bluuebunny/crossref_metadata_2025_split huggingface dataset:
The Ecology of Stress: linking life-history traits with physiological control mechanisms in free-living guanacos
Authors: Ovejero Aguilar Ramiro J.A. , Jahn Graciela A , Soto-Gamboa Mauricio , Novaro Andrés , Carmanchahi Pablo 
Published: January 2018

Background-Providing the context for the evolution of life-history traits, habitat features constrain successful ecological and physiological strategies. In vertebrates, a key response to life's challenges is the activation of the Stress (HPA) and Gonadal (HPG) axes. Much of the interest in stress ecology is motivated by the desire to understand the physiological mechanisms in which the environment affects fitness. As reported in the literature, several intrinsic and extrinsic factors affect variability in hormone levels. In both social and non-social animals, the frequency and type of interaction with conspecifics, as well as the status in social species, can affect HPA axis activity, resulting in changes in the reproductive success of animals. We predicted that a social environment can affect both guanaco axes by increasing the secretion of testosterone (T) and Glucocorticoid (GCs) in response to individual social interactions and the energetic demands of breeding. Assuming that prolonged elevated levels of GCs over time can be harmful to individuals, it is predicted that the HPA axis suppresses the HPG axis and causes T levels to decrease, as GCs increase.
Methods-All of the data for individuals were collected by non-invasive methods (fecal samples) to address hormonal activities. This is a novel approach in physiological ecology because feces are easily obtained through non-invasive sampling in animal populations.
Results- As expected, there was a marked adrenal (p-value= .344e-12) and gonadal (p-value= 0.002656) response due to seasonal variation in Lama guanicoe. No significant differences were found in fecal GCs metabolites between males/females*season for the entire study period (p-value= 0.2839). Despite the seasonal activity variation in the hormonal profiles, our results show a positive correlation (p-value= 1.952e-11,COR=0.50) between the adrenal and gonadal system. The marked endocrine (r2 = 0.806) and gonad (r2 = 0.7231) response due to seasonal variation in male guanaco individuals highlights the individual’s energetic demands according to life-history strategies. This is a remarkable result because no inhibition was found between the axes as theory suggests. Finally, the dataset was used to build a reactive scope model for guanacos.
Discussion-Guanacos cope with the trade-off between sociability and reproductive benefits and costs, by regulating their GCs and T levels on a seasonal basis, suggesting an adaptive role of both axes to different habitat pressures. The results presented here highlight the functional role of stress and gonad axes on a critical phase of a male mammal's life—the mating period—when all of the resources are at the disposal of the male and must be used to maximize the chances for reproductive success.
Walking on the Moon
Authors: Schlacht Irene Lia , Rittweger Jörn , Foing Bernard H. , Daumer Martin , Masali Melchiorre 
Published: January 2018

How high do we jump on the Moon? Should we build architecture with steps or should we support climbing? The hypogravity will lead to vestibular system malfunction, loss of muscular mass, and stiffness of the legs, negatively affecting a person’s balance: Yes, we can climb, but we can also easily lose our balance and trip up.
To avoid all of this, we need to better understand gait and balance on the Moon. This research will investigate a methodology that focuses on the collection of basic anthropometrical and postural data needed to develop interfaces for the Moon and Mars gravity environments and habitat.
Assessment of spectral properties of Apollo 12 landing site
Authors: Chemin Yann H , Crawford Ian A , Grindrod Peter , Alexander Louise 
Published: January 2018

The geology and mineralogy of the Apollo 12 landing site has been the subject of recent studies that this research attempts to complement from a remote sensing point of view using the Moon Mineralogy Mapper (M3) sensor data, onboard the Chandrayaan-1 lunar orbiter. It is a higher spatial-spectral resolution sensor than the Clementine UVVis sensor and gives the opportunity to study the lunar surface with a comparatively more detailed spectral resolution.
The M3 signatures are showing a monotonic featureless increment, with very low reflectance, suggesting a mature regolith. The regolith maturity is splitting the landing site in a younger Northwest and older Southeast. The mineral identification using the lunar sample spectra from within the Relab database found some similarity to a basaltic rock/glass mix. The spectrum features of clinopyroxene have been found in the Copernican rays and at the landing site. Lateral mixing increases FeO content away from the central part of the ray. The presence of clinopyroxene in the pigeonite basalt in the stratigraphy of the landing site brings forth some complexity in differentiating the Copernican ray’s clinopyroxene from the local source, as the spectra are twins but for their vertical shift in reflectance, reducing away from the central part of the ray.
Spatial variations in mineralogy were not found mostly because of the pixel size compared to the landing site area. The contribution to stratigraphy is limited to the topmost layer which is a clinopyroxene-dominated basalt belonging to the most remote tip of a Copernican ray and its resulting local regolith mix.
Structural models of the human iron exporter ferroportin in the inward- and outward- open states
Authors: Tortosa Valentina , Polticelli Fabio 
Published: January 2018

Motivation
Ferroportin (Fpn) is a membrane protein belonging to the Major Facilitator Superfamily of transporters. It is the only vertebrate iron exporter known so far. Several Fpn mutations lead to the so-called ‘ferroportin disease’ or type 4 haemochromatosis, characterized by two distinct iron accumulation phenotypes depending on whether the mutations affects the protein’s activity or its degradation pathway (1). Despite a general agreement of the scientific community on a 12 transmembrane helices topology, no experimental data are available on human Fpn (HsFpn) three-dimensional structure. Thus, important features of HsFpn remain to be clarified. Recently, the crystal structures of a HsFpn homologue from the predatory Gram-negative bacterium Bdellovibrio bacteriovorus (BbFPN), in both the outward- (Figure 1 A) and inward-open states (Figure 1 B), has been reported (2). The residues essential for iron binding and transport in HsFpn are conserved in BbFPN (3). The conservation of these functionally relevant residues prompted us to exploit the two BbFPN structures to construct reliable models of HsFPN.
Methods
The structural models of HsFpn in were built in both the outward- and inward-open states through the ab initio/threading strategy implemented in the I-TASSER server (4). The overall quality of the models generated has been evaluated using PROCHECK (5) and the model quality parameters provided in the I-TASSER output, such as the C-score. Putative iron binding sites have been detected using LIBRA (6).
Results
The models display the typical fold of MFS proteins with 12 TMs spanning the membrane and the N- and C-termini located on the intracellular side (Figure 1). LIBRA analysis of the models has led to the identification of potential iron binding sites in the inward-open state allowing to propose an iron traslocation mechanism. Further, the outward-open model uncovers details of the interaction site of the peptide hormone hepcidin, a regulator of HsFpn function. Fin ally, the HsFPN models provide a mechanistic interpretation for the disease-related mutations that cause hereditary hemochromatosis.
The mass, metabolism and length explanation can simultaneously calculate an animal’s mass and metabolic rate from its characteristic length
Authors: Frasier Charles C 
Published: January 2018

It is shown that the mass, metabolism and length explanation (MMLE) can simultaneously compute an animal’s body mass and BMR given its characteristic length using data for humans.
MMLE was advanced in 1984 to explain the relationship between metabolic rate and body mass for birds and mammals. It was modernized in 2015 by explicitly treating dynamic similarity of mammals’ skeletal musculature and revising the treatment of BMR. Using two primary equations MMLE deterministically computes the absolute value of Basal Metabolic Rate (BMR) and body mass for individual animals as functions of an individual animal’s characteristic length and sturdiness factor. The characteristic length is a measureable skeletal length associated with an animal’s means of propulsion. The sturdiness factor expresses how sturdy or gracile an animal is. Eight other parameters occur in the equations that vary little among animals in the same phylogenetic group. A mass and length data set with 575 entries from the orders Rodentia, Chiroptera, Artiodactyla, Carnivora, Perissodactyla and Proboscidea and a BMR and mass data set with 436 entries from the orders Rodentia, Chiroptera, Artiodactyla and Carnivora were used to estimate values for the parameters occurring in the equations. With the estimated values MMLE can exactly compute every BMR and mass datum from the BMR and mass data set. Furthermore, MMLE can exactly compute every body mass datum from the mass and length data set. Since there is not a data set that simultaneously reports body mass, BMR and characteristic length for individual animals from the mammal orders that were analyzed it could not be determined whether or not MMLE could simultaneously compute both an animal’s BMR and body mass given its characteristic length.
There are large data sets that report body mass, BMR and height for humans. A human’s characteristic length can be estimated from height. In this paper human data categorized by sex, age and body mass index (BMI) are used to show that MMLE can indeed simultaneously compute a human’s body mass and BMR given his or her characteristic length.
The MMLE body mass equation is modified to explicitly address body fat because it appears that humans are fatter than other running/walking placental mammals. Differences in body fat seem to account for body mass and BMR sexual dimorphism among humans. The impact on BMR of the large and metabolically expensive human brain is addressed. Also mitochondria capability decline with age is addressed.
HiPPO and PANDA: two bioinformatics tools to support analysis of high-dimensional mass cytometry data
Authors: Pirrò Stefano , Cerquone Perpetuini Andrea , Marinkovic Milica , Perfetto Livia , Petrilli Lucia Lisa , Rosina Marco , Spada Filomena , Castagnoli Luisa , Cesareni Gianni 
Published: January 2018

Biological processes are modulated by the interaction of different cell types and their study requires technologies able to analyse single cells in heterogeneous populations.
High-dimensional mass cytometry enables the single cell analysis of more than 40 parameters. Several computational approaches have been proposed to reduce the multidimensionality of the datasets produced by this technology (i.e. SPADE and viSNE for clustering and visualization).
We have developed two new bioinformatics tools that help overcoming some of the limitations of the available toolboxes by defining quasi homogeneous cell populations (HIPPO) and by matching their expression profiles with that of cell populations described in the literature.
HiPPO uses a supervised quantitation approach to discretize the expression distribution curves generated for each marker monitored in the experiments. Cells in the continuous, multidimensional dataset are converted into a bi-dimensional matrix where row and columns are events (cells) and markers, respectively.
In order to characterize cell populations, HiPPO queries PANDA, a manually-curated database which stores expression profiles for selected markers of primary cells. The comparison and PANDA discrete expression profiles with those identified by PANDA in the populations under study, allow to monitor cell type abundance.
Moreover, given a set of experiments in different conditions, HiPPO can evaluate the variation of protein expression levels, for any identified population. This is performed by the use of Kolmogorov-Smirnov non-parametric test, evaluating empirical distribution differences of two samples. The analysis is conducted interactively, through a user-friendly web application.
HiPPO ability to identify populations and rapidity of execution have been evaluated and compared with the popular SPADE and viSNE tools. For benchmarking we have used a published dataset of healthy human bone marrow biopsies analysed with the CyTOF platform by simultaneously measuring 34 parameters in single cells [1]. As use case, we focused on 5 cell populations (Mature/Naïve T-helper cells, Mature/Naïve T-cytotoxic cells, B cells). The abundance of cell populations identified by HiPPO is highly-comparable to SPADE and viSNE analysis conducted by the authors. On the other hand HIPPO is 2,15X faster in completing the analysis.
Hippo is a resource that can be easily used to analyze high-throughput multi-dimensional data. The synergy with PANDA represent a substantial improvement in the analysis pipeline and helps overcoming some of the shortcomings of other tools.
HiPPO is freely available at http://160.80.35.248/hippo, PANDA at http://160.80.35.248/panda
Receptor flexibility in molecular cross-docking
Authors: Sessa Lucia , Di BIasi Luigi , Parisi Rosaura , Concilio Simona , Piotto Stefano 
Published: January 2018

Motivation

Molecular docking is an efficient method to predict the conformations adopted by the ligand within the target binding site. Usually, standard docking protocol involves only one structure to represent the receptor, overlooking the changes in the binding pocket geometry induced by ligand binding. In our previous work, we observed that different conformations of the same target show different volume and shape of the internal cavities (Sessa et al., 2016). Different ligands may stabilize different receptor conformations with different internal cavities. Consequently, the crystallographic data represent the adaptation of a protein to a particular ligand. Cross-docking is a validation procedure consisting in docking a series of ligands into different conformation of the same receptor. Since the structures of the same receptor can be rather different, the cross-docking analyses are typically very poor. In these cases the internal cavity of the buried binding pocket does not have space enough to accommodate all ligands and this can radically affect the outcome and alter the cross-docking results. The changes of the cavity volume might explain the failure of traditional docking method and support the hypothesis that a single representative structure for the receptor is not enough. Keeping target proteins flexible during the docking has a high computational cost. To overcome this limit, our docking strategy is to represent receptor flexibility through an inexpensive method that generates a series of target structures. Starting from a known target structure, we used the molecular dynamics (MD) simulations to explore the conformational changes induced by ligand binding and to collect several snapshots of receptor structures to perform the cross-docking studies. To validate the accuracy of our flexible protocol in docking, we used a set of 10 crystallographic conformations of Androgen Receptor with the same target but with a different ligand. We performed two parallel experiments of docking, one with a rigid protein target and one considering flexible receptor structures. In addition, we compared the results for both experiments in the re-docking and in the cross-docking analysis.

Methods

Ten receptor structures complexed with a ligand were extracted from the X-ray structures in the PDB database (Berman et al., 2000). Several conformations for each receptor were selected from the molecular dynamics simulations (MD) at regular time intervals (each 500 ps). The MD simulations were performed with the software YASARA Structure 16.2.14 (Krieger & Vriend, 2014) using AMBER14 as force field. The molecular docking simulations were performed using VINA provided in the YASARA package.
"Abstract truncated at 3,000 characters - the full version is available in the pdf file"
IVaCS: an Integrated Variant Calling System
Authors: Chiara Matteo , Chillemi Giovanni , D'Antonio Mattia , D'Onorio De Meo Paolo , Flati Tiziano , Gioiosa Silvia , Picardi Ernesto , Pesole Graziano , Castrignanò Tiziana 
Published: January 2018

The reduction in sequencing costs associated with next generation sequencing technologies (NGS) has led to a rapid upsurge in the amount of genome re-sequencing data, paving the way for the advent of personalized genomics and precision medicine. Accurate genotyping is crucial for effective analyses of these data, and in particular for the correct identification of candidate causal mutations in diagnostic screenings. The body of genome resequencing data will likely see exponential growth in the next few years, underlining the need for publicly available, accurate and time-effective bioinformatics systems for data analysis. Ideally, such systems should be easy to use and constantly updated as new genomes and software tools are released.
Here we present IVaCS, a fully automated, highly accurate system with a web based graphical interface for genotyping and variant annotation. IVaCS offers state of the art tools for variant calling and annotation along with expert made pipelines for the analysis of whole genome sequencing (WGS), whole-exome sequencing (WES) and targeted resequencing (TGS) data, performing all steps from quality trimming to variant annotation.
The system is specifically designed to assist users with little or no bioinformatics skills and all the pipelines are available through a user friendly web interface. The final output is provided in the form of a dynamic web page where variants can be selected on the base of user defined hard filters. A comprehensive report containing detailed information and statistics concerning the execution of each step of the pipelines is also generated.
Extensive tests on publicly available genome resequencing data (Illumina platinum genome NA12878), show that our system recovers a slightly better sensitivity and a higher specificity than the commercial Illumina VCAT 2.0 software. IVaCS is implemented with a modular architecture and each module (quality trimming, reads mapping, variant calling, variant annotation) can be used independently. IVaCS may manage all the major commercial kits for exome sequencing, such as Illumina, Agilent or Nimblegen, along with a comprehensive collection of reference genomes (all the Illumina genomes, including human, mouse and cow, among the others) with corresponding genomic annotations. Finally, the software leverages an ensemble of publicly available resources (e.g., dbSNP, OMIM, COSMIC and ClinVar among others) for the functional annotation of human variants. Advanced users needing more control over the single steps might also request the command-line version of the software which is more flexible and easy to customize. IVaCS has a very active and growing community. The system is under constant development and new reference genomes, databases and bioinformatics tools are added to IvaCS on a regular basis. IVACS is available at: https://bioinformatics.cineca.it/ivacs
Investigating the opening mechanism of topoisomerase I B in complex with DNA by means of metadynamics
Authors: Morozzo della Rocca Blasco , Coletta Andrea , Iacovelli Federico , Desideri Alessandro 
Published: January 2018

Motivations: Topoisomerases play a central role in DNA homeostasis and act on them through a catalytic cycle that comprises the opening of the protein clamp to embrace the DNA (at the beginning of the cycle) and opening to allow the release of the topologically relaxed substrate. Protein opening is hard to follow experimentally thus computational techniques are very handy in dealing with this transitions, although classical molecular dynamics is limited in following big conformational changes and slowly occurring transitions. Therefore we present a well-tempered Metadynamics study of hToP1 clamp opening in presence of a 22-bp long ds-DNA substrate.
Methods: The protein structure of wild type hTopIB in complex with DNA has been obtained as previously reported. The hTopIB clamp around the DNA molecule has been destabilized by means of metadynamics using Gromacs-4.5.5 with the PLUMEDv1.3 patch. In the simulation, two Collective Variables have been used to describe the clamp opening: the distance between the center of mass of Cα atoms of the lip1 and of the lip2; and the number of hydrogen bonds between the protein and DNA.Free-energy surface (FES) and the minimum energy path (MEP) connecting different minima were reconstructed using in-house written codes in Python. Salt bridge analysis was conducted via Salt bridges extension of the VMD program and other analyses were performed with the tools of the GROMACS package.
Results: Results indicate that the lobes of the protein retain their domain structure during the opening that is characterized by an energy barrier of about 50 Kjoul/mole. Furthermore the DNA remains in contact with the Cap lobe, a fact that would enable the protein to perform 1D-diffusion in the DNA strand to enhance the specific activity by reducing the dimensional space it has to search between relaxation events.
Implementing an open source spatio-temporal search platform for Spatial Data Infrastructures
Authors: Corti Paolo , Lewis Benjamin G , Kralidis Tom , Mwenda Jude 
Published: January 2018

A Spatial Database Infrastructure (SDI) is a framework of geospatial data, metadata, users and tools intended to provide the most efficient and flexible way to use spatial information. One of the key software component of a SDI is the catalogue service, needed to discover, query and manage the metadata. Catalogue services in a SDI are typically based on the Open Geospatial Consortium (OGC) Catalogue Service for the Web (CSW) standard, that defines common interfaces to access the metadata information.
A search engine is a software system able to perform very fast and reliable search, with features such as full text search, natural language processing, weighted results, fuzzy tolerance results, faceting, hit highlighting and many others.
The Centre of Geographic Analysis (CGA) at Harvard University is trying to integrate within its public domain SDI (named WorldMap), the benefits of both worlds (OGC catalogs and search engines).
Harvard Hypermap (HHypermap) is a component that will be part of WorldMap, totally built on an open source stack, implementing an OGC catalog, based on pycsw, to provide access to metadata in a standard way, and a search engine, based on Solr/Lucene, to provide the advanced search features typically found in search engines.