bluuebunny/crossref_metadata_2025 huggingface dataset:
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

Characteristics of late maturity in fruits are good agronomic traits for extending the harvest period and marketing time. However, underlying molecular basis of the late-maturing 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-maturing characteristics from a late-maturing mutant ‘Huawan Wuzishatangju’ (HWWZSTJ) (Citrus reticulata Blanco) and its original line ‘Wuzishatangju’ (WZSTJ). A total of approximately 17.0 Gb and 84.2 M paried-end reads were obtained. DEGs were significantly enriched in the pathway of 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 maturing 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 (AB1) and 9-cis-epoxycarotenoid dioxygenase (NCED1) from ABA metabolism were cloned and analyzed. The expression pattern of NCED1 indicates its role in the late-maturing characteristics of HWWZSTJ. There were 270 consecutive bases missing in HWWZSTJ in comparison with full-length sequences of NCED1 cDNA from WZSTJ. Those results suggested that NCED1 might play an important role in late maturity of HWWZSTJ. This study provides new information of complex process that results in late maturity of Citrus fruit at the transcriptional level.
The first reported ceratopsid dinosaur from eastern North America (Owl Creek Formation, Late Cretaceous, Mississippi, USA)
Authors: Farke Andrew A. , Phillips George E.
Published: January 2018

Ceratopsids (“horned dinosaurs”) are known from numerous specimens in western North America and Asia, a distribution reflecting the inferred subaerial link between the two landmasses during the Late Cretaceous. However, this clade was previously unknown from eastern North America, presumably due to limited outcrop of the appropriate age and depositional environment as well as the separation of eastern and western North America by the Western Interior Seaway during much of the Late Cretaceous. A dentary tooth from the Owl Creek Formation (late Maastrichtian) of Union County, Mississippi, represents the first reported occurrence of Ceratopsidae from eastern North America. This tooth shows a combination of features typical of Ceratopsidae, including a double root and a prominent, blade-like carina. Based on the age of the fossil, we hypothesize that it is consistent with a dispersal of ceratopsids into eastern North America during the very latest Cretaceous, after the two halves of North America were reunited following the retreat of the Western Interior Seaway.
Evolution of anatomical concept usage over time: Mining 200 years of biodiversity literature
Authors: Manda Prashanti , Vision Todd J
Published: January 2018

The scientific literature contains an historic record of the changing ways in which we describe the world. Shifts in understanding of scientific concepts are reflected in the introduction of new terms and the changing usage and context of existing ones. We conducted an ontology-based temporal data mining analysis of biodiversity literature from the 1700s to 2000s to quantitatively measure how the context of usage for vertebrate anatomical concepts has changed over time. The corpus of literature was divided into nine non-overlapping time periods with comparable amounts of data and context vectors of anatomical concepts were compared to measure the magnitude of concept drift both between adjacent time periods and cumulatively relative to the initial state. Surprisingly, we found that while anatomical concept drift between adjacent time periods was substantial (55% to 68%), it was of the same magnitude as cumulative concept drift across multiple time periods. Such a process, bound by an overall mean drift, fits the expectations of a mean-reverting process.
Automatic characterization of ambulatory patterns of utilitarian and leisure trips
Authors: Härmä Aki , de Groot Koen
Published: January 2018

In the health self-management services it is beneficial to identify and address the already existing healthy activity patterns of the user. Some of these healthy activity patterns might be of a utilitarian nature, e.g. commuting to work by bike or on foot, or might be for leisure, like taking a walk in a park. In the paper we discuss one possibility to detect the utilitarian or leisure nature of a particular ambulatory path based on the geometry of the trajectory. In essence, a leisure trip is more commonly a round-trip while an utilitarian A-to-B trips follow the single shortest path between A and B. We define a generic measure for the characterization of utilitarian and leisure paths based on GPS location data and develop an algorithm for approaching the same based on only magnetometric data from a wearable device.
Assessing strengths and weaknesses of DNA metabarcoding based macroinvertebrate identification for routine stream monitoring
Authors: Elbrecht Vasco , Vamos Edith , Meissner Kristian , Aroviita Jukka , Leese Florian
Published: January 2018

1) DNA metabarcoding holds great promise for the assessment of macroinvertebrates in stream ecosystems. However, few large-scale studies have compared the performance of DNA metabarcoding with that of routine morphological identification.

2) We performed metabarcoding using four primer sets on macroinvertebrate samples from 18 stream sites across Finland. The samples were collected in 2013 and identified based on morphology as part of a Finnish stream monitoring program. Specimens were morphologically classified, following standardised protocols, to the lowest taxonomic level for which identification was feasible in the routine national monitoring.

3) DNA metabarcoding identified more than twice the number of taxa than the morphology-based protocol, and also yielded a higher taxonomic resolution. For each sample, we detected more taxa by metabarcoding than by the morphological method, and all four primer sets exhibited comparably good performance. Sequence read abundance and the number of specimens per taxon (a proxy for biomass) were significantly correlated in each sample, although the adjusted R2 were low. With a few exceptions, the ecological status assessment metrics calculated from morphological and DNA metabarcoding datasets were similar. Given the recent reduction in sequencing costs, metabarcoding is currently approximately as expensive as morphology-based identification.

4) Using samples obtained in the field, we demonstrated that DNA metabarcoding can achieve comparable assessment results to current protocols relying on morphological identification. Thus, metabarcoding represents a feasible and reliable method to identify macroinvertebrates in stream bioassessment, and offers powerful advantage over morphological identification in providing identification for taxonomic groups that are unfeasible to identify in routine protocols. To unlock the full potential of DNA metabarcoding for ecosystem assessment, however, it will be necessary to address key problems with current laboratory protocols and reference databases.
High definition video loggers provide new insights into behaviour, physiology, and the oceanic habitat of marine top predators
Authors: Mattern Thomas , McPherson Michael D , Ellenberg Ursula , van Heezik Yolanda , Seddon Philipp J
Published: January 2018

1. Camera loggers are increasingly used to examine behavioural aspects of free-ranging animals. However, often video loggers are deployed with a focus on specific behavioural traits utilizing small cameras with a limited field of view, poor light performance and video quality. Yet rapid developments in consumer electronics provide new devices with much improved visual data allowing a wider scope for studies employing this novel methodology.

2. We developed a camera logger that records full HD video through a wide-angle lens, providing high resolution footage with a greater field of view than other camera loggers. Main goal was the analysis of foraging behaviour of a marine top-predator, the Yellow-eyed penguin in New Zealand, in the context habitat characteristics. Frame-by-frame analysis allowed accurate timing of prey pursuits and time spent over certain seafloor types. Similarly, it was possible to time breathing intervals between dives and quantify exhalation events during prey events, a previously undescribed behaviour. Screen overlays facilitate analysis of flipper angles and beat frequencies throughout various stages of the dive cycle.

3. The recorded video footage showed that prey species were associated with certain seafloor types, revealed different predator evasion strategies by benthic fishes, and highlighted varying energetic consequences for penguins pursuing certain types of prey. Flipper movement analysis confirmed decreasing effort during descent phases as the bird gained depth, and that ascent was principally passive. Breathing episodes between dives were short (<1 s) while the majority of the time was devoted to subsurface scanning with a submerged head.

4. Video data recorded on free-ranging animals not only provides a wealth of information recorded from a single deployment but also necessitates new approaches with regards to analysis of visual data. Here, we demonstrate the diversity of information that can be gleaned from video logger data, if devices with high video resolution and wide field of view are utilized
USMI Galaxy Demonstrator (UGD): a collection of tools to integrate microorganisms information
Authors: Colobraro Daniele Pierpaolo , Romano Paolo
Published: January 2018

Due to the fragmentation of microbial information and the several branch of human activities encompassed by microorganism applications, a comprehensive approach for merging information on microbes is needed. Although on line service providers collect several data on microorganisms and provide services for microbial Biological Resource Centres (mBRCs), such services are still limited both in contents and aims. The USMI Galaxy Demonstrator (UGD), an implementation of the Galaxy framework exploiting the XML-based Microbiological Common Language (MCL), is meant to support researchers to make an integrated access to enriched information from microbial catalogues, as well as to help mBRC curators in validating and enriching the contents of their catalogues. Researchers and mBRC curators may exploit the UGD to avoid manual, potentially long, searches on the web and to identify and select microorganisms of interest.

UGD tools are written in Python, version 2.7. They allow to enrich the basic information provided by catalogues with related taxonomy, literature, sequence and chemical compound data retrieved from some of the main databases on the basis of the strain number, i.e. the unique identifier for a given culture, and the species names. The data is retrieved by querying database Web Services using either the Simple Object Access Protocol (SOAP) or the Representational State Transfer (REST) access protocols. The MCL format provides a versatile way to archive and exchange data among mBRCs.

Galaxy is a well-known, open, web-based platform which offers many tools to retrieve, manage and analyze different kind of information arising from any life science domain. By exploiting Galaxy flexibility,UGD implements some tools and workflows that can be used to find and integrate several information on microorganisms. UGD tools integrate basic information which may support mBRC staff in the insertion of all fundamental strain information in a proper format allowing integration and interoperability with external databases. They also extend the output by adding information on source materials, including species and strain numbers, and retrieve associated microorganisms which use a compound or an enzyme in whatever metabolic pathway by returning the accession number, synonyms, links to external databases, taxon name, and strain number of the requested molecule.
How long should the fully hillside-closed forest protection be implemented on the Loess Plateau, Shaanxi, China?
Authors: Hou Lin , Hou Sijia
Published: January 2018

Background. Restoration of degraded forest ecosystem is crucial for regional sustainable development. To protect the country’s fragile and fragmented environment, the Chinese government has initiated an ecological engineering, the Natural Forest Protection Program in seventeen provinces in China since 1998. Fully hillside-closed forest protection (vegetation restoration naturally without any artificial disturbance) was one of vital measures of the Natural Forest Protection Program applied national wide. Whether plant diversity, biomass and age structure of dominant tree species and soil nutrients in protected stands may become better with increase of protected period are still open problems.

Methods. We investigated community diversity, biomass of dominant tree species, age structures, and analyzed soil chemical properties of a Pinus tabulaeformis population at protected sites representing different protected ages at Huanglongshan Forest Bureau on the Loess Plateau, Shaanxi, China.

Results. Plant species richness of Pinus tabulaeformis community was significantly affected (p<0.05) by forest protection and the effect attenuated with protection age.Shannon evenness index of plant species generally increased with protection age. Stands protected for 45 years had the highest tree biomass and considerable natural regeneration capacity. Contents of organic carbon, available phosphorus and available potassium in top soil increased in protected stands less than 45 years, however decreased significantly thereafter. Long-term forest protection also decreased content of mineral nitrogen in top soil.

Discussion. We found that richness of shrubs and herbs was significantly affected by forest protection, and evenness indices of tree, shrub and herb increased inconsistently with protected ages. Forest protection created more complex age structures and tree densities with increasing age of protection. Content of soil mineral nitrogen at 0-20 cm soil depth showed a decreasing trend in stands of up to 30 years. Soil available phosphorus and potassium contents were higher in stands with greater proportions of big and middle trees. Long-term protection (> 45 years) of Pinus tabulaeformisstand in southeast Loess Plateau, China, may be associated with decreasing plant species richness, proportion of medium to large trees, dominant biomass of Pinus tabulaeformis and soil nutrients.
Genetic and structural study of DNA-directed RNA polymerase II of Trypanosoma brucei, towards the designing of novel antiparasitic agents
Authors: Papageorgiou Louis , Megalooikonomou Vasileios , Vlachakis Dimitrios
Published: January 2018

Trypanosoma brucei brucei (TBB) belongs to the unicellular parasitic protozoa organisms, specifically to the Trypanosoma genus of the Trypanosomatidae class. A variety of different vertebrate species can be infected by TBB including humans and animals. Under particular conditions, the TBB can be hosted by wild and domestic animals; thereby an important reservoir of infection always remains available to transmit through the tsetse flies. Although the TBB parasite is one of the leading causes of death in the most underdeveloped countries, to date, there is neither vaccination available nor any drug against TBB infection. The subunit RPB1 of the TBB DNA-directed RNA polymerase II (DdRpII) constitutes an ideal target for the design of novel inhibitors, since it is instrumental role is vital for the parasite’s survival, proliferation, and transmission. A major goal of the described study is to provide insights for novel anti-TBB agents via a state of the art drug discovery approach of the TBB DdRpII RPB1. In an attempt to understand the function and action mechanisms of this parasite enzyme related to its molecular structure, an in-depth evolutionary study has been conducted in parallel to the in silico molecular designing of the 3D enzyme model, based on state of the art comparative modelling and molecular dynamics techniques. Based on theevolutionary studies results nine new invariant, first-time reported, highly conserved regions have been identified within the DdRpII family enzymes. Consequently, those patches have been examined both at the sequence and structural level and have been evaluated in regards to their pharmacological targeting appropriateness. Finally, the pharmacophore elucidation study enabled us to virtually in silico screenhundreds of compounds and evaluate their interaction capabilities with the enzyme. It was found that a series of Chlorine-rich set of compounds were the optimal inhibitors for the TBB DdRpII RPB1 enzyme. All-in-all, herein we present a series of new sites on the TBB DdRpII RPB1 of high pharmacological interest, alongside the construction of the 3D model of the enzyme and the suggestion of a new in silico pharmacophore model for fast screening of potential inhibiting agents.
Effect of light on aggregational behavior of planarian Dugesia tigrina
Authors: Lee Jaemin
Published: January 2018

Introduction. Planarians are renowned for their regenerative ability due to pluripotent stem cells, as well as their peculiar photophobic response. However, few facts are known about their aggregational behavior. This study aims to reveal the effect of light on aggregational behavior. Reynierse (1966) suggested that light has a negative effect on the formation of aggregations. However, one of his objectives for aggregational behavior was inappropriate. This study reevaluated the effect of existence of light on aggregational behavior, as well as ascertained the effect of wavelength on the formation of aggregations.

Methods. In this study, the ratio of individuals participating in aggregations was measured as a criterion to determine aggregational behavior. Aggregational behavior was measured after two hours from the initial exposure to different light sources. The behaviors under white LED light and under shade were compared, as well as the behaviors under five different light sources: infrared lamp, red, green, blue LED, and ultraviolet lamp.

Results. The existence of light interfered the formation of aggregations (t-test, p < 0.0001), which supports the former study of Reynierse. Also, aggregational behavior differed under different wavelengths (ANOVA, p < 0.0001). Except for the infrared light which emitted a wide range of wavelengths, the behavior showed hierarchy: decreasing aggregational behavior in accordance with decreasing wavelength. UV light has the most significant negative effect on the formation of aggregations.

Discussion. Exposure to light caused negative effects on performing aggregational behavior. Participation in aggregations appears to be influenced by photophobic response, especially under lights of short wavelength. Disintegrating aggregations under exposure to lights can potentially bring evolutionary benefit. This behavior possibly makes the aggregating planarians altogether exposed to a higher risk or predation, considering that they lack defense mechanisms. Planarians can lower the risk and continue the populations by disintegrating the aggregational behavior under the existence of UV and lights of higher wavelength, which are indicatives of daytime. Understanding aggregational behavior of animals of a lower order would give better insight on general herding behavior, and potentially help interpreting more complex behaviors of higher animals.
Asymmetric cell-cell adhesion can trigger mitochondriogenesis: A hypothesis
Authors: Naito Yasuhiro
Published: January 2018

Without exception, modern hypotheses explaining the origin of eukaryotes assume evolution from two (or more) distinct prokaryotes. Almost all prokaryotic cell membranes possess a chemiosmosis system, whereas eukaryotic cell membranes have lost that ability. Nevertheless, no hypothesis describes how chemiosmosis might have been lost from one symbiont. This work proposes a novel hypothesis for the origin of eukaryotes, invoking the adhesion of two chemiosmosis-bearing membranes to promote eukaryogenesis. The intermembrane space between the adhered cell membranes accumulates protons, and the enhanced proton gradient across the membranes accelerates ATP synthesis in both symbionts. Next, the smaller symbiont is engulfed by the larger symbiont to expand the intermembrane space, and then the engulfed symbiont starts to supply a large quantity of ATP to the surrounding host to improve the evolutionary fitness of the whole symbiotic union. Finally, the host cell membrane acquires pluripotent membrane excitation in exchange for its own chemiosmosis system.
Direct imaging of APP proteolysis in living cells
Authors: Parenti Niccoló , Del Grosso Ambra , Antoni Claudia , Cecchini Marco , Corradetti Renato , Pavone Francesco S , Calamai Martino
Published: January 2018

It is now widely accepted that oligomers consisting of Aβ peptide are the cytotoxic species contributing mostly to the development of Alzheimer’s disease. Aβ peptide production results from the specific proteolytic processing of the amyloid precursor protein (APP). Deciphering the factors governing the activity of the secretases responsible for the cleavage of APP is still a critical issue. Kits available commercially measure the enzymatic activity of the secretases from cells lysates, in vitro. By contrast, we have developed a prototypal rapid bioassay that provides visible information on the proteolytic processing of APP directly in living cells. APP was fused to a monomeric variant of the green fluorescent protein and a monomeric variant of the red fluorescent protein at the C-terminal and N-terminal, respectively. Changes in the proteolytic processing rate in transfected human neuroblastoma and rat neuronal cells were imaged with confocal microscopy as changes in the red/green fluorescence intensity ratio. The significant decrease in the mean red/green ratio observed in cells over-expressing the β-secretase BACE1 fused to a monomeric blue fluorescent protein confirms that the proteolytic site is still accessible. Specific siRNA was used to evaluate the contribution of endogenous BACE1. Interestingly, we found that the degree of proteolytic processing of APP is not completely homogeneous within the same single cell, and that there is a high degree of variability between cells of the same type. We were also able to follow with a fluorescence spectrometer the changes in the red emission intensity of the extracellular medium when BACE1 was overexpressed. This represents a complementary approach to fluorescence microscopy for rapidly detecting changes in the proteolytic processing of APP in real time. Moreover, we obtained a quantitatively robust estimate of the changes in the red/green ratio for the above conditions by using a flow cytometer able to simultaneously excite and measure the red and green fluorescence. Our novel approach lay the foundation for a bioassay suitable to study the effect of drugs or particular conditions, to investigate in an unbiased way the the proteolytic processing of APP in single living cells in order, and to elucidate the causes of the variability and the factors driving the processing of APP.
Genome-wide analysis of WRKY transcription factors in wheat (Triticum aestivum L.) and differential expression under water deficit treatment
Authors: Ning Pan , Liu Congcong , Kang Jingquan , Lv Jinyin
Published: January 2018

WRKY proteins, comprising one of the largest transcription factor families in plant kingdom, play crucial roles in the plant development and stress responses. Despite several studies on WRKYs in wheat (Triticum aestivum L.) were investigated, functional annotation information about wheat WRKYs was limited. Here, 171 TaWRKY transcription factors (TFs) were identified from the whole wheat genome and compared with proteins from other 19 species representing nine major plant lineages. A phylogenetic analysis, coupled with gene structure analysis and motif determination, divided these TaWRKYs into seven subgroups (Group I, IIa-e, III). Chromosomal location showed that the most TaWRKY genes were enriched on four chromosomes, especially on chromosome 3B, and 85 (49.7%) genes were either tandem (5) or segmental duplication (80), which suggested that though tandem duplication has contributed to the expansion of TaWRKY family, segmental duplication probably played a more pivotal role. The cis-acting elements analysis revealed putative functions of WRKYs in wheat during development as well as under numerous biotic and abiotic stresses. Finally, the expression of TaWRKY genes in flag leaves, glumes and lemmas under water stress were analyzed, and we found different TaWRKY genes preferentially express in specific tissue during the grain-filling stage. Our results provide a more extensive knowledge on TaWRKYs, which helps to complete the information of WRKY gene family in wheat, and also contribute to screen more candidate genes for further investigation on function characterization of WRKYs under various stresses.
Computer modelling reveals new conformers of the ATP binding loop of Na+/K+-ATPase involved in the transphosphorylation process of the sodium pump
Authors: Tejral Gracian , Sopko Bruno , Necas Alois , Schoner Wilhelm , Amler Evzen
Published: January 2018

Hydrolysis of ATP by Na+/K+-ATPase, a P-Type ATPase, catalyzing active Na+ and K+ transport through cellular membranes leads transiently to a phosphorylation of its catalytical α-subunit. Surprisingly, 3-dimensional molecular structure analysis of P-type ATPases reveals that binding of ATP to the N-domain connected by a hinge to the P-domain is much too far away from the Asp369 to allow the transfer of ATP’s terminal phosphate to its aspartyl-phosphorylation site. In order to get information how the transfer of the γ‑phosphate group of ATP to the Asp369 is achieved, analogous molecular modeling of the M4-M5 loop of ATPase was performed using the crystal data of Na+/K+-ATPase of different species. Analogous molecular modeling of the cytoplasmic loop between Thr338 and Ile760 of the α2-subunit of Na+/K+-ATPase and the analysis of distances between the ATP binding site and phosphorylation site revealed the existence of 2 ATP binding sites in the open conformation, the first one close to Phe475 in the N-domain, the other one close to Asp369 in the P-domain. However, binding of Mg2+•ATP to any of these sites in the “open conformation” may not lead to phosphorylation of Asp369. Additional conformations of the cytoplasmic loop were found wobbling between “open conformation” <==> “semi-open conformation <==> “closed conformation” in the absence of 2Mg2+•ATP. The cytoplasmic loop’s conformational change to the “semi-open conformation” -- characterized by a hydrogen bond between Arg543 and Asp611 -- triggers by binding of 2Mg2+•ATP to a single ATP site and conversion to the “closed conformation” the phosphorylation of Asp369 in the P-domain, and hence the start of Na+/K+-activated ATP hydrolysis.
The impact of using large training data set KDD99 on classification accuracy
Authors: Özgür Atilla , Erdem Hamit
Published: January 2018

This study investigates the effects of using a large data set on supervised machine learning classifiers in the domain of Intrusion Detection Systems (IDS). To investigate this effect 12 machine learning algorithms have been applied. These algorithms are: (1) Adaboost, (2) Bayesian Nets, (3) Decision Tables, (4) Decision Trees (J48), (5)Logistic Regression, (6) Multi-Layer Perceptron, (7) Naive Bayes, (8) OneRule, (9)Random Forests, (10) Radial Basis Function Neural Networks, (11) Support Vector Machines (two different training algorithms), and (12) ZeroR. A well-known IDS benchmark dataset, KDD99 has been used to train and test classifiers. Full training data set of KDD99 is 4.9 million instances while full test dataset is 311,000 instances. In contrast to similar previous studies, which used 0.08%–10% for training and 1.2%–100% for testing, this study uses full training dataset and full test dataset. Weka Machine Learning Toolbox has been used for modeling and simulation. The performance of classifiers has been evaluated using standard binary performance metrics: Detection Rate, True Positive Rate, True Negative Rate, False Positive Rate, False Negative Rate, Precision, and F1-Rate. To show effects of dataset size, performance of classifiers has been also evaluated using following hardware metrics: Training Time, Working Memory and Model Size. Test results shows improvements in classifiers in standard performance metrics compared to previous studies.
Landscapes of fear: from trophic cascades to applied management and population ecology
Authors: Bleicher Sonny S
Published: January 2018

Predator-Prey dynamics, and their trophic impacts, have functioned as a focal point in both community and population biology for five decades. The work-group focusing on these dynamics has however largely changed the focus of their work from trophic effects to the study of non-consumptive effects of predation-- the “ecology of fear”. An increasing number of studies chose to spatially chart wildlife populations’ risk assessment and of those the majority use optimal patch-use (giving-up densities) as a continuous measure of fear. These charts, “landscapes-of-fear” (LOFs) originated in conservation literature and the reintroduction of wolves to Yellowstone. Today, they are used to study population habitat selection and venture into the evolutionary context with studies examining the mechanisms by which species coexist in the same physical space. This review predicts increase in, and encourages the use of, LOFs: as a conservation tool to assess species land-use; as a bridge between ecology and neurology with stress hormones as indicators fear; and as a tool to compare species’ evolutionary dynamics within a community context.
The influence of soil microbial community structure on carbon and nitrogen partitioning in plant/soil ecosystems
Authors: Johnson David C.
Published: January 2018

A greenhouse study was conducted to evaluate the influence of increasing soil fungal-to-bacterial ratios (F:B) on the allocation of plant-photosynthate carbon into the carbon (C) and nitrogen (N) partitions (g) of plant components (root, shoot and fruit), New-Soil C and N, and Soil-Respiration C (CO2). Six (6) experimental treatment soils were formulated to provide linearly increasing: initial-soil C% (0.14% – 5.3%); initial-soil N% (0.01% - 0.40%); and soil microbial community (SMC) populations progressing from bacterial dominant (F:B=0.04) to fungal dominant (F:B=3.68) while still maintaining significant SMC population homogeneity. In an 86-day greenhouse experiment, growing chile plants (Capsicum annuum) in treatment soils with increasing F:B (0.4-3.68), the following was observed: a) a continuous linear increase (3% up to 56%) in the partitioning of total plant-photosynthate C into plant biomass (root, shoot and fruit) when regressed to initial F:B (m=0.13; r2=0.96); b) approximately 93% of the flow of plant-photosynthate C was partitioned into New-Soil C in Treatment 0 (F:B = 0.04), to a minimum of 47% in Treatment 5 (F:B = 3.68) demonstrating a negative linear correlation to treatment Initial-Soil C mass (m= -0.12; r2 = 0.97); c) conditional and coordinated flow of system C resources into nitrogen (N) fixation (est. C cost for N fixation at 6:1), with 1.21 g C partitioned to N fixation in Treatment 0 (F:B=0.04), peaking at 6.92 g C in Treatment 2 (F:B=1.6), and final C partitioning to N fixation of 2.91 g C in Treatment 5 (F:B=3.68), following a 3rd order polynomial trendline (r2=0.99) when correlated with initial treatment soil C mass; d) decreases in soil respiration, from 44% of Initial-Soil C substrate respired in bacterial-dominant low-C (0.14%) soils (F:B = 0.04) to 11% in fungal dominant (F:B = 3.68), high-C percent (5.30% C) soils (y = -0.108ln(x)+ 0.4987; r2= 0.95). Increasing the F:B in the soils of agroecosystems may provide more efficient accumulation and partitioning of photosynthate C into plant and soil biomass, improved N fixation and beneficial increases in total carbon use efficiencies. Collectively, these benefits could provide a practical and cost-effective path towards: improving crop production, reducing N-fertilizer inputs, promoting a more sustainable agricultural system, while providing a cost-effective approach for capturing and storing atmospheric carbon (CO2) in soils of agroecosystems.
Sequential language learning versus language immersion in bilingualism: Diffusion MRI connectometry reveals microstructural evidence
Authors: Khazaei Razieh , Sobhani Soheila , Rahmani Farzaneh , Aarabi Mohammad Hadi
Published: January 2018

Background: Bilingualism is a universal phenomenon. Study of bilingual brain has provided evidence to probable advantageous outcomes of early second language learning and brain structural correlates to these outcomes. Preservation of cognitive function with aging and executive dexterity are amongst proposed benefits. Method: Using the data deposited by Pliatsikas we analyzed through diffusion MRI connectometry structural difference in white matter tracts in 20 healthy sequential bilingual adults, who used English as a second language on a daily basis, and 25 controls in fiber differentiation analyses. Significant tracts were extracted with and without regression against language immersion period. Results: Connectometry results revealed increased connectivity in corpus callosum (CC), bilateral cingulum, arcuate fasciculus (AF), and left Inferior fronto occipital fasciculus (IFOF), of sequential bilingual adults. Also bilateral IFOF, AF as well as body and genu of corpus callosum were positively correlated with language immersion time. Conclusion: Mentioned white matter tracts with diffusion structural significance in young adults with long immersion into the second language, confirm results of previous results. These are also in consort with known pathways involved in neurophysiological processes in speech stream and in cognitive performance. Insertion of immersion time as a variable in the model, yielded the same results with higher FDR values, except for arcuate fasciculus. Future studies are warranted to address structural differences with larger samples, investigating the effects of early language immersion on white matter tracts versus individual and social variables that interfere with white matter maturation and integrity.
Fertilization and stocking of unmanaged ponds through temporal plankton community structure map (PCSM): A nascent concept in aquaculture planning
Authors: Roy Koushik
Published: January 2018

Background: This paper deals with a non-conventional approach called PCSM model. It was developed to aid in horizontal expansion of aquaculture through utilization of unmanaged ponds for modified extensive aquaculture. This model applies to small lentic water bodies like ponds (<10 ha area) where plankton count and limnological parameters are naturally within permissible range for fish culture or survival. It can only help in – ‘modified extensive aquaculture’ by increasing the abundance of plankton groups that are most preferred. This is only applicable for culturing planktophagus fishes.

Methods: PCSM incorporates annual plankton community dynamics (data) of some representative ‘unmanaged’ ponds of the region. Only the dynamics of top two highly palatable and highly preferable Phytoplankton (Chlorophyceae and Bacillariophyceae) and Zooplankton (Rotifera and Copepoda) groups for Indian Major Carps were focused upon. The monthly composition of each plankton group in each pond of the region was averaged and plotted into a graphical model called Multiple Spline Curve with 5% padding using SigmaPlot.

Results: The model here has been developed in reference to pond based polyculture of 3 Indian Major Carps (Catla catla, Labeo rohita and Cirrhinus mrigala), which is still a dominant practice in the unmanaged freshwater ponds in India. The model can help in deciding two things – Fertilization timing (PCSM: Fertilization Module) and Stocking time (PCSM: Stocking Module). It is region specific and presently developed for Raipur district of Chhattisgarh, India.

Discussions: Through PCSM, effective pond fertilization period is 7 months out of 12 (April, June, August, September, October, December and February). Moreover, year round multiple stocking multiple harvesting based fish culture can be ensured in unmanaged pond through PCSM guided stocking schedule (June, August, November and December).
On the connection between supersaturation in the upper airways and «humid-rainy» and «cold-dry» seasonal patterns of influenza
Authors: Ishmatov Aleksandr N
Published: January 2018

We have originally shown for the first time the two different climatic patterns of seasonality of influenza and common colds have an only one common “link”. It is the effect of supersaturation and condensational growth in the upper airways which occurs under specific environmental conditions when flu seasons take place in the tropical/subtropical and temperate regions.

We have found that under climatic conditions which are peculiar to the seasonal patterns of influenza and common colds (“humid-rainy” and “cold-dry”) the effect of supersaturation and condensational growth may be additional factor/reason leading to the next:

- dramatic rise of deposition rate of infectious agents from inhaled air in the upper airways;

- additional acidification of epithelial lining fluid in the local areas of the respiratory tract, and, as a result, may lead to destructive impacts on host cells and weakening of the defense mechanisms of the airways;

- additional affecting on the critical local cooling and reducing (as a consequence) the antiviral immune response of the airway epithelial cells.

Thus, the effect of supersaturation and condensational growth in the upper airways can act as a common trigger for influenza, common colds and other respiratory infection in both mid-latitudes and in the tropics/subtropics.
Probability that p-value provides misleading evidence cannot be controlled by sample size
Authors: Grendar Marian , Judge George G
Published: January 2018

A measure of statistical evidence should permit the sample size determination so that the probability M of obtaining (strong) misleading evidence can be held as low as desired. On this desideratum the p-value fails completely, as it leads either to an arbitrary sample size if M >= 0.01 or no sample size at all, if M < 0.01.

Unlike the p-value, the ratio of likelihoods, the ratio of posteriors, as well as the Bayes Factor, permit controlling the probability of misleading evidence by the sample size.
Finding the optimal bayesian network given a constraint graph
Authors: Schreiber Jacob M , Noble William S
Published: January 2018

Despite recent algorithmic improvements, learning the optimal structure of a Bayesian network from data is typically infeasible past a few dozen variables. Fortunately, domain knowledge can frequently be exploited to achieve dramatic computational savings, and in many cases domain knowledge can even make structure learning tractable. Several methods have previously been described for representing this type of structural prior knowledge, including global orderings, super-structures, and constraint rules. While super-structures and constraint rules are flexible in terms of what prior knowledge they can encode, they achieve savings in memory and computational time simply by avoiding considering invalid graphs. We introduce the concept of a "constraint graph" as an intuitive method for incorporating rich prior knowledge into the structure learning task. We describe how this graph can be used to reduce the memory cost and computational time required to find the optimal graph subject to the encoded constraints, beyond merely eliminating invalid graphs. In particular, we show that a constraint graph can break the structure learning task into independent subproblems even in the presence of cyclic prior knowledge. These subproblems are well suited to being solved in parallel on a single machine or distributed across many machines without excessive communication cost.
Achilles heel of a powerful invader: restrictions on distribution and disappearance of feral pigs from a protected area in Northern Pantanal, Western Brazil
Authors: Cordeiro Jose L P , Hofmann Gabriel S , Fonseca Carlos , Oliveira Luiz Flamarion B
Published: January 2018

This paper focus a rare case of natural disappearance of feral pigs (Sus scrofa) in an extensive area without using traditional methods of eradication programs. The study was conducted both in the Private Reserve of Natural Heritage (PRNH) Sesc Pantanal and in an adjacent traditional private cattle ranch. In 1998 feral pigs were abundant and widely distributed in the PRNH. However, the feral pigs were gradually disappeared from the area and currently the absence of pigs in the PRNH contrasts with the adjacent cattle ranch where the species is abundant. To understand the current distribution of feral pigs in the region we partitioned the effects of variation of feral pigs presence considering the habitat structure (local), landscape composition and the occurrence of potential predators. Additionally, we modeled the distributions of feral pigs in Northern Pantanal, projecting into the past using the classes of vegetation cover before the PRNH implementation (year 1988). Our results show areas with more suitability for feral pigs in region are a landscape dominated by pastures and permeated by patches of Seasonal Dry Forest. The species tends to avoid predominantly forested areas. Additionally, we recorded that the environmental suitability for feral pigs decreases exponentially as the distance from water bodies increases. The disappearance of feral pigs into PRNH area seems to be associated with changes in the landscape and vegetation structure after the removal of the cattle. In the Brazilian Pantanal the feral pigs occurrence seems strongly conditioned to environmental changes associated to livestock activity.
Short-term deleterious effects of standard isolation and cultivation methods on new tropical freshwater microalgae strains
Authors: Aray-Andrade M. Magdalena , Uyaguari-Diaz Miguel I , Bermúdez Monsalve J. Rafael
Published: January 2018

Algae with potential biotechnological applications in different industries are commonly isolate from the environment in order to obtain pure (axenic) stocks that can be safely stored for long periods of time. To obtain axenic cultures, antibiotics are frequently used, and cryopreservation is applied to keep standing stocks. However, many of these now standard methods were developed using strains coming from pristine-to-low intervened environments and cold-to-temperate regions. Thus, it is still not well understand the potential effect of said methods on the life cycle and biochemical profile of algae isolates from hiper-eutrophic and constant high-temperature tropical regions, which could potentially render them unsuitable for their intended biotechnological application. In this study, we conducted a genetic characterization (18S rRNA) and evaluated the effect of purification (use of the antibiotic chloramphenicol, CPA) and cryopreservation (dimethyl sulfoxide (DMSO)-sucrose mix and Glycerol) on the growth rate and lipid content of four new tropical freshwater algal isolates: Chorella sp. M2, Chlorella sp. M6, Scenedesmus sp. R3, and Coelastrella sp. A2, from the Ecuadorian coast. The genetic characterization showed a clear discrimination between strains. All strains cultured with CPA had a lower growth rate. After cryopreservation Coelastrella sp. A2 did not grow with both methods; Chorella sp. M2, Chlorella sp. M6 and Scenedesmus sp. R3 presented no significant difference in growth rate between the cryopreservants. A significantly higher lipid content was observed in biomass cryopreserved with glycerol in relation to DMSO-sucrose, with Chorella sp. M2 and Chlorella sp. M6 having twice as much in the first treatment. The results highlight the relevance of choosing an appropriate method for storage as the materials used can affect the biological performance of different tropical species, although is still to determine if the effects observed here are long lasting in subsequent cultures of these algae.
An empirical analysis of the Docker container ecosystem on GitHub
Authors: Cito Jürgen , Schermann Gerald , Wittern Erik , Leitner Philipp , Zumberi Sali , Gall Harald C.
Published: January 2018

Docker allows packaging an application with its dependencies into a standardized, self-contained unit (a so-called container), which can be used for software development and to run the application on any system. Dockerfiles are declarative definitions of an environment that aim to enable reproducible builds of the container. They can often be found in source code repositories and enable the hosted software to come to life in its execution environment. We conduct an exploratory empirical study with the goal of characterizing the Docker ecosystem, prevalent quality issues, and the evolution of Dockerfiles. We base our study on a data set of over 70000 Dockerfiles, and contrast this general population with samplings that contain the Top-100 and Top-1000 most popular Docker-using projects. We find that most quality issues (28.6%) arise from missing version pinning (i.e., specifying a concrete version for dependencies). Further, we were not able to build 34% of Dockerfiles from a representative sample of 560 projects. Integrating quality checks, e.g., to issue version pinning warnings, into the container build process could result into more reproducible builds. The most popular projects change more often than the rest of the Docker population, with 5.81 revisions per year and 5 lines of code changed on average. Most changes deal with dependencies, that are currently stored in a rather unstructured manner. We propose to introduce an abstraction that, for instance, could deal with the intricacies of different package managers and could improve migration to more light-weight images.