Miracle-dz/UniFAR-FTUs huggingface dataset:
AmoebaDB and MicrosporidiaDB: functional genomic resources for Amoebozoa and Microsporidia species

AmoebaDB (http://AmoebaDB.org) and MicrosporidiaDB (http://MicrosporidiaDB.org) are new functional genomic databases serving the amoebozoa and microsporidia research communities, respectively. AmoebaDB contains the genomes of three Entamoeba species (E. dispar, E. invadens and E. histolityca) and microarray expression data for E. histolytica. MicrosporidiaDB contains the genomes of Encephalitozoon cuniculi, E. intestinalis and E. bieneusi. The databases belong to the National Institute of Allergy and Infectious Diseases (NIAID) funded EuPathDB (http://EuPathDB.org) Bioinformatics Resource Center family of integrated databases and assume the same architectural and graphical design as other EuPathDB resources such as PlasmoDB and TriTrypDB. Importantly they utilize the graphical strategy builder that affords a database user the ability to ask complex multi-data-type questions with relative ease and versatility. Genomic scale data can be queried based on BLAST searches, annotation keywords and gene ID searches, GO terms, sequence motifs, protein characteristics, phylogenetic relationships and functional data such as transcript (microarray and EST evidence) and protein expression data. Search strategies can be saved within a user’s profile for future retrieval and may also be shared with other researchers using a unique strategy web address.
Visualising Environmental Corrosion in Outdoor Augmented Reality

This paper provides a description of outdoor visualisation of environmental corrosion data. This system was developed to aid in the visual understanding of data from wireless sensors used to monitor large structures. Due to the laborious manual inspections required for large structures (such as bridges), wireless environmental sensors have been designed to automate this process. Our system visualizes this information in its real-world context using the Tinmith mobile outdoor augmented reality system. We provide an overview of the visualizations, outlining a user study that was conducted to determine the effectiveness of the visualizations in providing the user with context-sensitive information, along with the preliminary results of this study. The paper concludes with an overview of future work on the system and final thoughts.
Estimates of the Continuously Publishing Core in the Scientific Workforce

Background The ability of a scientist to maintain a continuous stream of publication may be important, because research requires continuity of effort. However, there is no data on what proportion of scientists manages to publish each and every year over long periods of time. Methodology/Principal Findings Using the entire Scopus database, we estimated that there are 15,153,100 publishing scientists (distinct author identifiers) in the period 1996–2011. However, only 150,608 (<1%) of them have published something in each and every year in this 16-year period (uninterrupted, continuous presence [UCP] in the literature). This small core of scientists with UCP are far more cited than others, and they account for 41.7% of all papers in the same period and 87.1% of all papers with >1000 citations in the same period. Skipping even a single year substantially affected the average citation impact. We also studied the birth and death dynamics of membership in this influential UCP core, by imputing and estimating UCP-births and UCP-deaths. We estimated that 16,877 scientists would qualify for UCP-birth in 1997 (no publication in 1996, UCP in 1997–2012) and 9,673 scientists had their UCP-death in 2010. The relative representation of authors with UCP was enriched in Medical Research, in the academic sector and in Europe/North America, while the relative representation of authors without UCP was enriched in the Social Sciences and Humanities, in industry, and in other continents. Conclusions The proportion of the scientific workforce that maintains a continuous uninterrupted stream of publications each and every year over many years is very limited, but it accounts for the lion’s share of researchers with high citation impact. This finding may have implications for the structure, stability and vulnerability of the scientific workforce.
Towards Visual Reflexion Models

Source code and models of a software system, like architectural views, tend to evolve separately and drift apart over time. Previous research has shown that it is possible to effectively relate them through a reflex ion model, defined as a "summarization of a software system from the viewpoint of a particular high-level model". While effective, the process of constructing and analyzing reflex ion models was supported by text-based tools with limited visual representation. With the original approach, it was relatively hard to understand which parts of the system were represented, and which parts of the system contributed to specific relations in the reflexion model. We present our vision on augmenting the construction and analysis of reflex ion models with visual support, effectively providing the basis for visual reflex ion models. We describe our approach, implemented as a web-based application, and two promising case studies involving two open-source projects.
Sized Type Analysis for Logic Programs

We present a novel analysis for relating the sizes of terms and subterms occurring at different argument positions in logic predicates. We extend and enrich the concept of sized type as a representation that incorporates structural (shape) information and allows expressing both lower and upper bounds on the size of a set of terms and their subterms at any position and depth. For example, expressing bounds on the length of lists of numbers, together with bounds on the values of all of their elements. The analysis is developed using abstract interpretation and the novel abstract operations are based on setting up and solving recurrence relations between sized types. It has been integrated, together with novel resource usage and cardinality analyses, in the abstract interpretation framework in the Ciao preprocessor, CiaoPP, in order to assess both the accuracy of the new size analysis and its usefulness in the resource usage estimation application. We show that the proposed sized types are a substantial improvement over the previous size analyses present in CiaoPP, and also benefit the resource analysis considerably, allowing the inference of equal or better bounds than comparable state of the art systems.
Endothelial cell apoptosis in brown adipose tissue of rats induced by hyperinsulinaemia: the possible role of TNF-α

The aim of the present study was to investigate whether hyperinsulinaemia, which frequently precedes insulin resistance syndrome (obesity, diabetes), induces apoptosis of endothelial cells (ECs) in brown adipose tissue (BAT) and causes BAT atrophy and also, to investigate the possible mechanisms underlying ECs death. In order to induce hyperinsuli-naemia, adult male rats of Wistar strain were treated with high dose of insulin (4 U/kg, intraperitonely) for one or three days. Examinations at ultrastructural level showed apoptotic changes of ECs, allowing us to point out that changes mainly but not exclusively, occur in nuclei. Besides different stages of condensation and alterations of the chromatin, nuclear fragmentation was also observed. Higher number of ECs apoptotic nuclei in the BAT of hyperinsulinaemic rats was also confirmed by propidium iodide staining. Immunohistochemical localization of tumor necrosis factor-alpha (TNF-α) revealed increased expression in ECs of BAT of hyperinsulinaemic animals, indicating its possible role in insulin-induced apoptotic changes. These results suggest that BAT atrophy in hyperinsulinaemia is a result of endothelial and adipocyte apoptosis combined, rather than any of functional components alone.
Mycotoxin Production in Liquid Culture and on Plants Infected with Alternaria spp. Isolated from Rocket and Cabbage

Fungi belonging to the genus Alternaria are common pathogens of fruit and vegetables with some species able to produce secondary metabolites dangerous to human health. Twenty-eight Alternaria isolates from rocket and cabbage were investigated for their mycotoxin production. Five different Alternaria toxins were extracted from synthetic liquid media and from plant material (cabbage, cultivated rocket, cauliflower). A modified Czapek-Dox medium was used for the in vitro assay. Under these conditions, more than 80% of the isolates showed the ability to produce at least one mycotoxin, generally with higher levels for tenuazonic acid. However, the same isolates analyzed in vivo seemed to lose their ability to produce tenuazonic acid. For the other mycotoxins; alternariol, alternariol monomethyl ether, altenuene and tentoxin a good correlation between in vitro and in vivo production was observed. In vitro assay is a useful tool to predict the possible mycotoxin contamination under field and greenhouse conditions.
SERIES A Generic Framework for Computational Spatial Modelling

In this paper, we develop a generic framework for comparing spatial models whose dynamics ranges from comparative static equilibrium structures to fully dynamic models. In the last 40 years, a variety of spatial models have been suggested. Until the mid 1980s, most models were static in structure and tended to embrace detailed mechanisms involving spatial economics and social physics. Typical examples were Land Use Transportation Interaction (LUTI) models that embraced theories of spatial interaction and discrete choice modelling. During this earlier period, the problems of making these models dynamic and more disaggregate was broached but progress was slow largely because of problems in collecting requisite data and problems of increasing the complexity of such models to the point where they could be properly validated in traditional ways. 20 years or more ago, new modelling approaches from very different sources came onto the horizon: in particular, dynamic models based in Cellular Automata (CA) which were largely physical in nature and Agent-Based Models (ABM) providing explicit behavioural processes that often rested alongside these automata. Systems Dynamics Models (SDM), Spatial Econometric Models (SEM) and Micro-simulation Models (MM) all informed the debate. It is tempting to see these models as all being of different genera but here we attempt to see them as part of an integrated whole, introducing a framework for their elaboration and comparison. After the framework is introduced, we review these six model types and choose three – CA, ABM and LUTI models – that we then work up in more detail to illustrate these comparisons. We conclude with the conundrums and paradoxes that beset this field.
High throughput microscopy identifies bisphenol AP, a bisphenol A analog, as a novel AR down-regulator

Prostate cancer remains a deadly disease especially when patients become resistant to drugs that target the Androgen Receptor (AR) ligand binding domain. At this stage, patients develop recurring castrate-resistant prostate cancers (CRPCs). Interestingly, CRPC tumors maintain dependency on AR for growth; moreover, in CRPCs, constitutively active AR splice variants (e.g., AR-V7) begin to be expressed at higher levels. These splice variants lack the ligand binding domain and are rendered insensitive to current endocrine therapies. Thus, it is of paramount importance to understand what regulates the expression of AR and its splice variants to identify new therapeutic strategies in CRPCs. Here, we used high throughput microscopy and quantitative image analysis to evaluate effects of selected endocrine disruptors on AR levels in multiple breast and prostate cancer cell lines. Bisphenol AP (BPAP), which is used in chemical and medical industries, was identified as a down-regulator of both full length AR and the AR-V7 splice variant. We validated its activity by performing time-course, dose-response, Western blot and qPCR analyses. BPAP also reduced the percent of cells in S phase, which was accompanied by a ~60% loss in cell numbers and colony formation in anchorage-independent growth assays. Moreover, it affected mitochondria size and cell metabolism. In conclusion, our high content analysis-based screening platform was used to classify the effect of compounds on endogenous ARs, and identified BPAP as being capable of causing AR (both full-length and variants) down-regulation, cell cycle arrest and metabolic alterations in CRPC cell lines.
Periodic solutions of the non-autonomous lagrange systems

This paper presents a robust distributed localization approach which employs weighted least squares scaling with soft constrains. It incorporates the a priori deployment constraints, i.e., minimum and maximum node separation among 2-hop nodes, into localization as soft constraints and penalizes pairs of 2-hop nodes whose assigned coordinates violate the minimum and maximum constraints. Combined with applying consistency checking and statistical filtering of ranging measurements, we improve the location estimates compared with classical least squares scaling. For received signal strength based range measurements, extensive simulation results confirm that this localization scheme outperforms classical least squares scaling and is resilient against large ranging errors and sparse range measurements, which are common in wireless sensor network deployments. Gained a theorem about existent periodic solutions of the non-autonomous lagrange systems with minimal action principle.
Multi-Temporal Time-Dependent Terrain Visualization through Localized Spatial Correspondence Parameterization

Visualizing quantitative time-dependent changes in the topography requires relying on a series of discrete given multi-temporal topographic datasets that were acquired on a given time-line. The reality of physical phenomenon occurring during the acquisition times is complex when trying to mutually model the datasets; thus, different levels of spatial inter-relations and geometric inconsistencies among the datasets exist. Any straight forward simulation will result in a truncated, ill-correct and un-smooth visualization. A desired quantitative and qualitative modelling is presumed to describe morphologic changes that occurred, so it can be utilized to carry out more precise and true-to-nature visualization tasks, while trying to best describe the reality transition as it occurred. This research paper suggests adopting a fully automatic hierarchical modelling mechanism, hence implementing several levels of spatial correspondence between the topographic datasets. This quantification is then utilized for the datasets morphing and blending tasks required for intermediate scene visualization. The establishment of a digital model that stores the local spatial transformation parameterization correspondences between the topographic datasets is realized. Along with designated interpolation concepts, this complete process ensures that the visualized transition from one topographic dataset to the other via the quantified correspondences is smooth and continuous, while maintaining morphological and topological relations.
A Modem Link Strategy for Optimization of LEO Satellite Throughput

This paper presents a means for optimizing the data throughput for low earth orbit (LEO) satellites by implementing a mission specific error control strategy. Due to limited connectivity and very limited overflight time exposure offered by LEO satellites, it is imperative to volumetrically optimize the data throughput. With power limitations on the space segment and remote groundstations, hardware utilization efficiency need to be optimized to reduce power consumption. Most protocols focus on correcting congestion related link errors, but with beam shaping introduced for satellite communication, error control strategies optimized for correcting link related bit errors need to be investigated and implemented. Low density parity check (LDPC) codes have been shown to achieve error performance near the Shannon limit, and with its sparse matrix property, decoding complexity is very low. Using a special class of LDPC codes, called quasi-cyclic (QC) LDPC codes the encoding complexity is also dramatically reduced. With iterative decoding, LDPC codes show large coding gains with low processing power requirements. With its advantages in parallel processing an field-programmable gate array (FPGA) will be used to implement the error control coding (ECC).
Framework of integrated Semantic Web Services and Ontology Development for Telecommunication Industry

The concept of web services is loosely coupled, location transparent, and protocol-independent software system for distributed platform. Literature review indicates that existing web services content is composed for humans to read whereas Semantic Web Services (SWS) have emerged as a new paradigm for meaningful data retrieval in a distributed environment. SWS have automated the information processing by interpreting human and machines content comprehensively. Telecommunications industry with its increasing demand of services and adapting nature of frequent changes forces service providers to support automated service discovery for cutting cost and response time. The objective of this paper is not only to overcome the existing limitation of automated discovery for heterogeneous and homogenous services in one model for industrial application as discussed in this paper but also to provide a way for an integrated enhancement of semantic web services. The proposed framework is an integrated approach for enhancement for goal based services discovery for telecommunication industry. We have developed domain and billing application ontologies and a prototype to validate the proposed framework by integrating Web Service Execution Environment (WSMX) and Internet Reasoning Service (IRS-III).
Acute hypertension provokes acute trafficking of distal tubule Na-Cl cotransporter (NCC) to subapical cytoplasmic vesicles.

When blood pressure (BP) is elevated above baseline, a pressure natriuresis-diuresis response ensues, critical to volume and BP homeostasis. Distal convoluted tubule Na(+)-Cl(-) cotransporter (NCC) is regulated by trafficking between the apical plasma membrane (APM) and subapical cytoplasmic vesicles (SCV). We aimed to determine whether NCC trafficking contributes to pressure diuresis by decreasing APM NCC or compensates for increased volume flow to the DCT by increasing APM NCC. BP was raised 50 mmHg (high BP) in rats by arterial constriction for 5 or 20-30 min, provoking a 10-fold diuresis at both times. Kidneys were excised, and NCC subcellular distribution was analyzed by 1) sorbitol density gradient fractionation and immunoblotting and 2) immunoelectron microscopy (immuno-EM). NCC distribution did not change after 5-min high BP. After 20-30 min of high BP, 20% of NCC redistributed from low-density, APM-enriched fractions to higher density, endosome-enriched fractions, and, by quantitative immuno-EM, pool size of APM NCC decreased 14% and SCV pool size increased. Because of the time lag of the response, we tested the hypothesis that internalization of NCC was secondary to the decrease in ANG II that accompanies high BP. Clamping ANG II at a nonpressor level by coinfusion of captopril (12 microg/min) and ANG II (20 ng.kg(-1). min(-1)) during 30-min high BP reduced diuresis to eightfold and prevented redistribution of NCC from APM- to SCV-enriched fractions. We conclude that DCT NCC may participate in pressure natriuresis-diuresis by retraction out of apical plasma membranes and that the retraction is, at least in part, driven by the fall in ANG II that accompanies acute hypertension.
Point-Based Multi-Scale Surface Representation

In this paper we present a new multi-scale surface representation based on point samples. Given an unstructured point cloud as input, our method first computes a series of point-based surface approximations at successively higher levels of smoothness, i.e., coarser scales of detail, using geometric low-pass filtering. These point clouds are then encoded relative to each other by expressing each level as a scalar displacement of its predecessor. Low-pass filtering and encoding are combined in an efficient multi-level projection operator using local weighted least squares fitting. Our representation is motivated by the need for higher level editing semantics, which allow surface modifications at different scales. The user is enabled to edit the surface at different approximation levels to perform coarse-scale edits on the whole model as well as very localized modifications on the surface detail. Additionally, the multi-scale representation provides a separation in geometric scale, which can be understood as a spectral decomposition of the surface geometry. Based on this observation, advanced geometric filtering methods can be implemented, that mimic the effects of Fourier filters to achieve effects such as smoothing, enhancement or band-bass filtering.
Average Bit Erasure Probability of Regular LDPC Code Ensembles under MAP Decoding over BEC

The average bit erasure probability of a binary linear code ensemble under maximum a-posteriori probability (MAP) decoding over binary erasure channel (BEC) can be calculated with the average support weight distribution of the ensemble via the EXIT function and the shortened information function. In this paper, we formulate the relationship between the average bit erasure probability under MAP decoding over BEC and the average support weight distribution for a binary linear code ensemble. Then, we formulate the average support weight distribution and the average bit erasure probability under MAP decoding over BEC for regular LDPC code ensembles.
Multiclass Support Vector Machines With Example-Dependent Costs Applied to Plankton Biomass Estimation

In many applications, the mistakes made by an automatic classifier are not equal, they have different costs. These problems may be solved using a cost-sensitive learning approach. The main idea is not to minimize the number of errors, but the total cost produced by such mistakes. This brief presents a new multiclass cost-sensitive algorithm, in which each example has attached its corresponding misclassification cost. Our proposal is theoretically well-founded and is designed to optimize cost-sensitive loss functions. This research was motivated by a real-world problem, the biomass estimation of several plankton taxonomic groups. In this particular application, our method improves the performance of traditional multiclass classification approaches that optimize the accuracy.
Weight-based contrast administration in the computerized tomography evaluation of acute pulmonary embolism

Abstract Compare individualized contrast protocol, or weight-based protocol, to standard methodology in evaluating acute pulmonary embolism. Retrospective chart review was performed on patients undergoing computed tomography angiography with standard contrast protocol (n = 50) or individualized protocol (n = 50). Computerized tomography images were assessed for vascular enhancement and image quality. Demographics were comparable, however, more patients in the individualized group were admitted to intensive care unit (48% vs 16%, P = 0.004). Vascular enhancement and image quality were also comparable, although individualized protocol had significantly fewer contrast and motion artifact limitations (28% vs 48%, P = 0.039). Fifteen percent decrease in intravenous contrast volume was identified in individualized group with no compromise in image quality. Individualized contrast protocol provided comparable vascular enhancement and image quality to the standard, yet with fewer limitations and lower intravenous contrast volume. Catheter-gauge flow rate restrictions resulting in inconsistent technologist exam execution were identified, supporting the need for further investigation of this regimen.