Miracle-dz/UniFAR-FTUs huggingface dataset:
Towards a comprehensive atlas of cortical connections in a primate brain: Mapping tracer injection studies of the common marmoset into a reference digital template

The marmoset is an emerging animal model for large‐scale attempts to understand primate brain connectivity, but achieving this aim requires the development and validation of procedures for normalization and integration of results from many neuroanatomical experiments. Here we describe a computational pipeline for coregistration of retrograde tracing data on connections of cortical areas into a 3D marmoset brain template, generated from Nissl‐stained sections. The procedure results in a series of spatial transformations that are applied to the coordinates of labeled neurons in the different cases, bringing them into common stereotaxic space. We applied this procedure to 17 injections, placed in the frontal lobe of nine marmosets as part of earlier studies. Visualizations of cortical patterns of connections revealed by these injections are supplied as Supplementary Materials. Comparison between the results of the automated and human‐based processing of these cases reveals that the centers of injection sites can be reconstructed, on average, to within 0.6 mm of coordinates estimated by an experienced neuroanatomist. Moreover, cell counts obtained in different areas by the automated approach are highly correlated (r = 0.83) with those obtained by an expert, who examined in detail histological sections for each individual. The present procedure enables comparison and visualization of large datasets, which in turn opens the way for integration and analysis of results from many animals. Its versatility, including applicability to archival materials, may reduce the number of additional experiments required to produce the first detailed cortical connectome of a primate brain. J. Comp. Neurol. 524:2161–2181, 2016. © 2016 The Authors The Journal of Comparative Neurology Published by Wiley Periodicals, Inc.
Structured Factored Inference: A Framework for Automated Reasoning in Probabilistic Programming Languages

Reasoning on large and complex real-world models is a computationally difficult task, yet one that is required for effective use of many AI applications. A plethora of inference algorithms have been developed that work well on specific models or only on parts of general models. Consequently, a system that can intelligently apply these inference algorithms to different parts of a model for fast reasoning is highly desirable. We introduce a new framework called structured factored inference (SFI) that provides the foundation for such a system. Using models encoded in a probabilistic programming language, SFI provides a sound means to decompose a model into sub-models, apply an inference algorithm to each sub-model, and combine the resulting information to answer a query. Our results show that SFI is nearly as accurate as exact inference yet retains the benefits of approximate inference methods.
Combinaciones de retroalimentación e igualación de la muestra generalizada bajo estímulos y relaciones de igualación familiares y no familiares

Six groups of high-school students were exposed to a second-order matching-to-sample task and generalization tests trials using familiar and unfamiliar stimuli as well as a new matching relation. For two groups correct and incorrect matching responses produced the correspondently feedback according to continuous and intermittent schedules, respectively. Correct responses produced feedback and incorrect responses produced blanks and vice versa for other two groups, respectively. Two additional groups were exposed to similar feedback-blanks combinations but participants were instructed about the “meaning” of blanks before training. Extra-relational generalized matching-to-sample performance with either familiar or unfamiliar stimuli was observed after training conditions in which intermittent right-wrong feedback was scheduled, as well as when incorrect matching responses produced blanks and correct responses produced the correspondently feedback.Instructions about the meaning of blanks produced generalized performances slightly higher to those observed after continuous right-wrong feedback, which in turn were similar to performances observed after the uninstructed right-blank feedback combination condition. Results confirm an initial tendency to treat blanks as if they mean right and suggest a common“detachment” processes between intermittent feedback and the wrong-blanks feedback combination.
Word Sense Induction & Disambiguation Using Hierarchical Random Graphs

Graph-based methods have gained attention in many areas of Natural Language Processing (NLP) including Word Sense Disambiguation (WSD), text summarization, keyword extraction and others. Most of the work in these areas formulate their problem in a graph-based setting and apply unsupervised graph clustering to obtain a set of clusters. Recent studies suggest that graphs often exhibit a hierarchical structure that goes beyond simple flat clustering. This paper presents an unsupervised method for inferring the hierarchical grouping of the senses of a polysemous word. The inferred hierarchical structures are applied to the problem of word sense disambiguation, where we show that our method performs significantly better than traditional graph-based methods and agglomerative clustering yielding improvements over state-of-the-art WSD systems based on sense induction.
Myelin is dependent on the Charcot–Marie–Tooth Type 4H disease culprit protein FRABIN/FGD4 in Schwann cells

Studying the function and malfunction of genes and proteins associated with inherited forms of peripheral neuropathies has provided multiple clues to our understanding of myelinated nerves in health and disease. Here, we have generated a mouse model for the peripheral neuropathy Charcot–Marie–Tooth disease type 4H by constitutively disrupting the mouse orthologue of the suspected culprit gene FGD4 that encodes the small RhoGTPase Cdc42-guanine nucleotide exchange factor Frabin. Lack of Frabin/Fgd4 causes dysmyelination in mice in early peripheral nerve development, followed by profound myelin abnormalities and demyelination at later stages. At the age of 60 weeks, this was accompanied by electrophysiological deficits. By crossing mice carrying alleles of Frabin/Fgd4 flanked by loxP sequences with animals expressing Cre recombinase in a cell type-specific manner, we show that Schwann cell-autonomous Frabin/Fgd4 function is essential for proper myelination without detectable primary contributions from neurons. Deletion of Frabin/Fgd4 in Schwann cells of fully myelinated nerve fibres revealed that this protein is not only required for correct nerve development but also for accurate myelin maintenance. Moreover, we established that correct activation of Cdc42 is dependent on Frabin/Fgd4 function in healthy peripheral nerves. Genetic disruption of Cdc42 in Schwann cells of adult myelinated nerves resulted in myelin alterations similar to those observed in Frabin/Fgd4-deficient mice, indicating that Cdc42 and the Frabin/Fgd4–Cdc42 axis are critical for myelin homeostasis. In line with known regulatory roles of Cdc42, we found that Frabin/Fgd4 regulates Schwann cell endocytosis, a process that is increasingly recognized as a relevant mechanism in peripheral nerve pathophysiology. Taken together, our results indicate that regulation of Cdc42 by Frabin/Fgd4 in Schwann cells is critical for the structure and function of the peripheral nervous system. In particular, this regulatory link is continuously required in adult fully myelinated nerve fibres. Thus, mechanisms regulated by Frabin/Fgd4–Cdc42 are promising targets that can help to identify additional regulators of myelin development and homeostasis, which may crucially contribute also to malfunctions in different types of peripheral neuropathies.
Cell cultivation under different gravitational loads using a novel random positioning incubator

Important in biotechnology is the establishment of cell culture methods that reflect the in vivo situation accurately. One approach for reaching this goal is through 3D cell cultivation that mimics tissue or organ structures and functions. We present here a newly designed and constructed random positioning incubator (RPI) that enables 3D cell culture in simulated microgravity (0 g). In addition to growing cells in a weightlessness‐like environment, our RPI enables long‐duration cell cultivation under various gravitational loads, ranging from close to 0 g to almost 1 g. This allows the study of the mechanotransductional process of cells involved in the conversion of physical forces to an appropriate biochemical response. Gravity is a type of physical force with profound developmental implications in cellular systems as it modulates the resulting signaling cascades as a consequence of mechanical loading. The experiments presented here were conducted on mouse skeletal myoblasts and human lymphocytes, two types of cells that have been shown in the past to be particularly sensitive to changes in gravity. Our novel RPI will expand the horizon at which mechanobiological experiments are conducted. The scientific data gathered may not only improve the sustainment of human life in space, but also lead to the design of alternative countermeasures against diseases related to impaired mechanosensation and downstream signaling processes on earth. Biotechnol. Bioeng. 2014;111: 1180–1190. © 2013 The Authors. Biotechnology and Bioengineering Published by Wiley Periodicals, Inc.
Evolution- and Structure-Based Computational Strategy Reveals the Impact of Deleterious Missense Mutations on MODY 2 (Maturity-Onset Diabetes of the Young, Type 2)

Heterozygous mutations in the central glycolytic enzyme glucokinase (GCK) can result in an autosomal dominant inherited disease, namely maturity-onset diabetes of the young, type 2 (MODY 2). MODY 2 is characterised by early onset: it usually appears before 25 years of age and presents as a mild form of hyperglycaemia. In recent years, the number of known GCK mutations has markedly increased. As a result, interpreting which mutations cause a disease or confer susceptibility to a disease and characterising these deleterious mutations can be a difficult task in large-scale analyses and may be impossible when using a structural perspective. The laborious and time-consuming nature of the experimental analysis led us to attempt to develop a cost-effective computational pipeline for diabetic research that is based on the fundamentals of protein biophysics and that facilitates our understanding of the relationship between phenotypic effects and evolutionary processes. In this study, we investigate missense mutations in the GCK gene by using a wide array of evolution- and structure-based computational methods, such as SIFT, PolyPhen2, PhD-SNP, SNAP, SNPs&GO, fathmm, and Align GVGD. Based on the computational prediction scores obtained using these methods, three mutations, namely E70K, A188T, and W257R, were identified as highly deleterious on the basis of their effects on protein structure and function. Using the evolutionary conservation predictors Consurf and Scorecons, we further demonstrated that most of the predicted deleterious mutations, including E70K, A188T, and W257R, occur in highly conserved regions of GCK. The effects of the mutations on protein stability were computed using PoPMusic 2.1, I-mutant 3.0, and Dmutant. We also conducted molecular dynamics (MD) simulation analysis through in silico modelling to investigate the conformational differences between the native and the mutant proteins and found that the identified deleterious mutations alter the stability, flexibility, and solvent-accessible surface area of the protein. Furthermore, the functional role of each SNP in GCK was identified and characterised using SNPeffect 4.0, F-SNP, and FASTSNP. We hope that the observed results aid in the identification of disease-associated mutations that affect protein structure and function. Our in silico findings provide a new perspective on the role of GCK mutations in MODY2 from an evolution-based structure-centric point of view. The computational architecture described in this paper can be used to predict the most appropriate disease phenotypes for large-genome sequencing projects and to provide individualised drug therapy for complex diseases such as diabetes.
Brain Activity Evoked by the Perception of Human Walking: Controlling for Meaningful Coherent Motion

Many functional neuroimaging studies of biological motion have used as stimuli point-light displays of walking figures and compared the resulting activations with those evoked by the same display elements moving in a random or noncoherent manner. Although these studies have established that biological motion activates the superior temporal sulcus (STS), the use of random motion controls has left open the possibility that coordinated and meaningful nonbiological motion might activate these same brain regions and thus call into question their specificity for processing biological motion. Here we used functional magnetic resonance imaging and an anatomical region-of-interest approach to test a hierarchy of three questions regarding activity within the STS. First, by comparing responses in the STS with animations of human and robot walking figures, we determined (1) that the STS is sensitive to biological motion itself, not merely to the superficial characteristics of the stimulus. Then we determined that the STS responds more strongly to biological motion (as conveyed by the walking robot) than to (2) a nonmeaningful but complex nonbiological motion (a disjointed mechanical figure) and (3) a complex and meaningful nonbiological motion (the movements of a grandfather clock). In subsequent whole-brain voxel-based analyses, we confirmed robust STS activity that was strongly right lateralized. In addition, we observed significant deactivations in the STS that differentiated biological and nonbiological motion. These voxel-based analyses also revealed regions of motion-related positive activity in other brain regions, including MT or V5, fusiform gyri, right premotor cortex, and the intraparietal sulci.
Measuring Student Debt and Its Performance

Studies continue to indicate that higher education is frequently a worthwhile investment for individuals and that it raises the productivity of the workforce as a whole. While the rising cost of post-secondary education has not eliminated this "college premium," it has raised new questions about how growing numbers of students can make these investments. One solution to this problem is student loans, which have come to play an increasingly important role in financing higher education. Yet, despite its importance, educational debt is not well understood. Among the reasons is that there exist few central repositories of information on the characteristics and performance of all student loans, which currently include loans made by both government and private lenders. In this paper, we bring a new data set to bear on this important issue and present a brief analysis of the historical and current levels of student debt and how those loans are performing. We also briefly discuss the implications of student loans for borrowers and the economy.
Serum Cytokine Responses over the Entire Clinical-Immunological Spectrum of Human Leishmania (L.) infantum chagasi Infection

The clinical-immunological spectrum of human Leishmania (L.) infantum chagasi infection in Amazonian Brazil was recently reviewed based on clinical, DTH, and IFAT (IgG) evaluations that identified five profiles: three asymptomatic (asymptomatic infection, AI; subclinical resistant infection, SRI; and indeterminate initial infection, III) and two symptomatic (symptomatic infection, SI; American visceral leishmaniasis, AVL; and subclinical oligosymptomatic infection, SOI). TNF-α, IL-4, IL-6, and IL-10 serum cytokines were analyzed using multiplexed Cytometric Bead Array in 161 samples from endemic areas in the Brazilian Amazon: SI [AVL] (21 cases), III (49), SRI (19), SOI (12), AI (36), and a control group [CG] (24). The highest IL-6 serum levels were observed in the SI profile (AVL); higher IL-10 serum levels were observed in SI than in SOI or CG and in AI and III than in SOI; higher TNF-α serum levels were seen in SI than in CG. Positive correlations were found between IL-6 and IL-10 serum levels in the SI and III profiles and between IL-6 and TNF-α and between IL-4 and TNF-α in the III profile. These results provide strong evidence for associating IL-6 and IL-10 with the immunopathogenesis of AVL and help clarify the role of these cytokines in the infection spectrum.
AR-42 induces apoptosis in human hepatocellular carcinoma cells via HDAC5 inhibition

Histone deacetylases (HDACs) play critical roles in apoptosis and contribute to the proliferation of cancer cells. AR-42 is a novel Class I and II HDAC inhibitor that shows cytotoxicity against various human cancer cell lines. The present study aims to identify the target of AR-42 in hepatocellular carcinoma (HCC) as well as evaluate its therapeutic efficacy. We found that HDAC5 was upregulated in HCC tissues compared to adjacent normal tissues, and this was correlated with reduced patient survival. CCK8 and colony-formation assays showed that HDAC5 overexpression promotes proliferation in HCC cell lines. Treatment with AR-42 decreased HCC cell growth and increased caspase-dependent apoptosis, and this was rescued by HDAC5 overexpression. We demonstrated that AR-42 can inhibit the deacetylation activity of HDAC5 and its downstream targets in vitro and in vivo. Taken together, these results demonstrate for the first time that AR-42 targets HDAC5 and induces apoptosis in human hepatocellular carcinoma cells. AR-42 therefore shows potential as a new drug candidate for HCC therapy.
Cost effective management frameworks for intrusion detection systems

This paper discusses the financial benefit of intrusion detection systems (IDS) deployment techniques and addresses the problems of bridging the gap between technical security solutions and the business need for it. This is an area of interest to both the research and the business community; most IDSes balance host and network monitoring, but the decision about how to adjust usage of each technique tends to be made in a rather ad-hoc way, or based upon effectiveness of detection only without regard to cost of technique. In practice, selections based on how well a strategy helps a company to perform are preferable and methodologies supporting a selection process of this type will assist an Information Technology officer to explain security mechanism selections more effectively to CEOs. In this context, the approach we propose could be applied when choosing one intrusion detection system over another based on which has a better or higher return on investment for the company.Through a case study, we illustrate the benefits of a better IDS management that leads to a positive Return on Investment (ROI) for IDS deployment. We conceive strategies and approaches to support effective decision-making about which techniques are appropriate for the cost effective management of the IDS in a given environment. It is our intent that this research will serve as a foundation for the formal description of cost structures, analysis, and selection of effective implementation approaches to support the management of IDS deployments.
Magnetotactic Bacteria and Their Significance for P Systems and Nanoactuators

In the framework of the dialog between P systems and Microbiology, in this paper we focus on the magnetotactic behavior of magnetotactic bacteria, namely the orientation along the Earth’s geomagnetic field lines. Magnetic properties and magnetotactic behavior could be used to obtained microand nanoactuators for the desired distribution at nanometer level of either intact magnetotactic bacteria or isolated intact magnetosomes with significant potential application in the construction of magnetic logic gates. Furthermore, (precise) distribution of intact magnetotactic bacteria or isolated intact magnetosomes by carefully using rather strong external magnetic fields could be described by P systems as a discontinuous process, whose potential for nanoactuators and magnetic microchips is increasing in evidence.
Rhythmic categories in spoken-word recognition

Rhythmic categories such as morae in Japanese or stress units in English play a role in the perception of spoken language. We examined this role in Japanese, since recent evidence suggests that morae may intervene as structural units in word recognition. First, we found that traditional puns more often substituted part of a mora than a whole mora. Second, when listeners reconstructed distorted words, e.g. panorama from panozema, responses were faster and more accurate when only a phoneme was distorted (panozama, panorema) than when a whole CV mora was distorted (panozema). Third, lexical decisions on the same nonwords were better predicted by duration and number of phonemes from nonword uniqueness point to word end than by number of morae. Our results indicate no role for morae in early spoken-word processing; we propose that rhythmic categories constrain not initial lexical activation but subsequent processes of speech segmentation and selection among word candidates.
Exploring the Origins and Information Processing Differences Between Men and Women: Implications for Advertisers

Sanjay Putrevu is Associate Professor of Marketing, Brock University, St. Catharines, Ontario CANADA L2S 3A1, (905) 688-5550 ext. 3997, sputrevu@spartan.ac. brocku.ca. The author wishes to thank the special issue editor, James Gentry, and three anonymous reviewers for their helpful comments on earlier drafts of this article. This article is part of a special issue on "Gender Issues in Consumer Research" edited by James Gentry, Seungwoo Chun, Suraj Commuri, Eileen Fischer, Sunkyu Jun, Lee McGinnis, Kay Palan, and Michal Strahilevitz.
First X-Ray Observations of the Young Pulsar J1357–6429

The first short Chandra and XMM-Newton observations of the young and energetic pulsar J1357-6429 provided indications of a tail-like pulsar wind nebula associated with this object as well as pulsations of its X-ray flux with a pulsed fraction pf ≳ 50% and a thermal component dominating at energies E ≲ 2 keV. The putative nebula is very compact in size and might be interpreted as evidence for a pulsar jet. The thermal radiation is most plausibly emitted from the entire neutron star surface of a 10 km radius and a 1.0 ± 0.1 MK temperature, covered with a hydrogen atmosphere. At higher energies, the pulsar's emission is of a nonthermal origin, with a power-law spectrum of a photon index Γ = 1.1 ± 0.2. This makes the properties of PSR J1357-6429 very similar to those of the young pulsars J1119-6127 and Vela with detected thermal radiation.