Miracle-dz/UniFAR-FTUs huggingface dataset:
Endoreduplication Mediated by the Anaphase-Promoting Complex Activator CCS52A Is Required for Symbiotic Cell Differentiation in Medicago truncatula Nodules Article, publication date, and citation information can be found at www.plantcell.org/cgi/doi/10.1105/tpc.014373.

In Medicago nodules, endoreduplication cycles and ploidy-dependent cell enlargement occur during the differentiation of bacteroid-containing nitrogen-fixing symbiotic cells. These events are accompanied by the expression of ccs52A, a plant ortholog of the yeast and animal cdh1/srw1/fzr genes, acting as a substrate-specific activator of the anaphase-promoting complex (APC) ubiquitin ligase. Because CCS52A is involved in the transition of mitotic cycles to endoreduplication cycles, we investigated the importance of somatic endoploidy and the role of the M. truncatula ccs52A gene in symbiotic cell differentiation. Transcription analysis and ccs52A promoter–driven β-glucuronidase activity in transgenic plants showed that ccs52A was dispensable for the mitotic cycles and nodule primordium formation, whereas it was induced before nodule differentiation. The CCS52A protein was present in the nucleus of endoreduplication-competent cells, indicating that it may activate APC constitutively during the endoreduplication cycles. Downregulation of ccs52A in transgenic M. truncatula plants drastically affected nodule development, resulting in lower ploidy, reduced cell size, inefficient invasion, and the maturation of symbiotic cells, accompanied by early senescence and finally the death of both the bacterium and plant cells. Thus, ccs52A expression is essential for the formation of large highly polyploid symbiotic cells, and endoreduplication is an integral part of normal nodule development.
A Digital Synthesis Procedure Under Function Symmetries and Mapping Methods

A new mathematically based method of synthesis for combinational digital networks is presented, based upon the recognition of symmetry patterns in the functions being synthesized. The design procedure is structured such that at each stage of the synthesis a relevant gate assembly is indicated, which leaves a simplified "remainder" function to be synthesized at the next stage of the realization. This decomposition procedure optimally uses gates with a fan in of two, but post-synthesis reconfiguration for amalgamation into larger fan-in gates is available.
GRIN: A Graph Based RDF Index

RDF ("Resource Description Framework") is now a widely used World Wide Web Consortium standard. However, methods to index large volumes of RDF data are still in their infancy. In this paper, we focus on providing a very lightweight indexing mechanism for certain kinds of RDF queries, namely graph-based queries where there is a need to traverse edges in the graph determined by an RDF database. Our approach uses the idea of drawing circles around selected "center" vertices in the graph where the circle would encompass those vertices in the graph that are within a given distance of the "center" vertex. We come up with methods of finding such "center" vertices and identifying the radius of the circles and then leverage this to build an index called GRIN. We compare GRIN with three existing RDF indexex: Jena, Sesame. and RDFBroker. We compared (i) the time to answer graph based queries, (ii) memory needed to store the index, and (iii) the time to build the index. GRIN outperforms Jena, Sesame and RDFBroker on all three measures for graph based queries (for other types of queries, it may be worth building one of these other indexes and using it), at the expense of using a larger amount of memory when answering queries.
The Maker Movement in Education

The Maker Movement is a broad international movement celebrating making with a wide range of tools and media, including an evolving array of new tools and processes for digital fabrication such as 3D printers and laser cutters. This article discusses who makers are in education, what that making entails, and where that making happens. akers are people of all ages who find digital and physical forums to share their products and processes. Educators and researchers in the Maker Movement in education are working to expand who makers are, providing critiques of traditional conceptions of maker identities and seeking to broaden participation in terms of race, gender, socioeconomic status, and ability status. Making entails a diversity of media, tools, processes and practices. Likewise, the Maker Movement in education purposefully transcends academic disciplines, drawing both on traditional academic subjects like engineering and math along with everyday life skills like sewing, carpentry and metalwork. Making happens across a variety of spaces where there is an educational focus, both informal (museums, community centers, libraries, and online) and formal (from K–12 to higher education, to teacher education). In these spaces, the specific goals and practices of the supporting organizations are woven together with those of the Maker Movement to support a range of learners and outcomes, including family inquiry, equity, access to technology, virtual community and support, social interaction, creativity, engineering education, and teacher candidate confidence. Maker education is often framed as a reaction to more “traditional” educational approaches and frequently involves the incorporation of making into STEM (science, technology, engineering, and math) and STEAM (science, technology, engineering, art, and math) approaches.
Major depressive disorder: Findings of reduced homotopic connectivity and investigation of underlying structural mechanisms

Depression has been associated with various alterations in magnetic resonance imaging (MRI) derived resting‐state functional connectivity. Recently, homotopic connectivity, defined as functional connectivity between homotopic regions across hemispheres, has been reported to be reduced in patients with major depressive disorder (MDD). However, little is known about structural factors underlying alterations of homotopic connectivity, which would contribute to the understanding of the altered neurophysiological architecture in patients with MDD. We compared 368 patients with MDD and 461 never‐depressed controls regarding voxel‐mirrored homotopic connectivity (VMHC) and potential underlying mechanisms such as the structural connectivity of the corpus callosum, measured by DTI‐derived fractional anisotropy (FA), and left–right symmetries in homotopic gray matter volumes. Compared to controls, patients with MDD exhibited reduced VMHC in the cuneus, putamen, superior temporal gyrus, insula, and precuneus. Within these regions, no differences in left–right symmetries in homotopic gray matter volumes were evident across cohorts. FA of the corpus callosum correlated with VMHC in the entire sample. However, patients with MDD and controls did not differ with regard to callosal FA. The findings indicate that MDD is associated with a loss of interhemispheric synchrony in regions known to be implicated in self‐referential and reward processing. They also suggest that additional mechanisms are implicated in altered homotopic connectivity of patients with MDD, other than direct callosal fiber pathways or asymmetries in homotopic gray matter volumes. Hum Brain Mapp 37:1209–1217, 2016. © 2015 Wiley Periodicals, Inc.
Morphologies of synaptic protein membrane fusion interfaces

Significance Neurotransmitter release occurs upon fusion of synaptic vesicles with the plasma membrane, and it is orchestrated by synaptic proteins, including SNAREs, synaptotagmin, complexin, and other factors. The system is exquisitely fine-tuned to increase the probability of membrane fusion by orders of magnitude upon Ca2+ binding to a Ca2+ sensor, such as synaptotagmin. Although crystal structures are available for some of the key complexes of soluble fragments of synaptic proteins, and the process has been reconstituted, the association of these complexes with the synaptic and plasma membranes remains unclear. We visualized functionally active synaptic proteins reconstituted into proteoliposomes and their interactions in a native membrane environment by electron cryotomography with a Volta phase plate for improved resolvability. Neurotransmitter release is orchestrated by synaptic proteins, such as SNAREs, synaptotagmin, and complexin, but the molecular mechanisms remain unclear. We visualized functionally active synaptic proteins reconstituted into proteoliposomes and their interactions in a native membrane environment by electron cryotomography with a Volta phase plate for improved resolvability. The images revealed individual synaptic proteins and synaptic protein complex densities at prefusion contact sites between membranes. We observed distinct morphologies of individual synaptic proteins and their complexes. The minimal system, consisting of neuronal SNAREs and synaptotagmin-1, produced point and long-contact prefusion states. Morphologies and populations of these states changed as the regulatory factors complexin and Munc13 were added. Complexin increased the membrane separation, along with a higher propensity of point contacts. Further inclusion of the priming factor Munc13 exclusively restricted prefusion states to point contacts, all of which efficiently fused upon Ca2+ triggering. We conclude that synaptic proteins have evolved to limit possible contact site assemblies and morphologies to those that promote fast Ca2+-triggered release.
Migration, Resilience and Security: Responses to New Inflows of Asylum Seekers and Migrants

The ubiquity of resilience—the process of patterned adjustments adopted by a society or an individual in the face of endogenous or exogenous shocks—across the broad social sciences spectrum is undisputable. Yet, migration scholars have been relatively absent from this vibrant discussion. The present article suggests a theorisation of the link between migration, resilience and security by examining ways in which resilience precedes a socially constructed understanding of international migration as a security issue. The article explores how the surge in worldwide refugee numbers and associated mass migration phenomena were not only interpreted as a shock in post-Cold War France, but also instrumentalised by dominant discourses to underscore the necessity of adopting a particular pattern of adjustments to uphold the status quo against changes provoked by these migratory events. The social construction of refugee movements and mass migration as a significant disturbance requiring France to opt for a resilient strategy has led, ultimately, to the securitisation of migration. In a broader sense, the article presents a new lens through which to analyse situations and conditions in which resilience has led to and induced the securitisation of migration.
Adaptationism and Early Confucian Moral Psychology

Ryan Nichols in his recent article ‘A genealogy of early Confucian moral psychology’ argues that the discussion of Confucius and Mencius on moral emotions can be provided an evolutionary analysis. Nichols’ argument is based on the evolutionary value of kin-relations and the origin of emotions toward kin in human society. In this article I argue that Nichols’ argument is flawed because he endorses an adaptationist program of human moral psychology. The adaptationists treat kin-relations and our emotions toward kin as a straightforward result of natural selection and adaptation. They ignore any non-adaptationist interpretation of biological traits. As more and more evolutionary biologists discover that the adaptationist program is too simplistic to understand the diverse evolutionary pathways of living beings, Nichols’ project is not justified due to its reliance on this problematic adaptationist program.
Social Anxiety Scale for Children-Revised: Factor Structure and Concurrent Validity

Examined the factor structure, internal reliabilities, and concurrent validity of a revised form of the Social Anxiety Scale for Children (SASC-R) with fourth through sixth graders (N = 587). Factor analysis on a subsample (n = 459) yielded three factors: Fear of Negative Evaluation From Peers, Social Avoidance and Distress Specific to New Situations, and Generalized Social Avoidance and Distress. Confirmatory factor analysis with another subsample (n = 128)revealed a good fit for the three-factor model of social anxiety. In addition, high-socially-anxious children perceived their social acceptance and global self-worth to be low. Neglected and rejected children reported more social anxiety than accepted classmates. The data support the reliability and validity of the SASC-R.
Immunohistochemical expression of chemokine receptor CXCR3 and its ligand CXCL10 in low-grade astrocytomas and glioblastoma multiforme: A tissue microarray-based comparison.

UNLABELLED Glioblastoma multiforme (GBM) and diffuse astrocytoma (DA) are the most frequently encountered gliomas. Due to poor prognosis and limited success of the currently available treatment modalities there is a need to identify new therapeutic targets. Chemokines (CKs) regulate cellular functions like chemotaxis, angiogenesis, apoptosis, and cell cycle progression that play role in tumor growth. OBJECTIVE To study comparative immunoexpression of CXCR3 and CXCL10 in DA and GBM using a high-throughput tissue microarray (TMA). MATERIALS AND METHODS A TMA of 1.0 mm core diameter was made from formalin-fixed, paraffin-embedded donor blocks of 25 pilocytic astrocytomas (PA), 45 DA, and 75 GBM. Immunohistochemical staining for CXCR3 and CXCL10 was performed. RESULTS Out of 145, 129 cores were suitable for immunohistochemical evaluation after processing and immunohistochemistry. Strong CXCR3 immunoexpression was observed in 72.7% cases of GBM as compared to 31.8% cases of DA. 50.7% of GBM and 24.5% of DA showed strong immunoexpression of CXCL10. Overall comparisons between DA and GBM for CXCR3 and CXCL10 showed statistically significant correlation between the two with P < 0.001 and P = 0.02, respectively. A positive correlation was observed between CXCR3 and MIB-1. Pearson's correlation coefficient r = 0.548 and 0.330 for DA and GBM, respectively with P < 0.01. CONCLUSION GBM shows overexpression of CXCR3 and CXCL10 in comparison to DA, indicating that they play an important role in tumor growth and progression. Inhibition of this receptor-ligand axis may be a potential therapeutic target for arresting tumor growth and development of a glioblastoma.
Intra‐aortic injection of myoblasts in mdx mice: Genetic and technetium‐99m cell labeling and biodistribution

Dystrophin is a muscle subsarcolemmal protein rethe reporter gene pCMVlacZ (a cytomegalovirus promoter driving the expression of Escherichia coli bquired to anchor membrane proteins (DAGs). 5 The complete lack of dystrophin in humans causes galactosidase) and pY3 (a plasmid conferring resistance to the toxic hygromycin B). 1 The transfected Duchenne’s muscular dystrophy (DMD) and partial deficiency Becker’s muscular dystrophy (BMD). No G-8 mouse myoblast cells2 were grown in Dulbecco therapy, so far, is available in dystrophinopathies; modified Eagle medium (DMEM) supplemented however, gene replacement is appealing as a potenwith 4.5 g/L glucose, 10% fetal bovine serum (FBS), tial therapy. Since myoblasts injected into patient’s 10% horse serum (HS), and 100 eg/mL hygromycin muscles are capable of expressing dystrophin, in the B (Boehringer Mannheim). Resistant cell colonies present work we analyze the myoblast-mediated gene were collected after 7 days of selection and distribtransfer through intra-aortic injection in mdx mice. uted in aliquots, each containing 2 3 105 cells in 100 This approach has the potential of a widespread diseL of phosphate-buffered saline (PBS), then they tribution of the gene transfer through the blood were ready for injection. Three C57B6L mice and stream, in muscle lacking dystrophin. The cell migra5 dystrophic mutant mdx mice were injected with tion in the muscle and the possible diffusion in differbupivacaine (BVC) on the left tibialis anterior (TA) ent tissues has been studied by genetic and technemuscle 24 h prior to the transplant. They were immutium-99m (Tc-99m) cell labeling. nosuppressed with daily IV injections of 10 mg/kg of cyclosporin A. The mice were anesthetized with an
Butyl paraben‐induced changes in DNA methylation in rat epididymal spermatozoa

Parabens have been shown to affect male rodent reproductive parameters, including testosterone levels and sperm production. In this study, we examined the effect of long‐term exposure to butyl paraben (BP) on rat epididymal sperm DNA methylation. Adult male rats were exposed to BP (0, 10, 100 and 1000 mg kg−1 per day) according to OECD TG407 for a repeated 28‐day oral toxicity study. Sperm DNA methylation was examined by differential display random amplification of polymorphic DNA (RAPD) following methylation‐specific restriction digestion of DNA. Among the 57 RAPD amplicons, six were methylation specific. Of these, five amplicons increased by 1.4‐ to 3.8‐fold in epididymal sperm DNA at testing dose of BP. This indicates that BP can cause DNA hypermethylation in germ cells from the mitotic through post‐meiotic stage in adult rat testes. To our knowledge, this is the first report on the epigenetic modification of sperm DNA by parabens.
An Improved Oracle for Dependency Parsing with Online Reordering

We present an improved training strategy for dependency parsers that use online reordering to handle non-projective trees. The new strategy improves both efficiency and accuracy by reducing the number of swap operations performed on non-projective trees by up to 80%. We present state-of-the-art results for five languages with the best ever reported results for Czech.
Fall detection and activity identification using wearable and hand-held devices

Human motion data captured from wearable devices such as smart watches can be utilized for activity recognition and emergency event detection, especially in the case of elderly or disabled people living independently in their homes. The output of such sensors is streams of physical activity data that require real-time recognition, especially in emergency situations. This paper presents a novel application that utilizes the low-cost Pebble Smart Watch together with an Android device (i.e. a smart phone) and allows the efficient capturing, transmission, storage and processing of such motion data. The paper includes the technical details of the stream data capturing and processing methodology, along with a comparison of the major algorithms used for the classification of physical activity type (i.e. Mild, Moderate, Intense and Sleep). An initial evaluation of the achieved accuracy in recognizing activity type, calculating the energy consumption and detecting falls, is also included and the corresponding results are discussed. The reported results are quite promising and can enable the development of intelligent systems, capable of analyzing human behavior and triggering alarms related to human activity in addition to fall detection.
Web-based assessment of depression in patients treated in clinical practice: reliability, validity, and patient acceptance.

OBJECTIVE Calls for the use of standardized assessments in clinical practice have been increasing. A Web-based administration of outcome assessments offers several potential advantages over paper-and-pencil assessments, such as patient convenience, reduced missing data, reduced costs, automatic scoring, and generation of large databases. The present study from the Rhode Island Methods to Improve Diagnostic Assessments and Services (MIDAS) project evaluated the acceptability, reliability, and validity of a Web-based administration of a depression scale in patients receiving ongoing care for depression. METHOD From June 2009 to July 2010, fifty-three depressed outpatients completed a Web-based and a paper version of the Clinically Useful Depression Outcome Scale (CUDOS). The vast majority of patients met DSM-IV criteria for either major depressive disorder (n = 36) or bipolar disorder (n = 9). Patients were also asked to complete a brief 6-question survey of the acceptability of the 2 modes of scale administration. At the time of the visit, the patients' psychiatrist completed the Montgomery-Asberg Depression Rating Scale (MADRS) and rated patients on the Clinical Global Impressions-Severity of Illness (CGI-S) scale and Global Assessment of Functioning (GAF). RESULTS The correlation between the Web-administered and paper versions of the CUDOS was high (P < .001). The mean scores were similar on the paper and Internet administrations. The internal consistency of the paper and Internet administrations of the CUDOS was high (both values, Cronbach α = .93), and all item-scale correlations for the paper and Internet versions were significant (median for paper administration = 0.76; median for Internet administration = 0.74). The paper and Internet versions of the CUDOS were equally correlated with clinicians' ratings on the MADRS, CGI-S, and GAF (all P values < .001). Patients reported high levels of satisfaction with Internet administration and preferred this method of monitoring outcome to paper administration in the office (all P values < .001). CONCLUSIONS The results of this first study of the use of a Web-based system of monitoring outcome in routine clinical practice supported the reliability and validity of Internet administration of a depression scale, and patients clearly preferred Internet administration to completion of a paper-and-pencil questionnaire in the office.
Automatic salient object extraction with contextual cue

We present a method for automatically extracting salient object from a single image, which is cast in an energy minimization framework. Unlike most previous methods that only leverage appearance cues, we employ an auto-context cue as a complementary data term. Benefitting from a generic saliency model for bootstrapping, the segmentation of the salient object and the learning of the auto-context model are iteratively performed without any user intervention. Upon convergence, we obtain not only a clear separation of the salient object, but also an auto-context classifier which can be used to recognize the same type of object in other images. Our experiments on four benchmarks demonstrated the efficacy of the added contextual cue. It is shown that our method compares favorably with the state-of-the-art, some of which even embraced user interactions.
Topological Birkhoff

One of the most fundamental mathematical contributions of Garrett Birkhoff is the HSP theorem, which implies that a finite algebra B satisfies all equations that hold in a finite algebra A of the same signature if and only if B is a homomorphic image of a subalgebra of a finite power of A. On the other hand, if A is infinite, then in general one needs to take an infinite power in order to obtain a representation of B in terms of A, even
Parallel Data Mining on Multicore Systems

The ever increasing number of cores per chip will be accompanied by a pervasive data deluge whose size will probably increase even faster than CPU core count over the next few years. This suggests the importance of parallel data analysis and data mining applications with good multicore, cluster and grid performance. This paper considers data clustering, mixture models and dimensional reduction presenting a unified framework applicable to bioinformatics, cheminformatics and demographics. Deterministic annealing is used to lessen effect of local minima. We present performance results on 8-core systems identifying effects from cache, runtime fluctuations, synchronization and memory bandwidth. We discuss needed programming model and compare with MPI and other approaches