Miracle-dz/UniFAR-FTUs huggingface dataset:
Mutagenesis in monkey cells of a vector containing a single d(GPG) cis- diamminedichloroplatinum(II) adduct placed on codon 13 of the human H- ras proto-oncogene

Cisplatin (cis-[Pt(NH3)2Cl2]) is a widely used antitumor agent whose mutagenic activity raises the possibility of the induction of secondary cancer as a result of treatment. Mutation of the proto-oncogene H-ras is found in more than 30% of all human tumors, where it has been postulated to contribute to the initiation and progression of human cancers. Activating mutations in the H-ras gene are predominantly single-base substitutions, most frequently at codons 12, 13 and 61. In the present work we have studied the mutational spectra induced by a single cis-[Pt(NH3)2d(GpG)] adduct, the most frequent DNA crosslink formed by cisplatin. We have constructed a 25-mer-Pt oligonucleotide singly modified at codon 13 (GGT) within the human H-ras DNA sequence and we have inserted it into a single-stranded SV40-based shuttle vector able to replicate in simian COS7 cells. After replication in the mammalian host, vectors were extracted, amplified in bacteria and DNA from 124 randomly chosen colonies was sequenced. The observed mutation frequency was 21%. Base substitutions were the most frequent modification. 92% of the mutagenic events occurred at one or both of the platinated guanines of codon 13. The single G-->T transversion accounted for 65% of the total mutations scored. All single base substitutions were located at the G in the 3' position showing, for the first time, that the guanine at the 3' side of a cis-[Pt(NH3)2d(GpG)] adduct may be a preferential site for cisplatin induced mutations. The substitution G-->T at this position of the codon 13 of the H-ras proto-oncogene is known to induce the oncogenic properties of the p21ras protein.
Homography-based orientation estimation for capsule endoscope tracking

Wireless capsule endoscopy (WCE) is a developing imaging technology for screening the gastrointestinal system. Tracking of the swallowable capsule endoscope within the human body is typically performed by external sensor arrays enabling approximate localization and detection of its orientation. In this paper we propose a method for capsule orientation estimation based only on image features, without the requirement of any external equipment. The proposed method involves two steps: a) salient point detection and extraction of image features from these points, and b) detection of feature correspondences between consecutive frames and homography estimation. The capsule orientation is estimated by decomposition of the homography matrix into rotation and translation components. The results obtained by the application of this method on WCE video frames indicate its effectiveness and improved performance over the state of the art.
Analysis of the Electromechanical Activity of the Heart from Synchronized ECG and PCG Signals of Subjects Under Stress

In this exploratory study we propose to analyze, in healthy adult volunteers, the heart electrical (electrocardiogram, ECG) and mechanical (phonocardiogram, PCG) activity during exercise. Heart sounds amplitude, frequency content, and RS2, may be important features in the non-invasive assessment of heart activity, such as for the estimation of cardiac output and blood pressure. Nine healthy volunteers were monitored with ECG and PCG simultaneously, under a stress test. After each workload level a 10 s window of signal was collected. PCG first (S1) and second (S2) heart sounds were manually annotated, based on time of QRS complex occurrence. A QRS detector was implemented to detect the QRS complex, and time intervals between electrical and mechanical events. Extracted features were analyzed in relation to heart rate (HR), including RS2, S1 and S2 amplitudes, and high frequency content of S1 and S2. Spearman correlation was used. Changes between baseline and maximum workload stage/HR for each volunteer were analyzed. Significant correlation was observed between HR, and all characteristics extracted (P<0.01). There was a clear difference between all variables from baseline to maximum workload level: with increasing workload/HR heart sounds amplitude increased (more pronounced in S1), RS2 decreased, and high frequency content of S2 decreased in relation to the high frequency content of S1, demonstrating that dynamic cardiovascular relations are individualized during cardiac stress and that assumptions for resting conditions may not be assumed.
Lifetime cigarette smoking is associated with striatal volume measures

Nicotine, the primary addictive component of tobacco, affects the mammalian brain. Smokers' brains have smaller cortical grey matter volumes and/or lower densities compared with non‐smokers'. Differences in subcortical structures like the striatum are however, less clear. A high concentration of nicotinic receptors makes the striatum a potential target for nicotine. In addition, striatal nuclei are essential components of the reward/reinforcement pathway involved in addiction. The aim of this study was to explore the relationship between striatal nuclei (caudate, putamen and nucleus accumbens area) volumes and lifetime smoking in a large community‐based sample of ‘young–old’ individuals. Brain volumes were measured using a semi‐automated method in 315 participants aged 64–70 years who were selected from a larger randomly sampled cohort and who consented to a magnetic resonance imaging scan. Multiple regression analysis was used to assess the relationship between striatal volumes and cigarette smoking measures while controlling for age, sex, intracranial and total brain volumes and general physical and mental health measures. Greater lifetime use of cigarettes (measured in pack‐years) was associated with smaller left nucleus accumbens area volume (P = 0.018) and larger left putamen volume (P = 0.025). Greater putaminal volume was also associated with a lower age at smoking initiation (P = 0.004). In this generally healthy cohort, lifetime use of cigarettes is significantly associated with striatal volume measures. These changes could indicate predisposing factors for nicotine addiction, or an effect of chronic nicotine exposure or a combination of both.
Do financial markets care about social and environmental disclosure?: Further evidence and exploration from the UK

Purpose – The purpose of the paper is to explore whether there is any relationship(s) between social and environmental disclosure and the financial market performance of the UK's largest companies. Design/methodology/approach – Two data sets were used in the study. The CSEAR database of UK companies provided the social and environmental disclosure component. The second data were the stock market returns earned by the largest UK companies as listed by The Times 1,000. A series of statistical tests was performed to examine whether any relationship could be detected in either the cross sectional or longitudinal data over a period of ten years. Findings – No direct relationship between share returns and disclosure was found. Neither had such a relationship been expected, in keeping with the prior literature. However, the longitudinal data revealed a convincing relationship between consistently high(low) returns and the predilection to high(low) disclosure. There is no single convincing theoretical explanation as to why this might be. Originality/value – This paper demonstrates the importance of examining a range of hypotheses on longitudinal data when other research suggests that any relationships are unlikely to be unstable year on year. More significantly, this paper is motivated not by a concern to understand better how investors' already-high returns may be bettered, but rather to explore how the alleged potential of financial markets to contribute to social responsibility and sustainability might be engaged.
Comparative analysis of fiber‐type composition in the iliofibularis muscle of phrynosomatid lizards (Squamata)

The lizard family Phrynosomatidae comprises three subclades: the closely related sand and horned lizards, and their relatives the Sceloporus group. This family exhibits great variation in ecology, behavior, and general body plan. Previous studies also show that this family exhibits great diversity in locomotor performance abilities; as measured on a high‐speed treadmill, sand lizards are exceptionally fast sprinters, members of the Sceloporus group are intermediate, and horned lizards are slowest. These differences are paralleled by differences in relative hindlimb span. To determine if muscle fiber‐type composition also varies among the three subclades, we examined the iliofibularis (IF), a hindlimb muscle used in lizard locomotion, in 11 species of phrynosomatid lizards. Using histochemical assays for myosin ATPase, an indicator of fast‐twitch capacity, and succinic dehydrogenase, denoting oxidative capacity, we classified fiber types into three categories based on existing nomenclature: fast‐twitch glycolytic (FG), fast‐twitch oxidative‐glycolytic (FOG), and slow‐twitch oxidative (SO). Sand lizards have a high proportion of FG fibers (64–70%) and a low proportion of FOG fibers (25–33%), horned lizards are the converse (FG fibers 25–31%, FOG fibers 56–66%), and members of the Sceloporus group are intermediate for both FG (41–48%) and FOG (42–45%) content. Hence, across all 11 species %FOG and %FG are strongly negatively correlated. Analysis with phylogenetically independent contrasts indicate that this negative relationship is entirely attributable to the divergence between sand and horned lizards. The %SO also varies among the three subclades. Results from conventional nested ANCOVA (with log body mass as a covariate) indicate that the log mean cross‐sectional area of individual muscle fibers differs among species and is positively correlated with body mass across species, but does not differ significantly among subclades. The log cross‐sectional area of the IF varies among species, but does not vary among subclades. Conversely, the total thigh muscle cross‐sectional area does not vary among species, but does vary among subclades; horned lizards have slimmer thighs. Muscle fiber‐type composition appears to form part of a coadapted suite of traits, along with relative limb and muscle sizes, that affect the locomotor abilities of phrynosomatid lizards. J. Morphol. 250:265–280, 2001. © 2001 Wiley‐Liss, Inc.
epresenting composition , spatial structure and management ntensity of European agricultural landscapes : A new typology mma

Comprehensive maps that characterize the variation in agricultural landscapes across Europe are lacking. In this paper we present a new Europe-wide, spatially-explicit typology and inventory of the diversity in composition, spatial structure and management intensity of European agricultural landscapes. Agricultural landscape types were characterized at a 1 km2 resolution based on Europe-wide datasets that represent land cover, landscape structure and land management intensity. Two alternative approaches for typology development were used: an expert-based top-down approach, and a bottom-up approach based on automated clustering using Self Organizing Maps (SOMs). Comparison with available national and European landscape typologies showed that our typology deviates from existing biophysical and
On the SPN Estimation in Image Forensics: A Systematic Empirical Evaluation

Extracting a fingerprint of a digital camera has fertile applications in image forensics, such as source camera identification and image authentication. In the last decade, photo response non_uniformity (PRNU) has been well established as a reliable unique fingerprint of digital imaging devices. The PRNU noise appears in every image as a very weak signal, and its reliable estimation is crucial for the success rate of the forensic application. In this paper, we present a novel methodical evaluation of 21 state-of-the-art PRNU estimation/enhancement techniques that have been proposed in the literature in various frameworks. The techniques are classified and systematically compared based on their role/stage in the PRNU estimation procedure, manifesting their intrinsic impacts. The performance of each technique is extensively demonstrated over a large-scale experiment to conclude this case-sensitive study. The experiments have been conducted on our created database and a public image database, the “Dresden image database. ”
Separability of spatial manipulations in multi-touch interfaces

Multi-touch interfaces allow users to translate, rotate, and scale digital objects in a single interaction. However, this freedom represents a problem when users intend to perform only a subset of manipulations. A user trying to scale an object in a print layout program, for example, might find that the object was also slightly translated and rotated, interfering with what was already carefully laid out earlier. We implemented and tested interaction techniques that allow users to select a subset of manipulations. Magnitude Filtering eliminates transformations (e.g., rotation) that are small in magnitude. Gesture Matching attempts to classify the user's input into a subset of manipulation gestures. Handles adopts a conventional single-touch handles approach for touch input. Our empirical study showed that these techniques significantly reduce errors in layout, while the Handles technique was slowest. A variation of the Gesture Matching technique presented the best combination of speed and control, and was favored by participants.
Learning Non-Linear Feature Maps

Feature selection plays a pivotal role in learning, particularly in areas were parsimonious features can provide insight into the underlying process, such as biology. Recent approaches for non-linear feature selection employing greedy optimisation of Centred Kernel Target Alignment(KTA), while exhibiting strong results in terms of generalisation accuracy and sparsity, can become computationally prohibitive for high-dimensional datasets. We propose randSel, a randomised feature selection algorithm, with attractive scaling properties. Our theoretical analysis of randSel provides strong probabilistic guarantees for the correct identification of relevant features. Experimental results on real and artificial data, show that the method successfully identifies effective features, performing better than a number of competitive approaches.
Implementing reusable software components for SNOMED CT diagram and expression concept representations

SNOMED CT is a vital component in the future of semantic interoperability in healthcare as it provides the meaning to EHRs via its semantically rich, controlled terminology. Communicating the concepts of this terminology to both humans and machines is crucial therefore formal guidelines for diagram and expression representations have been developed by the curators of SNOMED CT. This paper presents a novel, model-based approach to implementing these guidelines that allows simultaneous editing of a concept via both diagram and expression editors. The implemented extensible software component can be embedded both both desktop and web applications.
Molecular characterization of spa type t127, sequence type 1 methicillin-resistant Staphylococcus aureus from pigs.

OBJECTIVES The aim of this study was to provide molecular characterization of methicillin-resistant Staphylococcus aureus (MRSA) spa type t127, sequence type (ST) 1 isolates, detected in a European baseline survey in holdings of breeding pigs, to determine phenotypic and genotypic drug resistance and to compare the results with those obtained from a collection of t127, ST1 MRSA and methicillin-susceptible S. aureus (MSSA) clinical isolates. METHODS Twenty-four t127, ST1 MRSA from dust sampled in different breeding holdings in Italy, Spain and Cyprus were studied, along with 2 t127, ST1 MRSA from fattening pigs and 11 human t127, ST1 MRSA and MSSA. Genotyping was performed using multilocus sequence typing (MLST), spa typing and PFGE. SCCmec elements were characterized by multiplex-PCR and resistance and pathogenicity genes by PCR and microarray. RESULTS PFGE patterns separated a porcine cluster (PC) from a human cluster (HC), with 75% similarity. The PC carried SCCmec cassette type V, while all isolates of the HC carried SCCmec cassette type IVa. Kanamycin resistance mediated by aadD, fluoroquinolone and erm(A)-mediated macrolide resistance and the absence of the sakA gene were features of the PC only. All isolates of both clusters were positive for LukE-LukD and LuF-LukS-HlgA leukotoxin genes and one human MSSA harboured Panton-Valentine leucocidin genes. CONCLUSIONS Despite differences in the host-specific genetic features, the possibility of PC transmission to humans cannot be excluded. MRSA spa type t127, ST1 from pigs possesses several virulence and resistance genes towards major classes of antimicrobials and may represent a serious therapeutic challenge in case of invasive infections in humans.
Probabilistic asr feature extraction applying context-sensitive connectionist temporal classification networks

This paper proposes a novel automatic speech recognition (ASR) front-end that unites the principles of bidirectional Long Short-Term Memory (BLSTM), Connectionist Temporal Classification (CTC), and Bottleneck (BN) feature generation. BLSTM networks are known to produce better probabilistic ASR features than conventional multilayer perceptrons since they are able to exploit a self-learned amount of temporal context for phoneme estimation. Combining BLSTM networks with a CTC output layer implies the advantage that the network can be trained on unsegmented data so that the quality of phoneme prediction does not rely on potentially error-prone forced alignment segmentations of the training set. In challenging ASR scenarios involving highly spontaneous, disfluent, and noisy speech, our BN-CTC front-end leads to remarkable word accuracy improvements and prevails over a series of previously introduced BLSTM-based ASR systems.
Direction selectivity in the visual system of the zebrafish larva

Neural circuits in the vertebrate retina extract the direction of object motion from visual scenes and convey this information to sensory brain areas, including the optic tectum. It is unclear how computational layers beyond the retina process directional inputs. Recent developmental and functional studies in the zebrafish larva, using minimally invasive optical imaging techniques, indicate that direction selectivity might be a genetically hardwired property of the zebrafish brain. Axons from specific direction-selective (DS) retinal ganglion cells appear to converge on distinct laminae in the superficial tectal neuropil where they serve as inputs to DS postsynaptic neurons of matching specificity. In addition, inhibitory recurrent circuits in the tectum might strengthen the DS response of tectal output neurons. Here we review these recent findings and discuss some controversies with a particular focus on the zebrafish tectum’s role in extracting directional features from moving visual scenes.
Common metrics framework for ATM performance assessment and monitoring

Across the air traffic management (ATM) discipline there is a long-standing problem of inconsistencies in assessing and monitoring system performance. Research has offered limited solutions so far, and has failed to offer an internationally acceptable performance definition methodology that provides the ability to: (1) compare the analogous performance metrics and evaluations obtained by various organizations; (2) roll-up measures to the organizational goals; and (3) comprehend the impact of a change in metric-value onto the overall performance. This paper describes the initial results of an on-going work proposed by FAA, Eurocontrol and their partners, that addresses the ATM performance measurement discrepancies. The problem is approached in a systematic manner by dissecting the ATM system into the smallest elements and processes, and by studying the International Standardization Organization (ISO) definition of quality of service (QoS) in information technology (IT). A common metric taxonomy is developed to provide for unambiguous translation of the terminology and metric specifications used by different organizations, and to facilitate developing a collection of the existing metrics to enable maintaining the connection between the identical metrics, metrics with identical definitions but different names, and metrics with identical names but different definitions. A common ATM performance framework is built upon the International Civil Aviation Organization (ICAO) concepts of required ATM system performance (RASP) and required total system performance (RTSP). Illustrated through cause-effect diagrams, the framework maintains the connectivity between different levels of performance evaluation, performance aspects, and performance measures, and enables rolling-up measures to the performance requirements and organizational goals. A common 'dashboard' for presenting the achieved or expected performance is developed using radar diagrams to clearly and effectively accommodate simultaneous display of large amount of information. As such, this methodology enables common ATM performance monitoring, operational concept validation and comparison, and target setting. The proposed framework is briefly illustrated on the safety-evaluation example, and the further research guidelines are briefly described.
The Vps4p AAA ATPase regulates membrane association of a Vps protein complex required for normal endosome function

Vps4p is an AAA‐type ATPase required for efficient transport of biosynthetic and endocytic cargo from an endosome to the lysosome‐like vacuole of Saccharomyces cerevisiae. Vps4p mutants that do not bind ATP or are defective in ATP hydrolysis were characterized both in vivo and in vitro. The nucleotide‐free or ADP‐bound form of Vps4p existed as a dimer, whereas in the ATP‐locked state, Vps4p dimers assembled into a decameric complex. This suggests that ATP hydrolysis drives a cycle of association and dissociation of Vps4p dimers/decamers. Nucleotide binding also regulated the association of Vps4p with an endosomal compartment in vivo. This membrane association required the N‐terminal coiled‐coil motif of Vps4p, but deletion of the coiled‐coil domain did not affect ATPase activity or oligomeric assembly of the protein. Membrane association of two previously uncharacterized class E Vps proteins, Vps24p and Vps32p/Snf7p, was also affected by mutations in VPS4. Upon inactivation of a temperature‐conditional vps4 mutant, Vps24p and Vps32p/Snf7p rapidly accumulated in a large membrane‐bound complex. Immunofluorescence indicated that both proteins function with Vps4p at a common endosomal compartment. Together, the data suggest that the Vps4 ATPase catalyzes the release (uncoating) of an endosomal membrane‐associated class E protein complex(es) required for normal morphology and sorting activity of the endosome.
An integrated scheduling algorithm based on users' diversity for cognitive radio

The introduction of cognitive radio relieves the pressure brought by the lack of spectrum resources. However, it also brings new problems to the resources scheduling. The currently existed scheduling algorithms have not considered the different identities of primary users (PUs) and secondary users (SUs), delay urgency and implementation progress. Considering the different demands on the spectrum scheduling timeliness, this paper proposes an integrated scheduling algorithm based on users' diversity. Simulation results show that the algorithm proposed not only ensures the PUs' quality of service but also improves the SUs' performance and system throughput. Additionally, the novel algorithm makes the resources allocation between PUs and SUs more fair.