bluuebunny/crossref_metadata_2025 huggingface dataset:
pathVar: a new method for pathway-based interpretation of gene expression variability
Authors: de Torrente Laurence , Zimmerman Samuel , Taylor Deanne , Hasegawa Yu , Wells Christine A , Mar Jessica C
Published: January 2018

Identifying the pathways that control a cellular phenotype is the first step to building a mechanistic model. Recent examples in developmental biology, cancer genomics, and neurological disease have demonstrated how changes in the variability of gene expression can highlight important genes that are under different degrees of regulatory control. Simple statistical tests exist to identify differentially-variable genes; however, methods for investigating how changes in gene expression variability in the context of pathways and gene sets are under-explored. Here we present pathVar, a new method that provides functional interpretation of gene expression variability changes at the level of pathways and gene sets. pathVar is based on a multinomial exact test, or an asymptotic Chi-squared test as a more computationally-efficient alternative. The method can be used for gene expression studies from any technology platform in all biological settings either with a single phenotypic group, or two-group comparisons. To demonstrate its utility, we applied the method to a diverse set of diseases, species and samples. Results from pathVar are benchmarked against analyses based on average expression via GSEA, and demonstrate that analyses using both statistics are useful for understanding transcriptional regulation.
Studying the consistency of star ratings and the complaints in 1 & 2-star user reviews for top free cross-platform Android and iOS apps
Authors: Hu Hanyang , Bezemer Cor-Paul , Hassan Ahmed E
Published: January 2018

How users rate a mobile app via star ratings and user reviews is of utmost importance for the success of an app. Recent studies and surveys show that users rely heavily on star ratings and user reviews that are provided by other users, for deciding which app to download. However, understanding star ratings and user reviews is a complicated matter, since they are influenced by many factors such as the actual quality of the app and how the user perceives such quality relative to their expectations, which are in turn influenced by their prior experiences and expectations relative to other apps on the platform (e.g., iOS versus Android). Nevertheless, star ratings and user reviews provide developers with valuable information for improving the software quality of their app. In an effort to expand their revenue and reach more users, app developers commonly build cross-platform apps, i.e., apps that are available on multiple platforms. As star ratings and user reviews are of such importance in the mobile app industry, it is essential for developers of cross-platform apps to maintain a consistent level of star ratings and user reviews for their apps across the various platforms on which they are available. In this paper, we investigate whether cross-platform apps achieve a consistent level of star ratings and user reviews. We manually identify 19 cross-platform apps and conduct an empirical study on their star ratings and user reviews. By manually tagging 9,902 1 & 2-star reviews of the studied cross-platform apps, we discover that the distribution of the frequency of complaint types varies across platforms. Finally, we study the negative impact ratio of complaint types and find that for some apps, users have higher expectations on one platform. All our proposed techniques and our methodologies are generic and can be used for any app. Our findings show that at least 68% of the studied cross-platform apps do not have consistent star ratings, which suggests that different quality assurance efforts need to be considered by developers for the different platforms that they wish to support.
Male moths that shed their genital spines inside the female: A survey of male mating costs and material investment during copulation
Authors: Camacho-García Jaime , Pineda Samuel , Cordero Carlos
Published: January 2018

In some insects, males produce costly ejaculates that reduce the typical sexual imbalance in potential reproductive rates thus influencing the mode and intensity of sexual selection. In Lepidoptera, in particular, males tend to invest heavily in mate searching, courtship and ejaculate production; furthermore, in some species males shed genital spines (deciduous cornuti) within the female genital tract during copulation. We studied experimentally the potential mating costs incurred by males of a moth with deciduous cornuti, Amorbia cuneana (Tortricidae). In the first experiment, we tested the prediction that mating costs result in a reduction in male longevity and survival rate. Our results did not support this prediction because virgin and mated males had similar longevity and survival rate. This result is somewhat surprising considering the substantial resource investment in mating found in the second experiment. In their first mating males invested in the ejaculate 9% of their body weight and transferred virtually all their deciduous cornuti; furthermore, few males were able to mate a second time (although we do not know if this was due to female rejection), these males produced smaller ejaculates and there was no evidence of cornuti regrowth. We hypothesize that reduced mating opportunities have selected for males that are ready to transfer large ejaculates at any moment and thus against the diversion of resources from reproductive tissues to somatic maintenance in unmated males; the transfer of the full set of deciduous cornuti in first copulations is consistent with this hypothesis.
Statistical quality scale 6 (SQS6)
Authors: de Morais Jose Fausto , Borges Gecilmar Pereira , do Prado Gilmar Fernandes
Published: January 2018

Context. The statistical analysis is an important part of the process of assessing the quality of randomized controlled trials, unfortunately it tends to be underestimated or even omitted by editors, in this sense, scales that cover this gap becomes necessary. Objective. To build a definition and a scale for assessing the quality of statistical analysis in randomized controlled trials. Methods. A content analysis on 16 biostatistics texts was considered in the building of the definition and of the scale. The indicators of quality were based on the description and presentation of results of articles. Results. We identify 32 quality indicators grouping in six dimensions: randomization and management of lost; sample size computation; use of mean and median; statistical test; use and interpretation of confidence interval and P-values. The scale range from 0 to 6 and score greater than three identify article with appropriate statistical analysis. Conclusions. The scale presented three dimensions linked to quality of description and three linked to quality of used strategy.
Ethylene induces endophyte bacteria to control early and late stage development in several plant species
Authors: Perry Guenevere
Published: January 2018

Plant growth promoting bacteria (PGPB) can modify plant growth and increase nutrient uptake. This study focuses on additional applications for PGPB in pre-harvest and post-harvest biotechnology.In this study a Bacillus sp. were exposed to urea, cobalt, and iron cofactors and induced with ethylene gas. The induced bacteria enhanced early stage development in cucumber plants. The bacetria increased seed germination by 25% and increased the number of blossoms per plant increased by over 50%. The induced Bacillus sp. controlled late stage development inseveral plants species. The bacteria delayed the effects of climacteric ripening in bananas and peaches. The PGPB may biosynthesize a compound that is released into the surrounding environment that affects early stage development and late stage development in several species of plants.
Mapping and studying an urban red fox (Vulpes vulpes) population using social media
Authors: Soysal Ahsennur , Hooper-Bui Linda M , Laws Edward A
Published: January 2018

Foxes are timid yet resourceful animals that are integrated into many urban environments. Because they are elusive, collecting information about the number of urban foxes, their diet and spatial distribution, their interactions with the ecological community in their urban habitat, as well as residents’ response to them, is difficult. Involving stakeholders to participate in the data collection on wildlife via citizen science on social media is one way to overcome this complication, while simultaneously engaging residents in the ecology happening around them. Therefore, we used social media as the platform to engage the public to document and map the foxes in Baton Rouge, LA. Local residents were asked to post sightings and/or photographs of foxes they observed, with the location, onto our Facebook Page at Fox Finders of Baton Rouge, on Twitter at @FoxFindersBR, or on Twitter and Instagram with the hashtag #findfoxlsu. This information was added onto an ArcGIS story map. Types of public responses and engagement over time were also measured. The authors clarified people’s misconceptions about foxes when questions were asked on our Facebook Page. On-site observations and trail cameras were also used in common locations to monitor the urban foxes.

While we received only one fox sighting via Instagram and Twitter each, our Facebook Page generated 1132 “likes” and an average of 14% Page Engagement Rate during the first eight months. Along with Baton Rouge, people from 384 different cities and 16 countries have engaged with the page. In addition, 180 sightings of about 140 different foxes—including 61 photographs and eight videos—were submitted, with eight of the sightings coming from areas surrounding the city—outside the study area. Seven common fox locations in the city were identified, all of which were adjacent to a source of water. Results showed that urban foxes have become habituated to the urban environment and may serve as an umbrella species. From the many positive and enthusiastic feedback we have received on our Facebook Page, our research model successfully promoted citizen science by easily connecting residents to science, enabling them to engage with our team and local residents directly to learn about the wildlife around them, efficiently documented and mapped many local urban foxes, and provided a preliminary count of foxes for benchmark data for future studies.
Biological facilitation of the giant tree fern Angiopteris evecta in the germination of the invasive velvet tree Miconia calvescens
Authors: Lee Jaemin
Published: January 2018

Background. Biological facilitation is a type of relationship between two taxa that benefits at least one of the participants and harms neither. Although native species are widely known to compete with native taxa, recent studies suggest that invasive and native species can have positive relationships. This study aims to examine the biological facilitation of the germination of invasive Miconia calvescens by giant tree fern Angiopteris evecta , native to French Polynesia.

Methods. Field surveys were conducted to measure A. evecta and M. calvescens by applying the 10 × 10 m 2 quadrat survey method. The density of seedlings, saplings, and matures of M. calvescens growing on the rhizomes of A. evecta and on bare soil was compared, and the correlation between the size of the rhizomes and the number of M. calvescens growing on them was checked. Comparative soil nutrient experiments were done for the substrates of the rhizomes of A. evecta, soil under the rhizomes, and bare soils to check whether the rhizomes are chemically different than other microenvironments.

Results. Field surveys show that there is a greater number of seedlings and saplings of M. calvescens growing on the rhizomes of A. evecta as compared to bare soil. Furthermore, there is a positive correlation between the size of rhizomes and the number of M. calvescens growing on them. Substrates of A. evecta had higher phosphorus and potassium contents compared to other soils and substrates.

Discussion. Angiopteris evecta is facilitating the germination of M. calvescens, supported by the much higher number of seedlings and saplings growing on the rhizomes and the positive correlation between the size of the rhizome and the number of M. calvescens growing on it. Microslopes on the rhizomes of A. evecta prevent leaf litter from accumulating on the rhizomes, and enable more sunlight to reach and facilitate the germination of M. calvescens seeds. Also, field observations suggest that A. evecta has fast decomposing leaves, which can induce the germination and the recruitment of M. calvescens in forest understories dominated by A. evecta by preventing the accumulation of leaf litter on the ground and enabling more sunlight to reach to the seed bank. The germination of trees in tropical rainforest is known to be limited by the availability for potassium, suggesting that the rhizomes of A. evecta might be favored chemically. However, further studies are needed to verify whether potassium is a limiting factor of the germination of M. calvescens. Biological facilitation of the germination of invasive M. calvescens by native A. evecta can give better understanding on the invasion success and the relationship between the native and invasive species. Invasion of A. evecta can induce and promote further invasion of M. calvescens. Therefore, thorough management of ongoing invasion of A. evecta in some places is especially required.
The impact of archaeological clearing on secondary succession in a tropical rainforest
Authors: Herbert Allison J
Published: January 2018

Disturbance events can often create an environment that allows invasive species to colonize, particularly on susceptible island ecosystems. An increasingly common form are anthropogenic disturbances, which are caused by human interactions with the environment. The ‘Opunohu Valley on the island of Mo’orea, French Polynesia experiences continuous disturbance events in the form of forest clearing for archaeological excavations and mapping. This study examined whether archaeological clearing events increased the number of invasive plants during secondary regrowth by surveying four previously clear-cut archaeological sites for invasive vascular plants. There appeared to be no difference across treatments when looking at non-native species, but there was a difference in recent invaders. There was high variation between sites, indicating a possible confounding variable of previous habitation use or number of times cleared which varied across sites. The highest proportion of invasive species were found in a site that was repeatedly cleared for tourism purposes. Cleared archaeological sites overall had no effect on the invasion of non-native species, but may have helped distribute more recent invasive species. Thus, forest management organizations should take more precautions when conducting archaeological clearing and rebuilding prehistoric sites.
Genetic diversity and population structure of Gerbera delavayi Franch. revealed by newly developed genic-SSR markers
Authors: Zheng Wei , Xu Xiaodan
Published: January 2018

Background: Gerbera delavayi Franch., a perennial herb native to southwest China, is of important and special value in textile and culture. Its abaxial leaves have a layer of soft fibers, which can be manually peeled, twisted into a yarn, and applied in textiles for hand-made clothes. The particular craftsmanship, unique all over the world, is a part of the intangible cultural heritage in Yunnan and Sichuan Province. To date, the wild species has become endangered because its leaves are excessively harvested for textile applications. Estimating the genetic variation of plant species is crucial for plant conservation and breeding. So, the aim of this study was to (1) provide an accurate outline of the genetic diversity and population structure of G. delavayi and (2) propose targeted conservation strategies for these wild resources.

Methods: Simple sequence repeats (SSR) markers were developed from the G. delavayi transcriptome for its genetic analysis. A total of 5,179 genic-SSR markers were identified and 350 primer pairs were selected for PCR validation. After primary screening , 19 polymorphic and neutral primer pairs were used to analyze the genetic diversity and population structure of nine wild fireweed populations (a total of 204 individuals) collected from Southwest China.

Results: Moderate genetic diversity (allelic richness (Ar)=3.436, Shannon’s information index (I)=0.789 , observed heterozygosity (Ho)=0.304 , and expected heterozygosity (He)=0.415) and moderate differentiation (FST=0.110, P=0.000) were found among nine populations. The lowest genetic diversity (Ar=2.351, I=0.497, Ho=0.178, and He=0.284) and highest inbreeding (inbreeding coefficient (FIS)=0.365) were both detected within the isolated population PE. Furthermore, high genetic differentiation, limited gene flow, and clear genetic barrier were detected between PE and other populations, showing the significant effects of habitat fragmentation on the genetic differentiation of these G. delavayi populations.

Conclusions: Our results showed that human overexploitation has led to moderate genetic diversity in G.delavayi populations. Furthermore, habitat fragmentation has resulted in clear genetic barrier and high differentiation between the isolated and concentrated populations. Upon the genetic features of wild G. delavayi populations, we proposed several strategies for protecting and utilizing the current wild resources.
Hormone-injected leaf cutting, a new efficient in vivo multiplication protocol for two succulent plants
Authors: Xu Xiaodan , Zheng Wei
Published: January 2018

This study aimed to establish a simple and efficient in vivo multiplication protocol by leaf cutting to satisfy the supply of young succulent ornamentals Pachyveria pachytoides and Sedum morganianum. The regenerability of leaves injected with 6-benzylaminopurine (BAP) and α-naphthalene acetic acid (NAA) in vivo were tested with common leaf cutting as control. Results showed a 100% shoot induction frequency using hormone-injeceted methods for the two species. The number of shoots per leaf of 4.0 or 6.0 mg l −1 BAP and 0.1 mg l −1 NAA injected in vivo (5.08-5.14 in P. pachytoides, and 6.22-6.74 for S. morganianum) were significantly greater than that of the other treatments. Since the h ormone-injected leaf cutting needs no aseptic operation which is necessary for in vitro multiplication, it is simple for the commercial production of the two species. The new in vivo propagation method would be of great interest for growers and breeders of succulent plants.
The oldest vertebrate trace fossils from Comb Ridge (Bears Ears Region, southeastern Utah)
Authors: Gay Robert J , Jenkins Xavier A , Lepore Taormina
Published: January 2018

Vertebrate trace fossils are common in Upper Triassic deposits across the American southwest. These ichnofauna are dominated by Grallator, Brachycheirotherium, and Pseudotetrasauropus and lack ichnotaxa traditionally considered to be Early Jurassic in age, such as Eubrontes and Anomoepus. While known from Indian Creek and Lisbon Valley, vertebrate trace fossils have not been previously reported from Comb Ridge. This is despite lithostratigraphic work having been conducted at the elsewhere-fossiliferous “Big Indian Rock Beds” at the US Highway 163 roadcut since the 1990s. 2016 fieldwork by the Museums of Western Colorado: Dinosaur Journey recovered two sandstone slabs that had been dislodged from a river channel sand in the Church Rock Member of the Chinle Formation. The slabs preserve the first documented vertebrate trace fossils from Comb Ridge: a single pes impression of the ichnogenus Grallator, and several manus and at least one pes impression of a small archosaur. We tentatively refer this second track set to the ichnogenus Brachychierotherium. Taken together, these specimens provide evidence for a more diverse vertebrate fauna in the Church Rock Member of the Chinle Formation at Comb Ridge than indicated by the body fossil record.
Is there a connection between peptide bond geometry and aminoacid residue conformational preferences?
Authors: Balasco Nicole , Esposito Luciana , Vitagliano Luigi
Published: January 2018

The definition of the structural basis of the conformational preferences of the genetically encoded aminoacid residues is crucial to decipher the physical code of protein folding and would have a huge impact on our understanding of protein structure and function. Indeed, although a large number of computational and experimental investigations have highlighted that the different protein residues show distinct conformational propensities, none of the current hypotheses is able to satisfactorily explain these preferences. In the last decades, we and others have clearly demonstrated that several geometrical parameters of protein backbone (bond angles, peptide bond distortions from planarity, and pyramidalization of the carbonyl carbon atom) are heavily dependent on the local conformation (φ/ψ dihedral angles) [1-8]. Moreover, a correlation between bond distances such as CO and CN has been detected in ultrahigh resolution protein structures [9]. Concerning bond angles, most of these investigations have been focused on the NCαC (τ) angle, shown to be significantly affected by both φ/ψ dihedral angles. In this framework, we here evaluated the impact of the local geometry on the residues conformational preferences by performing statistical analyses on a dataset of non-redundant protein chains selected from the Protein data Bank (PDB). Our data highlight a clear link between residue conformational preferences and local geometry.

References

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Proposal of a new genome-based taxonomy for Cyanobacteria
Authors: Walter Juline M , Coutinho Felipe H , Dutilh Bas E , Thompson Fabiano , Thompson Cristiane C
Published: January 2018

Cyanobacteria are major contributors to global biogeochemical cycles. The genetic diversity among Cyanobacteria enables them to thrive across many habitats. However, the taxonomy of Cyanobacteria remains unstable because of an inadequate taxonomic classification system. Taxa within Cyanobacteria have historically been classified using morphological traits, which is inadequate to categorize the diversity within this phylum. The aim of this study was to propose a new taxonomic framework for Cyanobacteria using whole-genome-based taxonomic analysis including in silico Genome-to-Genome hybridization (GGH), Average Amino acid Identity (AAI), Average Nucleic acid Identity (ANI), phylogenetic reconstruction using a set of conserved marker genes (MLST), and 16S rRNA gene sequences. Applying these genomic signatures to a set of 100 cyanobacterial genomes allowed 86 species and 43 genera to be identified, among which 32 species and 19 genera were found to be novel. By exploring changes in the relative abundances of the analyzed genomes throughout diverse marine and freshwater ecosystems, we determined the ecological niches occupied by these taxa, adding another level to our proposed taxonomic scheme.
Assessing value of biomedical digital repositories
Authors: Hsu Chun-Nan , Bandrowski Anita , Grethe Jeffery S , Martone Maryann
Published: January 2018

Digital repositories bring direct impacts and influence to the research community and society but at the moment it is challenging to objectively measure their value. We distinguished the difference between impacts and influence and discussed measures and mentions as the basis of a quality metric of a digital repository. It is challenging to define a single perfect metric that covers all quality aspects. We argue that these challenges may potentially be overcome through the introduction of standard resource identification and data citation practices. We briefly summarized our research and experience in the Neuroscience Information Framework, the BD2K BioCaddie project on data citation, and the Resource Identification Initiative. We outline our accomplishments and challenges ahead. Full implementation of these standards will depend on cooperation from all stakeholders --- digital repositories, authors, publishers, and funding agencies, for which we have been gaining support with endorsements and resource investments.
A scale to classify plastic marine debris into physical degradation stages
Authors: Siqueira Sara C W , Costa Monica F , Barletta Mario , Dantas David V
Published: January 2018

Marine debris are a widespread problem that affects every river basin, costal and marine environment ever studied for this pollutant. Its full characterization is paramount in the efforts to identify and abate sources, as well as in the raising filed of risk studies. In addition to variables as material, size, colour and shape, state of degradation is also an important feature to be observed, registered and included in numerical analysis that aim at describing marine debris spatio-temporal patterns of distribution. A scale that attributes three degrees, or states, of degradation (1 recent; 2 intermediate; 3 old) to individual marine debris items was created. It is described here together with the criteria adopted to classify among its categories. The scale allows for the inclusion of a relatively difficult to determine factor into statistical analysis as a categorical variable through recognizable levels of physical abrasion. Although degradation is a continuous process, when surveying plastic marine debris the large amount of items does not allow for detailed individual assessment (through chemical and mechanical tests, for instance), and therefore a quick direct observation method adds value to the work without overloading personnel, being time-consuming or resulting in excessive financial costs. We suggest that, until further studies are conduced, the scale is used to compare marine plastic debris items, mainly within surveys.
Exposure to dense bacteria lawns does not cause the social amoeba Dictyostelium discoideum to carry bacteria through the social stage
Authors: Brock Debra A , Canas Alicia , Jones Kai , Queller David C , Strassmann Joan E
Published: January 2018

Background. Interactions between eukaryotic amoebae and bacteria are understudied and important. Bacteria inside of amoebae are protected from external forces including antibiotics. An excellent model for bacteria-amoeba interactions is the social amoeba Dictyostelium discoideum and its associated bacteria. A third of wild-collected clones of the soil-dwelling amoeba Dictyostelium discoideum exhibit a suite of characteristics that make them simple farmers of bacteria. They carry bacteria internally through the social spore-making stage. They then release these bacteria to grow and subsequently eat them, prudently stopping before they are entirely consumed so some bacteria can be carried to the next generation. D. discoideum defend their food bacteria with other inedible bacteria that produce compounds toxic to non-farmers. Both carried bacteria and social amoeba hosts have demonstrated co-evolved characteristics. Most farmer clones discovered to date carry inedible Burkholderia in addition to food bacteria, but it is not clear whether or not a preponderance of naïve bacteria might induce the farming state by overwhelming the phagocytic actions of the host amoebae. In this study we address this question with D. discoideum clones that naturally carry bacteria and those that do not. Will naïve bacteria in large numbers succeed in colonizing the amoebae?

Methods. We grew five non-farmer clones and five farmer clones of wild-collected Dictyostelium discoideum on three different concentrations of a highly palatable bacterial food source, Klebsiella pneumoniae. We then tested them to see if they carried bacteria through the social stage.

Results. We found that bacterial density did not have a significant effect on whether or not the clones carried bacteria through the social stage. Even those grown in very dense bacterial cultures were able to shed them successfully unless they were also carrying Burkholderia.

Discussion. Our results indicate that even a preponderance of food bacteria cannot overwhelm the ability of social amoebae to digest and not carry bacteria. Apparently, only the inedible Burkholderia have that effect. This points to the importance of understanding co-infection with multiple bacteria because those that cannot induce carriage can nevertheless become carried, foiling digestive processes, but only in the presence of another bacterium. Future studies of host bacteria interactions should consider using multiple bacteria simultaneously.
Rates of morphological evolution in Captorhinidae: An adaptive radiation of Permian herbivores
Authors: Brocklehurst Neil
Published: January 2018

The evolution of herbivory in early tetrapods was crucial in the establishment of terrestrial ecosystems, although it is so far unclear what effect this innovation had on the macro-evolutionary patterns observed within this clade. The clades which entered this under-filled region of ecospace might be expected to have experienced an “adaptive radiation”: an increase in rates of morphological evolution and speciation driven by the evolution of a key innovation. However such inferences are often circumstantial, being based on the coincidence of a rate shift with the origin of an evolutionary novelty. The conclusion of an adaptive radiation may be made more robust by examining the pattern of the evolutionary shift; if the evolutionary innovation coincides not only with a shift in rates of morphological evolution, but specifically in the morphological characteristics relevant to the ecological shift of interest, then one may more plausibly infer a causal relationship between the two. Here I examine the impact of diet evolution on rates of morphological change in one of the earliest tetrapod clades to evolve high-fibre herbivory: Captorhinidae. Using a method of calculating heterogeneity in rates of discrete character change across a phylogeny, it is shown that a significant increase in rates of evolution coincides with the transition to herbivory in captorhinids. Theherbivorous captorhinids also exhibit greater morphological disparity than their faunivorous relatives, indicating more rapid exploration of new regions of morphospace. As well as an increase in rates of evolution, there is a shift in the regions of the skeleton undergoing the most change; the character changes in the herbivorous lineages are concentrated in the manible and dentition. The fact that the increase in rates of evolution coincides with increased change in characters relating to food acquisition provides stronger evidence for a causal relationship between the herbivorous diet and the radiation event.
Disc-shaped fossils resembling porpitids (Cnidaria: Hydrozoa) or eldonids from the early Cambrian (Series 2: Stage 4) of western U.S.A.
Authors: Lieberman Bruce S , Kurkewicz Richard , Shinogle Heather , Kimmig Julien , MacGabhann Breandán Anraoi
Published: January 2018

The morphology and affinities of newly discovered disc-shaped soft-bodied fossils from the early Cambrian (Series 2: Stage 4, Dyeran) Carrara Formation are discussed. These specimens show some similarity to the Ordovician Discophyllum Hall, 1847; traditionally this taxon had been treated as a fossil porpitid. However, recently it has instead been referred to another clade, the eldonids, which includes the enigmatic Eldonia Walcott, 1911 that was originally described from the Cambrian Burgess Shale. The status of various Proterozoic and Phanerozoic taxa previously referred to porpitids and eldonids is also briefly considered. To help ascertain that the specimens were not dubio- or pseudofossils, elemental mapping using energy dispersive X-ray spectroscopy (EDS) was conducted. This, in conjunction with the morphology of the specimens, indicated that the fossils were not hematite, iron sulfide, pyrolusite, or other abiologic mineral precipitates. Instead, their status as biologic structures and thus actual fossils is supported. Enrichment in the element carbon, and also possibly to some extent the elements magnesium and iron, seems to be playing some role in the preservation process.
Investigation of Diadema savignyi’s role in shaping the abundance of the brown microalga, Sargassum Pacificum, in Mo’orea, French Polynesia
Authors: Bednarski Valerie R
Published: January 2018

The role of Diadema savignyi in controlling the brown microalga, Sargassum pacificum, was studied on the barrier reef of Mo’orea, French Polynesia. A survey of the area was conducted to determine if there was a trend between the number of D. savignyi and the amount of S. pacificum on a coral bommie; no correlation was found. A field experiment involved relocating D. savignyi by placing groups of seven on coral bommies in the backreef outside of Cooks Bay. At the end of the experiment, Sargassum pacificum cover was compared in urchin manipulated coral bommies and non-manipulated bommies. Manipulated bommies experienced a statistically greater decrease in S. pacificum cover. However, the control bommies experienced almost no change, indicating that the increased density of urchins on a bommie caused an increased feeding rate.
Splice variants’ role in mediating different disease states in tissue requiring ion transduction through calcium channel for function
Authors: Ng Wenfa
Published: January 2018

Structure informs function, and this may be the evolutionary reason why alternative splicing, which is capable of generating different variants of the same protein, arise. But, given the energetic cost of generating different splice variants for testing their capability at a specific task, which incurs cellular functional uncertainty; as well as the exertion of differing physiological effects on cells that may translate into diseased states, what is the evolutionary advantage of this process? Additionally, what are the factors that select a specific variant for a presented task? Using heart tissue samples exposed to hypoxia stress as model system, this research idea entails the illumination of single nucleotide polymorphisms (SNP) of the calcium channel transporter, Cav 1.2 gene in the population through gene sequencing followed by bioinformatic analysis for alternative splice sites. This would be followed by a scan for alternative splice variants through colony polymerase chain reaction using universal primers for Cav 1.2 gene. Confirmation of splice variant identity through Western blot laid the stage for subsequent efforts at cloning and expressing the variant gene in HEK 293 cells lacking endogenous expression of Cav 1.2, for biophysical characterization of calcium conduction through patch clamp electrophysiology. In parallel, structural elucidation efforts necessitate the purification of the calcium channel via hydrophobic interaction or reversed phase liquid chromatography after its heterologous expression in a bacterial host. But, biophysical and biochemical characterization does not speak of the signaling and metabolic pathways laying the path to generation of the splice variant(s). Hence, discovery approaches such as RNA-seq and mass spectrometry proteomics could uncover the molecular mysteries at the transcript and protein level that help guide the selection of specific splice variant in response to hypoxic stress, where HIF is a candidate pathway. Implementing this approach from the retrospective angle of examining diseased human tissue samples provide one important facet for uncovering possible mechanisms driving the generation of a splice variant. However, the complementary prospective approach of identifying the molecular basis and processes for responding to hypoxia in a cell line such as HEK 293 would help provide confirmatory evidence in understanding the key drivers of physiological response to lack of oxygen at the cellular level. Collectively, this research route would illuminate both the nucleotide informational basis of alternative splicing in calcium channel Cav 1.2 as well as identify the molecular mechanisms enabling the selection of specific splice variants useful for conferring, at the cell and tissue level, ability to withstand hypoxic stress without significant negative effects on cell function. Interested readers can expand on the ideas presented.
Pharmacophore modeling, virtual computational screening and biological evaluation studies
Authors: Dotolo Serena , Facchiano Angelo
Published: January 2018

Drug discovery process plays an important role in identifying new investigational drug-likes and developing new potential inhibitors related to a determinate target, in biopharmaceutical field [1]. An alternative promising and efficient used to identify new active substances is Pharmacophore modeling method.We defined a new computational strategy protocol characterized by the use of bioinformatics online tools and by the application of locally installed tools, for lead candidates generation-optimization able to reduce the cycle time and cost of this process and to promote the next steps of study [2].Hence, we have tried to apply this new computational procedure, in a more detailed screening, of small bioactive molecules, searching and identifying new candidates as “lead compounds”, potentially able to inhibit biological target AKT1 human protein and its related molecular mechanisms [3].The workflow executed in our work has been characterized by a multi-step design, which concerns different topics: search in PDB database of a model structure for AKT1, pharmacophore modeling and virtual computational screening, biological evaluation divided in two parts (molecular validation of selected compounds and study of physical-chemical properties related to pharmacokinetic/pharmacodynamics prediction models). All these step have been performed through PHARMIT (http://pharmit.csb.pitt.edu) and Discovery Studio 4.5 platform.We selected the PDB structure 3O96 as the reference complex (protein-ligand), and we analyzed it by means of PHARMIT and Discovery Studio, to generate four different “pharmacophore models” with four different list of natural compounds.It is performed a thorough screening of compounds applying several filters, to find some good candidates as possible natural AKT1 allosteric inhibitors.The compounds that match a well-defined pharmacophore have been analyzed through direct molecular docking, for selecting only the best candidates and studying the protein-ligand interactions. Selected compounds have been investigated in more details, to trace their origin, by their chemical-physical properties.This information can help us to predict some plausible enzyme-catalyzed reaction pathways, through PathPred web-server and KEGG compound database, in order to highlight the most important reactions for biosynthesis of compounds and obtain PharmacoKinetics/PharmacoDynamics (PK/PD) models, to investigate the ADMET properties of these lead compounds and to study their behavior in some biological systems, for the next experimental assays.This new computational strategy has been very efficient in showing what could be good “lead compounds” and potential natural inhibitors of AKT1 and PI3K/AKT1 signaling cascade. Therefore, the next steps could be the experimental analysis of pharmacokinetics-pharmacodynamics and toxicity properties “in vitro/in vivo”, in order to evaluate the results obtained “in silico”.
Lifting the curse of stringly-typed code
Authors: Santos Eddie A , Ali Karim
Published: January 2018

How often do JavaScript programmers embed structured languages into strings literals? We conduct an empirical investigating mining nearly 500 thousand JavaScript source files from almost ten thousand repositories from GitHub. We parsed each string literal with seven separate common grammars, and found the most common data type that is hidden within the confines of string literals. To reduce the overuse of strings for structured data types, we present a simple static program analyzer that finds embedded languages and warns the developer, providing an optional fix.
A residence-time framework for biodiversity
Authors: Locey Kenneth J , Lennon Jay T
Published: January 2018

Residence time (τ) is the average amount of time that particles spend in an ecosystem. Often estimated from the ratio of volume to flow rate, τ equates the physical environment with dynamics of growth. Here, we propose that τ is key to understanding relationships between biodiversity and the physical ecosystem. We hypothesize that τ acts as a force of selection on traits related to growth and persistence by coupling dispersal and resource supply. We test a suite of predictions using >10,000 stochastic individual-based models that simulate resource-limited life history among ecologically distinct species within complex environments. Predicted relationships between τ and abundance, productivity, and diversity emerged alongside realistic macroecological patterns. Abundance and productivity were greatest when τ equaled an emergent property ϕ, which captures energy-based trade-offs between growth and persistence. From individual metabolism to the dynamics of bioreactors, soils, lakes, and oceans, ecological systems should inherently be governed by τ.
Effects of pre-mature harvest and heat exposure on physical and mechanical properties of Pandanus tectorius leaves
Authors: Toman John A
Published: January 2018

Plant materials have long been utilized for human use because of their wide range of physical properties and incredible mechanical efficiency as eco-friendly structures. One example of their use today is the practice of using the sturdy leaves of Pandanus tectorius for thatching purposes. An increase in modern demand for P. tectorius is pressuring farmers to deviate from traditional harvesting methods in an attempt to increase leaf yield. With little knowledge of the repercussions of their new practice, modern farmers are pre-maturely harvesting leaves through heat-induced leaf drying while the leaves remain on the tree. In this study, life-history characteristics, physical and mechanical properties of P. tectorius leaves on Mo’orea, French Polynesia are examined to determine whether or not this deviation from traditional harvest methods reduces leaf efficacy as a thatching material. Quantitative measures of P. tectorius leaves suggest that pre-mature harvest does not alter the size of collected leaves for thatch because most leaves on a tree have already reached maximum growth. Heat-induced leaf drying, however, reduces the tensile strength of P. tectorius leaves by about 25%. Further research may find that this loss in leaf tensile strength may correlate to less robust roofing structures, hindered longevity and ultimately an increase in energy cost to repair and rebuild such structures.
­Isochoric refrigeration of food products
Authors: Lyu Chenang , Nastase Gabriel , Ukpai Gideon , Serban Alexandru , Rubinsky Boris
Published: January 2018

Background: Food preservation is essential to the growing world population, food economy. Freezing is a commonly used method for food preservation. While extending the life of the product, freezing has detrimental effects. It is causing loss of food weight and is causing changes in food quality, e.g. enzymatic browning.

Method: Freezing of food is usually done under constant atmospheric pressure (isobaric). We have developed a new technology in which biological materials are preserved at subfreezing temperatures in an isochoric (constant volume) system. Experiments were performed with a food product, potato, in a thermodynamic isochoric device designed by us, that is robust and has no moving parts.

Results: We have shown that under similar storage conditions, freezing to -5°C, the isochoric preserved potato experienced no weight loss and limited enzymatic browning. In contrast the -5°C isobaric frozen potato experienced substantial weight loss and substantial enzymatic browning. Microscopic analysis, shows that the mechanism responsible for the different results is related to the integrity of the cell and the cell membrane, which are maintain during freezing in the isochoric system and lost during freezing in the isobaric system.

Discussion: The main mechanism of cell damage during isobaric freezing are the increase in extracellular osmolality and the mechanical damage by ice crystals. In contrast, during isochoric freezing the cells in the preserved material are under conditions in which the intracellular osmolality is comparable to the extracellular osmolality and they are not affected by ice mechanical damage. The conditions during isochoric freezing result in improved quality of the preserved food products.

Conclusion: We have shown that the quality of food products preserved by isochoric freezing is better than the quality of food preserved to the same temperature in isobaric conditions. This is only a preliminary study on isochoric preservation of food. However, it illustrates the potential of the technology.
Comparative transcriptome analyses of a late-ripening mandarin mutant and its original cultivar reveals gene expression profiling associated with citrus fruit ripening
Authors: Lu Wang , Qingzhu Hua , Yuewen Ma , Guibing Hu , Yonghua Qin
Published: January 2018

Late-ripening characteristics of a fruit is a good agronomic trait for extending both the harvest period and marketing time. However, underlying molecular basis of the late-ripening mechanism in fruit is largely unknown. In this study, RNA sequencing (RNA-seq) technology was used to identify differentially expressed genes (DEGs) related to late-ripening characteristics from a late-ripening mutant ‘Huwan Wuzishatangju’ (HWWZSTJ) (Citrus reticulata Blanco) and its original line ‘Wuzishatangju’ (WZSTJ). A total of approximately 17.0 G base and 84.2 M paried-end reads were obtained. DEGs were mainly enriched in processes including photosynthesis, phenylpropanoid biosynthesis, carotenoid biosynthesis, chlorophyll and abscisic acid (ABA) metabolism. Thirteen candidate transcripts related to chlorophyll metabolism, carotenoid biosynthesis and ABA metabolism were analyzed using real-time quantitative PCR (qPCR) at all fruit maturation stages of HWWZSTJ and WZSTJ. Chlorophyllase (CLH) and divinyl reductase (DVR) from chlorophyll metabolism, phytoene synthase (PSY) and capsanthin/capsorubin synthase (CCS) from carotenoid biosynthesis, abscisic acid 8'-hydroxylase (AB) and 9-cis-epoxycarotenoid dioxygenase (NCED1) from ABA metabolism were cloned and analyzed. NCED1 is probably responsible for the formation of late-repining of HWWZSTJ based on sequence and expression analyses. The preliminary study provides new information to better understand the complex process of late-ripening in Citrus at the transcriptional level.