bluuebunny/crossref_metadata_2025 huggingface dataset:
Cannibalism as cell differentiation meant that Bacillus subtilis NRS-762 is not suitable as model organism in survivability studies of microbes
Authors: Ng Wenfa
Published: January 2018

Survival of microbes on various surfaces and environment is a question of importance to basic science, as well as health care, water treatment and distribution, ecology, and search for life in other planetary bodies. To this end, various model organisms, known to be resilient against a variety of environmental insults are used for understanding the mechanisms underlying survival in extreme environments, or conditions mimicking those of the investigated habitats. Serendipitous observations of drastic decline in optical density of Bacillus subtilis NRS-762 (ATCC 8473) in LB Lennox and Tryptic Soy Broth (TSB) at temperatures of 25, 30 and 37 oC, after the aerobic culture reached maximal cell density at stationary phase, pointed to possible cell lysis as mechanism for cell death. Specifically, optical density of the bacterium declined from 5.4 at 22.5 hours post inoculation in LB Lennox to 2.5 after 38 hours of culture at 25 oC and 250 rpm rotational shaking. Similarly, optical density of B. subtilis also precipitously declined from 6.4 at 33 hours of culture to 1.8 at 51 hours post inoculation at 37 oC in TSB. This is in stark contrast to aerobic growth of Escherichia coli DH5α (ATCC 53868) in LB Lennox at 37 oC and 250 rpm, where optical density remained stable during stationary phase. More importantly, observations of B. subtilis culture after autoclave decontamination revealed lack of cellular debris; thereby, indicating massive cell lysis resulting in population collapse. Although B. subtilis is known to enter into various cellular differentiation programmes upon nutrient starvation such as onset of stationary phase in cell culture, complete absence of cell debris that usually settle at the bottom of the shake flask after autoclave decontamination, pointed to cannibalism or prophage induced cell lysis as key reasons underlying observed drastic decline in optical density of the culture. Specifically, prophage induced cell lysis may be discounted as this would have destroyed the entire cell population expeditiously shortly after entry into stationary phase. Hence, cannibalism, where a subpopulation of B. subtilis cells secrete cell lysis factors which other B. subtilis cells are not resistant to, likely result in massive cell lysis that generated cellular contents that could serve as nutrients for the surviving cell population resistant to the cell lysis factors, and may be the dominant mechanism underpinning observed rapid decline in optical density after entry into stationary phase. Collectively, B. subtilis NRS-762 is not suitable as model organism for microbial survivability studies given its tendency to undergo differentiation into the cannibalism programme, which in killing a significant fraction of cells upon nutrient deprivation, would also confound experiments aimed at understanding the resilience of cells towards various extraneous environmental factors not common in the microbe’s favoured habitats.
Evaluation of potential reference genes for real-time qPCR analysis in a biparental beetle, Lethrus apterus (Coleoptera: Geotrupidae)
Authors: Nagy Nikoletta A , Németh Zoltán , Juhász Edit , Póliska Szilárd , Rácz Rita , Kosztolányi András , Barta Zoltán
Published: January 2018

Hormones play an important role in the regulation of physiological, developmental and behavioural processes. Many of these mechanisms in insects, however, are still not well understood. One way to investigate hormonal regulation is to analyse gene expression patterns of hormones and their receptors in question by real-time quantitative polymerase chain reaction (RT-qPCR). This method, however, requires stably expressed reference genes for normalisation. In the present study, we evaluated 11 candidate housekeeping genes as reference genes in samples of Lethrus apterus, an earth-boring beetle with biparental care, collected from a natural population. For identifying the most stable genes we used the following computational methods: geNorm, NormFinder, BestKeeper, comparative delta Ct method and RefFinder. Based on our results, the two body regions sampled (head and thorax) differ in which genes are most stably expressed. We identified two candidate reference genes for each region investigated: ribosomal protein L7A and RP18 in samples extracted from the head, and ribosomal protein L7A and RP4 extracted from the muscles of the thorax. These reference genes can be used to study the hormonal regulation of reproduction and parental care in Lethrus apterus in the future.
Finding and correcting syntax errors using recurrent neural networks
Authors: Santos Eddie A , Campbell Joshua C , Hindle Abram , Amaral José Nelson
Published: January 2018

Minor syntax errors are made by novice and experienced programmers alike; however, novice programmers lack the years of intuition that help them resolve these tiny errors. Standard LR parsers typically resolve syntax errors and their precise location poorly. We propose a methodology that helps locate where syntax errors occur, but also suggests possible changes to the token stream that can fix the error identified. This methodology finds syntax errors by checking if two language models “agree” on each token. If the models disagree, it indicates a possible syntax error; the methodology tries to suggest a fix by finding an alternative token sequence obtained from the models. We trained two LSTM (Long short-term memory) language models on a large corpus of JavaScript code collected from GitHub. The dual LSTM neural network model predicts the correct location of the syntax error 54.74% in its top 4 suggestions and produces an exact fix up to 35.50% of the time. The results show that this tool and methodology can locate and suggest corrections for syntax errors. Our methodology is of practical use to all programmers, but will be especially useful to novices frustrated with incomprehensible syntax errors.
A simple encryption algorithm
Authors: St. Pierre Joseph Keenan
Published: January 2018

In this paper I present a Simple Encryption Algorithm (SEAL), by which 128-bit long blocks can be quickly encrypted/decrypted. The algorithm is designed to run efficiently in software without any specialized hardware while still guaranteeing a strong degree of confidentiality. The cipher is composed entirely of simple bit-wise operations, such as the exclusive or, and modular addition, thereby making it exceedingly easy to implement in most programming languages as well as efficient in terms of performance.
A simple encryption algorithm
Authors: St. Pierre Joseph Keenan
Published: January 2018

In this paper I present a Simple Encryption Algorithm (SEAL), by which 128-bit long blocks can be quickly encrypted/decrypted. The algorithm is designed to run efficiently in software without any specialized hardware while still guaranteeing a strong degree of confidentiality. The cipher is composed entirely of simple bit-wise operations, such as the exclusive-or and circular shift, in addition to modular addition, thereby making it exceedingly easy to implement in most programming languages as well as efficient in terms of performance.
Upper Karoo vertebrate assemblages (Late Triassic/Early Jurassic) of the Lake Kariba region, Zimbabwe
Authors: Barrett Paul M , Broderick Tim , Chapelle Kimberley , Choiniere Jonah , Edwards Steve , Munyikwa Darlington , Viglietti Pia , Zondo Michel
Published: January 2018

Southern Africa provides critical information on Late Triassic–Early Jurassic terrestrial tetrapod faunas. Most of the localities in this region are in South Africa and Lesotho, but preliminary work in Zimbabwe has revealed significant potential. Early Jurassic Zimbabwean localities have yielded the basal sauropodomorph Massospondylus, the early sauropod Vulcanodon and theropod material. Late Triassic localities are also known, but have yielded only fragmentary specimens thus far.

In early 2017, a joint South African-Zimbabwean-UK team conducted fieldwork in the upper Karoo-aged deposits along the shores of Lake Kariba, northern Zimbabwe (Mid-Zambesi Basin). We relocated the Vulcanodon type locality on Island 126/127 and found that, contrary to previous reports suggesting a Toarcian age, the quarry was in a horizon pre-dating the onset of Drakensburg volcanism (= Batoka Basalts). It is situated instead within the earlier Lower Jurassic Forest Sandstone. This indicates that Vulcanodon is 10–15 million years older than thought previously, recalibrating several nodes within Sauropoda and indicating extensive overlap between true sauropods and 'prosauropods'.

Other new vertebrate localities show that sauropodomorphs are present in the Forest Sandstone and upper Tashinga (Late Triassic) formations, but a grey mudstone facies within the Pebbly Arkose Member of the latter unit yields a more aquatic fauna, including lungfish and phytosaurs, but lacking sauropodomorphs. The phytosaur occurrence is the first in Africa south of the Sahara. Faunal and sedimentological evidence indicates that the Late Triassic and Early Jurassic sites in this region were deposited under more mesic environments than their lateral equivalents in South Africa.
CITED1 is a novel binding partner of MITF that influences the MITF-directed transcriptional profile in melanoma
Authors: Lettiero Barbara , Lauss Martin , Borg Ake , Gruvberger-Saal Sofia , Jönsson Goran B , Howlin Jillian
Published: January 2018

We previously demonstrated how CITED1 knockdown in melanoma cells had the capacity to perturb expression of a significant number of genes that comprised MITF and several of its known transcriptional targets. This manifest as a switch from a more invasive to a more proliferative gene signature phenotype. We now demonstrate by using MITF ChIP-seq, that altered CITED1 expression affects MITF transcription factor binding to its targets across the genome. We show that silencing CITED1 effectively amplifies the MITF chromatin-binding signal response while we also demonstrate for the first time that CITED1 and MITF co-localise in a nuclear complex using an in-situ ligation proximity assay. We propose that CITED1-MITF binding is capable of altering both the affinity of chromatin association and transcriptional response to MITF at the target regions in the genome where MITF is either directly or indirectly bound to DNA. As CITED1/SMAD2 has been shown to mediate TGFβ-driven transcription that induces amoeboid-like invasion in melanoma cells we hypothesis that the MITF/CITED1 driven transcriptional response dominates in MITF-high/low-invasive environment or proliferative signature cell phenotype, whereas the SMAD2/CITED1 transcriptional response is dominant in a low-MITF/ high-invasive signature environment.
Virulence test using nematodes to prescreen Nocardia species capable of inducing neurodegeneration and behavioral disorders
Authors: Claire Bernardin-Souibgui , Anthony Zoropogui , Jeremy Voisin , Sebastien Ribun , Valentin Vasselon , Petar Pujic , Veronica Rodriguez-Nava , Patrick Belly , Benoit Cournoyer , Blaha Didier
Published: January 2018

Background. Parkinson’s disease (PD) is a disorder characterized by dopaminergic neuron programmed cell death. The etiology of PD remains uncertain—some cases are due to selected genes associated with familial heredity, others are due to environmental exposure to toxic components, but over 90% of cases have a sporadic origin. Nocardia are Actinobacteria that can cause human diseases like nocardiosis. This illness can lead to lung infection or central nervous system (CNS) invasion in both immunocompromised and immunocompetent individuals. The main species involved in CNS are N. farcinica, N. nova, N. brasiliensis and N. cyriacigeorgica. Some studies have highlighted the ability of N. cyriacigeorgica to induce Parkinson’s disease-like symptoms in animals. Actinobacteria are known to produce a large variety of secondary metabolites, some of which can be neurotoxic. We hypothesized that neurotoxic secondary metabolite production and the onset of PD-like symptoms in animals could be linked. Methods. Here we used a method to screen bacteria that could induce dopaminergic neurodegeneration before performing mouse experiments. Results.The nematode Caenorhabditis elegans allowed us to demonstrate that Nocardia strains belonging to N. cyriacigeorgica and N. farcinica species can induce dopaminergic neurodegeneration. Strains of interest involved with the nematodes in neurodegenerative disorders were then injected in mice. Infected mice had behavioral disorders that may be related to neuronal damage, thus confirming the ability of Nocardia strains to induce neurodegeneration. These behavioral disorders were induced by N. cyriacigeorgica species (N. cyriacigeorgica GUH-2 and N. cyriacigeorgica 44484) and N. farcinica 10152. Discussion.We conclude that C. elegans is a good model for detecting Nocardia strains involved in neurodegeneration. This model allowed us to detect bacteria with high neurodegenerative effects and which should be studied in mice to characterize the induced behavioral disorders and bacterial dissemination.
Preprints as medium for communicating new ideas, hypotheses, data, analysis and beyond
Authors: Ng Wenfa
Published: January 2018

Preprints emerged as a medium for exchanging ideas and new research data in the physics and mathematics community through the arXiv preprint server, and the phenomenon has since spread to biology and chemistry, with the promulgation of a variety of preprint servers such as PeerJ Preprints and bioRxiv. Partly as a response to the slow publication process where it could take months or even years to publish a manuscript, which leads to latency in the distribution of ideas and data useful to other researchers, preprints have also been conferred with the status of citability, and thus, a source of recognition for the work of the authors. Specifically, preprints could be used as an indication of the first publication of an idea. From my experience with publication of preprints on PeerJ Preprints and figshare, I see preprints as a publication format that liberates citizen scientists and afford an opportunity for common people with an interest in science to participate in the scientific dialogue. Beyond exchange of ideas and data, as well as laying an indication to the novelty of a work, preprints also allow the publication of hypotheses and research ideas of benefit to other researchers. For example, I share, using preprints, my research ideas on other areas of science which I lack the resources to partake. Additionally, commentary and perspective manuscripts could also be published, which democratizes the sharing of scientific ideas and enriches the scientific dialogue, as well as prevents the published literature from being monopolized by limited number of school of thoughts. Datasets could also be shared with others as preprints, and being citable, provides a platform for gaining credit, as well as a means for data comparison and reuse by others. In addition, presentations and posters, which are typically not published, could also be published as preprints; thereby, providing authors with a forum to communicate their preliminary findings expeditiously. Finally, with individual journals placing implicit restrictions on the style of communication and what should be described (for example, disallowing the publication of hypotheses papers), preprints afford authors' freedom to express their ideas in a format they think would best showcase their work in an understandable manner. Hence, preprint is an alternative scientific arena that works in complement to the published literature in enabling a wider and richer discussion of ideas, hypotheses, commentary and critique amongst scientists. With lower barriers to entry and the willingness to communicate as the only constraints, preprints may be identifiable as a revolution in scientific communication, aided by the low cost model of Web publication, which in adding to the diversity of ideas made known to scientists, non-scientists and policy makers, help anchor science firmly in any intellectual discussion of importance to society.
GIS-based seismic hazard prediction system for urban earthquake disaster prevention planning
Authors: Zhai Yongmei , Chen Shenglong , OuYang Qianwen
Published: January 2018

A basic framework of a GIS-based seismic hazard prediction system for urban earthquake disaster prevention planning is developed in this study, incorporating structural vulnerability analysis, program development, and GIS. The system is integrated with proven building vulnerability analysis models, data search function, spatial analysis function, and plotting function, realizing the batching and automation of seismic hazard prediction and the interactive visualization of predicted results. The system is applied to a test area and the results are compared with results from previous studies to verify that the system can provide data support and aid decisionmaking for the establishment and implementation of urban earthquake disaster prevention planning. Results from this study are essentially the same as the results of 2003 and slightly better than the results of 1993, which highlights the reliability of the fragility analysis method applied in this system.
Declutter your R workflow with tidy tools
Authors: Ross Zev , Wickham Hadley , Robinson David
Published: January 2018

The R language has withstood the test of time. Forty years after it was initially developed (in the form of the S language) R is being used by millions of programmers on workflows the inventors of the language could never have imagined. Although base R packages perform well in most settings, workflows can be made more efficient by developing packages with more consistent arguments, inputs and outputs and emphasizing constantly improving code over historical code consistency. The universe of R packages known as the tidyverse, including dplyr, tidyr and others, aim to improve workflows and make data analysis as smooth as possible by applying a set of core programming principles in package development.
An improved method for utilizing high-throughput amplicon sequencing to determine the diets of insectivorous animals
Authors: Jusino Michelle A , Banik Mark T , Palmer Jonathan M , Wray Amy K , Xiao Lei , Pelton Emma , Barber Jesse R , Kawahara Akito Y , Gratton Claudio , Peery M. Zachariah , Lindner Daniel L
Published: January 2018

DNA analysis of predator feces using high-throughput amplicon sequencing (HTS) enhances our understanding of predator-prey interactions. However, conclusions drawn from this technique are constrained by biases that occur in multiple steps of the HTS workflow. To better characterize insectivorous animal diets, we used DNA from a diverse set of arthropods to assess PCR biases of commonly used and novel primer pairs for the mitochondrial gene, cytochrome oxidase C subunit 1 (CO1). We compared diversity recovered from HTS of bat guano samples using a commonly used primer pair “ZBJ” to results using the novel primer pair “ANML”. To parameterize our bioinformatics pipeline, we created an arthropod mock community consisting of single-copy (cloned) CO1 sequences. To examine biases associated with both PCR and HTS, mock community members were combined in equimolar amounts both pre- and post-PCR. We validated our system using guano from bats fed known diets and using composite samples of morphologically identified insects collected in pitfall traps. In PCR tests, the ANML primer pair amplified 58 of 59 arthropod taxa (98%) whereas ZBJ amplified 24 of 59 taxa (41%). Furthermore, in an HTS comparison of field-collected samples, the ANML primers detected nearly four-fold more arthropod taxa than the ZBJ primers. The additional arthropods detected include medically and economically relevant insect groups such as mosquitoes. Results revealed biases at both the PCR and sequencing levels, demonstrating the pitfalls associated with using HTS read numbers as proxies for abundance. The use of an arthropod mock community allowed for improved bioinformatics pipeline parameterization.
Improved query reformulation for concept location using CodeRank and document structures
Authors: Rahman Mohammad Masudur , Roy Chanchal
Published: January 2018

During software maintenance, developers usually deal with a significant number of software change requests. As a part of this, they often formulate an initial query from the request texts, and then attempt to map the concepts discussed in the request to relevant source code locations in the software system (a.k.a, concept location). Unfortunately, studies suggest that they often perform poorly in choosing the right search terms for a change task. In this paper, we propose a novel technique –ACER– that takes an initial query, identifies appropriate search terms from the source code using a novel term weight –CodeRank, and then suggests effective reformulation to the initial query by exploiting the source document structures, query quality analysis and machine learning. Experiments with 1,675 baseline queries from eight subject systems report that our technique can improve 71% of the baseline queries which is highly promising. Comparison with five closely related existing techniques in query reformulation not only validates our empirical findings but also demonstrates the superiority of our technique.
Improved query reformulation for concept location using CodeRank and document structures
Authors: Rahman Mohammad Masudur , Roy Chanchal
Published: January 2018

During software maintenance, developers usually deal with a significant number of software change requests. As a part of this, they often formulate an initial query from the request texts, and then attempt to map the concepts discussed in the request to relevant source code locations in the software system (a.k.a., concept location). Unfortunately, studies suggest that they often perform poorly in choosing the right search terms for a change task. In this paper, we propose a novel technique --ACER-- that takes an initial query, identifies appropriate search terms from the source code using a novel term weight --CodeRank, and then suggests effective reformulation to the initial query by exploiting the source document structures, query quality analysis and machine learning. Experiments with 1,675 baseline queries from eight subject systems report that our technique can improve 71% of the baseline queries which is highly promising. Comparison with five closely related existing techniques in query reformulation not only validates our empirical findings but also demonstrates the superiority of our technique.
Packaging data analytical work reproducibly using R (and friends)
Authors: Marwick Ben , Boettiger Carl , Mullen Lincoln
Published: January 2018

Computers are a central tool in the research process, enabling complex and large scale data analysis. As computer-based research has increased in complexity, so have the challenges of ensuring that this research is reproducible. To address this challenge, we review the concept of the research compendium as a solution for providing a standard and easily recognisable way for organising the digital materials of a research project to enable other researchers to inspect, reproduce, and extend the research. We investigate how the structure and tooling of software packages of the R programming language are being used to produce research compendia in a variety of disciplines. We also describe how software engineering tools and services are being used by researchers to streamline working with research compendia. Using real-world examples, we show how researchers can improve the reproducibility of their work using research compendia based on R packages and related tools.
Disparities in availability of essential medicines to treat non-communicable diseases in Uganda: a Poisson analysis using the Service Availability and Readiness Assessment
Authors: Armstrong-Hough Mari , Kishore Sandeep , Byakika Sarah , Mutungi Gerald , Nunez-Smith Marcella , Schwartz Jeremy
Published: January 2018

Objective Although the WHO-developed Service Availability and Readiness Assessment (SARA) tool is a comprehensive and widely applied survey of health facility preparedness, SARA data have not previously been used to model predictors of readiness. We sought to demonstrate that SARA data can be used to model availability of essential medicines for treating non-communicable diseases (EM-NCD). Methods We fit a Poisson regression model using 2013 SARA data from 196 Ugandan health facilities. The outcome was total number of different EM-NCD available. Basic amenities, equipment, region, health facility type, managing authority, NCD diagnostic capacity, and range of HIV services were tested as predictor variables. Findings In multivariate models, we found significant associations between EM-NCD availability and region, managing authority, facility type, and range of HIV services. For-profit facilities’ EM-NCD counts were 98% higher than public facilities (p<.001). General hospitals and referral health centers had 98% (p=.004) and 105% (p=.002) higher counts compared to primary health centers. Facilities in the North and East had significantly lower counts than those in the capital region (p=0.015; p=0.003). Offering HIV care was associated with 35% lower EM-NCD counts (p=0.006). Offering HIV counseling and testing was associated with 57% higher counts (p=0.048). Conclusion We identified multiple within-country disparities in availability of EM-NCD in Uganda. Our findings can be used to identify gaps and guide distribution of limited resources. While the primary purpose of SARA is to assess and monitor health services readiness, we show that it can also be an important resource for answering complex research and policy questions requiring multivariate analysis.
Sex differences in the use of social information emerge under conditions of risk
Authors: Brand Charlotte Olivia , Brown Gillian R , Cross Catharine P
Published: January 2018

Social learning provides an effective route to gaining up-to-date information, particularly when information is costly to obtain asocially. Theoretical work predicts that the willingness to switch between using asocial and social sources of information will vary between individuals according to their risk tolerance. We tested the prediction that, where there are sex differences in risk tolerance, altering the variance of the payoffs of using asocial and social information differentially influences the probability of social information use by sex. In a computer-based task that involved building a virtual spaceship, men and women (N=88) were given the option of using either asocial or social sources of information to improve their performance. When the asocial option was risky (i.e., the participant’s score could markedly increase or decrease) and the social option was safe (i.e., their score could slightly increase or remain the same), women, but not men, were more likely to use the social option than the asocial option. In all other conditions, both women and men preferentially used the asocial option to a similar degree. We therefore found both a sex difference in risk aversion and a sex difference in the preference for social information when relying on asocial information was risky, consistent with the hypothesis that levels of risk-aversion influence the use of social information.
Kinematic parameters of goats walking on different slopes and biomimetic walking mechanisms
Authors: Zhang Fu , Wang Yafei , Wang Wei ,   Fu Zhangfu， PhD, Professor, Master supervisor. Research interests: the biomimetic materials and the intelligent agricultural.
Yafei Wang, Master student ,Research interests: the biomimetic materials and the intelligent agricultural.
Wei Wang,PhD,  Research interests: the biomimetic materials and the intelligent agricultural.
Published: January 2018

A comparative analysis of the kinematic parameters of a goat on different slopes was conducted to study the kinematic parameters of goats on different slopes with walking mechanics. The uphill walking processes on different slopes (0°, 5°, 10°, 15°, 20°, 25° and 30°) were recorded by a high speed video system (VRI Phantom M110). The experimental image results were processed and analyzed using PCC and MATLAB software. The kinematic parameters were obtained from the goat walking on different slopes; these parameters are the changes of centroid with displacement, speed with time, and acceleration with time. As the gradient in the uphill process increases, the range of centroid fluctuation ranges from 0.079 to 0.59 and the rate of change ranges from 0.4 to 2.2 m/s, while the acceleration of the goat slope decreases. The present research can provide theoretical basis and experimental data for the design of a biomimetic agricultural slope walking mechanism.
Chemical properties and fertility analysis of dredger-fill silt during soil formation: The tianjin dredge–fill project
Authors: Gu Huijun , Sui Xin , Zhang Guogang , Jia Meiqing
Published: January 2018

Dredger-fill silt has been used in the port of Tianjin, China to reclaim land; however, the dredger-fill silt has no soil ecological function. Translating the silt into soil rapidly and accelerating the soil-forming process are key to solving the ecological problems of the Dredge–Fill project. This study measured 15 chemical properties of the dredger-fill silt for 8 years of the soil forming process to explore fertility changes and the critical factors affecting soil formation. The results showed that: (1) the salinity of silt changed from severe to mild with a reduction in Na+ and Cl- concentration. Other ion concentrations changed slightly. (2) Effective nutrients significantly decreased during soil formation. Soil organic matter (SOM)，the nitrate-nitrogen, available phosphorus (A-P) and available potassium (A-K) decreased by 26.22%, 86.23%, 45.92%, 33.61% respectively, indicating severe nutrients loss. (3) Principal component analysis showed that silt fertility decreased significantly and the total soil fertility loss was severe. This study has significance for the artificial improvement of silt.
Crustacean amphipods from marsh ponds: a nutritious feed resource with potential application in Integrated Multi-Trophic Aquaculture.
Authors: Jiménez-Prada Pablo , Hachero-Cruzado Ismael , Giráldez Inmaculada , Fernández-Diaz Catalina , Vilas César , Cañavate José Pedro , Guerra-garcía José Manuel
Published: January 2018

Coastal protection, nutrient cycling, erosion control, water purification, and carbon sequestration are ecosystem services provided by salt marshes. Additionally, the salt ponds offers coastal breeding and nursery habitat to fishes and invertebrates providing abundant amphipods potentially useful as a resource in aquaculture. Fishmeal and fish oil are necessary food resources to support aquaculture of carnivorous species due to their omega-3 long-chain polyunsaturated fatty acids (n-3 LC-PUFA). Their dependence on limited fisheries constrains growth of aquaculture and the need for n-3 LC-PUFA recommends the development of more sustainable food sources. Due to their extensive feeding on detritus and primary producers, amphipods appear as potential and high quality alternative feed resource for aquaculture. Hence, a nutritional study was carried out for main amphipods species -Microdeutopus gryllotalpa, Monocorophium acherusicum, Gammarus insensibilis, Melita palmata and Cymadusa filosa- at South Spain aquaculture terrestrial ponds . These species showed a high protein content (up to 40%), high n-3 PUFA and phospholipid levels, and high levels of phophatidylcholine (PC), phosphatidylethanolamine (PE) and triacylglycerols(TAG), the latter significantly high for M. acherusicum . M. gryllotalpa and M. acherusicum showed the highest proportion of lipids (19.15% and 18.35%, respectively). Isoleucine, glycine and alanine were the dominant amino acids in all species. In addition, amphipods collected from ponds showed low levels of heavy metals. Furthermore, the biochemical profile of the five amphipods have been compared with other studied alternatives preys. Therefore, amphipods of ponds are good candidates to be used as feed, and are proposed as a new sustainable economic resource to use in aquaculture. G. insensibilis may be the best to be intensively cultured as an alternative feed resource because shows: 1) adequate PUFAS n-3 and PL composition; 2) high levels of glycine, alanine, tyrosine, isoleucine and lysine; 3) high natural densities; 4) large body size ( ≥ 1 cm) and 5) high concentration of Calcium. Moreover, a combined culture of amphipods and fishes in these marsh ponds seems a promising and environmentally sustainable way to develop Integrate Multi-Trophic Aquaculture (IMTA) in these ecosystems.
DeepBlueR: Large-scale epigenomic analysis in R
Authors: List Markus , Albrecht Felipe , Bock Christoph , Lengauer Thomas
Published: January 2018

Epigenetic research focuses on understanding non-inheritable factors influencing gene regulation and covers various cellular mechanisms such as DNA methylation, histone modification, miRNA function and transcription factor binding sites. Recent advances in high-throughput profiling technologies allow for systematically collecting data on each of these mechanisms in large-scale experiments. These efforts are fostered and concerted by international collaborations, such as the International Human Epigenome Consortium (IHEC) and its members. As a result of these collaborations, researchers can exploit massive amounts of publicly available epigenomic data on dozens of cell types, cell lines and tissues. Access to these data is streamlined by existing data portals and, in principle, allows for answering important biomedical questions.

However, working with such data requires a suitable computational infrastructure not accessible ubiquitously. This creates a serious bottleneck in research and, as a result, data from these costly experiments are currently underused. To address this issue, we developed a new web resource, the DeepBlue Epigenomic Data Server to provide access to more than 40,000 experimental files from four major epigenome projects: ENCODE, ROADMAP, BLUEPRINT, the German Epigenome Program DEEP, the Canadian CEEHRC, and the Japanese CREST.

A common challenge with this resources is that researchers are typically interested in a small fraction of the available epigenomic data to answer specific biomedical questions. Using a typical data repository to solve this task would require the user to download several files amounting to gigabytes of data that subsequently need to be filtered locally. In addition, it is often important to perform memory- and cpu-intensive operations to transform or aggregate these data, while the necessary computational resources are not accessible to every user. Therefore, the DeepBlue Data Server offers features beyond those of a centralized epigenomic data repository. It has a comprehensive programmatic interface (API) to enable users to perform complex data operations, such as searching, selecting, filtering, summarizing, and downloading of epigenomic data of interest. These operations can be combined into custom workflows, thus offering nearly the same degree of flexibility as a local programming environment.

Here, we present DeepBlueR, a new R/Bioconductor package that enables users to engage with the DeepBlue server in a seamless fashion from within the R environment. DeepBlueR mirrors all DeepBlue data operations as R commands and provides additional features for compressing, downloading and transforming aggregated epigenomic data into suitable R data structures. A mechanism for local caching guarantees that complex scripts can be executed without the need to download previously requested data from the server.
Effects of shinbuto and ninjinto on prostaglandin E2 production in lipopolysaccharide-treated human gingival fibroblasts
Authors: Ara Toshiaki , Sogawa Norio
Published: January 2018

Previously, we revealed that several kampo medicines that are used for patients with excess and/or medium patterns [kakkonto (TJ-1), shosaikoto (TJ-9), hangeshashinto (TJ-14), and orento (TJ-120)] reduced prostaglandin (PG)E<2 levels using LPS-treated human gingival fibroblasts (HGFs). Recently, we examined other kampo medicines used for patients with the deficiency pattern [bakumondoto (TJ-29), shinbuto (TJ-30), ninjinto (TJ-32), and hochuekkito (TJ-41)] and the herbs comprising shinbuto and ninjinto using the same experimental model. Shinbuto and ninjinto concentration-dependently reduced LPS-induced PGE2 production by HGFs, whereas hochuekkito weakly reduced and bakumondoto did not reduce PGE2 production. Shinbuto and ninjinto did not alter cyclooxygenase (COX) activity or the expression of molecules involved in the arachidonic acid cascade. Therefore, we next examined which herbs compromising shinbuto and ninjinto reduce LPS-induced PGE2 production. Among these herbs, shokyo (Zingiberis Rhizoma) and kankyo (Zingiberis Processum Rhizoma) strongly and concentration-dependently decreased LPS-induced PGE2 production. However, both shokyo and kankyo increased the expression of cytosolic phospholipase (cPL)A2 but did not affect annexin1 or COX-2 expression. These results suggest that shokyo and kankyo suppress cPLA2 activity. We demonstrated that kampo medicines suppress inflammatory responses in patients with the deficiency pattern, and in those with excess or medium patterns. Moreover, kampo medicines that contain shokyo or kankyo are considered to be effective for the treatment of inflammatory diseases.
Best practices for conducting benchmarking in the most comprehensive and reproducible way
Authors: Mangul Serghei , Martin Lana S. , Distler Margaret , Eskin Eleazar , Flint Jonathan
Published: January 2018

Computational biology is rapidly advancing thanks to the many new tools developed and published each month. A systematic benchmarking practice would help biomedical researchers leverage this technological expansion to optimize their projects. Several aspects of algorithm publication and distribution contribute to this challenge. We address these challenges and present seven principles to guide researchers in designing a benchmarking study. Our proposed steps show how benchmarking can create a framework for comparison of newly published algorithms.
Towards combining occurrence and abundance distribution models of Great Bustard for conservation: A global research template from Bohai Bay?
Authors: Mi Chunrong , Huettmann Falk , Sun Rui , Guo Yumin
Published: January 2018

Species distribution models (SDMs) have become important and essential tools in conservation and management. However, SDMs built with count data, commonly referred to as species abundance models (SAMs), are still less used so far. SDMs are increasingly used now in conservation decisions, whereas SAMs are still not widely employed. Species occurrence and abundance do not frequently display similar patterns, often they are not even well correlated. This leads to an insufficient or misleading conservation. How to combine information from SDMs and SAMs all together for unified conservation remains a challenge. In this study, we put forward for the first time a priority protection index (PI). The PI combines the prediction results of occurrence and abundance models. We used the best-available presence and count records for an endangered farmland species, Great Bustard (Otis tarda dybowskii) in Bohai Bay, China, as a case study. We then applied the advanced Random Forest algorithm (Salford Systems Ltd. implementation), a powerful machine learning method, with eleven predictor variables to forecast the spatial occurrence as well as the abundance distribution. The results show that the occurrence model had a decent performance (ROC: 0.77) and the abundance model had a RMSE 26.54. It is of note that environmental variables influenced bustard occurrence and abundance differently. We found that occurrence and abundance models display different spatial distribution patterns. Still, combining occurrence and abundance indices to produce a priority protection index (PI) used for conservation could guide the protection of the areas with high occurrence and high abundance (e.g. in Strategic Conservation Planning). Due to the widespread use of SDMs and the rel. easy subsequent employment of SAMs these ﬁndings have a wide relevance and applicability, worldwide. We promote and strongly encourage to further test, apply and update the priority protection index (PI) elsewhere in order to explore the generality of these ﬁndings and methods readily available now for researchers.
GenHap: A novel computational method based on genetic algorithms for haplotype assembly
Authors: Tangherloni Andrea , Spolaor Simone , Rundo Leonardo , Nobile Marco S , Merelli Ivan , Cazzaniga Paolo , Besozzi Daniela , Mauri Giancarlo , Liò Pietro
Published: January 2018

The process of inferring a full haplotype of a cell is known as haplotyping, which consists in assigning all heterozygous Single Nucleotide Polymorphisms (SNPs) to exactly one of the two chromosomes. In this work, we propose a novel computational method for haplotype assembly based on Genetic Algorithms (GAs), named GenHap. Our approach could efficiently solve large instances of the weighted Minimum Error Correction (wMEC) problem, yielding optimal solutions by means of a global search process. wMEC consists in computing the two haplotypes that partition the sequencing reads into two unambiguous sets with the least number of corrections to the SNP values. Since wMEC was proven to be an NP-hard problem, we tackle this problem exploiting GAs, a population-based optimization strategy that mimics Darwinian processes. In GAs, a population composed of randomly generated individuals undergoes a selection mechanism and is modified by genetic operators. Based on a quality measure (i.e., the fitness value), inspired by Darwin’s “survival of the fittest” laws, each individual is involved in a selection process.

Our preliminary experimental results show that GenHap is able to achieve correct solutions in short running times. Moreover, this approach can be used to compute haplotypes in organisms with different ploidity. The proposed evolutionary technique has the advantage that it could be formulated and extended using a multi-objective fitness function taking into account additional insights, such as the methylation patterns of the different chromosomes or the gene proximity in maps achieved through Chromosome Conformation Capture (3C) experiments.
Multiplication and Division over Extended Galois Field GF(p^q): A new Approach to find Monic Irreducible Polynomials over any Galois Field GF(p^q).
Authors: Dey Sankhanil , Ghosh Ranjan
Published: January 2018

Irreducible Polynomials (IPs) have been of utmost importance in generation of substitution boxes in modern cryptographic ciphers. In this paper an algorithm entitled Composite Algorithm using both multiplication and division over Galois fields have been demonstrated to generate all monic IPs over extended Galois Field GF(p^q) for large value of both p and q. A little more efficient Algorithm entitled Multiplication Algorithm and more too Division Algorithm have been illustrated in this Paper with Algorithms to find all Monic IPs over extended Galois Field GF(p^q) for large value of both p and q. Time Complexity Analysis of three algorithms with comparison to Rabin’s Algorithms has also been exonerated in this Research Article.
Collinearity does not affect Procrustes analysis outputs: directions for plant and soil ecologists
Authors: Lisboa Francy , Mitchell Ruth , Chapman Stephen J , Potts Jacqueline , Berbara Ricardo
Published: January 2018

Background. The Procrustean residual vector (or PAM, an acronym for the alternative equivalent term Procrustean association metric) derived from Procrustes analysis can be seen as the univariate form of relationship between two or more data tables, which provides an interesting way for ecologists to place multivariate relationships as the central object of investigation in more familiar statistical approaches such as ANOVA and post hoc tests. However, many aspects need to be elucidated to make ecologists more confident in using Procrustes in their studies going beyond the simple comparisons. We attempted to address two questions: 1) How does the increasing number of correlated columns within an entire data table affect the Procrustes results? 2) Can the PAM be used for detecting how the correlation is partitioned across treatment levels within the original data table? Methods. Question 1) two data tables, X and Y, from a previous research were used to conduct the study. Four levels of correlation between variables (0.9, 0.7, 0.5, and 0.2) within the X data table were imposed to an increasing number of variables (6, 9, 12, and 15) to assess their effects on Procrustes relationship and its significance. Question 2) two simulated data tables covering four hypothetical categorical predictors (A, B, C, D) were created varying the relationship between them regarding the treatment A (0.2, 0.5, 0.7, 0.9) in order to assess the association between Procrustes and multiple mean comparisons method. Results. for the first question, we found that increasing the number of correlated variables across different imposed correlation levels (0.9, 0.7, 0.5, and 0.2) in the data table not subject to Procrustean linear transformation (translation and rotation), i.e. the X data table, had no effects either on the classical Procrustes outcomes related to the fit between data tables (R statistic and its P value), or on the significance of the ANOVA using the Procrustes association metric (PAM), which summarizes the multivariate correlation between two data tables, as the response variable. For the second question, increasing the between correlation levels between X and Y data tables for a specific set of rows in these tables corresponding to a hypothetical treatment A resulted in PAMs that, when used in mean multiple comparisons, did show this treatment A as different from all others treatments B, C, and D from which X and Y were not related above (0.1). Discussion. Our results support that the Procrustes fit is only dependent on the information between data tables instead of within a data table. Finally, we showed that PAM, in fact, reflects the differences in multivariate correlation across data tables which can be useful for ecological questions addressing the partitioning of the multivariate correlation among different categorical levels (e.g. plots, time, land use type, etc.).
Crypto-Archaeology: unearthing design methodology of DES s-boxes
Authors: Dey Sankhanil , Ghosh Ranjan
Published: January 2018

US defence sponsored the DES program in 1974 and released it in 1977. It remained as a well-known and well accepted block cipher until 1998. Thirty-two 4-bit DES S-Boxes are grouped in eight each with four and are put in public domain without any mention of their design methodology. S-Boxes, 4-bit, 8-bit or 32-bit, find a permanent seat in all future block ciphers. In this paper, while looking into the design methodology of DES S-Boxes, we find that S-Boxes have 128 balanced and non-linear Boolean Functions, of which 102 used once, while 13 used twice and 92 of 102 satisfy the Boolean Function-level Strict Avalanche Criterion. All the S-Boxes satisfy the Bit Independence Criterion. Their Differential Cryptanalysis exhibits better results than the Linear Cryptanalysis. However, no S-Boxes satisfy the S-Box-level SAC analyses. It seems that the designer emphasized satisfaction of Boolean-Function-level SAC and S-Box-level BIC and DC, not the S-Box-level LC and SAC.