Miracle-dz/UniFAR-FTUs huggingface dataset:
Goal-directed imitation through repeated trial-and-error interactions between agents

Imitation or learning by demonstration is one of the holy grails in robotics. Wouldn’t it be great to show a service robot how to do the laundry or to show an edutainment robot how to clear up the kids’ toys at the end of the day? However, the community is still at a stage where we can only dream from such applications. Most if not all researchers have been concentrating on sub problems of imitation, such as imitation using logic programming (Kuniyoshi et al. 1994), imitation between agents with different embodiments (Alissandrakis et al. 2004) or the metrics for deciding what to imitate (Billard, this volume); the work presented in this paper is not any different. In the last years insights from cognitive science and developmental psychology have provided new impetus in artificial imitation research (see among others Dautenhahn and Nehaniv (2002)). It is this work that inspired us to build a new model for agents to imitate the intention of observed behaviour. In previous work we have demonstrated how a group of agents can agree on imitating gestures (a class of imitation which Byrne and Russon (1998) have dubbed action-level imitation) and how we avoided to need for an explicit measure of imitation quality. This was done by letting the initiator judge if the imitator’s behaviour corresponded to the demonstrated action (Jansen 2003; Jansen et al. 2004; Belpaeme et al. 2005). In this paper we wish to present some of our ongoing research in goal-level imitation, where agents learn to imitate the goal of an action. This is a natural continuation of action-level imitation, and has been recognised as a notoriously difficult problem as the imitator needs to solve two difficult problems. First, it needs to understand the goal of the observed behaviour, something which is immediately obvious to us, but is hard to grasp if you not do have the necessary world knowledge to deduce the goal. If you see someone sweeping the patio with a broom, is the goal then the sweeping motion itself? Or the swishing noise made by the broom? Or the fact that the
Genetic basis of the association of resistance genes mef(I) (macrolides) and catQ (chloramphenicol) in streptococci

In streptococci mef(I) and catQ, two relatively uncommon macrolide and chloramphenicol resistance genes, respectively, are typically linked in a genetic module designated IQ module. Though variable, the module consistently encompasses, and is sometimes reduced to, a conserved ∼5.8-kb mef(I)-catQ fragment. The prototype IQ module was described in Streptococcus pneumoniae. IQ-like modules have subsequently been detected in Streptococcus pyogenes and in different species of viridans group streptococci, where mef(E) may be found instead of mef(I). Three genetic elements, one carrying the prototype IQ module from S. pneumoniae and two carrying different, defective IQ modules from S. pyogenes, have recently been characterized. All are integrative and conjugative elements (ICEs) belonging to the Tn5253 family, and have been designated ICESpn529IQ, ICESpy029IQ and ICESpy005IQ, respectively. ICESpy029IQ and ICESpy005IQ were the first Tn5253 family ICEs to be described in S. pyogenes. A wealth of new information has been obtained by comparing their genetic organization, chromosomal integration, and transferability. The origin of the IQ module is unknown. The mechanism by which it spreads in streptococci is discussed.
Privacy preserving protocol for detecting genetic relatives using rare variants

Motivation: High-throughput sequencing technologies have impacted many areas of genetic research. One such area is the identification of relatives from genetic data. The standard approach for the identification of genetic relatives collects the genomic data of all individuals and stores it in a database. Then, each pair of individuals is compared to detect the set of genetic relatives, and the matched individuals are informed. The main drawback of this approach is the requirement of sharing your genetic data with a trusted third party to perform the relatedness test. Results: In this work, we propose a secure protocol to detect the genetic relatives from sequencing data while not exposing any information about their genomes. We assume that individuals have access to their genome sequences but do not want to share their genomes with anyone else. Unlike previous approaches, our approach uses both common and rare variants which provide the ability to detect much more distant relationships securely. We use a simulated data generated from the 1000 genomes data and illustrate that we can easily detect up to fifth degree cousins which was not possible using the existing methods. We also show in the 1000 genomes data with cryptic relationships that our method can detect these individuals. Availability: The software is freely available for download at http://genetics.cs.ucla.edu/crypto/. Contact: fhormoz@cs.ucla.edu or eeskin@cs.ucla.edu Supplementary information: Supplementary data are available at Bioinformatics online
Genetic Control of Osmoadaptive Glycine Betaine Synthesis in Bacillus subtilis through the Choline-Sensing and Glycine Betaine-Responsive GbsR Repressor

ABSTRACT Synthesis of the compatible solute glycine betaine confers a considerable degree of osmotic stress tolerance to Bacillus subtilis. This osmoprotectant is produced through the uptake of the precursor choline via the osmotically inducible OpuB and OpuC ABC transporters and a subsequent two-step oxidation process by the GbsB and GbsA enzymes. We characterized a regulatory protein, GbsR, controlling the transcription of both the structural genes for the glycine betaine biosynthetic enzymes (gbsAB) and those for the choline-specific OpuB transporter (opuB) but not of that for the promiscuous OpuC transporter. GbsR acts genetically as a repressor and functions as an intracellular choline sensor. Spectroscopic analysis of the purified GbsR protein showed that it binds the inducer choline with an apparent KD (equilibrium dissociation constant) of approximately 165 μM. Based on the X-ray structure of a protein (Mj223) from Methanococcus jannaschii, a homology model for GbsR was derived. Inspection of this GbsR in silico model revealed a possible ligand-binding pocket for choline resembling those of known choline-binding sites present in solute receptors of microbial ABC transporters, e.g., that of the OpuBC ligand-binding protein of the OpuB ABC transporter. GbsR was not only needed to control gbsAB and opuB expression in response to choline availability but also required to genetically tune down glycine betaine production once cellular adjustment to high osmolarity has been achieved. The GbsR regulatory protein from B. subtilis thus records and integrates cellular and environmental signals for both the onset and the repression of the synthesis of the osmoprotectant glycine betaine.
Children obesity treatment support with telemedicine

Obesity is considered an endemic within the whole European continent, just as in most part of the developed world. Obesity poses an increasing risk, childhood obesity has more than doubled in children and tripled in adolescents in the past 30 years. To assess the impact of obesity we need to take into account the severity of the problems that obesity might cause, as risk is usually interpreted as the product of probability of occurrence and severity. In the last few decades, increased occurrence of several morbidities was casually linked to obesity. Recently health problems targeting children have increasing trends in well developed countries. Our research is focusing on obesity related health problems in children, and our offered ICT solutions enables healthcare service providers to remotely monitor patient's (children's) activities and weight. The solution also helps to assign workout programs to the children according to the collected sensor data. The used workout programs base not only on widely used sport activities (etc. running or gymnastics), but cover non-conventional sport activities like playing with interactive game consoles at home. The system contains an Android based DAQ (Data Acquisition Device), sensors and a server side portal, which collects all measured patient information in the data center. The solution combines existing; self developed client and server side applications and frameworks, and commodity sensor solutions. The main goal of our work is to adapt the already existing monitoring solution to children. Kids behave and use such monitoring environments differently due to their different perception and knowledge level. They need different GUIs; they live different lifestyle as elderly patients. The communication lines of the system are compliant to the EU and national regulations. The developed system was tested and a prototype system was installed successfully in a real environment. Sensor data acquisition on the personal mobile device enables both end-users and care givers/professionals to provide better and more effective health monitoring and facilitate patient's treatment. The paper describes the internal architecture of the software solution and its main functionalities.
Distinctive Cytokines as Biomarkers Predicting Fatal Outcome of Severe Staphylococcus aureus Bacteremia in Mice

Invasive Staphylococcus aureus infections are frequently associated with bacteraemia. To support clinical decisions on antibiotic therapy, there is an urgent need for reliable markers as predictors of infection outcome. In the present study in mice, bacteraemia was established by intravenous inoculation of a clinical S. aureus isolate at the LD50 inoculum. As potential biomarkers for fatal outcome, blood culture (qualitative and quantitative), serum levels of C-reactive protein (CRP), as well as 31 selected cytokines and chemokines were assessed during the first three days of infection. A positive S. aureus blood culture, the quantitative blood culture, CRP levels, and levels of eight cytokines were indicative for the presence of S. aureus bacteraemia. However, only tumor necrosis factor (TNF) α, interleukin (IL) 1α, and keratinocyte chemoattractant (KC; a functional homologue of human IL-8) were each significantly elevated in eventually non-surviving infected mice versus eventually surviving infected mice. In severe S. aureus bacteraemia in mice, TNF-α, IL-1α, and KC are biomarkers predicting fatal outcome of infection. KC was a biomarker elevated irrespective the progression of infection, which is very interesting regarding clinical application in view of the heterogeneity of patients experiencing bacteraemia in this respect.
The Weighted Factors Automaton : A Tool for DNA Sequences Analysis

A lot of computing tools are often used for analyzing DNA sequences like trees, automata, dictionaries, every one being reserved for a particular problem. A. Blumer and al. have proposed a more general computing tool : the smaller automaton recognizing the subwords of a text (DAWG). In this paper we propose the concept of “weighted factors automaton” producing every occurrence of any factor. Its transitions are labeled by the read letter and weighted by the set of the indices of the factors beginnings. The factors are obtained by concatenating the read letters and the indices of the factors beginnings are obtained by computing the intersection of the weighting sets, when advancing from the initial state to a final state. We think that this automaton can be more easily processed than DAWG and we present a comparison between DAWG and our automaton: the set of the factors beginnings indices and the factors frequency are more easily obtained by our automaton and the restriction of our automaton to the factors of length k maintains the automaton structure, when DAWG cannot be easily restricted. The applications are numerous: By selecting factors of length 1, we obtain the coding regions, factors of length 3, we obtain the expression level of some gene. The “weighted factors automaton” allows us to find matches of pattern, to study homology, FASTA and BLAST algorithms being significantly simplified.
Cardiotoxicity of chemotherapeutic agents and radiotherapy-related heart disease: ESMO Clinical Practice Guidelines.

New anticancer therapies have led to a long life expectancy for many patients; however, treatment-related comorbidities have become an issue for long-term cancer survivors. Cardiac toxicity is one of most feared side-effects of anticancer agents so that the gain in life expectancy due to anticancer therapy might be countered by increased mortality due to cardiac problems, above all heart failure (HF), but also myocardial ischaemia, arrhythmias, hypertension, thromboembolism. Detection of cardiac injury is crucial since it may facilitate early therapeutic measures. The incidence of cardiotoxicity depends on different factors related to oncological therapies (type of drug, dose administered during each cycle, cumulative dose, schedule of administration, route of administration, combination of other cardiotoxic drugs or association with radiotherapy) and to patient [age, presence of cardiovascular (CV) risk factors, previous cardiovascular disease (CVD), prior mediastinal radiation therapy]. Adverse cardiotoxic effects induced by chemotherapy are summarized in Table 1.
Lateral regionalization and diffusion of a maturation-dependent antigen in the ram sperm plasma membrane

We have used a monoclonal antibody ESA 152 in fluorescence recovery after photobleaching (FPR) studies of a maturation-dependent surface antigen of ram sperm. The antibody is an immunoglobulin G secreted by a hybridoma derived from NS1 mouse myeloma cells. The ESA 152 antigen is not detectable in testicular sperm. It is localized on the surface of ejaculated sperm where it is present on all regions of the surface, but tends to be concentrated on the posterior region of the head. The ESA 152 antigen can be extracted by detergents or chloroform-methanol. The extracted antigen is sensitive to proteases and migrates with an apparent Mr approximately 30,000 in SDS-containing 10-20% polyacrylamide gradient gels. FPR measurements of ESA 152 lateral mobility in the membrane yield diffusion coefficients in the range 10(- 9)-10(-8) cm2/s, values typical of lipids but observed for proteins only at the fluid dynamic limit where diffusion is controlled by lipid fluidity. Immobile fractions, typical of membrane proteins, are observed on all regions. When the antigen is stained by a fluoresceinated Fab fragment of the ESA 152 antibody, the diffusibility is highly regionalized, with particularly low, but rapid, recovery on the midpiece. Cross-linking of the antigen with the intact ESA 152 antibody induces a redistribution in which the antigen is excluded from the posterior head region. This cross-linking is accompanied by increases in ESA 152 diffusibility on both the anterior head and the midpiece.
Set-Constrained Delivery Broadcast: Definition, Abstraction Power, and Computability Limits

This paper introduces a new communication abstraction, called Set-Constrained Delivery Broadcast (SCD-broadcast), whose aim is to provide its users with an appropriate abstraction level when they have to implement objects or distributed tasks in an asynchronous message-passing system prone to process crash failures. This abstraction allows each process to broadcast messages and deliver a sequence of sets of messages in such a way that, if a process delivers a set of messages including a message m and later delivers a set of messages including a message m', no process delivers first a set of messages including m' and later a set of message including m. After having presented an algorithm implementing SCD-broadcast, the paper investigates its programming power and its computability limits. On the "power" side it presents SCD-broadcast-based algorithms, which are both simple and efficient, building objects (such as snapshot and conflict-free replicated data), and distributed tasks. On the "computability limits" side it shows that SCD-broadcast and read/write registers are computationally equivalent.
Comparison of Gen-Probe Transcription-Mediated Amplification, Abbott PCR, and Roche PCR Assays for Detection of Wild-Type and Mutant Plasmid Strains of Chlamydia trachomatis in Sweden

ABSTRACT The clinical performance of two nucleic acid amplification assays targeting the cryptic plasmid and two assays targeting rRNA molecules in Chlamydia trachomatis was examined. First-catch urine samples from Malmoe, Sweden, were tested for C. trachomatis with the Abbott real-time PCR assay m2000 and an in-house PCR for the new variant strain of C. trachomatis with a deletion in the cryptic plasmid. Aliquots of the urine samples were sent to Aarhus, Denmark, and further examined with the Roche COBAS Amplicor CT (RCA) PCR, the Gen-Probe Aptima Combo 2 assay (AC2) targeting the C. trachomatis 23S rRNA, and the Aptima C. trachomatis assay (ACT) targeting the 16S rRNA molecule. A positive prevalence of 9% (163/1,808 urine samples examined) was detected according to the combined reference standard. The clinical sensitivity and specificity of the four assays were as follows: for ACT, 100% (163/163) and 99.9% (1,643/1,645), respectively; for AC2, 100% (163/163) and 99.6% (1,640/1,645); for m2000, 68.7% (112/163) and 99.9% (1,644/1,645); for RCA, 63.8% (104/163) and 99.9% (1,643/1,645). The two Gen-Probe assays detected all mutant strains characterized by the in-house PCR as having the deletion in the cryptic plasmid, whereas the Roche and the Abbott PCRs targeting the plasmid were both unable to detect the plasmid mutant. The difference in clinical sensitivity between the plasmid PCR assays m2000 and RCA, on the one hand, and the rRNA assays AC2 and ACT, on the other, could be attributed almost exclusively to the presence of the plasmid mutant in about one-quarter of the Chlamydia-positive samples examined.
Proximity of thiol esters and bait region in human alpha 2-macroglobulin: paramagnetic mapping.

The two key structural features of alpha 2-macroglobulin (alpha 2M) involved in inhibitory caging of proteases are the thiol ester and the bait region. This paper examines the environment of the hydrolyzed thiol ester in methylamine-treated human alpha 2M and the separation between the bait region and the thiol ester and between the four thiol esters in the tetramer to try to further our understanding of how bait region proteolysis triggers thiol ester cleavage. The sulfhydryl groups of Cys-949, formed upon cleavage of the thiol ester by methylamine, were specifically labeled with the nitroxide spin-labels 3-(2-iodoacetamido)-PROXYL (iodo-I) (PROXYL = 2,2,5,5-tetramethylpyrrolidine-1-oxyl), 3-[2-(2-iodoacetamido)acetamido]-PROXYL (iodo-II), and 4-(2-iodoacetamido)-2,2,6,6-tetramethylpiperidine-1-oxyl (iodo-III). ESR spectra of these alpha 2M derivatives showed that label I is firmly held and label II has limited freedom of rotation consistent with location of the cysteine residue in a narrow cavity. Label III has much greater motional freedom. From the absence of dipole-dipole splittings in the ESR spectra, it is concluded that the four nitroxide groups in the tetramer are more than 20 A apart for both label I and label II. Label I broadens 1H NMR signals from one phenylalanyl, one tyrosyl, and four histidyl residues in the bait region. Separations of 11-17 A are estimated between the nitroxide of label I and these residues. Label II is further away and only broadens resonances from one of the histidines. (ABSTRACT TRUNCATED AT 250 WORDS)
Mismatch repair deficiency endows tumors with a unique mutation signature and sensitivity to DNA double-strand breaks

DNA replication errors that persist as mismatch mutations make up the molecular fingerprint of mismatch repair (MMR)-deficient tumors and convey them with resistance to standard therapy. Using whole-genome and whole-exome sequencing, we here confirm an MMR-deficient mutation signature that is distinct from other tumor genomes, but surprisingly similar to germ-line DNA, indicating that a substantial fraction of human genetic variation arises through mutations escaping MMR. Moreover, we identify a large set of recurrent indels that may serve to detect microsatellite instability (MSI). Indeed, using endometrial tumors with immunohistochemically proven MMR deficiency, we optimize a novel marker set capable of detecting MSI and show it to have greater specificity and selectivity than standard MSI tests. Additionally, we show that recurrent indels are enriched for the ‘DNA double-strand break repair by homologous recombination’ pathway. Consequently, DSB repair is reduced in MMR-deficient tumors, triggering a dose-dependent sensitivity of MMR-deficient tumor cultures to DSB inducers. DOI: http://dx.doi. org/10.7554/eLife.02725. 001
Atoll-scale patterns in coral reef community structure: Human signatures on Ulithi Atoll, Micronesia

The dynamic relationship between reefs and the people who utilize them at a subsistence level is poorly understood. This paper characterizes atoll-scale patterns in shallow coral reef habitat and fish community structure, and correlates these with environmental characteristics and anthropogenic factors, critical to conservation efforts for the reefs and the people who depend on them. Hierarchical clustering analyses by site for benthic composition and fish community resulted in the same 3 major clusters: cluster 1–oceanic (close proximity to deep water) and uninhabited (low human impact); cluster 2–oceanic and inhabited (high human impact); and cluster 3–lagoonal (facing the inside of the lagoon) and inhabited (highest human impact). Distance from village, reef exposure to deep water and human population size had the greatest effect in predicting the fish and benthic community structure. Our study demonstrates a strong association between benthic and fish community structure and human use across the Ulithi Atoll (Yap State, Federated States of Micronesia) and confirms a pattern observed by local people that an ‘opportunistic’ scleractinian coral (Montipora sp.) is associated with more highly impacted reefs. Our findings suggest that small human populations (subsistence fishing) can nevertheless have considerable ecological impacts on reefs due, in part, to changes in fishing practices rather than overfishing per se, as well as larger global trends. Findings from this work can assist in building local capacity to manage reef resources across an atoll-wide scale, and illustrates the importance of anthropogenic impact even in small communities.
Frequent occurrence of UVB-induced sister chromatid exchanges in telomere regions and its implication to telomere maintenance

Sister chromatid exchanges (SCEs) are symmetrical exchanges between newly replicated chromatids and their sisters. While homologous recombination may be one of the principal mechanisms responsible for SCEs, the full details of their molecular basis and biological significance remain to be elucidated. Following exposure to ultraviolet light B (UVB), mitomycin C (MMC) and cisplatin, we analyzed the location of SCEs on metaphase chromosomes in Chinese hamster CHO cells. The frequency of SCEs increased over the spontaneous level in proportion to the agent’s dose. UVB-induced SCEs occurred frequently in telomere regions, as cisplatin-induced SCEs did, differing from MMC-induced ones. The remarkable difference of intrachromosomal distribution among the three mutagens may be attributed to the specificity of induced DNA lesions and structures of different chromosome regions. Telomeric DNA at the end of chromosomes is composed of multiple copies of a repeated motif, 5′-TTAGGG-3′ in mammalian cells. Telomeric repeats may be potential targets for UVB and cisplatin, which mainly form pyrimidine dimers and intrastrand d(GpG) cross-links, respectively, resulting in SCE formation. UVB irradiation shortened telomeres and augmented the telomerase activity. The possible implications of the frequent occurrence of SCEs in telomere regions are discussed in connection with the maintenance of telomere integrity.