Miracle-dz/UniFAR-FTUs huggingface dataset:
Gapped consensus motif discovery : evaluation of a new algorithm based on local multiple alignments and a sampling strategy

We check the efficiency and faisability of a novel method designed for the discovery of a priori unknown motifs described as gaps alternating with specific regions. Such motifs are searched for as consensi of non homologous biological sequences. The only specifications required concern the maximal gap length, the minimal frequency for specific characters and the minimal percentage (quorum) of sequences sharing the motif. Our method is based on a cooperation between a multiple alignment method for a quick detection of local similarities and a sampling strategy running candidate position specific scoring matrices to convergence. This rather original way implemented for converging to the solution proves efficient both on simulated data, gapped instances of the so-called challenge problem, promoter sites in Dicot plants and transcription factor binding sites in E.Coli. Our algorithm compares favorably with the MEME and STARS approaches in terms of accuracy.
The role of local design factors for newspaper reading behaviour – an eye-tracking perspective

Newspaper design is a creative art, and the possibilities to vary design are endless. Basically, newspaper designers judge the value of a designed spread by looking at it themselves and imagining how readers could perceive it or sense what it feels like. Actual feedback on readers perception of the design is very scarce. The only method widely in use is target group interviews. Interviews can cover large samples from a reader population, but readers have only a very limited self-knowledge and memory of their own reading (Helander, Landauer and Prabhu 1997). Also, very few general interview questions are asked. It is unlikely that these can reflect all potentially interesting details and processes that occur during the half hour that Scandinavian readers on average spend with their newspaper.
A Disease Modification Effect of APOE E4 on the Association between Urinary Albumin Excretion and Cognition in Korean Adults

Background. No previous study examined a disease modifying effect of APOE E4 status on the association between the urinary albumin-to-creatinine ratio (UACR) and cognition. This study aimed to investigate whether APOE E4 modified the association in Korean adults. Methods. We performed a cross-sectional study in adults aged 45 to 74 who were living in Namwon City, Republic of Korea. Cognitive function was measured with the Korean version of modified Mini-Mental State Examination (K-mMMSE) and cognitive impairment was defined as scores falling below the 25th percentile of the K-mMMSE according to age, sex, and educational attainments. Results. A total of 10,190 participants (4006 men and 6184 women) were analyzed in the present study. Of these, 1698 subjects (16.7%) were APOE E4 carriers. The UACR values were negatively associated with the K-mMMSE scores, even after adjusting for potential confounders including age, sex, education, and vascular risk factors. APOE E4 modified the association significantly, resulting in a steeper decline of cognitive function with the increase in UACR in E4 carriers (P for interaction = 0.021). Conclusion. Higher UACR values were significantly associated with cognitive dysfunction in the general Korean population, with cognition in APOE E4 carriers being more severely affected by increased UACR.
Distinguishing between Abstract Art by Artists vs. Children and Animals

Abstract expressionism is a school of art characterized by nonrepresentational paintings where color, composition, and brush strokes are used to express emotion. These works are often misunderstood by the public who see them as requiring no skill and as images that even a child could have created. However, a recent series of studies has shown that ordinary adults untrained in art or art history, as well as young children, can differentiate paintings by abstract expressionists and superficially similar works by preschool children and even animals (monkeys, apes, elephants). Adults perform this distinction with an accuracy rate of ∼64%, significantly higher than chance. Here we ask whether machine perception can do as well. Using the same paintings, we show that in ∼68% of the cases the computer algorithm can discriminate between abstract paintings and the work of children and animals. We also applied a method that computes the correlation between the degree of artisticity deduced from human perception of the paintings and the visual content of the images, and we show significant correlation between perceived artisticity and visual content. The image content descriptor that was the strongest predictor of correct identification was the fractality of the painting. We also show that the computer algorithm predicts the perceived intentionality of the paintings by humans. These results confirm perceptible differences between works by abstract expressionists and superficially similar ones by the untrained and show that people see more than they think they see when looking at abstract expressionism.
Effects of Short Term Exposure of Atrazine on the Liver and Kidney of Normal and Diabetic Rats

The present study evaluates the effects of short term (15 days) exposure of low dose (300 μg kg−1) of atrazine (2-chloro-4-ethylamino-6-isopropylamino-1,3,5-triazine) on antioxidant status and markers of liver and kidney damage in normal (nondiabetic) and diabetic male Wistar rats. Rats were divided into four groups: Group I as normal control, Group II as atrazine treated, Group III as diabetic control, and Group IV as atrazine treated diabetic rats. Atrazine administration resulted in increased MDA concentration as well as increased activities of SOD, CAT, and GPx in both liver and kidney of atrazine treated and atrazine treated diabetic rats. However, GSH level was decreased in both liver and kidney of atrazine treated and atrazine treated diabetic rats. Atrazine administration led to significant increase in liver damage biomarkers such as AST, ALT, and ALP as well as kidney damage biomarkers such as creatinine and urea in both normal and diabetic rats, but this increase was more pronounced in diabetic rats when compared to normal rats. In conclusion, the results of the present study demonstrate that short term exposure of atrazine at a dose of 300 μg kg−1 could potentially induce oxidative damage in liver and kidney of both normal and diabetic rats.
UML-Checker: An Approach for Verifying UML Behavioral Diagrams

UML is a visual modeling language used for specifying, visualizing, constructing, and documenting software artifacts. Despite having many features to model systems, conducting verifications and validations on UML models is not an easy task. In this paper, the problem of performing verification of UML models is discussed through a translation of UML behavioral diagrams into formal models to be verified by a symbolic model checker. An approach and tool (UML checker) is presented in order to conduct verifications on UML diagrams. The main ideas are: (a) provide an approach to perform the translation of activity, state and use case diagrams to the formal input language of the NuSMV checker; (b) automate the translation of UML diagrams to a formal language; and (c) provide a set of predefined validations that are used to check the diagrams.
Distribution of porin and lipopolysaccharide antigens on a Pseudomonas aeruginosa permeability mutant

Pseudomonas aeruginosa common surface antigens were compared in a permeability mutant (PCC118) and its parent (PAO503). The distribution of lipopolysaccharide and porin antigens in the mutant supports the conclusion that beta-lactam permeability was affected by lipopolysaccharide-side chain presentation rather than by a change in porin number.
Peptide Conjugates of Oligonucleotide Analogs and siRNA for Gene Expression Modulation

18.1 The Challenge of Delivery of Oligonucleotide Analogs and siRNA into Cells in Culture and In Vivo 313 18.2 Chemical Synthesis of Peptide–Oligonucleotide Conjugates 314 18.2. 1 Synthesis of CPP Conjugates to Phosphate-Containing Oligonucleotides 315 18.2. 2 Synthesis of PNA–Peptide Conjugates 318 18.3 Gene Expression Modulation by Peptide Conjugates of Antisense or Steric Block Oligonucleotides 318 18.3. 1 Anionic Oligonucleotide Analog Conjugates with CPPs . 318 18.3. 2 Charge-Neutral PNA and PMO Oligonucleotide Conjugates with CPPs 320 18.4 Gene Expression Inhibition by Peptide Conjugates of siRNA 323 18.5 Future Perspectives 324 Acknowledgments 325 References 325
Secure agreement protocols: reliable and atomic group multicast in rampart

Reliable and atomic group multicast have been proposed as fundamental communication paradigms to support secure distributed computing in systems in which processes may behave maliciously. These protocols enable messages to be multicast to a group of processes, while ensuring that all honest group members deliver the same messages and, in the case of atomic multicast, deliver these messages in the same order. We present new reliable and atomic group multicast protocols for asynchronous distributed systems. We also describe their implementation as part of Rampart, a toolkit for building high-integrity distributed services, i.e., services that remain correct and available despite the corruption of some component servers by an attacker. To our knowledge, Rampart is the first system to demonstrate reliable and atomic group multicast in asynchronous systems subject to process corruptions.
Advances in gene therapy technologies to treat retinitis pigmentosa

Retinitis pigmentosa (RP) is a class of diseases that leads to progressive degeneration of the retina. Experimental approaches to gene therapy for the treatment of inherited retinal dystrophies have advanced in recent years, inclusive of the safe delivery of genes to the human retina. This review is focused on the development of gene therapy for RP using recombinant adenoassociated viral vectors, which show a positive safety record and have so far been successful in several clinical trials for congenital retinal disease. Gene therapy for RP is under development in a variety of animal models, and the results raise expectations of future clinical application. Nonetheless, the translation of such strategies to the bedside requires further understanding of the mutations and mechanisms that cause visual defects, as well as thorough examination of potential adverse effects.
Water Stress Deforms Tracheids Peripheral to the Leaf Vein of a Tropical Conifer1

Just as a soggy paper straw is prone to yielding under the applied suction of a thirsty drinker, the xylem tracheids in leaves seem prone to collapse as water potential declines, impeding their function. Here we describe the collapse, under tension, of lignified cells peripheral to the leaf vein of a broad-leaved rainforest conifer, Podocarpus grayi de Laub. Leaves of Podocarpus are characterized by an array of cylindrical tracheids aligned perpendicular to the leaf vein, apparently involved in the distribution of water radially through the mesophyll. During leaf desiccation the majority of these tracheids collapsed from circular to flat over the water potential range −1.5 to −2.8 MPa. An increase in the percentage of tracheids collapsed during imposed water stress was mirrored by declining leaf hydraulic conductivity (Kleaf), implying a direct effect on water transport efficiency. Stomata responded to water stress by closing at −2.0 MPa when 45% of cells were collapsed and Kleaf had declined by 25%. This was still substantially before the initial indications of cavitation-induced loss of hydraulic conductance in the leaf vein, at −3 MPa. Plants droughted until 49% of tracheids had collapsed were found to fully recover tracheid shape and leaf function 1 week after rewatering. A simple mechanical model of tracheid collapse, derived from the theoretical buckling pressure for pipes, accurately predicted the collapse dynamics observed in P. grayi, substantiating estimates of cell wall elasticity and measured leaf water potential. The possible adaptive advantages of collapsible vascular tissue are discussed.
Dual loops meshing

We present a theoretical framework and practical method for the automatic construction of simple, all-quadrilateral patch layouts on manifold surfaces. The resulting layouts are coarse, surface-embedded cell complexes well adapted to the geometric structure, hence they are ideally suited as domains and base complexes for surface parameterization, spline fitting, or subdivision surfaces and can be used to generate quad meshes with a high-level patch structure that are advantageous in many application scenarios. Our approach is based on the careful construction of the layout graph's combinatorial dual. In contrast to the primal this dual perspective provides direct control over the globally interdependent structural constraints inherent to quad layouts. The dual layout is built from curvature-guided, crossing loops on the surface. A novel method to construct these efficiently in a geometry- and structure-aware manner constitutes the core of our approach.
Cerebrospinal fluid Aβ levels correlate with structural brain changes in Parkinson's disease

ParkWest is a large Norwegian multicenter study of newly diagnosed drug‐naïve subjects with Parkinson's disease (PD). Cognitively normal PD subjects (PDCN) and PD subjects with mild cognitive impairment (PDMCI) from this cohort have significant hippocampal atrophy and ventricular enlargement, compared to normal controls. Here, we aimed to investigate whether the same structural changes are associated with cerebrospinal fluid (CSF) levels of amyloid beta (Aβ)38, Aβ40, Aβ42, total tau (t‐tau), and phosphorylated tau (p‐tau). We performed three‐dimensional radial distance analyses of the hippocampi and lateral ventricles using the MRI data from ParkWest subjects who provided CSF at baseline. Our sample consisted of 73 PDCN and 18 PDMCI subjects. We found significant associations between levels of all three CSF Aβ analytes and t‐tau and lateral ventricular enlargement in the pooled sample. In the PDCN sample, all three amyloid analytes showed significant associations with the radial distance of the occipital and frontal horns of the lateral ventricles. CSF Aβ38 and Aβ42 showed negative associations, with enlargement in occipital and frontal horns of the lateral ventricles in the pooled sample, and a negative association with the occipital horns in PDMCI. CSF Aβ levels in early PD correlate with ventricular enlargement, previously associated with PD dementia. Therefore, CSF and MRI markers may help identify PD patients at high risk for developing cognitive decline and dementia in the course of their illness. Contrary to Alzheimer's disease, we found no associations between CSF t‐tau and p‐tau and hippocampal atrophy. © 2013 Movement Disorder Society
EARNINGS SMOOTHING AMONG GROWTH AND VALUE FIRMS

This research examines earnings management practices of growth vis-à-vis value firms. It proposes that growth firms have more incentive to 'manage their earnings' and that they do so more aggressively as compared to value firms. The primary reason for this behavior is that information asymmetries are more severe for growth firms. Using a sample of firms over the period from 1997 through 2001, this study finds that growth firms tend to manage their earnings upward and downward more aggressively than value firms. These results are robust to using different components of discretionary total accruals as a measure for earnings management and after controlling for other factors.
Persephin: A potential key component in human oral cancer progression through the RET receptor tyrosine kinase‐mitogen‐activated protein kinase signaling pathway

Persephin (PSPN) is a neurotrophic factor of the glial cell line‐derived neurotrophic factor (GDNF) family that promotes survival of multiple populations of neurons. Little is known about the relevance of PSPN in human malignancy including oral squamous cell carcinoma (OSCC). This study was undertaken to evaluate PSPN mRNA and protein expression by analyzing cellular proliferation and the cell cycle in PSPN knockdown cells in vitro. PSPN mRNA and protein were significantly (P < 0.05) up‐regulated in OSCC‐derived cells compared with human normal oral keratinocytes (n = 7). Cellular proliferation decreased significantly (P < 0.05) in PSPN knockdown cells with reduced receptor tyrosine kinase (RTK) signaling, and cell‐cycle arrest at the G1 phase resulted from up‐regulation of the cyclin‐dependent kinase inhibitors (p21Cip1, p27Kip1, p15INK4B, and p16INK4A). Furthermore, the PSPN protein expression in 101 primary OSCCs was significantly (P < 0.05) higher than in normal counterparts. Among the clinical variables analyzed, overexpression of PSPN also was related closely (P < 0.05) to tumoral size. Our results suggested that PSPN is a possible key regulator of OSCC progression via PSPN‐RET‐mitogen‐activated protein kinase activation and that PSPN overexpression may have diagnostic potential for OSCC. © 2013 Wiley Periodicals, Inc.
Evaluation of environmental scanning electron microscopy for analysis of Proteus mirabilis crystalline biofilms in situ on urinary catheters

Proteus mirabilis is a common cause of catheter-associated urinary tract infections and frequently leads to blockage of catheters due to crystalline biofilm formation. Scanning electron microscopy (SEM) has proven to be a valuable tool in the study of these unusual biofilms, but entails laborious sample preparation that can introduce artefacts, undermining the investigation of biofilm development. In contrast, environmental scanning electron microscopy (ESEM) permits imaging of unprocessed, fully hydrated samples, which may provide much insight into the development of P. mirabilis biofilms. Here, we evaluate the utility of ESEM for the study of P. mirabilis crystalline biofilms in situ, on urinary catheters. In doing so, we compare this to commonly used conventional SEM approaches for sample preparation and imaging. Overall, ESEM provided excellent resolution of biofilms formed on urinary catheters and revealed structures not observed in standard SEM imaging or previously described in other studies of these biofilms. In addition, we show that energy-dispersive X-ray spectroscopy (EDS) may be employed in conjunction with ESEM to provide information regarding the elemental composition of crystalline structures and demonstrate the potential for ESEM in combination with EDS to constitute a useful tool in exploring the mechanisms underpinning crystalline biofilm formation.
Neighborhood watch: security and privacy analysis of automatic meter reading systems

Research on smart meters has shown that fine-grained energy usage data poses privacy risks since it allows inferences about activities inside the home. While smart meter deployments are very limited, more than 40 million meters in the United States have been equipped with Automatic Meter Reading (AMR) technology over the past decades. AMR utilizes wireless communication for remotely collecting usage data from electricity, gas, and water meters. Yet to the best of our knowledge, AMR has so far received no attention from the security research community. In this paper, we conduct a security and privacy analysis of this technology. Based on our reverse engineering and experimentation, we find that the technology lacks basic security measures to ensure privacy, integrity, and authenticity of the data. Moreover, the AMR meters we examined continuously broadcast their energy usage data over insecure wireless links every 30s, even though these broadcasts can only be received when a truck from the utility company passes by. We show how this design allows any individual to monitor energy usage from hundreds of homes in a neighborhood with modest technical effort and how this data allows identifying unoccupied residences or people's routines. To cope with the issues, we recommend security remedies, including a solution based on defensive jamming that may be easier to deploy than upgrading the meters themselves.
Common Genetic Variants and Response to Atrial Fibrillation Ablation

Background—Common single nucleotide polymorphisms (SNPs) at chromosomes 4q25 (rs2200733, rs10033464 near PITX2), 1q21 (rs13376333 in KCNN3), and 16q22 (rs7193343 in ZFHX3) have consistently been associated with the risk of atrial fibrillation (AF). Single-center studies have shown that 4q25 risk alleles predict recurrence of AF after catheter ablation of AF. Here, we performed a meta-analysis to test the hypothesis that these 4 AF susceptibility SNPs modulate response to AF ablation. Methods and Results—Patients underwent de novo AF ablation between 2008 and 2012 at Vanderbilt University, the Heart Center Leipzig, and Massachusetts General Hospital. The primary outcome was 12-month recurrence, defined as an episode of AF, atrial flutter, or atrial tachycardia lasting >30 seconds after a 3-month blanking period. Multivariable analysis of the individual cohorts using a Cox proportional hazards model was performed. Summary statistics from the 3 centers were analyzed using fixed effects meta-analysis. A total of 991 patients were included (Vanderbilt University, 245; Heart Center Leipzig, 659; and Massachusetts General Hospital, 87). The overall single procedure 12-month recurrence rate was 42%. The overall risk allele frequency for these SNPs ranged from 12% to 35%. Using a dominant genetic model, the 4q25 SNP, rs2200733, predicted a 1.4-fold increased risk of recurrence (adjusted hazard ratio,1.3 [95% confidence intervals, 1.1–1.6]; P=0.011). The remaining SNPs, rs10033464 (4q25), rs13376333 (1q21), and rs7193343 (16q22) were not significantly associated with recurrence. Conclusions—Among the 3 genetic loci most strongly associated with AF, the chromosome 4q25 SNP rs2200733 is significantly associated with recurrence of atrial arrhythmias after catheter ablation for AF.
Magnetic resonance imaging of contaminated and damaged core cells in polymer composite sandwich panels

Computed tomography magnetic resonance imaging has been successfully applied to fully detect typical aircraft hydrogen-rich liquid contaminants entrapped in honeycomb core cells of structural polymer composite sandwich panels. With the aid of Bayesian-based image processing toolbox, the quantification, identification, and discrimination of the contaminants were also rapidly accomplished. Computed tomography magnetic resonance imaging has also been auspiciously applied to accurately define the extent of crushed-core damage in liquid impregnated honeycomb cells. Presented results strengthen the potential of magnetic resonance imaging as safe, fast, reliable, and user-friendly nondestructive testing technique to all engineering fields employing composite sandwich panels as high-demanding structural members.
AI-KU: Using Substitute Vectors and Co-Occurrence Modeling For Word Sense Induction and Disambiguation

Word sense induction aims to discover different senses of a word from a corpus by using unsupervised learning approaches. Once a sense inventory is obtained for an ambiguous word, word sense discrimination approaches choose the best-fitting single sense for a given context from the induced sense inventory. However, there may not be a clear distinction between one sense and another, although for a context, more than one induced sense can be suitable. Graded word sense method allows for labeling a word in more than one sense. In contrast to the most common approach which is to apply clustering or graph partitioning on a representation of first or second order co-occurrences of a word, we propose a system that creates a substitute vector for each target word from the most likely substitutes suggested by a statistical language model. Word samples are then taken according to probabilities of these substitutes and the results of the co-occurrence model are clustered. This approach outperforms the other systems on graded word sense induction task in SemEval-2013.