Miracle-dz/UniFAR-FTUs huggingface dataset:
AGO1 defines a novel locus of Arabidopsis controlling leaf development

An allelic series of the novel argonaute mutant (ago1‐1 to ago1‐6) of the herbaceous plant Arabidopsis thaliana has been isolated. The ago1 mutation pleotropically affects general plant architecture. The apical shoot meristem generates rosette leaves and a single stem, but axillary meristems rarely develop. Rosette leaves lack a leaf blade but still show adaxial/abaxial differentiation. Instead of cauline leaves, filamentous structures without adaxial/abaxial differentiation develop along the stem and an abnormal inflorescence bearing infertile flowers with filamentous organs is produced. Two independent T‐DNA insertions into the AGO1 locus led to the isolation of two corresponding genomic sequences as well as a complete cDNA. The AGO1 locus was mapped close to the marker mi291a on chromosome 1. Antisense expression of the cDNA resulted in a partial mutant phenotype. Sense expression caused some transgenic lines to develop goblet‐like leaves and petals. The cDNA encodes a putative 115 kDa protein with sequence similarity to translation products of a novel gene family present in nematodes as well as humans. No specific function has been assigned to these genes. Similar proteins are not encoded by the genomes of yeast or bacteria, suggesting that AGO1 belongs to a novel class of genes with a function specific to multicellular organisms.
Fragile X Mental Retardation Protein is Involved in Protein Synthesis-Dependent Collapse of Growth Cones Induced by Semaphorin-3A

Fragile X syndrome, the most frequent form of familial mental retardation, is caused by mutation of the Fmr1 gene. Fmr1 encodes the fragile X mental retardation protein (FMRP), an mRNA binding protein regulating local, postsynaptic mRNA translation along dendrites necessary for long-term synaptic plasticity. However, recent studies on FMRP localization in axons and growth cones suggest a possible function in the regulation of local protein synthesis needed for axon guidance. Here, we have demonstrated that FMRP is involved in axonal and growth cone responses induced by the axon guidance factor, Semaphorin-3A (Sema3A). In cultured hippocampal neurons from wild type mice, Sema3A-induced growth cone collapse was protein synthesis-dependent. In contrast, Sema3A-induced growth cone collapse was attenuated in Fmr1 knock-out (KO) neurons and insensitive to protein synthesis inhibitors, suggesting that FMRP is involved in protein synthesis-dependent growth cone collapse. Sema3A increased phosphorylation of eukaryotic initiation factor 4E (eIF4E), an indicator of local translation, in distal axons and growth cones of wild type, but not Fmr1 KO neurons. Furthermore, Sema3A rapidly induced a protein synthesis-dependent increase in levels of microtubule associated protein 1B (MAP1B) in distal axons of wild type neurons, but this response was attenuated in Fmr1 KO neurons. These results suggest a possible role of FMRP to regulate local translation and axonal protein localization in response to Sema3A. This study reveals a new link between FMRP and semaphorin signaling in vitro, and raises the possibility that FMRP may have a critical role in semaphorin signaling in axon guidance during brain development.
3D-Jury: A Simple Approach to Improve Protein Structure Predictions

MOTIVATION Consensus structure prediction methods (meta-predictors) have higher accuracy than individual structure prediction algorithms (their components). The goal for the development of the 3D-Jury system is to create a simple but powerful procedure for generating meta-predictions using variable sets of models obtained from diverse sources. The resulting protocol should help to improve the quality of structural annotations of novel proteins. RESULTS The 3D-Jury system generates meta-predictions from sets of models created using variable methods. It is not necessary to know prior characteristics of the methods. The system is able to utilize immediately new components (additional prediction providers). The accuracy of the system is comparable with other well-tuned prediction servers. The algorithm resembles methods of selecting models generated using ab initio folding simulations. It is simple and offers a portable solution to improve the accuracy of other protein structure prediction protocols. AVAILABILITY The 3D-Jury system is available via the Structure Prediction Meta Server (http://BioInfo.PL/Meta/) to the academic community. SUPPLEMENTARY INFORMATION 3D-Jury is coupled to the continuous online server evaluation program, LiveBench (http://BioInfo.PL/LiveBench/)
Initial Study on 3D Porous Silk Fibroin Scaffold: Preparation and Morphology

Objective. The aim of the present study is to prepare a 3D porous silk fibroin scaffold with a hierachical structure that can meet the demands for bone tissue engineering. Materials and Methods. 3D fibroin scaffold was prepared by the methods of partial dissolution in acid solution and freeze drying fibroin solution. Results. The nets were composed of a mesh of randomly oriented fibers that ranged between 10 ? m and 30 ? m in diameter. Branchpoints and three dimensional open spaces were distributed throughout the structure with an average pore size of about 177.9 Â± 40.0 ? m. Conclusion. With the methods of non-woven silk fibroin net preparation and frozen-dried technics, it is possible to prepare a 3D porous silk fibroin scaffold with hierachical fine structure.
An a priori typology of sentential negation from an HPSG perspective

In this paper I explore the logical range of sentential negation types predicted by the theory of HPSG. I find that typological surveys confirm that attested simple negation strategies neatly line up with the types of lexical material given by assuming Lexical Integrity and standard Phrase Structure Grammar dependencies. I then extend the methodology to bipartite negation and derive a space of predicted sentential negation types. I present details of the analysis for each type and relevant examples where possible.
Plan Recognition as Planning Revisited

Recent work on plan recognition as planning has shown great promise in the use of a domain theory and general planning algorithms for the plan recognition problem. In this paper, we propose to extend previous work to (1) address observations over fluents, (2) better address unreliable observations (i.e., noisy or missing observations), and (3) recognize plans in addition to goals. To this end, we introduce a relaxation of the plan-recognition-as-planning formulation that allows unreliable observations. That is, in addition to the original costs of the plan, we define two objectives that account for missing and noisy observations, and optimize for a linear combination of all objectives. We approximate the posterior probabilities of generated plans by taking into account the combined costs that include penalties for missing or noisy observations, and normalizing over a sample set of plans generated by finding either diverse or high-quality plans. Our experiments show that this approach improves goal recognition in most domains when observations are unreliable. In addition, we evaluate plan recognition performance and show that the high-quality plan generation approach should be preferred in most domains.
Phylogenetic Relationships of 3 Korean Neodiplostomum Species (Digenea: Neodiplostomidae) Based on Partial CO1 Gene

The phylogenetic relationships of the 3 Neodiplostomum spp. (Digenea: Neodiplostomidae) occurring in Korea (N. seoulense, N. leei, and N. boryongense) were analyzed using the partial mitochondrial cytochrome c oxidase subunit 1 (CO1) gene. The adult flukes were recovered from Sprague-Dawley rats (N. seoulense) and newborn chicks (N. leei and N. boryongense) experimentally infected with the neodiplostomula from the grass snake, Rhabdophis tigrinus tigrinus. The genomic DNA was amplified using specific primers, and the sequence of CO1 was obtained. According to the results, the pairwise similarity was 96.1% between N. boryongense and N. seoulense, but was 95.0% between N. boryongense and N. leei and 94.2% between N. leei and N. seoulense. The results demonstrated a closer phylogenetic relationship between N. seoulense and N. boryongense. This high relationship of N. seoulense and N. boryongense may be related to their similar morphologic features including the limited distribution of vitellaria and the presence of a genital cone. N. leei is distinct on the other hand with an extensive distribution of vitellaria and the absence of a genital cone.
Text Classification for Student Data Set using Naive Bayes Classifier and KNN Classifier

— In this Information Era, Text documents with large features are available in plenty. Correct classification of this text documents into predefined set is a critical task. Text document classification is an emerging field in the area of text mining. Text classification is gorgeous because it eliminates the need of manually organizing documents based on their content and provides good accuracy. For Automated Text Classification a number of classifiers are available. I n this paper, our focus is on text classification using Naïve Bayes classifier and K-Nearest Neighbour classifier and to emphasize on performance and accuracy of these classifiers using Rapid miner for Student Data Set.
Building an urban identity. Cultural space and civic boosterism in a 'new' industrial town: Burslem, 1761-1911

In 1761 the residents of Burslem in the Staffordshire Potteries built a town hall. It was the first civic building in a rapidly growing industrial settlement and is frequently seen as marking the birth of Burslem as a town. One hundred and fifty years later the borough council spent over £35,000 on a new town hall – a last defiant act before Burslem was amalgamated with five neighbouring towns in the new county borough of Stoke-on-Trent. These two projects form the opening and closing chapters in a narrative of civic enterprise in Burslem. They also serve to define the discourse of urban identity in the town: a discourse which, as we shall see, was shaped by external/spatial relationships – rivalries with neighbouring places – as well as internal/social processes. Identity as and of a town has multiple layers. For many places, it was linked to the possession and nature of a charter along with the associated coat of arms and civic trappings, including municipal records. These might be augmented by a tradition of town histories, celebrating the glories of the past, highlighting recent development or calling for greater activity in future. Many of the manufacturing towns of the Midlands and North gained such formal accoutrements only in the midor late nineteenth century, often after decades if not centuries of functioning and being generally acknowledged as towns. In these places especially, civic culture – the construction of town halls, museums, libraries, concert halls and the like – was central to identity and image, both of the town and its elite. In all towns, such investment vastly increased in scale and importance with the expansion of the powers, responsibilities, roles and, of course, the budgets of municipal government in the second half of the nineteenth century. It also changed in nature. The eighteenth-century emphasis on polite
Feature Selection Based on the SVM Weight Vector for Classification of Dementia

Computer-aided diagnosis of dementia using a support vector machine (SVM) can be improved with feature selection. The relevance of individual features can be quantified from the SVM weights as a significance map (p-map). Although these p-maps previously showed clusters of relevant voxels in dementia-related brain regions, they have not yet been used for feature selection. Therefore, we introduce two novel feature selection methods based on p-maps using a direct approach (filter) and an iterative approach (wrapper). To evaluate these p-map feature selection methods, we compared them with methods based on the SVM weight vector directly, t-statistics, and expert knowledge. We used MRI data from the Alzheimer's disease neuroimaging initiative classifying Alzheimer's disease (AD) patients, mild cognitive impairment (MCI) patients who converted to AD (MCIc), MCI patients who did not convert to AD (MCInc), and cognitively normal controls (CN). Features for each voxel were derived from gray matter morphometry. Feature selection based on the SVM weights gave better results than t-statistics and expert knowledge. The p-map methods performed slightly better than those using the weight vector. The wrapper method scored better than the filter method. Recursive feature elimination based on the p-map improved most for AD-CN: the area under the receiver-operating-characteristic curve (AUC) significantly increased from 90.3% without feature selection to 92.0% when selecting 1.5%-3% of the features. This feature selection method also improved the other classifications: AD-MCI 0.1% improvement in AUC (not significant), MCI-CN 0.7%, and MCIc-MCInc 0.1% (not significant). Although the performance improvement due to feature selection was limited, the methods based on the p-map generally had the best performance, and were therefore better in estimating the relevance of individual features.
New stability conditions for semilinear diffusion systems with time-delays

In the present paper, sufficient conditions for the exponential stability of nonlinear diffusion systems with infinite distributed and discrete time-varying delays are derived. Such systems arise in many applications, e.g. in population dynamics. The existing Lyapunov-based results on the stability of diffusion nonlinear systems treat either systems with infinite delays or the ones with discrete slowly varying delays (with the delay derivatives smaller than 1), where the conditions are delay-independent in the discrete delays. We introduce the Lyapunov-based analysis of systems with fast varying (without any constraints on the delay-derivative) discrete and infinite distributed delays. We derive delay-independent with respect to discrete delays stability criterion via a novel combination of Lyapunov-Krasovskii functionals and of the Halanay inequality in terms of Linear Matrix Inequalities (LMIs). Numerical examples illustrate the efficiency of the method.
Development of a low-noise wide-band phased-array feed

Low-noise phased-array feeds are a new way to expand the field of view of radio telescopes at centimetre wavelengths. First generation engineering demonstrators of this technology have been constructed and tested by several institutes worldwide. The development of second-generation phased-array feeds is now underway. We describe one effort to design and build an astronomy-capable phased-array feed using techniques to reduce front-end noise and increase system bandwidth.
Transfer Learning of a Temporal Bone Performance Model via Anatomical Feature Registration

Evaluation of the outcome (end-product) of surgical procedures carried out in virtual reality environments is an essential part of simulation-based surgical training. Automated end-product assessment can be carried out by performance classifiers built from a set of expert performances. When applied to temporal bone surgery simulation, these classifiers can evaluate performance on the bone specimen they were trained on, but they cannot be extended to new specimens. Thus, new expert performances need to be recorded for each new specimen, requiring considerable time commitment from time-poor expert surgeons. To eliminate this need, we propose a transfer learning framework to adapt a classifier built on a single temporal bone specimen to multiple specimens. Once a classifier is trained, we translate each new specimens' features to the original feature space, which allows us to carry out performance evaluation on different specimens using the same classifier. In our experiment, we built a surgical end-product performance classifier from 16 expert trials on a simulated temporal bone specimen. We applied the transfer learning approach to 8 new specimens to obtain machine generated end-products. We also collected end-products for these 8 specimens drilled by a single expert. We then compared the machine generated end-products to those drilled by the expert. The drilled regions generated by transfer learning were similar to those drilled by the expert.
Intelligent Multimedia Indexing and Retrieval through Multi-source Information Extraction and Merging

This paper reports work on automated meta-data creation for multimedia content. The approach results in the generation of a conceptual index of the content which may then be searched via semantic categories instead of keywords. The novelty of the work is to exploit multiple sources of information relating to video content (in this case the rich range of sources covering important sports events). News, commentaries and web reports covering international football games in multiple languages and multiple modalities is analysed and the resultant data merged. This merging process leads to increased accuracy relative to individual sources.
Follow-Up of Coiled Cerebral Aneurysms at 3T: Comparison of 3D Time-of-Flight MR Angiography and Contrast-Enhanced MR Angiography

BACKGROUND AND PURPOSE: Our aim was to compare contrast-enhanced MR angiography (CE-MRA) and 3D time-of-flight (TOF) MRA at 3T for follow-up of coiled cerebral aneurysms. MATERIALS AND METHODS: Fifty-two patients treated with Guglielmi detachable coils for 54 cerebral aneurysms were evaluated at 3T MRA. 3D TOF MRA (TR/TE = 23/3.5; SENSE factor = 2.5) and CE-MRA by using a 3D ultrafast gradient-echo sequence (TR/TE = 5.9/1.8; SENSE factor = 3) enhanced with 0.1-mmol/kg gadobenate dimeglumine were performed in the same session. Source images, 3D maximum intensity projection, 3D shaded surface display, and/or 3D volume-rendered reconstructions were evaluated in terms of aneurysm occlusion/patency and artifact presence. RESULTS: In terms of clinical classification, the 2 MRA sequences were equivalent for 53 of the 54 treated aneurysms: 21 were considered fully occluded, whereas 16 were considered to have a residual neck and 16 were considered residually patent at follow-up MRA. The remaining aneurysm appeared fully occluded at TOF MRA but had a residual patent neck at CE-MRA. Visualization of residual aneurysm patency was significantly (P = .001) better with CE-MRA compared with TOF MRA for 10 (31.3%) of the 32 treated aneurysms considered residually patent with both sequences. Coil artifacts were present in 5 cases at TOF MRA but in none at CE-MRA. No relationship was apparent between the visualization of patency and either the size of the aneurysm or the interval between embolization and follow-up. CONCLUSION: At follow-up MRA at 3T, unenhanced TOF and CE-MRA sequences are similarly effective at classifying coiled aneurysms as occluded or residually patent. However, CE-MRA is superior to TOF MRA for visualization of residual patency and is associated with fewer artifacts.
Becoming Seen, Becoming Known: Lesbian Women's Self-Disclosures of Sexual Orientation to Mental Health Service Providers

Self-disclosure of sexual orientation has been reported to be important to quality health care interactions for lesbians. Existing research literature is limited in that it does not address self-disclosure of sexual orientation within psychiatric and mental health settings generally and self-disclosure strategies specifically. This article describes how lesbians respond to the imperative to make decisions about, and negotiate, self-disclosure of sexual orientation over a period of extensive interactions with mental health service providers by describing three strategies for self-disclosure: (a) unprompted, explicit self-disclosure; (b) prompted, explicit self-disclosure; and (c) subtle, tentative self-disclosure.
Characterization and regulation of an additional actin-filament-binding site in large isoforms of the stereocilia actin-bundling protein espin

The espin actin-bundling proteins, which are produced as isoforms of different sizes from a single gene, are required for the growth of hair cell stereocilia. We have characterized an additional actinfilament-binding site present in the extended amino-termini of large espin isoforms. Constitutively active in espin 2, the site increased the size of actin bundles formed in vitro and inhibited actin fluorescence recovery in microvilli. In espin 1, which has an Nterminal ankyrin repeat domain, the site was autoinhibited by binding between the ankyrin repeat domain and a peptide near the actin-binding site. Deletion of this peptide from espin 1 activated its actin-binding site. The peptide resembled tail homology domain I of myosin III, a ligand of the ankyrin repeat domain localized with espin 1 at the tip of stereocilia. A myosin III tail homology domain I peptide, but not scrambled control peptides, inhibited internal binding of the ankyrin repeat domain and released the espin 1 actin-binding site from autoinhibition. Thus, this regulation could result in local activation of the additional actin-binding site of espin 1 by myosin III in stereocilia.
21. Making the Most of Multiple-Choice Questions: Getting Beyond Remembering

Multiple-choice questions are widely used in higher education and have some important advantages over constructed-response test questions. It seems, however, that many teachers underestimate the value of multiple-choice questions, believing them to be useful only for assessing how well students can memorize information, but not for assessing higher-order cognitive skills. Several strategies are presented for generating multiple-choice questions that can effectively assess students’ ability to understand, apply, analyze, and evaluate information.
Twinkle: Interacting with physical surfaces using handheld projector

We propose a novel interface called Twinkle for interacting with an arbitrary physical surface using a handheld projector and a camera. When a user flashes a projection light on an object, the projected images react as if the user touched the object with the light. The handheld device recognizes the features of the physical environment and displays images and sounds that are generated in real-time according to the user's motion and collisions of projected images with objects. We realize this system by using several image-processing techniques and a collision detection algorithm. We also use an acceleration sensor to compensate for the image processing. In this paper, we explain the principle of interacting with a physical surface. Then, we describe the implementation of the prototype system and some application examples.
A foot in many camps: literacy teacher educators acquiring knowledge across many realms and juggling multiple identities

This study involved 28 literacy/English teachers in four countries: Canada, the USA, the UK and Australia. The goal of the study was to examine their backgrounds, knowledge, research activities, identity and support within the university. The teacher educators had a range of classroom teaching experience which they drew on in many ways. Most went far beyond simply telling stories about their previous work. All were heavily influenced by their own childhood experiences, which continue to affect their current work. Many felt that they needed to hold dual identities, teacher and academic, because they were still heavily involved in schools through their research and in-service activities. Several felt that there was a hierarchy in their department with those most removed from schooling at the highest tier. Most saw themselves in the field of literacy not teacher education and gravitate towards literacy-focused conferences and journals rather than those in teacher education.