Miracle-dz/UniFAR-FTUs huggingface dataset:
Endogenous Myc controls mammalian epidermal cell size, hyperproliferation, endoreplication and stem cell amplification

The transcription factor Myc (c-Myc) plays an important role in cell growth and cell death, yet its physiological function remains unclear. Ectopic activation of Myc has been recently suggested to regulate cell mass, and Drosophila dmyc controls cellular growth and size independently of cell division. By contrast, it has been proposed that in mammals Myc controls cell division and cell number. To gain insights into this debate we have specifically knocked out Myc in epidermis. Myc epidermal knockout mice are viable and their keratinocytes continue to cycle, but they display severe skin defects. The skin is tight and fragile, tears off in areas of mechanical friction and displays impaired wound healing. Steady-state epidermis is thinner, with loss of the proliferative compartment and premature differentiation. Remarkably, keratinocyte cell size, growth and endoreplication are reduced, and stem cell amplification is compromised. The results provide new and direct evidence for a role for endogenous Myc in cellular growth that is required for hyperproliferative cycles and tissue homeostasis.
Density Formula and Concentration Inequalities with Malliavin Calculus

We show how to use the Malliavin calculus to obtain a new exact formula for the density $\rho$ of the law of any random variable $Z$ which is measurable and differentiable with respect to a given isonormal Gaussian process. The main advantage of this formula is that it does not refer to the divergence operator $\delta$ (dual of the Malliavin derivative $D$). The formula is based on an auxilliary random variable $G:= _H$, where $L$ is the generator of the so-called Ornstein-Uhlenbeck semigroup. The use of $G$ was first discovered by Nourdin and Peccati (PTRF 145 75-118 2009 MR-2520122 ), in the context of rates of convergence in law. Here, thanks to $G$, density lower bounds can be obtained in some instances. Among several examples, we provide an application to the (centered) maximum of a general Gaussian process. We also explain how to derive concentration inequalities for $Z$ in our framework.
Structure of Burkholderia cepacia UDP-Glucose Dehydrogenase (UGD) BceC and Role of Tyr10 in Final Hydrolysis of UGD Thioester Intermediate

ABSTRACT Members of the Burkholderia cepacia complex (BCC) are serious respiratory pathogens in immunocompromised individuals and in patients with cystic fibrosis (CF). They are exceptionally resistant to many antimicrobial agents and have the capacity to spread between patients, leading to a decline in lung function and necrotizing pneumonia. BCC members often express a mucoid phenotype associated with the secretion of the exopolysaccharide (EPS) cepacian. There is much evidence supporting the fact that cepacian is a major virulence factor of BCC. UDP-glucose dehydrogenase (UGD) is responsible for the NAD-dependent 2-fold oxidation of UDP-glucose (UDP-Glc) to UDP-glucuronic acid (UDP-GlcA), which is a key step in cepacian biosynthesis. Here, we report the structure of BceC, determined at 1.75-Å resolution. Mutagenic studies were performed on the active sites of UGDs, and together with the crystallographic structures, they elucidate the molecular mechanism of this family of sugar nucleotide-modifying enzymes. Superposition with the structures of human and other bacterial UGDs showed an active site with high structural homology. This family contains a strictly conserved tyrosine residue (Y10 in BceC; shown in italics) within the glycine-rich motif (GXGYXG) of its N-terminal Rossmann-like domain. We constructed several BceC Y10 mutants, revealing only residual dehydrogenase activity and thus highlighting the importance of this conserved residue in the catalytic activity of BceC. Based on the literature of the UGD/GMD nucleotide sugar 6-dehydrogenase family and the kinetic and structural data we obtained for BceC, we determined Y10 as a key catalytic residue in a UGD rate-determining step, the final hydrolysis of the enzymatic thioester intermediate.
Grading of Subarachnoid Hemorrhage: Modification of the World Federation of Neurosurgical Societies Scale on the Basis of Data for a Large Series of Patients

OBJECTIVEThe goals of this study were to use a large, prospectively collected, multicenter database for patients with aneurysmal subarachnoid hemorrhage (SAH) who were treated between 1991 and 1997 to determine the prognostic significance of clinical and radiological factors for outcomes and to use those factors to develop a grading scale to predict outcomes. METHODSA total of 3567 patients with SAH who were entered into four randomized clinical trials of tirilazad were studied. Outcomes were assessed 3 months after SAH, with the Glasgow Outcome Scale. Twenty clinical and radiological factors were entered into univariate and multivariate analyses, to determine factors prognostic for outcomes. Grading scales based on the most powerful prognostic parameters were statistically derived and validated and were compared with the World Federation of Neurosurgical Societies (WFNS) grading scale. RESULTSFactors predictive of outcomes included age, WFNS grade, history of hypertension, systolic blood pressure at admission, ruptured aneurysm location and size, blood clot thickness on computed tomographic scans, and angiographic vasospasm at admission. A grading scale using these factors could be derived; it predicted outcomes more accurately than did the WFNS scale, although it would be more complex to use. CONCLUSIONOutcome prediction after SAH can be improved by adding additional clinical and radiological factors to the WFNS scale, albeit with added complexity.
No Smurfs: Revealing Fraud Chains in Mobile Money Transfers

Mobile Money Transfer (MMT) services provided by mobile network operators enable funds transfers made on mobile devices of end-users, using digital equivalent of cash (electronic money) without any bank accounts involved. MMT simplifies banking relationships and facilitates financial inclusion, and, therefore, is rapidly expanding all around the world, especially in developing countries. MMT systems are subject to the same controls as those required for financial institutions, including the detection of Money Laundering (ML) - a source of concern for MMT service providers. In this paper we focus on an often practiced ML technique known as micro-structuring of funds or smurfing and introduce a new method for detection of fraud chains in MMT systems. Whereas classical detection methods are based on machine learning and data mining, this work builds on Predictive Security Analysis at Runtime (PSA@R), a model-based approach for event-driven process analysis. We provide an extension to PSA@R which allows us to identify fraudsters in an MMT service monitoring network behavior of its end-users. We evaluate our method on simulated transaction logs, containing approximately 460,000 transactions for 10,000 end-users, and compare it with classical fraud detection approaches. With 99.81% precision and 90.18% recall, we achieve better recognition performance in comparison with the state of the art.
Frequency Agile 90° Hybrid Coupler Using Barium Strontium Titanate Varactors

This paper presents a tunable quadrature hybrid coupler realized using integrated lumped components. The centre frequency of the hybrid is tuned by controlling the DC bias across barium strontium titanate (BST) varactors. The hybrid was designed to tune from 1710-2170 MHz. Varactors were fabricated by sputtering a 700 nm BST film on a c-plane sapphire substrate and patterning interdigital electrodes on top of the BST film. Promising results were achieved from the first prototype, with a maximum insertion loss of 3.5 dB and minimum return loss of 12.2 dB across the tuning range. Phase quadrature between the coupled ports is within 90plusmn5deg from 1710-2170 MHz.
On a Theory of Nonparametric Pairwise Similarity for Clustering: Connecting Clustering to Classification

Pairwise clustering methods partition the data space into clusters by the pairwise similarity between data points. The success of pairwise clustering largely depends on the pairwise similarity function defined over the data points, where kernel similarity is broadly used. In this paper, we present a novel pairwise clustering framework by bridging the gap between clustering and multi-class classification. This pairwise clustering framework learns an unsupervised nonparametric classifier from each data partition, and search for the optimal partition of the data by minimizing the generalization error of the learned classifiers associated with the data partitions. We consider two nonparametric classifiers in this framework, i.e. the nearest neighbor classifier and the plug-in classifier. Modeling the underlying data distribution by nonparametric kernel density estimation, the generalization error bounds for both unsupervised nonparametric classifiers are the sum of nonparametric pairwise similarity terms between the data points for the purpose of clustering. Under uniform distribution, the nonparametric similarity terms induced by both unsupervised classifiers exhibit a well known form of kernel similarity. We also prove that the generalization error bound for the unsupervised plug-in classifier is asymptotically equal to the weighted volume of cluster boundary [1] for Low Density Separation, a widely used criteria for semi-supervised learning and clustering. Based on the derived nonparametric pairwise similarity using the plug-in classifier, we propose a new nonparametric exemplar-based clustering method with enhanced discriminative capability, whose superiority is evidenced by the experimental results.
ChangeScribe: A Tool for Automatically Generating Commit Messages

During software maintenances tasks, commit messages are an important source of information, knowledge, and documentation that developers rely upon. However, the number and nature of daily activities and interruptions can influence the quality of resulting commit messages. This formal demonstration paper presents ChangeScribe, a tool for automatically generating commit messages. ChangeScribe is available at http://www.cs. wm.edu/semeru/changescribe (Eclipse plugin, instructions, demos and the source code).
An Efficient Hardware design and Implementation of Advanced Encryption Standard (AES) Algorithm

We propose an efficient hardware architecture design & implementation of Advanced Encryption Standard (AES). The AES algorithm defined by the National Institute of Standard and Technology (NIST) of United States has been widely accepted. The cryptographic algorithms can be implemented with software or built with pure hardware. However Field Programmable Gate Arrays (FPGA) implementation offers quicker solution and can be easily upgraded to incorporate any protocol changes. This contribution investigates the AES encryption cryptosystem with regard to FPGA and Very High Speed Integrated Circuit Hardware Description language (VHDL). Optimized and Synthesizable VHDL code is developed for the implementation of 128- bit data encryption process. AES encryption is designed and implemented in FPGA, which is shown to be more efficient than published approaches. Xilinx ISE 12.3i software is used for simulation. Each program is tested with some of the sample vectors provided by NIST and output results are perfect with minimal delay. The throughput reaches the value of 1609Mbit/sec for encryption process with Device XC6vlx240t of Xilinx Virtex Family.
Semi-Markov Models for Brownian Dynamics Permeation in Biological Ion Channels

Constructing accurate computational models that explain how ions permeate through a biological ion channel is an important problem in biophysics and drug design. Brownian dynamics simulations are large-scale interacting particle computer simulations for modeling ion channel permeation but can be computationally prohibitive. In this paper, we show the somewhat surprising result that a small-dimensional semi-Markov model can generate events (such as conduction events and dwell times at binding sites in the protein) that are statistically indistinguishable from Brownian dynamics computer simulation. This approach enables the use of extrapolation techniques to predict channel conduction when performing the actual Brownian dynamics simulation that is computationally intractable. Numerical studies on the simulation of gramicidin A ion channels are presented.
Genealogical Relationships between Early Medieval and Modern Inhabitants of Piedmont

In the period between 400 to 800 AD, also known as the period of the Barbarian invasions, intense migration is documented in the historical record of Europe. However, little is known about the demographic impact of these historical movements, potentially ranging from negligible to substantial. As a pilot study in a broader project on Medieval Europe, we sampled 102 specimens from 5 burial sites in Northwestern Italy, archaeologically classified as belonging to Lombards or Longobards, a Germanic people ruling over a vast section of the Italian peninsula from 568 to 774. We successfully amplified and typed the mitochondrial hypervariable region I (HVR-I) of 28 individuals. Comparisons of genetic diversity with other ancient populations and haplotype networks did not suggest that these samples are heterogeneous, and hence allowed us to jointly compare them with three isolated contemporary populations, and with a modern sample of a large city, representing a control for the effects of recent immigration. We then generated by serial coalescent simulations 16 millions of genealogies, contrasting a model of genealogical continuity with one in which the contemporary samples are genealogically independent from the medieval sample. Analyses by Approximate Bayesian Computation showed that the latter model fits the data in most cases, with one exception, Trino Vercellese, in which the evidence was compatible with persistence up to the present time of genetic features observed among this early medieval population. We conclude that it is possible, in general, to detect evidence of genealogical ties between medieval and specific modern populations. However, only seldom did mitochondrial DNA data allow us to reject with confidence either model tested, which indicates that broader analyses, based on larger assemblages of samples and genetic markers, are needed to understand in detail the effects of medieval migration.
Volumes of Velopharyngeal and Glossopharyngeal Airway Were Not Changed after Uvulopalatopharyngoplasty: Report of Three Cases

Objective. The aim of this study was to investigate the changes in velopharyngeal and glossopharyngeal airway morphology and volume after uvulopalatopharyngoplasty in three adult obstructive sleep apnea syndrome patients who had bilateral large tonsils using three-dimensional computed tomography. Case Report. All three patients (one male and two females) who presented with a history of heavy snoring and excessive daytime sleepiness were examined with overnight nocturnal polysomnography, which indicated moderate-to-severe obstructive sleep apnea syndrome. Because all patients had large tonsils, uvulopalatopharyngoplasty was expected to enlarge the pharyngeal airway. Polysomnography and three-dimensional computed tomography scanning were performed and compared, both before and 3 months after uvulopalatopharyngoplasty. Results. Unexpectedly, although the morphology of the glossopharyngeal airway clearly changed after UPPP, the volume changes in the velopharyngeal and glossopharyngeal airways were negligible.
Transplantation of a tyrosine editing domain into a tyrosyl-tRNA synthetase variant enhances its specificity for a tyrosine analog

To guarantee specific tRNA and amino acid pairing, several aminoacyl-tRNA synthetases correct aminoacylation errors by deacylating or “editing” misaminoacylated tRNA. A previously developed variant of Escherichia coli tyrosyl-tRNA synthetase (iodoTyrRS) esterifies or “charges” tRNATyr with a nonnatural amino acid, 3-iodo-l-tyrosine, and with l-tyrosine less efficiently. In the present study, the editing domain of phenylalanyl-tRNA synthetase (PheRS) was transplanted into iodoTyrRS to edit tyrosyl-tRNATyr and thereby improve the overall specificity for 3-iodo-l-tyrosine. The β-subunit fragments of the PheRSs from Pyrococcus horikoshii and two bacteria were tested for editing activity. The isolated B3/4 editing domain of the archaeal PheRS, which was exogenously added to the tyrosylation reaction with iodoTyrRS, efficiently reduced the production of tyrosyl-tRNATyr. In addition, the transplantation of this domain into iodoTyrRS at the N terminus prevented tyrosyl-tRNATyr production most strongly among the tested fragments. We next transplanted this archaeal B3/4 editing domain into iodoTyrRS at several internal positions. Transplantation into the connective polypeptide in the Rossmann-fold domain generated a variant that efficiently charges tRNATyr with 3-iodo-l-tyrosine, but hardly produces tyrosyl-tRNATyr. This variant, iodoTyrRS-ed, was used, together with an amber suppressor derived from tRNATyr, in a wheat germ cell-free translation system and incorporated 3-iodo-l-tyrosine, but not l-tyrosine, in response to the amber codon. Thus, the editing-domain transplantation achieved unambiguous pairing between the tRNA and the nonnatural amino acid in an expanded genetic code.
Cationic lipid-coated PEI/DNA polyplexes with improved efficiency and reduced cytotoxicity for gene delivery into mesenchymal stem cells

Background Effective gene transfection without serum deprivation is a prerequisite for successful stem cell-based gene therapy. Polyethylenimine (PEI) is an efficient nonviral gene vector, but its application has been hindered by serum sensitivity and severe cytotoxicity. Methods To solve this problem, a new family of lipopolyplexes was developed by coating PEI/DNA polyplexes with three serum-resistant cationic lipids, namely, lysinylated, histidylated, and arginylated cholesterol. The physical properties, transfection efficiency, cellular uptake, subcellular distribution, and cytotoxicity of the lipopolyplexes was investigated. Results The outer coat composed of lysinylated or histidylated cholesterol remarkably improved the transfection efficiency of the polyplex with a low PEI/DNA ratio of 2 in the presence of serum. The resulting lysinylated and histidylated cholesterol lipopolyplexes were even more efficient than the best performing polyplex with a high PEI/DNA ratio of 10. Results from cellular uptake and subcellular distribution studies suggest that their higher transfection efficiency may result from accelerated DNA nuclear localization. The superiority of the lipopolyplexes over the best performing polyplex was also confirmed by delivering the therapeutic gene, hVEGF165. Equally importantly, the lipid coating removed the necessity of introducing excess free PEI chains into the transfection solution for higher efficiency, generating lipopolyplexes with no signs of cytotoxicity. Conclusion Noncovalent modification of polyplexes with lysinylated and histidylated cholesterol lipids can simultaneously improve efficiency and reduce the toxicity of gene delivery under serum conditions, showing great promise for genetic modification of bone marrow stem cells.
The NICE.I: Noisy Iris Challenge Evaluation - Part I

This paper gives an overview of the NICE.I : Noisy Iris Challenge Evaluation -Part I contest. This contest differs from others in two fundamental points. First, instead of the complete iris recognition process, it exclusively evaluates the iris segmentation and noise detection stages, allowing the independent evaluation of one of the main recognition error sources. Second, it operates on highly noisy images that were captured to simulate less constrained imaging environments and constitute the second version of the UBIRIS database (UBIRIS.v2).
Simple method for characterization a ferroelectric material.

Jean-Michel Guy Le Floch was born in February 1977. He received his PhD degree from both the University of Limoges, France and the University of Western Australia, Perth, Australia. During his thesis, he studied high Q dielectric resonators using Bragg reflectors and also whispering gallery modes for metrology applications. In 2007, he was working as a CNRS postdoctoral fellow at XLIM institute in Limoges on thin film ferroelectric microwave devices.
The interaction site of Flap Endonuclease-1 with WRN helicase suggests a coordination of WRN and PCNA

Werner and Bloom syndromes are genetic RecQ helicase disorders characterized by genomic instability. Biochemical and genetic data indicate that an important protein interaction of WRN and Bloom syndrome (BLM) helicases is with the structure-specific nuclease Flap Endonuclease 1 (FEN-1), an enzyme that is implicated in the processing of DNA intermediates that arise during cellular DNA replication, repair and recombination. To acquire a better understanding of the interaction of WRN and BLM with FEN-1, we have mapped the FEN-1 binding site on the two RecQ helicases. Both WRN and BLM bind to the extreme C-terminal 18 amino acid tail of FEN-1 that is adjacent to the PCNA binding site of FEN-1. The importance of the WRN/BLM physical interaction with the FEN-1 C-terminal tail was confirmed by functional interaction studies with catalytically active purified recombinant FEN-1 deletion mutant proteins that lack either the WRN/BLM binding site or the PCNA interaction site. The distinct binding sites of WRN and PCNA and their combined effect on FEN-1 nuclease activity suggest that they may coordinately act with FEN-1. WRN was shown to facilitate FEN-1 binding to its preferred double-flap substrate through its protein interaction with the FEN-1 C-terminal binding site. WRN retained its ability to physically bind and stimulate acetylated FEN-1 cleavage activity to the same extent as unacetylated FEN-1. These studies provide new insights to the interaction of WRN and BLM helicases with FEN-1, and how these interactions might be regulated with the PCNA–FEN-1 interaction during DNA replication and repair.
Automatic Acquisition of Language Model based on Head-Dependent Relation between Words

Language modeling is to associate a sequence of words with a priori probability, which is a key part of many natural language applications such as speech recognition and statistical machine translation. In this paper, we present a language modeling based on a kind of simple dependency grammar. The grammar consists of head-dependent relations between words and can be learned automatically from a raw corpus using the reestimation algorithm which is also introduced in this paper. Our experiments show that the proposed model performs better than n-gram models at 11% to 11.5% reductions in test corpus entropy.