Miracle-dz/UniFAR-FTUs huggingface dataset:
Automated offline design of algorithms

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Predicting program behavior using real or estimated profiles

A brush bristle cleaning system (10) which includes a handle member (16) adapted to be held in one hand of a user. The handle member (16) passes in a longitudinal direction (18). A first wire element (20) extends in an arcuate closed contour and is secured to the first handle member (16) on one end thereof. A first helical wire element (24) defining a plurality of first helical loops (26) pass around a portion of the closed contour of the first wire element (20). A second wire element (30) which extends in the longitudinal direction (18) is secured to the handle member (16) on a first end and is secured to the first wire element (20) on a second end thereof. A second helical wire element (36) passes around the second wire element (30) and defines a plurality of second helical loops (38). A brush (12) having brush bristles (14) is either longitudinally moved or transversely contacted with the helical loops of (38) and (26) to provide a cleansing action for the bristles of (14). A receptacle (44) is provided wherein the first wire elements (20) and second wire elements (30) may be releasably mounted for capturing a material being displaced from the brush bristles (14).
Security for smart mobile networks: The NEMESYS approach

The growing popularity of smart mobile devices such as smartphones and tablets has made them an attractive target for cyber-criminals, resulting in a rapidly growing and evolving mobile threat as attackers experiment with new business models by targeting mobile users. With the emergence of the first large-scale mobile botnets, the core network has also become vulnerable to distributed denial-of-service attacks such as the signaling attack. Furthermore, complementary access methods such as Wi-Fi and femtocells introduce additional vulnerabilities for the mobile users as well as the core network. In this paper, we present the NEMESYS approach to smart mobile network security, to develop novel security technologies for seamless service provisioning in the smart mobile ecosystem, and to improve mobile network security through a better understanding of the threat landscape.
Same talker, different language

When discriminating between unknown foreign languages, infants, young children, and adult listeners are able to make same-language/different-language discrimination judgments at better than chance levels. In these studies (Lorch & Meara, 1989; Mehler et al., 1988; Stockmal, 1995), foreign language samples have often been provided by different talkers, confounding voice characteristics and language characteristics. In Experiments 1 and 2, using the same talkers for different pairs of languages, we found that listeners were able to discriminate between languages they did not know, even when spoken by the same talker. That is, listeners were able to separate talker from language characteristics. Experiment 3 used multidimensional scaling to explore the bases of listener judgments. Listeners were attentive to prosodic properties and influenced by their familiarity with the test languages.
TRRUST v2: an expanded reference database of human and mouse transcriptional regulatory interactions

Abstract Transcription factors (TFs) are major trans-acting factors in transcriptional regulation. Therefore, elucidating TF–target interactions is a key step toward understanding the regulatory circuitry underlying complex traits such as human diseases. We previously published a reference TF–target interaction database for humans—TRRUST (Transcriptional Regulatory Relationships Unraveled by Sentence-based Text mining)—which was constructed using sentence-based text mining, followed by manual curation. Here, we present TRRUST v2 (www.grnpedia.org/trrust) with a significant improvement from the previous version, including a significantly increased size of the database consisting of 8444 regulatory interactions for 800 TFs in humans. More importantly, TRRUST v2 also contains a database for TF–target interactions in mice, including 6552 TF–target interactions for 828 mouse TFs. TRRUST v2 is also substantially more comprehensive and less biased than other TF–target interaction databases. We also improved the web interface, which now enables prioritization of key TFs for a physiological condition depicted by a set of user-input transcriptional responsive genes. With the significant expansion in the database size and inclusion of the new web tool for TF prioritization, we believe that TRRUST v2 will be a versatile database for the study of the transcriptional regulation involved in human diseases.
Enhanced Frequency Response Strategy for a PMSG-Based Wind Energy Conversion System Using Ultracapacitor in Remote Area Power Supply Systems

Conventional generators in wind–diesel hybrid remote-area power supply (RAPS) systems are likely to be heavily stressed during frequency disturbances due to poor frequency response of power electronic interfaced wind energy conversion systems (WECSs). Hence, it is imperative for the WECS to provide frequency support during frequency excursions. However, existing frequency control strategies are slow and will also impose severe mechanical/electromagnetic stress on WECSs. In this paper, frequency response strategies for the PMSG-based WECS are explored, and an enhanced frequency response strategy is investigated to regulate the RAPS system frequency jointly with the integrated ultracapacitors. The proposed short-term frequency response strategy utilizes a virtual inertial technique along with the supplementary droop control. Suboptimal power-point-tracking is also implemented at the PMSG to improve the active power reserve. The enhanced frequency response strategy can regulate the RAPS system frequency while alleviating high rate-of-change-of-power, and thus stresses on both the conventional generator and PMSG under frequency disturbances. Proposed control strategies are validated by both simulations and experiments.
Whole-genome analyses resolve early branches in the tree of life of modern birds

To better determine the history of modern birds, we performed a genome-scale phylogenetic analysis of 48 species representing all orders of Neoaves using phylogenomic methods created to handle genome-scale data. We recovered a highly resolved tree that confirms previously controversial sister or close relationships. We identified the first divergence in Neoaves, two groups we named Passerea and Columbea, representing independent lineages of diverse and convergently evolved land and water bird species. Among Passerea, we infer the common ancestor of core landbirds to have been an apex predator and confirm independent gains of vocal learning. Among Columbea, we identify pigeons and flamingoes as belonging to sister clades. Even with whole genomes, some of the earliest branches in Neoaves proved challenging to resolve, which was best explained by massive protein-coding sequence convergence and high levels of incomplete lineage sorting that occurred during a rapid radiation after the Cretaceous-Paleogene mass extinction event about 66 million years ago.
The lysine-rich motif of intrinsically disordered stress protein CDeT11-24 from Craterostigma plantagineum is responsible for phosphatidic acid binding and protection of enzymes from damaging effects caused by desiccation

The late embryogenesis abundant (LEA)-like protein CDeT11-24 is one of the major desiccation-related phosphoproteins of the resurrection plant Craterostigma plantagineum. In this study, it was shown that CDeT11-24 is mostly intrinsically disordered and protects two different enzymes, citrate synthase and lactate dehydrogenase, against damaging effects caused by desiccation. Lipid-binding assays revealed that CDeT11-24 is able to interact with phosphatidic acid, although electrostatic repulsion was expected due to the overall negative net charge of the protein under the tested physiological conditions. CDeT11-24 carries an N-terminal lysine-rich sequence, which is predicted to form an amphipathic α-helix. Analysis of the truncated CDeT11-24 protein identified this region to be responsible for both activities: enzyme protection and phosphatidic acid interaction. Possible functions of the CDeT11-24 protein are discussed in the context of desiccation tolerance. Abbreviations:ABA abscisic acid;CD circular dichroism;CS citrate synthase;IDP intrinsically disordered protein;LDH lactate dehydrogenase;LEA late embryogenesis abundant;PA phosphatidic acid;PC phosphatidylcholine;TFE trifluoroethanol.
The NIHR public health research programme: intervention approaches to tackle health inequalities

Background The National Institute for Health Research (NIHR) Public Health Research (PHR) Programme evaluates interventions intended to improve the health of the public and reduce inequalities in health in the UK. The aim of the research was to establish how projects funded by the PHR Programme between 2009 and 2014 addressed health inequalities. Methods A health inequalities intervention framework developed by Bambra et al. was used to map PHR funded studies to a typology. The framework is based on interventions that are characterized by their level of action and their approach to tackling inequalities. Results A total of 57 primary research projects funded by the PHR Programme were categorized using the framework; 16 PHR research projects were classified as strengthening individuals, 24 strengthening communities, 15 improving living and school/work conditions and 2 promoting healthy macro policies. Eighteen were classified as targeted interventions whereas 39 were universal. Conclusions Mapping the interventions being evaluated by the PHR Programme to a typology differentiated health inequality interventions and illustrates how they are expected to have an impact. Emerging findings will contribute to the evidence base for addressing health inequalities to inform research and future commissioning of public health services.
Maternal Separation Impairs Cocaine-Induced Behavioural Sensitization in Adolescent Mice

Adverse early-life conditions induce persistent disturbances that give rise to negative emotional states. Therefore, early life stress confers increased vulnerability to substance use disorders, mainly during adolescence as the brain is still developing. In this study, we investigated the consequences of maternal separation, a model of maternal neglect, on the psychotropic effects of cocaine and the neuroplasticity of the dopaminergic system. Our results show that mice exposed to maternal separation displayed attenuated behavioural sensitization, while no changes were found in the rewarding effects of cocaine in the conditioned place preference paradigm and in the reinforcing effects of cocaine in the self-administration paradigm. The evaluation of neuroplasticity in the striatal dopaminergic pathways revealed that mice exposed to maternal separation exhibited decreased protein expression levels of D2 receptors and increased levels of the transcriptional factor Nurr1. Furthermore, animals exposed to maternal separation and treated with cocaine exhibited increased DA turnover and protein expression levels of DAT and D2R, while decreased Nurr1 and Pitx3 protein expression levels were observed when compared with saline-treated mice. Taken together, our data demonstrate that maternal separation caused an impairment of cocaine-induced behavioural sensitization possibly due to a dysfunction of the dopaminergic system, a dysfunction that has been proposed as a factor of vulnerability for developing substance use disorders.
Oseltamivir- and Amantadine-Resistant Influenza Viruses A (H1N1)

Surveillance of amantadine and oseltamivir resistance among influenza viruses was begun in Hong Kong in 2006. In 2008, while both A/Brisbane/59/2007-like and A/Hong Kong/2652/2006-like viruses (H1N1) were cocirculating, we detected amantadine and oseltamivir resistance among A/Hong Kong/2652/2006-like viruses (H1N1), caused by genetic reassortment or spontaneous mutation.
Efficient Inference of Haplotypes from Genotypes on a Pedigree

We study haplotype reconstruction under the Mendelian law of inheritance and the minimum recombination principle on pedigree data. We prove that the problem of finding a minimum-recombinant haplotype configuration (MRHC) is in general NP-hard. This is the first complexity result concerning the problem to our knowledge. An iterative algorithm based on blocks of consecutive resolved marker loci (called block-extension) is proposed. It is very efficient and can be used for large pedigrees with a large number of markers, especially for those data sets requiring few recombinants (or recombination events). A polynomial-time exact algorithm for haplotype reconstruction without recombinants is also presented. This algorithm first identifies all the necessary constraints based on the Mendelian law and the zero recombinant assumption, and represents them using a system of linear equations over the cyclic group Z2. By using a simple method based on Gaussian elimination, we could obtain all possible feasible haplotype configurations. A C++ implementation of the block-extension algorithm, called PedPhase, has been tested on both simulated data and real data. The results show that the program performs very well on both types of data and will be useful for large scale haplotype inference projects.
Comparative Analysis of Secretomes from Ectomycorrhizal Fungi with an Emphasis on Small-Secreted Proteins

Fungi are major players in the carbon cycle in forest ecosystems due to the wide range of interactions they have with plants either through soil degradation processes by litter decayers or biotrophic interactions with pathogenic and ectomycorrhizal symbionts. Secretion of fungal proteins mediates these interactions by allowing the fungus to interact with its environment and/or host. Ectomycorrhizal (ECM) symbiosis independently appeared several times throughout evolution and involves approximately 80% of trees. Despite extensive physiological studies on ECM symbionts, little is known about the composition and specificities of their secretomes. In this study, we used a bioinformatics pipeline to predict and analyze the secretomes of 49 fungal species, including 11 ECM fungi, wood and soil decayers and pathogenic fungi to tackle the following questions: (1) Are there differences between the secretomes of saprophytic and ECM fungi? (2) Are small-secreted proteins (SSPs) more abundant in biotrophic fungi than in saprophytic fungi? and (3) Are there SSPs shared between ECM, saprotrophic and pathogenic fungi? We showed that the number of predicted secreted proteins is similar in the surveyed species, independently of their lifestyle. The secretome from ECM fungi is characterized by a restricted number of secreted CAZymes, but their repertoires of secreted proteases and lipases are similar to those of saprotrophic fungi. Focusing on SSPs, we showed that the secretome of ECM fungi is enriched in SSPs compared with other species. Most of the SSPs are coded by orphan genes with no known PFAM domain or similarities to known sequences in databases. Finally, based on the clustering analysis, we identified shared- and lifestyle-specific SSPs between saprotrophic and ECM fungi. The presence of SSPs is not limited to fungi interacting with living plants as the genome of saprotrophic fungi also code for numerous SSPs. ECM fungi shared lifestyle-specific SSPs likely involved in symbiosis that are good candidates for further functional analyses.
Medicaid Savings From The New York University Caregiver Intervention for Families with Dementia

Purpose of the study The economic burden of dementia is substantially borne by state Medicaid programs. We estimated savings, from the state payer perspective, from offering the New York University Caregiver Intervention (NYUCI), a well-studied caregiver support and counseling program, to eligible Minnesota Medicaid enrollees. Design and Methods A population-based microsimulation Markov model predicted and compared costs over 15 years with and without implementation of the NYUCI for family caregivers of community-based Medicaid eligibles with dementia. The model was informed by primary analysis of Minnesota Department of Human Services (MN DHS) data, and literature on the epidemiology, natural history, costs, and evidence-based management of the disease. Primary outcomes were predicted cumulative total direct costs, including medical, facility, and waiver-program payments for eligibles, and estimated costs of providing the NYUCI. Results Approximately 5-6% more eligibles with dementia would remain in the community annually from year 3 (2014) on, so that over 15 years 17% fewer would die in nursing homes (NH) if their caregivers received the NYUCI. After 15 years, MN DHS could realize savings of $40.4 million (2011 dollars, discounted at 3%) if all eligibles/caregivers enrolled. Savings were expected 5 years after implementation. Multiple sensitivity analyses, including best-and worst-case scenarios, estimated results ranging from 15-year cumulative savings of $178.9 million to a cumulative loss of $7.3 million, respectively, driven largely by assumed program effectiveness. Implications State payers can use enhanced caregiver support to moderate the growing tax burden of dementia, even without a breakthrough in the pharmacologic treatment of the disease.
The burden of proof for a cultural group selection account

Abstract Richerson et al. establish cultural group selection as a plausible force in human social evolution. However, they do not demonstrate its causal precedence for any trait, let alone its “essentialness. ” To do so, they must show that a particular group trait was caused by cultural transmission, and directly caused differences in group fitness.
Preventing Central Line-Associated Bloodstream Infections

TODAY, INFECTIONS CONTRACTED in the hospital and other health care settings represent one of the greatest risks to the health and well-being of patients. Health care– associated infections (HAIs) occur throughout the world, affecting hundreds of millions of patients each year.1 The Centers for Disease Control and Prevention estimates that 5% to 10% of hospitalized patients develop an HAI.2 There were an estimated 1.7 million infections and 99 000 associated deaths in hospitals in 2002.3 Another estimated 1.6 million to 3.8 million infections occur in long-term care facilities each year.4 Recent evidence that HAIs are largely preventable has created new opportunities to implement relatively simple practices to reduce or even eliminate the burden associated with such infections. Central line–associated bloodstream infections (CLABSIs) are one such type of infection that appear to be largely
PlasFlow: predicting plasmid sequences in metagenomic data using genome signatures

Abstract Plasmids are mobile genetics elements that play an important role in the environmental adaptation of microorganisms. Although plasmids are usually analyzed in cultured microorganisms, there is a need for methods that allow for the analysis of pools of plasmids (plasmidomes) in environmental samples. To that end, several molecular biology and bioinformatics methods have been developed; however, they are limited to environments with low diversity and cannot recover large plasmids. Here, we present PlasFlow, a novel tool based on genomic signatures that employs a neural network approach for identification of bacterial plasmid sequences in environmental samples. PlasFlow can recover plasmid sequences from assembled metagenomes without any prior knowledge of the taxonomical or functional composition of samples with an accuracy up to 96%. It can also recover sequences of both circular and linear plasmids and can perform initial taxonomical classification of sequences. Compared to other currently available tools, PlasFlow demonstrated significantly better performance on test datasets. Analysis of two samples from heavy metal-contaminated microbial mats revealed that plasmids may constitute an important fraction of their metagenomes and carry genes involved in heavy-metal homeostasis, proving the pivotal role of plasmids in microorganism adaptation to environmental conditions.
SOI : Materials to Systems

There is increased interest in the steam oxidation of AlxGat-xAs, following the pioneering work done at University of Illinoisl. We report the first demonstration of p-HEMTs in GaAs On Insulator (GOI) technology using Alz03 formed by the steam oxidation of AlAs as the buffer insulator. p-HEMT is one of the most widely used device in high speed applicatilons,including wireless communications. The GOI p-HEMT promises to be a high output resistance, high efficiency, high linearity device, attractive for high frequency communication applications.
On the specialization of online program specializers

Abstract A common technique for improving the speed of program specialization is to specialize the program specializer itself on the program to be specialized, creating a custom program generator. Much research has been devoted to the problem of generating efficient program generators, which do not perform reductions at program generation time which could instead have been performed when the program generator was constructed. The conventional wisdom holds that only program specializers using binding-time approximations can be specialized into such efficient program generators. This paper argues that this is not the case, and demonstrates that the specialization of a nontrivial online program specializer similar to the original ‘naive MIX’ can indeed yield an efficient program generator. The key to our argument is that, while the use of binding-time information at program generator generation time is necessary for the construction of an efficient custom specializer, the use of explicit binding-time approximation techniques is not. This allows us to distinguish the problem at hand (i.e. the use of binding-time information during program generator generation) from particular solutions to that problem (i.e. offline specialization). We show that, given a careful choice of specializer data structures, and sufficiently powerful specialization techniques, binding-time information can be inferred and utilized without explicit approximations. This allows the construction of efficient, optimizing program generators from online program specializers.
Cooperative converters in power electronic systems

The specifications of power electronic systems are becoming ever more exigent - better performance (dynamic and steady state), increased efficiency, reliability, and quality, and decreased power rating, size (volume and weight), and cost. One strategy for the overall improvement of these systems is to use various cooperating converters with the system functions being shared among them, optimizing each converter for the functions assigned it. The result will be a converter with better characteristics than a conventional design based on a single converter (or on a simple parallel association of converters) responsible for all the functions assigned to the system. This paper analyzes the possibilities of such cooperative converters, considering the filtering inductor size, and the efficiency, reliability, and power rating.