bluuebunny/crossref_metadata_2025 huggingface dataset:
Body and skull morphometric variations between two shovel-headed species of Amphisbaenia (Reptilia: Squamata) with morphofunctional inferences on burrowing
Authors: Hohl Leandro , Loguercio Mariana , Sicuro Fernando , Barros-Filho José , Rocha-Barbosa Oscar
Published: January 2018

Background. Morphological descriptions comparing Leposternon microcephalum and L. scutigerum are known. However, these taxa lack of a formal quantitative morphological characterization and comparison between their morphometric patterns. Studies suggest that morphology and burrowing performance seem to be related. For example, the robustness of the head in L. microcephalum is positively associated to the digging force. The excavatory movements of this species were described in detail. However, there is a lack of studies comparing locomotor patterns and/or performance among different amphisbaenids sharing the same skull pattern. Likewise, morphofunctional interpretations of the morphological variations are scarce. This paper presents the first study of comparative morphometric variations between two adaptively close amphisbaenid species,L. microcephalum and L. scutigerum, with functional inferences of fossorial locomotion efficiency.

Methods. Inter-specific morphometric variations were verified through statistical analyses of body and cranial measures of L. microcephalum and L. scutigerum specimens. Their burrowing activity was assessed through X-ray videoflouroscopy and then compared. The influence of morphological variations on the speed of the digging performance was tested among Leposternon individuals.

Results. Leposternon microcephalum and L. scutigerum are morphometrically distinct species. The first is shorter and robust with a wider head while the other is more elongated and slim with a narrower head. They seem to share the same excavatory movements. However, L. scutigerum presented higher averages for speed, travel distance and frequency of excavatory cycles, and lower values for cycle duration in relation to that found for L. microcephalum. The animals analyzed reached relatively high speeds, but individuals with narrower skulls dig faster. A negative correlation between the speed and the width of skull was determined, but not with total length or diameter of the body.

Discussion. The morphometric differences between L. microcephalum and L. scutigerum are in accord with morphological variations previously described. Since these species performed the same excavation pattern, we may infer that adaptively close amphisbaenids with the same skull type would exhibit the same excavatory pattern. The locomotor performance values suggested that L. scutigerum is a faster digger than L. microcephalum. Such differences are supported by morphometric and morphological features. The negatively correlation between head width and excavation speed is also observed in others fossorial squamates. The robustness of the skull is also related to compression force in L. microcephalum. Individuals with wider heads are stronger. Thus, we suggested trade-offs between excavation speed and compression force during burrowing activity for this species.
Antagonism and population dynamics of Acinetobacter baumannii from US military treatment centers
Authors: Heitkamp Rae A , Zale Amy M , Kirkup Benjamin C
Published: January 2018

Antibiotic-resistant bacteria complicate many infections and can be difficult to eradicate from hospitals. The population dynamics and ecology of these organisms in the hospital setting, however, is not well understood. Here, we report extensive strain-based antagonistic interactions occurring in military clinical isolates of Acinetobacter baumannii, a bacterial species that causes many drug-resistant hospital-associated infections. Sequence-based phylogenetic analysis of isolates allowed for differentiation to two major clades, with one of the clades representing two closely related genetic groups. Antagonistic activity was detected using a spot-plate assay to test pairwise interactions of all isolates. Isolates exhibited extensive and diverse patterns of antagonism against other isolates. One major clade of isolates had a distinct change in antagonism phenotype between isolates that differed by one base pair out of ~1500bp sequenced, with consistent antagonism of one group of isolates by the other. Both the antagonistic and the sensitive group exhibited extensive drug resistance. The first isolate of the antagonistic group was cultured in May 2010. The proportion of isolates from the antagonistic group collected before and after July 2010 increased from 2% to 76%. The results of this early study of the ecology of hospital-associated bacterial populations are discussed in the context of the species ecology of bacteria in natural environments. This work is a potential starting point for investigations into ecological interventions for infection control in hospitals.
How to conduct meta-analysis: a basic tutorial
Authors: Basu Arindam
Published: January 2018

Meta analysis refers to a process of integration of the results of many studies to arrive at evidence syn- thesis. Meta analysis is similar to systematic review; however, in addition to narrative summary that is conducted in systematic review, in meta analysis, the analysts also numerically pool the results of the studies and arrive at a summary estimate. In this paper, we discuss the key steps of conducting a meta analysis. We will discuss the steps of a simple meta-analysis with a demonstration of the key steps based on a published paper on meta-analysis and systematic review of the effectiveness of salt restricted diet on blood pressure control. This paper is a basic introduction to the process of meta-analysis. In subsequent papers in this series, we will show how you can conduct meta-analysis of diagnostic and screening studies, network meta analyses, and those of diagnostic and screening studies.
Littorally adaptive? Testing the link between habitat, morphology, and reproduction in the intertidal sculpin subfamily Oligocottinae (Pisces: Cottoidea)
Authors: Buser Thaddaeus J , Burns Michael D , López J. Andrés
Published: January 2018

While intertidal habitats are often productive, species-rich environments, they are also harsh and highly dynamic. Organisms that live in these habitats must possess morphological and physiological adaptations that enable them to do so. Intertidal fishes are generally small, often lack scales, and the diverse families represented in intertidal habitats often show convergence into a few general body shapes. However, few studies have quantified the relationship between phenotypes and intertidal living. Likewise, the diversity of reproductive traits and parental care in intertidal fishes has yet to be compared quantitatively with habitat. We examine the relationship of these characters in the sculpin subfamily Oligocottinae using a phylogenetic hypothesis, geometric morphometrics, and phylogenetic comparative methods to provide the first formal test of associations between fish phenotypes and reproductive characters with intertidal habitats. We show that the ability to live in intertidal habitats, particularly in tide pools, is likely a primitive state for Oligocottinae, with a single species that has secondarily come to occupy only subtidal habitats. Contrary to previous hypotheses, maximum size and presence of scales do not show a statistically significant correlation with depth. However, the maximum size for all species is generally small (250mm or less) and all show a reduction in scales, as would be expected for an intertidal group. Also contrary to previous hypotheses, we show that copulation and associated characters are the ancestral condition in Oligocottinae, with copulation most likely being lost in a single lineage within the genus Artedius. Lastly, we show that body shape appears to be constrained among species with broader depth ranges, but lineages that occupy only a narrow range of intertidal habitats display novel body shapes, and this may be associated with habitat partitioning, particularly as it relates to the degree of wave exposure.
Project level effects of gender on contribution evaluation on GitHub
Authors: Brokmeier Pascal
Published: January 2018

Distributed open source software development has largely turned to GitHub, a pull-based software development collaboration platform. Recent studies have deployed data science techniques on the large datasets available about millions of projects on GitHub. Some research has focused on pull request (PR) acceptance predictors and evidence was found of sexual discrimination among members. In this paper I analyzed the influence of gender on PR acceptance on a project level, comparing different popular projects regarding their discrimination factors. Several projects were identified that have significant differences between male and female PR acceptance rates.
bioPDFX: preparing PDF scientific articles for biomedical text mining
Authors: Bhargava Shitij , Kuo Tsung-Ting , Goyal Ankit , Kuri Vincent , Lin Gordon , Hsu Chun-Nan
Published: January 2018

Background. There is huge amount of full-text biomedical literatures available in public repositories like PubMed Central (PMC). However, a substantial number of the papers are in Portable Document Format (PDF) and do not provide plain text format ready for text mining and natural language processing (NLP). Although there exist many PDF-to-text converters, they still suffer from several challenges while processing biomedical PDFs, such as the correct transcription of titles/abstracts, segmenting references/acknowledgements, special characters, jumbling errors (the wrong order of the text), and word boundaries.

Methods. In this paper, we present bioPDFX, a novel tool which complements weaknesses with strengths of multiple state-of-the-art methods and then applies machine learning methods to address all issues above

Results. The experiment results on publications of Genome Wide Association Studies (GWAS) demonstrated that bioPDFX significantly improved the quality of XML comparing to state-of-the-art PDF-to-XML converter, leading to a biomedical database more suitable for text mining.

Discussion. Overall, the whole pipeline developed in this paper makes the published literature in form of PDF files much better suited for text mining tasks, while slightly improving the overall text quality as well. The service is open to access freely at URL: http://textmining.ucsd.edu:9000 . A list of PubMed Central IDs of the 941 articles (see Supplemental File 1) used in this study is available for download at the same URL. The instructions of how to run the service with a PubMed ID are described in Supplemental File 2.
Secure trustless text processing of sensitive documents
Authors: Coelho Flávio C , Cuconato Bruno
Published: January 2018

Scaling up the analysis of sensitive or confidential documents frequently stumbles on the limited number of individuals with the necessary clearance to access the documents. The availability of cryptographic protocols compatible with text processing methods can greatly improve this situation allowing for the automated processing of large corpora of confidential documents by ``untrusted'' third-parties. In this paper we propose a protocol which allows for secure outsourcing of text analytics tasks without compromising the confidentiality of documents. The method scales to large corpora, and presents linear time complexity on the size of the corpus.
A hybrid-hierarchical genome assembly strategy to sequence the invasive golden mussel Limnoperna fortunei
Authors: Uliano da Silva Marcela , Dondero Francesco , Otto Thomas , Costa Igor , Lima Nicholas CB , Americo Juliana A , Mazzoni Camila , Prosdocimi Francisco , Rebelo Mauro F
Published: January 2018

Background: For more than 25 years the golden mussel Limnoperna fortunei has been an aggressive invader in South America freshwaters, having travelled more than 5,000 km upstream across 5 countries. The mussel has outcompeted native species in the invaded environments and since chemicals in the water have been unable to control infestation in closed environments, it has economically harmed aquaculture, hydroelectric generation and ship transit. We sequenced the complete genome of the golden mussel to try to understand the molecular basis of its invasiveness and search for ways to control it. Findings: We have assembled the 1.6 Gb genome into 20548 scaffolds with a N50 length of 312 Kb using a hybrid and hierarchical assembly strategy from short and long DNA reads and transcriptomes. A total of 60717 coding genes were inferred from a customized transcriptome-trained AUGUSTUS run. We also compared predicted protein sets with those of complete molluscan genomes, revealing an exacerbation of protein-binding domains in L. fortunei. Conclusions: We assembled one of the best bivalve genomes available using a cost-effective approach using Illumina pair-end, mate pair and PacBio long reads. We expect the continuous and careful annotation of L. fortunei’s genome to aid to the investigation of bivalve genetics, evolution and invasiveness, as well as the development of biotechnological tools for aquatic pest control.
Diversity, abundance, and host relationships in the avian malaria community of New Mexico pine forests
Authors: Marroquin-Flores Rosario A. , Williamson Jessie L. , Chavez Andrea N. , Bauernfeind Selina M. , Baumann Matthew J. , Gadek Chauncey R. , Johnson Andrew B. , McCullough Jenna M. , Witt Christopher C. , Barrow Lisa N.
Published: January 2018

Avian malaria parasites (genera Haemoproteus, Plasmodium, and Leucocytozoon) affect bird demography, distribution limits, and community structure, yet most bird communities and populations remain unsurveyed. We conducted a community-level survey of these vector-transmitted parasites in New Mexico, USA, to describe the diversity, abundance, and host associations. We focused on the breeding-bird community in the transition zone between piñon-juniper woodland and ponderosa pine forests (elevational range: 2150–2460 meters). We screened 186 birds representing 49 species using both standard PCR and microscopy techniques to detect infections of all three avian malaria genera. The combined infection rate was 36.6%, with the highest infection rate for Haemoproteus (20.9%), followed by Leucocytozoon (13.4%), then Plasmodium (8.0%). We sequenced mtDNA for 77 infections representing 43 haplotypes (25 Haemoproteus, 12 Leucocytozoon, 6 Plasmodium). When compared to all previously known lineages in the MalAvi and GenBank databases, 65% (28) of the haplotypes that we recovered were novel. We found evidence for host specificity at the avian clade and species level, but this specificity was variable among parasite genera. Haemoproteus and Leucocytozoon were each restricted to three avian host-clades or groups (out of six), while Plasmodium occurred in all groups except non-passerines. We found striking variation in infection rate among host species, with nearly universal infection among vireos and no infection among nuthatches. Using rarefaction and extrapolation, we estimated the total avian malaria diversity to be 70 haplotypes (95% CI: 43–98); thus, we may have already sampled ~60% of the diversity of avian malaria in New Mexico pine forests. It is possible that future studies will find higher diversity in microhabitats or host species that are under-sampled or unsampled in the present study. Fortunately, this study is fully extendable via voucher specimens, frozen tissues, blood smears, parasite images, and documentation provided in open-access databases (MalAvi, Genbank, and ARCTOS).
Disguised executable files in spear-phishing emails: Detecting the point of entry in advanced persistent threat
Authors: Ghafir Ibrahim , Hammoudeh Mohammad , Prenosil Vaclav
Published: January 2018

Advanced Persistent Threat (APT) is one of the most serious types of cyber attacks, which is a new and more complex version of multi-step attack. Within the APT life cycle, the most common technique used to get the point of entry is spear-phishing emails which may contain disguised executable files. This paper presents the disguised executable file detection (DeFD) module, which aims at detecting disguised exe files transferred over the connections. The detection is based on a comparison between the MIME type of the transferred file and the file name extension. This module was experimentally evaluated and the results show successful detection of disguised executable files.
Can editors protect peer review from bad reviewers?
Authors: D'Andrea Rafael , O'Dwyer James P
Published: January 2018

Peer review is the golden standard for scientific communication, but its ability to guarantee the quality of published research remains difficult to verify. Recent modeling studies suggest that peer review is sensitive to misbehavior by reviewers, and it has been claimed that referees who sabotage work they perceive as competition may severely undermine the quality of publications. Here we examine which aspects of suboptimal reviewing practices most strongly impact quality, and test different mitigating strategies that editors may employ to counter them. We find that the biggest hazard to the quality of published literature is not selfish rejection of high-quality manuscripts but indifferent acceptance of low-quality ones. Blacklisting bad reviewers and consulting additional reviewers to settle disagreements can reduce but not eliminate the impact. The other editorial strategies we tested do not significantly improve quality, but pairing manuscripts to reviewers unlikely to selfishly reject them and allowing revision of rejected manuscripts minimize rejection of above-average manuscripts. In its current form, peer review offers few incentives for disinterested reviewing efforts. Editors can help, but structural changes are more likely to have a stronger impact.
Transitioning “Open Data” from a NOUN to a VERB
Authors: varma D Aadinarayana , Sharma Sheevendra
Published: January 2018

Research assessment is the process or a metric which aims to assess the impact of the research study. The assessment may include the process that aims in evaluating the quality or intellect of a researcher given the notion that qualified scientists are more productive and may drive quality research in the process of Scholarly Communications. Over time, we have become used to equating the quality of the research with the quality or performance of the researcher. The emphasis over publications may encourage unethical practices, Which may be extrapolated to the evolution of problems like, Irreproducibility, Scientific fraud. Over the past century, a myriad of activities has been undertaken or are still being taken to improve the ways by which research can be assessed. Beginning with the first evolution of the Impact Factor and more recently other, Citation metrics, Altmetrics, etc. have resulted from this work. In this article, we discuss around the myriad of strategies that may play a significant role in the cultural transition of Science and Scientists that is still ongoing. And also highlight the reasons why we should not only look at research assessment but should also be keen on researcher evaluations and differentiate them from one another. Reflecting this, the title of the article signals how the strategies that researchers may need to consider might impact the way they interact with the Open Data movement.
Fighting fungi with fungi: the mycobiome contribution to emerging disease in amphibians
Authors: Kearns Patrick , Fischer Sarah , Fernández-Beaskoetxea Saioa , Gabor Caitlin , Bosch Jaime , Bowen Jennifer L , Tlusty Michael F , Woodhams Douglas
Published: January 2018

Emerging infectious diseases caused by fungal taxa are increasing and are placing a substantial burden on economies and ecosystems worldwide. Of the emerging fungal diseases, chytridomycosis caused by the fungus Batrachochytrium dendrobatidis (hereafter Bd) is causing a global amphibian extinction. The host frog does have come internal innate immunity, as well as additional resistance through cutaneous microbial communities, leading to the development of probiotic bacterial therapies with mixed results. Unknown is the role of fungi in the protection against Bd infection, and as such, we examined the overlapping roles of bacterial and fungal microbiota in pathogen defense with a combination of high-throughput sequencing and culturing of symbiotic fungi from poison arrow frogs (Dendrobates sp.). Our analyses revealed that abundance of cutaneous fungi contributed more to pathogen defense (~45%), than bacteria (~10%) and these differed from environmental microbiota. Further, we demonstrated that a fungal probiotic therapy did not induce an endocrine-immune reaction in contrast to bacterial probiotics that stressed amphibian hosts and suppressed antimicrobial peptide responses, limiting their long-term colonization potential. Our results suggest that probiotic strategies against amphibian fungal pathogens should refocus on host-associated and environmental fungi such as Penicillium and member of the families Chaetomiaceae and Lasiosphaeriaceae.
Human agency beliefs influence behaviour during virtual social interactions
Authors: Caruana Nathan , Spirou Dean , Brock Jon
Published: January 2018

In recent years, with the emergence of relatively inexpensive and accessible virtual reality technologies, it is now possible to deliver compelling and realistic simulations of human-to-human interaction. Neuroimaging studies have shown that, when participants believe they are interacting via a virtual interface with another human agent, they show different patterns of brain activity compared to when they know that their virtual partner is computer-controlled. The suggestion is that users adopt an “intentional stance” by attributing mental states to their virtual partner. However, it remains unclear how beliefs in the agency of a virtual partner influence participants’ behaviour and subjective experience of the interaction. We investigated this issue in the context of a cooperative “joint attention” game in which participants interacted via an eye tracker with a virtual onscreen partner, directing each other’s eye gaze to different screen locations. Half of the participants were correctly informed that their partner was controlled by a computer algorithm (“Computer” condition). The other half were misled into believing that the virtual character was controlled by a second participant in another room (“Human” condition). Those in the “Human” condition were slower to make eye contact with their partner and more likely to try and guide their partner before they had established mutual eye contact than participants in the “Computer” condition. They also responded more rapidly when their partner was guiding them, although the same effect was also found for a control condition in which they responded to an arrow cue. Results confirm the influence of human agency beliefs on behaviour in this virtual social interaction context. They further suggest that researchers and developers attempting to simulate social interactions should consider the impact of agency beliefs on user experience in other social contexts, and their effect on the achievement of the application’s goals.
Tropical ash (Fraxinus udhei) invading Andean forest remnants in Northern South America
Authors: Saavedra-Ramírez Kelly A , Etter Andrés , Ramírez Alberto
Published: January 2018

Exotic invasive species represent a major driver of the loss of biological diversity and services provided by ecosystems globally. An important source of species becoming invasive are the commercial afforestation projects using fast growing and adaptable exotic species, which may become invasive impacting natural environments. The Tropical Ash (Fraxinus uhdei) native to México has been widely introduced for many decades to Colombia and other countries for timber, live fences and urban greening, is now common in many areas of the tropical mountains, and has been observed expanding into native forests in Colombia. This study explores the invasion of Tropical Ash in remnant Andean forests in Colombia, to understand the invasion pattern and the demographic structure of Tropical Ash. The analysis took into account biotic and physical factors, such as distance to the propagule source, vegetation cover types, and density of the understory and canopy cover. Although the reproductive strategy of the Tropical Ash is of “r” type with low survival rates, the results show evidence for an active process of invasion characterized by an aggregated distribution pattern. The study shows the existence of an interaction between the distance to the propagule source and the vegetation cover, which has an additive effect on the demographic structure of the population.
Fish Ontology framework for taxonomy-based fish recognition
Authors: Ali Najib M. , Khan Haris A. , Then Amy Y-Hui , Ving Ching Chong , Dhillon Sarinder Kaur
Published: January 2018

Life science ontologies play an important role in semantic web. In the fish and fisheries research field, it is imperative to have an ontology that can automatically provide information for biological objects annotations and links to relevant data pieces. As such, we introduce the Fish Ontology (FO), an automated classification architecture of existing fish taxa which provides taxonomic information of unknown fish based on metadata restrictions. It is designed to support knowledge discovery, providing semantic annotation of fish and fisheries resources, data integration, and information retrieval. The automated classification for unknown specimen is a feature not existing in other known ontologies covering fish species proﬁling and fisheries data. Examples of automated classification for major groups of fish are demonstrated, showing the inferred information by introducing several restrictions at the species or specimen level. The current version of FO has 1830 classes, includes widely used fisheries terminology, and models major aspects of fish taxonomy, grouping, and character. With more than 30,000 known fish species globally, the FO will be an indispensable tool for fish scientists and other interested users.
Region level risk factors for the Ebola virus disease in West Africa
Authors: Levy Benjamin , Odoi Agricola
Published: January 2018

Background. The Ebola Virus Disease (EVD) is a highly infectious disease that has claimed over 25,000 cases in the past 50 years. While many past outbreaks of EVD resulted in relatively few incidents, the 2014 outbreak in West Africa was the most deadly occurrence of EVD to date producing over 15,000 confirmed cases.

Objective. In this study we relate total confirmed case counts of EVD to predictor variables at the region level in Sierra Leone, Liberia, and Guinea.

Methods. We used a Poisson framework and negative binomial framework to relate the predictors to the outcome. A spatial analysis was conducted to further our understanding and help interpret results.

Results. Results indicate that the percent of the population living in urban areas, percent of household with a bad quality or no toilet, and percent of married men working in blue collar jobs protect against the transmission of EVD. Our study also shows that mean years of education contributes to increased case counts of the disease.

Conclusions. Each significant predictor are associated with the types of dynamics that either protect against, or exacerbate, the spread of EVD. While having limited contact with the bodily fluids of others, reduced person-to-person contact, and isolated population clusters protect against the spread of EVD, the types of daily interactions an educated individual will experience leads to higher incidence rates. This information can be used to identify potential transmission routes and prevent future outbreak of this deadly disease.
Indigenous Australian household structure: a simple data collection tool and implications for close contact transmission of communicable diseases
Authors: Vino Thiripura , Singh Gurmeet R , Davison Belinda , Campbell Patricia T , Lydeamore Michael , Robinson Andrew , McVernon Jodie , Tong Steven YC , Geard Nicholas
Published: January 2018

Households are an important location for the transmission of communicable diseases. Social contact between household members is typically more frequent, of greater intensity, and is more likely to involve people of different age groups than contact occurring in the general community. Understanding household structure in different populations is therefore fundamental to explaining patterns of disease transmission in these populations. Indigenous populations in Australia tend to live in larger households than non Indigenous populations, but limited data is available on the structure of these households, and how they differ between remote and urban communities. We have developed a novel approach to the collection of household structure data, suitable for use in a variety of contexts, which provides a detailed view of age,gender, and room occupancy patterns in remote and urban Australian Indigenous households. Here we report analysis of data collected using this tool, which quantifies the extent of crowding in Indigenous households, particularly in remote areas. We use this data to generate matrices of age-specific contact rates, as used by mathematical models of infectious disease transmission. To demonstrate the impact of household structure, we use a mathematical model to simulate an influenza-like illness in different populations. Our simulations suggest that outbreaks in remote populations are likely to spread more rapidly and to a greater extent than outbreaks in non-Indigenous populations.
Control study of short-term after effect in diving exposure related pulmonary ventilation function
Authors: Cheng Hua
Published: January 2018

Objective: Ventilation attenuation often happened in professional divers due to long-term cumulative effects in diving exercises. By case-control experiments, we observed the immediate effects of pulmonary ventilation before and after the exposure of 12m-depth underwater for 20 min to discuss the relationships between the short-term and long-time effects caused by diving environment.

Methods: Participants were randomly assigned into the Experimental Group (EG) who stayed for 20 min under 12-m water environment or the Control Group (CG) who stayed in hyperbaric chamber under the pressure of 2.2ATA. Pulmonary ventilation function parameters including VC, FVC, MVV and MV were detected respectively before and after hyperbaric exposure by the Spirometer. Immediate effects of pulmonary ventilation before and after diving were compared by paired t test to reveal the different influence caused by environmental pressure.

Results: The value of VC appears to rise while the MV, MVV were detected decreased after the exposure of 2.2ATA of environment pressure for 20min in the two groups. VC increased more significantly in the CG (t=-1.26, p=0.23) after hyperbaric exposure, that leads to the FEV1.0%t (=FEV1.0/VC %) increase in EG (t=-0.73, p=0.48) while decrease in CG (t=0.42, p=0.17). The same trend in VC, MV and MVV after high pressure exposure in the two groups mainly due to the effect of common factors –the pressure. In addition to the impact of the pressure itself, EG members also face diving related immersion effect, influence of diving equipment load and water under low temperature. The FVC is detected decreased in EG (t=1.21, P =0.25) while it increased in CG (t=-0.42, P =0.68)，but the differences are not significant and couldn’t affect the measured FEV1.0% (=FEV1.0/FVC %) values showed both increasing in EG(t=-1.48, P =0.16) and in CG(t=-0.23, P =0.82). The expiratory flow rate including PEF, FEF25-75, MEF75, MEF50 increased in EG (t are -0.72, -0.69, -0.87 and -0.36 respectively with P all greater than 0.05) while decreased in CG (t are 1.67, 0.50, 1.53 and 0.71 respectively with P all greater than 0.05). MEF25 is the expiratory flow index of not affected by respiratory muscle force and the measured values of MEF25 increased in the EG (t=-0.68, P =0.51) and in the CG (t=-0.36, P =0.72).

Conclusion: Water immersion and water temperature during diving exposure could cause and accelerate hemodynamic changes in pulmonary circulation induced pulmonary interstitial edema and led to the increase of external respiratory work. Instant effects of diving exposure in the study are quite consistent with the long-term cumulative effect of professional divers in previous research, which is FVC reduced because small airway become narrower. The results illustrate even the small depth of short-range diving exercise have definite influences on pulmonary ventilation, which mainly comes from the environmental factor but not the pressure increases.
De novo gene evolution: How do we transition from non-coding to coding?
Authors: Ruiz-Orera Jorge , Villanueva-Cañas José Luis , Blevins William , Albà M.Mar
Published: January 2018

Recent years have witnessed the discovery of protein–coding genes which appear to have evolved de novo from previously non-coding sequences. This has changed the long-standing view that coding sequences can only evolve from other coding sequences. However, there are still many open questions regarding how new protein-coding sequences can arise from non-genic DNA.

Two prerequisites for the birth of a new functional protein-coding gene are that the corresponding DNA fragment is transcribed and that it is also translated. Transcription is known to be pervasive in the genome, producing a large number of transcripts that do not correspond to conserved protein-coding genes, and which are usually annotated as long non-coding RNAs (lncRNA). Recently, sequencing of ribosome protected fragments (Ribo-Seq) has provided evidence that many of these transcripts actually translate small proteins. We have used mouse non-synonymous and synonymous variation data to estimate the strength of purifying selection acting on the translated open reading frames (ORFs). Whereas a subset of the lncRNAs are likely to actually be true protein-coding genes (and thus previously misclassified), the bulk of lncRNAs code for proteins which show variation patterns consistent with neutral evolution. We also show that the ORFs that have a more favorable, coding-like, sequence composition are more likely to be translated than other ORFs in lncRNAs. This study provides strong evidence that there is a large and ever-changing reservoir of lowly abundant proteins; some of these peptides may become useful and act as seeds for de novo gene evolution.
Quercivorol as a lure for the polyphagous and Kuroshio shot hole borers, Euwallacea spp. nr. fornicatus (Coleoptera: Scolytinae), vectors of Fusarium dieback
Authors: Dodge Christine , Coolidge Jessica , Cooperband Miriam , Cossé Allard , Carrillo Daniel , Stouthamer Richard
Published: January 2018

The polyphagous shot hole borer and Kuroshio shot hole borer, two members of the Euwallacea fornicatus species complex (Coleoptera: Curculionidae: Scolytinae), are invasive ambrosia beetles that harbor distinct species of Fusarium fungal symbionts. Together with the damage caused by gallery construction, these two phytopathogenic Fusarium species are responsible for the emerging tree disease Fusarium dieback, which affects over 50 common tree species in Southern California. Host trees suffer branch dieback as the xylem is blocked by invading beetles and fungi, forcing the costly removal of dead and dying trees in urban areas. The beetles are also threatening natural riparian habitats, and avocado is susceptible to Fusarium dieback as well, resulting in damage to the avocado industries in California and Israel. Currently there are no adequate control mechanisms for shot hole borers. This paper summarizes efforts to find a suitable lure to monitor shot hole borer invasions and dispersal. Field trials were conducted in two counties in Southern California over a span of two years. We find that the chemical quercivorol is highly attractive to these beetles, and perform subsequent field experiments attempting to optimize this lure. We also explore other methods of increasing trap catch and effects of other potential attractants, as well as the deterrents verbenone and piperitone.
Estimating the number of lionfish (Pterois volitans) that colonized the Atlantic Ocean
Authors: Selwyn Jason D , Johnson John E , Downey-Wall Alan M , Bynum Adam M , Hamner Rebecca M , Hogan J Derek , Bird Christopher E
Published: January 2018

The invasion of the western Atlantic Ocean by the Indo-Pacific red lionfish (Pterois volitans) has had devastating consequences for marine ecosystems. Estimating the number of colonizing lionfish can be useful in identifying the introduction pathway and can inform policy decisions aimed at preventing similar invasions. It is well-established that at least ten lionfish were initially introduced. However, that estimate has not faced statistical scrutiny and is based solely on the number of haplotypes in the maternally-inherited mitochondrial control region observed in samples from the western Atlantic Ocean. To rigorously estimate the number of lionfish introduced, we used a forward-time, Wright-Fisher, population genetic model of the mitochondrial control region in concert with a demographic life-history model to simulate the invasion. The colonization of the western North Atlantic and subsequent spread to the Caribbean and Gulf of Mexico were modeled as single introductions of 1-800 females, which should conservatively estimate the most likely number of colonizing lionfish relative to a model with multiple introductions. Assuming a balanced sex ratio and no Allee effects, the simulations indicate that the Atlantic population was most likely founded by 118 (54-514, 95% HPD) lionfish from the Indo-Pacific, the Caribbean by 84 (22-328, 95% HPD) lionfish from the Atlantic, and the Gulf of Mexico by at least 114 (no upper bound on 95% HPD) lionfish from the Caribbean. Considering the additional possibilities that (1) multiple Indo-Pacific populations colonized the Atlantic and (2) Allee effects (e.g. 50% reduction in fecundity) plagued the colonists, the most likely number of lionfish increased to 180 (88-416, 95% HPD). These results, in combination with all other published data, support the hypothesis that lionfish were introduced to the Atlantic via the aquarium trade, rather than shipping. The most parsimonious introduction pathway is a single release of lionfish in one location, but it seems likely that a combination of smaller and larger releases from a variety of aquarium trade stakeholders occurred near Miami, Florida. Efforts to prevent future invasions via the aquarium trade should focus on the education of stakeholders and the prohibition of release, with adequate rewards for compliance and penalties for violations.
DNA barcode-based survey of Trichoptera in the Crooked River reveals three new species records for British Columbia
Authors: Erasmus Daniel J , Yurkowski Emily A , Huber Dezene PW
Published: January 2018

Anthropogenic pressures on aquatic systems have placed a renewed focus on biodiversity of aquatic macroinvertebrates. By combining classical taxonomy and DNA barcoding we identified 39 species of caddisflies from the Crooked River, a unique and sensitive system in the southernmost arctic watershed in British Columbia. Our records include three species never before recorded in British Columbia: Lepidostoma togatum (Lepidostomatidae), Ceraclea annulicornis (Leptoceridae), and Cheumatopsyche harwoodi (Hydropsychidae). Three other specimens may represent new occurrence records and a number of other records seem to be substantial observed geographic range expansions within British Columbia.
Genome-wide survey of single-nucleotide polymorphisms reveals fine-scale population structure and signs of selection in the threatened Caribbean elkhorn coral, Acropora palmata
Authors: Durante Meghann D , Baums Iliana B
Published: January 2018

The advent of next-generation sequencing tools has made it possible to conduct fine-scale surveys of population differentiation and genome-wide scans for signatures of selection in non-model organisms. Such surveys are of particular importance in sharply declining coral species, since knowledge of population boundaries and signs of local adaptation can inform restoration and conservation efforts. Here, genome-wide surveys of single-nucleotide polymorphisms in the threatened Caribbean elkhorn coral, Acropora palmata, reveal fine-scale population structure and place the major barrier to gene flow that separates the eastern and western Caribbean populations between the Bahamas and Puerto Rico. The exact location of this break had been subject to discussion because two previous studies based on microsatellite data had come to differing conclusions. We investigate this contradiction by analyzing an extended set of 12 microsatellite markers including the five previously employed and discovered that one of the original microsatellite loci is apparently under selection. Exclusion of this locus reconciles the results from the SNP and the microsatellite datasets. Scans for outlier loci in the SNP data detected 12 candidate loci under positive selection. Together, these results suggest that restoration of populations should use local sources and utilize existing functional variation among populations in ex situ crossing experiments to improve stress resistance of this species.
Benchmarking viromics: An in silico evaluation of metagenome-enabled estimates of viral community composition and diversity
Authors: Roux Simon , Emerson Joanne B , Eloe-Fadrosh Emiley A , Sullivan Matthew B
Published: January 2018

Background. Viral metagenomics (viromics) is increasingly used to obtain uncultivated viral genomes, evaluate community diversity, and assess ecological hypotheses. While viromic experimental methods are relatively mature and widely accepted by the research community, robust bioinformatics standards remain to be established. Here we used in silico mock viral communities to evaluate the viromic sequence-to-ecological-inference pipeline, including (i) read pre-processing and metagenome assembly, (ii) thresholds applied to estimate viral relative abundances based on read mapping to assembled contigs, and (iii) normalization methods applied to the matrix of viral relative abundances for alpha and beta diversity estimates. Results. Tools specifically designed for metagenomes, specifically metaSPAdes and MEGAHIT, were the most effective at assembling viromes. Read pre-processing, such as partitioning, had virtually no impact on assembly output, but may be useful when hardware is limited. Viral populations with 2–5x coverage typically assembled well, whereas lesser coverage led to fragmented assembly. Strain heterogeneity within populations hampered assembly, especially when strains were closely related (average nucleotide identity, or ANI ≥ 97%) and when the most abundant strain represented < 50% of the population. Viral community composition assessments based on read recruitment were generally accurate when the following thresholds for detection were applied: (i) ≥ 10kb contig lengths to define populations, (ii) coverage defined from reads mapping at ≥ 90% identity, and (ii) ≥ 75% of contig length with ≥ 1x coverage. Finally, although data are limited to the most abundant viruses in a community, alpha and beta diversity patterns were robustly estimated (±10%) when comparing samples of similar sequencing depth, but more divergent (up to 80%) when sequencing depth was uneven across the dataset. In the latter cases, the use of normalization methods specifically developed for metagenomes provided the best estimates. Conclusions. These simulations provide benchmarks for selecting analysis cut-offs and establish that an optimized sample-to-ecological-inference viromics pipeline is robust for making ecological inferences from natural viral communities. Continued development to better accessing RNA, rare, and/or diverse viral populations and improved reference viral genome availability will alleviate many of viromics remaining limitations.
Meiotic Error-Correction: How sexual reproduction may facilitate a trans-generational repair mechanism that can bias meiotic gene conversion against new mutations and in favor of ancestral alleles
Authors: Reese Virgil
Published: January 2018

Highly conserved DNA (where selection has most consistently punished variation) is comprised of elements of life’s code where mutations pose an especially highly risk. Thus, any difference between homologous chromosomes in these regions can warn of a potentially dangerous mutation; yet this warning is of little use to an organism, unless it can find some way to discern which of the two strands (paternal or maternal) harbors the mutation. Sexual reproduction may be addressing this challenge. If a sexual organism can just pass on to its offspring the suspicion that a particular DNA variant has a 50% chance of being a mutation, this offspring’s separately derived homologous chromosome can serve as both an independent check, and a correction template. This Meiotic Error-Correction process could work as follows - During the close association of homologous chromosomes in synapsis, primordial germ cells create a trans-generational epigenetic signature at (or near) an isolated DNA variant, thereby marking as ‘suspect’ both [mutant and normal] alleles. After fertilization, when one of these two ‘suspect-alleles’ is paired with a new homolog (in the subsequent meiosis) any persisting heterozygosity will again indicate a potential mutation; but now the marked suspect-allele can be recognized as the likely culprit. If this suspect-allele acts to promote meiotic homologous strand exchange, the ensuing mismatch can be resolved by gene conversion biased in favor of the less-suspect allele from the new chromosome, thus removing this mutation from the new organism’s germline.
A Study on Immunological and Molecular Genetic Test Methods of Bacterial Sexually Transmitted Diseases Reagents
Authors: Kim Geun Soo , Kim San , Han Hye Youn , Kwon Eunji
Published: January 2018

Chlamydia trachomatis is usally isolated only from humans and is often infected together with other sexually transmitted diseases(STD). C. trachomatis is a serious disease which infects 500 million people per year globally and causes blindness in 7 to 9 million people per year due to continuous infection. Thus, it is urgent to develop (draft) guidelines on the test methods for performance evaluation of medical devices for in vitro diagnosis of bacterial STD(C. trachomatis) based on molecular diagnosis. In this study, in reference to the U.S. FDA Guidance, has derived essential methods for testing performance which are applicable to medical device for in vitro diagnosis of bacterial STD which are used in the field of melecular diagnosis. Because of the establish of the test method for performance evaluation of medical devices, it could provide consistent performance evaluation standards for the approval and examination of products, promote the improvement of the quality and safety of products. This will contribute to the development of the quality and safety of products. This will contribute to the development of medical device for in vitro diagnosis in Korea
Taxonomy is not beholden to its dependencies: a rebuttal to Garnett and Christidis (2017)
Authors: Jackson Morgan D. , Scherz Mark D. , Zona Scott
Published: January 2018

Garnett and Christidis (2017) slammed taxonomy for hampering conservation. They painted a picture of capricious taxonomists arbitrarily creating or dismissing species and claimed “the scientific community's failure to govern taxonomy threatens the effectiveness of global efforts to halt biodiversity loss, damages the credibility of science, and is expensive to society”. We reject their premise that taxonomy is but a service in need of governance, rather than an independent—and foundational—scientific discipline.