Miracle-dz/UniFAR-FTUs huggingface dataset:
A comparison of key aspects of gene regulation in Streptomyces coelicolor and Escherichia coli using nucleotide-resolution transcription maps produced in parallel by global and differential RNA sequencing

Streptomyces coelicolor is a model for studying bacteria renowned as the foremost source of natural products used clinically. Post‐genomic studies have revealed complex patterns of gene expression and links to growth, morphological development and individual genes. However, the underlying regulation remains largely obscure, but undoubtedly involves steps after transcription initiation. Here we identify sites involved in RNA processing and degradation as well as transcription within a nucleotide‐resolution map of the transcriptional landscape. This was achieved by combining RNA‐sequencing approaches suited to the analysis of GC‐rich organisms. Escherichia coli was analysed in parallel to validate the methodology and allow comparison. Previously, sites of RNA processing and degradation had not been mapped on a transcriptome‐wide scale for E. coli. Through examples, we show the value of our approach and data sets. This includes the identification of new layers of transcriptional complexity associated with several key regulators of secondary metabolism and morphological development in S. coelicolor and the identification of host‐encoded leaderless mRNA and rRNA processing associated with the generation of specialized ribosomes in E. coli. New regulatory small RNAs were identified for both organisms. Overall the results illustrate the diversity in mechanisms used by different bacterial groups to facilitate and regulate gene expression.
CTX-M-32 beta-lactamase-producing uropathogenic Escherichia coli isolated in Latin America.

Background Uropathogenic Escherichia coli (UPEC) is the most important pathogen involved in urinary tract infections (UTIs). Beta-lactam antibiotics have been widely used to treat UPEC infections; however, extended-spectrum beta-lactamases (ESBLs) create significant therapeutic problems by inactivating almost all beta-lactams except cephamycins and carbapenems [1,2]. The CTX-M-type beta-lactamases are members of a lineage of ESBLs currently recognized as the most widespread worldwide, both in clinical and community settings. Based on their amino-acid sequence diversity, more than 135 of the CTX-M identified variants have been classified into six major clusters: CTX-M-1, -2, -8, -9, -25 and -45. (www.lahey.org/studies/webt.stm) [3-5]. These betalactamases predominantly hydrolyze cefotaxime (or ceftriaxone) but are weakly active against ceftazidime. However, to date the CTX-M-1 cluster is the most diversified group and includes more efficient CTX-M variants with a strong hydrolytic activity against ceftazidime, as is the case for CTX-M-32 [6]. In 2004, blaCTX-M-32 was first reported in an E. coli isolate from Spain [7]. Since then, CTX-M-32 continues to spread mainly in Mediterranean countries [3]. In Latin America, the prevalence of CTX-M beta-lactamases is represented by the CTX-M-2, but other variants such as CTX-M-1, CTX-M-8, CTX-M-9, CTX-M-12, CTX-M-14, CTX-M-15, CTX-M-16, CTX-M-24 and CTX-M-56 have been identified in this continent [4,8]. In this report, we describe the first detection of CTXM-32 in uropathogenic Escherichia coli from Venezuela, which is also the first report of this enzyme in Latin America.
A New Measure of Word Semantic Similarity Based on WordNet Hierarchy and DAG Theory

The problem of measuring the semantic similarity between words has been considered a fundamental operation in the field of computational lexical semantics, but the accuracy of existing computational methods is not very close to what humans would perceive. This paper presents a new approach to measure the semantic similarity between words in the hierarchy of WordNet. Our approach considers not only the semantic distance between two words but also the feature information of the DAG (Directed Acyclic Graph). A common data set of word pairs is used to evaluate the proposed approach: we first calculate the semantic similarities of 30 word pairs, then the correlation coefficient between human judgement and six computational measures are calculated, the experiment shows our approach is better than other existing computational models.
A Deterministic Equivalent for the Analysis of Correlated MIMO Multiple Access Channels

In this article, novel deterministic equivalents for the Stieltjes transform and the Shannon transform of a class of large dimensional random matrices are provided. These results are used to characterize the ergodic rate region of multiple antenna multiple access channels, when each point-to-point propagation channel is modelled according to the Kronecker model. Specifically, an approximation of all rates achieved within the ergodic rate region is derived and an approximation of the linear precoders that achieve the boundary of the rate region as well as an iterative water-filling algorithm to obtain these precoders are provided. An original feature of this work is that the proposed deterministic equivalents are proved valid even for strong correlation patterns at both communication sides. The above results are validated by Monte Carlo simulations.
Genetic Evidence for Interdomain Regulation of the Phenol-responsive 54-dependent Activator DmpR*

The σ54-dependent DmpR activator regulates transcription of the dmp operon that encodes the enzymes for catabolism of (methyl)phenols. DmpR is expressed constitutively, but its transcriptional promoting activity is controlled positively in direct response to the presence of aromatic pathway substrates (effectors). DmpR has a distinct domain structure with the amino-terminal A-domain controlling the specificity of activation of the regulator by aromatic effectors (signal reception), a central C-domain mediating an ATPase activity essential for transcriptional activation, and a carboxyl-terminal D-domain involved in DNA binding. Deletion of the A-domain has been shown previously to result in an effector-independent transcriptional activator with constitutive ATPase activity. These results, in conjunction with the location of mutations within the A- and C-domains which exhibit an effector-independent (semiconstitutive) property, have led to a working model in which the A-domain serves to mask the ATPase and transcriptional promoting activity of the C-domain in the absence of effectors. To investigate the mechanism by which the A-domain exerts its repressive effect, we developed a genetic system to select positively for intramolecular second site revertants of DmpR. The results demonstrate (i) that mutations within the A-domain can suppress the semiconstitutive activity of C-domain located mutations and vice versa; (ii) that the C-domain located mutations do not influence the intrinsic ATPase and transcriptional promoting property of the C-domain in the absence of the A-domain; and (iii) that semiconstitutive mutations of the A- and C-domain have an additive effect. Taken together these results support a model in which the A-domain represses the function(s) of the C-domain by direct interactions between residues of the two domains.
VELOCITY TRENDS IN THE DEBRIS OF SAGITTARIUS AND THE SHAPE OF THE DARK-MATTER HALO OF THE GALAXY

Recently, radial velocities have been measured for a large s ample of M giants from the 2MASS catalog, selected to be part of the Sgr dwarf leading and trailing streams. Here we present a comparison of their kinematics to models of the Sgr dwarf debris orbiting Galactic potentials , with halo components of varying degrees of flattening and elongation. This comparison shows that the portion of th e trailing stream mapped so far is dynamically young and hence does not provide very stringent constraints on the shape of the Galactic dark-matter halo. The leading stream, however, contains slightly older debris, and its ki nematics provide for the first time direct evidence that the dark-matter halo of the Galaxy has a prolate shape with an average density axis ratio within the orbit of Sgr close to 5/3. Subject headings: dark-matter – Galaxy: halo, kinematics and dynamics, struc tu e, fundamental parameters
Architectures for function evaluation on FPGAs

This paper presents a new family of architectures for multi-cycle area-efficient evaluation of elementary and composite functions, and an exploration of the design tradeoffs for implementation on Field Programmable Gate Arrays (FPGAs). The method is exemplified with two common functions, sine and power-of-2. To test the performance of each design, we compare the proposed architecture to an established table-based method for several different input word-lengths and output precision requirements. FPGA-based results are presented, illustrating both the technology-independent and the technology-specific attributes of the tradeoff of area and speed between the proposed techniques.
Adrenomedullin 2/intermedin: a putative drug candidate for treatment of cardiometabolic diseases

Adrenomedullin (ADM) 2/intermedin (IMD) is a short peptide that belongs to the CGRP superfamily. Although it shares receptors with CGRP, ADM and amylin, ADM2 has significant and unique functions in the cardiovascular system. In the past decade, the cardiovascular effect of ADM2 has been carefully analysed. In this review, progress in understanding the effects of ADM2 on the cardiovascular system and its protective role in cardiometabolic diseases are summarized.
Continuing coevolution of virus and defective interfering particles and of viral genome sequences during undiluted passages: virus mutants exhibiting nearly complete resistance to formerly dominant defective interfering particles

We quantitatively analyzed the interference interactions between defective interfering (DI) particles and mutants of cloned vesicular stomatitis virus passaged undiluted hundreds of times in BHK-21 cells. DI particles which predominated at different times in these serial passages always interfered most strongly (and very efficiently) with virus isolated a number of passages before the isolation of the DI particles. Virus isolated at the same passage level as the predominant DI particles usually exhibited severalfold resistance to these DI particles. Virus mutants (Sdi- mutants) isolated during subsequent passages always showed increasing resistance to these DI particles, followed by decreasing resistance as new DI particles arose to predominate and exert their own selective pressures on the virus mutant population. It appears that such coevolution of virus and DI particle populations proceeds indefinitely through multiple cycles of selection of virus mutants resistant to a certain DI particle (or DI particle class), followed by mutants resistant to a newly predominant DI particle, etc. At the peak of resistance, virus mutants were isolated which were essentially completely resistant to a particular DI particle; i.e., they were several hundred thousand-fold resistant, and they formed plaques of normal size and numbers in the presence of extremely high multiplicities of the DI particle. However, they were sensitive to interference by other DI particles. Recurring population interactions of this kind can promote rapid virus evolution. Complete sequencing of the N (nucleocapsid) and NS (polymerase associated) genes of numerous Sdi- mutants collected at passage intervals showed very few changes in the NS protein, but the N gene gradually accumulated a series of stable nucleotide and amino acid substitutions, some of which correlated with extensive changes in the Sdi- phenotype. Likewise, the 5' termini (and their complementary plus-strand 3' termini) continued to accumulate extensive base substitutions which were strikingly confined to the first 47 nucleotides. We also observed addition and deletion mutations in noncoding regions of the viral genome at a level suggesting that they probably occur at a high frequency throughout the genome, but usually with lethal or debilitating consequences when they occur in coding regions.
Visualizing a set of olfactory sensory neurons responding to a bile salt

SUMMARY In the present study, we exposed the olfactory epithelia of crucian carp, Carassius carassius, and brown trout, Salmo trutta, to dextran coupled with Alexa dyes together with odorants. Dye uptake was severely reduced after pre-exposure to nocodazole, an inhibitor of microtubule polymerization that impairs endocytosis, supporting the hypothesis that odour-activated olfactory receptor molecules undergo endocytosis. Application of the bile acid taurolithocholate, a potent and specific odorant for fish, resulted in the labelling of a sparse (less than 3%) cell population with the typical morphology of ciliated sensory neurons (CSNs) – long dendrites and cell somata deep in the sensory epithelium. The dye was distributed throughout the sensory neuron, also revealing axons and target glomeruli. Stained axons redistribute at the entrance of the olfactory bulb and terminate in two small target areas, a dorsal and a medial one. These results are consistent with the notion that taurolithocholate is detected specifically by a few ciliated sensory neurons. Application of the olfactory epithelium of brown trout to bile acid stained cells with the appearance of CSNs. Application of an alarm agonist, hypxanthine-3-N-oxide, to crucian carp olfactory organ caused staining of another set of sensory neurons. Furthermore, our results show that odour-induced uptake of a dye can serve to identify the subtype of olfactory sensory neurons responding to a particular odorant, and to pinpoint the target regions of these neurons in the olfactory bulb as a first step to elucidating the neuronal network responding to a particular odour.
5Cam: a multicamera system for panoramic capture of videos

This paper presents a multicamera system for panoramic video capture. The system, named 5Cam, is constructed from low-cost digital cameras and standard PCs running on Windows. The approach for panoramic video generation consists of three phases (camera calibration, image fusion and synchronization, video stream production), which are described in detail in the paper. Using this approach, a 5Cam prototype has been implemented and evaluated. Initial experiments has shown that 5Cam system is effective, obtaining sufficiently high frame rate and quality for 360 degree video capture.
A photometric stereo approach to face recognition

Face recognition has received much interest in the last decade, as the need for reliable personal identification security has become ever more critical. At present for face recognition to be a viable personal identification method an accurate low cost solution is required. Many two-dimensional (2D) face recognition systems have been implemented, which demonstrate the potential of using face recognition, although at present these systems are often unreliable. To produce more reliable face recognition systems, a recent trend has been to use three-dimensional (3D) data, which as research has shown is more accurate and robust than traditional 2D techniques. 3D face recognition systems, however, are often expensive relative to 2D alternatives, as precise capture equipment is required. This research project has identified photometric stereo as a low cost 3D capture system, which has been little researched in the area of face recognition. An investigation is presented, which evaluates the capabilities of photometric stereo for use in the area of face recognition by means of a number of experiments. These experiments are conducted using a photometric stereo system, designed and implemented for this research project.
Investigation of Elements Sufficient To Imprint the Mouse Air Promoter

ABSTRACT Imprinted maternal-allele-specific expression of the mouse insulin-like growth-factor type 2 receptor (Igf2r) gene depends on a 3.7-kb element named region 2, located in the second intron of the gene. Region 2 carries a maternal-allele-specific methylation imprint and contains an imprinted CpG island promoter (Air) that expresses a noncoding antisense RNA from the paternal inherited allele only. Here, we use transgenes to test the minimal requirements for imprinting of Air and to test if the action of region 2 is restricted to Igf2r. Transgenes up to 9 kb with Air as a single promoter are expressed but not imprinted. When coupled to the Igf2rCpG island promoter on a 44-kb transgene, Air was imprinted in one of three lines. However, Air on a 4.6-kb fragment is also imprinted in 2 of 14 lines when inserted in an intron of an adenine phosphoribosyltransferase (Aprt) transgene, and in one line, the imprinted methylation and expression ofAir have been transferred onto the AprtCpG island promoter. These data suggest that a dual CpG island promoter setting may facilitate Air imprinting as a short transgene and also show that Air can transfer imprinting onto other genes. However, for reliable Air imprinting, elements are necessary that are located outside a 44-kb region spanning the Air-Igf2r promoters.
NKp44 Triggers NK Cell Activation through DAP12 Association That Is Not Influenced by a Putative Cytoplasmic Inhibitory Sequence 1

NKp44 (NCR2) is a member of the natural cytotoxicity receptor (NCR) family that is expressed on activated human NK cells. We dissected structural attributes of NKp44 to determine their contributions to receptor function. Our results demonstrate that surface expression and NK cell activation by NKp44 is mediated through noncovalent association with the immunoreceptor tyrosine-based activation motif-containing protein, DAP12. Physical linkage to DAP12 requires lysine-183 in the NKp44 transmembrane domain. Intriguingly, the cytoplasmic domain of NKp44 also contains a sequence that matches the immunoreceptor tyrosine-based inhibitory motif (ITIM) consensus. By expressing a chimeric receptor in an NK-like cell line, we found that this ITIM-like motif from NKp44 lacks inhibitory capacity in a redirected cytotoxicity assay. The NKp44 cytoplasmic tyrosine was efficiently phosphorylated in the chimeric receptor upon treating the cells with pervanadate, but it was unable to recruit ITIM-binding negative effector phosphatases. We also generated NK-like cell lines expressing epitope-tagged wild-type or tyrosine to phenylalanine mutant (Y238F) versions of NKp44 and compared their capacities to induce activation marker expression, promote IFN-γ production, or stimulate target cell cytotoxicity. We did not detect any tyrosine-dependent reduction or enhancement of NK cell activation through wild-type vs. Y238F mutant NKp44. Finally, the cytoplasmic tyrosine-based sequence did not provide a docking site for the AP-2 clathrin adaptor, nor did it potentiate receptor internalization. In summary, all activating properties and surface expression of NKp44 are mediated through its association with DAP12, and the putative ITIM in the NKp44 cytoplasmic domain does not appear to attenuate activating function.
INFLAMMATION AND INFLAMMATORY BOWEL DISEASE Distribution and partial characterisation of IgG Fc binding protein in various mucin producing cells and body fluids

Background and aims: Mucus released from goblet cells is important in intestinal mucosal defence, and mucin glycoproteins are thought to be major components of mucus. Recently, we identified and cloned another component of human colonic mucus, IgG Fc binding protein (FcγBP). FcγBP is immunologically distinct from known Fcγ receptors and its structure contains repeated cysteine rich unit sequences resembling those present in mucins. In this work, we assessed the tissue distribution of FcγBP, its binding activity in various body fluids, and its ability to inhibit complement mediated haemolysis. Methods: Immunohistochemical localisation of FcγBP, using monoclonal antibodies against FcγBP (K9 or K17) and labelled IgG, was conducted in various mucin producing tissues: colon, small intestine, stomach, gall bladder, cystic duct, choledochus, bronchus, submandibular gland, conjunctiva, and cervix uteri. The binding activity of FcγBP in mucus extracted from colon, gastric juice, bile, nasal discharges, saliva, sputum, and tears was also examined by immunodotblot and immunoprecipitation using these monoclonal antibodies. Inhibition of complement mediated haemolysis by FcγBP was investigated using sheep red blood cells (SRBC) and anti-SRBC IgG. Results: The immunohistochemical study revealed that mucin secreting cells in the colon, small intestine, gall bladder, cystic duct, choledochus, bronchus, submandibular gland, and cervix uteri contained FcγBP, and immunodotblot and immunoprecipitation analysis using IgG and monoclonal antibodies demonstrated that the fluids secreted by these cells were capable of binding IgG. Mucin producing cells of the conjunctiva did not express FcγBP molecules or bind to IgG. The surface mucus cells in the stomach were variably positive for FcγBP. Perhaps because of proteolytic degradation, FcγBP in gut lavage fluid did not have IgG binding activity, although this activity was present in the mucus covering the colon. FcγBP suppressed complement mediated haemolysis of SRBC. Conclusions: FcγBP is widely expressed on mucosal surfaces and in external secretions. It is functionally intact in several fluids. These findings lend support to the concept that FcγBP is an important component of mucosal immunological defences.
Efficient pricing of Asian options under Lévy processes based on Fourier cosine expansions. Part II. Early-exercise features and GPU implementation

In this article, we propose an efficient pricing method for Asian options with early–exercise features. It is based on a two–dimensional integration and a backward recursion of the Fourier coefficients, in which several numerical techniques, like Fourier cosine expansions, Clenshaw–Curtis quadrature and the Fast Fourier transform (FFT) are employed. Rapid convergence of the pricing method is illustrated by an error analysis. Its performance is further demonstrated by various numerical examples, where we also show the power of an implementation on the Graphics Processing Unit (GPU).