bluuebunny/crossref_metadata_2025 huggingface dataset:
Patient, staffing and health centre factors associated with annual testing for sexually transmissible infections in remote primary health centres
Authors: Hengel Belinda , Wand Handan , Ward James , Rumbold Alice , Garton Linda , Taylor-Thomson Debbie , Silver Bronwyn , McGregor Skye , Dyda Amalie , Mein Jacqueline , Knox Janet , Maher Lisa , Kaldor John , Guy Rebecca , on behalf of the STRIVE Investigators
Published: November 2018

Background: In high-incidence Chlamydia trachomatis (CT) and Neisseria gonorrhoeae (NG) settings, annual re-testing is an important public health strategy. Using baseline laboratory data (2009–10) from a cluster randomised trial in 67 remote Aboriginal communities, the extent of re-testing was determined, along with the associated patient, staffing and health centre factors. Methods: Annual testing was defined as re-testing in 9–15 months (guideline recommendation) and a broader time period of 5–15 months following an initial negative CT/NG test. Random effects logistic regression was used to determine factors associated with re-testing. Results: Of 10 559 individuals aged ≥16 years with an initial negative CT/NG test (median age = 25 years), 20.3% had a re-test in 9–15 months (23.6% females vs 15.4% males, P < 0.001) and 35.2% in 5–15 months (40.9% females vs 26.5% males, P < 0.001). Factors independently associated with re-testing in 9–15 months in both males and females were: younger age (16–19, 20–24 years); and attending a centre that sees predominantly (>90%) Aboriginal people. Additional factors independently associated with re-testing for females were: being aged 25–29 years, attending a centre that used electronic medical records, and for males, attending a health centre that employed Aboriginal health workers and more male staff. Conclusions: Approximately 20% of people were re-tested within 9–15 months. Re-testing was more common in younger individuals. Findings highlight the importance of recall systems, Aboriginal health workers and male staff to facilitate annual re-testing. Further initiatives may be needed to increase re-testing.
Distribution of 40K, 232Th and 238U in Soils of Southern and Western Coasts of Viti Levu, Fiji
Authors: Garimella Sitaram , Prasad Umawatti
Published: November 2018

Abstract A 10 cm (diameter) x 7.5 cm NaI(Tl) gamma-ray spectrometer was used to measure the concentrations of 40K, 232Th and 238U in 50 samples of top soils of the southern and western coasts of Viti Levu, the largest island of the Republic of Fiji Islands. The average activities of 232Th, 238U and 40K in soils of this region were 2.8, 3.6 and 160 Bq kg-1, respectively. The average external gamma-dose, which is likely to be delivered to the local population in this region, is estimated to be 10.3 nGy h-1, well below the world average.
Potassium Studies on Some Sugarcane Growing Soils in Fiji
Authors: Gawander J.S. , Gangaiya P. , Morrison R.J.
Published: November 2018

This study investigated the potassium (K) status of sugarcane growing soils in Fiji, using samples taken from fields under cultivation and also from sites that had not been cultivated for at least 30 years. Five sites were on highly weathered oxyhydroxide soils where the total K contents and K retention capacities were generally low. The two less weathered soils containing significant amounts of 2:1 expanding clay minerals had much higher total K and non-exchangeable K. Exchangeable K and soil solution K contents varied significantly, but were generally low for most soils. Exchangeable K contents were lower in the regularly cultivated fields at five sites out of the eight, were higher at 2 sites, while for one site there was no change. These variations may be due to different levels of K input, uptake by crop and losses due to leaching and erosion. The two less weathered soils (Sigatoka and Nawaicoba) had lower contents of both non-exchangeable and exchangeable K in the cultivated soil when compared with the fallow sites suggesting net loss of K due to cultivation. These soils, however, also had high surface negative charge and thus a better capacity to retain K. Since the K requirement of sugarcane is characteristically high and large amounts of K are removed in the harvested crop, K fertilizer practices need to be scrutinized carefully in Fiji.
Walks on graphs as symmetric or asymmetric tools to encrypt data
Authors: Ustimenko V. A. , Khmelevsky Y. M.
Published: November 2018

New results on graph theoretical method of encryption will be presented. The general idea is to treat vertices of a graph as messages, and walks of a certain length as ecnryption tools. We will construct one-time pad algorithms with a certain resistance to attacks when the adversary knows plaintext and ciphertext. Special linguistic graphs of high girth whose vertices (messages) and walks (encoding tools) could be both naturally identified with vectors over the finite field, and with the so-called parallelotopic graphs, which turn out to be efficient tools for symmetric encryption. We will formulate criteria when parallelotopic graph (or the more general graph of tactical configuration) is a graph of absolutely optimal encryption scheme, producing asymptotic one-time pad algorithm. We will show how to convert one-time pads, which are related to geometries of rank 2 of simple groups of Lie type, to a real-life encryption scheme involving potentially infinite text and flexible passwords.
We will discuss families of linguistic and parallelotopic graphs of increasing girth as the source for the generation of asymmetric cryptographic functions and related open key algorithms. We will construct new families of such graphs via group theoretical and geometrical technique.
The software for symmetric and asymmetric ecnryption (prototype model of the package) is ready for demonstration.
Solving the three-dimensional findpath problem via Liapunov's method
Authors: Sharma B
Published: November 2018

This paper presents a method for solving the findpath problem. Commonly known as the second or direct method of Liapunov, the method is used to solve this geometric problem of finding collision-free trajectories of moving solid objects amongst other fixed and moving solid objects. A Liapunov function is proposed for a n-point dynamical system in three-space. Computer simulations are carried out to show the effectiveness of the proposed Liapunov function-based feedback controllers.
Methane Concentration in Fiji Air: A Study of its Emission Trends and Source Strengths
Authors: Mani Francis , Koshy Kanayathu , Maata Matakite
Published: November 2018

In this study we have developed an in house capacity at the Chemistry Department, the University of the South Pacific, to analyze methane in ambient air to a precision of 1.5% using a custom converted Gas Chromatograph with FID detector. The technical support to develop this capacity was provided by our overseas partner, National Institute of Water and Atmospheric Research (NIWA). The air samples were collected from known sources of methane such as the digester at the sewage treatment plant, rubbish dump, wetlands, sugar cane burning in the western side of Viti Levu, geothermal emission in Vanua Levu, rice farms and cattle farms from September 2001 to June 2002 and were analyzed. Through inter-laboratory measurements involving NIWA a mean drift of 0.8% was obtained. The methane concentration in the ambient air has a seasonal cycle with a minimum during late January and a maximum during the July to August period. The digester at the sewage plant recorded the maximum concentration of approximately 70 ppmv followed by Lami rubbish dump with values ranging from 4.37 ? 13.35 ppmv. The data from cattle farms, wetlands, rice farms and hot springs recorded emissions in the range of 2.00 ? 5.11 ppmv, 1.85 ? 4.25 ppmv, 1.77 ? 2.62 ppmv and 2.06 ? 1.90 ppmv respectively.
A Novel Method of Assessing Bioerosion by the Sea Urchin Echinometra sp. A on a Fijian Reef
Authors: Appana Subhashni D. , Vuki Veikila C.
Published: November 2018

Sea urchins are major substratum eroders of coral reefs and the calcium carbonate condition of coral reefs may therefore reflect the abundance of sea urchins. The omnivorous urchins, Echinometra spp. are known as ?rock -borers? and are agents of large-scale bioerosion, particularly in the Caribbean, Eastern Pacific and Western Indian Ocean. By burrowing into coral rocks they protect themselves from predators, wave and current action, and to some extent from desiccation at low tide. Bioerosion estimates are known for a few specific reefs only. Although the Echinometra sp. A have not been named yet, they were mistaken for Echinometra mathaei for long in Fiji. This novel study attempted to estimate bioerosion rates of the low but consistent numbers of sea urchins, Echinometra sp. A (green-white-tipped) on the Nukubuco reef, Fiji by calculation of the net carbonate accumulation. Cage experiments reported bioerosion rates (kg CaCO3/m2/urchin/d) of 35-37 x 10-3 at the reef crest and 30-43 x 10-3 at the reef flat. This method of assessing bioerosion showed both strengths and weaknesses. However, the Nukubuco reef balance between reef growth and reef destruction is shifting, with bioerosion becoming the dominant process.
Nutrient levels in sea and river water along the ‘Coral Coast’ of Viti Levu, Fiji
Authors: Mosley Luke M. , Aalbersberg William G. L.
Published: November 2018

Nutrient (nitrate and phosphate) levels potentially damaging to coral reefs have been detected at several sites along the Coral Coast of Viti Levu, Fiji. Nutrient concentrations were determined using standard techniques on an autoanalyser capable of measuring to sub-micromolar levels. The mean nitrate level for 34 seawater samples was 1.69 mM and the mean phosphate level was 0.21 mM which exceeded levels considered to be harmful to coral reef ecosystems (>1.0 mM N, >0.1 mM P). It is proposed that these elevated nutrient levels coupled with overfishing of herbivore species have contributed to the recent widespread growth of macro -algae species along this coast. Nutrient levels were highest at sites located near hotels and other populated sites. At sites not significantly influenced by human activity, levels were comparable to that of non-polluted sites elsewhere in Fiji. Concentrations of nutrients in rivers along the coast were generally higher than in seawater. Urgent action is needed at community, regional and government levels to try and reduce the nutrient inputs to this coast.
A note on optimum allocation in multivariate stratified sampling
Authors: Khan M. G. M. , Ahsan M. J.
Published: November 2018

In stratified random sampling when several characteristics are to be estimated simultaneously, an allocation that is optimum for one characteristic may be far away from optimum for others. To
resolve this conflict the authors formulate the problem of determining optimum compromise allocation as a nonlinear programming problem (NLPP). The allocation obtained is optimum in the sense that it minimizes the sum of weighted variances of the estimated population means of the characteristics subject to a fixed sampling cost. The formulated NLPP is treated as multistage decision problem and solved using dynamic programming technique. A numerical example is presented to illustrate the computational details.
Supercomputing in the South Pacific: performance of a parallel cluster using existing USP facilities
Authors: Blanke William J , Hussein Imtiyaz
Published: November 2018

This paper presents the details of a parallel computing cluster built using existing computing resources at the University of the South Pacific. Benchmarking tests using the High Performance Linpack Benchmark were done in order to measure the gigaflops (billions of floating point operations per second) ratings for solving large systems of linear equations while varying the number of computers and Ethernet switches used. These tests provided an overall maximum gigaflops rating which allowed comparison of USP's cluster with leading edge clusters from around the world. Efficiency results also provided insight in how improving the existing network infrastructure might improve the performance of USP's cluster and increase its gigaflops rating. Further tests revealed that the number of Ethernet switches used in USP's current network layout is a definite contributor to the low efficiency of the system as a whole.
Aspergilli and rhizobia are better co-inoculants as biofertilizers
Authors: James Dilip , Predeepa Rachel J.
Published: November 2018

The application of synthetic phosphorous fertilizer is a routine agricultural practice. However, in nature in the soil, several phosphate-solubilising microbes (PSM) have been identified in the rhizosphere, and are of significance in organic farming. Two major PSM are Rhizobium sp. and Aspergillus sp. that has been identified to have the potential to establish as biofilms in the soil root-zone environment. As the fungi are capable of solubilising both organic and rock phosphates, co-inoculation of these two microbes will enhance the availability of available phosphates to plants and in turn will reduce the requirement of synthetic fertilizers. The present study aims to evaluate the survivability of these two organisms in vitro conditions as co-inoculants. Aspergillus sp. seemed to be more synergistic or associative in growth with the rhizobial strains, and this organism is known well as a rigorous PSM. The effect of rhizobial toxins on the isolated fungal strains and the fungal toxins on the isolated rhizobial strains were tested in this study. Results show that Aspergillus flavus 2 and Rhizobium sp. K 1 strains were found to be highly antagonistic and will be eliminated for further studies. Nevertheless, synergism was found to be highly variable amongst not only within rhizobial strains, but also amongst the isolated fungal strains.
Sea level changes in the Pacific region and impacts of the 2009 El Niño in Fiji waters [assessment from 18 years land-based data]
Authors: Aung Than , Singh Awnesh , Maryam Dayang Siti
Published: November 2018

The sea level rise issue is one of the major topics that has gained increasing global attention. In particular, its impacts on many Pacific island countries and other low lying countries have been more prevalent over the last two decades. Sea level data from the AusAID funded South Pacific Sea Level and Climate Monitoring Project will be focused in this study despite the fact that the length of data is not sufficiently long. The project was set up in response to concerns raised by Pacific island countries over the potential impacts of an enhanced greenhouse effect on climate and sea levels in the South Pacific initially for 20 years and probably more. Based upon 18 years of sea level data from the project, the range of sea level rise rate in the Pacific region is between 3.1 mm y–1 (Kiribati) and 8.4 mm y–1 (Tonga) as of June 2011. This is 3–4 times higher than the global average of 1–2 mm y–1. Although the data length is for the last 18 years, the sea level trend values do not fluctuate significantly since 2002. It simply indicates that the rate of sea level rise in the Pacific region is not accelerating as anticipated by the local community. Interestingly, the profound effects of El Niño on sea level changes are quite unpredictable even during the 2009 mild El Niño. In two particular spots in the Pacific and their vicinities (at latitude 12°S & longitude 180°E and latitude 14°S & longitude 157°E) sea level drop in these areas is ~40 cm during March 2010. Although the present effect of El Niño on sea level changes is isolated and not Pacific wide like in 1997–98 El Niño, it simply indicates the complexity of sea level issue and danger of projecting future sea level trends at a particular area.
Field studies on Fiji’s endemic swallowtail butterfly, Papilio schmeltzi: habitat, activity patterns, phenology and distribution
Authors: Chandra Visheshni , Inoue Takashi A. , Khurma Uma R.
Published: November 2018

Fiji’s swallowtail butterfly, Papilio schmeltzi, is a Rutaceae feeding, tropical Papilionid butterfly that is endemic to the Fiji islands and generally occurs in low density. Field observations on habitat and the seasonal activity patterns of P. schmeltzi were carried out in the Vatukarasa area in Korolevu, Sigatoka over the course of one year. P. schmeltzi adults were found throughout the year but with dry and wet seasonal variation in abundance. High abundance was recorded for all the P. schmeltzi stages during the dry season (May to September). Adults and larvae were the most abundant when compared to eggs and pupae, and showed the greatest variation with respect to distribution of life stages throughout the year. P. schmeltzi currently occurs at four localities on the mainland and ten localities in the outer islands, with high abundance in Sigatoka and Koro Island. Adults of the species mainly occupy isolated forest edge habitat and gardens near forested areas and display a strong affinity for running water. At least two larval host plants, Micromelum minutum and Citrus reticulata, were found to sustain populations of P. schmeltzi, in its natural environment.
A fuzzy goal programming approach in stochastic multivariate stratified sample surveys
Authors: Gupta Neha , Ali Irfan , Shafiullah  , Bari Abdul
Published: November 2018

This paper deals with fuzzy goal programming (FGP) approach to stochastic multivariate stratified sampling with non linear objective function and probabilistic non linear cost constraint which is formulated as a multiobjective non linear programming problem (MONLPP). In the model formulation of the problem, we first determine the individual best solution of the objective functions subject to the system constraints and construct the non linear membership functions of each objective. The non linear membership functions are then transformed into equivalent linear membership functions by first order Taylor series at the individual best solution point. Fuzzy goal programming approach is then used to achieve maximum degree of each of the membership goals by minimizing negative deviational variables and finally obtain the compromise allocation. A numerical example is presented to illustrate the computational procedure of the proposed approach.
Quantifying role of seaweed (Caulerpa racemosa) harvesting in livelihood system of some coastal communities in Fiji
Authors: Loumoli Hikaione , Bhati Jagdish Prasad
Published: November 2018

The relative contributions of various work activities in the rural livelihood systems are not well understood. This study investigates roles of various work activities in the household income and employment in coastal areas of Fiji. Data were obtained by personal interview method from a random sample survey 48 households from four coastal villages in Fiji. Study revealed that workers in the coastal areas have work opportunities for only 20 h per week against a 40 h work norm. About 76% of their total work time was devoted to sea-based resources (58% for seaweed harvesting and 18% for fishing). Coconut collection and handicraft activities accounted for 17 and 7 percent of their work time, respectively. Overall, average weekly income of workers was about FJ$110.The share of income from seaweeds was about 50% and the shares of income from fishing, coconut activities and handicrafts were 21.9, 20.5 and 8 percent, respectively. Hence, it is clear that although seaweed harvesting activity in the overall economy of Fiji is still at the subsistence level, but this activity plays a very critical and substantial role in the food and nutrition security of the coastal communities.
Are less vocal rainforest mammals susceptible to impacts from traffic noise?
Authors: Byrnes Peter , Goosem Miriam , Turton Stephen M.
Published: November 2018

Context
Traffic noise is believed to cause road avoidance and other barrier effects in a variety of wildlife species, and to force changes to call pitch or loudness in others; however, this has never been tested in the absence of other road impacts. Noise impacts on species that do not frequently vocalise are also poorly understood. We investigated traffic-noise impacts on the following three rainforest mammals that do not often vocalise: Hypsiprymnodon moschatus, Uromys caudimaculatus and Perameles nasuta. These species have previously been observed to exhibit varying levels of road avoidance.

Aims
To determine whether traffic noise affects movement and behaviour of medium-sized, ground-dwelling rainforest mammals in the absence of other road-associated variables and potential impacts. We hypothesised that noise impacts would be greatest for species previously shown to avoid roads. Noise impacts on these less vocal species compared with more vocal species is also discussed.

Methods
In north-eastern Queensland, Australia, mammals captured at least 500 m from any road were tracked after fitting with spool-and-line equipment. On noisy nights, traffic noise at levels similar to a busy highway was played continuously throughout the night from a line of 12 speakers mounted on trees. Speakers were silent on quiet nights.

Key results
Traffic noise caused no increase in avoidance of the speaker line and was not a barrier to movements across the line. Overall, movement paths on noisy nights appeared similar in pattern (tortuosity) to those of quiet nights. At a finer scale, movements of H. moschatus and P. nasuta became more tortuous later in the track, suggesting a return to normal foraging behaviour and possible habituation to the noise.

Conclusions
These three species with varying levels of previously recorded road avoidance, did not respond negatively to traffic noise. There was, however, a suggestion of habituation by H. moschatus and P. nasuta in response to the noise.

Implications
The demonstrated lack of response to traffic noise in these less vocal species means that traffic noise is unlikely to cause road avoidance or barrier effects. Instead, lack of response and possible habituation to traffic noise may increase vulnerability to road mortality.
An Aerial Survey of Nests of Malleefowl Leipoa ocellata Gould (Megapodidae) in Central New South Wales
Authors: Brickhill J
Published: November 2018

Malleefowl nests were surveyed by air, in six breeding seasons, in Round Hill Nature Reserve in central New South Wales. A technique for marking the nests from a helicopter so that they can be easily relocated was used. In an area of 20 800 ha, a total of 19 1 old nests were marked, only three nests being used for breeding in 1979-80. Correction factors from a ground survey show that about 43% of the nests present were found in 22 days aerial survey. The results show a very low population of malleefowl on Round Hill Nature Reserve and suggest a decline in the population in the last few decades.
Formal ontology for discourse analysis of a corpus of court interpreting
Authors: Pease Adam , Pease Jennifer Cheung , Cheung Andrew K. F.
Published: November 2018

We develop a new method of discourse analysis using speech act theory and formal ontology. The method constitutes an attempt to make discourse analysis more formal and repeatable. We apply the method to a corpus of bi-lingual, interpreted legal dialogue, focusing on the speech act of clarification and its component acts. While discourse analysis is primarily a qualitative tool, it can be applied quantitatively by counting certain types of discourse, such as clarification speech acts. Dialogues are still analysed, utterances are classified as speech acts and their semantic relationships are qualitatively assessed. Subjectivity of human analysis is minimised using a new method of discourse analysis that employs a formal ontology. The ontology is stated in higher-order logic making the annotation of the corpus more objective, formal and repeatable than prior research.
GenCoF: a graphical user interface to rapidly remove human genome contaminants from metagenomic datasets
Authors: Czajkowski Matthew D , Vance Daniel P , Frese Steven A , Casaburi Giorgio
Published: November 2018

The removal of human genomic reads from shotgun metagenomic sequencing is a critical step in protecting subject privacy. Freely available tools addressing this issue require advanced programing knowledge or are limited by analytical time and data load due to their server-based nature. Here, we compared the most cited tools for host-DNA removal using synthetic and real metagenomic datasets. Then, we integrated the most efficient pipeline in a graphical user interface to make these tools available without command line use. This interface, GenCoF, rapidly removes human genome contaminants from metagenomic datasets. Additionally, the tool offers quality-filtering, data reduction and interactive modification of any parameter in order to customize the analysis. GenCoF offers both quality and host-associated filtering in a non-commercial, freely available tool in a local, interactive and easy-to-use interface.

Availability and implementation

GenCoF is freely available (under a GPL license) for Mac OS and Linux at https://github.com/MattCzajkowski/GenCoF.

Supplementary information

Supplementary data are available at Bioinformatics online.
Nestin Regulates Neurogenesis in Mice Through Notch Signaling From Astrocytes to Neural Stem Cells
Authors: Wilhelmsson Ulrika , Lebkuechner Isabell , Leke Renata , Marasek Pavel , Yang Xiaoguang , Antfolk Daniel , Chen Meng , Mohseni Paria , Lasič Eva , Bobnar Saša Trkov , Stenovec Matjaž , Zorec Robert , Nagy Andras , Sahlgren Cecilia , Pekna Marcela , Pekny Milos
Published: November 2018

The intermediate filament (nanofilament) protein nestin is a marker of neural stem cells, but its role in neurogenesis, including adult neurogenesis, remains unclear. Here, we investigated the role of nestin in neurogenesis in adult nestin-deficient (Nes–/–) mice. We found that the proliferation of Nes–/– neural stem cells was not altered, but neurogenesis in the hippocampal dentate gyrus of Nes–/– mice was increased. Surprisingly, the proneurogenic effect of nestin deficiency was mediated by its function in the astrocyte niche. Through its role in Notch signaling from astrocytes to neural stem cells, nestin negatively regulates neuronal differentiation and survival; however, its expression in neural stem cells is not required for normal neurogenesis. In behavioral studies, nestin deficiency in mice did not affect associative learning but was associated with impaired long-term memory.
Screening questions for the diagnosis of restless legs syndrome in hemodialysis
Authors: Collister David , Rodrigues Jennifer C , Mazzetti Andrea , Salisbury Kelsi , Morosin Laura , Rabbat Christian , Brimble K Scott , Walsh Michael
Published: November 2018

Background

Restless legs syndrome (RLS) is common in end-stage renal disease and is associated with reduced health-related quality of life. Simple and accurate screening instruments are needed since RLS is underdiagnosed and treatable. We examined the operating characteristics of screening questions and a disease-specific measurement tool for the diagnosis of RLS in hemodialysis.

Methods

We conducted a cohort study of prevalent adult hemodialysis patients in Hamilton, Canada. The diagnosis of RLS was made using the 2012 Revised International Restless Legs Syndrome Study Group (IRLSSG) criteria. All participants received three screening instruments: (i) a single screening question for RLS derived from a nondialysis population; (ii) a single question from the Edmonton Symptom Assessment System (ESAS); and (iii) the IRLSSG Rating Scale (IRLS). All instruments were compared with the reference standard using logistic regression from which receiver operating characteristics curves were generated. Cutoffs associated with maximum performance were identified.

Results

We recruited 50 participants with a mean (SD) age of 64 (12.4) years, of whom 52% were male and 92% were on three times weekly hemodialysis. Using the reference standard, 14 (28%) had a diagnosis of RLS. The single screening question for RLS had an area under the receiver operating curve (AUROC) of 0.72 with a sensitivity of 85.7% and specificity of 58.3%. An ESAS cutoff of ≥1 had the highest AUROC at 0.65 with a sensitivity of 79% and specificity of 56%. An IRLS cutoff of ≥20 had the highest AUROC at 0.75 with a sensitivity of 71% and specificity of 81%.

Conclusion

IRLS had better specificity than the single question or ESAS for the diagnosis of RLS.
The genome of an underwater architect, the caddisfly Stenopsyche tienmushanensis Hwang (Insecta: Trichoptera)
Authors: Luo Shiqi , Tang Min , Frandsen Paul B , Stewart Russell J , Zhou Xin
Published: November 2018

Background

Caddisflies (Insecta: Trichoptera) are a highly adapted freshwater group of insects split from a common ancestor with Lepidoptera. They are the most diverse (>16,000 species) of the strictly aquatic insect orders and are widely employed as bio-indicators in water quality assessment and monitoring. Among the numerous adaptations to aquatic habitats, caddisfly larvae use silk and materials from the environment (e.g., stones, sticks, leaf matter) to build composite structures such as fixed retreats and portable cases. Understanding how caddisflies have adapted to aquatic habitats will help explain the evolution and subsequent diversification of the group.

Findings

We sequenced a retreat-builder caddisfly Stenopsyche tienmushanensis Hwang and assembled a high-quality genome from both Illumina and Pacific Biosciences (PacBio) sequencing. In total, 601.2 M Illumina reads (90.2 Gb) and 16.9 M PacBio subreads (89.0 Gb) were generated. The 451.5 Mb assembled genome has a contig N50 of 1.29 M, has a longest contig of 4.76 Mb, and covers 97.65% of the 1,658 insect single-copy genes as assessed by Benchmarking Universal Single-Copy Orthologs. The genome comprises 36.76% repetitive elements. A total of 14,672 predicted protein-coding genes were identified. The genome revealed gene expansions in specific groups of the cytochrome P450 family and olfactory binding proteins, suggesting potential genomic features associated with pollutant tolerance and mate finding. In addition, the complete gene complex of the highly repetitive H-fibroin, the major protein component of caddisfly larval silk, was assembled.

Conclusions

We report the draft genome of Stenopsyche tienmushanensis, the highest-quality caddisfly genome so far. The genome information will be an important resource for the study of caddisflies and may shed light on the evolution of aquatic insects.
A unique nanoparticulate TLR9 agonist enables a HA split vaccine to confer FcγR-mediated protection against heterologous lethal influenza virus infection
Authors: Yamamoto Takuya , Masuta Yuji , Momota Masatoshi , Kanekiyo Masaru , Kanuma Tomohiro , Takahama Shoukichi , Moriishi Eiko , Yasutomi Yasuhiro , Saito Takashi , Graham Barney S , Takahashi Yoshimasa , Ishii Ken J
Published: November 2018

The development of a universal influenza vaccine that can provide a robust and long-lasting protection against a broader range of influenza virus strains is a global public health priority. One approach to improve vaccine efficacy is to use an adjuvant to boost immune responses to the target antigens; nevertheless, the role of adjuvants in the context of influenza vaccines is not fully understood. We have previously developed the K3-schizophyllan (SPG) adjuvant, which is composed of nanoparticulated oligodeoxynucleotides K3, a TLR9 agonist, with SPG, a non-agonistic β-glucan ligand of Dectin-1. In this study, K3-SPG given with conventional influenza hemagglutinin (HA) split vaccine (K3-SPG HA) conferred protection against antigenically mismatched heterologous virus challenge. While K3-SPG HA elicited robust cross-reactive HA-specific IgG2c and CD8 T-cell responses, CD8 T-cell depletion had no impact on this cross-protection. In contrast, K3-SPG HA was not able to confer protection against heterologous virus challenge in FcRγ-deficient mice. Our results indicated that FcγR-mediated antibody responses induced by the HA antigen and K3-SPG adjuvant were important for potent protection against antigenically mismatched influenza virus infection. Thus, we demonstrated that the K3-SPG-adjuvanted vaccine strategy broadens protective immunity against influenza and provides a basis for the development of next-generation influenza vaccines.
Suzaku detection of enigmatic geocoronal solar wind charge exchange event associated with coronal mass ejection
Authors: Ishi Daiki , Ishikawa Kumi , Numazawa Masaki , Miyoshi Yoshizumi , Terada Naoki , Mitsuda Kazuhisa , Ohashi Takaya , Ezoe Yuichiro
Published: November 2018

Suzaku detected an enhancement of the soft X-ray background associated with solar eruptions on 2013 April 14–15. The solar eruptions were accompanied by an M6.5 solar flare and a coronal mass ejection with magnetic flux ropes. The enhanced soft X-ray background showed a slight variation over half a day and then a clear one in a few hours. The former spectrum was composed of oxygen emission lines, while the later one was characterized by a series of emission lines from highly ionized carbon to silicon. The soft X-ray enhancement originated from geocoronal solar wind charge exchange. However, there appeared to be no significant time correlation with the solar wind proton flux measured by the ACE and WIND satellites. From other solar wind signatures, we considered that an interplanetary shock associated with the coronal mass ejection and a turbulent sheath immediately behind the shock compressed the ambient solar wind ions and then resulted in the soft X-ray enhancement. Furthermore, the enriched emission lines were presumed to be due to an unusual set of ion abundances and ionization states within the coronal mass ejection. We found a better time correlation with the solar wind alpha flux rather than the solar wind proton flux. Our results suggest that the solar wind proton flux is not always a good indicator of geocoronal solar wind charge exchange, especially associated with coronal mass ejections. Instead, the solar wind alpha flux should be investigated when such a soft X-ray enhancement is detected in astronomical observations.
Regional reinfection by Dengue: a network approach using data from Mexico
Authors: Núñez-López Mayra , Alarcón-Ramos Luis , Velasco-Hernández Jorge X.
Published: November 2018

Most of the recent epidemic outbreaks in the world have a strong immigration component as a trigger rather than the dynamics implied by the basic reproduction number. In this work we present and discuss an approach to the problem of pathogen reinfections in a given area that associates people mobility and transmission of dengue, using a Markov-chain Susceptible-Infected-Susceptible (SIS) metapopulation model over a network. Our model postulates a parameter that we have named the effective inoculum size which represents a local measure of the population size of infected hosts that arrive at a given location as a function of population size, current incidence at neighboring locations and the connectivity of the patches. This parameter can be interpreted as an indicator of outbreak risk of any location. Our model also incorporates climate variability represented by an index based upon precipitation data. We replicate observed patterns of incidence at a regional scale using data from epidemics in Mexico.
Noise-Cancelling Repeat Finder: Uncovering tandem repeats in error-prone long-read sequencing data
Authors: Harris Robert S. , Cechova Monika , Makova Kateryna D.
Published: November 2018

Tandem DNA repeats can be sequenced with long-read technologies, but cannot be accurately deciphered due to the lack of computational tools taking high error rates of these technologies into account. Here we introduce Noise-Cancelling Repeat Finder (NCRF) to uncover putative tandem repeats of specified motifs in noisy long reads produced by Pacific Biosciences and Oxford Nanopore sequencers. Using simulations, we validated the use of NCRF to locate tandem repeats with motifs of various lengths and demonstrated its superior performance as compared to two alternative tools. Using real human whole-genome sequencing data, NCRF identified long arrays of the (AATGG)n repeat involved in heat shock stress response.

Availability and implementation

NCRF is implemented in C, supported by several python scripts. Source code, under the MIT open source license, and simulation data are available at https://github.com/makovalab-psu/NoiseCancellingRepeatFinder, and also in bioconda.
Refinement of metabolite detection in cystic fibrosis sputum reveals heme negatively correlates with lung function
Authors: Glasser Nathaniel R. , Hunter Ryan C. , Liou Theodore G. , Newman Dianne K. ,   Mountain West CF Consortium Investigators
Published: November 2018

Pseudomonas aeruginosalung infections are a leading cause of morbidity and mortality in cystic fibrosis (CF) patients (1, 2). Our laboratory has studied a class of small molecules produced byP. aeruginosaknown as phenazines, including pyocyanin and its biogenic precursor phenazine-1-carboxylic acid (PCA). As phenazines are known virulence factors (3), we and others have explored the possibility of using phenazine concentrations as a marker for disease progression (4–6). Previously, we reported that sputum concentrations of pyocyanin and PCA negatively correlate with lung function in cystic fibrosis patients (6). Our study used high performance liquid chromatography (HPLC) to quantify phenazines by UV–vis absorbance after extraction from lung sputum. Since our initial study, methods for metabolite analysis have advanced considerably, aided in large part by usage of mass spectrometry (LC-MS) and tandem mass spectrometry (LC-MS/MS). Because a more recent study employing LC-MS/MS revealed a surprising decoupling ofP. aeruginosametabolites in sputum and the detection ofP. aeruginosathrough culturing or microbiome profiles (4), we decided to check whether we could reproduce our previous findings by analyzing sputum samples from a different patient cohort with a new LC-MS instrument in our laboratory. Our new samples were provided by the Mountain West CF Consortium Sputum Biomarker study (7). In the course of performing our new analyses, comparison of our old HPLC data to our new LC-MS data led us to realize that the peak previously assigned to PCA instead originates from heme, and the peak assigned to pyocyanin originates from an as-yet unknown compound. This correction only affects the measurements of phenazines in sputum, and we are confident in the phenazine measurements from isolated cultures and the 16S rRNA gene sequencing data from that study (6). Here we outline the basis for our correction and present additional data showing that heme concentration negatively correlates with lung function in cystic fibrosis patients.
High-resolution mass spectrometry-based non-targeted metabolomic discovery of disease and glucocorticoid biomarkers in an animal model of muscular dystrophy
Authors: Thangarajh Mathula , Boca Simina M. , Zhang Aiping , Gill Kirandeep , Ressom Habtom , Li Zhenzhi , Hoffman Eric P. , Nagaraju Kanneboyina , Hathout Yetrib
Published: November 2018

Urine is increasingly being considered as a source of biomarker development in Duchenne Muscular Dystrophy (DMD), a severe, life-limiting disorder that affects approximately 1 in 4500 boys. In this study, we used the mdx mice—a murine model of DMD—to discover biomarkers of disease, as well as pharmacodynamic biomarkers responsive to prednisolone, commonly used to treat DMD. Longitudinal urine samples were analyzed from male age-matched mdx and wild-type mice randomized to prednisolone or vehicle. We used high-resolution mass spectrometry to discover metabolic biomarkers of both disease and glucocorticoid treatment. A large number of metabolites (869 out of 6,334) were found to be significantly different between mdx and wild-type mice at baseline (Bonferroni-adjusted p-value < 0.05), thus being associated with disease status. These included a peak with m/z=357 and creatine, which were also discovered in a previous human study looking at serum. Novel observations included biliverdin and hypusine. These four peaks were also significantly higher in mdx mice compared to wild-type, as well as significantly associated with time after the baseline. Creatine and biliverdin were also associated with treatment after the baseline, but the association with creatine may have been driven by an imbalance at baseline. In conclusion, our study reports a number of biomarkers, both known and novel, which may be related to either the mechanisms of muscle injury in DMD and/or prednisolone treatment.
Campylobacter jejunitransmission and colonisation in broiler chickens is inhibited by Faecal Microbiota Transplantation
Authors: Gilroy Rachel , Chaloner Gemma , Wedley Amy , Lacharme-Lora Lizeth , Jopson Sue , Wigley Paul
Published: November 2018

BACKGROUND

Campylobacter jejuni,the most frequent cause of foodborne bacterial infection, is found on around 70% of retail chicken. As such there is a need for effective controls in chicken production. Microbial-based controls such as probiotics are attractive to the poultry industry, but of limited efficacy. Furthermore, as commercially-produced chickens have no maternal contact, their pioneer microbiome is likely to come from the hatchery environment. Early delivery of microbials that lead to a more ‘natural avian’ microbiome may, therefore, improve bird health and reduce susceptibility toC.jejunicolonisation.

A faecal microbiota transplant (FMT) was used to transfer a mature cecal microbiome to newly-hatched broiler chicks and its effects onC.jejunichallenge assessed. We used both a seeder-bird infection model that mimics natural bird-to-bird infection alongside a direct-challenge model. We used a 16S rRNA gene sequencing-based approach to characterize the transplant material itself alongside changes to the chicken microbiome following FMT.

RESULTS

FMT changes the composition of the chicken intestinal microbiome. We observed little change in species richness following FMT compared to untreated samples, but there is an increase in phylogenetic diversity within those species. The most significant difference in the ceca is an increase inLactobacilli,although not a major component of the transplant material, suggesting the FMT results in a change in the intestinal milieu as much as a direct change to the microbiome.

Upon direct challenge, FMT resulted in lower initial intestinal colonisation withC.jejuni.More significantly, in a seeder-bird challenge of infection transmission, FMT reduced transmission and intestinal colonisation until common UK retail age of slaughter. In a repeat experiment, transmission was completely blocked following FMT treatment. Delayed FMT administration at 7 days of-age had limited effect on colonisation and transmission.

CONCLUSIONS

We show that transfer of a whole mature microbiome to newly-hatched chicks reduces transmission and colonisation ofC.jejuni.This indicates that modification of the broiler chick microbiome can reduce intestinal colonisation ofC.jejunito levels projected to lead to lower the human infection rate. We believe these findings offer a way to identify key taxa or consortia that are effective in reducingC.jejunicolonisation and improving broiler gut health.
Predicting precision grip grasp locations on three-dimensional objects
Authors: Klein Lina K. , Maiello Guido , Paulun Vivian C. , Fleming Roland W.
Published: November 2018

We rarely experience difficulty picking up objects, yet of all potential contact points on the surface, only a small proportion yield effective grasps. Here, we present extensive behavioral data alongside a normative model that correctly predicts human precision grasping of unfamiliar 3D objects. We tracked participants’ forefinger and thumb as they picked up objects of 10 wood and brass cubes configured to tease apart effects of shape, weight, orientation, and mass distribution. Grasps were highly systematic and consistent across repetitions and participants. We employed these data to construct a model which combines five cost functions related to force closure, torque, natural grasp axis, grasp aperture, and visibility. Even without free parameters, the model predicts individual grasps almost as well as different individuals predict one another’s, but fitting weights reveals the relative importance of the different constraints. The model also accurately predicts human grasps on novel 3D-printed objects with more naturalistic geometries and is robust to perturbations in its key parameters. Together, the findings provide a unified account of how we successfully grasp objects of different 3D shape, orientation, mass, and mass distribution.

Author Summary

A model based on extensive behavioral data unifies the varied and fragmented literature on human grasp selection by correctly predicting human grasps across a wide variety of conditions.
Isolation and characterization of extracellular vesicles from Caenorhabditis elegans for multi-omic analysis
Authors: Russell Joshua C. , Merrihew Gennifer E. , Robbins Julia E. , Postupna Nadia , Kim Tyek-Kyun , Golubeva Alexandra , Noori Ayush , Wang Kai , Keene C. Dirk , MacCoss Michael J. , Kaeberlein Matt
Published: November 2018

Cells from bacteria to human release vesicles into their extracellular environment. These extracellular vesicles (EVs) contain multiple classesof molecules, including nucleic acids, proteins, and lipids. The isolation and analysis of EV cargos from mammalian cell culture and liquid biopsysamples has become a powerful approach for uncovering the messages that are packaged into these organelles. However, this approach has not been tenable in invertebrate model systems due to lack of sufficient amounts of pure EVs. Here we report a robust and reproducible procedure to isolateEVs from Caenorhabditis elegans with yields similar to those obtained from human cell culture. Through nanoparticle tracking, transmission electron microscopy, flow cytometry, mass spectrometry, RNAseq, and immunoaffinity analysis we provide the first ever detailed characterization of C. elegans EV composition and demonstrate that C. elegans EVs share fundamentally similar properties with their mammalian counterparts. These include vesicle size, enrichment for lipid rafts, and similar types of RNA and protein cargos. This ability of isolate pure EVs on ascale amenable to multiple types of downstream analyses permits, multi-omics characterization of EV cargos in an invertebrate model system.
Pipeliner: A Nextflow-based framework for the definition of sequencing data processing pipelines
Authors: Federico Anthony , Karagiannis Tanya , Karri Kritika , Kishore Dileep , Koga Yusuke , Campbell Joshua D. , Monti Stefano
Published: November 2018

The advent of high-throughput sequencing technologies has led to the need for flexible and user-friendly data pre-processing platforms. The Pipeliner framework provides an out-of-the-box solution for processing various types of sequencing data. It combines the Nextflow scripting language and Anaconda package manager to generate modular computational workflows. We have used Pipeliner to create several pipelines for sequencing data processing including bulk RNA-seq, single-cell RNA-seq (scRNA-seq), as well as Digital Gene Expression (DGE) data. This report highlights the design methodology behind Pipeliner which enables the development of highly flexible and reproducible pipelines that are easy to extend and maintain on multiple computing environments. We also provide a quick start user guide demonstrating how to setup and execute available pipelines with toy datasets.