bluuebunny/crossref_metadata_2025 huggingface dataset:
Project report: intelligent semantic oriented agent based Search
Authors: Ahmed Zeeshan
Published: January 2018

Product Data Management (PDM) produced desktop and web based systems to maintain the organizational technical and managerial data to increase the quality of products by improving the processes of development, business process flows, change management, product structure management, project tracking and resource planning. Though PDM is heavily benefiting industry but PDM community is facing some serious unresolved issues in PDM System development. i.e., unfriendly graphical user interfaces and unintelligent search. PDM Systems offer different many services and functionalities at a time but the graphical user interfaces of most of the PDM Systems are not designed in a way that a user (especially a new user) can easily learn and use them. Moreover, PDM Systems contain and manage heavy amount of data but the search mechanism of most of the PDM System is not intelligent which can process user’s structured or unstructured natural language based queries to extract desired information. Targeting above discussed two serious PDM based issues a thorough research is conducted in fields of Product Data Management (PDM), Human Machine Interfaces (HMI) and Semantic Web (SW). Concerning PDM, conducted research discusses PDM desktop and web based systems, PDM system development guidelines and some existing PDM Systems. Concerning HMI, conducted research provide information about HMI Designing including Ideologies, Principles, Patterns, Design Guidelines, Basic Design Goals, Problems and Rich Internet Applications (RIA) for Web based HMI Development. Concerning SW, conducted research provides information about Web based information modeling and processing, Ontologies and semantic oriented information modeling based approaches. Using conducted research based information and keeping some existing solutions toward targeted PDM community’s issues in mind a semantic oriented, information processing and intelligent graphical user interface based solution is proposed. i.e., Intelligent Semantic Oriented Agent based Search (I-SOAS). Describing the proposition in detail the main concept, implementation designs and developed prototype of I-SOAS is discussed in this dissertation.
An energetics-based honeybee nectar-foraging model used to assess the potential for landscape-level pesticide exposure dilution
Authors: Baveco Johannes M , Focks Andreas , Belgers Dick , van der Steen Jozef JM , Boesten Jos JTI , Roessink Ivo
Published: January 2018

Estimating the exposure of honeybees to pesticides on a landscape scale requires models of their spatial foraging behaviour. For this purpose, we developed a mechanistic, energetics-based model for a single day of nectar foraging in complex landscape mosaics. The hive population was assumed to select the resource patch with highest net energetic efficiency in perfect knowledge of its environment. During the day the optimal patch could change, due to resource depletion or related to the characteristics of the resource (i.e., the period flowers were open and provided nectar). By quantifying foraging costs and yield in terms of energy, we accounted for the impact of field distance and size, the occurrence of resource depletion and the characteristics of the resource type (crops and wild flowers), like seasonal and diurnal patterns in availability.From the model we derived simple rules for resource patch selection, e.g., for landscapes with mass-flowering crops, the net energetic efficiency would be proportional to the ratio of the energetic content of the nectar of the crop divided by distance of crop field to the hive. Also, we determined maximum distances at which resources like oilseed rape and clover could still be energetically attractive.We used the model to assess the potential for pesticide exposure dilution in landscapes of different composition and complexity. Dilution implied a lower average concentration in nectar arriving at the hive, resulting from foraging effort being diverted away from treated fields. Applying the model for all possible hive locations in a landscape, landscape-specific distributions of dilution values were obtained.For a case study area for which detailed spatial data were available, we tested three scenarios that were expected to lead to exposure dilution: the presence of i) equally attractive crop fields in the neighbourhood of a treated field, ii) highly attractive flowers strips of different widths at the edges of treated fields (off-crop in-field resources), and iii) highly attractive resources on off-field (semi-natural) habitats. The results indicated significant dilution at landscape scale only from flowers strips of more than 5 m wide and off-field habitats. On an area-base, flowers strips were approximately 10 times as effective as off-field habitats, the main reason being that the flowers strips had an optimal location, always at the edges of treated fields.
Arboreal spiders in coffee agroecosystems: Untangling the web of local and landscape influences driving diversity
Authors: Hajian-Forooshani Zachary , Gonthier David , Marín Linda , Iverson Aaron L , Perfecto Ivette
Published: January 2018

Agricultural intensification is implicated as a major driver of global biodiversity loss. Local management and landscape scale factors both influence biodiversity in agricultural systems, but there are relatively few studies to date looking at how local and landscape scales influence biodiversity in tropical agroecosystems. Understanding what drives the diversity of groups of organisms such as spiders is important from a pragmatic point of view because of the important biocontrol services they offer to agriculture. Spiders in coffee are somewhat enigmatic because of their positive or lack of response to agricultural intensification. In this study, we provide the first analysis, to our knowledge, of the arboreal spiders in the shade trees of coffee plantations. In the Soconusco region of Chiapas, Mexico we sampled across 38 sites on 9 coffee plantations. Tree and canopy connectedness were found to positively influence overall arboreal spider richness and abundance. We found that different functional groups of spiders are responding to different local and landscape factors, but overall elevation was most important variable influencing arboreal spider diversity. Our study has practical management applications that suggest having shade grown coffee offers more suitable habitat for arboreal spiders due to a variety of the characteristics of the shade trees. Our results which show consistently more diverse arboreal spider communities in lower elevations are important in light of looming global climate change. As the range of suitable elevations for coffee cultivation shrinks promoting arboreal spider diversity will be important in sustaining the viability of coffee.
Probable impact of age and hypoxia on proliferation and microRNA expression profile of bone marrow-derived human mesenchymal stem cells
Authors: Mohd Ali Norlaily , Boo Lily , Yeap Swee Keong , Ky Huynh , Satharasinghe Dilan A , Liew Woan Charn , Ong Han Kiat , Cheong Soon Keng , Kamarul Tunku
Published: January 2018

Decline in the therapeutic potential of bone marrow-derived mesenchymal stem cells (MSC) is often seen with older donors as compared to young. Although hypoxia is known as an approach to improve the therapeutic potential of MSC in term of cell proliferation and differentiation capacity, its effects on MSC from aged donors have not been well studied. To evaluate the influence of hypoxia on different age groups, MSC from young (<30 years) and aged (>60 years) donors were expanded under hypoxic (5% O2) and normal (20% O2) culture conditions. MSC from old donors exhibited a reduction in proliferation rate and differentiation potential together with the accumulation of senescence features compared to that of young donors. However, MSC cultured under hypoxic condition showed enhanced self-renewing and proliferation capacity in both age groups as compared to normal condition. Bioinformatic analysis of the gene ontology (GO) and KEGG pathway under hypoxic culture condition identified hypoxia-inducible miRNAs that were found to target transcriptional activity leading to enhanced cell proliferation, migration as well as decrease in growth arrest and apoptosis through the activation of multiple signaling pathways. Overall, differentially expressed miRNA provided additional information to describe the biological changes of young and aged MSCs expansion under hypoxic culture condition at the molecular level. Based on our findings, the therapeutic potential hierarchy of MSC according to donor’s age group and culture conditions can be categorized in the following order: young (hypoxia)> young (normoxia) > old aged (hypoxia) > old aged (normoxia).
Validation of the electronic prescription as a method of measurement of treatment adherence in hypertension
Authors: Marquez-Contreras Emilio , López  García-Ramos Lourdes , Martell-Claros Nieves , Gil-Guillen Vicente F , Márquez-Rivero Sara , Pérez-López Elena , Garrido-Lopez Maria Angeles , Farauste Celia , Lopez-Pineda Adriana , Casado-Martínez Jose Joaquín , Carratala-Munuera Concepcion
Published: January 2018

Background. The diagnosis of non-adherence is complex and there are no completely reliable methods that can be used widely in daily practice. The aim of this study was to validate electronic prescriptions as a method of measuring treatment adherence in patients with mild-moderate hypertension.

Methods. We conducted a prospective, longitudinal, multicenter study in primary care centers. The study involved 120 patients treated for hypertension and included in the electronic prescription program of the centers. Five visits were made: initial, 6, 12, 18 and 24 months. Adherence was measured using an electronic monitor [medication event monitoring system (MEMS)] and through the electronic prescription program. We calculated the adherence rate (AR) using the MEMS and the electronic prescriptions, with the Medication Possession Ratio (MPR). Adherent patients were considered to be those whose AR was 80-100%. To validate the electronic prescription, its data were compared to the pill count by MEMS (Method of certainty). Sensitivity, specificity, positive (PPV) and negative (NPV) predictive values, and positive (LR+) and negative (LR-) likelihood ratios were calculated. The Kappa concordance index and the area under the ROC curve were also determined.

Results. The study was completed by 108 patients (mean age 61.06 years, SD 9.08). Adherence was 77.4% by MEMS (95% CI: 66.8-88%) and 80.4% (95% CI=70.3-90.5) by MPR. At 24 months the sensitivity was 87%, specificity 93.7%, PPV 80%, NPV 96.1%, LR+ 13.8 and LR- 0.1. The K was 0.782 and the AUC was 0.903 (95% CI: 0.817-0.989). Therapeutic complexity was associated with pharmacological non-adherence (OR=1.35, p<0.01).

Discussion. The electronic prescription was an excellent method to measure non-adherence in hypertensive patients included in this program for over two years. Therapeutic simplicity improved treatment adherence.
PATACSDB - The database of polyA translational attenuators in coding sequences
Authors: Habich Malgorzata , Djuranovic Sergej , Szczesny Pawel
Published: January 2018

Recent addition to the repertoire of gene expression regulatory mechanisms are polyadenylate (polyA) tracks encoding for poly-lysine runs in protein sequences. Such tracks stall translation apparatus and induce frameshifting independently of the effects of charged nascent poly-lysine sequence on the ribosome exit channel. As such they substantially influence the stability of mRNA and amount of protein produced from a given transcript. Single base changes in these regions are enough to exert a measurable response on both protein and mRNA abundance, and makes each of these sequences potentially interesting case studies for effects of synonymous mutation, gene dosage balance and natural frameshifting. Here we present the PATACSDB, a resource that contain comprehensive list of polyA tracks from over 250 eukaryotic genomes. Our data is based on Ensembl genomic database of coding sequences and filtered with algorithm of 12A-1 which selects sequences of polyA tracks with a minimal length of 12 A's allowing for one mismatched base. The PATACSDB database is accesible at: http://sysbio.ibb.waw.pl/patacsdb. Source code is available for download from GitHub repository at http://github.com/habich/PATACSDB, including the scripts to recreate the database from the scratch on user's own computer.
The sea urchin Diadema antillarum – keystone herbivore or redundant species?
Authors: Precht Lindsey L. , Precht William F.
Published: January 2018

Two main hypotheses have been developed for describing the role and importance of the sea urchin Diadema antillarum on reefs of the Caribbean region in both space and time. The first and most crucial is whether D. antillarum was the most important “keystone” grazer on Caribbean reefs? The alternate to this hypothesis is that D. antillarum was merely a redundant species, playing a secondary role to herbivorious fishes which only came into dominance after herbivorous fishes had been removed by man through exploitive fishing practices. To resolve this debate, we pose the question: “What is the role of Diadema antillarum in altering the composition of the benthic community on Caribbean coral reefs in time and space?” The interpretation presented herein implies that D. antillarum was and is the most important shallow-water herbivore on Caribbean coral reefs. This is contrary to a prevailing model but in substantial agreement with the historical importance of the species. If correct, the continued and future recovery of this sea urchin may be the key ingredient to facilitating coral reef recovery throughout the region. In addition, on coral reefs where the natural recovery of Diadema has been delayed or is absent (e.g. the Florida Reef Tract); measures to actively restore these urchins may be the most efficient and cost-effective tool for conserving and enhancing the ecological function of reefs. This debate also emphasizes the requirement for implementing ecologically-based, not ideologically-based management of natural systems.
Assessing migration patterns in Passerina ciris using the world’s bird collections as an aggregated resource
Authors: Linck Ethan , Bridge Eli S , Duckles Jonah M , Navarro-Sigüenza Adolfo G , Rohwer Sievert
Published: January 2018

Natural history museum collections (NHCs) represent a rich and largely untapped source of data on demography and population movements. NHC specimen records can be corrected to a crude measure of collecting effort and reflect relative population densities with a method known as abundance indices. We plot abundance index values from georeferenced NHC data in a 12-month series for the new world migratory passerine Passerina ciris across its molting and wintering range in Mexico and Central America. We illustrate a statistically significant change in abundance index values across regions and months that suggests a quasi-circular movement around its non-breeding range, and use enhanced vegetation index (EVI) analysis of remote sensing plots to demonstrate non-random association of specimen record density with areas of high primary productivity. We demonstrate how abundance indices from NHC specimen records can be applied to infer previously unknown migratory behavior, and be integrated with remote sensing data to allow for a deeper understanding of demography and behavioral ecology across space and time.
Kinect controlled dinosaur simulations for education and public outreach
Authors: Sellers William I , Pond Stuart B
Published: January 2018

Dinosaurs are a source of enormous public interest and as such are useful for fostering greater interest in basic science and technology. With the increasing popularity of dinosaur films that claim to portray realistic dinosaur behaviour, one question that is regularly posed for palaeontologists to answer is how we know that our reconstructions are accurate. Dinosaur locomotion is no exception to this line of questioning and one technique for estimating how dinosaurs may have moved is multibody dynamic simulation (MBDA) of high biofidelity musculoskeletal computer models. Such simulations uses Newton's Law's of Motion to calculate how the different parts of the animals body would have moved depending on the internal forces generated by the muscles and the external forces due to gravity and physical contact with the ground. In this project we designed a system that allowed the user to directly control the muscles forces generated using a Kinect for Xbox One sensor attached to a PC using the Kinect Adaptor for Windows. The Kinect output is used to drive the muscles using customised software and models (Tyrannosaurus, Triceratops, Brachiosaurus, Edmontonia, Edmontosaurus, Gorgosaurus) based on our standard GaitSym MBDA system. The initial system was trialled over 7 days at the 2015 Cheltenham Science Festival which showed that the bipedal models were relatively easy to control using human body movements and provided a good vehicle to explain how the physics and physiology behind dinsoaur locomotor reconstruction. The quadrupedal models in their current form are much more difficult to control and further work is needed in this area. The 3D models and software for this project are freely available to download (http://www.animalsimulation.org or DOI: 10.6084/m9.figshare.2008977) and it is hoped that they will find further uses in areas such as 3D printing for anatomical education and virtual world simulations.
BBCC2015 Tenth edition of “Bioinformatics and Computational Biology in Campania”
Authors: Facchiano Angelo
Published: January 2018

BBCC represents the meeting point of researchers with a common interest for bioinformatics, in the Italian region Campania. I organize it yearly since 2006, so it reaches now the tenth edition. The birth of this meeting was the consideration of the high number of research institutes in this region, with many teams involved in bioinformatics studies, and many others in biomedical area, as well as in mathematics and informatics, so they may be interested to approach the bioinformatics community. At the end of 2006, I was involved with other colleagues in the organization of the meeting (April 2007, Naples) of the Bioinformatics Italian Society, BITS (www.bioinformatics.it). The Italian national community of bioinformatics has an annual meeting, since 2004 in the form of the society meeting, and also before the foundation of BITS. However, no specific event was regularly organized at regional level, as an opportunity for bioinformaticians in Campania to meet and discuss as an unique community. Therefore, I decided to organize a meeting of bioinformatics for the Campania region researchers, also for stimulating the local community in the view of the approaching annual meeting in Naples. In December 2006, the meeting registered the participation of about 100 researchers and students, an unexpected success and a strong motivation to repeat the meeting as an annual appointment. Since that first edition, the meeting has been held in the last months of the year, having every year about 100 participants. The formula of the meeting is very simple: a single-day event, with speakers on very different topics, open to the participation of colleagues from other regions and countries that introduced other ideas and suggestions for the community. This is the origin and ten years of life of the “Bioinformatica e Biologia Computazionale in Campania - BBCC” meeting series. For the tenth annual edition of BBCC meeting, 27 abstracts have been proposed for oral presentations or posters. A Program Committee has been created to evaluate the level of the proposals, and a good average evaluation has been reached.
Strategies and difficulties in assembling highly recombinogenic plant organelle genomes: a case study
Authors: Cantarella Concita , Tamburino Rachele , Scotti Nunzia , Cardi Teodoro , D'Agostino Nunzio
Published: January 2018

Mitochondrial genomes in plants are larger and more complex than in other eukaryotes due to their recombinogenic nature as widely demonstrated. The mitochondrial DNA (mtDNA) is usually represented as a single circular map, the so-called master molecule. This molecule includes repeated sequences, some of which are able to recombine, generating sub-genomic molecules in various amounts, depending on the balance between their recombination and replication rates. Recent advances in DNA sequencing technology gave a huge boost to plant mitochondrial genome projects. Conventional approaches to mitochondrial genome sequencing involve extraction and enrichment of mitochondrial DNA, cloning, and sequencing. Large repeats and the dynamic mitochondrial genome organization complicate de novo sequence assembly from short reads. The PacBio RS long-read sequencing platform offers the promise of increased read length and unbiased genome coverage and thus the potential to produce genome sequence data of a finished quality (fewer gaps and longer contigs). However, recently published articles revealed that PacBio sequencing is still not sufficient to address mtDNA assembly-related issues. Here we present a preliminary hybrid assembly of a potato mtDNA based on both PacBio and Illumina reads and debate the strategies and obstacles in assembling genomes containing repeated sequences that are recombinationally active and serve as a constant source of rearrangements.
Transcriptome analysis of Solanum lycopersicum roots provides novel insights into the plant response to a beneficial fungus
Authors: Salzano Maria , De Palma Monica , D'Agostino Nunzio , Lorito Matteo , Ruocco Michelina , Tucci Marina
Published: January 2018

The globally pressing need for increasing agriculture yield while reducing environmental impact has promoted the utilization of sustainable plant protection strategies based on natural biocontrol agents, among which, rhizosphere-competent Plant-Growth-Promoting Fungi (PGPF) have inspired great interest. In this scenario, beneficial strains of Trichoderma have proved to be very effective for crop protection against pathogens. Therefore, “omic” data of the plant response to Trichoderma can be effectively exploited in sustainable agriculture and could also be a useful model of the plant-beneficial microorganism interaction through “translational research”. Our work investigated the transcriptional response of tomato roots (Solanum lycopersicum) to Trichoderma harzianum strain T22 at early stages of the interaction (24, 48 and 72 h), using a Next Generation Sequencing approach (RNA-seq). This analysis revealed an intense remodelling of the plant transcriptome already after 24 h, involving more than 75% of the detected Differentially Expressed Genes (DEGs), while smaller effects on gene expression were observed at 48 and 72 h. Enrichment analysis of the 24 h DEGs based on Gene Ontology (GO) showed involvement of “defence response” and “cell wall organization” activities as well as of macromolecules “metabolism”, “transport” and “localization”. Data inspection via the MapMan tool assigned 151 DEGs to bin 27 (“RNA”-related), suggesting the activation of the transcriptional machinery in tomato roots responding to the PGPF. Moreover, MapMan annotation highlighted a considerable enrichment of bin 35 (i.e. “not assigned”) over the three time points, mostly due to the large presence (155) of proteins with unknown functions. Along with plant transcripts, RNA-sequencing of roots also identified 448 Trichoderma genes, which were searched for differential expression over the time course. GO enrichment analysis of the differentially expressed genes revealed that, at 24-48 h, ‘macromolecules metabolic processes’ were affected; on the other hand, “response to stimulus”–related, as well as cellular processes (“communication”, “amino acid metabolism”) and their regulation, were involved at 48-72 h. Taken together, our data were used to develop a model of the early tomato root response (within 72 h) to stimulation by the beneficial fungus T. harzianum.
The linkage of human circadian rhythms and hepatocellular carcinoma (HCC) through network analysis
Authors: Singh Sakshi , Colonna Giovanni , Ciliberto Gennaro , Costantini Susan
Published: January 2018

Human circadian rhythms connect internal biological clock and external environmental through earth’s day and night alternating. The human circadian clocks, present in each organs, are controlled by a main pace-maker situated in SCN (suprachiasmatic nuclei) of hypothalamus which is synchronized to the daily photoperiod. Clock disturbances are involved in many diseases like diabetes, obesity, depression, bipolar disease, and many types of cancers like breast cancer, colon cancer as well as hepatocellular carcinoma which is the third most life claiming cancer around the world. In this work the protein- protein interaction networks were analyzed using Cytoscape software. The human circadian network consists of 2151 nodes and 75821 interactions making it a huge network. It is very centralized with the value of 0.235. The density of the network is 0.033 and heterogeneity of 1.012. The characteristic path length is 2.373 while the average number of neighbors is equal to 70.5. Recently we performed a network analysis on gene expression data obtained in our group from HepG2 cells, a liver cancer cell line that lacks the viral infection, identifying 26 HUB genes [1]. Among these genes, 20 of them resulted present in the human circadian rhythm network. All these 20 genes had high degree values in the circadian network, ranging from 287 to 77 indicating that they control a large number of functional interactions and the information flow through the circadian network. However, by merging the network of genes involved in human circadian rhythms as well HepG2, we found that 83 hub nodes are common. This establishes strong relationships between liver cancer and circadian rhythms.
Effects of trait variation, environment, and phylogeny on the air pollutant removal capacity of indoor plants
Authors: Lu Shan , Hu Guang , Chen Bo , Zheng Ye , Lai Yi'nan , Jing Jing
Published: January 2018

Although it is well known that plants have the capacity to remove indoor air pollutants, there has been little research to investigate how this ability is regulated by the environment and evolutionary processes. In this study, we tested the capacity of 58 common indoor plants to remove three specific air pollutants. We also measured the traits, phylogenetic signals, and cultivated environments of these plants to analyze their relationship with the air pollutant removal capacity using Spearman’s correlation, Blomberg’s K test, and phylogenetic generalized least-squares. While we found trait variation had a significant correlation with removal capacity, we did not, however, detect a phylogenetic signal with removal capacity. Trait variation and environmental factors both contributed to the removal capacity in phylogenetic generalized least-squares, but again, without phylogeny. Our results show that plant trait variation, especially total leaf area, could play an important role in plant’s capacity to remove pollutants from indoor air. Moreover, environmental changes, not the phylogeny, could result in trait modification, improving the tolerance and purification capacities of these plants. The findings outlined here will help to explain how plants living with air pollution can adapt as well as the application of plants for the purpose of indoor air purification.
Derivation of kernel of dynamic support vector machines: Stochastic and deterministic data process
Authors: Sato Masamichi
Published: January 2018

We give an analytic derivation of kernel of dynamic support vector machine (DSVM). We show them for the cases of the data processes with stochastic and deterministic changes. We derive the kernels by solving Bellman equations. For the stochastic case, Gaussian kernel is naturally derived. For the deterministic case, the kernel is derived in the form of traveling wave. We also give comments from physical viewpoints in the context of information geometry. Physical comments include the equivalence principle in information geometric context and the relation to AdS/CFT correspondence.
Treating patients with compounds or biological agents that pass the safety-test
Authors: Zhang Jianyi
Published: January 2018

There are numerous medical disorders without effective treatments. It is possible that many of un-treatable conditions need more than one compound co-operatively for improvement or cure. Approval of drugs in the U.S. is governed by a rigorous review process by the Food and Drug Administration (FDA) regulation. A sponsor must demonstrate the drug’s safety and efficacy in well controlled clinical trials in the proper patient population for which it is indicated. Development of a new compound entity (NCE) is a very costly and time-consuming process; it takes roughly 15 years and 1.5 billion dollars on average. The high cost of the process makes the development of a new drug with multiple NCEs almost impossible. There are many compounds or biological agents which pass the safety test, but fail in the efficacy test. Those compounds might be critical for treatment of these medical conditions. The author suggests that compounds or biological agents, which pass the safety test, but the fail in efficacy test, should be allowed to use in clinical setting. The safety of those compounds is comparable with any other drugs approved by FDA. Benefits would heavily outweigh risks for patients treated by those compounds. The same principle should also be applied to biological agents, such as vaccines against HIV infection, cancers, etc.
Investigation of the abundance, distribution and composition of microplastics at coastal upwelling sites in the Atlantic Ocean
Authors: Kanhai La Daana K , Officer Rick , O'Connor Ian , Thompson Richard C
Published: January 2018

Microplastics are an issue of international concern due to the fact that these substances may potentially threaten biota by (i) causing physical harm, (ii) transporting persistent, bioaccumulating and toxic (PBT) substances and, (iii) leaching plastic additives. Within the world’s oceans, areas which experience coastal upwelling are biota rich due to their high levels of primary productivity. The assessment of microplastic presence in areas which experience coastal upwelling is vital as it will indicate whether microplastics are an issue of concern in areas which support key biological resources. The null hypothesis of the present study is that microplastic abundance will be lower in areas where there is upwelling. As such, the present study aims to investigate whether microplastic abundance in upwelled areas in the Atlantic Ocean is significantly different from non-upwelled areas. Based on an opportunistic voyage aboard the RV Polarstern, microplastics will be sampled in sub-surface waters along a diverse latitudinal gradient in the Atlantic Ocean i.e. from Bremerhaven (Germany) to Cape Town (South Africa). Based on the proposed route, it will be possible to determine microplastic levels at two areas of coastal upwelling in the Atlantic Ocean (i) Canary Upwelling Ecosystem (CUE) and (ii) Benguela Upwelling Ecosystem (BUE). The results will then be analysed to determine whether there was a statistically significant difference between ‘upwelled areas’ and ‘non-upwelled areas’.
Integration of biochar and chemical fertilizer to enhance quality of soil and wheat crop (Triticum aestivum L.)
Authors: Khalid Chaudhry Usman , Shahzad Salman , Nadir Naqqash Muhammad , Saboor Abdul , Yaqoob Sana , Salim Muhammad , Khalid Muhammad
Published: January 2018

A wide variety of soil amendments like manures, compost, humic acid and bio-sorbents have been used to make nutrients available to crops as well as to protect them from toxic elements. Among soil amendments, biochar has been known to improve soil crumping, soil nutrients’ availability to plants and ultimately the yield of crops. A field experiment was conducted by using biochar prepared from Dalbergia sissoo Roxb. wood by brick batch process. Two doses of biochar were applied to soil 0 and 12 t ha-1. Fertilizer rates used in the experiments were 25% recommended doses of fertilizers (RDF), 50% RDF, 75% RDF and 100% RDF alone & with biochar applied under two factorial randomized complete block design in natural field conditions (RDF of NPK fertilizer is 120-60-60 kg ha-1) . Soil physico-chemical properties viz., bulk density, particle density, porosity, pH, electrical conductivity, organic matter, soil organic carbon, total nitrogen, available phosphorus, available potassium, soil organic carbon, soil microbial biomass carbon and soil microbial biomass nitrogen were measured from the soil samples collected from 0-30 cm depth. All these parameters varied significantly among the treatments. A combined treatment of biochar and 50% of the recommended dose of NPK was most effective for soil conditioning. Agronomic parameters were also measured by standard methods. Due to chelation of heavy metal ions and availability of nutrients to the soil, yield of the crop may significantly increase due to cumulative treatment of fertilizer and biochar but upto a certain limit.
Structural characterization of the Hepatitis C Virus E2 glycoprotein: computational and experimental approaches
Authors: Barone Daniela , Balasco Nicole , Autiero Ida , Vitagliano Luigi
Published: January 2018

Hepatitis C virus (HCV) infection is a major cause of chronic liver disease worldwide. Although effective therapeutic approaches, based on specific inhibitors of HCV proteins NS3/4A and NS5B, have been recently discovered, their use is limited by the elevated costs of these drugs. Currently, there is neither an effective immune globulin for prophylaxis nor a vaccine for the prevention of hepatitis C. A particularly attracting target is represented by the immunogenic E2 glycoprotein, a key factor for HCV entry in host cells. This protein has been the subject of recent structural studies that have greatly expand our current knowledge of HCV pathogenicity (Khan et al. 2015; Khan et al. 2014; Kong et al. 2013). In this framework, we have recently undertaken studies aimed at evaluating the potential of some regions of the protein as vaccine candidates (Sandomenico et al. 2015, under review). We here investigated the structural/dynamic features of the E2 protein, whose structure has been recently solved by two independent groups in complex with antibodies. Molecular dynamics simulations carried out on the protein core provided interesting information on both global dynamics of the protein and on local features of important regions. Moreover, a combined experimental/computational analysis shows that the epitope I region (residues 412-422) is endowed with an elevated structural versatility. Collectively these findings provide useful information for future studies aimed at designing anti-HCV vaccines.ReferencesKhan AG, Miller MT, and Marcotrigiano J. 2015. HCV glycoprotein structures: what to expect from the unexpected. Current opinion in virology 12:53-58. 10.1016/j.coviro.2015.02.004 Khan AG, Whidby J, Miller MT, Scarborough H, Zatorski AV, Cygan A, Price AA, Yost SA, Bohannon CD, Jacob J, Grakoui A, and Marcotrigiano J. 2014. Structure of the core ectodomain of the hepatitis C virus envelope glycoprotein 2. Nature 509:381-384. 10.1038/nature13117 Kong L, Giang E, Nieusma T, Kadam RU, Cogburn KE, Hua Y, Dai X, Stanfield RL, Burton DR, Ward AB, Wilson IA, and Law M. 2013. Hepatitis C virus E2 envelope glycoprotein core structure. Science 342:10901094. 10.1126/science.1243876
Gamma-H2AX biodosimetry for use in large scale radiation incidents: comparison of a rapid lyse/fix protocol with a routine method
Authors: Moquet Jayne , Barnard Stephen G R , Rothkamm Kai
Published: January 2018

Following a radiation incident, preliminary dose estimates made by γ-H2AX foci analysis can supplement the early triage of casualties based on clinical symptoms. Sample processing time is important when many individuals need to be rapidly assessed. A protocol was therefore developed for high sample throughput that requires less than 0.1 ml blood, thus enabling finger prick sampling. The technique combines red blood cell lysis and leukocyte fixation in one step on a 96 well plate, in contrast to the routine protocol, where lymphocytes are separated by Ficoll density gradient centrifugation with subsequent washing and fixation steps. The rapid lyse/fix method reduced the estimated sample processing time for 96 samples to about 4 h compared to 15 h using the routine protocol. However, scoring 20 cells in 96 samples prepared by the rapid protocol took longer than for the routine method (3.1 versus 1.5 h at zero dose; 7.0 versus 6.1 h for irradiated samples). Similar foci yields were scored for both protocols and reliable dose estimates were obtained for coded samples, with mean absolute differences from the actual doses of 0.26 and 0.27 Gy for the routine and lyse/fix method, respectively. The lyse/fix protocol can therefore facilitate high throughput processing for γ-H2AX biodosimetry for use in large scale radiation incidents, at the cost of somewhat longer foci scoring times.
Cell cycle progression in glioblastoma cells is unaffected by pathophysiological levels of hypoxia
Authors: Richards Rosalie , Jenkinson Michael D , Haylock Brian J , See Violaine
Published: January 2018

Hypoxia is associated with the increased malignancy of a broad range of solid tumours; however, whilst very severe hypoxia has been widely shown to induce cell cycle arrest, the impact of pathophysiological hypoxia on tumour cell proliferation is poorly understood. The aim of this study was to investigate the effect of different oxygen levels on glioblastoma (GBM) cell proliferation and survival. GBM is an extremely aggressive brain tumour with a heterogeneous oxygenation pattern. The effect of a range of oxygen tensions on GBM cell lines and primary cells were assessed using flow cytometry. Results indicate that cell cycle distribution and viability are unaffected by long term exposure (up to 4 days) to pathophysiological levels of oxygen (1-8% O 2). Both transient cell cycle arrest and small amounts of cell death could only be detected when cells were exposed to severe hypoxia (0.1% O2). No significant changes in p21 protein expression levels were detected. These findings reinforce the importance of using physiologically relevant oxygen tensions when investigating tumour hypoxia, and help to explain how solid tumours can be both hypoxic and highly proliferative, as is the case with GBM.
Genetic characterization of colorectal cancer using a next generation sequencing approach to identify a specific pattern of somatic alterations in tumors arising from different anatomic sites
Authors: Laudanna Carmelo , Santamaria Gianluca , Migliozzi Simona , Mendes Oliveira Duarte , Malanga Donatella , Sacco Rosario , Rizzuto Antonia , Viglietto Giuseppe
Published: January 2018

Colorectal cancer (CRC) is the third leading cause of cancer-related deaths worldwide, with nearly 1.4 million new cases diagnosed in 2012. CRC results from the accumulation of multiple genetic and epigenetic aberrations. Tumor localization in the large intestine tract determines different surgical approaches and treatment options. Considering the heterogeneous nature of these tumors we hypothesized that different patterns of molecular alterations could be associated with a specific anatomical location. To identify distinct genomic alterations (e.g, copy number variations and mutations) associated to different CRC anatomical sites we sequenced 32 CRCs samples from different location (right-sided, left-sided etc.) using the Ion AmpliSeq™ Comprehensive Cancer Panel that covered the whole coding sequence of 409 tumor suppressor genes and oncogenes frequently altered in cancer. Interestingly left-sided tumors were generally more altered respect to right-sided ones. Cluster analysis of all samples allowed the identification of 21-gene core that were significantly mutated in all sample groups. As expected, KRAS and APC mutations were frequently in the tumors resected from different anatomical localizations. Unsupervised analysis of copy number variations reveals a core of 160-gene significantly altered. In addition to the expected SRC, MYC and CEBPA, we found interestingly genes in validation status. Despite missing a significant number of cases, gene panel provides a solid alternative approach to WES in order to characterize a signature of alterations correlated with CRC tumor and the identification of novel biomarkers in colorectal carcinoma that could be used as potential clinical target.
Metagenomic analysis exploring taxonomic and functional diversity of soil microbial communities in Chilean vineyards and surrounding native forests
Authors: Castañeda Luis E , Barbosa Olga
Published: January 2018

Mediterranean biomes are biodiversity hotspots and also have been historically related to wine production. During the last decades, land occupied by vineyards has increased considerably threatening these Mediterranean ecosystems. Land use change and agricultural management affect soil biodiversity, changing physical and chemical properties of soil. These changes may have consequences on wine production, especially because soil is a key component of wine identity or terroir. Here, we characterized the taxonomic and functional diversity of bacterial and fungal communities present in soil from vineyards in Central Chile. To accomplish this goal we collected soil samples from organic vineyards from Central Chile and employed a shotgun metagenomic approach. Additionally, we also studied the surrounding native forest as a picture of the soil conditions prior to the establishment of the vineyard. Our metagenomic analyses revealed that both habitats shared most of the soil microbial species. In general, bacteria were more abundant than fungi in both types of habitats, including soil-living genera such as Candidatus Solibacter, Bradyrhizobium and Gibberella. Interestingly, we found presence of lactic bacteria and fermenting yeasts in soil, which are key during wine production. However, their abundances were extremely low, suggesting unlikeness of soil as a potential reservoir in Chilean vineyards. Regarding functional diversity, we found that genes for metabolism of amino acids, fatty acids, nucleotides and secondary metabolism were enriched in forest soils, whereas genes for metabolism of potassium, proteins and miscellaneous functions were more abundant in vineyard soils. Our results suggest that organic vineyards have similar soil community composition than forest habitats. Additionally, we suggest that native forests surrounding vineyards may be acting as microbial reservoir buffering the land conversion. We conclude that the implementation of environmentally friendly practices by the wine industry may help to maintain the microbial diversity and ecosystem functions related to natural habitats.
Sentieon DNA pipeline for variant detection - Software-only solution, over 20× faster than GATK 3.3 with identical results
Authors: Weber Jessica A. , Aldana Rafael , Gallagher Brendan D. , Edwards Jeremy S.
Published: January 2018

Sentieon DNA Software is a suite of tools that allow running DNA sequencing secondary analysis pipelines. The Sentieon DNA Software produces results identical to the Genome Analysis Toolkit (GATK) Best Practice Workflow using HaplotypeCaller, with more than 20x increase in processing speed on the same hardware. This paper presents a benchmark analysis of both speed comparison and output concordance between using GATK and Sentieon DNA software on publically available datasets from the 100 genomes database.
Morphometric comparisons of plant-mimetic juvenile fish associated with plant debris observed on Kuchierabu-jima Island, southern Japan
Authors: Queiroz Alexya C , Sakai Yoichi , Vallinoto Marcelo , Barros Breno
Published: January 2018

The general morphological shape of plant-resembling fish and plant parts were compared using a geometric morphometrics approach. Lobotes surinamensis (Lobotidae), Platax orbicularis (Ephippidae) and Canthidermis maculata (Balistidae), three plant-mimetic fish species, were compared during their early developmental stages with accompanying plant parts (i.e. leaves of several taxa) in the coastal subtropical waters of Kuchierabu-jima Island, closely facing the Kuroshio Current. The degree of similarity shared between the plant parts and co-occurring fish species was quantified, however fish remained morphologically distinct from their plant models. Such similarities were corroborated by a linear model, in which relative body areas of fish and plant models were strongly interdependent. Our results strengthen the paradigm that morphological clues can lead to ecological evidence to allow predictions of behavioural and habitat choice by mimetic fish, according to the degree of similarity shared with their respective models. The resemblance to plant parts detected in the three fish species may provide fitness advantages via convergent evolutionary effects.
Using a pacifier to decrease sudden infant death syndrome: An emergency department educational intervention
Authors: Walsh Paul , Veith Teri , Rodriguez Carolina , Molina Rogelio , Lona Nicole , Habebo Emnet , Caldera Enrique , Garcia Cynthia , Veazy Gregory
Published: January 2018

Background: Pacifier use decreases the risk of sudden infant death syndrome (SIDS). An emergency department (ED) visit may provide an opportunistic ‘teachable moment’ for parents. Objectives: To test the hypotheses (1) that caregivers were less familiar with the role of pacifiers in sudden infant death (SIDS) prevention than other recommendations, and (2) that an ED educational intervention would increase pacifier use in infants younger than six months, and (3) that otitis media would not occur more frequently in pacifier users. Methods: An intervention-group-only longitudinal study in a county hospital ED. We measured pacifier use infants and baseline knowledge of SIDs prevention recommendations in caregivers. We followed up three months later to determine pacifier use, and 12 months later to determine episodes of otitis media. Results: We analyzed data for 780 infants. Parents knew of advice against co-sleeping in 469/780 (60%), smoking in 660/776 (85%), and prone sleeping in 613/780 (79%). Only 268/777 (35%) knew the recommendation to offer a pacifier at bedtime. At enrollment 449/780 (58%) did not use a pacifier. Of 210/338 infants aged less than 6 months followed up 41/112 (37%) non-users had started using a pacifier at bedtime (NNT 3). Over the same period, 37/98 (38%) users had discontinued their pacifier. Otitis media did not differ between users and non-users at 12 months. Conclusion: Caregiver knowledge of the role of pacifiers in SIDS prevention was less than for other recommendations. Our educational intervention appeared to increase pacifier use. Pacifier use was not associated with increased otitis media.