bluuebunny/crossref_metadata_2025_split huggingface dataset:
Implementing an open source spatio-temporal search platform for Spatial Data Infrastructures
Authors: Corti Paolo , Lewis Benjamin G , Kralidis Tom , Mwenda Jude 
Published: January 2018

A Spatial Data Infrastructure (SDI) is a framework of geospatial data, metadata, users and tools intended to provide an efficient and flexible way to use spatial information. One of the key software components of an SDI is the catalogue service which is needed to discover, query and manage the metadata. Catalogue services in an SDI are typically based on the Open Geospatial Consortium (OGC) Catalogue Service for the Web (CSW) standard which defines common interfaces for accessing the metadata information.
A search engine is a software system capable of supporting fast and reliable search, with features such as full text search, natural language processing, weighted results, fuzzy tolerance results, faceting, hit highlighting and many others. In this paper we will be focusing on the Lucene, a powerful Javabased search library.
The Centre of Geographic Analysis (CGA) at Harvard University is trying to integrate within its public domain SDI (WorldMap http://worldmap.harvard.edu), the benefits of both worlds (OGC catalogues and search engines).
Harvard Hypermap (HHypermap) is a component that will be part of WorldMap, built on an open source stack. The system implements an OGC catalogue based on pycsw, to provide access to metadata in a standard way, and uses a search engine based on Solr/Lucene, to provide advanced search features typically found in search engines.
Implementing an open source spatio-temporal search platform for Spatial Data Infrastructures
Authors: Corti Paolo , Lewis Benjamin G , Kralidis Athanasios Tom , Mwenda Ntabathia Jude 
Published: January 2018

A Spatial Data Infrastructure (SDI) is a framework of geospatial data, metadata, users and tools intended to provide an efficient and flexible way to use spatial information. One of the key software components of an SDI is the catalogue service which is needed to discover, query, and manage the metadata. Catalogue services in an SDI are typically based on the Open Geospatial Consortium (OGC) Catalogue Service for the Web (CSW) standard which defines common interfaces for accessing the metadata information.
A search engine is a software system capable of supporting fast and reliable search, which may use “any means necessary” to get users to the resources they need quickly and efficiently. These techniques may include features such as full text search, natural language processing, weighted results, fuzzy tolerance results, faceting, hit highlighting, recommendations, feedback mechanisms based on log mining, usage statistic gathering, and many others. In this paper we will be focusing on improving geospatial search with a search engine platform that uses Lucene, a Java-based search library, at its core.
In work funded by the National Endowment for the Humanities, the Centre for Geographic Analysis (CGA) at Harvard University is in the process of re-engineering the search component of its public domain SDI (WorldMap http://worldmap.harvard.edu ) which is based on the GeoNode platform. In the process the CGA has developed Harvard Hypermap (HHypermap), a map services registry and search platform independent from WorldMap.
The goal of HHypermap is to provide a framework for building and maintaining a comprehensive registry of web map services, and because such a registry is expected to be large, the system supports the development of clients with modern search capabilities such as spatial and temporal faceting and instant previews via an open API. Behind the scenes HHypermap scalably harvests OGC and Esri service metadata from distributed servers, organizes that information, and pushes it to a search engine. The system monitors services for reliability and uses that to improve search. End users will be able to search the SDI metadata using standard interfaces provided by the internal CSW catalogue, and will benefit from the enhanced search possibilities provided by an advanced search engine. HHypermap is built on an open source software source stack.
MetaCRAST: Reference-guided extraction of CRISPR spacers from unassembled metagenomes
Authors: Moller Abraham G , Liang Chun 
Published: January 2018

Summary: Clustered regularly interspaced palindromic repeat (CRISPR) systems are prokaryotic adaptive immune systems against phage infection. CRISPR spacer sequences can provide valuable ecological insights by linking environmental viruses to their microbial hosts. Despite this importance, metagenomic CRISPR detection remains a major challenge. Here we present a reference-guided CRISPR detection tool (Metagenomic CRISPR Reference-Aided Search Tool - MetaCRAST) that constrains searches based on user-specified direct repeats. These DRs could be expected from assembly or taxonomic profiles of metagenomic sequence data. Our evaluation shows MetaCRAST improves CRISPR spacer detection in real metagenomes compared to de novo detection methods. Simulations show it performs better than comparable tools when analyzing Illumina metagenomes.
Availability and implementation: MetaCRAST is implemented in Perl and takes metagenomic sequence reads and direct repeat queries in FASTA format as input. It is freely available for download at https://github.com/molleraj/MetaCRAST .
Differences in pollination success between local and foreign flower color phenotypes: a translocation experiment with Gentiana lutea (Gentianaceae)
Authors: Guitián Javier A , Sobral Mar , Veiga Tania , Losada María , Guitián Pablo , Guitián José M 
Published: January 2018

Background. The adaptive maintenance of flower color variation is frequently attributed to pollinators in part because they preferentially visit certain flower phenotypes. We test whether Gentiana lutea – which shows a flower color variation (from orange to yellow) in the Cantabrian Mountains range (north of Spain) − is locally adapted to the pollinator community.
Methods. We transplant orange-flowering individuals to a population with yellow-flowering individuals and vice-versa, to assess whether there is a pollination advantage in the local morph comparing its visitation rate with the foreign morph.
Results. Our reciprocal transplant experiment showed no clear signal of local morph advantage at one site; thus, there is no evidence of local adaptation in Gentiana lutea to the pollinator assemblage. However, some floral visitor groups (such as Bombus pratorum, B. soroensis ancaricus and B. lapidarius decipiens) consistently preferred the local morph to the foreign morph whereas others (such as Bombus terrestris) consistently preferred the foreign morph.
Discussion. We concluded that there is no evidence of local adaptation to the pollinator community in each of the two G. lutea populations studied. The consequences for local adaptation to pollinator on G. lutea flower color would depend on the variation along the Cantabrian Mountains range in morph frequency and pollinator community composition.
S-phase kinase-associated protein 2 positively controls mitotic arrest deficient 2 in lung cancer cells
Authors: Huang Tonghai , Yang Lin , Wang Guangsuo , Ding Guanggui , Peng Bin , Wen Yuxin , Wang Zheng 
Published: January 2018

Background. Mitotic arrest deficient 2 (Mad2) is a key component of spindle assembly checkpoint and overexpressed in human lung cancers, but the mechanism of the deregulation of Mad2 in lung cancer is largely unknown. We aim to investigate the regulation of Mad2 by S-phase kinase-associated protein 2 (Skp2) in human lung cancer cells.
Methods. Human lung cancer A549 and NCI-H1975 cells were transfected with MAD2 and SKP2 siRNAs or plasmids to silence or overexpress MAD2 and SKP2. Flavopiridol and HLM006474 were used to inhibit cyclin dependent kinases (CDKs) and E2F1, respectively. mRNA and protein levels were determined by real-time PCR and Western blot, respectively. Cell cycle progression was assayed by flow cytometery.
Results. Knockdown of Skp2 by siRNA decreased Mad2 mRNA and protein levels in A549 and NCI-H1299 cells, accompanied with upregulation of p27 but decrease of the phosphorylation of retinoblastoma (Rb). In contrast, ectopic overexpression of Skp2 increased Mad2 mRNA and protein levels and phosphorylation of Rb, while decreased p27. Pharmacological inhibition of CDK1/2 by flavopiridol or E2F1 with HLM006474 led to downregulation of Mad2 expression, and prevented the increase of Mad2 expression by Skp2. Accordingly, silencing of either Mad2 or Skp2 impaired the mitosis arrest in response to nocadazole.
Conclusion. SKP2 positively regulates the gene expression of MAD2 through p27-CDKs-E2F1 signaling pathway, suggesting that deregulation of Skp2 may lead to upregulation of Mad2 via enhancing the activity of CDKs in human lung cancers. Our findings may provide an explanation of the simultaneous upregulation of MAD2 and SKP2 in lung cancer and potential targets for the development of molecular targeted therapy for lung cancers.
A new specimen-dependent method of estimating felid body mass
Authors: Sherani Shaheer 
Published: January 2018

Background. The estimation of body mass of long extinct species of the family Felidae has been a focus of paleontology. However, most utilized methods impose expected proportions on the fossil specimens being estimated, resulting in a high chance of underestimation or overestimation. This study proposes a new method of estimating felid body mass by accounting for osteological proportionality differences between the extinct taxa being estimated and the living species being used as comparisons.
Method. Using a manipulation of the cube law, 36 equations were formulated that estimate body mass based on certain humeral and femoral dimensions. The formulated equations were used to examine whether the mass of living comparison species, namely the tiger (Panthera tigris), the lion (Panthera leo), and the jaguar (Panthera onca), depends equally on a select set of long bone dimensions. The body mass of five extinct felids, namely Panthera atrox, Panthera spelaea, Panthera tigris soloensis, Smilodon populator, and Smilodon fatalis, was also estimated.
Results. Living comparisons species were found to somewhat incorrectly estimate other living comparison species. All five extinct taxa were found to weigh well over 300 kg, with the largest of the species weighing nearly 500 kg.
Discussion. The inability of one living comparison species to predict the mass of another with strong accuracy suggests that bone dimensions do not solely influence body mass. Discrepancies between the masses of Smilodon populator and Smilodon fatalis were likely the product of the difference in available niches in late Pleistocene North and South America. The masses of Panthera spelaea and Panthera atrox indicate a discrepancy in sociality between the two closely related species. Lastly, the extreme body mass of Panthera tigris soloensis points to great plasticity within the tiger lineage in terms of size, indicating that such variations among tiger populations may not warrant subspeciation.
Bovine tuberculosis in cattle from 1986 to 2012 in and around badger-culled areas of the RBCT
Authors: Hendy David 
Published: January 2018

In 2007 the Independent Scientific Group (ISG) reported to the UK government the impact on bovine tuberculosis (TB) in cattle of a trial where badgers were culled between 1998 and 2005. This trial, known as the Randomised Badger Culling Trial (RBCT), was performed across 100 km2 (nominal) zones in the West of England. The results were based on a model of new herd incidence data. It was concluded that reactive culling generated overall detrimental effects, while proactive culling achieved very modest overall benefits at the cost of elevated incidence on neighbouring farms.
This work looks at more extensive RBCT data to examine if these findings hold true. Instead of presenting the results of a model, this work directly illustrates data supplied in March 2016 by the Animal and Plant Health Agency. Such data covers a greater number of years (1986 to 2012) and includes the prevalence of herd restrictions as well as herd incidence.
It appears that whilst cattle TB noticeably reduced in areas subjected to proactive culling, TB did not significantly increase in the surrounding areas. The more limited reactive culls were found to have no significant impact either positively or negatively. This applied to both the treated and surrounding areas.
The more extensive data also showed that culling badgers only reduced confirmed TB with no significant impact on unconfirmed TB. This was also found by the ISG in 2007 when using their model.
The delay before culling benefit became apparent was about 5 years after the first substantial cull. This has implications for the culls which started in South West England in 2013. If account is taken for the need to average the data, the number of years needed to see TB drop, and the reporting delay, it may not be until September 2023 before the impact of these culls become clear. Also, if culls stop after year four in each zone, this risks benefits falling short of those achieved in the RBCT.
Randomised Badger Culling Trial: Impact, based on more extensive data
Authors: Hendy David 
Published: January 2018

In 2007 the Independent Scientific Group (ISG) reported to the UK government the impact on bovine tuberculosis (TB) in cattle of the Randomised Badger Culling Trial (RBCT). Badgers were culled between 1998 and 2005 across 100 km2 (nominal) zones in the West of England. The results were based on a model of New Herd Incidence (NHI). It was concluded that reactive culling generated overall detrimental effects, while proactive culling achieved very modest overall benefits at the cost of elevated incidence in surrounding areas.
This work looks at more extensive RBCT data to examine if these findings hold true. Instead of presenting the results of a model, this work directly illustrates the data. The Animal and Plant Health Agency supplied this data in March 2016. Such data covers a greater number of years (1986 to 2012) and includes the prevalence of herd restrictions as well as herd incidence.
Whilst the proactive culls substantially and sustainably reduced cattle TB in treated areas, such culls did not significantly increase TB in the surrounding areas. In fact NHIs between 2006 and 2012 dropped by 28%, 1% and 18% in the treated, outer 2km ring, and combined areas respectively. Based on the number of NHIs prevented since 1998, a break-even cost to complete a badger removal exercise was calculated to be £8,693 per km2. This figure may be under-estimated because it takes no account of any NHIs prevented after 2012.
The more limited reactive culls had no impact on both the treated area and outer 2km ring. Proactive culling only reduced confirmed TB with no significant impact on unconfirmed TB.
Conclusions in the RBCT Final Report, which were based on the results of a model of time-shifted early data, poorly reflect the greater benefits seen in this more extensive data. Badger culling is highly contentious in the UK and many press reports adversely report the effectiveness of badger culling in general and the culls which started in 2013 in particular. Unfortunately the RBCT conclusions are often cited to add credence to these press reports. In the RBCT, after the first year of substantial culling, this work found that 9 years of data were needed to clearly see the full extent by which TB dropped when plotted against calendar year. The impact of the culls, which started in late 2013, may not become clear until late 2023 after a 2-year reporting delay.
This work was restricted to looking at data showing total TB breakdowns over all triplets. Further work to examine breakdowns by triplet or groups of triplets should reveal more.
Supply-side barriers to maternal health care utilization at health sub-centres in India
Authors: Singh Aditya 
Published: January 2018

Introduction: There exist several barriers to maternal health service utilization in developing countries. Most of the previous studies conducted in India have focused on demand-side barriers, while only a few have touched upon supply-side barriers. None of the previous studies in India have investigated the factors that affect maternal health care utilization at Health Sub-Centers (HSC) in India, despite the fact that these institutions, as the nearest available public healthcare facilities in rural areas, play a significant role in providing affordable maternal health care. Therefore, this study aims to examine the supply-side determinants of maternal service utilization at HSCs in rural India.
Data and Methods: This study uses health facility data from the nationally representative District-Level Household Survey, which was collected in 2007–2008 to examine the effect of supply-side variables on the utilization of maternal healthcare services across HSCs in rural India. Since the dependent variables (the number of antenatal registrations, in-facility deliveries, and postnatal care services) are count variables with considerable dispersion, the data has been analyzed using negative binomial regression instead of Poisson regression.
Results: The results show that those HSCs run by a contractual auxiliary nurse midwife (ANM) are likely to offer a lower volume of services when compared to those run by a permanent ANM. The availability of obstetric drugs, weighing scale, blood pressure equipment is associated with the increased utilization of antenatal and postnatal services. The unavailability of labor/examination table and bed screen is associated with a reduction in the number of safe deliveries and postnatal services. The utilization of services is expected to increase if essential facilities, such as water, telephone, toilet, and electricity, are available at HSCs. Monitoring of an ANM’s work by the Village Health and Sanitation Committee (VHSC) and the in-service training of ANMs appear to have a positive impact on the utilization of services. The distance of an ANM’s actual residence from the sub-center village where she works is negatively associated with the utilization of delivery and postnatal services. These findings are robust to the inclusion of several demand-side factors.
Conclusion: To improve maternal healthcare utilization at sub-centers, the government should ensure the availability of basic infrastructure, drugs, and equipment at all sub-centers. Monitoring of ANMs’ work by VHSCs could play an important role in improving healthcare utilization at the HSCs; therefore, it is important to establish VHSCs in each sub-center village. The issue of the relatively low utilization of maternity services in the HSCs that are run solely by contractual ANMs needs to be investigated further.
Bioinformatics support for the Tubiom community gut microbiome project
Authors: Beier Sina , Gorska Anna , Grupp Patrick , Harbig Theresa Anisja , Flade Isabell , Huson Daniel H 
Published: January 2018

The Tübiom project is a community-based project aimed at constructing a large, representative reference database of human gut microbiome profiles. The goal is to collect 10 000 profiles, along with detailed metadata on each participants health and lifestyle. All samples will be processed using identical sequencing and analysis protocols to ensure comparability. The project has four technical components: sequencing, sequence analysis, data storage and visualisation.
The project website http://www.tuebiom.de allows interested people to learn about the project, order a sampling kit and fill-in the metadata questionnaire. Once a sample as been submitted and processed, a participant can explore the taxonomic profile of their gut microbiome and compare it to the typical profile of different comparison groups.This community-based project also hopes to engage participants in science-propagation, spread knowledge about the gut microbiome and the importance of this area of research.
Here we provide a brief introduction to the Tübiom project and describe the bioinformatics framework that we have developed for it.
In-silico prediction and modeling of the Entamoeba histolytica proteins: Serine-rich Entamoeba histolytica protein and peroxiredoxin
Authors: Manochitra Kumar , Parija Subhash Chandra 
Published: January 2018

Background: Amoebiasis is the third most common parasitic cause of morbidity and mortality particularly in countries with poor hygienic settings. There exists an ambiguity in the diagnosis of amoebiasis, and hence arises a necessity for a better diagnostic approach. Serine-rich Entamoeba histolytica protein (SREHP), peroxiredoxin and Gal/GalNAc lectin are pivotal in E. histolytica virulence and are extensively studied as diagnostic and vaccine targets. For elucidating the cellular function of these proteins, details regarding their respective quaternary structures are essential which are not available till date. Hence, this study was carried out to predict the structure of these target proteins and characterize them structurally as well as functionally using relevant in-silico methods.
Methods:The amino acid sequences of the proteins were retrieved from National Centre for Biotechnology Information database and aligned using ClustalW. Bioinformatic tools were employed in the secondary structure and tertiary structure prediction. The predicted structure was validated, and final refinement was carried out.
Results: The protein structures predicted by i-TASSER were found to be more accurate than Phyre2 based on the validation using SAVES server. The prediction suggests SREHP to be a extracellular protein, peroxiredoxin was a peripheral membrane protein, while Gal/GalAc was found to be a cell-wall protein. Signal peptides were found in the amino-acid sequences of SREHP and Gal/GalNAc, whereas they were not present in the peroxiredoxin sequence. Gal/GalNAc lectin showed better antigenicity than the other two proteins studied. All three proteins exhibited similarity in their structures and were mostly composed of loops.
Discussion:The structures of SREHP and peroxiredoxin were predicted successfully, while the structure of Gal/GalNAc lectin could not be predicted as it was a complex protein composed of three sub-units. Also, this protein showed less similarity with the available structural homologs. The quaternary structures predicted from this study would provide better structural and functional insights into these proteins and may aid in development of newer diagnostic assays or enhancement of the available treatment modalities.
The man-machine integration era
Authors: Bilar Daniel 
Published: January 2018

Through sensor ubiquity, the man-machine integration era is upon us. This integration is taking place in distributed, continuously changing, optimizing/learning, finite precision feedback systems. Security challenges of such systems abound, also due to constantly co-evolving threat actors and changing environments. Are we adequately preparing to defend such systems, and more importantly: how do we ensure they are worth defending?
This position paper posits we are ill-prepared, due to perverse incentives affecting methodology, results and foundational corpuses. With respect to the first question, we will corroborate this ill-preparedness in the context of a basic requirement – situational awareness – for so-called Moving Target Defenses. We’ll argue that the second question hinges on a deceptively straightforward permanence invariant: The ability to robustly encode the infinite value of a human being in finite precision systems. Here too, we are failing to develop needed toolsets and skills.
Successfully tackling both questions may determine the future winning model of the man-machine integration era; whether we’ll lose the Republic of the People to the People’s Republic.