Miracle-dz/UniFAR-FTUs huggingface dataset:
A Gain-of-Function Mutation in a Cytokinin Receptor Triggers Spontaneous Root Nodule Organogenesis

Legume root nodules originate from differentiated cortical cells that reenter the cell cycle and form organ primordia. We show that perception of the phytohormone cytokinin is a key element in this switch. Mutation of a Lotus japonicus cytokinin receptor gene leads to spontaneous development of root nodules in the absence of rhizobia or rhizobial signal molecules. The mutant histidine kinase receptor has cytokinin-independent activity and activates an Escherichia coli two-component phosphorelay system in vivo. Mutant analysis shows that cytokinin signaling is required for cell divisions that initiate nodule development and defines an autoregulated process where cytokinin induction of nodule stem cells is controlled by shoots.
Efficient use of large don't cares in high-level and logic synthesis

This paper describes optimization techniques using don't-care conditions that span the domain of high-level and logic synthesis. The following three issues are discussed: (1) how to describe and extract don't-care conditions from high-level descriptions; (2) how to pass don't-care conditions from high-level to logic synthesis; and (3) how to optimize the logic using don't-care conditions. Efficient techniques are given for these three problems which allow the use of large don't-care sets. Results from several examples demonstrate that these techniques are very effective for both area and delay minimization.
Integrating Learning, Problem Solving, and Engagement in Narrative-Centered Learning Environments

A key promise of narrative-centered learning environments is the ability to make learning engaging. However, there is concern that learning and engagement may be at odds in these game-based learning environments. This view suggests that, on the one hand, students interacting with a game-based learning environment may be engaged but unlikely to learn, while on the other hand, traditional learning technologies may promote deep learning but provide limited engagement. This paper presents findings from a study with human participants that challenges the view that engagement and learning need be opposed. A study was conducted with 153 middle school students interacting with a narrative-centered learning environment. Rather than finding an oppositional relationship between learning and engagement, the study found a strong positive relationship between learning outcomes, in-game problem solving and increased engagement. Furthermore, the relationship between learning outcomes and engagement held even when controlling for students' background knowledge and game-playing experience. Additional analyses revealed that males tended to report significantly greater presence in the virtual environment than girls, and students with more game-playing experience reported significantly greater presence in the virtual environment than students with minimal game-playing experience. Follow up analyses suggested that differences in presence may be more strongly associated with game-playing experience than gender.
Pigmented Villonodular Synovitis for Combined Therapy

Pigmented villonodular synovitis (PVNS), inflammatory proliferative disease resulting from synovial cells, has progressive course similar neoplastic local expansion. We followed up a case with effective combined therapy for diffuse PVNS despite incomplete response to its components and reviewed therapies based on MedLine for PVNS. Due to US data residue synovitis after open radical synovectomy, we made decision about external beam radiotherapy. Photon radiation with linear accelerator energy of 6 MV was applied for two fields: anterior and posterior. The total dose was 20 Gy, delivered in 2 Gy a day, five times a week. Due to postoperative pain and the rest of synovial tissue on US study, pharmacologic therapy with salazopyrine and celecoxib was added. For several weeks, the knee pain became episodic and further disappeared. Six months later, the patient feels healthy and continues to take salazopyrine permanently and celecoxib as needed. We conclude high rate response analyzing literature data and our case to combined therapy: arthroscopic or open surgery followed by RT along with complimentary pharmacotherapy. J Med Cases. 2014;5(3):147-151 doi: http://dx.doi. org/10.14740/jmc1656e
Word-length effect in verbal short-term memory in individuals with Down's syndrome.

BACKGROUND Many studies have indicated that individuals with Down's syndrome (DS) show a specific deficit in short-term memory for verbal information. The aim of the present study was to investigate the influence of the length of words on verbal short-term memory in individuals with DS. METHODS Twenty-eight children with DS and 10 control participants matched for memory span were tested on verbal serial recall and speech rate, which are thought to involve rehearsal and output speed. RESULTS Although a significant word-length effect was observed in both groups for the recall of a larger number of items with a shorter spoken duration than for those with a longer spoken duration, the number of correct recalls in the group with DS was reduced compared to the control subjects. The results demonstrating poor short-term memory in children with DS were irrelevant to speech rate. In addition, the proportion of repetition-gained errors in serial recall was higher in children with DS than in control subjects. CONCLUSIONS The present findings suggest that poor access to long-term lexical knowledge, rather than overt articulation speed, constrains verbal short-term memory functions in individuals with DS.
Allele-specific imbalance of oxidative stress-induced growth inhibitor 1 associates with progression of hepatocellular carcinoma.

BACKGROUND & AIMS Although there are a few highly penetrant mutations that are linked directly to cancer initiation, more less-penetrant susceptibility alleles have been associated with cancer risk and progression. We used RNA sequence analysis to search for genetic variations associated with pathogenesis of hepatocellular carcinoma (HCC). METHODS We analyzed 400 paired HCC and adjacent nontumor tissues, along with clinical information, from patients who underwent surgery at Sun Yat-Sen University in Guangzhou, China. Total RNA was extracted from tissues and sequenced, and variations with allele imbalance were identified. Effects of variants on cell functions were investigated in HCC cell lines and tumor xenografts in mice. Variants were associated with patient outcomes. RESULTS We found a high proportion of allele imbalance in genes related to cellular stress. A nucleotide variation in the Oxidative Stress-Induced Growth Inhibitor 1 (OSGIN1) gene (nt 1494: G-A) resulted in an amino acid substitution (codon 438: Arg-His). The variant form of OSGIN1 was specifically retained in the tumor tissues. Functional assays showed that the common form of OSGIN1 functioned as a tumor suppressor, sensitizing HCC cells to chemotherapeutic agents by inducing apoptosis. However, the variant form of OSGIN1 was less effective. It appeared to affect the translocation of OSGIN1 from the nucleus to mitochondria, which is important for its apoptotic function. The expression pattern and localization of OSGIN1 was altered in HCC specimens, compared with adjacent liver tissue. Levels of OSGIN1 messenger RNA were reduced in 24.7% of HCC specimens, and down-regulation was associated with shorter overall and disease-free survival times of patients. Patients with the OSGIN1 1494A variant had the shortest mean survival time (32.68 mo) among patient subgroups, and their tumor samples had the lowest apoptotic index. CONCLUSIONS We identified OSGIN1 as a tumor suppressor that is down-regulated or altered in human HCCs. Variants of OSGIN1 detected in HCC samples reduce apoptosis and are associated with shorter survival times of patients.
A robotic nursing bed design and its control system

A kind of new robotic nursing bed is designed in this paper, which has the functions of raising back, curling legs, side turning over from left to right separately, and voice recognition control, according to paralyzed patient's repuirement. The bed is designed based on the robot's behave planning and the characteristics of multi-axis control and templet matching theory, to improve living standard of the paralyzed patients. The work focuses on technical solutions for human-friendly assistance in structure design of the nursing bed and voice recognition that provide convenience control of all assistive robotic systems. The designed nursing bed has been tried out, the trial results show the practicality and reliability of the designed hospital beds, and fully meet the needs of patients.
A New Application of MEG and DTI on Word Recognition

This paper presented a novel application of Magneto encephalography (MEG) and diffusion tensor image (DTI) on word recognition, in which the spatiotemporal signature and the neural network of brain activation associated with word recognition were investigated. The word stimuli consisted of matched and mismatched words, which were visually and acoustically presented simultaneously. Twenty participants were recruited to distinguish and gave different reactions to these two types of stimuli. The neural activations caused by their reactions were recorded by MEG system and 3T magnetic DTI scanner. Virtual sensor technique and wavelet beam former source analysis, which were state-of-the-art methods, were used to study the MEG and DTI data. Three responses were evoked in the MEG waveform and M160 was identified in the left temporal-occipital junction. All the results coincided with the previous studies’ conclusions, which indicated that the integration of virtual sensor and wavelet beam former were effective techniques in analyzing the MEG and DTI data.
Binding of tetrodotoxin to squid nerve fibers. Two kinds of receptors?

The effect of tetrodotoxin on the sodium currents of the squid (Doryteuthis plei and Sepioteuthis sepiodea) giant axons was studied under potential control conditions. The axons were immersed in artificial seawater at 21 degrees C and pH 7.5. When the effect of the toxin is studied in concentrations ranging from 0.1 to 50 nM the Eadie- Haldane plot is not a straight line and indicates that there are two populations of sodium channels open during activity. 19.0 +/- 4.7% of the channels are accociated to receptors with an apparent dissociation constant of 0.11 +/- 0.05 nM and 84.0 +/- 4.1% of the channels are related to receptors having an affinity constant of 4.90 +/- 0.49 nM (nine nerves).
Holonic Dynamic Scheduling Architecture and Services

Departamento de Engenharia InformaticaInstituto Superior de Engenharia do PortoInstituto Politecnico do PortoRua de S. Tome, s/n4200 Porto - PortugalTel. : +351 2 8340500 Fax: +351 2 821159e-mail: {nsilva, csr}@dei.isep.ipp.pthttp:// www.dei.isep.ipp. pt/~{nsilva, csr}Abstract: Manufacturing systems are changing its structure and organisation. Supply chain are evolving to morecoupled organisations, like virtual enterprises, though maintaining the single entities autonomy, adaptabilityand dynamism properties. Such organisations are very different, which imply organisational and technologicalshift through agility, distribution, decentralisation, reactivity and flexibility. New organisational andtechnological paradigms are needed in order to reply to the modern manufacturing systems needs. This paperpresent a holonic manufacturing system architecture and complementary services supplied to assist overallCommunication, Security, Reliability, Information Management, Co-operation and Co-ordination.Keywords: HMS, MAS, Architecture and Services
Targeting of Arf-1 to the early Golgi by membrin, an ER-Golgi SNARE

Arf and Rab family GTPases regulate membrane traffic in cells, yet little is known about how they are targeted to distinct organelles. To identify sequences in Arf-1 necessary for Golgi targeting, we examined the localization of chimeras between Arf-1 and Arf-6. Here, we identify a 16–amino acid sequence in Arf-1 that specifies Golgi targeting and contains a motif (MXXE) that is important for Arf-1 binding to membrin, an ER-Golgi SNARE protein. The MXXE motif is conserved in all Arfs known to localize to the Golgi and enables Arf-1 to localize to the early Golgi. Arf-1 lacking these 16 aa can still localize to the late Golgi where it displays a more rapid Golgi-cytosol cycle than wild-type Arf-1. These studies suggest that membrin recruits Arf-1 to the early Golgi and reveal distinct kinetic cycles for Arf-1 at early and late Golgi determined by different sets of Arf regulators and effectors.
A Categorical Treatment of Ornaments

Ornaments aim at taming the multiplication of special-purpose datatypes in dependently typed programming languages. In type theory, purpose is logic. By presenting datatypes as the combination of a structure and a logic, ornaments relate these special-purpose datatypes through their common structure. In the original presentation, the concept of ornament was introduced concretely for an example universe of inductive families in type theory, but it was clear that the notion was more general. This paper digs out the abstract notion of ornaments in the form of a categorical model. As a necessary first step, we abstract the universe of datatypes using the theory of polynomial functors. We are then able to characterise ornaments as cartesian morphisms between polynomial functors. We thus gain access to powerful mathematical tools that shall help us understand and develop ornaments. We shall also illustrate the adequacy of our model. Firstly, we rephrase the standard ornamental constructions into our framework. Thanks to its conciseness, we gain a deeper understanding of the structures at play. Secondly, we develop new ornamental constructions, by translating categorical structures into type theoretic artefacts.
Deep Sequencing of the Trypanosoma cruzi GP63 Surface Proteases Reveals Diversity and Diversifying Selection among Chronic and Congenital Chagas Disease Patients

Background Chagas disease results from infection with the diploid protozoan parasite Trypanosoma cruzi. T. cruzi is highly genetically diverse, and multiclonal infections in individual hosts are common, but little studied. In this study, we explore T. cruzi infection multiclonality in the context of age, sex and clinical profile among a cohort of chronic patients, as well as paired congenital cases from Cochabamba, Bolivia and Goias, Brazil using amplicon deep sequencing technology. Methodology/ Principal Findings A 450bp fragment of the trypomastigote TcGP63I surface protease gene was amplified and sequenced across 70 chronic and 22 congenital cases on the Illumina MiSeq platform. In addition, a second, mitochondrial target—ND5—was sequenced across the same cohort of cases. Several million reads were generated, and sequencing read depths were normalized within patient cohorts (Goias chronic, n = 43, Goias congenital n = 2, Bolivia chronic, n = 27; Bolivia congenital, n = 20), Among chronic cases, analyses of variance indicated no clear correlation between intra-host sequence diversity and age, sex or symptoms, while principal coordinate analyses showed no clustering by symptoms between patients. Between congenital pairs, we found evidence for the transmission of multiple sequence types from mother to infant, as well as widespread instances of novel genotypes in infants. Finally, non-synonymous to synonymous (dn:ds) nucleotide substitution ratios among sequences of TcGP63Ia and TcGP63Ib subfamilies within each cohort provided powerful evidence of strong diversifying selection at this locus. Conclusions/Significance Our results shed light on the diversity of parasite DTUs within each patient, as well as the extent to which parasite strains pass between mother and foetus in congenital cases. Although we were unable to find any evidence that parasite diversity accumulates with age in our study cohorts, putative diversifying selection within members of the TcGP63I gene family suggests a link between genetic diversity within this gene family and survival in the mammalian host.
Empirical development of a heuristic evaluation methodology for shared workspace groupware

Good real time groupware products are hard to develop, in part because evaluating their support for basic teamwork activities is difficult and costly. To address this problem, we are developing discount evaluation methods that look for groupware-specific usability problems. In a previous paper, we detailed a new set of usability heuristics that evaluators can use to inspect shared workspace groupware to see how they support teamwork. We wanted to determine whether the new heuristics could be integrated into a low-cost methodology that parallels Nielsen's traditional heuristic evaluation (HE). To this end, we examined 27 evaluations of two shared workspace groupware systems and analysed the inspectors' relative performance and variability. Similar to Nielsen's findings for traditional HE, individual inspectors discovered about a fifth of the total known teamwork problems, and that there was only modest overlap in the problems they found. Groups of three to five inspectors would report about 40-60% of the total known teamwork problems. These results suggest that heuristic evaluation using our groupware heuristics can be an effective and efficient method for identifying teamwork problems in shared workspace groupware systems.
Partial order embedding with multiple kernels

We consider the problem of embedding arbitrary objects (e.g., images, audio, documents) into Euclidean space subject to a partial order over pair-wise distances. Partial order constraints arise naturally when modeling human perception of similarity. Our partial order framework enables the use of graph-theoretic tools to more efficiently produce the embedding, and exploit global structure within the constraint set. We present an embedding algorithm based on semidefinite programming, which can be parameterized by multiple kernels to yield a unified space from heterogeneous features.
A song of fire and water: will climate change interacting with fire affect the distribution of vegetation in the Australian Wet Tropics?

Complex landscapes interact with meteorological processes to generate climatically suitable habitat (refuges) in otherwise hostile environments. Locating these refuges has practical importance in tropical montane regions where a high diversity of climatically specialized species is threatened by climate change. Here, we use a combination of weather data and spatial modeling to quantify thermally buffered environments in a regional tropical rainforest. We do this by constructing a spatial surface of maximum air temperature that takes into account important climatemediating processes. We find a strong attenuating effect of elevation, distance from coast and foliage cover on maximum temperature. The core habitat of a disproportionately high number of endemic species (45%) is encompassed within just 25% of the coolest identified rainforest. We demonstrate how this data can be used to (i) identify important areas of cool habitat for protection and (ii) efficiently guide restoration in degraded landscapes to expand extant networks of critical cool habitat.
New Methodology for Feasible Reconfigurable Real-Time Network-on-Chip NoC

The current research paper is interested in flexible reconfigurable real-time Network-on-Chip (NoC) in Multiprocessors System-on-Chip MPSoC architectures. A NoC is composed of several nodes where each one consists of a processor and a router. The reconfiguration of a processor is any operation that permits the addition-removal-update of periodic dependent OS (Operating System) tasks that are sharing resources. For two added dependent tasks assigned to different processors, a message is added automatically on the NoC. After any reconfiguration scenario, several real-time constraints cannot be satisfied since a task can miss its deadline and a message can take a long time to arrive to its destination. In order to re-obtain the system feasibility, we propose a new approach that is called CRM (abrev. Cynapsys Reconfigurable MPSoC). A multi-agent architecture based on a master/slave model is defined where a slave agent is assigned to each node to control its local feasibility after any reconfiguration scenario, and a master is proposed for the whole architecture if any perturbation occurs at run-time by proposing software or hardware solutions. A developed tool at LISI laboratory and Cynapsys is implemented for a real case study in order to evaluate the paper’s contribution.
Dengue Virus Nonstructural Protein 5 (NS5) Assembles into a Dimer with a Unique Methyltransferase and Polymerase Interface

Flavivirus nonstructural protein 5 (NS5) consists of methyltransferase (MTase) and RNA-dependent RNA polymerase (RdRp) domains, which catalyze 5’-RNA capping/methylation and RNA synthesis, respectively, during viral genome replication. Although the crystal structure of flavivirus NS5 is known, no data about the quaternary organization of the functional enzyme are available. We report the crystal structure of dengue virus full-length NS5, where eight molecules of NS5 are arranged as four independent dimers in the crystallographic asymmetric unit. The relative orientation of each monomer within the dimer, as well as the orientations of the MTase and RdRp domains within each monomer, is conserved, suggesting that these structural arrangements represent the biologically relevant conformation and assembly of this multi-functional enzyme. Essential interactions between MTase and RdRp domains are maintained in the NS5 dimer via inter-molecular interactions, providing evidence that flavivirus NS5 can adopt multiple conformations while preserving necessary interactions between the MTase and RdRp domains. Furthermore, many NS5 residues that reduce viral replication are located at either the inter-domain interface within a monomer or at the inter-molecular interface within the dimer. Hence the X-ray structure of NS5 presented here suggests that MTase and RdRp activities could be coordinated as a dimer during viral genome replication.
The Calderón problem with partial data in two dimensions

We prove for a two dimensional bounded domain that the Cauchy data for the Schrodinger equation measured on an arbitrary open subset of the boundary determines uniquely the potential. This implies, for the conductivity equation, that if we measure the current fluxes at the boundary on an arbitrary open subset of the boundary produced by voltage potentials supported in the same subset, we can determine uniquely the conductivity. We use Carleman estimates with degenerate weight functions to construct appropriate complex geometrical optics solutions to prove the results.