Miracle-dz/UniFAR-FTUs huggingface dataset:
Brain size, innovative propensity and migratory behaviour in temperate Palaearctic birds

The evolution of migration in birds remains an outstanding, unresolved question in evolutionary ecology. A particularly intriguing question is why individuals in some species have been selected to migrate, whereas in other species they have been selected to be sedentary. In this paper, we suggest that this diverging selection might partially result from differences among species in the behavioural flexibility of their responses to seasonal changes in the environment. This hypothesis is supported in a comparative analysis of Palaearctic passerines. First, resident species tend to rely more on innovative feeding behaviours in winter, when food is harder to find, than in other seasons. Second, species with larger brains, relative to their body size, and a higher propensity for innovative behaviours tend to be resident, while less flexible species tend to be migratory. Residence also appears to be less likely in species that occur in more northerly regions, exploit temporally available food sources, inhabit non-buffered habitats and have smaller bodies. Yet, the role of behavioural flexibility as a response to seasonal environments is largely independent of these other factors. Therefore, species with greater foraging flexibility seem to be able to cope with seasonal environments better, while less flexible species are forced to become migratory.
Novel chemotherapeutics and other therapies for treating high-grade glioma

Introduction: Despite extensive research, high-grade glioma (HGG) remains a dire diagnosis with no change in the standard of care in almost a decade. However, recent advancements uncovering molecular biomarkers of brain tumors and tumor-specific antigens targeted by immunotherapies provide opportunities for novel personalized treatment regimens to improve survival. Areas covered: In this review, the authors provide a comprehensive overview of recent therapeutic advancements in HGG. Furthermore, they describe new molecular biomarkers and molecular classifications, in addition to updated research on bevacizumab, targeted molecular therapies, immunotherapy and alternative delivery methods that overcome the blood–brain barrier to reach the target tumor tissue. Challenges regarding each therapy are also outlined. The authors also provide some insight into a novel non-chemotherapeutic treatment for malignant glioma, NovoTTFA, as well as a summary of current treatment options for recurrence. Expert opinion: Current research for treating malignant gliomas are paving the path to personalized therapy, including immunotherapy, that involve integrated genomic and histolopathologic data, as well as a multi-modal treatment regimen. Immunotherapy will potentially be the next addition to the current standard of care, specialized to the antigens presented on the tumors. The results of the current trials of multi-antigen vaccines are eagerly anticipated.
Mobile visual clothing search

We present a mobile visual clothing search system whereby a smart phone user can either choose a social networking photo or take a new photo of a person wearing clothing of interest and search for similar clothing in a retail database. From the query image, the person is detected, clothing is segmented, and clothing features are extracted and quantized. The information is sent from the phone client to a server, where the feature vector of the query image is used to retrieve similar clothing products from online databases. The phone's GPS location is used to re-rank results by retail store location. State of the art work focusses primarily on the recognition of a diverse range of clothing offline and pays little attention to practical applications. Evaluated on a challenging dataset, the system is relatively fast and achieves promising results.
TIGRFAMs and Genome Properties: tools for the assignment of molecular function and biological process in prokaryotic genomes

TIGRFAMs is a collection of protein family definitions built to aid in high-throughput annotation of specific protein functions. Each family is based on a hidden Markov model (HMM), where both cutoff scores and membership in the seed alignment are chosen so that the HMMs can classify numerous proteins according to their specific molecular functions. Most TIGRFAMs models describe ‘equivalog’ families, where both orthology and lateral gene transfer may be part of the evolutionary history, but where a single molecular function has been conserved. The Genome Properties system contains a queriable set of metabolic reconstructions, genome metrics and extractions of information from the scientific literature. Its genome-by-genome assertions of whether or not specific structures, pathways or systems are present provide high-level conceptual descriptions of genomic content. These assertions enable comparative genomics, provide a meaningful biological context to aid in manual annotation, support assignments of Gene Ontology (GO) biological process terms and help validate HMM-based predictions of protein function. The Genome Properties system is particularly useful as a generator of phylogenetic profiles, through which new protein family functions may be discovered. The TIGRFAMs and Genome Properties systems can be accessed at and .
Scanning Electrochemical Microscopy: Preparation of Submicrometer Electrodes

In this report, we describe two procedures for the construction of submicrometer microelectrodes particularly suited for use in SECM. In one, an electrochemically sharpened Pt wire is sealed in a glass capillary and the submicrometer tip is exposed via mechanical polishing, and in the other, electron beam lithography using a commercial scanning electron microscope is used to produce submicrometer features at the tip of a polymer-coated polyshed Pt wire
Changes in Brain Size during the Menstrual Cycle

Background There is increasing evidence for hormone-dependent modification of function and behavior during the menstrual cycle, but little is known about associated short-term structural alterations of the brain. Preliminary studies suggest that a hormone-dependent decline in brain volume occurs in postmenopausal, or women receiving antiestrogens, long term. Advances in serial MR-volumetry have allowed for the accurate detection of small volume changes of the brain. Recently, activity-induced short-term structural plasticity of the brain was demonstrated, challenging the view that the brain is as rigid as formerly believed. Methodology/Principal Findings We used MR-volumetry to investigate short-term brain volume changes across the menstrual cycle in women or a parallel 4 week period in men, respectively. We found a significant grey matter volume peak and CSF loss at the time of ovulation in females. This volume peak did not correlate with estradiol or progesterone hormone levels. Men did not show any significant brain volume alterations. Conclusions/Significance These data give evidence of short-term hormone-dependent structural brain changes during the menstrual cycle, which need to be correlated with functional states and have to be considered in structure-associated functional brain research.
Properties of Hamster Embryo Fibroblasts Transformed In Vitro After Exposure to Ultraviolet-Irradiated Herpes Simplex Virus Type 2

An in vitro method which led to the transformation of hamster embryo fibroblasts after exposure to herpes simplex virus type 2 (HSV-2) inactivated with ultraviolet irradiation is described. The transformed cells (333-8-9) produced tumors when inoculated into newborn Syrian hamsters but not when injected into weanling Syrian hamsters of the same LSH inbred strain. However, after one in vivo passage, the 333-8-9 cells became highly oncogenic in weanling hamsters. No infectious virus was recovered from these cells. Herpes simplex virus antigens were detected in the transformed cells by the indirect immunofluorescence technique. Sera from tumor-bearing hamsters contained antibody with highly specific neutralizing activity against HSV-2. These studies indicate the continued involvement of the HSV-2 genome in an oncogenic cell line.
Real-time human posture estimation using monocular thermal images

This paper introduces a new real-time method to estimate the posture of a human from thermal images acquired by an infrared camera regardless of the background and lighting conditions. Distance transformation is performed for the human body area extracted from the thresholded thermal image for the calculation of the center of gravity. After the orientation of the upper half of the body is obtained by calculating the moment of inertia, significant points such as the top of the head, the tips of the hands and foot are heuristically located. In addition, the elbow and knee positions are estimated from the detected (significant) points using a genetic algorithm based learning procedure. The experimental results demonstrate the robustness of the proposed algorithm and real-time (faster than 20 frames per second) performance.
Talairach‐Based Parcellation of Neonatal Brain Magnetic Resonance Imaging Data: Validation of a New Approach

Background and Purpose. Talairach‐based parcellation (TP) of human brain magnetic resonance imaging (MRI) data has been used increasingly in clinical research to make regional measurements of brain structures in vivo. Recently, TP has been applied to pediatric research to elucidate the changes in regional brain volumes related to several neurological disorders. However, all freely available tools have been designed to parcellate adult brain MRI data. Parcellation of neonatal MRI data is very challenging owing to the lack of strong signal contrast, variability in signal intensity within tissues, and the small size and thus difficulty in identifying small structures used as landmarks for TP. Hence the authors designed and validated a new interactive tool to parcellate brain MRI data from newborns and young infants. Methods. The authors' tool was developed as part of a postprocessing pipeline, which includes registration of multichannel MR images, segmentation, and parcellation of the segmented data. The tool employs user‐friendly interactive software to visualize and assign the anatomic landmarks required for parcellation, after which the planes and parcels are generated automatically by the algorithm. The authors then performed 3 sets of validation experiments to test the precision and reliability of their tool. Results. Validation experiments of intra‐and interrater reliability on data obtained from newborn and 1‐year‐old children showed a very high sensitivity of >95% and specificity >99.9%. The authors also showed that rotating and reformatting the original MRI data results in a statistically significant difference in parcel volumes, demonstrating the importance of using a tool such as theirs that does not require realignment of the data prior to parcellation. Conclusions. To the authors' knowledge, the presented approach is the first TP method that has been developed and validated specifically for neonatal brain MRI data. Their approach would also be valuable for the analysis of brain MRI data from older children and adults.
Human Alveolar Epithelial Cells Attenuate Pulmonary Microvascular Endothelial Cell Permeability under Septic Conditions

Acute lung injury (ALI) and its most severe form, acute respiratory distress syndrome (ARDS), are characterised by high-protein pulmonary edema and severe hypoxaemic respiratory failure due to increased permeability of pulmonary microvascular endothelial cells (PMVEC). Alveolar epithelial cells (AEC) contribute importantly to normal alveolar function, and AEC dysfunction in ALI/ARDS is associated with worse outcomes. We hypothesized that AEC can modulate human PMVEC barrier function, and investigated the effects of AEC presence on human PMVEC barrier under septic conditions in vitro. PMVEC isolated from human lung were treated in vitro with septic stimulation (lipopolysaccharide [LPS], a mixture of clinically-relevant cytokines [cytomix], or plasma from patients with severe sepsis), and the trans-PMVEC leak of Evans Blue dye-labeled albumin assessed. PMVEC septic responses were compared in the presence/absence of co-cultured A549 epithelial cell line or primary human AEC. Septic stimulation with LPS, cytomix, or septic plasma induced marked PMVEC hyper-permeability (10.2±1.8, 8.9±2.2, and 3.7±0.2 fold-increase vs. control, respectively, p<0.01 for all). The presence of A549 cells or primary human AEC in a non-contact co-culture model attenuated septic PMVEC hyper-permeability by 39±4% to 100±3%, depending on the septic stimulation (p<0.05). Septic PMVEC hyper-permeability was also attenuated following treatment with culture medium conditioned by previous incubation with either naïve or cytomix-treated A549 cells (p<0.05), and this protective effect of A549 cell-conditioned medium was both heat-stable and transferable following lipid extraction. Cytomix-stimulated PMN-dependent PMVEC hyper-permeability and trans-PMVEC PMN migration were also inhibited in the presence of A549 cells or A549 cell-conditioned medium (p<0.05). Human AEC appear to protect human PMVEC barrier function under septic conditions in vitro, through release of a soluble mediator(s), which are at least partly lipid in nature. This study suggests a scientific and potential clinical therapeutic importance of epithelial-endothelial cross talk in maintaining alveolar integrity in ALI/ARDS.
Towards fault tolerant perception for autonomous vehicles: Local fusion

Many robust sensor fusion strategies have been developed in order to reliably detect the surrounding environments of an autonomous vehicle. However, in real situations there is always the possibility that sensors or other components may fail. Thus, internal modules and sensors need to be monitored to ensure their proper function. This paper introduces a general view of a perception architecture designed to detect and classify obstacles in an autonomous vehicle's environment using a fault tolerant framework, whereas elaborates the object detection and local fusion modules proposed in order to achieve the modularity and real-time process required by the system.
Dicer Functions in Aquatic Species

Dicer is an RNase III enzyme with two catalytic subunits, which catalyzes the cleavage of double-stranded RNA to small interfering RNAs and micro-RNAs, which are mainly involved in invasive nucleic acid defense and endogenous genes regulation. Dicer is abundantly expressed in embryos, indicating the importance of the protein in early embryonic development. In addition, Dicer is thought to be involved in defense mechanism against foreign nucleic acids such as viruses. This paper will mainly focus on the recent progress of Dicer-related research and discuss potential RNA interference pathways in aquatic species.
A Semisupervised Approach to the Detection and Characterization of Outliers in Categorical Data

In this paper, we introduce a new approach of semisupervised anomaly detection that deals with categorical data. Given a training set of instances (all belonging to the normal class), we analyze the relationship among features for the extraction of a discriminative characterization of the anomalous instances. Our key idea is to build a model that characterizes the features of the normal instances and then use a set of distance-based techniques for the discrimination between the normal and the anomalous instances. We compare our approach with the state-of-the-art methods for semisupervised anomaly detection. We empirically show that a specifically designed technique for the management of the categorical data outperforms the general-purpose approaches. We also show that, in contrast with other approaches that are opaque because their decision cannot be easily understood, our proposed approach produces a discriminative model that can be easily interpreted and used for the exploration of the data.
News Retrieval Based On Latent Semantic Index And Clustering

Web is a collection of heterogeneous as well as unstructured set of news articles. This paper presents a novel approach to retrieve relevant news articles from heterogeneous and unstructured collection of articles. Efficient retrieval requires analysis of news articles based on keyword. Two problems that occur in the analysis of news articles are synonymy and polysemy. In this paper, we present a News Retrieval approach based on Latent Semantic Index (LSI) and Clustering. It includes projection of keyword-news article matrix into small spaces called clusters. After that, clustering approach is used to group relevant articles into clusters.
Effect of Mycobacterium bovis BCG Vaccination on Interleukin-1β and RANTES mRNA Expression in Guinea Pig Cells Exposed to Attenuated and Virulent Mycobacteria

ABSTRACT The effect of Mycobacterium bovis BCG vaccination on interleukin-1β (IL-1β) or regulated-upon-activation, normally T-cell-expressed and -secreted chemokine (RANTES) mRNA expression in guinea pig spleen cells stimulated with concanavalin A, lipopolysaccharide (LPS), phorbol myristate acetate (PMA) plus ionomycin, or purified protein derivative (PPD) was studied in vitro. Similarly, peritoneal exudate cell-derived macrophages from naïve and BCG-vaccinated guinea pigs were infected with M. bovis BCG, Mycobacterium avium, the attenuated Mycobacterium tuberculosis H37Ra strain, or virulent strains H37Rv and Erdman of M. tuberculosis. Total RNA was subjected to Northern blot analysis using probes generated from guinea pig IL-1β or RANTES cDNA. Although IL-1β and RANTES mRNA could be detected in the spleen cells from naïve animals stimulated with LPS or PMA plus ionomycin, the levels were significantly enhanced after BCG vaccination. mRNA expression was also elevated in macrophages infected with live mycobacteria after BCG vaccination. However, macrophages infected with the virulent H37Rv strain of M. tuberculosis showed 75 to 90% reductions in IL-1β expression and 25 to 60% reductions in RANTES mRNA expression compared with macrophages infected with the attenuated H37Ra strain. The IL-1β mRNA levels peaked as soon as 1 h after PPD stimulation and 4 h after M. tuberculosis H37Rv infection of macrophages. In contrast, RANTES mRNA expression was delayed until 48 h after infection. These results indicate that molecular mediators produced in response to various stimuli associated with protective immunity against mycobacteria are upregulated after BCG vaccination; however, a significantly weaker response was observed with virulent M. tuberculosis. These initial studies indicate that BCG vaccination has a positive effect on IL-1β and RANTES mRNA expression by host cells in a highly relevant animal tuberculosis model.
Bibliographical Research Method for Business Administration Studies: a Model Based on Scientific Journal Ranking

This article proposes a three-stage method, with the use of multiple rankings as a starting point in the first stage to help carry out bibliographical research in a more effective and systematic fashion. The relevance of this method is made evident by way of a pioneer empirical investigation on the use and importance of scientific journal rankings as perceived by Brazilian professors in the practice of bibliographical research in the field of Business Administration. The results suggest that, although there is an awareness of the importance of ranking as a criterion for bibliographical research, with a view to identifying the state of the art and relevant research gaps, ranking is in fact hardly used on a regular basis. It is believed that the proposed method can help overcome this problem and contribute to more effective literature reviews and research.
Ice Nucleation Measurement and Parameterizations and the Broad Impact of Associated Ocean and Atmospheric Interactions Within the Global Climate

Current climate models attempt to represent the frequency and characteristics of mixedphase and ice clouds in the atmosphere. Ice crystals have the ability to scatter incoming solar radiation, which may have a net cooling effect on the Earth’s energy budget. Ice forms in the atmospheric by either homogenous freezing at temperatures colder than -36°C, or by heterogeneous freezing, which requires an ice nucleating particle (INP) to initiate freezing at temperatures warmer than -36°C. The stochastic nature of ice formation requires more rigorous development and testing of model parameterizations that aim to predict ice formation. In this study, we have measured the immersion freezing temperatures of sea surface microlayer (SML) samples collected in the North Atlantic Ocean and used our results to examine the accuracy of a global ice nucleation parameterization to predict marine INP concentrations. SML samples from the fourth NASA North Atlantic Aerosol and Marine Ecosystem Study (NAAMES4) field campaign were evaluated for freezing temperature on a custom built ice microscope. Primary marine aerosols generated by the SML have been found to freeze from -28.041°C to -21.341°C showing they are moderately effective INP. DeMott et al. 2010 developed a global parameterization to predict the concentration of INP that is dependent on both the temperature and size of aerosol particles. To apply the parameterization, Scanning Electrical Mobility Sizer (SEMS) size distribution measurements collected concurrently with the SML samples during NAAMES4 were used to select aerosol particles larger than 0.5 μm to input into the parameterization. Results of the comparison between observed and predicted number concentration of INP show that the parameterization does not represent the high degree of variability present in the observed concentrations of the marine INP in this study. Further refinement of this global parameterization may improve its ability to accurately predict number concentrations of INP produced in a marine environment. A detailed overview of the measurements and parametrizations for INP concentrations will be provided. In addition, an examination of the climate implications of this ocean-atmospheric interaction will also be
Effects of partially thiolated polycytidylic acid on the clonogenicity of murine leukemic stem cells.

The effect of partially thiolated polycytidylic acid (MPC) on the colony-forming ability of the progenitor cells (CFUC) of RF/Un leukemic mice was investigated using the plasma clot method in order to study the mode of action of the modified polynucleotide. The results showed that MPC inhibited the CFUC in a dose-dependent and time-dependent manner. Once a maximum level of inhibition of CFUC (approximately 40%) was observed, no further inhibition occurred whether the concentration of MPC was increased or whether the duration of incubation was lengthened. High-specific-activity [3H]thymidine, an S-phase-specific agent, showed a similar inhibition profile on the CFUC as did MPC. When MPC and high-specific-activity [3H]thymidine were incubated together with the bone marrow cells, there was no additive or synergistic inhibitory effect on the CFUC. Thus, it appears that MPC is an S-phase-specific agent. When injected i.v. into the mice, MPC decreased the number of CFUC of both the bone marrow and the spleen significantly.
Creating Large-scale Training and Test Corpora for Extracting Structured Data from the Web

For making the web of linked data grow, information extraction methods are a good alternative for manual dataset curation, since there is an abundance of semi-structured and unstructured information which can be harvested that way. At the same time, existing structured data sets can be used for training and evaluating such information extraction systems. In this paper, we introduce a method for creating training and test corpora from websites annotated with structured data. Using different classes in schema.org and websites annotated with Microdata, we show how training and test data can be curated at large scale and across various domains. Furthermore, we discuss how negative examples can be generated as well as open challenges and future directs for this kind of training data curation.