechanics, the physics of vocal fold vibration and sound production, and laryngeal muscular control of the fundamental frequency of voice, vocal intensity, and voice quality. Current efforts to develop mechanical and computational models of voice production are also critically reviewed. Finally, issues and future challenges in developing a causal theory of voice production and perception are discussed.
Assessment of traffic noise levels in urban areas using different soft computing techniques
Authors: Tomić J. , Bogojević N. , Pljakić M. , Šumarac-Pavlović D.
Published: October 2016

Available traffic noise prediction models are usually based on regression analysis of experimental data, and this paper presents the application of soft computing techniques in traffic noise prediction. Two mathematical models are proposed and their predictions are compared to data collected by traffic noise monitoring in urban areas, as well as to predictions of commonly used traffic noise models. The results show that application of evolutionary algorithms and neural networks may improve process of development, as well as accuracy of traffic noise prediction.
The bursts of stops can convey dialectal information
Authors: Themistocleous Charalambos
Published: October 2016

This study investigates the effects of the dialect of the speaker on the spectral properties of stop bursts. Forty-five female speakers—20 Standard Modern Greek and 25 Cypriot Greek speakers—participated in this study. The spectral properties of stop bursts were calculated from the burst spectra and analyzed using spectral moments. The findings show that besides linguistic information, i.e., the place of articulation and the stress, the speech signals of bursts can encode social information, i.e., the dialects. A classification model using decision trees showed that skewness and standard deviation have a major contribution for the classification of bursts across dialects.
Superradiance on the millihertz linewidth strontium clock transition
Authors: Norcia Matthew A. , Winchester Matthew N. , Cline Julia R. K. , Thompson James K.
Published: October 2016

Researchers demonstrate superradiant emission from the 150-s lifetime strontium clock transition.
Genome Sequence of the Enterohemorrhagic Escherichia coli Bacteriophage UFV-AREG1
Authors: Lopez Maryoris E. Soto , Batalha Laís Silva , Vidigal Pedro Marcus Pereira , Albino Luiz Augusto A. , Boggione Delaine Meireles Gouveia , Gontijo Marco Tulio Pardini , Bazzolli Denise M. Soares , Mendonca Regina C. Santos
Published: October 2016

Here, we present the genome sequence of the
Escherichia coli
bacteriophage UFV-AREG1. This phage was isolated from cowshed wastewater and showed specificity for enterohemorrhagic
E. coli
O157:H7 (ATCC 43895),
E. coli
0111 (CDC O11ab) and
E. coli
(ATCC 23229).
Complete Genome Sequence of NC983, a Live Attenuated Strain of Salmonella enterica Serovar Typhimurium
Authors: Troxell Bryan , Fink Ryan C. , Dickey Allison N. , Scholl Elizabeth H. , Hassan Hosni M.
Published: October 2016

Foodborne infections caused by
Salmonella enterica
serovars are a significant problem worldwide. Presented here is the genome sequence of the nontyphoidal
S. enterica
serovar Typhimurium mutant strain NC983, a potential vaccine candidate.
Whole-Genome Sequence of a Beak and Feather Disease Virus Isolate from a Fledgling Red-Capped Parrot (
Purpureicephalus spurius
)
Authors: Das Shubhagata , Subir Sarker , Forwood Jade K. , Ghorashi Seyed A. , Raidal Shane R.
Published: October 2016

The complete genome sequence of beak and feather disease virus (BFDV) from a fledgling red-capped parrot (
Purpureicephalus spurius
) was assembled and characterized. The genome consists of 1,995 nucleotides and encodes two major proteins in opposing directions. This is the first evidence of BFDV infectivity and a complete genome sequence for this novel host.
Complete Genome Sequence of Zika Virus Isolated from Semen
Authors: Atkinson Barry , Graham Victoria , Miles Rory W. , Lewandowski Kuiama , Dowall Stuart D. , Pullan Steven T. , Hewson Roger
Published: October 2016

Zika virus (ZIKV) is an emerging pathogenic flavivirus currently circulating in numerous countries in South America, the Caribbean, and the Western Pacific Region. Using an unbiased metagenomic sequencing approach, we report here the first complete genome sequence of ZIKV isolated from a clinical semen sample.
Genome Sequence of Mycoplasma hyorhinis Isolated from Cell Cultures
Authors: Cibulski Samuel Paulo , Siqueira Franciele Maboni , Teixeira Thais Fumaco , Mayer Fabiana Quoos , Almeida Luiz Gonzaga , Roehe Paulo Michel
Published: October 2016

Mycoplasmas are major contaminants of mammalian cell cultures. Here, the complete genome sequence of
Mycoplasma hyorhinis
recovered from Madin-Darby bovine kidney (MDBK) cells is reported.
Draft Genome Sequence of Tenacibaculum soleae UCD-KL19
Authors: Lujan Karley M. , Eisen Jonathan A. , Coil David A.
Published: October 2016

Here, we present the draft genome sequence of
Tenacibaculum soleae
strain UCD-KL19. The assembly contains 3,012,701 bp in 46 contigs. This strain was isolated from a seagrass leaf (
Zostera marina
) collected from Bodega Bay, CA, as a part of an undergraduate student research project on isolating bacteria from seagrass.
Draft Genome Sequence of
Gordonia
sp. Strain UCD-TK1 (Phylum
Actinobacteria
)
Authors: Koenigsaecker Tynisha M. , Eisen Jonathan A. , Coil David A.
Published: October 2016

Here, we present the draft genome of
Gordonia
sp. strain UCD-TK1. The assembly contains 5,470,576 bp in 98 contigs. This strain was isolated from a disinfected ambulatory surgery center.
Draft Genome Sequences of Four Salmonella enterica Strains Isolated from Turkey-Associated Sources
Authors: Khajanchi Bijay K. , Han Jing , Gokulan Kuppan , Zhao Shaohua , Gies Allen , Foley Steven L.
Published: October 2016

We report the draft genomes of four
Salmonella enterica
isolates evaluated for the contribution of plasmids to virulence. Strains SE163A, SE696A, and SE710A carry plasmids demonstrated to facilitate plasmid-associated virulence, while SE819 is less virulent and has been used as a recipient for conjugation experiments to assess plasmid-encoded virulence mechanisms.
Complete Genome Sequences of Bordetella flabilis, Bordetella bronchialis, and “
Bordetella pseudohinzii
”
Authors: Spilker Theodore , Darrah Rebecca , LiPuma John J.
Published: October 2016

We report here the complete genome sequences of
Bordetella flabilis
and
Bordetella bronchialis
recovered from cultures of individuals with cystic fibrosis (CF), and “
Bordetella pseudohinzii
” recovered from a CF mouse model.
Introduction to Preharvest Food Safety
Authors: Torrence Mary E.
Published: October 2016

This introductory article provides an overview of preharvest food safety activities and initiatives for the past 15 years. The section on traditional areas of preharvest food safety focuses on significant scientific advancements that are a culmination of collaborative efforts (both public health and agriculture) and significant research results. The highlighted advancements provide the foundation for exploring future preharvest areas and for improving and focusing on more specific intervention/control/prevention strategies. Examples includeEscherichia coliand cattle,SalmonellaandCampylobacterin poultry, and interventions and prevention and control programs. The section on “nontraditional” preharvest food safety areas brings attention to potential emerging food safety issues and to future food safety research directions. These include organic production, the FDA’s Produce Rule (water and manure), genomic sequencing, antimicrobial resistance, and performance metrics. The concluding section emphasizes important themes such as strategic planning, coordination, epidemiology, and the need for understanding food safety production as a continuum. Food safety research, whether at the pre- or postharvest level, will continue to be a fascinating complex web of foodborne pathogens, risk factors, and scientific and policy interactions. Food safety priorities and research must continue to evolve with emerging global issues, emerging technologies, and methods but remain grounded in a multidisciplinary, collaborative, and systematic approach.
Neonatal vaccination of low birthweight infants in Ghana
Authors: O'Leary Maureen , Edmond Karen , Floyd Sian , Hurt Lisa , Shannon Caitlin , Thomas Gyan , Newton Sam , Kirkwood Betty , Thomas Sara
Published: October 2016

Objectives

Global vaccination policy advocates for identifying and targeting groups who are underserved by vaccination to increase equity and uptake. We investigated whether birth weight and other factors are determinants of neonatal BCG vaccination in order to identify infants underserved by vaccination.

Methods

We used logistic regression to calculate adjusted ORs (AORs) for the association between birth weight (categorised as non-low birth weight (NLBW) (≥2.50 kg) and low birth weight (LBW) (2–2.49 kg, 1.50–1.99 kg and <1.50 kg)) and non-vaccination with BCG at the end of the neonatal period (0–27 days). We assessed whether this association varied by place of delivery and infant illness. We calculated how BCG timing and uptake would improve by ensuring the vaccination of all facility-born infants prior to discharge.

Results

There was a strong dose–response relationship between LBW and not receiving BCG in the neonatal period (p-trend<0.0001). Infants weighing 1.50–1.99 kg had odds of non-vaccination 1.6 times (AOR 1.64; 95% CI 1.30 to 2.08), and those weighing <1.50 kg 2.4 times (AOR 2.42; 95% CI 1.50 to 3.88) those of NLBW infants. Other determinants included place of delivery, distance to the health facility and socioeconomic status. Neither place of delivery nor infant illness modified the association between birth weight and vaccination (p-interaction all >0.19). Facility-born infants were vaccinated at a mean of 6 days, suggesting that they were not vaccinated in the facility at birth but were referred for vaccination.

Conclusions

LBW is a risk factor for neonatal under-vaccination, even for facility-born infants. Ensuring vaccination at facility births would substantively improve timing and equitable BCG vaccination.
Development of a DNA aptamer that binds specifically to group AStreptococcusserotype M3
Authors: Alfavian Hanif , Mousavi Gargari Seyed Latif , Rasoulinejad Samaneh , Medhat Arvin
Published: October 2016

Group A streptococcus (GAS) is an important Gram-positive pathogen that causes various human diseases ranging from peripheral lesions to invasive infections. The M protein is one of the main virulence factors present on the cell surface and is associated with invasive GAS infections. Compared with other M types, serotype M3 has a predominant role in lethal infections and demonstrates epidemic behaviors, including streptococcal toxic shock syndrome, bacteremia, and necrotizing fasciitis. Traditional methods for M typing are time-consuming, tedious, contradictory, and generally restricted to reference laboratories. Therefore, development of a new M-typing technique is needed. Aptamers with the ability to detect their target with a high degree of accuracy and specificity can be ideal candidates for specific M-typing of Streptococcus pyogenes. In this study DNA aptamers with a high binding affinity towards S. pyogenes serotype M3 were selected through 12 iterative rounds of the Systematic Evolution of Ligands by EXponential (SELEX) enrichment procedure using live cells as a target. We monitored the progress of the SELEX procedure by flow cytometry analysis. Of several aptamer sequences analyzed, 12L18A showed the highest binding efficiency towards S. pyogenes type M3, with an apparent dissociation constant (Kd) of 7.47 ± 1.72 pmol/L being the lowest. Therefore the isolated aptamer can be used in any tool, such as a biosensor, for the detection of S. pyogenes and can be used in the development of a novel M-typing system.
On the cohomology of almost-complex and symplectic manifolds and proper surjective maps
Authors: Tardini Nicoletta , Tomassini Adriano
Published: October 2016

Let [Formula: see text] be an almost-complex manifold. In [Comparing tamed and compatible symplectic cones and cohomological properties of almost-complex manifolds, Comm. Anal. Geom. 17 (2009) 651–683], Li and Zhang introduce [Formula: see text] as the cohomology subgroups of the [Formula: see text]th de Rham cohomology group formed by classes represented by real pure-type forms. Given a proper, surjective, pseudo-holomorphic map between two almost-complex manifolds, we study the relationship among such cohomology groups. Similar results are proven in the symplectic setting for the cohomology groups introduced in [Cohomology and Hodge Theory on Symplectic manifolds: I, J. Differ. Geom. 91(3) (2012) 383–416] by Tseng and Yau and a new characterization of the hard Lefschetz condition in dimension [Formula: see text] is provided.
The DAMA project
Authors: Bernabei R.
Published: October 2016

The DAMA project at the Laboratori Nazionali del Gran Sasso (LNGS) of the I.N.F.N. has realized and developed many low background scintillators for rare event searches, as investigation of Dark Matter, double beta decay, etc. A short introduction to the project and a summary of the past and present activities will be given here.
Reduced Complexity Linearity Improved Threshold Quantized Comparator Based Flash ADC
Authors: Palsodkar Prachi , Dakhole Pravin , Palsodkar Prasanna
Published: October 2016

This paper describes a standard cell-based new approach of comparator design for flash ADC. Conventional flash ADC comparator consumes up to 60% of the power due to resistive ladder network and analog comparators. Threshold inverter quantized (TIQ) comparators reported earlier have improved speed and provide low-power, low-voltage operation. But they need feature size variation and have non-linearity issues. Here, a new standard cell comparator is proposed which retains all advantages of TIQ comparator and provides improved linearity with reduced hardware complexity. A 4-bit ADC designed using the proposed comparator requires 206 minimum-sized transistors and provides large area saving compared to previously proposed designs. Thermometer code is partitioned using algebraic division theorem. This conversion is used for mathematical modeling and complexity reduction of decoder circuit using semi-parallel organization of comparators. Circuit is designed using 90 nm technology which exhibits satisfactory performance even in process variation.
Novikov homology and non-commutative Alexander polynomials
Authors: Friedl Stefan
Published: October 2016

In the early 2000's Cochran and Harvey introduced non-commutative Alexander polynomials for 3-manifolds. Their degrees give strong lower bounds on the Thurston norm. In this paper, we make the case that the vanishing of a certain Novikov–Sikorav homology module is the correct notion of a monic non-commutative Alexander polynomial. Furthermore we will use the opportunity to give new proofs of several statements about Novikov–Sikorav homology in the three-dimensional context.
Complements of connected hypersurfaces in S4
Authors: Hillman Jonathan A.
Published: October 2016

Let [Formula: see text] and [Formula: see text] be the complementary regions of a closed hypersurface [Formula: see text] in [Formula: see text]. We use the Massey product structure in [Formula: see text] to limit the possibilities for [Formula: see text] and [Formula: see text]. We show also that if [Formula: see text] then it may be modified by a 2-knot satellite construction, while if [Formula: see text] and [Formula: see text] is abelian then [Formula: see text] or [Formula: see text]. Finally we use TOP surgery to propose a characterization of the simplest embeddings of [Formula: see text].
A homotopy+ solution to the A-B slice problem
Authors: Freedman Michael , Krushkal Vyacheslav
Published: October 2016

The A-B slice problem, a reformulation of the four-dimensional topological surgery conjecture for free groups, is shown to admit a link-homotopy[Formula: see text] solution. The proof relies on geometric applications of the group-theoretic [Formula: see text]-Engel relation. Implications for the surgery conjecture are discussed.
Quantum leaps of black holes: Magnifying glasses of quantum gravity
Authors: Chakraborty Sumanta , Lochan Kinjalk
Published: October 2016

We show using simple arguments, that the conceptual triad of a classical black hole, semi-classical Hawking emission and geometry quantization is inherently, mutually incompatible. Presence of any two explicitly violates the third. We argue that geometry quantization, if realized in nature, magnifies the quantum gravity features hugely to catapult them into the realm of observational possibilities. We also explore a quantum route towards extremality of the black holes.
Unconditionally Secure Credit/Debit Card Chip Scheme and Physical Unclonable Function
Authors: Kish Laszlo B. , Entesari Kamran , Granqvist Claes-Göran , Kwan Chiman
Published: October 2016

The statistical-physics-based Kirchhoff-law–Johnson-noise (KLJN) key exchange offers a new and simple unclonable system for credit/debit card chip authentication and payment. The key exchange, the authentication and the communication are unconditionally secure so that neither mathematics- nor statistics-based attacks are able to crack the scheme. The ohmic connection and the short wiring lengths between the chips in the card and the terminal constitute an ideal setting for the KLJN protocol, and even its simplest versions offer unprecedented security and privacy for credit/debit card chips and applications of physical unclonable functions (PUFs).
Dynamic behavior of stochastic p-Laplacian-type lattice equations
Authors: Gu Anhui , Li Yangrong
Published: October 2016

In this paper, we consider the dynamic behavior of stochastic [Formula: see text]-Laplacian-type lattice equations perturbed by a multiplicative noise. Under weaker dissipative conditions compared to the cases of stochastic [Formula: see text]-Laplacian-type equations in bounded and unbounded domains, we first obtain the existence of a unique random attractor. We also establish the approximation of the random attractors from finite lattice to infinite lattice, which indicates that the family of random attractors is upper and lower semi-continuous when the number of the lattice nodes tends to infinity.
Theoretical calculations of intramolecular hydrogen bond of the 2-Amino-2, 4, 6-cycloheptatrien-1-one in the gas phase and solution: Substituent effects and their positions
Authors: Toosy Narges Khatoon Attaran , Raissi Heidar , Zaboli Maryam
Published: October 2016

The density functional theory (DFT) method with 6-311[Formula: see text]G[Formula: see text] basis set has been used to calculate the intramolecular hydrogen bond, molecular structure, vibrational frequencies, nuclear quadrupole resonance (NQR) parameters, 1HNMR, and resonance parameters of 2-Amino-2, 4, 6-cycloheptatrien-1-one (2-amino tropone) and its 18 derivatives in 5 positions. The natural bonding orbital (NBO) and quantum theory of atoms in molecules (QTAIM) analyses have been studied. The strongest and weakest hydrogen bonds exist for NO2 substituent in R3 position and OH in R7 position, respectively. In general, the substituted systems in position 3 indicate the stronger hydrogen bond in comparison with the parent molecule (R[Formula: see text]H), while, it is comparatively weaker for position 5. The energy of the N-H[Formula: see text]O interaction is found to be medium in strength ([Formula: see text][Formula: see text]kJ mol[Formula: see text] to [Formula: see text][Formula: see text]kJ mol[Formula: see text]). The low [Formula: see text], positive [Formula: see text] values and [Formula: see text] show that the nature of O [Formula: see text] H bonding is electrostatic. Also, our theoretical results show that the hydrogen bond strength in solution phase and the first singlet excited state is weaker in comparison with the gas phase ground state.