bluuebunny/crossref_metadata_2025 huggingface dataset:
Photosynthesis is not a universal feature of the phylum Cyanobacteria
Authors: Soo Rochelle M , Skennerton Connor T , Sekiguchi Yuji , Imelfort Michael , Paech Samuel J , Dennis Paul G , Steen Jason A , Parks Donovan H , Tyson Gene W , Hugenholtz Philip
Published: January 2018

Molecular surveys of aphotic habitats have indicated the presence of major uncultured lineages phylogenetically classified as members of the Cyanobacteria. One of these lineages has recently been proposed as a non-photosynthetic sister phylum to the Cyanobacteria, the Melainabacteria, based on recovery of standard draft population genomes from human gut and groundwater samples. Here, we expand the phylogenomic representation of the Melainabacteria through sequencing of six diverse population genomes from gut and bioreactor samples supporting the inference that this lineage is non-photosynthetic, but not the assertion that they are strictly fermentative. We propose that the Melainabacteria is a class within the phylogenetically defined Cyanobacteria based on robust monophyly and shared ancestral traits with photosynthetic representatives. Our findings are consistent with theories that photosynthesis occurred late in the Cyanobacteria and involved extensive lateral gene transfer, and refutes the long held belief that oxygenic photosynthesis is a universal feature of this phylum.
Self-concept in poor readers: a systematic review protocol
Authors: McArthur Genevieve M , Francis Deanna , Caruana Nathan , Boyes Mark E , Badcock Nicholas A
Published: January 2018

Individuals with poor reading ability are at greater risk of educational and occupational difficulties. In addition to this, these individuals are also at greater risk of poor health outcomes, particularly mental health. At least some of this association may be underpinned by poor self-concept; however, the evidence for this relationship is mixed. In this systematic review protocol, we outline an approach to adjudicate between three reasons for these mixed results: (1) poor reading is more closely associated with some types of self-concept than others; (2) low self-concept is more closely associated with some types of poor reading than others; and (3) low self-concept is not associated with poor reading per se, but is associated with co-morbid problems with language or attention. The protocol proposes a review (based on PRSIMA-P guidelines) to use the existing literature to explore the evidence for these possibilities to better understand the association between poor reading and low self-concept.
SymPy: Symbolic computing in Python
Authors: Meurer Aaron , Smith Christopher P , Paprocki Mateusz , Čertík Ondřej , Kirpichev Sergey B , Rocklin Matthew , Kumar AMiT , Ivanov Sergiu , Moore Jason K , Singh Sartaj , Rathnayake Thilina , Vig Sean , Granger Brian E , Muller Richard P , Bonazzi Francesco , Gupta Harsh , Vats Shivam , Johansson Fredrik , Pedregosa Fabian , Curry Matthew J , Terrel Andy R , Roučka Štěpán , Saboo Ashutosh , Fernando Isuru , Kulal Sumith , Cimrman Robert , Scopatz Anthony
Published: January 2018

SymPy is an open source computer algebra system written in pure Python. It is built with a focus on extensibility and ease of use, through both interactive and programmatic applications. These characteristics have led SymPy to become the standard symbolic library for the scientific Python ecosystem. This paper presents the architecture of SymPy, a description of its features, and a discussion of select domain specific submodules. The supplementary materials provide additional examples and further outline details of the architecture and features of SymPy.
Considerations of context and scale when using fecal glucocorticoids to indicate stress in large mammals: a study of wild American plains bison
Authors: Ranglack Dustin H , Neuman-Lee Lorin A , French Susannah S , du Toit Johan T
Published: January 2018

Non-invasive measures of the stress response are used to understand the impacts of natural and anthropogenic disturbances on wild animals. They can, however, be challenging to interpret without additional contextual information and specifics of the animals in question. Here, we used fecal samples collected from the Henry Mountains bison herd in Utah to measure the glucocorticoid hormone corticosterone (CORT), which is indicative of stress. We compared site-specific measures of fecal CORT concentration with measures of covariates related to geography (elevation, slope, aspect, distance to roads, distance to water, food quality, habitat type, season), bison physiology (body condition, parasite load, sex), and human activity (traffic volume at multiple time scales, hunting seasons). Our aim was to determine whether an unexpected habitat selection pattern could be a response to human disturbance, and thus whether ecological covariates could explain variations in fecal CORT concentration in free-ranging bison. No meaningful relationships were found for any of the covariates included in the study. At least some of those covariates should be related to the stress state of the herd, but in large and highly mobile species such as bison there is a scale mismatch between the physiological stress response of an animal and the spatiotemporal distribution of fresh feces left on the landscape. We offer our assessment of fecal CORT in bison as a case study demonstrating the utility and complications associated with using fecal indicators of stress in wildlife populations.
The HOSPITAL score as a predictor of 30 day readmission in a university affiliated community hospital
Authors: Robinson Robert
Published: January 2018

Introduction Hospital readmissions are common, expensive, and a key target of the Medicare Value Based Purchasing (VBP) program. Risk assessment tools have been developed to identify patients at high risk of hospital readmission so they can be targeted for interventions aimed at reducing the rate of readmission. One such tool is the HOSPITAL score that uses 7 readily available clinical variables to predict the risk of readmission within 30 days of discharge. The HOSPITAL score has been internationally validated in large academic medical centers. This study aims to determine if the HOSPITAL score is similarly useful in a moderate sized university affiliated hospital in the midwestern United States. Materials and Methods All adult medical patients discharged from the SIU-SOM Hospitalist service from Memorial Medical Center from October 15, 2015 to March 16, 2016, were studied retrospectively to determine if the HOSPITAL score was a significant predictor of hospital readmission within 30 days. Results During the study period, 998 discharges were recorded for the SIU-SOM Hospitalist service. The analysis includes data for the 963 patients who were discharged alive. Of these patients, 118 (12%) were readmitted to the same hospital within 30 days. The patients who were readmitted were less likely to have a length of stay greater than or equal to 5 days (45% vs. 59%, p = 0.003) but were more likely to have been admitted to the hospital within the last year. A receiver operating characteristic evaluation of the HOSPITAL score for this patient population shows a C statistic of 0.762 (95% CI 0.720 - 0.805), indicating good discrimination for hospital readmission. Kaplan-Meier analysis of 30-day readmission free survival showed a significant (p < 0.001) increase in the risk of readmission in patients with a HOSPITAL score of 5 or more. Discussion This single center retrospective study indicates that the HOSPITAL score has good discriminatory ability to predict hospital readmissions within 30 days for a medical hospitalist service a university-affiliated hospital. This data for all causes of hospital readmission is comparable to the discriminatory ability of the HOSPITAL score in the international validation study (C statistics of 0.72 vs. 0.762) conducted at considerably larger hospitals (975 average beds vs 507 at Memorial Medical Center) for potentially avoidable hospital readmissions. Higher risk patients, identified as having a HOSPITAL score of 5 or more, clearly show an increased risk of hospital readmission within 30 days. Conclusions The internationally validated HOSPITAL score may be a useful tool in moderate sized community hospitals to identify patients at high risk of hospital readmission within 30 days. This easy to use scoring system using readily available data can be used as part of interventional strategies to reduce the rate of hospital readmission.
Development of a bacterial culture medium from avocado seed waste
Authors: Tzintzun-Camacho Olivia , Sánchez-Segura Lino , Minchaca-Acosta Alexis Z , Rosales-Colunga Luis M , Hernández-Orihuela Ana L , Martínez-Antonio Agustino
Published: January 2018

Avocado (Persea americana Mill) seeds, a rich source of starch and micronutrients, are a major waste product from the agroindustrial processing of avocados. Here we designed and developed an experimental culture medium (ECM) from hydrolysed avocado seeds, supplemented with M9 salts (10% v/v). Breaking of starch granules of avocado seeds due to hydrolysis treatments was analysed by morphology and morphometry of granules. We evaluated the ECM functionality by measuring the growth of Escherichia coli as affected by (i) the carbon source (reducing sugars concentration), (ii) the nitrogen source, and (iii) mixing and aeration in a stirred tank bioreactor. ECM containing 13.33 and 20 g/L of reducing sugars reached a biomass production of 1.75 and 2.22 gDCW/L, respectively. The biomass yield from ECM was at least 2.5-fold higher than that obtained using Luria-Bertani Broth (LB) medium (0.23 vs 0.09). In addition, the growth rate increased with the agitation velocity (0.44 h-1 at 200 rpm; 0.36 h-1 at 150 rpm). Our findings suggest that avocado seeds represent a cost-effective material for producing a sustainable culture medium for bacterial growth of E. coli and other strains of interest in biotechnological processes.
Meter scale variation in shrub dominance and soil moisture structure Arctic arthropod communities
Authors: Hansen Rikke Reisner , Hansen Oskar Liset Pryds , Bowden Joseph J , Treier Urs A , Normand Signe , Høye Toke
Published: January 2018

The Arctic is warming at twice the rate of the rest of the world. This impacts Arctic species both directly, through increased temperatures, and indirectly, through structural changes in their habitats. Species are expected to exhibit idiosyncratic responses to structural change, which calls for detailed investigations at the species and community level. Here, we investigate how arthropod assemblages of spiders and beetles respond to variation in habitat structure at small spatial scales. We sampled transitions in shrub dominance and soil moisture between three different habitats (fen, dwarf shrub heath, and tall shrub tundra) at three different sites along a fjord gradient in southwest Greenland, using yellow pitfall cups. We identified 2547 individuals belonging to 47 species. We used species richness estimation, indicator species analysis and latent variable modeling to examine differences in arthropod community structure in response to habitat variation at local (within site) and regional scales (between sites). We estimated species responses to the environment by fitting species-specific generalized linear models with environmental covariates. Species assemblages were segregated at the habitat and site level. Each habitat hosted significant indicator species, and species richness and diversity were significantly lower in fen habitats. Assemblage patterns were significantly linked to changes in soil moisture and vegetation height, as well as geographic location. We show that meter-scale variation among habitats affects arthropod community structure, supporting the notion that the Arctic tundra is a heterogenous environment. To gain sufficient insight into temporal biodiversity change, we require studies of species distributions detailing species habitat preferences.
Enhancing physical activity on the dance floor through a mobile phone application
Authors: Ly Kien Hoa , Beauchamp Daniel , Andersson Gerhard
Published: January 2018

Research indicates that there is a potential for persuasive technologies to be used as a means for increasing physical activity. In this exploratory work, we developed a mobile web application to gather movement data to explore the potential of a health tool in the context of a dance floor to promote physical activity. We wanted to explore if the mobile application in combination with the context and mechanisms seen in other health applications could drive physical activity. In total, 208 participants generated 20,279 data points through the mobile application on the dance floor. The result from this work points out that the concept should be further investigated in more studies.
In situ effects of simulated overfishing and eutrophication on settlement of benthic coral reef invertebrates in the Central Red Sea
Authors: Jessen Christian , Voolstra Christian R. , Wild Christian
Published: January 2018

In the Central Red Sea, relatively pristine coral reefs meet intense coastal development, but data on the effects of related stressors for reef functioning are lacking. This in situ study therefore investigated the independent and combined effects of simulated overfishing and eutrophication on settlement of reef associated invertebrates on light-exposed and -shaded tiles over 4 months. Findings revealed that at the end of the study period invertebrates had almost exclusively colonized shaded tiles, indicating that algae were superior settling competitors on light-exposed tiles. On the shaded tiles, simulated overfishing prevented settlement of hard corals, but significantly increased settlement of polychaetes, while simulated eutrophication only significantly decreased hard coral settlement relative to controls. The combined treatment significantly increased settlement of bryozoans and bivalves compared to controls and individual manipulations, but significantly decreased polychaetes compared to simulated overfishing. These results suggest settlement of polychaetes and hard corals as potential bioindicators for overfishing and eutrophication, respectively, and settlement of bivalves and bryozoans for a combination of both. Therefore, if investigated stressors are not controlled, phase shifts from dominance by hard corals to that by other invertebrates may occur at shaded reef locations in the Central Red Sea.
Demonstration of antibiotic-induced tolerance development in tropical agroecosystems through physiological profiling of sediment microbial communities
Authors: Arias-Andrés Maria , Ruepert Clemens , García Fernando , Rodríguez César
Published: January 2018

Agricultural use of antibiotics differs quantitatively and qualitatively in tropical and temperate countries. To gain insight into the nature and magnitude of physiological adaptations prompted by these drugs in microbial communities from tropical agroecosystems, we compared community-level physiological profiles of sediment bacteria from a protected wetland (PV), a pig farm (RD), treated (TIL1) and untreated effluents (TIL2) from a tilapia farm, an estuary close to shrimp farms (CA), and an irrigation channel adjacent to a rice plantation (AZ) exposed to a range of oxytetracycline (OTC) concentrations in Ecoplates (Biolog®). In addition, we used LC/MS/MS and plate counts to determine the concentration of OTC and the number of OTC-resistant bacteria in the samples, respectively. Water samples collected at RD contained maximum amounts of OTC (640 ng L-1), followed by TIL2 (249 ng L-1), TIL1 (72 ng L-1), and CA (85 ng L-1). In average, the microbial community of RD was more tolerant to OTC (EC50: 14.30 ± 3.12 mg L-1) than bacteria from CA (8.83 ± 1.85 mg Ll-1), TIL2 (EC50: 4.97 ± 1.43 mg L-1), TIL1 (4.25 ± 0.60 mg L-1), AZ (3.66 ± 0.97 mg L-1) and PV (3.77 ± 0.62 mg L-1). Congruently, PV, AZ, TIL1, CA, TIL2, and RD appeared in that order in a cumulative distribution of individual EC50 values and higher plate counts of bacteria resistant to 10 µg mL-1 (5.0x105- 1.5x107) and 100 µg mL-1 of OTC (1.5x104-8.4x105) were obtained for RD than for the other sites (10 µg ml-1: 4.8x104-3.3x105 and 100 µg mL-1: 1.0x102-4.4x103). These results are compatible with a scenario in which the basal level of tolerance to OTC that characterizes pristine environments (PV) is amplified in proportion to the intensity of antibiotic exposure (agriculture<aquaculture<swine farming).
Can pseudocomplementary peptide nucleic acid nucleases (pcPNANs) be a new tool for genetic engineering?
Authors: Shi Penghui
Published: January 2018

Zinc-finger nucleases (ZFNs) and transcription activator-like effector nucleases (TALENs) comprise a powerful class of tools that are redefining the boundaries of biological research. Although these technologies have begun to enable targeted genome modifications, there remains a need for new technologies that are scalable, affordable, and easy to engineer. In this paper, we propose a new tool for genetic engineering, the pseudocomplementary peptide nucleic acid nucleases (pcPNANs), which are composed of a pseudocomplementary PNA (pcPNA) specific for a DNA target sequence, a FokI nuclease cleavage domain and a nuclear localization signal. pcPNANs may induce targeted DNA double-strand breaks that activate DNA damage response pathways and enable custom alterations. Their cleavage-site is determined by simple Watson-Crick rule, and thus pcPNANs for aimed cleavage of genomes can be straightforwardly designed and synthesized without any selection procedure. Accordingly, the cleavage-site and site-specificity are freely chosen by changing the sequences and the lengths of pcPNA strands. We believe that the potentiality of pcPNAN as a new tool for genetic engineering will be confirmed in the future.
The angular gyrus model of consciousness
Authors: Smith Graeme E
Published: January 2018

The Angular Gyrus sits at the point where the Temporal and Parietal Lobes join. It is a point where integrative processes link together the Where and What pathways through the brain and link them to time. It is also the most likely location for at least two centers of consciousness. In this article the location is discussed and it's potential for a model of consciousness that replaces the Declarative Memory Model of Consciousness previously put forward. It's main benefit over the Declarative Memory Model of Consciousness is that it allows for the preservation of consciousness despite the loss of declarative memory in the cases of Medial Temporal Lobe injury/disease. However Connectome studies might support this model in that the TemporoParietal Fiber Intersection Area provides 7 different white matter tracts that intersect in this area.
Regional variation in digital cushion pressure in the forefeet of horses and elephants.
Authors: Warner Sharon E , Henry Victoria , Roskilly Kyle , Hildebrandt Thomas , Panagiotopoulou Olga , Hutchinson John R
Published: January 2018

Horses and elephants have extreme foot designs; horses have an unguligrade foot posture with small, single-toed, rigid hooves housing a small fibrous digital cushion, whereas elephants have large, multi-toed, functionally plantigrade, compliant feet with large adipose filled digital cushions. The morphology of the digital cushion is divergent in these species, in terms of its size, shape, volume, composition and organisation. In the context of foot-ground contact this is interesting, because feet nonetheless have to perform similar mechanical functions in all terrestrial species. How well the digital cushion functions under load may contribute to the aetiopathogenesis of foot disease; a sub-optimal digital cushion is less likely to distribute (and thus reduce) high pressures, moderate impact shock and vibration, or prevent unwarranted bone displacement.

In this study, we seek to understand how the digital cushion morphologies evident in horse and elephant feet influence internal and external foot pressures. Our novel use of invasive blood pressure monitoring equipment, combined with a pressure pad and force plate, enabled measurements of (ex vivo) digital cushion pressure under increasing axial loads in seven horse and six elephant forefeet. Linear mixed effects models (LMER) revealed that internal digital cushion pressures increase under load and differ depending on region; elephant feet experienced higher magnitudes of medial digital cushion pressure, whereas horse feet experienced higher magnitudes of centralised digital cushion pressure. Direct comparison of digital cushion pressure magnitudes in both species, at equivalent loads relative to body weight, revealed that medial and lateral pressures increased more rapidly with load in elephant limbs. Within the same approximate region, internal pressures exceeded external, palmar pressures (on the sole of the foot), supporting previous Finite Element (FE) predictions. High pressures and large variations in pressure may relate to the development of foot pathology, which is a major concern in horses and elephants in a captive/domestic environment.

We suggest that heterogeneity within the digital cushion allows it to perform conflicting mechanical functions during locomotion; different digital cushion regions may be responsible for specific functions and therefore feature appropriate properties to do so. Determining how internal structures such as the digital cushion respond to locomotor loading is essential to understanding foot health and pathology, as well as the functional consequences of evolutionary changes in foot morphology.
Biblio-MetReS for user-friendly mining of genes and biological processes in scientific documents
Authors: Usie Anabel , Karathia Hiren , Teixidó Ivan , Solsona Francesc , Alves Rui
Published: January 2018

One way to initiate the reconstruction of molecular circuits is by using automated text-mining techniques. Developing more efficient methods for such reconstruction is a topic of active research, and those methods are typically included by bioinformaticians in pipelines used to mine and curate large literature datasets. Nevertheless, experimental biologists have a limited number of available user-friendly tools that use text-mining for network reconstruction and require no programming skills to use. One of these tools is Biblio-MetReS. Originally, this tool permitted an on-the-fly analysis of documents contained in a number of web-based literature databases to identify co-occurrence of proteins/genes. This approach ensured results that were always up-to-date with the latest live version of the databases. However, this “up-to-dateness” came at the cost of large execution times. Here we report an evolution of the application Biblio-MetReS that permits constructing co-occurrence networks for genes, GO process, Pathways, or any combination of the three types of entities and graphically represent those entities. We show that the performance of Biblio-MetReS in identifying gene co-occurrence is as least as good as that of other comparable applications (STRING and iHOP). In addition, we also show that the identification of GO processes is on par to that reported in the latest BioCreAtIvE challenge. Finally, we also report the implementation of a new strategy that combines on-the-fly analysis of new documents with preprocessed information from documents that were encountered in previous analyses. This combination simultaneously decreases program run time and maintains “up-to-dateness” of the results. Availability: http://metres.udl.cat/index.php/downloads Contact: metres.cmb@gmail.com
The evolution of Predictive Adaptive Responses in human life history
Authors: Nettle Daniel , Frankenhuis Willem E , Rickard Ian J
Published: January 2018

Many studies have shown that adverse experience in early life is associated with accelerated reproductive timing in humans. There are two different classes of adaptive explanation for such associations. Both can be seen as predictive adaptive responses (PARs). According to external PAR hypotheses, early-life adversity provides a ‘weather forecast’ of the environmental conditions into which the individual will mature, and it is adaptive for the individual to develop an appropriate phenotype for this anticipated environment. In internal PAR hypotheses, early-life adversity has a lasting negative impact on the individual’s somatic state, such that her health is likely to fail more rapidly as she gets older, and there is an advantage to adjusting her reproductive schedule accordingly. We use a model of fluctuating environments to derive evolveability conditions for acceleration of reproductive timing in response to early-life adversity. For acceleration to evolve via the external PAR process, early-life cues must have a high degree of validity and the level of annual autocorrelation in the individual’s environment must be almost perfect. For acceleration to evolve via the internal PAR process requires that early-life experience must determine a significant fraction of the variance in survival prospects in adulthood. The two processes are not mutually exclusive, and mechanisms for calibrating reproductive timing on the basis of early experience could evolve through a combination of the predictive value of early-life adversity for the later environment and its negative impact on somatic state.
Fuelling in front of the barrier - are there age based behavioral differences in Garden Warblers Sylvia borin?
Authors: Barboutis Christos , Henshaw Ian , Kullberg Cecilia , Nikolopoulou Stamatina , Fransson Thord
Published: January 2018

Garden Warblers Sylvia borin were studied during autumn stopover in Crete before crossing the barrier of the Mediterranean Sea and the Sahara desert. Birds followed with transmitters show extensive stopover periods, which were longer in first-year birds, 16 days, compared with adult birds, 14 days. The distribution of body masses from birds trapped in fig trees were used to estimate the departure body mass and the results found indicate that both age categories on average depart with a fuel load close to 100% of lean body mass. The movement of transmitter birds shows differences between first-year and adult birds. Adult birds move further away from the release site and many also left the study area. Several were found settled outside the study area, up to 17 km away, indicating that they regularly make longer stopover movements. It is suggested that this might be a result of that they return to a place where they stayed during an earlier migration. It was shown that stopover site fidelity exists and nine garden warblers were recaptured in the area during a following autumn. The results found highlights the importance of stopover areas close to the Sahara desert.
Differential genotoxicity of diphenyl diselenide (PhSe)2 and diphenyl ditelluride (PhTe)2
Authors: Rocha Joao B , Meinerz Daiane F. , Allebrandt Josiane , Pansera Waczuk Emily , Soares Felix , Hassan Waseem , Mariano Douglas
Published: January 2018

Organoselenium compounds have been pointed out as therapeutic agents. In contrast, the potential therapeutic aspects of tellurides have not yet been demonstrated. The present study evaluated the comparative toxicological effects of diphenyl diselenide (PhSe)2 and diphenyl ditelluride (PhTe)2 in mice after in vivo administration. Genotoxicity (as determined by comet assay) and mutagenicicity were used as end-points of toxicity. Subcutaneous administration of high doses of (PhSe)2 or (PhTe)2 (500 μmol/Kg) caused distinct genotoxicity in mice. (PhSe)2 significantly decreased the DNA damage index after 48 and 96 hours of its injection (p<0.05). In contrast, (PhTe) caused a significant increase in DNA damage (p<0.05) after 48 and 96 hours of intoxication. (PhSe)2 did not cause mutagenicity but (PhTe)2 increased the micronuclei frequency, indicating its mutagenic potential. The present study demonstrated that acute in vivo exposure to ditelluride caused genotoxicity in mice, which may be associated with pro-oxidant effects of diphenyl ditelluride. These results indicated that exposure to ditelluride can be genotoxic to mice and the use of this compound and possibly other related tellurides must be carefully controlled.
Next-generation sequencing reveals cryptic Symbiodinium diversity within Orbicella faveolata and Orbicella franksi at the Flower Garden Banks, Gulf of Mexico
Authors: Green Elizabeth , Davies Sarah W. , Matz Mikhail V. , Medina Mónica
Published: January 2018

The genetic composition of the resident Symbiodinium endosymbionts appears to strongly modulate the physiological performance of reef-building corals. Here, we used deep amplicon sequencing to quantitatively assess Symbiodinium genetic diversity for the two mountainous star corals, Orbicella franksi and Orbicella faveolata, from two reefs separated by 19 kilometers of deep water. We aimed to determine if symbiont diversity is largely partitioned with respect to coral host species or geographic location. Our results demonstrate that across the two reefs both coral species contained only Symbiodinium identifiable as clade B type B1, represented by five distinct haplotypes. Three of these haplotypes have not been previously described and may be endemic to the Flower Garden Banks. No consistent differences in symbiont composition were detected between the two coral species. However, significant quantitative differences were observed between the east and west banks for two of the five haplotypes. These results highlight the need for consistent molecular genotyping techniques to assess local community assemblages of Symbiodinium-host relationships, which could be largely irrespective of host genetic background. This deep-sequencing approach used to sensitively characterize cryptic genetic diversity of Symbiodinium will potentially contribute to the understanding of physiological variations among coral populations.
Strain- and plasmid-level deconvolution of a synthetic metagenome by sequencing proximity ligation products
Authors: Beitel Christopher W. , Froenicke Lutz , Lang Jenna M. , Korf Ian F. , Michelmore Richard W. , Eisen Jonathan A. , Darling Aaron E.
Published: January 2018

Metagenomics is a valuable tool for the study of microbial communities but has been limited by the difficulty of “binning” the resulting sequences into groups corresponding to the individual species and strains that constitute the community. Moreover, there are presently no methods to track the flow of mobile DNA elements such as plasmids through communities or to determine which of these are co-localized within the same cell. We address these limitations by applying Hi-C, a technology originally designed for the study of three-dimensional genome structure in eukaryotes, to measure the cellular co-localization of DNA sequences. We leveraged Hi-C data generated from a synthetic metagenome sample to accurately cluster metagenome assembly contigs into groups that contain nearly complete genomes of each species. The Hi-C data also reliably associated plasmids with the chromosomes of their host and with each other. We further demonstrated that Hi-C data provides a long-range signal of strain-specific genotypes, indicating such data may be useful for high-resolution genotyping of microbial populations. Our work demonstrates that Hi-C sequencing data provide valuable information for metagenome analyses that are not currently obtainable by other methods. This metagenomic Hi-C method could facilitate future studies of the fine-scale population structure of microbes, as well as studies of how antibiotic resistance plasmids (or other genetic elements) mobilize in microbial communities. The method is not limited to microbiology; the genetic architecture of other heterogeneous populations of cells could also be studied with this technique.
Re-examining the relationship between invasive lionfish and native grouper in the Caribbean
Authors: Valdivia Abel , Bruno John F , Cox Courtney , Hackerott Serena , Green Stephanie
Published: January 2018

Biotic resistance is the idea that native species negatively affect the invasion success of introduced species, but whether this can occur at large spatial scales is poorly understood. Here we re-evaluated the hypothesis that native large-bodied grouper and other predators are controlling the abundance of exotic lionfish (Pterois volitans/miles) on Caribbean coral reefs. We assessed the relationship between the biomass of lionfish and native predators at 71 reefs in three biogeographic regions while taking into consideration several cofactors that may affect fish abundance, including among others, proxies for fishing pressure and habitat structural complexity. Our results indicate that the abundance of lionfish, large-bodied grouper and other predators were not negatively related. Lionfish abundance was instead controlled by several physical site characteristics, and possibly by culling. Taken together, our results suggest that managers cannot rely on current native grouper populations to control the lionfish invasion.
Extraordinary incidence of cervical ribs indicates vulnerable condition in Late Pleistocene mammoths
Authors: Reumer Jelle W.F. , ten Broek Clara M.A. , Galis Frietson
Published: January 2018

The number of cervical vertebrae in mammals is highly conserved at seven. We have shown that changes of this number are selected against due to a coupling with major congenital abnormalities (pleiotropic effects, (Galis 1999, Galis et al. 2006, Varela-Lasheras et al. 2011, ten Broek et al. 2012)). Here we show that the incidence of abnormal cervical vertebral numbers in Late Pleistocene mammoths from the North Sea is high (33.3%) and approximately 10 times higher than that of extant elephants (3.6%). Abnormal numbers were due to the presence of large cervical ribs on the seventh vertebra, which we deduced from the presence of rib articulation facets on sixth (posterior side) and seventh (anterior side) cervical vertebrae. The incidence of abnormal cervical vertebral numbers in mammoths appears to be much higher than in other mammalian species, apart from exceptional sloths, manatees and dugongs (Varela-Lasheras, Bakker et al. 2011) and indicates a vulnerable condition. We argue that the increased incidence of cervical ribs in mammoths is probably caused by inbreeding and adverse conditions that impact early pregnancies in declining populations close to extinction in the Late Pleistocene.
SPRINGS: Prediction of Protein-Protein Interaction Sites Using Artificial Neural Networks
Authors: Singh Gurdeep , Dhole Kaustubh , Pai Priyadarshini P. , Mondal Sukanta
Published: January 2018

Knowledge of protein-protein interaction sites provides an important base for deciphering novel drug targets and applications of enzyme-based studies. But on account of biological complexity and transient forms, determination of these sites is a challenge in biology. Various computational approaches are being explored for relevant prediction based on available protein sequence-structure information. Here we propose a novel method SPRINGS (Sequence-based predictor of PRotein- protein interactING Sites) for identification of interaction sites based on sequences. It uses protein evolutionary information, averaged cumulative hydropathy and predicted relative solvent accessibility from amino acid chains in artificial neural network architecture with a promising performance for protein-protein interactions sites based research and applications.
Educational options for children with medical needs
Authors: Capurso Michele
Published: January 2018

Schooling is known to influence a wide range of economic, social and psychological aspects of people’s life, but children with medical needs are subject to school failure more often than their healthy peers. The aim of this paper is to review different school options available to the paediatrics community for the education of children with medical needs. Hospital school, home tuition and mainstream school re-entry are examined. Critical aspects for each type of solution are discussed. The provision and stability of adequate educational opportunities for children with medical needs represents an important area of collaboration between doctors, educators and parents for the prevention of long-term consequences of illnesses and therapies.
Evaluation of granular anaerobic ammonium oxidation process for the disposal of pre-treated swine manure
Authors: Ni Shou-Qing , Yang Ning
Published: January 2018

With rising environmental concerns on potable watersafety and eutrophication, increased media attention and tighter environmental regulations, managing animal wastes in an environmentally responsible and economically feasible way can be a challenge. In this study, the possibility of using granular anammox process for ammonia removal from swine waste treatment water was investigated. A rapid decrease of NO2 --N and NH4 +-N was observed during incubation with wastewater from an activated sludge deodorization reactor and anaerobic digestion-partial oxidation treatment process treating swine manure and its corresponding control artificial wastewaters. Ammonium removal dropped from 98.0 ± 0.6% to 66.9 ± 2.7% and nearly absent when the organic load in the feeding increased from 232 mg COD/L to 1160 mg COD/L and 2320 mg COD/L. The presence of organic carbon had limited effect on nitrite and total nitrogen removal. At a COD to N ratio of 0.9, COD inhibitory organic load threshold concentration was 727 mg COD/L. Mass balance indicated that denitrifiers played an important role in nitrite, nitrate and organic carbon removal. These results demonstrated that anammox system had the potential to effectively treat swine manure that can achieve high nitrogen standards at reduced costs.
Extreme undisclosed analytical flexibility in HRV with automated p‐mining software
Authors: Heathers James A , Holcombe Alex O
Published: January 2018

Heart rate variability (HRV) is the study of the beat‐to‐beat variability in the heart rate, which is a consequence of the immediate state of the autonomic nervous system. While it is a popular psychobiological technique, flexibility within analytical methods allows any finding to be presented as significant.Here we present a potential demonstration of this, by automating analytical decisions to manipulate findings into significance by automating an extreme number of different yet plausible paths for analysis (PMinerEKG).It should be possible to demonstrate ‘extremely significant’ ‐ and entirely spurious ‐ differences between even extremely similar datasets simply by performing enough analyses.
Heritability estimation of osteoarthritis in the pig-tailed macaque Macaca nemestrina
Authors: Chi Peter B , Duncan Andrea , Kramer Patricia Ann , Minin Vladimir
Published: January 2018

We examine heritability estimation of an ordinal trait for osteoarthritis, using a population of pig-tailed macaques from the Washington National Primate Research Center (WaNPRC). This estimation is non-trivial, as the data consist of ordinal measurements on 16 intervertebral spaces throughout each macaque's spinal cord, with many missing values. We examine the resulting heritability estimates from different model choices, and also perform a simulation study to compare the performance of heritability estimation with these different models under specific known parameter values. Under both the real data analysis and the simulation study, we find that heritability estimates from an assumption of normality of the trait differ greatly from those of ordered probit regression, which considers the ordinality of the trait. This finding indicates that some caution should be observed regarding model selection when estimating heritability of an ordinal quantity. Furthermore, w e find evidence that our real data have little information for valid heritability estimation under ordered probit regression. We thus conclude with an exploration of sample size requirements for heritability estimation under this model. For an ordinal trait, an incorrect assumption of normality can lead to severely biased heritability estimation. Sample size requirements for heritability estimation of an ordinal trait under the threshold model depends on the pedigree structure, trait distribution and the degree of relatedness between each phenotyped individual. Our sample of 173 monkeys did not have enough information from which to estimate heritability, but estimable heritability can be obtained with as few as 180 related individuals under certain scenarios examined here.
On growth and form of a heteromorphic terrestrial snail: Plectostoma concinnum (Fulton, 1901) (Mollusca: Gastropoda: Diplommatinidae)
Authors: Liew Thor-Seng , Kok Annebelle CM , Schilthuizen Menno , Urdy Severine
Published: January 2018

The molluscan shell can be viewed as a petrified representation of the organism’s ontogeny and thus can be used as a record of changes in form during growth. However, little empirical data is available on the actual growth and form of shells, as these are hard to quantify and examine simultaneously. To address these issues, we studied the growth and form of a heteromorphic and heavily ornamented land snail – Plectostoma concinnum. The growth data were collected in a natural growth experiment and the actual form changes of the aperture during shell ontogeny were quantified. We used an ontogeny axis that allows data of growth and form to be analysed simultaneously. Then, we examined the association between the growth and the form during three different whorl growing phases, namely, the regular coiled spire phase, the transitional constriction phase, and the distortedly-coiled tuba phase. In addition, we also explored the association between growth rate and the switching between whorl growing mode and rib growing mode. As a result, we show how the changes in the aperture ontogeny profiles in terms of aperture shape, size and growth trajectory, and the changes in growth rates, are associated with the different shell forms at different parts of the shell ontogeny. These associations suggest plausible constraints that underlie the three different shell ontogeny phases and the two different growth modes. We found that the mechanism behind the heteromorphy is the rotational changes of the animal’s body and mantle edge with respect to the previously secreted shell. Overall, we propose that future study should focus on the role of the mantle and the columellar muscular system in the determination of shell form.
The Vertebrate Taxonomy Ontology: A framework for reasoning across model organism and species phenotypes
Authors: Midford Peter E , Dececchi T Alex , Balhoff James P , Dahdul Wasila M , Ibrahim Nizar , Lapp Hilmar , Lundberg John G , Mabee Paula M , Sereno Paul C , Westerfield Monte , Vision Todd J , Blackburn David C
Published: January 2018

Background: A hierarchical taxonomy of organisms is a prerequisite for semantic integration of biodiversity data. Ideally, there would be a single, expansive, authoritative taxonomy that includes extinct and extant taxa, information on synonyms and common names, and monophyletic supraspecific taxa that reflect our current understanding of phylogenetic relationships.

Description: As a step towards development of such a resource, and to enable large-scale integration of phenotypic data across the vertebrates, we created the Vertebrate Taxonomy Ontology (VTO), a semantically defined taxonomic resource derived from the integration of existing taxonomic compilations, and freely distributed under a Creative Commons Zero (CC0) public domain waiver. The VTO includes both extant and extinct vertebrates and currently contains 106,927 taxonomic terms, 23 taxonomic ranks, 104,506 synonyms, and 162,132 taxonomic cross-references. Key challenges in constructing the VTO included (1) extracting and merging names, synonyms, and identifiers from heterogeneous sources; (2) replacing subgroups with more authoritative local taxonomies; and (3) automating this process as much as possible to accommodate updates in source taxonomies.

Conclusions: The VTO is the primary source of taxonomic information used by the Phenoscape Knowledgebase (http://phenoscape.org/), which integrates genetic and evolutionary phenotype data across both model and nonmodel vertebrates. The VTO is useful for crudely inferring phenotypic changes on the vertebrate tree of life, which enables queries for candidate genes for different episodes in vertebrate evolution.
In a fit of pique: Analyzing microbial ChIP-Seq data with Pique
Authors: Neches Russell Y , Seitzer Phillip M , Wilbanks Elizabeth G , Facciotti Marc T
Published: January 2018

While numerous effective peak finders have been developed for eukaryotic systems, we have found that the approaches used can be error prone when run on high coverage bacterial and archaeal ChIP-Seq datasets. We have developed Pique, an easy to use ChIP-Seq peak finding application for bacterial and archaeal ChIP-Seq experiments. The software is cross-platform and Open Source, and based on only freely licensed dependencies. Output is provided in standardized file formats, and may be easily imported by the Gaggle Genome Browser (Bare et al. 2010) for manual curation and data exploration, or into statistical and graphics software such as R (R Core Team 2013) for further analysis. The software is available under the BSD-3 license, and tutorial and test data are included with the documentation.

http://github.com/ryneches/pique.
A complete, multi-level conformational clustering of antibody complementarity-determining regions.
Authors: Nikoloudis Dimitris , Pitts Jim E. , Saldanha José W.
Published: January 2018

Classification of antibody Complementarity-Determining Region (CDR) conformations is an important step that drives antibody modelling and engineering, prediction from sequence, directed mutagenesis and induced-fit studies, and allows inferences on sequence-to-structure relations. Most of the previous work performed conformational clustering on a reduced set of structures or after application of various structure pre-filtering criteria. In this study, it was judged that a clustering of every available CDR conformation would produce a complete and redundant repertoire, increase the number of sequence examples and allow better decisions on structure validity in the future. In order to cope with the potential increase in data noise, a first-level statistical clustering was performed using structure superposition Root-Mean-Square Deviation (RMSD) as a distance-criterion, coupled with second- and third-level clustering that employed Ramachandran regions for a deeper qualitative classification. The classification of a total of 12712 CDR conformations is thus presented, along with rich annotation and cluster descriptions, and the results are compared to previous major studies. The present repertoire has procured an improved image of our current CDR Knowledge-Base, with a novel nesting of conformational sensitivity and specificity that can serve as a systematic framework for improved prediction from sequence as well as a number of future studies that would aid in knowledge-based antibody engineering such as humanisation.