Miracle-dz/UniFAR-FTUs huggingface dataset:
At Least One Intron Is Required for the Nonsense-Mediated Decay of Triosephosphate Isomerase mRNA: a Possible Link between Nuclear Splicing and Cytoplasmic Translation

ABSTRACT Mammalian cells have established mechanisms to reduce the abundance of mRNAs that harbor a nonsense codon and prematurely terminate translation. In the case of the human triosephosphate isomerase (TPI gene), nonsense codons located less than 50 to 55 bp upstream of intron 6, the 3′-most intron, fail to mediate mRNA decay. With the aim of understanding the feature(s) of TPI intron 6 that confer function in positioning the boundary between nonsense codons that do and do not mediate decay, the effects of deleting or duplicating introns have been assessed. The results demonstrate that TPI intron 6 functions to position the boundary because it is the 3′-most intron. Since decay takes place after pre-mRNA splicing, it is conceivable that removal of the 3′-most intron from pre-mRNA “marks” the 3′-most exon-exon junction of product mRNA so that only nonsense codons located more than 50 to 55 nucleotides upstream of the “mark” mediate mRNA decay. Decay may be elicited by the failure of translating ribosomes to translate sufficiently close to the mark or, more likely, the scanning or looping out of some component(s) of the translation termination complex to the mark. In support of scanning, a nonsense codon does not elicit decay if some of the introns that normally reside downstream of the nonsense codon are deleted so the nonsense codon is located (i) too far away from a downstream intron, suggesting that all exon-exon junctions may be marked, and (ii) too far away from a downstream failsafe sequence that appears to function on behalf of intron 6, i.e., when intron 6 fails to leave a mark. Notably, the proposed scanning complex may have a greater unwinding capability than the complex that scans for a translation initiation codon since a hairpin structure strong enough to block translation initiation when inserted into the 5′ untranslated region does not block nonsense-mediated decay when inserted into exon 6 between a nonsense codon residing in exon 6 and intron 6.
Diagnosis and Treatment of Galactosaemia

to operate. No great difference, either in the level at which patency is established or in the appearance of tubal-contraction waves, is usually seen when insufflation is repeated even after several months. Rubin (1939) maintains that the tracings can be correlated with phases of endometrial or ovarian activity. I have not been able to confirm this. More active or more frequent peristalsis may be seen at various stages of the menstrual cycle and spasm may also be exhibited for no apparent reason. Moreover, if two or three insufflations are performed on the one day-that is, within a few hours of one another-the tracings obtained need not be closely similar.
Annotation sémantique par classification

Les systemes actuels d'annotation semantique exploitent peu les connaissances du domaine et fonctionnent essentiellement du texte vers l'ontologie. Pourtant, il est frequent qu'un element dans une page doive etre annote par un concept parce que certains autres elements de cette meme page sont annotes par d'autres concepts. Cet article propose une methode d'annotation prenant en compte cette dependance entre concepts, exprimee dans une ontologie sous forme de concepts definis. L'utilisation des logiques de descriptions comme mode de representation unifiee de la structure des documents, de l'ontologie et de l'annotation semantique du document permet de definir le processus d'annotation comme un mecanisme de classification et d'introduire la notion de classe d'annotation.
A Generic Non-linear Method for Fisheye Correction

With rapid advances in the field of vision based systems and ever increasing applications that they foster to; it brings along many challenges both in terms of algorithm design and associated hardware. One such widely used gadget is the fisheye camera that is used in myriad of applications in various fields owing to their wide Field of View. However, these lenses introduce distortions when any real-world object gets mapped on to the image plane. The amount of distortion in fish eye images increases while moving radially outward from the image centre. Therefore, the amount of correction to be applied should also vary accordingly based on the pixel location. This paper presents a fast and real-time implementable technique for fisheye correction. The proposed method uses non-linear radial stretching and scaling down of pixels thereafter; both in X and Y dimensions for correction. For real-time implementation of the proposed algorithm, we propose the use of inverse mapping matrix. This enables transformation of computationally extensive equations used for correction into a simple look-up table that can easily be implemented on a FPGA platform. General Terms Image Processing, Fisheye Images
Discrete-time stochastic optimal control via occupation measures and moment relaxations

We consider discrete-time nonlinear stochastic optimal control problems for which all the data are polynomial. For this class of problems we derive a hierarchy of linear matrix inequality relaxations which is based on occupation measures and moment theory. The dual of the convex problem obtained, which can be interpreted in terms of the Bellman equation, is then used to derive an almost optimal control law. A numerical example illustrates the effectiveness of the approach.
The face perception system becomes species-specific at 3 months: An eye-tracking study

The current study aimed at investigating own- vs. other-species preferences in 3-month-old infants. The infants’ eye movements were recorded during a visual preference paradigm to assess whether they show a preference for own-species faces when contrasted with other-species faces. Human and monkey faces, equated for all low-level perceptual characteristics, were used. Our results demonstrated that 3-month-old infants preferred the human face, suggesting that the face perception system becomes species-specific after 3 months of visual experience with a specific class of faces. The eye tracking results are also showing that fixations were more focused on the eye area of human faces, supporting the notion of their importance in holding visual attention.
Relation of infant diet to childhood health: seven year follow up of cohort of children in Dundee infant feeding study

Abstract Objective: To investigate the relation of infant feeding practice to childhood respiratory illness, growth, body composition, and blood pressure. Design: Follow up study of a cohort of children (mean age 7.3 years) who had detailed infant feeding and demographic data collected prospectively during the first two years of life. Setting: Dundee. Subjects: 674 infants, of whom 545 (81%) were available for study. Data on respiratory illness were available for 545 children (mean age 7.3 (range 6.1- 9.9) years); height for 410 children; weight and body mass index for 412 children; body composition for 405 children; blood pressure for 301 children (mean age 7.2 (range 6.9-10.0) years). Main outcome measures: Respiratory illness, weight, height, body mass index, percentage body fat, and blood pressure in relation to duration of breast feeding and timing of introduction of solids. Results: After adjustment for the significant confounding variables the estimated probability of ever having respiratory illness in children who received breast milk exclusively for at least 15 weeks was consistently lower (17.0% (95% confidence interval 15.9% to 18.1%) for exclusive breast feeding, 31.0% (26.8% to 35.2%) for partial breast feeding, and 32.2% (30.7% to 33.7%) for bottle feeding. Solid feeding before 15 weeks was associated with an increased probability of wheeze during childhood (21.0% (19.9% to 22.1%) v 9.7% (8.6% to 10.8%)). It was also associated with increased percentage body fat and weight in childhood (mean body fat 18.5% (18.2% to 18.8%) v 16.5% (16.0% to 17.0%); weight standard deviation score 0.02 (−0.02 to 0.06) v −0.09 (−0.16 to 0.02). Systolic blood pressure was raised significantly in children who were exclusively bottle fed compared with children who received breast milk (mean 94.2 (93.5 to 94.9) mm Hg v 90.7 (89.9 to 91.7) mm Hg). Conclusions: The probability of respiratory illness occurring at any time during childhood is significantly reduced if the child is fed exclusively breast milk for 15 weeks and no solid foods are introduced during this time. Breast feeding and the late introduction of solids may have a beneficial effect on childhood health and subsequent adult disease. Key messages Current guidelines in the United Kingdom recommend that babies are exclusively breast fed for the first 4 months of life, with solids being introduced thereafter This study found that exclusive breast feeding is associated with a significant reduction in childhood respiratory illness The early introduction of solids is associated with increased body fat and weight in childhood Exclusive bottle feeding is associated with higher systolic blood pressure in childhood Breast feeding and delaying the introduction of solids until after 15 weeks may have a beneficial effect on childhood health and subsequent adult disease
The HOLJ Corpus. Supporting Summarisation of Legal Texts

We describe an XML-encoded corpus of texts in the legal domain which was gathered for an automatic summarisation project. We describe two distinct layers of annotation: manual annotation of the rhetorical status of sentences and an entirely automatic annotation process incorporating a host of individual linguistic processors. The manual rhetorical status annotation has been developed as training and testing material for a summarisation system based on the work of Teufel and Moens, while the automatic layer of annotation encodes linguistic information as features for a machine learning approach to rhetorical status classification.
Putting OWL into Production at the European Bioinformatics Institute

The Experimental Factor Ontology (EFO) is an OWL based ontology of experimental variables used in a wide range of biomedical studies. EFO has been in use since 2007 and was the first OWL ontology to be used in production ready data services at the EBI. As the ontology content, application requirements and the OWL language have evolved over time, this has presented several challenges in how to develop EFO and how best to deploy this within the applications. In this paper we describe our experiences of using OWL and the challenges we have faced which include; managing imports from multiple ontologies, optimising axiomatisation for performance, displaying the ontology in domain specific views, incorporating the ontology into a continuous integration framework and deploying the ontology in applications and curation tools. We also describe some of the tools we have developed and applications EFO is now used in and, finally, discuss our future challenges.
WSN16-2: Load Sensitive Topology Control for Energy Conservation in Ad Hoc Sensor Networks

Sensor networks are usually composed of tiny and resource constraint devices, which make energy conservation a vital concern of their design. Reducing energy consumption has been addressed through different aspects till now. Topology control (TC), as the process of determining the transmission ranges of nodes to optimize energy utilization while keeping some network properties like connectivity, is a well-known approach. However, current TC schemes mostly account the transmission range of each node as the exclusive estimator for its energy consumption, while ignoring the amount of data it sends or relays. In this paper, we redefine the problem of topology control regarding both network load and transmission range parameters. Our approach is particularly formulated for sensor networks with one or more base stations. Then, under a certain modeling of environment, proper mathematical relations are provided to find the optimum solution. Finally, we show the advantages of our proposal through presenting analytical and experimental results.
The grassroots of a green revolution

A tread strip is positioned in proximity to the outer periphery of a tire carcass. A bonding substance is provided intermediate the carcass and the strip and has adhesive characteristics sufficient to temporarily bond the strip to the carcass when the strip and carcass are pressed together. The bonding substance is also sufficiently plastic to result in intimate contact by the substance of the facing surfaces of the strip and the carcass when the strip and carcass are pressed together. The bonding substance, for example unvulcanized rubber, is capable of permanently bonding the strip to the carcass when the bonding substance is sufficiently heated. Initially, the strip and carcass are pressed together in such a manner as to expel gases from between the strip and carcass and in such a manner as to cause the bonding substance to temporarily bond the strip to the carcass. The bonding substance is heated to a temperature resulting in permanent bonding of the strip to the carcass, and during the heating step, escape of the bonding substance from between the strip and the carcass is prevented.
Effect of Glycyrrhizin on Pseudomonal Skin Infections in Human-Mouse Chimeras

In our previous studies, peripheral blood lineage−CD34+CD31+ cells (CD31+ IMC) appearing in severely burned patients have been characterized as inhibitor cells for the production of β-defensins (HBDs) by human epidermal keratinocytes (NHEK). In this study, the effect of glycyrrhizin on pseudomonal skin infections was studied in a chimera model of thermal injury. Two different chimera models were utilized. Patient chimeras were created in murine antimicrobial peptide-depleted NOD-SCID IL-2rγnull mice that were grafted with unburned skin tissues of severely burned patients and inoculated with the same patient peripheral blood CD31+ IMC. Patient chimera substitutes were created in the same mice that were grafted with NHEK and inoculated with experimentally induced CD31+ IMC. In the results, both groups of chimeras treated with glycyrrhizin resisted a 20 LD50 dose of P. aeruginosa skin infection, while all chimeras in both groups treated with saline died within 3 days of the infection. Human antimicrobial peptides were detected from the grafted site tissues of both groups of chimeras treated with glycyrrhizin, while the peptides were not detected in the same area tissues of controls. HBD-1 was produced by keratinocytes in transwell-cultures performed with CD31+ IMC and glycyrrhizin. Also, inhibitors (IL-10 and CCL2) of HBD-1 production by keratinocytes were not detected in cultures of patient CD31+ IMC treated with glycyrrhizin. These results indicate that sepsis stemming from pseudomonal grafted site infections in a chimera model of burn injury is controllable by glycyrrhizin. Impaired antimicrobial peptide production at the infection site of severely burned patients may be restored after treatment with glycyrrhizin.
The New Registration Method Used in ARDK

A tool, called ARDK (Augmented Reality Development Kit), which has more advantages than former tools of this kind, is developed and represented in this paper. The advantages over others are as follows: without setting internal parameters of camera ahead of time, ARDK allows the system to automatically compute them at the real-time during the operating. It also solves the problem of being unable to change the internal parameters of camera when the system is running. This tool adopts a developed camera pose tracking method based on Homography Matrix to settle the problem of Registration when the mark is partly covered, and also enables the system to avoid the error from frames’ accumulation. This paper illustrates the camera pose tracking algorithm and the experiment results, as well as a virtual residential area planning system based on the Augmented Reality, which is completed by using ARDK
Highly Ionized High-Velocity Clouds: Intergalactic Gas in the Local Group or Distant Gas in the Galactic Halo?

In the course of our studies of the gaseous halo surrounding the Milky Way, we have recently identified several high-velocity clouds (HVCs; VLSR<-100 km s-1) in the directions of Mrk 509 and PKS 2155-304 that have unusual ionization properties. The clouds exhibit strong C IV absorption with little or no detectable low ion (C II, Si II) absorption or H I 21 cm emission down to very sensitive levels. As the closest known analog to the outer diffuse halos of damped Lyα absorbers and the low H I column density metal-line absorption systems seen in the spectra of high-redshift quasars, these "C IV HVCs" present unique opportunities for relating the conditions within the Milky Way halo and nearby intergalactic gas to the properties of galactic halos at higher redshift. In this paper we present new Goddard High Resolution Spectrograph (GHRS) intermediate-resolution measurements of the absorption lines within these C IV HVCs and study the ionization properties of the gas in detail. The present data represent the most complete set of measurements available for studying the ionization conditions within HVCs. The C IV HVCs have ionization properties consistent with photoionization by extragalactic background radiation, although some contribution by collisional ionization within a hot plasma cannot be ruled out. The clouds are probably low density (nH~10−4 cm-3), large (greater than several kiloparsecs), and mostly ionized (nHI/nH~10−3) regions located well beyond the neutral gas layer of the Galaxy. The presence of weak H I HVCs detected through their 21 cm emission near both sight lines indicates that the C IV HVCs trace the extended, ionized, low-density regions of the H I HVCs. Several lines of evidence, including very low thermal pressures (P/k ~2 cm-3 K), favor a location for the C IV HVCs in the Local Group or very distant Galactic halo. If the clouds are intergalactic in nature, their metallicities could be [Z/H]~-1 or lower, but higher metallicities [Z/H]>-1 are favored if the clouds are located in the distant Galactic halo since the cloud sizes scale inversely with metallicity. We provide a summary of the HVCs detected in absorption at intermediate resolution with the GHRS and the IUE satellite and find that C IV HVCs are detected along three of 10 extragalactic sight lines down to a level of logN(C IV)≈13.3 (3σ).
Detailed Architecture of the Barley ChloroplastpsbD-psbC Blue Light-responsive Promoter*

The photosystem II reaction center chlorophyll protein D2, is encoded by the chloroplast gene psbD. PsbDis transcribed from at least three different promoters, one which is activated by high fluence blue light. Sequences within 130 base pairs (bp) of the psbD blue light-responsive promoter (BLRP) are highly conserved in higher plants. In this study, the structure of thepsbD BLRP was analyzed in detail using deletion and site-directed mutagenesis and in vitro transcription. Deletion analysis showed that a 53-bp DNA region of thepsbD BLRP, from −57 to −5, was sufficient for transcription in vitro. Mutation of a putative prokaryotic −10 element (TATTCT) located from −7 to −12 inhibited transcription from the psbD BLRP. In contrast, mutation of a putative prokaryotic −35 element, had no influence on transcription. Mutation of a TATATA sequence located between the barley psbA −10 and −35 elements significantly reduced transcription from this promoter. However, site-directed mutation of sequences located between −35 and −10 had no effect on transcription from the psbDBLRP. Transcription from the psbD BLRP was previously shown to require a 22-bp sequence, termed the AAG-box, located between −36 and −57. The AAG-box specifically binds the protein complex AGF. Site-directed mutagenesis identified two different sequence motifs in the AAG-box that are important for transcription in vitro. Based on these results, we propose that positive factors bind to the AAG-box and interact with the chloroplast-encoded RNA polymerase to promote transcription from the psbD BLRP. Transcription from the psbD BLRP is thus similar to type II bacterial promoters that use activating proteins to stimulate transcription. Transcription of the psbD BLRP was ∼6.5-fold greater in plastid extracts from illuminated versus dark-grown plants. This suggests that light-induced activation of this promoter in vivo involves factors interacting with the 53-bp psbDBLRP in vitro.
Sialic acid–deficient invasive trophoblast antigen (sd‐ITA): a new urinary variant for gestational Down syndrome screening

Invasive trophoblast antigen (ITA), also known as hyperglycosylated hCG, is a glycosylation variant of hCG produced by invasive cytotrophoblast cells. Publications show that ITA is potentially a sensitive test for Down syndrome screening, reportedly detecting 38 and 80% of cases at a 5% false‐positive rate in the first and second trimesters of pregnancy respectively. ITA has six oligosaccharides varying greatly in terminal sialic acid content (0–19 residues), leading to wide‐charge heterogeneity. With the objective of developing an improved Down syndrome screening test, we examined the charge, or sialic acid variants, of ITA.
Disruption of innate immunity due to mitochondrial targeting of a picornaviral protease precursor

Mitochondrial antiviral signaling protein (MAVS) is an essential component of virus-activated signaling pathways that induce protective IFN responses. Its localization to the outer mitochondrial membrane suggests an important yet unexplained role for mitochondria in innate immunity. Here, we show that hepatitis A virus (HAV), a hepatotropic picornavirus, ablates type 1 IFN responses by targeting the 3ABC precursor of its 3Cpro cysteine protease to mitochondria where it colocalizes with and cleaves MAVS, thereby disrupting activation of IRF3 through the MDA5 pathway. The 3ABC cleavage of MAVS requires both the protease activity of 3Cpro and a transmembrane domain in 3A that directs 3ABC to mitochondria. Lacking this domain, mature 3Cpro protease is incapable of MAVS proteolysis. HAV thus disrupts host signaling by a mechanism that parallels that of the serine NS3/4A protease of hepatitis C virus, but differs in its use of a stable, catalytically active polyprotein processing intermediate. The unique requirement for mitochondrial localization of 3ABC underscores the importance of mitochondria to host control of virus infections within the liver.
Reconstruction and simplification of surfaces from contours

In this paper we consider the problem of reconstructing triangular surfaces from given contours. An algorithm solving this problem has to decide which contours of two successive slices should be connected by the surface (branching problem), and, given that, which vertices of the assigned contours should be connected for the triangular mesh (correspondence problem). We present a new approach that solves both tasks in an elegant way. The main idea is to employ discrete distance fields enhanced with correspondence information. This allows us not only to connect vertices from successive slices in a reasonable way but also to solve the branching problem by creating intermediate contours where adjacent contours differ too much. Last but not least we show how the 2D-distance fields used in the reconstruction step can be converted to a 3D-distance field that can be advantageously exploited for distance calculations during a subsequent simplification step.