bluuebunny/crossref_metadata_2025 huggingface dataset:
Distribution and abundance of Cymodocea nodosa meadows and Pinna nobilis populations in the Mar Menor coastal lagoon (Murcia, South East of Spain)
Authors: Belando Maria Dolores , García-Muñoz Rocio , Ramos Aranzazu , Franco Ignacio , Bernardeau-Esteller Jaime , García Pedro , Ruiz Juan Manuel
Published: January 2018

The Mar Menor (135 km2 ) is one of the most important hypersaline coastal lagoons in the Western Mediterranean Sea, its bottoms were originally colonized by monospecific meadows of the seagrass Cymodocea nodosa. However, since the 1970’s, drastic hydrographic changes caused by various human activities has seen the expansion of a number of species common in the adjacent Mediterranean waters, of which development had been limited up to now due to high salinities and temperatures. Among these species, the seaweed Caulerpa prolifera and the endangered fan mussel Pinna nobilis are those experiencing a broader spread in the lagoon and with a great potential to interact through both bottom-up and top-down processes have, as a result of which they have become key species of the lagoon ecosystem. In fact, previous maps of benthic vegetation suggest a huge decline of seagrass populations as C. prolifera has expanded. Moreover, both the algae and the filter feeder could play a key role in the control of planktonic communities, which development in the lagoon waters could have been accelerated in the last decades due to the great enhancement of eutrophication and pollution processes. Therefore, quantification of benthic vegetation communities, in particular C. nodosa meadows, and P. nobilis populations are crucial for the understanding of the Mar Menor ecosystem, but overall for the management of human activities and the implementation of conservation actions given its current protection status and the urgent need to obey European Directives (Habitats, Water Framework and Marine Strategy). In this context, precise maps of the distribution and abundance of benthic vegetation and P. nobilis in the Mar Menor was obtained during the spring-summer of 2014 by means of direct measurements (macrophytes cover, density and biomass and P. nobilis density) performed on 57 sampling points and qualitative observations (presence/absence) performed on 189 additional points as well as on 155.5 km of lineal transects using a trawled videocamera. Data obtained suggests that seagrass abundance in the lagoon is much higher than that reported in some previous studies and does not support the hypothesis of a long-term decline. P. nobilis has spread over a surface area 56.8% of the lagoon seafloor with a mean density of 2.17 ind.·100 m-2 and maximum values (up to 22.5 ind.·100 m-2) located in the northern part of the lagoon under the maximum influence of the Mediterranean waters.
Pinna nobilis within a Posidonia oceanica meadow: evidences of how hydrodynamics define this association in the Gulf of Oristano (West Sardinia, Italy)
Authors: Coppa Stefania , Cucco Andrea , De Falco Giovanni , Massaro Giorgio , Camedda Andrea , Marra Stefano , Simeone Simone , Conforti Alessandro , Tonielli Renato , de Lucia Giuseppe
Published: January 2018

The fan mussel Pinna nobilis is the largest bivalve of the Mediterranean Sea, declared protected since 1992. It is a sessile suspension feeder endemic of this basin which lives mainly on soft sediments colonized by seagrass meadows. This study considers a population living within a Posidonia oceanica bed in the Gulf of Oristano (W Sardinia, Italy), a site included within a Marine Protected Area and in two Sites of Community Importance. Based on field surveys conducted in 2007, 2009 and 2014 differences in density, size, and shell burial level of P. nobilis were investigated in relation to meadow's distribution and characteristics. Moreover, the spatial differences in density and orientation of P. nobilis were related to hydrological features. P. nobilis showed a mean density of 4.06±1.13 ind./100 m2 and a significant increase in population size was observed between 2009 and 2014. A high-resolution multibeam survey revealed that the P. oceanica bed was characterized by a striped structure. Toward the inner sheltered sector of Gulf, the meadow became hill-shaped. A comparison between meadow structure and P. nobilis distribution showed that specimens are mainly located at the edge of the channels within the striped meadow, whereas the edge effect resulted less noticeable within the hill-shaped meadow. The compactness of the seabed influences the shell stability: the burial level decreased with the increasing of fine sediments. Bottom current direction and speed are the main factors influencing shell orientation, whereas wave action is negligible. Where bottom current speed exceeded 0.07 m/s specimens resulted in line with the prevalent current direction with the ventral side exposed to incoming flow. These features suggest that feeding strategy is an important factor in determining shell orientation, possibly in addition to drag. Food availability could be the driving force in determining the patchiness distribution of P. nobilis population with higher values in those sites close to the mouth of the lagoons, in sedimentation area or in the meadow channels where the water flow is conveyed. These findings contribute to increase the knowledge on the P. nobilis-P. oceanica association and provide useful information for improving conservation measures.
Selection in the dopamine receptor 2 gene: New candidate SNPs for disease-related studies
Authors: Göllner Tobias , Fieder Martin
Published: January 2018

Dopamine is a major neurotransmitter in the human brain and is associated with various diseases. Schizophrenia, for example, is treated by blocking the dopamine receptors type 2. In 2009, Shaner, Miller and Mintz stated that schizophrenia was the low fitness variant of a highly variable mental trait. We therefore explore whether the dopamine receptor 2 gene (DRD2) underwent any selection processes. We acquired genotype data of the 1000 Genomes project (phase I), which contains 1093 individuals from 14 populations. We included only single nucleotide polymorphisms (SNPs) with a minor allele frequency (MAF) of over 0.05 in the analysis. This is equivalent to 151 SNPs for DRD2. We used two different approaches (an outlier approach and a Bayesian approach) to detect loci under selection. The combined results of both approaches yielded nine candidate SNPs under balancing selection. While directional selection strongly favours one allele over all others, balancing selection favours more than one allele. All candidates are in the intronic region of the gene and only one (rs12574471) has been mentioned in the literature. Two of our candidate SNPs are located in specific regions of the gene: rs80215768 lies within a promoter flanking region and rs74751335 lies within a transcription factor binding site. We strongly encourage research on our candidate SNPs and their possible phenotypic effects.
Turtles of the genus Sakya (Geoemydidae): new material from the late Miocene of Russia and Ukraine, new taxonomic diversity and expansion of the stratigraphic range
Authors: Syromyatnikova Elena , Danilov Igor
Published: January 2018

Background. Sakya Bogachev, 1960 is a genus of geoemydid turtles with unusual scalation of the carapace consisting of 9–10 vertebrals and 8–10 pairs of pleurals. It is known from Neogene localities of Eastern Europe and includes two species: Sakya riabinini (Khosatzky, 1946) (= S. pontica Bogachev, 1960), from the late Miocene (MN13) to early Pleistocene of Eastern Europe (Moldova, Romania, Russia, and Ukraine) and Sakya kolakovskii Chkhikvadze, 1968 from the Pliocene of Abkhazia. Attribution of Melanochelys etuliensis Khosatzky and Redkozubov, 1986 from the early Pliocene of Moldova to Sakya is poorly corroborated. Here we report new material of Sakya from the late Miocene of Russia and Ukraine, which, probably, belongs to one or two new species of this genus and expands its stratigraphic distribution. Methods. We examined new material of Sakya, that includes posterior part of carapace and incomplete plastron from Morskaya 2 locality (MN 13, Rostov Province, Russia), incomplete carapace and plastron from Egorovka locality (MN 12, Odessa Province, Ukraine), and fragmentary shell remains from Fortepianka locality (MN 11, Republic of Adygea, Russia). For comparison we used published data and personal observations on other specimens of Sakya. Results. The specimens from Morskaya 2 and Egorovka are assigned to Sakya based on the presence of increased number of vertebrals and pleurals. Both specimens differ from the described species of Sakya by reduced number of vertebrals (seven in the Morskaya 2 specimen, and five in the Egorovka specimen), and extension of the posteriormost vertebral onto pygal. In addition, they differ from S. riabinini in the presence of eight neurals, longer than wide pleurals, and from S. kolakovskii in the presence of two suprapygals and serrated posterior edge of the carapace. The material from Fortepianka is too fragmentary for detailed comparison, but also differs from S. riabinini in the reduced number of vertebrals. Discussion. The reported material may represent one or two new species of Sakya. The reduced number of vertebrals in these forms probably represents a primitive condition, whereas the extension of the posteriormost vertebral onto the pygal may be a synapomorphy, which unites the new forms. Thus, the Morskaya 2 and Egorovka specimens of Sakya may represent a separate primitive lineage of this genus. In this case, S. kolakovskii and S. riabinini form a more advanced clade with increased number of carapacial scales. These issues as well as phylogenetic position of Sakya within Geoemydidae will be checked by future phylogenetic analysis. The Sakya material from Fortepianka (MN11, late Sarmatian) represents the earliest reliable record of this genus, known previously beginning from MN 12 (Meotic).
Identification and management of physical health problems among an injecting drug using population
Authors: Patton Robert
Published: January 2018

Injecting drug use is highly prevalent in London and is associated with specific physical health problems. These problems are related to the toxicity of the substances, their mode of consumption and as a consequence of the drug taking lifestyle. Hepatitis B and C viral infections are common among drug users due to sharing of both needles and other drug taking paraphernalia. Hepatitis B infection can be prevented by immunisation. Hepatitis C infection can interact with alcohol consumption to accelerate liver damage. Sharing of drug injection equipment is high (up to 78%). Injecting drug users (IDUs) that live close to needle exchanges are significantly less likely to engage in sharing activities than those that live further away. Drug users are at particular risk of developing poor dental health, which is associated with morbidity and mortality, particularly cardio-vascular conditions and respiratory disease. Many female drug users have been involved with the commercial sex industry and are at risk of contracting blood borne viruses. Drug users who also use alcohol have an increased likelihood of physical morbidity and injury / trauma. Problem drug users have an increased likelihood of experiencing physical morbidity, but are less likely to engage with primary care services. Barriers to accessing primary care include convenience (access), apathy, procrastination and “self-medication”. Drug users are more likely to report physical health complications at an Accident & Emergency department (AED) than at a GP practice. Further investigation of local AEDs is required to ascertain their potential for assessing and referring drug users to specialist services and other primary care providers. Integration of primary care and drug treatment services may encourage drug users to engage in treatment for physical morbidity and promote retention within addictions services. Physical health of drug users may be assessed as part of a formal induction to treatment services, or opportunistically as appropriate. Drug users presenting to primary care services for prescriptions related to their addiction may not experience such an assessment. Increasing GPs knowledge and skills can lead to greater implementation of screening practices. The provision of primary care services to clients attending addiction treatment centres can lead to improvements in drug users’ physical health and enhanced treatment outcomes.
Liver 3D modeling and hepatectomy simulation for the residents’ preoperative education
Authors: Zygomalas Apollon , Megalooikonomou Vasileios , Koutsouris Dimitrios , Karavias Dimitrios , Karagiannidis Ioannis , Maroulis Ioannis , Giokas Konstantinos , Karavias Dionissios
Published: January 2018

Background. Liver segmentation from medical images produces high quality patient specific 3D liver models which are used for preoperative planning and intraoperative guidance. These 3D models can be manipulated and visualized in various ways and can be useful for residents’ education. Objective. The aim of this study was to evaluate the implementation of a novel liver segmentation and hepatectomy simulation application as a tool for the residents’ preoperative education. Method. We developed in MATLAB® 2013a a liver segmentation and preoperative planning application. Ten liver imaging datasets of a prospectively selected random sample of patients undergoing elective hepatectomies at our institution were used for liver segmentation and 3D modeling. Residents were asked to identify anatomical and pathological structures and propose liver resection plans. Intraoperatively, they could consult the computer models in real time. Their surgical scenarios were evaluated and discussed with specialized liver surgeons. Learning objectives were defined and their accomplishment was evaluated using the Kirkpatrick’s four levels model. Results. The residents learned to 1) identify anatomical and pathological structures 2) calculate future liver remnant volume (FLR) from segmented liver images 3) propose liver resection plans based on FLR and liver vascular tree and tumor relations 4) consult liver medical images (CT and MRI) 5) understand the role of computer assisted surgery. They evaluated in-vivo their preoperative planning decisions and understood better the surgical operations. Conclusions. Our proposed liver segmentation and hepatectomy simulation application appears to be appropriate for the preoperative education of resident surgeons.
PROV‐man: A PROV‐compliant toolkit for provenance management
Authors: Benabdelkader Ammar , van Kampen Antoine A.H.C. , Olabarriaga Silvia D
Published: January 2018

Discoveries in modern science can take years and involve the contribution of large amounts of data, many people and various tools. Although good scientific practice dictates that findings should be reproducible, in practice there are very few automated tools that actually support traceability of the scientific method employed, in particular when various experimental environments are involved at different research phases. Data provenance tracking approaches can play a major role in addressing many of these challenges. These approaches propose ways to capture, manage, and use of provenance information to support the traceability of the scientific methods in heterogeneous environments. PROV is a W3C standard that provides a comprensive model for data and semantics representation with common vocabularies and rich concepts to describe provenance. Nevertheless, it is difficult for domain scientists to easily understand and adopt all the richeness provided by PROV. In this paper we describe the design and implementation of the provenance manager PROV-man, a PROV-compliant framework that facilitates the tasks of scientists in integrating provenance capabilities into their data analysis tools. PROV-man provides functionalities to create and manipulate provenance data in a consistent manner and ensures its permanent storage. It also provides a set of interfaces to serialize and export provenance data into various data formats, serving interoperability. The open architecture of PROV-man, consisting of an API and a configurable database, allows for its easy deployment within existing and newly developed software tools. The paper presents examples illustrating the usage of PROV-man. The first example illustrates how to create and manipulate provenance data of an online newspaper article using PROV-man. The second example demonstrates and evaluates the PROV-man implementation in a more complex case for collection of provenance data about biomedical data analysis activities that are carried out using a distributed computing infrastructure.
Social media as a big public health data source: review of the international bibliography
Authors: Karamagioli Evika
Published: January 2018

Background: As the use of social media creates huge amounts of data, the need for big data analysis has to synthesize the information and determine which actions is generated. Online communication channels such as Facebook, Twitter, Instagram etc provide a wealth of passively collected data that may be mined for public health purposes such as health surveillance, health crisis management, and last but not least health promotion and education. Objective: We explore international bibliography on the potential role and perceptive of use for social media as a big data source for public health purposes. Method: Systematic literature review. Data extraction and synthesis was performed with the use of thematic analysis. Results: Examples of those currently collecting and analyzing big data from generated social content include scientists who are working with the Centers for Disease Control and Prevention to track the spread of flu by analyzing what user searches, and the World Health Organization is working on disaster management relief. But what exactly do we do with this big social media data? We can track real-time trends and understand them quicker through the platforms and processing services. By processing this big social media data, it is possible to determine specific patterns in conversation topics, users behaviors, overall trends and influencers, sociodemographic characteristics, lifestyle behaviors, and social and cultural constructs. Conclusion: The key to fostering big data and social media converge is process and analyze the right data that may be mined for purposes of public health, so as to provide strategic insights for planning, execution and measurement of effective and efficient public health interventions. In this effort, political, economic and legal obstacles need to be seriously considered.
Regional Internet-competition in English skills among Russian-speaking medical students: first experience
Authors: Mitrofanova Ksenia A. , Gavrilyuk Oksana A. , Chemezov Sergey A.
Published: January 2018

Currently being a highly qualified medical specialist means to be a member of an international medical society. One of the major resources to enter the international medical field is excellent English skills, as the English language has become a lingua franca in Medicine. Thus, our aim is to enhance students’ motivation to study English for professional purposes starting from the first year in the medical school. We organized the Internet competition in English skills among first-year students from two Russian medical schools (USMU in the Urals and KrasSMU in Siberia). The competition had three stages held during 30 days in November-December, 2014 via the Internet on the e-educational platforms of the universities. All tasks were related to medical profession. Overall 130 students took part in the competition doing the reading, listening and writing tasks at the first stage. The best 35 students continued their work at the second stage where they created a video on the topic “Health is not simply the absence of sickness”. Then 10 students were selected to participate in the final, which was held as a teleconference between the universities. The evaluation of students’ works was performed by competent English teachers. The results of the competition showed that medical students enthusiastically accepted new teaching methods developing their creativity. The first-year medical students expressed a desire for their involvement in unusual educational projects and were interested in studying English for professional purposes. Thus, we may include outstanding educational techniques in the studying process to keep medical students motivated and develop their individual skills and abilities. Moreover, such competitions promote better communication between the universities.
A systemic explanation of denial of pregnancy fitting clinical observations and previous models
Authors: Sandoz Patrick
Published: January 2018

Introduction: The etiology of denial of pregnancy remains poorly understood. Neither necessary nor sufficient conditions can be synthesized from the risk factors identified from psychological analyses. Furthermore, the involvement of mother-fetus interactions cannot result only from psychology causes in the mother. Although instructive, the few available evolutionary and systemic explanations proposed remain insufficient. This article synthesizes and extends previous knowledge within a systemic model which is fully compatible with clinical observations.

Methods: A systemic intrapersonal conflict theory opposing primitive, evolutionary-inherited forces to psycho-sociological forces embodied across individual’s childhood is developed.

Results: As members of a social species, human beings have a dual character of independent organisms and of social group members that is a source of customized intrapersonal conflicts. Authors explain denial of pregnancy as a standby-in-tension response to such an unresolved intrapersonal conflict between forand against-pregnancy forces. As long as the woman’s brain is unable to renounce one option in favor of the other, denial of pregnancy offers a standby-in-tension means to postpone conflict resolution. It may thus be considered as temporarily adaptive response.

Conclusions: The proposed systemic psycho-evolutionary explanation of denial of pregnancy is fully consistent with clinical observations. It brings into agreement the previously reported models with the advantage of being more synthetic. It is thus compatible with a large diversity of causative events in accordance with the actual life story of each woman concerned.

The systemic intrapersonal conflict approach developed herein provides a new means of investigating body-mind problems, especially pseudocyesis.
A comparison of two commercially available ELISA methods for the quantification of human plasma heat shock protein 70 during rest and exercise stress
Authors: Lee Ben J , Sukri Nursyuhada Mohd , Ogden Henry B , Vine Christopher , Thake Charles D , Turner James E , Bilzon James LJ
Published: January 2018

Background. This study compared resting and exercise heat/hypoxic-stress induced levels of plasma eHSP70 in humans using two commercially available ELISA kits. Methods. EDTA plasma samples were collected from 21 males during two separate investigations. Participants in Part A completed a 60 min treadmill run in the heat (HOT70; 33.0 ± 0.1 °C, 28.7 ± 0.8%, n = 6) at 70% V̇O2max. Participants in Part B completed 60 minutes of cycling exercise at 50% V̇O2max in either hot (HOT50; 40.5°C, 25.4 RH%, n = 7) or hypoxic (HYP50; FIO2 = 0.14, 21°C, 35% RH, n = 8) conditions. Samples were collected prior to and immediately upon termination of exercise and analysed for eHSP70 using EKS-715 high sensitivity HSP70 ELISA, and new ENZ-KIT-101 AMP’D™ HSP70 high sensitivity ELISA. Results. ENZ-KIT was superior in detecting resting eHSP70 (1.54 ± 3.27 ng.mL-1; range 0.08 to 14.01 ng.mL-1), with concentrations obtained from 100% of samples compared to 19% with EKS-715 assay. The ENZ-KIT requires optimisation prior to running samples in order to ensure participants fall within the standard curve, a step not required with EKS-715. Using ENZ-KIT, a 1:4 dilution allowed for quantification of resting HSP70 in 26/32 samples, with a 1:8 (n = 3) and 1:16 (n = 3) dilution required to determine the remaining samples. After exercise eHSP70 was detected in 6/21 and 21/21 samples using EKS-715 and ENZ-KIT respectively. eHSP70 was increased from rest after HOT70 (p < 0.05), but not HOT50 (p > 0.05) or HYP50 (p > 0.05) when analysed using ENZ-KIT. Conclusion. It is recommended that future studies requiring the precise determination of resting plasma eHSP70 use the ENZ-KIT (i.e., HSP70 Amp'd®ELISA) instead of the EKS-715 assay, despite additional assay development time and cost required.
Prioritization of potential policy actions to develop IT skills among healthcare workforce
Authors: Li Sisi , Bamidis Panagiotis D , Konstantinidis Stathis , Traver Vicente , Zary Nabil
Published: January 2018

Background: Health related information and communication technology is globally an important and growing sector. With the promise of more efficient and cost-effective care, eHealth is becoming a key priority to address the current challenges faced by health systems worldwide. Addressing IT skills for healthcare workforce is seen as an important element of achieving greater social inclusion.Objective: To identify the needs in the eHealth field across the EU health workforce and actions to improve the IT skills of healthcare professionals. In addition, to identify priorities among the identified actions. Methods: A diverse group of technical experts, representing different fields of expertise in healthcare and geographical locations across EU participated in the study. A scientific priority-setting methodology was used to systematically list and score actions that would improve IT skills among healthcare workforce. The participants evaluated the actions using several criteria: feasibility, effectiveness, deliverability, and maximum impact on IT skills improvement.Results: The actions that scored highest were related to appropriate training, integrating eHealth in curriculum, involving health workforce in the eHealth solution development, improving awareness of eHealth as well as learning arrangement. The actions that scored lowest related to the workforce management, identification of IT skills needed, joint funding for training program and training on potential workforce. Conclusion: To maintain a highly IT skilled health workforce, eHealth related knowledge and skills in current curricula, improving awareness of eHealth and continuous training according to the different professionals’ needs should be addressed. In addition, health professionals should be actively and continuously included in the development of eHealth solutions.
Prioritization of actions needed to develop IT skills among healthcare workforce
Authors: Li Sisi , Bamidis Panagiotis D , Konstantinidis Stathis , Traver Vicente , Zary Nabil
Published: January 2018

Background: Health related information and communication technology is globally an important and growing sector. With the promise of more efficient and cost-effective care, eHealth is becoming a key priority to address the current challenges faced by health systems worldwide. Addressing IT skills for healthcare workforce is seen as an important element of achieving greater social inclusion.Objective: To identify the actions needed to improve the IT skills of healthcare workforce across the EU. In addition, to identify priorities among the identified actions with collaboration of healthcare experts. Methods: A diverse group of technical experts, representing different fields of expertise in healthcare and geographical locations participated in the study. A scientific priority-setting methodology was used to systematically list and score actions that would improve IT skills among healthcare workforce. The participants evaluated the actions using several criteria: feasibility, effectiveness, deliverability, and maximum impact on IT skills improvement.Results: The actions that scored highest were related to appropriate training, integrating eHealth in curriculum, involving health workforce in the eHealth solution development, improving awareness of eHealth as well as learning arrangement. The actions that scored lowest related to the workforce management, identification of IT skills needed, joint funding for training program and training on potential workforce. Conclusion: To maintain a highly IT skilled health workforce, eHealth related knowledge and skills in current curricula, improving awareness of eHealth and continuous training according to the different professionals’ needs should be addressed. In addition, health professionals should be actively and continuously included in the development of eHealth solutions.
Why do women choose to start, continue or stop breastfeeding? a qualitative phenomenological interpretive analysis
Authors: Ryan Jessica , Norman Alyson
Published: January 2018

The statistics from the National Health Service in the United Kingdom show that despite the current advice to breastfeed an infant exclusively for the first six months of life, less than 1% of mothers are actually doing this. Therefore, it is important it understand the barriers to breastfeeding experiences by women. The study aimed to investigate why some women choose to continue breastfeeding their infant, whilst other women do not. A qualitative semi-structured approach was employed recruiting eight participants interviewed one-to-one and three participants via one mini focus group. It was decided to use a qualitative approach in order to understand the experiences of women who have breastfed. Ethical approval was received from University of Plymouth, Faculty of Health and Human Sciences. Data was analysed using interpretive phenomenological analysis. The analysis identified four main themes centred on; social and cultural expectations of women, the impact of breastfeeding on maternal role, the perceived impact of breastfeeding on the mother’s attachment to her infant, and finally, the information provision from health care professional involved throughout pregnancy and after. The study only employed 11 participants. It is hoped that this study can be extended in the future to better understand the experiences of a wider range of breastfeeding women. Increased support and resources are needed to support women through the early stages of breastfeeding. Women need more appropriate help and support from professionals to enable them to breast feed without undue pressure, particularly when breastfeeding becomes problematic. Future research should investigate when different forms of information provision should be provided.
PopAlu: population-scale discovery of Alu polymorphisms
Authors: Qian Yu , Kehr Birte , Halldórsson Bjarni V
Published: January 2018

Alu elements are sequences of approximately 300 basepairs that combined comprise more than 10% of the human genome. Due to their recent origin in primate evolution some Alu elements are polymorphic in humans, present in some individuals while absent in others. We present PopAlu, a tool to detect polymorphic Alu elements on a population scale from paired-end sequencing data. PopAlu uses read pair distance and orientation as well as split reads to identify the location and precise breakpoints of polymorphic Alus. Genotype calling enables us to differentiate between homozygous and heterozygous carriers, making the output of PopAlu suitable for use in downstream analyses such as genome-wide association studies (GWAS). We show on a simulated dataset that PopAlu calls Alu elements inserted and deleted with respect to a reference genome with high accuracy and high precision. Our analysis of real data of a human trio from the 1000 Genomes Project confirms that PopAlu is able to produce highly accurate genotype calls. To our knowledge, PopAlu is the first tool that identifies polymorphic Alu elements from multiple individuals simultaneously, pinpoints the precise breakpoints and calls genotypes with high accuracy.
A cost-efficient novel live-trap for demographic studies of small mammals
Authors: Locasciulli Osvaldo , Milana Giuliano , Rocchi Flavio , Luiselli Luca , Amori Giovanni
Published: January 2018

A new live-trap (named LOT trap) for small mammals is described herein. This trap is easily built and is considerably cheaper than commercial traps. The trap body is made of a PVC 8x8 cm pipe, with a tin door and a transparent plexiglas back door. The efficacy of this trap was tested in an experimental field study, and the results are presented and discussed. Capture rates were significantly different between types of trap, with 81.6% of captured rodents for LOT and 18.4% of rodents for multiple-capture traps.
A multi prototype classification algorithm and its application to multi class diagnostics
Authors: Ziller Mario
Published: January 2018

This paper introduces a novel, universal distance-based classification procedure. It is based on a simple geometric model. Considering all objects as points in a metric space, a class is imagined as covered by potentially differentsized hyperspheres, the centres of which are referred to as prototypes. The radii of the hyperspheres are individually optimised by a generalised ROC-analysis. For the approximate solution of the entire discrete optimisation problem, a greedy algorithm was developed and implemented in R. It runs in O(k2∙n2∙log(n)) time where k is the number of prototypes to be selected and n the number of training objects. For application to multi class problems, one against all approach is performed. The diagnostic decision is finalised for that class of maximum positive predictive value when in doubt. Objects not recognised as a member of any of the classes are assigned to an additional residual class. The performance of the classification system presented is demonstrated on various data examples, and in comparison with other methods.
A redundancy-removing feature selection algorithm for nominal data
Authors: Li Zhihua
Published: January 2018

No order correlation or similarity metric exists in nominal data, and there will always be more redundancy in a nominal dataset, which means that an efficient mutual information-based nominal-data feature selection method is relatively difficult to find. In this paper, a nominal-data feature selection method based on mutual information without data transformation, called the redundancy-removing more relevance less redundancy algorithm, is proposed. By forming several new information-related definitions and the corresponding computational methods, the proposed method can compute the information-related amount of nominal data directly. Furthermore, by creating a new evaluation function that considers both the relevance and the redundancy globally, the new feature selection method can evaluate the importance of each nominal-data feature. Although the presented feature selection method takes commonly used MIFS-like forms, it is capable of handling high-dimensional datasets without expensive computations. We perform extensive experimental comparisons of the proposed algorithm and other methods using three benchmarking nominal datasets with two different classifiers. The experimental results demonstrate the average advantage of the presented algorithm over the well-known NMIFS algorithm in terms of the feature selection and classification accuracy, which indicates that the proposed method has a promising performance.
Education of IT skills for the healthcare workforce in EU-US: Analysis of opportunities
Authors: Traver Vicente , Konstantinidis Stathis , Bamidis Panagiotis , Zary Nabil
Published: January 2018

Physicians, nurses and other professionals interact with patients every day, and ICT, especially the internet, can enhance the communication processes among them, providing timely information to patients about disease prevention, health promotion, as well as treatment of diseases. ICT skills are: access to health science information, management of health information and knowledge, generation and dissemination of health knowledge. The development of these new ICT skills requires digital literate people.

Funded by the CAMEI EC funded project, a whitepaper has been produced, identifying some key recommendations about how USA organisations and communities can cooperate with EU organisations in order to empower sharing, reuse, repurposing and creation of educational material applied in different context and promote renewal of programmes.

After the analysis of opportunities about education of IT skills for the healthcare workforce in EU-US, authors conclude that:

- Common challenges and opportunities on providing IT skills for healthcare workforce have been identified, assessing the cooperation potential among the EU and the US.

- A benchmark in detail policy priorities of US on IT skills for Healthcare workforce and research sub-areas with those of EU (i2010, FP7-ICT strategic priorities, Horizon 2020) has been performed to help partners from the other side to be involved in joint related activities.

- Open Education and the creation of some educational frameworks have been identified as the means and the guidelines of sharing, re-using, and repurposing technologies of new educational material and programs for IT-skilled workforce in healthcare applied in the different context, different languages and cultures in the EU and US.

- A prominent base of cooperation where mutual benefits can be generated for both regions has been located, identifying key players from the EU and US.
Irrigation and avifaunal change in Coastal Northwest Mexico: Has irrigated habit attracted threatened migratory species?
Authors: Rohwer Sievert , Grason Emily W. , Navarro-Sigüenza Adolfo G
Published: January 2018

Irrigation in desert ecosystems can either reduce or increase species diversity. Groundwater pumping often lowers water tables and reduces natural wetlands, while canal irrigation often creates mesic habitat, resulting in great increases in avian diversity from irrigation. Here we use remotely-sensed data sets to show that 60% of the land in the coastal plain of southern Sonora and northern Sinaloa lying below 200m elevation has been converted by irrigation to more mesic habitats. We then use the record of bird specimens in the world’s museums from this same region of Mexico to examine the avian community before and after the development of extensive irrigation. In general these museum records show an increase in the abundance and diversity of breeding birds associated with mesic habitats. Although thorn forest birds have likely decreased in total numbers, most are common enough in the remaining thorn forest that collection records did not indicate their probable decline. Four migrants having most of their breeding ranges in the U.S. or Canada, Yellow-billed Cuckoo, Cliff Swallow, Bell’s Vireo, and Orchard Oriole, apparently have increased dramatically as breeders in irrigated habitats of NW Mexico. Because these species have decreased or even largely disappeared as breeding birds in parts of the U.S. or Canada, further research should assess whether their increases in new mesic habitats of NW Mexico are linked to their declines as breeding birds in Canada and the U.S. For Bell’s Vireo recent specimens from Sinaloa suggest its new breeding population in NW Mexico may be composed partly of the endangered Least Bell’s Vireo.
The fitness consequences of honesty: under-signalers have a survival advantage in song sparrows
Authors: Akçay Çağlar , Campbell S. Elizabeth , Beecher Michael D.
Published: January 2018

How honest or reliable signaling can evolve and be maintained has been a major question in evolutionary biology. The question is especially puzzling for a particular class of signals used in aggressive interactions: threat signals. Here we report a study on song sparrows (Melospiza melodia) in which we assayed males with playbacks on their territories to quantify their aggressiveness (flights and close proximity) and aggressive signaling levels (rates of soft song, a close range signal reliably predicting attack) and asked whether these traits affect individuals’ survival on territory. We found that the effect of aggressive signaling via soft song interacted with aggressive behaviors such that there was a negative correlational selection: among males with low aggression, those males that signaled at higher levels (over-signalers) had higher survival whereas among males with high aggression those that signaled at low levels (under-signalers) survived longer. In other words, males who deviate from reliable signaling have a survival advantage. These results, along with previous research that suggested most of the deviation from reliable signaling in this system is in the form of under-signaling (high aggression males signaling at low levels) pose a puzzle for future research on how this reliable signaling system is maintained.
Goal-oriented evaluation of species distribution models’ accuracy and precision: True Skill Statistic profile and uncertainty maps
Authors: Ruete Alejandro , Leynaud Gerardo C
Published: January 2018

The use of species distribution models’ (SDM) is limited by its performance in terms of accuracy, precision, or the spatial distribution of model errors. Despite the wide acceptance of some standard statistics used to evaluate SDM, there is currently a strong on-going debate as to their use. The “area under the curve” (AUC) is a popular measure used to evaluate SDMs; however, it does not provide complete information about model accuracy. The maximum True Skill Statistic (TSS) is another statistic that is gaining acceptance. However, evaluations of a model’s accuracy solely based on this statistic may also be misleading. We investigate the use of alternative methods to evaluate the performance of SDMs, to objectively compare among different modelling approaches. We evaluate the performance of SDMs fitted to simulated and real data by contrasting model predictions to additional validation datasets. We propose visualising TSS scores over the whole detection threshold range (TSS profile). We show how models with similarly good performance according to AUC, present very different results and may serve to different purposes. Also, a high maximum TSS may not guarantee accurate predictions and should be accompanied by the threshold where the maximum is reached (t*). We observe that the higher t* the better predicted observations correlate with confirmed observations. Also, SDM predictions should be accompanied with the corresponding uncertainty map to avoid misleading conclusions. Too high or too widely spread uncertainty on such maps would question the overall accuracy of the model. Whether the model is intended to detect all potential observation sites (sensitive model) or to accurately predict where confirmed observations could be found (specific model) sets a different performance targets to be achieved by the model. The approach proposed helps to discern which SDM may best suit the intended goals. Furthermore, the TSS profile helps i) to evaluate the overall performance of SDMs and compare among them, ii) to identify the main source of error, and iii) to select a detection threshold depending on the maps intended use.
Swarm v2: highly-scalable and high-resolution amplicon clustering
Authors: Mahé Frédéric , Rognes Torbjørn , Quince Christopher , de Vargas Colomban , Dunthorn Micah
Published: January 2018

Previously we presented Swarm v1, a novel and open source amplicon clustering program that produced fine-scale molecular operational taxonomic units (OTUs), free of arbitrary global clustering thresholds and input-order dependency. Swarm v1 worked with an initial phase that used iterative single-linkage with a local clustering threshold (d), followed by a phase that used the internal abundance structures of clusters to break chained OTUs. Here we present Swarm v2 that has two important novel features: 1) a new algorithm for d = 1 that allows the computation time of the program to scale linearly with increasing amounts of data; and 2) the new fastidious option that reduces under-grouping by grafting low abundant OTUs (e.g., singletons and doubletons) onto larger ones. Swarm v2 also directly integrates the clustering and breaking phases, dereplicates sequencing reads with d = 0, outputs OTU representatives in fasta format, and plots individual OTUs as two-dimensional networks.
Buyanghuanwu decoction inhibited TLR4-induced activation of nuclear factor-kappa B in acute carbon monoxide poisoning rats
Authors: Li Weirong , Wang Xiuwei , Guan Zhen , Zheng Yufei , Zhang Xiaodong , Shi Jing , Niu Bo
Published: January 2018

Acute carbon monoxide poisoning (ACMP) is one of the most common types of poisoning worldwide, and may result in delayed encephalopathy, however, its pathogenesis remains obscure and there is no optimal treatment strategy for the patients with ACMP. Here, we developed the ACMP rat model to observe the protective effects of Buyanghuanwu decoction (BYHWD) on hippocampal neuron. BYHWD (per 5 g/kg) were intragastric administration to rats twice each day for 28 days after ACMP. In ACMP + BYHWD group rats, the neuronal injury in the hippocampal region was significantly less than that of ACMP group’s. BYHWD of intragastric administration also markedly decreased the expression of the TLR4, MyD88, NF-κB P65 after acute carbon monoxide poisoning (P<0.05). TNF-α、IL-1β protein level in ACMP + BYHWD group was lower than that of ACMP group (P<0.05). Our results suggested that decreased the activation of TLR4- NF-κB signal pathway due to BYHWD may partially account for its effect of neuroprotection standing against ACMP, and inhibited the inflammatory reaction to promote the ability recovery of learning and memory in ACMP rats.
Song characteristics of Oriental Cuckoo Cuculus optatus and Himalayan Cuckoo Cuculus saturatus and implications for taxonomy and distribution
Authors: Xia Canwei , Liang Wei , Carey Geoff J , Zhang Yanyun
Published: January 2018

Song features during the breeding season are important for determining classifications. Whether Oriental Cuckoo Cuculus optatus and Himalayan Cuckoo C. saturatus inhabiting the Palearctic and Oriental realms respectively can be distinguished according to song characteristics is uncertain. In this study, we performed a thorough investigation of the song characteristics of these taxa by collecting and analyzing recordings of song in their areas of distribution. We found that these cuckoos could be divided into two groups based on the number of notes in their songs. In addition, we observed significant differences in song duration and frequencies such that these two species could be clearly distinguished based on discriminant analysis of song features. Songs of Oriental cuckoos had two notes, whereas songs of Himalayan cuckoos had more than two notes. Thus, our data supported the separation of the two species based on their song features. The areas of distribution of the two species are thus refined, with Oriental Cuckoo distributed in Northeast China, Xinjiang in northwest China, Japan and Russia, and Himalayan Cuckoo distributed in the Himalayas through central and northern China to northeast Hebei, and the northern part of southeast Asia (Guangxi, China). The taxonomic status of birds in Taiwan indicates a closer relationship to C. optatus, which is contrary to the prevailing interpretation and requires further study.