bluuebunny/crossref_metadata_2025 huggingface dataset:
Phenotypic plasticity promotes recombination and gene clustering in periodic environments
Authors: Gulisija Davorka , Plotkin Joshua B.
Published: January 2018

While theory offers clear predictions for when recombination will evolve in changing environments, it is unclear what natural scenarios can generate the necessary conditions. The Red Queen hypothesis provides one such scenario in natural populations, but it requires interaction with antagonistic species such as host-parasite systems. We present a novel scenario for the evolution of recombination in finite populations: the genomic storage effect due to phenotypic plasticity. Using an analytic approximation and Monte Carlo simulations we demonstrate that balanced polymorphism and recombination evolve between a target locus that codes for a seasonally selected trait and a plasticity modifier locus that modulates the effects of target-locus alleles. Unlike in prior models, evolution of recombination by this plasticity effect does not require antagonistic inter-specific interactions or a steady influx of mutation, and it occurs even when a single target locus expresses a trait under selection. Furthermore, we show that selection will suppress the recombination rate among multiple polymorphic target loci, even in the absence of epistasis among them, which produces a cluster of linked loci under selection. These results provide a novel biological scenario for the evolution of recombination and supergenes.
Seasonal and year-round use of the Ramsar-listed Kushiro Wetland by sika deer (Cervus nippon yesoensis)
Authors: Takafumi Hino , Kamii Tatsuya , Murai Takunari , Yoshida Ryoto , Sato Atsuki , Tachiki Yasuyuki , Akamatsu Rika , Yoshida Tsuyoshi
Published: January 2018

The sika deer (Cervus nippon yesoensis) population in the Ramsar-listed Kushiro Wetland has increased in recent years, and the Ministry of the Environment of Japan has decided to take measures to reduce the impact these sika deer are having on the ecosystem. However, their seasonal movement patterns, i.e., when and how the deer inhabit the wetland, remain unclear. Thus, we examined seasonal movement patterns and the population structure of sika deer in the Kushiro Wetland from 2013 to 2015 by analyzing GPS location data for 28 hinds captured at three sites in the wetland. Seasonal movement patterns were quantitatively classified as seasonal migration, dispersal, nomadic, resident, or atypical, and the degree of wetland utilization for each individual was estimated. The overlap areas of population-level home ranges among capture sites were calculated for both the entire year and for individual seasons. Our results showed that approximately one-third of the individuals moved into and out of the wetland during the year as either seasonal migrants or individuals with atypical movement. Some of the individuals migrated to farmland areas outside the wetland (the farthest being 64 km away). Half of the individuals inhabited the wetland all or most of the year, i.e., 81–100% of their annual home range was within the wetland area. The movement patterns of these deer were classified not only as resident but also as seasonal migration, dispersal, nomadic, and atypical. Even among individuals captured at the same site, various seasonal movement patterns were identified. Annual population-level home ranges showed little to no overlap, and seasonal population-level home ranges were completely segregated among capture sites. Individual deer used the wetland either seasonally or year-round, and some populations inhabiting the wetland had sub-populations with different seasonal movement patterns, which need to be considered to achieve more effective ecosystem management including deer management in the wetland.
Ontogeny of long-range vocalizations in a Neotropical fossorial rodent: the Anillaco Tuco-Tuco (Ctenomys sp.)
Authors: Amaya Juan Pablo , Areta Juan Ignacio
Published: January 2018

Adult vocalizations can develop following three alternative modes; by retention of juvenile vocalizations, through the modification of juvenile precursors or by a de novo appearance in adults. Vocalizations that develop from juvenile precursors may develop following two pathways; vocal learning (implying the ability of juveniles to modify their vocalizations based on an external auditory input) and/or vocal tract maturation (involving the improvement of the capacity of juveniles to generate progressively more adult-like vocalizations by the tuning of an innate motor program). The emission of adult vocalizations requires the synchronization of neuromuscular and anatomical structures, and the lack of maturation and/or precise coupling between them would lead to the production of abnormal vocalizations. Tuco-tucos (Ctenomys spp.) are subterranean rodents that produce territorial, high intensity long-range vocalizations (LRVs) of, broadband and low frequency that are essential for long-distance communication between individuals in different tunnel systems. Despite their importance, the developmental modes, pathways and developmental sequences of LRVs remain poorly understood. In adult Anillaco Tuco-Tucos (Ctenomys sp.) the LRV is composed by two types of syllables (series and individual notes) that are repeated a variable number of times. We studied the development of the LRV in 8 juveniles of the Anillaco Tuco-Tuco ranging from 14 to 108 days after birth. The LRV exhibited a mixed developmental mode: while series developed from juvenile precursors whose acoustic features gradually approached those of adults, individual notes appeared later in the ontogeny and de novo, with acoustic features undistinguishable from those of adults. Vocalizations became progressively longer, but the series types shown by adults were evident in juveniles at an early age. All three acoustic features of series (triad) notes studied correlated with age in both sexes (duration 90% increased through development, while bandwidth 90% and peak frequency decreased). LRV developed normally in juveniles acoustically isolated from adults, supporting the vocal tract maturation hypothesis and possibly rejecting the vocal learning hypothesis. Juveniles emmitted a higher proportion (7.4%) of abnormal vocalizations than adults (0.3%), as expected in the development of any complex behavior that requires practice to be mastered. The maturation of the LRV occurred well before the sexual maturation, presumably due to the protracted time needed to acquire or build a burrow system long before mating is possible. We propose that protracted vocal development is another component in the slow developmental strategy of Ctenomys and subterranean rodents in general.
Profiling soil microbial communities with next-generation sequencing: the influence of DNA kit selection and technician technical expertise
Authors: Soliman Taha , Yang Sung-Yin , Yamazaki Tomoko , Jenke-Kodama Holger
Published: January 2018

Structure and diversity of microbial communities are an important research topic in biology, since microbes play essential roles in the ecology of various environments. Different DNA isolation protocols can lead to data bias and can affect results of next-generation sequencing. To evaluate the impact of protocols for DNA isolation from soil samples and also the influence of individual handling of samples, we compared results obtained by two researchers (R and T) using two different DNA extraction kits: (1) MO BIO PowerSoil® DNA Isolation kit (MO_R and MO_T) and (2) NucleoSpin® Soil kit (MN_R and MN_T). Samples were collected from six different sites on Okinawa Island, Japan. For all sites, differences in the results of microbial composition analyses (bacteria, archaea, fungi, and other eukaryotes), obtained by the two researchers using the two kits, were analyzed. For both researchers, the MN kit gave significantly higher yields of genomic DNA at all sites compared to the MO kit (ANOVA; P <0.006). In addition, operational taxonomic units for some phyla and classes were missed in some cases: Micrarchaea were detected only in the MN_T and MO_R analyses; the bacterial phylum Armatimonadetes was detected only in MO_R and MO_T; and WIM5 of the phylum Amoebozoa of eukaryotes was found only in the MO_T analysis. Our results suggest the possibility of handling bias; therefore, it is crucial that replicated DNA extraction be performed by at least two technicians for thorough microbial analyses and to obtain accurate estimates of microbial diversity.
Preventive effects of salvia officinalis leaf extract on insulin resistance and inflammation, in high fat diet-induced-obesity mice model
Authors: Ben Khedher Mohamed Raafet , Hammami Mohamed , Arch Jonathan Robert , Hislop David Christopher , Eze Dominic Anthony , Wargent Edward Taynton , Kępczyńska Małgorzata Anna , Zaibi Mohamed Sghaier
Published: January 2018

Background: Salvia officinalis (sage) is a native plant to the Mediterranean region and has been used for a long time in traditional medicine for various diseases. We investigated possible anti-diabetic, anti-inflammatory and anti-obesity effects of sage methanol (MetOH) extract in a nutritional mouse model of obesity, inflammation and insulin resistance, as well as its effects on lipolysis and lipogenesis in 3T3-L1 cells.

Methods: Diet-induced obese (DIO) mice were treated for 5 weeks with sage methanol extract (100 and 400 mg.kg -1 /day. bid), or rosiglitazone (3 mg.kg -1 /day. bid), as a positive control. Energy expenditure, food intake, body weight, fat mass, liver glycogen and lipid content were evaluated. Blood glucose, and plasma levels of insulin, lipids leptin and pro- and anti-inflammatory cytokines were measured throughout the experiment. The effects of sage MetOH extract on lipolysis and lipogenesis were tested in vitro in 3T3-L1 cells.

Results: After two weeks of treatment, the lower dose of sage MetOH extract decreased blood glucose and plasma insulin levels during an oral glucose tolerance test (OGTT). An insulin tolerance test (ITT), performed at day 29 confirmed that sage improved insulin sensitivity. Groups treated with low dose sage and rosiglitazone showed very similar effects on OGTT and ITT. Sage also improved HOMA-IR, triglycerides and NEFA. Treatment with the low dose increased the plasma levels of the anti-inflammatory cytokines IL-2, IL-4 and IL-10 and reduced the plasma level of the pro-inflammatory cytokines IL-12, TNF-α, and KC/GRO. The GC analysis revealed the presence of two PPARs agonist in sage MetOH extract. In vitro, the extract reduced in a dose-related manner the accumulation of lipid droplets; however no effect on lipolysis was observed.

Conclusions: Sage MetOH extract at low dose exhibits similar effects to rosiglitazone. It improves insulin sensitivity, inhibits lipogenesis in adipocytes and reduces inflammation as judged by plasma cytokines. Sage presents an alternative to pharmaceuticals for the treatment of diabetes and associated inflammation.
The role of biotic factors during plant establishment in novel communities assessed with an agent-based simulation model
Authors: Radny Janina , Meyer Katrin M
Published: January 2018

Background. Establishment success of non-native species can be influenced by interactions with native competitors and novel enemies. Magnitude of interactions between species is mediated by traits, e.g. reflecting competitive strength or defence mechanisms. We combine the concepts to investigate the importance of species traits for successful establishment in a novel community exhibiting biotic resistance in the form of competition and herbivory.

Methods. We developed an individual-based simulation model that tracks survival rate of non-native plants in a native community. Non-native plants are characterized by high or low values of traits relevant for interaction with competitors and herbivores.

Results. Traits related to competition had a much greater impact on survival of non-native species than traits related to defence. Survival rates of strong competitors never fell below 50% while survival of weak competitors averaged about 10%. Weak competitors were also much more sensible to competitive pressures including community density, composition and asymmetry while strong competitors responded negatively to changes in competition intensity but hardly to composition or density of native community. High initial numbers of non-native individuals did decrease survival rate of strong competitors but slightly increased survival rate of weak competitors. In the current model configuration we detected only minor advantages in terms of higher survival from high defensive ability as compared to low defensive ability under enemy attack. Surprisingly, herbivory increased survival rate of species classified as weak competitors.

Discussion. High survival rates of strong competitors relate to a higher chance of establishment as compared to weak competitors. However, the negative effect of high initial numbers for strong competitive non-natives indicates a self-thinning effect, probably through creation of a highly competitive milieu. For weak competitors, our model predicted increasing survival rates at high initial densities. Positive effects of high propagule pressure have been proposed in field studies and are underlined with this model. However, our model largely overestimated mortality as compared to the preceding experiment. This could be improved by implementing more sophisticated competition modes and traits reflecting tolerance and avoidance of competition by non-native plants. This would, however, be very costly in terms of parameterization. Herbivory had a very low negative effect on survival in general and an advantage of high defence was almost untraceable. However, the positive effect of herbivory on survival of weak competitors indicated that herbivory should not be neglected in estimation of establishment success of species. Although the immediate and expected effect of herbivory might be small, side effects as weakening of resident competitors might play an important role for establishment in a new community.
Sicegar: R package for sigmoidal and double-sigmoidal curve fitting
Authors: Caglar M. Umut , Teufel Ashley I. , Wilke Claus O
Published: January 2018

Sigmoidal and double-sigmoidal dynamics are commonly observed in many areas of biology. Here we present sicegar, an R package for the automated fitting and classification of sigmoidal and double-sigmodial data. The package categorizes data into one of three categories, "no signal", "sigmodial", or "double sigmoidal", by rigorously fitting a series of mathematical models to the data. The data is labeled as "ambiguous" if neither the sigmoidal nor double-sigmoidal model fit the data well. In addition to performing the classification, the package also reports a wealth of metrics as well as biologically meaningful parameters describing the sigmoidal or double-sigmoidal curves. In extensive simulations, we find that the package performs well, can recover the original dynamics even under fairly high noise levels, and will typically classify curves as "ambiguous" rather than misclassifying them. The package is available on CRAN and comes with extensive documentation and usage examples.
Evolution of body size in Crocodylomorpha in a multi-regime evolutionary landscape
Authors: Godoy Pedro L , Benson Roger B J , Bronzati Mario , Butler Richard J
Published: January 2018

Body size is strongly related to physiology and ecology, and its evolution has been studied intensely for many animal groups. Crocodylomorphs occupy the intermediate–large range of body sizes among extant tetrapods, and have a rich and diverse fossil record, ranging in size from less than 30 centimetres to over 10 metres in length. To investigate crocodylomorph body size evolution, we used maximum-likelihood to fit macroevolutionary models to body length data within a phylogenetic context. We focused on non-uniform Ornstein-Uhlenbeck (OU) models (“SURFACE” model). Under an OU process, lineages are attracted towards an adaptive trait optimum (theta, θ) through time. SURFACE allows multiple adaptive regimes (i.e. shifts in trait optima). We also fitted other models, and conducted analyses using alternate body length proxies, tree topologies and time-calibration methods, to assess the influence of analytical choices on results. The SURFACE model fit best to our data, suggesting convergent evolution of body size among macroevolutionary adaptive zones. Although different trees identify regime shifts in phylogenetically distinct positions, we recognized some shared patterns. For instance, non-Mesoeucrocodylia crocodylomorphs maintained relatively small sizes (θ = 0.646 m), and experienced no or few shifts, thriving until the Late Cretaceous. During the Late Jurassic and Cretaceous, crocodylomorph body size disparity increased, with a high number of regime shifts, particularly within Notosuchia and Thalattosuchia. Another important regime shift, towards larger body sizes (θ = 5.561 m), occurred in the lineage leading to extant crocodylians (Eusuchia), potentially related to an adaptive radiation of the group after the Cretaceous-Paleogene extinction.
PGxO: A very lite ontology to reconcile pharmacogenomic knowledge units
Authors: Monnin Pierre , Jonquet Clément , Legrand Joël , Napoli Amedeo , Coulet Adrien
Published: January 2018

We present in this article a lightweight ontology named PGxO and a set of rules for its instantiation, which we developed as a frame for reconciling and tracing pharmacogenomics (PGx) knowledge. PGx studies how genomic variations impact variations in drug response phenotypes. Knowledge in PGx is typically composed of units that have the form of ternary relationships gene variant–drug–adverse event, stating that an adverse event may occur for patients having the gene variant when being exposed to the drug. These knowledge units (i) are available in reference databases, such as PharmGKB, are reported in the scientific biomedical literature and (ii) may be discovered by mining clinical data such as Electronic Health Records (EHRs). Therefore, knowledge in PGx is heterogeneously described (i.e., with various quality, granularity, vocabulary, etc.). It is consequently worth to extract, then compare, assertions from distinct resources. Using PGxO, one can represent multiple provenances for pharmacogenomic knowledge units, and reconcile duplicates when they come from distinct sources.
The complicated and surprisingly early origin of the pterodactyloid bauplan
Authors: Unwin David M.
Published: January 2018

The origin of the pterodactyloid bauplan from that of non-monofenestratan (‘rhamphorhynchoid’) pterosaurs involved extensive anatomical changes and had profound consequences for the evolutionary history of Pterodactyloidea, a clade that dominated the aerial realm throughout the Cretaceous. This important evolutionary transformation, about which almost nothing was known for almost two centuries, is now rapidly coming into focus thanks to a plethora of new pterosaur fossils from the Middle and Upper Jurassic of South America, Europe and China. So far, however, these finds have largely been considered in isolation from each other and few have been thoroughly evaluated. Phylogenetic analysis, combined with improved stratigraphic data for all potentially relevant taxa including putative non-pterodactyloid monofenstratans (NPMs) and the oldest known pterodactyloids (e.g. Liaodactylus) was used to generate a new map of the anatomical transformations and temporal history of the non-monofenestratan–pterodactyloid transition. Evolution of the pterodactyloid skull construction predates the Middle Jurassic, but remains almost completely undocumented by fossils. Liaodactylus reveals that innovation in pterodactyloid skull anatomy and the appearance of derived features was well underway prior to the Upper Jurassic. Douzhanopterus, a derived NPM, demonstrates that elongation of the metacarpus and reduction of the tail and fifth toe (classic pterodactyloid synapomorphies) also predates the Upper Jurassic, but disjunction in the degree of their development across taxa is not consistent with simple explanations such as ‘adaptation for flight’. Overall, late Early to early Late Jurassic pterosaurs were much more diverse and had a far more complex evolutionary history than heretofore recognised.
A unique Morrison-Formation sauropod specimen with biconcave dorsal vertebrae
Authors: Taylor Michael P , Wedel Mathew J
Published: January 2018

AMNH FARB 291 is a unique sauropod dinosaur specimen, excavated in 1898 from the Bone Cabin Quarry of Wyoming (Upper Jurassic; Morrison Formation). It consists of a sequence of five contiguous dorsal vertebrae, all with biconvex centra: a morphology not previously observed in any sauropod, and which is very rare even in other amniotes.

The specimen was initially catalogued as Brontosaurus, one of only half a dozen sauropods then known. But it lacks diplodocid features such as bifid neural spines, short centra and dual centroprezygapophyseal laminae. Instead, it resembles Brachiosaurus in its elongated centra, forward-shifted neural arches and lobe-like transverse processes. Centrum lengths (from anteriormost to posteriormost) are 207, 205, 232, 222 and 207 mm, about 60% those of the Brachiosaurus holotype. This specimen could represent:

1. normal development: the condyle would have ossified separately but the individual died before this could happen;

2. a developmental anomaly;

3. a Brachiosaurus with a rare variation not previously seen due to paucity of specimens;

4. a bizarre taphonomic event;

5. a unique taxon in which this is a normal, inherited trait.

Vertebrae typically ossify as rings of bone around the notochord, which sometimes persists as a tunnel through the centrum. There is a developmental continuum from biconcave centra with a persistent notochordal tube (as in most fishes), through biconcave centra with the notochord persisting as intervertebral cartilage balls, to the normal amniote condition. However, all known baby sauropod presacrals have already ossified opisthocoelous or amphiplatyan centra, so the present specimen remains mysterious.
Reviewing the vertebrate fossil record
Authors: Naish Darren
Published: January 2018

The vastness of the vertebrate fossil record and its literature makes any effort to review it in entirety a difficult task; ‘a review’ is understood to be a work that discusses the evolution and diversity of a group, drawing in knowledge on taxonomy, morphology, ecology and distribution, with representative illustrations. Existing reviews of the entire vertebrate record have mostly been designed with teaching in mind and have focused on groups, trends and processes deemed of interest to students. As goes more specific reviews, some groups (Mesozoic dinosaurs in particular) are frequently reviewed; others are afflicted by their association with idiosyncratic authors, others have only been given partial treatment, and others are woefully under-represented. Biographical information on vertebrate palaeontologists themselves is scattered. An additional issue is that several excellent volumes (notably the Handbook volumes) are prohibitively expensive, rare or otherwise hard to obtain. Cenozoic fishes – in particular actinopterygians, the largest and richest vertebrate radiation – remain essentially untouched and it might not be obvious to non-specialists just how rich the fish record is. Indeed, an enormous number of lineages scarcely known to experts on modern fishes are present in the fossil record. The result of this skewed coverage is that both popular and technical perceptio n of the vertebrate fossil record is biased. Not only are there a huge number of groups that fail to attract students, a large number of research questions relevant to these groups remain un- or under-investigated because so few researchers are aware of their existence.
Unraveling a resilient reef: structure and composition of Varadero, an imperiled coral reef in the Colombian Caribbean
Authors: Pizarro Valeria , Rodríguez Sara C , López-Victoria Mateo , Zapata Fernando A , Zea Sven , Galindo-Martínez Claudia T , Iglesias-Prieto Roberto , Pollock Joseph , Medina Monica
Published: January 2018

Coral reefs supply millions of people with ecosystem goods and services, especially those living along tropical coastlines. Unfortunately, these ecosystems are disappearing at an alarming pace. In the Caribbean, the rate of coral loss is high (5.5 – 9.2% per year) and constant. In 2013, a healthy coral reef was discovered in one of the least expected places within the Colombian Caribbean: at the entrance of Cartagena Bay, a highly-polluted system that receives industrial and sewage waste, as well as high sediment and freshwater loads from an outlet of the Magdalena River (the longest and most populated river basin in Colombia). Here we provide the first characterization of Varadero Reef’s geomorphology and biological diversity. We also compare these characteristics with those of a nearby reference reef, Barú Reef, located in an area much less influenced by the described polluted system. Below the murky waters, we found high coral cover of 45.1% (± 3.9; up to 80% in some sectors), three species of lobster, eight of sea urchin, a fish community composed by 61 species from 24 families, and the typical zonation of a Caribbean fringing reef. All attributes found correspond to a reef that, according to current standards should be considered in "good condition". Current plans to dredge part of Varadero threaten the survival of this reef and could hinder efforts to uncover the underpinnings of this reef’s remarkable resilience. There is, therefore, an urgent need to describe the location and characteristics of Varadero as a first step towards gaining acknowledgement of its existence and garnering inherent legal and environmental protections.
Independent evolution of tetraloop in enterovirus oriL replicative element and its putative binding partners in protein 3C
Authors: Prostova Maria A , Deviatkin Andrey A , Tcelykh Irina O , Lukashev Alexander N , Gmyl Anatoly P
Published: January 2018

Background. Enteroviruses are small non-enveloped viruses with (+) ssRNA genome with one open reading frame. Enterovirus protein 3C (or 3CD for some species) binds replicative element oriL to initiate replication. The replication of enteroviruses features low fidelity that allows virus to adapt to changing environment on the one hand, and requires additional mechanisms to maintain the genome stability on the other. Structural disturbances in the apical region of oriL domain d can be compensated by amino acid substitutions in positions 154 or 156 of 3C (amino acid numeration corresponds to poliovirus 3C), thus suggesting co-evolution of these interacting sequences in nature. The aim of this work was to understand co-evolution patterns of two interacting replication machinery elements in enteroviruses, the apical region of oriL domain d and its putative binding partners in the 3C protein.

Methods.To evaluate the variability of the domain d loop sequence we retrieved all available full enterovirus sequences (>6400 nucleotides) that were present in the NCBI database on February 2017 and analyzed variety and abundance of sequences in domain d of replicative element oriL and in the protein 3C.

Results. A total of 2842 full genome sequences were analyzed. Majority of domain d apical loops were tetraloops, which belonged to consensus YNHG (Y=U/C, N=any nucleotide, H=A/C/U). Putative RNA-binding tripeptide 154-156 (Enterovirus C 3C protein numeration) was less diverse than the apical domain d loop region and, in contrast to it, was species-specific.

Discussion. Despite RNA-binding tripeptide is suggested to interact with apical region of domain d, they evolve independently in nature. Together, our data indicates plastic evolution of both interplayers of 3C-oriL recognition.
Surface water dependency among Kalahari Desert birds
Authors: Smit Ben , Woodborne Stephan , Wolf Blair O , McKechnie Andrew E
Published: January 2018

The availability of free-standing water sources is a key determinant of animal and plant community structure in arid environments, and an understanding of the extent to which particular species depend on drinking water is vital for modelling the effects of climate change on desert avifauna. We investigated interspecific variation in dependence on artificial water sources among birds in the Kalahari Desert, South Africa, by 1) observations at waterholes and 2) tracing spatial water-use patterns during summer using isotopically-labelled water and blood sampling. More than 50 % of the avian community (primarily insectivores and omnivores) were not observed to drink. The majority (53%) of species drinking at waterholes were granivorous, and most visited waterholes daily. Blood samples revealed that only 11 of 42 species (again, mostly granivores) showed evidence of drinking at a waterhole labelled with deuterium, with between 2.2 and 92.9 % of individual birds’ body water pools originating from the labelled waterhole. These findings illustrate how two methods employed in this study provide different but complementary data on the relative importance of a water source for an avian community. Although our results suggest that most species are independent of drinking, drinking patterns on the hottest days during our study period suggest that free-standing water might become more important for some of the non-drinking species under hotter climatic conditions.
Response to “An exceptionally preserved 110 million years old praying mantis provides new insights into the predatory behaviour of early mantodeans”
Authors: Brannoch Sydney K. , Svenson Gavin J.
Published: January 2018

Hörnig, Haug, & Haug (2017) published a description of a new specimen of Santanmantis axelrodi MB.I.2068, an extinct species of praying mantis from the Crato Formation of Brazil. According to Hörnig et al. (2017) the discovery of this new specimen brought with it implications for praying mantis character evolution and predatory behavior and it is with these lines of reasoning that we find fault. More specifically, we point to four flawed assumptions in their study that led to their unsubstantiated conclusion that S. axelrodi employed their mesothoracic legs in prey capture.
The evolutionary history of plant T2/S-type ribonucleases
Authors: Ramanauskas Karolis , Igić Boris
Published: January 2018

A growing number of T2/S-RNases are being discovered in plant genomes. Members of this protein family have a variety of known functions, but the vast majority are still uncharacterized. We present data and analyses of phylogenetic relationships among T2/S-RNases, and pay special attention to the group that contains the female component of the most widespread system of self-incompatibility in flowering plants. The returned emphasis on the initially identified component of this mechanism yields important conjectures about its evolutionary context. First, we find that the clade involved in self-rejection (class III) is found exclusively in core eudicots, while the remaining clades contain members from other vascular plants. Second, certain features, such as intron patterns, isoelectric point, and conserved amino acid regions, help differentiate S-RNases, which are necessary for expression of self-incompatibility, from other T2/S-RNase family members. Third, we devise and present a set of approaches to clarify new S-RNase candidates from existing genome assemblies. We use genomic features to identify putative functional and relictual S-loci in genomes of plants with unknown mechanisms of self-incompatibility. The widespread occurrence of possible relicts suggests that the loss of functional self-incompatibility may leave traces long after the fact, and that this manner of molecular fossil-like data could be an important source of information about the history and distribution of both RNase-based and other mechanisms of self-incompatibility. Finally, we release a public resource intended to aid the search for S-locus RNases, and help provide increasingly detailed information about their taxonomic distribution.
Infrastructure and tools for teaching computing throughout the statistical curriculum
Authors: Cetinkaya-Rundel Mine , Rundel Colin W
Published: January 2018

Modern statistics is fundamentally a computational discipline, but too often this fact is not reflected in our statistics curricula. With the rise of big data and data science it has become increasingly clear that students both want, expect, and need explicit training in this area of the discipline. Additionally, recent curricular guidelines clearly state that working with data requires extensive computing skills and that statistics students should be fluent in accessing, manipulating, analyzing, and modeling with professional statistical analysis software. Much has been written in the statistics education literature about pedagogical tools and approaches to provide a practical computational foundation for students. This article discusses the computational infrastructure and toolkit choices to allow for these pedagogical innovations while minimizing frustration and improving adoption for both our students and instructors.
Phytochemicals in Daucus carota and their importance in nutrition – Review article
Authors: Ahmad Tanveer , Cawood Maria , Batool Asmat , Tariq Rana Muhammad Sabir , Ghani Muhammad Awais , Azam Muhammad ,   All authors contributed to the review article equally.
Published: January 2018

Background. Carrot is a multi-nutritional food source. It is an important root vegetable, rich in natural bioactive compounds with health-promoting properties, such as antioxidants that have anti-carcinogenic properties. Aim. This review summarises the occurrences and biosynthesis of phytochemicals and factors affecting their concentration in carrot and their pharmacological functions related to human health. Method. 155 articles including original research papers, books, book chapters were downloaded and 94 articles (most relevant to the topic) were selected for writing the review article. The rejected research papers were too old or irrelevant. Results. Carrot contains important phytochemicals i.e. phenolic compounds, carotenoids, polyacetylenes and ascorbic acid which are bioactive compounds and recognised for their nutraceutical effects and health benefits. These chemicals aid in the prevention of cancer and cardiovascular diseases due to their antioxidant, anti-inflammatory, plasma lipid modification and anti-tumour properties. This vegetable can be used to improve the health of poor people, especially in developing countries. Discussion. We recommend carrot to be promoted as a food security and food safety crop in the future to meet the global food demands in developed as well as in developing countries. Future cultivation programmes should focus on the cultivation of carrot for its phytochemicals to improve the health of impoverished people.
The Modern Research Data Portal: A design pattern for networked, data-intensive science
Authors: Chard Kyle , Dart Eli , Foster Ian , Shifflett David , Tuecke Steven , Williams Jason
Published: January 2018

We describe best practices for providing convenient, high-speed, secure access to large data via research data portals. We capture these best practices in a new design pattern, the Modern Research Data Portal, that disaggregates the traditional monolithic web-based data portal to achieve orders-of-magnitude increases in data transfer performance, support new deployment architectures that decouple control logic from data storage, and reduce development and operations costs. We introduce the design pattern; explain how it leverages high-performance Science DMZs and cloud-based data management services; review representative examples at research laboratories and universities, including both experimental facilities and supercomputer sites; describe how to leverage Python APIs for authentication, authorization, data transfer, and data sharing; and use coding examples to demonstrate how these APIs can be used to implement a range of research data portal capabilities. Sample code at a companion web site, https://docs.globus.org/mrdp, provides application skeletons that readers can adapt to realize their own research data portals.
Teaching stats for data science
Authors: Kaplan Daniel T
Published: January 2018

The familiar mathematical topics of introductory statistics --- means, proportions, t-tests, normal and t distributions, chi-squared, etc. --- are a product of the first half of the 20th century. Naturally, they reflect the statistical conditions of that era: scarce, e.g. n < 10, data originating in benchtop or agricultural experiments; algorithms communicated via algebraic formulas. Today, applied statistics relates to a different environment: software is the means of algorithmic communication, observational and "unplanned" data are interpreted for causal relationships, and data are large both in n and the number of variables. This change in situation calls for a thorough rethinking of the topics in and approach to statistics education. This paper presents a set of ten organizing blocks for intro stats that are better suited to today's environment.
Opinionated analysis development
Authors: Parker Hilary
Published: January 2018

Traditionally, statistical training has focused primarily on mathematical derivations and proofs of statistical tests. The process of developing the technical artifact—that is, the paper, dashboard, or other deliverable—is much less frequently taught, presumably because of an aversion to cookbookery or prescribing specific software choices. In this paper I argue that it’s critical to teach analysts how to go about developing an analysis in order to maximize the probability that their analysis is reproducible, accurate, and collaborative. A critical component of this is adopting a blameless postmortem culture. By encouraging the use of and fluency in tooling that implements these opinions, as well as a blameless way of correcting course as analysts encounter errors, we as a community can foster the growth of processes that fail the practitioners as infrequently as possible.
An invitation to modeling: building a community with shared explicit practices
Authors: Dahlquist Kam D , Aikens Melissa L , Dauer Joseph T , Donovan Samuel S , Eaton Carrie Diaz , Highlander Hannah Callender , Jenkins Kristin P , Jungck John R , LaMar M Drew , Ledder Glenn , Mayes Robert L , Schugart Richard C
Published: January 2018

Models and the process of modeling are fundamental to the discipline of biology, and therefore should be incorporated into undergraduate biology courses. In this essay, we draw upon the literature and our own teaching experiences to provide practical suggestions for how to introduce models and modeling to introductory biology students. We begin by demonstrating the ubiquity of models in biology, including representations of the process of science itself. We advocate for a model of the process of science that highlights parallel tracks of mathematical and experimental modeling investigations. With this recognition, we suggest ways in which instructors can call students’ attention to biological models more explicitly by using modeling language, facilitating metacognition about the use of models, and employing model-based reasoning. We then provide guidance on how to begin to engage students in the process of modeling, encouraging instructors to scaffold a progression to mathematical modeling. We use the Hardy-Weinberg Equilibrium model to provide specific pedagogical examples that illustrate our suggestions. We propose that by making even a small shift in the way models and modeling are discussed in the classroom, students will gain understanding of key biological concepts, practice realistic scientific inquiry, and build quantitative and communication skills.
A computational framework to find novel therapeutics for autoimmunity
Authors: Banerjee Soumya
Published: January 2018

The immune system protects a host from foreign pathogens. In rare cases, the immune system can attack the cells of the host organism causing autoimmune diseases. We outline a computational framework that combines bioinformatics and network analysis with an emerging targets platform. The computational framework presented here can be used to find drug targets for autoimmune diseases. It can also be used to find existing drugs that can be repurposed to treat autoimmune diseases based on networks of interactions or similarities between different diseases. Information on which gene regions are associated with the disease (single nucleotide polymorphisms) can be used in gene therapy when that technique becomes viable. Our analysis also revealed immune cell subtypes that are implicated in these diseases. These immune cell subtypes can be selected for immunotherapy experiments. Finally, our analysis also reveals intra-cellular and protein-protein interaction networks and pathways that can be targeted with small molecule inhibitors. The downstream off-target effects of these inhibitors can also be determined from such a network analysis. In summary, our computational framework can be used to find novel therapeutics for autoimmune diseases and potentially even other dysfunctions.
Whole genome sequencing of Rhodotorula mucilaginosa isolated from the chewing stick (Distemonanthus benthamianus): insights into Rhodotorula phylogeny, mitogenome dynamics and carotenoid biosynthesis
Authors: Gan Han Ming , Thomas Bolaji N , Cavanaugh Nicole T , Morales Grace H , Mayers Ashley N , Savka Michael A , Hudson Andre O
Published: January 2018

In industry, the yeast Rhodotorula mucilaginosa is commonly used for the production of carotenoids. The production of carotenoids is important because they are used as natural colorants in food and some carotenoids are precursors of retinol (vitamin A). However, the identification and molecular characterization of the carotenoid pathway/s in species belonging to the genus Rhodotorula is scarce due to the lack of genomic information thus potentially impeding effective metabolic engineering of these yeast strains for improved carotenoid production. In this study, we report the isolation, identification, characterization and the whole nuclear genome and mitogenome sequence of the endophyte R. mucilaginosa RIT389 isolated from Distemonanthus benthamianus, a plant known for its anti-fungal and antibacterial properties and commonly used as chewing sticks. The assembled genome of R. mucilaginosa RIT389 is 19 Mbp in length with an estimated genomic heterozygosity of 9.29%. Whole genome phylogeny supports the species designation of strain RIT389 within the genus in addition to validating the monophyly of the genus Rhodotorula. Further, we report for the first time, the recovery of the complete mitochondrial genome of R. mucilaginosa using the genome skimming approach. The assembled mitogenome is at least 7,000 bases larger than that of Rhodotorula taiwanensis which is largely attributed to the presence of large intronic regions containing open reading frames coding for homing endonuclease from the LAGLIDADG and GIY-YIG families. Furthermore, genomic regions containing the key genes for carotenoid production were identified in R. mucilaginosa RIT389, revealing differences in gene synteny that may play a role in the regulation of the biotechnologically important carotenoid synthesis pathways in yeasts.
Predicting comorbidities of epilepsy patients using big data from Electronic Health Records combined with biomedical knowledge
Authors: Gerlach Thomas , Lu Chao , Fröhlich Holger
Published: January 2018

Epilepsy is a complex brain disorder characterized by repetitive seizure events. Epilepsy patients often suffer from various and severe physical and psychological comorbidities. While general comorbidity prevalence and incidences can be estimated from epidemiological data, such an approach does not take into account that actual patient specific risks can depend on various individual factors, including medication. This motivates to develop a machine learning approach for predicting individual comorbidities. To address these needs we used Big Data from electronic health records (~100 Million raw observations),which provide a time resolved view on an individual's disease and medication history. A specific contribution of this work is an integration of these data with information from 14 biomedical sources (DisGeNET, TTD, KEGG, Wiki Pathways, DrugBank, SIDER, Gene Ontology, Human Protein Atlas, ...) to capture putative biological effects of observed diseases and applied medications. In consequence we extracted >165,000 features describing the longitudinal patient journey of >10,000 adult epilepsy patients. We used maximum-relevance-minimum-redundancy feature selection in combination with Random Survival Forests (RSF) for predicting the risk of 9 major comorbidities after first epilepsy diagnosis with high cross-validated C-indices of 76 - 89% and analyzed the influence of medications on the risk to develop specific comorbidities. Altogether we see our work as a first step towards earlier detection and better prevention of common comorbidities of epilepsy patients.

Supplementary material: https://drive.google.com/file/d/0B4OhgVPeWvGTeUNFQVJLai1HRlk/view?usp=sharing , code: https://github.com/thomasmooon/GCB2017
A case of mistaken identity: ‘Latvius’ obrutus and new dipnoans from the Frasnian of Stolbovo, Russia
Authors: Challands Tom , Lebedev Oleg , Friedman Matt , Krupina Natasha
Published: January 2018

The village of Stolbovo, western Russia, has previously yielded a dipnoan fauna comprising the long-snouted form 'Rhinodipterus' stolbovi, but also a three-dimensionally preserved otoccipital region of a skull previously identified as the osteolepiform ‘Latvius’ obrutus. This identification was made from the density of lateral line canal pores in the skull roof bones in addition to what Vorobyeva (1977) described as the post-parietal, tabular and extratabular bones. Reexamination of this specimen does not recognise the osteolepiform dermal elements previously identified but rather a dipnoan configuration including a characteristic B-bone, lateral dermal elements and a dipnoan parasphenoid. rhinodipterid and dipterid dipnoans. Phylogenetic analysis resolves ‘Latvius’ obrutus as the primitive sister taxon to the ‘phaneropleurid-fleurantiid’ clade – a clade comprising derived Middle–Upper Devonian lungfishes. 'Rhinodipterus' stolbovi resolves among the more primitive griphognathids, typical Gondwanan forms, and is not a rhinodipterid. Additional isolated dipnoan skeletal elements from the site include tooth plates, parasphenoids, shoulder girdle elements and dermal elements and indicate at least an additional three lungfish taxa from Stolbovo. Of particular note is a ctenodiform tooth plate more characteristic of Carboniferous lungfishes. The new material and analyses not only demonstrate increased lungfish diversity from the Frasnian of Baltica but also probable interchange between Gondwana and Baltica during this time. Most importantly, Carboniferous-like forms appear more common in the Devonian than previously realised indicating that Carboniferous lungfishes likely represent a survival assemblage in addition to a new radiation of lungfish.