Miracle-dz/UniFAR-FTUs huggingface dataset:
A PEST‐like element in FREQUENCY determines the length of the circadian period in Neurospora crassa

FREQUENCY (FRQ) is a crucial element of the circadian clock in Neurospora crassa. In the course of a circadian day FRQ is successively phosphorylated and degraded. Here we report that two PEST‐like elements in FRQ, PEST‐1 and PEST‐2, are phosphorylated in vitro by recombinant CK‐1a and CK‐1b, two newly identified Neurospora homologs of casein kinase 1ϵ. CK‐1a is localized in the cytosol and the nuclei of Neurospora and it is in a complex with FRQ in vivo. Deletion of PEST‐1 results in hypophosphorylation of FRQ and causes significantly increased protein stability. A strain harboring the mutant frqΔPEST‐1 gene shows no rhythmic conidiation. Despite the lack of overt rhythmicity, frqΔPEST‐1 RNA and FRQΔPEST‐1 protein are rhythmically expressed and oscillate in constant darkness with a circadian period of 28 h. Thus, by deletion of PEST‐1 the circadian period is lengthened and overt rhythmicity is dissociated from molecular oscillations of clock components.
Blind equalization of square-QAM signals: a multimodulus approach

By generalizing and modifying some existing cost-functions, we present two new, generic and efficient multimodulus families of blind equalization algorithms for use in higher-order quadrature amplitude modulation based digital communication systems. Proposed algorithms are shown to be capable of blindly equalizing and recovering carrier-phase at convergence speed much faster than existing counterparts on certain QAM sizes. We show that particular examples of the proposed cost-functions include a number of existing algorithms. We also provide detailed dynamic convergence analysis which is found in good conformation with those obtained from Monte-Carlo experiments.
Speeded production of inflected words in children and adults

This study examines the production of regular and irregular participle forms of German with high and low frequencies using a speeded production task. 40 children in two age groups (five- to seven-year olds, eleven- to twelve-year olds) and 35 adult native speakers of German listened to stem forms of verbs presented in a sentential context and were asked to produce corresponding participle forms as quickly and accurately as possible. Dependent variables were the subjects' participle-production latencies and error rates. We found contrasts between the production of regular and irregular forms in both children and adults, with respect to the production latencies and types of morphological error. Children overapplied the regular patterns to forms that are irregular in the adult language, but not vice versa. High-frequency irregular participles were produced faster (and amongst the children more accurately) than low-frequency ones, whereas regular participles yielded a reverse frequency effect, i.e. longer production latencies for high-frequency forms than for low-frequency ones, in the two groups of children as well as in one subgroup of adults. We explain these findings from the perspective of dual-mechanism models of inflection arguing that the mental mechanisms and representations for processing morphologically complex words (‘words’ and ‘rules’) are the same in children and adults, and that the observed child/adult differences in participle production are due to slower and less accurate lexical access in children than in adults.
Hemodialysis versus Peritoneal Dialysis: A Comparison of Survival Outcomes in South-East Asian Patients with End-Stage Renal Disease

Background Studies comparing patient survival of hemodialysis (HD) and peritoneal dialysis (PD) have yielded conflicting results and no such study was from South-East Asia. This study aimed to compare the survival outcomes of patients with end-stage renal disease (ESRD) who started dialysis with HD and PD in Singapore. Methods Survival data for a maximum of 5 years from a single-center cohort of 871 ESRD patients starting dialysis with HD (n = 641) or PD (n = 230) from 2005–2010 was analyzed using the flexible Royston-Parmar (RP) model. The model was also applied to a subsample of 225 propensity-score-matched patient pairs and subgroups defined by age, diabetes mellitus, and cardiovascular disease. Results After adjusting for the effect of socio-demographic and clinical characteristics, the risk of death was higher in patients initiating dialysis with PD than those initiating dialysis with HD (hazard ratio [HR]: 2.08; 95% confidence interval [CI]: 1.67–2.59; p<0.001), although there was no significant difference in mortality between the two modalities in the first 12 months of treatment. Consistently, in the matched subsample, patients starting PD had a higher risk of death than those starting HD (HR: 1.73, 95% CI: 1.30–2.28, p<0.001). Subgroup analysis showed that PD may be similar to or better than HD in survival outcomes among young patients (≤65 years old) without diabetes or cardiovascular disease. Conclusion ESRD patients who initiated dialysis with HD experienced better survival outcomes than those who initiated dialysis with PD in Singapore, although survival outcomes may not differ between the two dialysis modalities in young and healthier patients. These findings are potentially confounded by selection bias, as patients were not randomized to the two dialysis modalities in this cohort study.
Frames: a corpus for adding memory to goal-oriented dialogue systems

This paper proposes a new dataset, Frames, composed of 1369 human-human dialogues with an average of 15 turns per dialogue. This corpus contains goal-oriented dialogues between users who are given some constraints to book a trip and assistants who search a database to find appropriate trips. The users exhibit complex decision-making behaviour which involve comparing trips, exploring different options, and selecting among the trips that were discussed during the dialogue. To drive research on dialogue systems towards handling such behaviour, we have annotated and released the dataset and we propose in this paper a task called frame tracking. This task consists of keeping track of different semantic frames throughout each dialogue. We propose a rule-based baseline and analyse the frame tracking task through this baseline.
Further development of a neurobehavioral profile of fetal alcohol spectrum disorders.

BACKGROUND Heavy prenatal alcohol exposure (AE) results in a broad array of neurobehavioral deficits. Recent research has focused on identification of a neurobehavioral profile or profiles that will improve the identification of children affected by AE. This study aimed to build on our preliminary neurobehavioral profile to improve classification accuracy and test the specificity of the resulting profile in an alternate clinical group. METHODS A standardized neuropsychological test battery was administered to 3 groups of children: subjects with AE (n = 209), typically developing controls (CON, n = 185), and subjects with attention-deficit/hyperactivity disorder (ADHD, n = 74). We assessed a large sample from 6 sites in the United States and South Africa, using standardized methodology. Data were analyzed using 3 latent profile analyses including (i) subjects with fetal alcohol syndrome (FAS) and controls, (ii) subjects with AE without FAS and controls, and (iii) subjects with AE (with or without FAS) and subjects with ADHD. RESULTS Classification accuracy was moderate but significant across the 3 analyses. In analysis 1, overall classification accuracy was 76.1% (77.2% FAS, 75.7% CON). In the second analysis, overall classification accuracy was 71.5% (70.1% AE/non-FAS, 72.4% CON). In the third analysis, overall classification accuracy was 73.9% (59.8% AE, 75.7% ADHD). Subjects that were misclassified were examined for systematic differences from those that were correctly classified. CONCLUSIONS The results of this study indicate that the neuropsychological effects of AE are clinically meaningful and can be used to accurately distinguish alcohol-affected children from both typically developing children and children with ADHD. Further, in combination with other recent studies, these data suggest that approximately 70% of children with heavy prenatal alcohol exposure are neurobehaviorally affected, while the remaining 30% are spared these often-devastating consequences, at least those in the domains under study. Refining the neurobehavioral profile will allow improved identification and treatment development for children affected by prenatal alcohol exposure.
Text Classification with Heterogeneous Information Network Kernels

Text classification is an important problem with many applications. Traditional approaches represent text as a bag-of-words and build classifiers based on this representation. Rather than words, entity phrases, the relations between the entities, as well as the types of the entities and relations carry much more information to represent the texts. This paper presents a novel text as network classification framework, which introduces 1) a structured and typed heterogeneous information networks (HINs) representation of texts, and 2) a meta-path based approach to link texts. We show that with the new representation and links of texts, the structured and typed information of entities and relations can be incorporated into kernels. Particularly, we develop both simple linear kernel and indefinite kernel based on meta-paths in the HIN representation of texts, where we call them HIN-kernels. Using Freebase, a well-known world knowledge base, to construct HIN for texts, our experiments on two benchmark datasets show that the indefinite HIN kernel based on weighted meta-paths outperforms the state-of-the-art methods and other HIN-kernels.
Integrating molecular, phenotypic and environmental data to elucidate patterns of crocodile hybridization in Belize

The genus Crocodylus comprises 12 currently recognized species, many of which can be difficult to differentiate phenotypically. Interspecific hybridization among crocodiles is known to occur in captivity and has been documented between some species in the wild. The identification of hybrid individuals is of importance for management and monitoring of crocodilians, many of which are Convention on International Trade in Endangered Species (CITES) listed. In this study, both mitochondrial and nuclear DNA markers were evaluated for their use in confirming a suspected hybrid zone between American crocodile (Crocodylus acutus) and Morelet’s crocodile (Crocodylus moreletii) populations in southern Belize where individuals and nests exhibiting atypical phenotypic features had previously been observed. Patterns observed in both phenotypic and molecular data indicate possible behavioural and ecological characteristics associated with hybridization events. The results of the combined analyses found that the majority of suspected hybrid samples represent crosses between female C. acutus and male C. moreletii. Phenotypic data could statistically identify hybrids, although morphological overlap between hybrids and C. moreletii reduced reliability of identification based solely on field characters. Ecologically, C. acutus was exclusively found in saline waters, whereas hybrids and C. moreletii were largely absent in these conditions. A hypothesized correlation between unidirectional hybridization and destruction of C. acutus breeding habitats warrants additional research.
DNA polymerases ζ and Rev1 mediate error-prone bypass of non-B DNA structures

DNA polymerase ζ (Pol ζ) and Rev1 are key players in translesion DNA synthesis. The error-prone Pol ζ can also participate in replication of undamaged DNA when the normal replisome is impaired. Here we define the nature of the replication disturbances that trigger the recruitment of error-prone polymerases in the absence of DNA damage and describe the specific roles of Rev1 and Pol ζ in handling these disturbances. We show that Pol ζ/Rev1-dependent mutations occur at sites of replication stalling at short repeated sequences capable of forming hairpin structures. The Rev1 deoxycytidyl transferase can take over the stalled replicative polymerase and incorporate an additional ‘C’ at the hairpin base. Full hairpin bypass often involves template-switching DNA synthesis, subsequent realignment generating multiply mismatched primer termini and extension of these termini by Pol ζ. The postreplicative pathway dependent on polyubiquitylation of proliferating cell nuclear antigen provides a backup mechanism for accurate bypass of these sequences that is primarily used when the Pol ζ/Rev1-dependent pathway is inactive. The results emphasize the pivotal role of noncanonical DNA structures in mutagenesis and reveal the long-sought-after mechanism of complex mutations that represent a unique signature of Pol ζ.
Modelling nanowires : crystals encapsulated in carbon nanotubes

Nanotube-encapsulated ionic materials can be usefully modelled using ab initio methods to inform and validate experiment. This thesis models these materials using density functional theory, explores the specific challenges these materials pose, and presents results only visible once these challenges are addressed. Chemical potentials and ab initio calculations are used to predict tube radii at which filling occurs for a range of filling conditions, which informs our choice of tube. The practice of fitting both ionic core and encapsulating tube into the same unit cell causes artificial strain. A method of quantifying this mismatch is developed and the associated strain energy and distortions predicted. Current methods of approximating the nanotube treat it as a smooth cylinder. We find significant texture which can resist core movement, allow metastable twisted states, and be used to determine which supercells have physically realistic mismatch strain. Cores have previously been relaxed in vacuo with limited justification. We find that, in general, cores are not stable without constraints. We guide three bare silver iodide ansatze to metastable saddle-points by applying artificial symmetry constraints during in vacuo relaxation. An investigation into their unconstrained unstable phonon modes reveals them to be stabilised by an encapsulating tube. Two classes of stabilisation are identified, one due to radial encapsulation and a second due to mismatch-like effects. Charge of a few tenths of e per core ion is seen to transfer from core to tube, with magnitude depending on tube radius. In order to approximate the charge field by atomic charges, four population analysis schemes are investigated. The Bader and Density Derived Electrostatic and Chemical (DDEC) population analyses agree to physically sensible values while using different approaches. A machine-learned model is trained using local chemical-environment descriptors to transferrably predict atomic charges to within 0:004 e of DDEC values with an orders-of-magnitude speedup.
A novel electrochemical comparative sensing interface of MgO nanoparticles synthesized by different methods

Recent advancements in nanotechnology, for the biosynthesis of metal nanoparticles through enormous techniques, showed multidimensional developments. One among many facets of nanotechnology is to procure and adopt new advancements for green technology over chemical reduction synthesis. This adaptation for acquiring green nanotechnology leads us to a new dimension of nanobiotechnology. In order to imply one such efforts, in this study the emphasis is being laid on the synthesis of MgO nanoparticles using green technology and eliminating chemical reduction methods. Different characterization techniques such as UV–Vis spectroscopy, transmission electron microscopy, and dynamic light scattering were used to carry out the experiments. The average size of MgO nanoparticles were obtained in the range of 85–95 nm, when synthesized by various sources. The extracts of plants were capable of producing MgO nanoparticles efficiently and exhibited good results during cyclic voltammetry and electrochemical impedance spectroscopy study. The electrode modified with MgO nanoparticles (plant extract) showed good stability (90 days) and high conductivity. This study reports cost-effective and environment-friendly method for synthesis of MgO nanoparticles using plant extracts. The process is rapid, simple, and convenient and can be used as an alternative to chemical method.
Traditional food attributes must be included in studies of food security in the Canadian Arctic

Objectives. The objective was to explore some typically understudied characteristics of food security in Arctic Canada: observed changes to traditional food systems, perceived advantages and health benefits of traditional food and traditional food preferences. Study Design. Data analysis used a cross-sectional survey of Yukon First Nations, Dene/Metis and Inuit women in 44 Arctic communities. Methods. Open-ended responses to 4 questions were used to qualitatively investigate roles traditional foods play in Arctic food security. Chi-square tests were applied to responses to ascertain differences by age and region. A fifth question explored agreement with cultural responses to harvesting and using traditional food. Results. Traditional food was regarded as natural and fresh, tasty, healthy and nutritious, inexpensive, and socially and culturally beneficial. Between 10% and 38% of participants noticed recent changes in the quality or health of traditional food species, with physical changes and decreasing availability being reported most often. Caribou, moose and seal were among the foods considered particularly healthy and held special values in these populations. The opinion that all traditional food was healthy was also popular. More than 85%, of participants agreed with most cultural attributes of traditional food. Conclusions. This study confirms that traditional food remains important to Arctic indigenous women and that food security in the Arctic is contingent upon access to these foods.
Induction and mode of action of suppressor cells generated against human gamma globulin. I. An immunologic unresponsive state devoid of demonstrable suppressor cells

A model of unresponsiveness to human gamma-globulin (HGG) which is maintained in the absence of demonstrable suppressor cells has been described. A/J mice were tolerized with deaggregated HGG purified from a variety of sources. The spleen cells from these tolerized mice were assessed for their ability to suppress the response of normal spleen cells to HGG when transferred into lethally irradiated mice. All of the HGG preparations obtained from commercial sources as Cohn fraction II of pooled, outdated plasma induced suppressor cells to HGG, although not of equal magnitude. However, suppressor cells could not be demonstrated in the spleens of mice tolerized with deaggregated HGG purified from the plasma of a healthy individual. This inability to detect suppression was independent of the method of purification of the HGG and of the time of assessment of the putative suppressor cells after tolerization. Similarly, deaggregated HGG isolated from an IgG1 lambda-myeloma protein induced unresponsiveness to HGG but did not stimulate demonstrable suppressor cells. These data suggest that suppressor T cells are not involved in the maintenance of tolerance to this antigen, although they may play a regulatory role in the immune response to HGG. Support for this concept was obtained by assessing the duration of unresponsiveness in the T and B lymphocytes of mice tolerized with the various HGG preparations. Mice tolerized with the HGG preparations that stimulated little or no suppression were among the last to recover responsiveness. Indeed, there was no consistent correlation between the level of suppressor cell activity and the degree of unresponsiveness in either the splenic T or B lymphocytes. Thus, although certain HGG preparations may provide a tool for the generation of antigen-specific suppressor T cells, the utilization of these suppressive preparations may be inappropriate for the investigation of the mechanisms of the induction and maintenance of the unresponsive state.
Improving search-based test suite generation with dynamic symbolic execution

Search-based testing can automatically generate unit test suites for object oriented code, but may struggle to generate specific values necessary to cover difficult parts of the code. Dynamic symbolic execution (DSE) efficiently generates such specific values, but may struggle with complex datatypes, in particular those that require sequences of calls for construction. The solution to these problems lies in a hybrid approach that integrates the best of both worlds, but such an integration needs to adapt to the problem at hand to avoid that higher coverage in a few corner cases comes at the price of lower coverage in the general case. We have extended the Genetic Algorithm (GA) in the Evosuite unit test generator to integrate DSE in an adaptive approach where feedback from the search determines when a problem is suitable for DSE. In experiments on a set of difficult classes our adaptive hybrid approach achieved an increase in code coverage of up to 63% (11% on average); experiments on the SF100 corpus of roughly 9,000 open source classes confirm that the improvement is of practical value, and a comparison with a DSE tool on the Roops set of benchmark classes shows that the hybrid approach improves over both its constituent techniques, GA and DSE.
Pointshop 3D: an interactive system for point-based surface editing

We present a system for interactive shape and appearance editing of 3D point-sampled geometry. By generalizing conventional 2D pixel editors, our system supports a great variety of different interaction techniques to alter shape and appearance of 3D point models, including cleaning, texturing, sculpting, carving, filtering, and resampling. One key ingredient of our framework is a novel concept for interactive point cloud parameterization allowing for distortion minimal and aliasing-free texture mapping. A second one is a dynamic, adaptive resampling method which builds upon a continuous reconstruction of the model surface and its attributes. These techniques allow us to transfer the full functionality of 2D image editing operations to the irregular 3D point setting. Our system reads, processes, and writes point-sampled models without intermediate tesselation. It is intended to complement existing low cost 3D scanners and point rendering pipelines for efficient 3D content creation.