bluuebunny/crossref_metadata_2025 huggingface dataset:
Melanoma expression analysis with Big Data technologies
Authors: Fernandez-Rovira Alicia , Lavado-Valenzuela Rocio , Berciano Guerrero Miguel Ángel , Navas-Delgado Ismael , Aldana-Montes José F
Published: January 2018

Melanoma is a highly immunogenic tumor. Therefore, in recent years physicians have incorporated drugs that alter the immune system into their therapeutic arsenal against this disease, revolutionizing in the treatment of patients in an advanced stage of the disease. This has led us to explore and deepen our knowledge of the immunology surrounding melanoma, in order to optimize its approach. At present, immunotherapy for metastatic melanoma is based on stimulating an individual’s own immune system through the use of specific monoclonal antibodies. The use of immunotherapy has meant that many of patients with melanoma have survived and therefore it constitutes a present and future treatment in this field. At the same time, drugs have been developed targeting specific mutations, specifically BRAF, resulting in large responses in tumor regression (set up in this clinical study to 18 months), as well as a higher percentage of long-term survivors. The analysis of the gene expression changes and their correlation with clinical changes can be developed using the tools provided by those companies which currently provide gene expression platforms. The gene expression platform used in this clinical study is NanoString, which provides nCounter. However, nCounter has some limitations as the type of analysis is restricted to a predefined set, and the introduction of clinical features is a complex task. This paper presents an approach to collect the clinical information using a structured database and a Web user interface to introduce this information, including the results of the gene expression measurements, to go a step further than the nCounter tool. As part of this work, we present an initial analysis of changes in the gene expression of a set of patients before and after targeted therapy. This analysis has been carried out using Big Data technologies (Apache Spark) with the final goal being to scale up to large numbers of patients, even though this initial study has a limited number of enrolled patients (12 in the first analysis). This is not a Big Data problem, but the underlaying study aims at targeting 20 patients per year just in Málaga, and this could be extended to be used to analyze the 3.600 patients diagnosed with melanoma per year.
A methodology for malaria programme impact evaluation
Authors: Pothin Emilie , Segura Luis , Galactionova Katya , Bohle Leah , Matthys Barbara , Briet Olivier J.T. , Smith Thomas A
Published: January 2018

This document describes a methodology for continual assessment of the impact of malaria interventions, and the efficiency of the malaria programme. The methodology is designed to be implemented recurrently on a cycle of 2–5 years, with the involvement of stakeholders, including National Malaria Control Programmes, development partners and other organizations active in the programme. Their participation should inform the impact and efficiency assessment, so that it is linked to subsequent decision making defining the nature and scope of malaria control interventions. The methodology is designed in a modular way, providing some flexibility with regard to which elements are implemented at any given time. Some modules require technical capabilities usually not available in a regular monitoring and evaluation (M&E) team, and will require contributions from other national and/or international partners.
Overexpression of VrPDF1 gene confers resistance to weevils in transgenic mung bean plant
Authors: Thao Hoang Thi , Ngoc Lan Nguyen Thi , Son Le Van , Hoang Mau Chu
Published: January 2018

Plant defensins are known for different biological functions such as insect resistance, antibacterial, antifungal and antiviral activities. The role of plant defensins against weevils is based on inhibitor of alpha-amylase activity in weevil gut, therefore, weevils can not digest starch and then die. The low content of Vigna radiata plant defensin 1 (VrPDF1) in mung bean seeds is promted researches to increase the VrPDF1content, in which leads to enhance alpha-amylase inhibition and improve bruchid resistance in mung bean. This article presents the results of overexpression of VrPDF1 gene in transgenic mung bean plants. VrPDF1 gene was successfully transferred into DX22 mung bean cultivar and expressed in T1 generation transgenic mung bean seeds. The extract containing recombinant VrPDF1 protein inhibited alpha-amylase of weevil larvae in its larval stage. The performance of alpha-amylase inhibitor of DX1-3 and DX1-7 transgenic mung bean lines increased by 166.40% and 178.19% respectively, in comparison with non-transgenic plants. The enhancement of alpha-amylase inhibitor ability of rVrPDF1 extracted from transgenic plants is scientifically fundamental to confirm the effectiveness of the application of gene technology in enhancement the ability of mung bean weevil resistance in particular and grain crops in general revenue.
Improved draft of the Mojave Desert tortoise genome, Gopherus agassizii, version 1.1
Authors: Webster Timothy H , Dolby Greer A. , Wilson Sayres Melissa , Kusumi Kenro
Published: January 2018

Exogenous sequence contamination presents a challenge in first-draft genomes because it can lead to non-contiguous, chimeric assembled sequences. This can mislead downstream analyses reliant on synteny, such as linkage-based analyses. Recently, the Mojave Desert Tortoise (Gopherus agassizii) draft genome was published as a resource to advance conservation efforts for the threatened species and discover more about chelonian biology and evolution. Here, we illustrate steps taken to improve the desert tortoise draft genome by removing contaminating sequences—actions that are typically carried out after the initial release of a draft genome assembly. We used information from NCBI’s Vecscreen output to remove intra-scaffold contamination and trim heading and trailing Ns. We then reordered and renamed scaffolds, and transferred the gene annotation onto this assembly. Finally, we describe the tools developed for this pipeline, freely available on Github (https://github.com/thw17/G_agassizii_reference_update), which facilitate post-assembly processing of other draft genomes. The new gopAga1.1 genome has an N50 of 251 KB, L50 of 2592 scaffolds, and its annotation retains 17,201 of the original 20,172 genes that were unaffected by the scaffold processing.
Assessing intraspecific genetic diversity from community DNA metabarcoding data
Authors: Elbrecht Vasco , Vamos Ecaterina Edith , Steinke Dirk , Leese Florian
Published: January 2018

DNA metabarcoding provides species composition data for entire communities, yet information on intraspecific diversity is usually lost during data analysis. The capacity to infer intraspecific genetic diversity within whole communities would, however, represent a leap forward for ecological monitoring and conservation. We developed an amplicon-based sequence denoising approach that allows the identification of haplotypes from metabarcoding data sets and demonstrate its power with two freshwater macroinvertebrate data sets.
On the efficiency of the Genetic Code after frameshift mutations
Authors: Geyer Regine , Madany Mamlouk Amir
Published: January 2018

Statistical and biochemical studies of the standard genetic code (SGC) have found evidence that the impact of mistranslations is minimized in a way that erroneous codes are either synonymous or code for an amino acid with similar polarity as the originally coded amino acid. It could be quantified that the SGC is optimized to protect this specific chemical property as good as possible. In recent work, it has been speculated that the multilevel optimization of the genetic code stands in the wider context of overlapping codes.

This work tries to follow the systematic approach on mistranslations and to extend those analyses to the general effect of frameshift mutations on the polarity conservation of amino acids: We generated one million random codes and compared their average polarity change over all triplets and the whole set of possible frameshift mutations. While the natural code - just as for the point mutations - appears to be competitively robust against frameshift mutations as well, we found that both optimizations appear to be independent of each other.

For both, better codes can be found, but it becomes significantly more difficult to find candidates that optimize all of these features - just like the SGC does. We conclude that the SGC is not only very efficient in minimizing the consequences of mistranslations, but rather optimized in amino acid polarity conservation for all three effects of code alteration, namely translational errors, point and frameshift mutations. In other words, our result demonstrates that the SGC appears to be much more than just "one in a million".
Landscape connectivity among remnant populations of guanaco (Lama guanicoe Müller, 1776) in an arid region of Chile impacted by global change
Authors: Espinosa Herazo Mara Ines , Gouin Nicolas , Squeo Porcile Francisco Antonio , López Aspe David , Bertin Angéline
Published: January 2018

Connectivity between populations plays a key role in the long-term persistence of species in fragmented habitats. It is an issue of concern for the preservation of biodiversity in drylands since landscapes in water limited environments are characterized by low habitat cover, high habitat fragmentation and harsh matrices, and are being rapidly degraded at the global scale. In this study, we modelled landscape connectivity between the 11 remnant coastal and Andean populations of the guanaco Lama guanicoe, an emblematic herbivore indigenous to South America, in Chile's arid Norte Chico. We first produced a habitat surface model to derive a regional surface resistance map; and we then used circuit theory to map functional connectivity, investigate the degree of isolation of the populations, and identify those that most contribute to the network patch connectivity. Predicted suitable habitat for L. guanicoe represented about 25% of the study region (i.e. 29,173 km2), and was heterogeneously distributed along a continuous stretch along the Andes, and discontinuous patches along the coast. As a result, we found that high connectivity current flows in the mid and high Andes formed a wide continuous connectivity corridor enabling connectivity between all the high Andean populations. Coastal populations, in contrast, were predicted to be more isolated. They only connect to medium and high altitude populations, and for two of them, animal movement was linked to the effectiveness of wildlife crossings. Based on the degree of connectivity, population size, and local threats, the coastal and the northernmost populations were identified as being most vulnerable, while the Andean populations appeared to be least at risk, even when located near areas of mining activity. Collectively, our results suggest that functional connectivity is an issue of concern for L. guanicoe in Chile’s Norte Chico, and that future conservation and management plans should adopt a landscape strategy aiming at conserving the functional connectivity between the coastal and Andean populations, and at protecting the habitat patches likely to act as stepping stones within the connectivity network.
Reproduction and community structure of fish from winter shrimp bycatch from the Southeast Gulf of California
Authors: Tirado-Ibarra Jorge de Jesus , Loya-Rodriguez Mariany , Morales-Arevalo Jose Carlos , Muñoz-Garcia Isabel Rosario , Ramirez-Perez Jorge Saul , Jimenez-Gutierrez Laura Rebeca
Published: January 2018

Shrimp fishery is one of the most important fisheries of the world. However, the low selectivity from trawl nets leads the capture of a large number of non-target species. Shrimp bycatch include a large number of fish and invertebrate species; of which fish species are the most abundant. The present study aims to determine the community structure as well as the average sizes at first maturity of the fish species from shrimp bycatch caught from industrial fisheries at the southeast of the Gulf of California from Sinaloa to Guerrero, Mexico; from January to March 2015. A total of 37 species of finfish were found; of which five were considered rare. The fish species with the highest Importance Value Index (IVI) were Pseudupeneus grandisquamis, Paralichthys woolmani, Lutjanus peru y Diapterus peruvianus. The average size at first maturity of 12 fish species was determined; nine of which have not been previously reported. Of the analyzed organisms 90% were in juvenile stage; including species with riverine and artisanal fisheries. The present study demonstrates the risk in marine populations of different non-target species due to the low selectivity of shrimp trawls.
Characterization of sympatric Platanthera bifolia and Platanthera chlorantha (Orchidaceae) populations with intermediate plants
Authors: Esposito Fabiana , Vereecken Nicolas J. , Gammella Maddalena , Rinaldi Rosita , Laurent Pascal , Tyteca Daniel
Published: January 2018

Platanthera bifolia and P. chlorantha are terrestrial and rewarding orchids with a wide Eurasian distribution. Although genetically closely related, they exhibit significant morphological, phenological and ecological differences that maintain reproductive isolation between the species. However, where both species co-occur, individuals with intermediate phenotypic traits, often considered as hybrids, are frequently observed. Here, we combined neutral genetic markers (AFLPs), morphometrics and floral scent analysis (GC-MS) to investigate two mixed Platanthera populations where morphologically intermediate plants were found. Self-pollination experiments revealed a low level of autogamy and artificial crossings combined with assessments of fruit set and seed viability, showed compatibility between the two species. The results of the genetic analyses showed the same genetic patterns of morphologically intermediate individuals with the P. bifolia group. These results are corroborated also by floral scent analyses, which confirmed a strong similarity in floral scent composition between intermediate morphotypes and P. bifolia. Therefore, this study provided a much more detailed picture of the genetic structure of a sympatric zone between two closely allied species and supports the hypothesis that intermediate morphotypes in sympatry could reflect an adaptive evolution in response to local pollinator-mediated selection.
Elephant dung, chewed antlers, weathered bones: documenting a unique taphonomic collection
Authors: Pappa Spyridoula , Adams Neil , Brewer Philippa , Parfitt Simon , Carnegie Gillian , Lewis Mark
Published: January 2018

The Antony John Sutcliffe Collection is a unique taphonomic reference collection held within the Department of Earth Sciences at the Natural History Museum (NHM). Sutcliffe was the Curator of Fossil Mammal at the NHM from 1957 to 1987, during which time he collected a large assemblage of modern comparative vertebrate material, including complete skulls, bones, teeth and soft tissues (skin and faeces) of numerous species from across the world including sites in East Africa, Canada, Alaska, Siberia and northwest Europe. Sutcliffe studied Pleistocene mammals and was particularly interested in the alterations to their remains after death and how they come to be fossilised, i.e., their taphonomy.

The specimens were either collected during Sutcliffe’s own fieldwork or gifted to him by international colleagues, and are often accompanied by detailed notes on their provenance and original letters of donation.

After a preliminary study in 2013, and given the value of the collection for future taphonomic studies, a curatorial project ran from 2015 to 2017 aiming to document the entire collection on EMu (the museum’s collection management system), recording the anatomy, taxonomy, previous and new locations within the museum, and any associated documentation of over 1500 specimens. Photographs of each object were included and all specimens have been registered, safely repacked and rehoused at Wandsworth museum store, where they are now accessible to researchers. The specimens have the potential to form curated taphonomic reference standards for use by researchers around the world.
Idea farming: it is a good idea to have bad ideas in science
Authors: Lortie Christopher J
Published: January 2018

There are few truly bad ideas in authentic science. We need to embrace science as a process- driven human endeavour to better understand the world around us. Products are important, but through better transparency, we can leverage ideas, good and bad, ours and others, to do better science. In a brief analysis here inspired by a recent discussion of the topic and previous introspections by other ecologists, it is proposed that whilst it is a good idea to track ideas and all the processes that generate outcomes such as publications, there is inherent merit in all scientific ideas. That said, organizing and framing our ideas into the networks that we already use to examine hypotheses and questions in science is a window into our workflows including ideation, implementation, data analyses, and how we can better map ideas into open science outcomes. Formalizing and describing the linkages between ideas, data, and projects we produce as scientists will enhance and diversify the value of the work we do individually and collectively.
Stability analysis of MTopGO for module identification in PPI networks
Authors: Vella Danila , Tucker Allan , Bellazzi Riccardo
Published: January 2018

MTopGo is a novel algorithm of module identification for PPI Network analysis, it is designed to consider two key aspects of these models, the topological properties of the network and the apriori knowledge about the proteins involved, represented by GO annotations.

MTopGO rely on random components, thus stability of the results across different runs is a critical aspect of the algorithm. Moreover, when evaluating an algorithm specific for PPI Networks an important aspect is the stability in presence of false positive and false negative edges. In this work, two different stability analyses have been executed to evaluate MTopGO performance. Firstly, one to evaluate the stability of the result over many runs starting from a same input, to consider the range of variability introduced by the random components of the algorithm; secondly, one to evaluate the robustness of the output clusters when the input is affected by noise and uncertainty.

The results showed that MTopGO was more stable in case of false negative edges than false positive edges (adding false edges to a PPI Network was more damaging than removing existing links).
Sublime recapitulation: Evolution of the appendicular skeleton of Australian Mekosuchinae crocodiles.
Authors: Stein Michael D
Published: January 2018

Australian mekosuchines (Crocodylia; Crocodyloidea) with their wide diversity of cranial shape and inferred hunting strategies present a fascinating window into the diversification processes of crocodilians. This includes lingering questions as to the extent of any terrestrial habitus. A direct morphological signal for locomotion can be expected in the postcrania, particularly the girdles and the limbs of the appendicular skeleton. After a lengthy survey, enough materials of the pelvic girdle are available to chart morphological variation in the subfamily from Eocene through to middle Miocene. Over this period, the pelvis has undergone a vigorous morphological radiation. An enclosed, ventrally oriented acetabulum in the ilium developed in one lineage that apparently recapitulates the pillar-erect configuration of the pelvic girdle seen in many Mesozoic crocodilian lineages, suggesting consistent use of erect high-walk in these mekosuchines. Other pelves from Oligo–Miocene deposits display morphology closer to modern crocodilians despite clearly representing derived forms themselves, indicating a partition of locomotory strategy in the fauna during the Oligo–Miocene. While materials of hindlimb remain frustratingly lacking in light of this discovery, enough materials of forelimb humeri have been uncovered to chart the morphological variation in the subfamily from Eocene through to Pleistocene, corroborating what is seen in the pelvic girdle. As such, a collaborative project has been started that aims to quantitatively asses shape and stress variation in the mekosuchine forelimb using geometric morphometric and finite element analyses.
Primary care consultations in the UK between 2006 and 2015: An analysis of electronic health records
Authors: Eaton Benjamin
Published: January 2018

Primary care accounts for the majority of patient contact within the NHS. Over time medical science and healthcare needs change, which may lead to differences in how patients are treated in primary care for good or ill. In this study over 700 million consultations were analysed over a 10 year period between 2006 and 2015 inclusively to examine the trends in how people access primary care. The number of consultations per person per year initially increased in the first two years from 5.81 to 5.92, an increase of 0.11(0.10 to 0.12 95% CI) before declining to 3.7 by 2015, a decrease of 2.21 from the peak in 2008(2.20 to 2.23 95% CI). Consultations were increasingly handled by health care assistants instead of Nurses and GPs, and increased slightly in duration for all types of staff. This reduction in number of consultations is theorized to be a consequence of the 2008 financial crisis and its aftermath, further research is recommended on the impact of economic recessions and austerity policies on health care provision.
GenotypeAnalytics: a RESTFul platform to mine multiple associations between SNPs and drug response in case-control studies
Authors: Agapito Giuseppe , Guzzi Pietro H , Cannataro Mario
Published: January 2018

We present GenotypeAnalytics (GA), a RESTFul service that makes it possible to mine association rules from Single Nucleotide Polymorphism (SNP) datasets using standard web browsers. GA can speed up and simplify the analysis of this massive amount of data, highlighting only the SNPs involved, for example, in the development of the disease or responsible for adverse drug reactions to the drug. In this way, the doctor may use this extracted knowledge for a significant improvement in the quality of the treatments.
4, 8, 32, 64 bit Substitution Box generation using Irreducible or Reducible Polynomials over Galois Field GF(pq)
Authors: Dey Sankhanil , Ghosh Ranjan
Published: January 2018

Substitution Box or S-Box had been generated using 4-bit Boolean Functions (BFs) for Encryption and Decryption Algorithm of Lucifer and Data Encryption Standard (DES) in late sixties and late seventies respectively. The S-Box of Advance Encryption Standard have also been generated using Irreducible Polynomials over Galois field GF(28) adding an additive constant in early twenty first century. In this paper Substitution Boxes have been generated from Irreducible or Reducible Polynomials over Galois field GF(pq). Binary Galois fields have been used to generate Substitution Boxes. Since the Galois Field Number or the Number generated from coefficients of a polynomial over a particular Binary Galois field (2q) is similar to log2q+1 bit BFs. So generation of log2q+1 bit S-Boxes is possible. Now if p = prime or non-prime number then generation of S-Boxes is possible using Galois field GF (pq ), where q = p-1.
R Python, and Ruby clients for GBIF species occurrence data
Authors: Chamberlain Scott A , Boettiger Carl
Published: January 2018

Background. The number of individuals of each species in a given location forms the basis for many sub-fields of ecology and evolution. Data on individuals, including which species, and where they're found can be used for a large number of research questions. Global Biodiversity Information Facility (hereafter, GBIF) is the largest of these. Programmatic clients for GBIF would make research dealing with GBIF data much easier and more reproducible.

Methods. We have developed clients to access GBIF data for each of the R, Python, and Ruby programming languages: rgbif, pygbif, gbifrb.

Results. For all clients we describe their design and utility, and demonstrate some use cases.

Discussion. Programmatic access to GBIF will facilitate more open and reproducible science - the three GBIF clients described herein are a significant contribution towards this goal.
Network diffusion on multiple-layers: current approaches and integrative analysis of Rheumatoid Arthritis data.
Authors: Di Nanni Noemi , Gnocchi Matteo , Moscatelli Marco , Milanesi Luciano , Mosca Ettore
Published: January 2018

Network Diffusion has been proposed in several applications, thanks to its ability of amplifying biological signals and prioritizing genes that may be associated with a disease. Not surprising, the success of Network Diffusion on a “single layer” led to the first approaches for the joint analysis of multi-omics data.

Here, we review integrative methods based on Network Diffusion that have been proposed with several aims (e.g. patient stratification, module detection, function prediction). We used Network Diffusion to analyse, in the context of physical and functional protein-protein interactions, genetic variation, DNA methylation and gene expression data from a study on Rheumatoid Arthritis. We identified functionally related genes with multiple alterations.
Drop-out from the tuberculosis contact investigation cascade in a routine public health setting in urban Uganda: A prospective, multi-center study
Authors: Armstrong-Hough Mari , Turimumahoro Patricia , Meyer Amanda , Ochom Emmanuel , Babirye Diana , Ayakaka Irene , Mark David , Ggita Joseph , Cattamanchi Adithya , Dowdy David , Mugabe Frank , Fair Elizabeth , Haberer Jessica , Katamba Achilles , Davis J. Lucian
Published: January 2018

Setting Seven public tuberculosis (TB) units in Kampala, Uganda, where Uganda’s national TB program recently introduced household contact investigation, as recommended by 2012 guidelines from WHO.

Objective To apply a cascade analysis to implementation of household contact investigation in a programmatic setting. Design Prospective, multi-center observational study.

Methods We constructed a cascade for household contact investigation to describe the proportions of: 1) index patient households recruited; 2) index patient households visited; 3) contacts screened for TB; and 4) contacts completing evaluation for, and diagnosed with, active TB.

Results 338 (33%) of 1022 consecutive index TB patients were eligible for contact investigation. Lay health workers scheduled home visits for 207 (61%) index patients and completed 104 (50%). Among 287 eligible contacts, they screened 256 (89%) for symptoms or risk factors for TB. 131 (51%) had an indication for further TB evaluation. These included 59 (45%) with symptoms alone, 58 (44%) children <5, and 14 (11%) with HIV. Among 131 contacts found to be symptomatic or at risk, 26 (20%) contacts completed evaluation, including five (19%) diagnosed with and treated for active TB, for an overall yield of 1.7%. The cumulative conditional probability of completing the entire cascade was 5%.

Conclusion Major opportunities exist for improving the effectiveness and yield of TB contact investigation by increasing the proportion of index households completing screening visits by lay health workers and the proportion of at-risk contacts completing TB evaluation.
Mechanism for the prevention of password reuse through Anonymized Hashes
Authors: Ali Junade
Published: January 2018

Password authentication is an essential and widespread form of user authentication on the Internet with no other authentication system matching its dominance. When a password on one website is breached, if reused, the stolen password can be used to gain access to multiple other authenticated websites. Even amongst technically educated users, the security issues surrounding password reuse are not well understood and restrictive password composition rules have been unsuccessful in reducing password reuse. In response, the US NIST have published standards outlining that, when setting passwords, authentication systems should validate that user passwords have not already been compromised or breached. We propose a mechanism to allows for clients to anonymously validate whether or not a password has been identified in a compromised database, without needing to download the entire database or send their password to a third-party service. A mechanism is proposed whereby password hash data is generalized such that it holds the k-anonymity property. An implementation is constructed to identify to what extent the data should be generalized for it to hold k-anonymity and additionally to group password hashes by their generalized anonymous value. The implementation is run on a database of over 320 million leaked passwords and the results of the anonymization process are considered.
An algebraic representation for tree alignment of RNA pseudoknotted structures
Authors: Quadrini Michela , Tesei Luca , Merelli Emanuela ,   BioShape & Data Science Lab
Published: January 2018

The methods proposed in the literature for RNA comparison focus mainly on pseudoknot free structures. The comparison of pseudoknotted structures is still a challenge. In this work, we propose a new algebraic representation of RNA secondary structures based on relations among hairpins in terms of nesting, crossing, and concatenation. Such algebraic representation is obtained from a defined multiple context-free grammar, which maps any kind of RNA secondary structures into extended trees, i.e., ordered trees where internal nodes are labeled with algebraic operators and leaves are labeled with loops. These extended trees permit the definition of the RNA secondary structure comparison as a tree alignment problem.
ISMARA: Completely automated inference of gene regulatory networks from high-throughput data
Authors: Pachkov Mikhail , Balwierz Piotr J , Arnold Phil , Gruber Andreas J , Zavolan Mihaela , van Nimwegen Erik
Published: January 2018

As the costs of high-throughput measurement technologies continue to fall, experimental approaches in biomedicine are increasingly data intensive and the advent of big data is justifiably seen as holding the promise to transform medicine. However, as data volumes mount, researchers increasingly realize that extracting concrete, reliable, and actionable biological predictions from high-throughput data can be very challenging. Our laboratory has pioneered a number of methods for inferring key gene regulatory interactions from high-throughput data. For example, we developed motif activity response analysis (MARA)[, which models genome-wide gene expression (RNA-Seq, or microarray) and chromatin state (ChIP-Seq) data in terms of comprehensive predictions of regulatory sites for hundreds of mammalian regulators (TFs and micro-RNAs). Using these models, MARA identifies the key regulators driving gene expression and chromatin state changes, the activities of these regulators across the input samples, their target genes, and the sites on the genome through which these regulators act. We recently completely automated MARA in an integrated web-server (ismara.unibas.ch) that allows researchers to analyze their own data by simply uploading RNA-Seq or ChIP-Seq datasets, and provides results in an integrated web interface as well as in downloadable flat form.
Evolutionary persistence in Gunnera and the contribution of southern plant groups to the tropical Andes biodiversity hotspot
Authors: Bacon Christine D. , Velásquez-Puentes Francisco , Hinojosa Luis Felipe , Schwartz Thomas , Oxelman Bengt , Pfeil Bernard , Arroyo Mary T. K. , Wanntorp Livia , Antonelli Alexandre
Published: January 2018

Several studies have demonstrated the contribution of northern immigrants to the flora of the tropical Andes – the world’s “hottest” biodiversity hotspot. However, much less is known about the biogeographic history and diversification of Andean groups with southern origins, although it has been suggested that northern and southern groups have contributed roughly equally to the high Andean (i.e. páramo) flora. Here we infer the evolutionary history of the southern hemisphere plant genus Gunnera, a lineage with a rich fossil history and an important ecological role as an early colonising species characteristic of wet, montane environments. Our results show striking contrasts in species diversification, where some species may have persisted for some 90 million years, whereas others date to less than 2 Ma since origination. The outstanding longevity of the group is likely linked to a high degree of niche conservatism across its highly disjunct range, whereby Gunnera tracks damp and boggy soils in cool habitats. Colonisation of the northern Andes is related to Quaternary climate change, with subsequent rapid diversification appearing to be driven by their ability to take advantage of environmental opportunities. This study demonstrates the composite origin of a mega-diverse biota.
Phylogeography and cryptic diversity of intertidal Ligia isopods (Crustacea, Isopoda, Ligiidae) across the southern Africa coastline
Authors: Greenan Taylor M , Griffiths Charles L , Santamaria Carlos A
Published: January 2018

The extensive coastlines of South Africa and Namibia extends from the Atlantic to the Indian Ocean and encompass several major biogeographic provinces, each characterized by unique faunal and floral assemblages. Recent biogeographic studies have led to competing biogeographic models of the southern African coastline. This has stimulated phylogeographic work to determine whether the distribution of genetic diversity within coastal invertebrate species match the proposed biogeographic regions. The lack of congruence between studies and the discovery of cryptic diversity indicating the possible existence of cryptic species in coastal isopods in the region underscore the need for additional phylogeographic research in southern Africa, particularly for organisms that have been shown to both harbor cryptic diversity and to retain signatures of past geological and oceanographic processes in their phylogeographic patterns. Isopods in the genus Ligia exhibit several biological traits that suggest they may be informative on phylogeographic patterns. They inhabit patchy rocky beaches, are direct developers, avoid the open water, and exhibit several biological traits that severely constrain their dispersal potential (e.g. poor desiccation resistance). These traits are thought to lead to long term isolation of populations, the retention of geological and oceanographic signatures in phylogeographic patterns of Ligia, and the presence of cryptic lineages. In this study, we used mitochondrial and nuclear markers to characterize Ligia collected in 18 localities across Namibia to the KwaZulu-Natal region of South Africa. We report the presence of cryptic lineages within Ligia species in the region, as well as distributional patterns that differ from those reported from other coastal taxa, but that broadly matches a widely used biogeographic model for the region.
The protective effect of palm tocotrienol-rich fraction against H2O2- induced oxidative stress in neonatal rat cardiomyocytes
Authors: Abdul Khalid Noor Shareena Aisha , Jubri Zakiah
Published: January 2018

Background: Oxidative stress plays an important role in the pathogenesis of heart diseases. Antioxidants such as palm tocotrienol-rich fraction (TRF) can reduce oxidative stress, hence preventing and reducing the risk of heart disease. This study was aimed to determine the protective effects of TRF against hydrogen peroxide (H2O2 ) - induced oxidative stress in neonatal rat cardiomyocytes (NRCM). Methods: The NRCM were divided into five groups: (1) control, (2) cells treated with TRF (10 µg/ml) for 24 hours, (3) cells subjected to H2O2 (0.5 mM ) for 30 minutes, (4) cells pre-treated with TRF, and (5) cells post-treated with TRF. The IC50 of H2O2 (0 – 5 mM ) and the effective dose of TRF (0 – 25 µg/ml) were determined using the MTS cell viability assay. Meanwhile, ELISA was used to measure the level of reactive oxygen species (ROS). The presence of superoxides and H2O2 were detected by dihydroethidium and 5-(and-6 ) - carboxy -2′,7′-dichlorodihydrofluorescein diacetate respectively. Flowcytometry analysis was conducted to determine the presence of apoptosis and measure the mitochondrial membrane potential, whereby the former involved the use of Annexin V-FITC stain while the latter JC-1 stain. The gene expressions of antioxidant (SOD, CAT, GPx) and apoptosis (Bax, Bcl-2, Caspase-3) enzymes were studied using qRT -PCR. Results: The IC50 of H2O2 was 0.5 mM while the effective dose of TRF 10 µg/ml. The cells which were subjected to H2O2 showed a decrease in NRCM viability and significant increase (p < 0.05) in ROS production. LDH activity and green fluorescence intensity (which indicated mitochondrial depolarisation ) were increased following H2O2 induction . With reference to the control, the H2O2- induced group had a higher percentage of late apoptotic cells, which was associated with the upregulation of the pro-apoptotic gene, Bax, and downregulation of the anti-apoptotic gene, Bcl-2 (p < 0.05). H2O2 also upregulated GPx expression , apart from downregulating CAT and Cu/Zn SOD expression (p < 0.05). The pre- and post-treatment groups had increased cell viability and reduced ROS production. Pre-treatment with TRF protected the cell membranes and mitochondria from H2O2- induced injury, as reflected by the reduction in extracellular LDH activity and apoptosis (the latter of which was associated with the downregulation of Bax). Meanwhile, the expression of GPx, Cat, and Cu/Zn SOD was reduced in the post-treatment group. Conclusion: By scavenging for ROS, palm TRF directly protects the cell membrane from H2O2- induced injury, leading to a decrease in oxidative stress. Thus, palm TRF maintains the mitochondrial membrane potential and prevents apoptosis secondary to decreased Bax expression.
Detecting significant features in modeling microRNA-target interactions
Authors: Coronnello Claudia , Perconti Giovanni , Rubino Patrizia , Contino Flavia , Bivona Serena , Feo Salvatore , Giallongo Agata
Published: January 2018

MicroRNAs (miRNAs) are small non-coding RNA molecules mediating the translational repression and degradation of target mRNAs in the cell. Mature miRNAs are used as a template by the RNA-induced silencing complex (RISC) to recognize the complementary mRNAs to be regulated. Up to 60% of human genes are putative targets of one or more miRNAs. Several prediction tools are available to suggest putative miRNA targets, however, only a small part of the interaction pairs has been validated by experimental approaches. The analysis of the expression profile of the RNA fraction immunoprecipitated (IP) with the RISC proteins is an established method to detect which genes are actually regulated by the RISC machinery. In fact, genes that result over-expressed in the IP sample with respect to the whole cell lysate RNA, are considered as involved in the RISC complex, then miRNA targets. Here, we aim to find the features useful to predict which genes are overexpressed in IP, i.e. miRNA targets, without actually performing the IP experiments. To this purpose, we compiled and analyzed a novel high throughput data set suitable to unravel the features involved in the miRNA regulatory activities. We analyzed IP samples obtained by the immunoprecipitation of two RISC proteins, AGO2 and GW182. The two proteins shows different behaviors, in terms of enriched genes and features characterizing the immunoprecipitated RNA fractio. Further analysis is needed to unravel the reason of such different behavior.
Application of network diffusion approaches to drug screenings: A perspective on multilayered networks derived from cell lines and drugs
Authors: Subramanian Vigneshwari , Szalai Bence , Tobalina Luis , Saez-Rodriguez Julio
Published: January 2018

Network diffusion approaches are frequently used for identifying the relevant disease genes and for prioritizing the genes for drug sensitivity predictions. Majority of these studies rely on networks representing a single type of information. However, using multiplex heterogeneous networks (networks with multiple interconnected layers) is much more informative and helps to understand the global topology. We built a multi-layered network that incorporates information on protein-protein interactions, drug-drug similarities, cell line-cell line similarities and co-expressed genes. We applied Random Walk with Restart algorithm to investigate the interactions between drugs, targets and cancer cell lines. Results of ANOVA models show that these prioritized genes are among the most significant ones that relate to drug response. Moreover, the predictive power of the drug response prediction models built using the gene expression data of only the top ranked genes is similar to the models built using all the available genes. Taken together, the results confirm that the multiplex heterogeneous network-based approach is efficient in identifying the most significant genes associated with drug response.
Resource management and security issues in mobile phone operating systems: A comparative analysis
Authors: Awan Khalid Mahmood , Waqar Muhammad , Faseeh Muhammad , Ullah Farman , Saleem Muhammad Qaiser
Published: January 2018

Nowadays Mobile phones are becoming more popular in our daily lives. Mobile technology has a great effect on human life. Our daily tasks are dependent on mobile devices. Memory Management (MM), Security and Performance plays an important role in every handheld device specially in mobile phones, which are very much dependent on their operating system (OS). These embedded operating systems are on the driving seat when we talk about efficient and useful memory management and secure handling. Three popular OS in mobile phones are Android, Windows and iOS (iPhone OS). Each OS has its own way of managing the memory and provide it to certain number of applications. Android is an open software available for the people to modify as per their needs. But Windows and iOS operating systems didn’t allow their software as open source. Researchers have done a large amount of work using different mechanisms and decision makings to develop new ways to manage the memory of these OS’s. This work shows a comparative analysis of different memory management and security related techniques in above three operating systems. In this paper, we present the analysis of memory management and security in mobile phone operating systems with respect to apps, main memory, cache memory and virtual memory. Also, we compare the overall performance of these OS’s in terms of MM, security concerns. This study will help in finding better operating system in terms of efficient memory management and security.
Potential conditional mutual information: Estimators and properties
Authors: Rahimzamani Arman , Kannan Sreeram
Published: January 2018

The conditional mutual information \(I(X;Y|Z)\) measures the average information that X and Y contain about each other given Z. This is an important primitive in many learning problems including conditional independence testing, graphical model inference, causal strength estimation and time-series problems. In several applications, it is desirable to have a functional purely of the conditional distribution \(p_{Y |X,Z}\) rather than of the joint distribution \(p_{X,Y,Z}\). We define the potential conditional mutual information as the conditional mutual information calculated with a modified joint distribution \(p_{Y |X,Z} q_{X,Z}\), where \(q_{X,Z}\) is a potential distribution, fixed airport. We develop K nearest neighbor based estimators for this functional, employing importance sampling, and a coupling trick, and prove the finite k consistency of such an estimator. We demonstrate that the estimator has excellent practical performance and show an application in dynamical system inference.
Publiphilia Impactfactorius: a new psychiatric syndrome among biomedical scientists?
Authors: Tijdink Joeri K , Smulders Yvo M , Bouter Lex M
Published: January 2018

Abstract

Introduction

Personality traits differ significantly between professionals, and the biomedical field is no exception. However, whether specific clusters of personality traits are indeed typical for biomedical scientists is unknown. This can be of particular interest since personality traits impact on behavior, and sloppy science or even scientific misconduct may be linked to specific clusters of personality traits. To explore clusters of personality traits among biomedical scientists, and to associate the clusters with academic position and research misbehaviour we designed a cross-sectional study with cluster analysis of personality traits among a stratified sample of Dutch biomedical scientists working in academic medical centers.

Methods

We used the NEO-BIG5, Rosenberg Self-esteem, Achievement Motivation Inventory and the Dark Triad (narcissistic, Machiavellianistic and psychopathic personality traits) as validated questionnaires. Self-reported research misconduct was assessed via a separate questionnaire.

Results

We included 537 active biomedical scientists completed a web-based survey (response rate 65%). Cluster analysis revealed the existence of three personality clusters among biomedical scientists: the ‘perfectionist’, the ‘ideal son-in-law’ and the ‘sneaky grandiose’. The latter cluster showed a consistent set of (subclinical) personality traits such as narcissism, psychopathy and Machiavellianism, that are indicative of the presence of a mental disorder, but could not be classified as such in terms of the DSM-IV TR or ICD-10. Male gender, higher academic hierarchical position, perceived publication pressure and, importantly, self-reported scientific misbehaviour were associated with the ‘sneaky grandiose’ personality cluster.

Discussion

These findings suggest that biomedical scientists in the ‘sneaky grandiose’ personality cluster have a relatively high propensity to engage in research misbehaviour. A small proportion of the ‘sneaky grandiose’ might suffer from a psychiatric condition characterized by pathological preoccupation with publishing and being cited. We therefore propose to name this syndrome ‘Publiphilia Impactfactorius’ (PI), and we suggest this affliction should be considered in revised versions of DSM5 and ICD-10. We provide tentative diagnostic criteria for PI. Early identification and intensive treatment or, alternatively, expulsion and annihilation of colleagues who suffer from PI may prevent further accumulation of research waste.