Miracle-dz/UniFAR-FTUs huggingface dataset:
The PAPI-1 pathogenicity island-encoded small RNA PesA influences Pseudomonas aeruginosa virulence and modulates pyocin S3 production

Small non-coding RNAs (sRNAs) are post-transcriptional regulators of gene expression that have been recognized as key contributors to bacterial virulence and pathogenic mechanisms. In this study, we characterized the sRNA PesA of the opportunistic human pathogen Pseudomonas aeruginosa. We show that PesA, which is transcribed within the pathogenicity island PAPI-1 of P. aeruginosa strain PA14, contributes to P. aeruginosa PA14 virulence. In fact, pesA gene deletion resulted in a less pathogenic strain, showing higher survival of cystic fibrosis human bronchial epithelial cells after infection. Moreover, we show that PesA influences positively the expression of pyocin S3 whose genetic locus comprises two structural genes, pyoS3A and pyoS3I, encoding the killing S3A and the immunity S3I proteins, respectively. Interestingly, the deletion of pesA gene results in increased sensitivity to UV irradiation and to the fluoroquinolone antibiotic ciprofloxacin. The degree of UV sensitivity displayed by the PA14 strain lacking PesA is comparable to that of a strain deleted for pyoS3A-I. These results suggest an involvement of pyocin S3 in DNA damage repair and a regulatory role of PesA on this function.
Les enjeux et les déclinaisons de la notion de « santé sexuelle et reproductive » au Maroc. Réflexions à partir du cas des grossesses hors mariage

Au Maroc les grossesses et les naissances hors mariage font l’objet de nombreuses initiatives surtout dans le domaine des organisations non-gouvernementales. Plusieurs de celles-ci demandent le changement du droit de la famille afin que les enfants nes hors mariage ne soient pas discrimines et luttent contre la marginalisation sociale des meres celibataires. Elles offrent a ces dernieres l’assistance medicale dont elles ont besoin et leur proposent des activites d’education a la sante, aussi dans le domaine de la sante sexuelle et reproductive. Les recherches de terrain que j’ai menees en 2011 et 2012 dans des hopitaux, des centres de sante, des ONG et aupres des femmes ayant enfante hors-mariage a Casablanca m’ont poussee a questionner les enjeux de la notion de sante sexuelle et reproductive (SSR), ses applications et ses appropriations par les acteurs locaux. Au-dela de l’information sur la contraception et les avortements illegaux, les activites pedagogiques promues par les ONG locales et destinees aux jeunes femmes non-mariees, visent a prevenir les « recidives » et a « responsabiliser » les beneficiaires de leurs services. Les trajectoires des meres celibataires revelent une grande vulnerabilite dans laquelle s’imbriquent des dimensions socio-economiques, de genre et de sante qui ne sont pas toujours prises en compte par les ONG locales. Est-ce que les discours, les politiques et les pratiques s’inspirant de la notion de SSR au Maroc se declinent en termes de droits ou produisent-ils des formes inedites de normalisation et de gouvernement des corps feminins ? La notion de SSR se revele parfois inadequate afin de saisir la complexite des realites locales et des experiences subjectives des meres celibataires. Le role des inegalites socio-economiques plus larges, des negociations morales ainsi que la creation de categories « cibles » de beneficiaires « vulnerables » au sein des organisations non-gouvernementales emergent plutot comme des elements a problematiser dans une anthropologie critique de la sante et de la reproduction au Maroc.
An optimal alignment of proteins energy characteristics with crisp and fuzzy similarity awards

We discuss the usage of constant and fuzzy similarity awards while establishing an optimal alignment between energy characteristics of two compared protein energy profiles. Single protein energy profile is a set of energy characteristics of various types of energy. The energy profile is determined for a given protein structure. We use these profiles to find protein molecules of the same structural protein family and inspect conformational modifications in their molecular structures as an effect of biochemical reactions or environmental influences. Energy profiles are received in the computational process based on the molecular mechanics theory. Afterwards, these profiles can be stored in the special purpose database (EDB) and used by the search engine to find similar fragments of protein structures on the energy level. To optimize the alignment path we use modified, energy-adapted Smith-Waterman method with one of the tested similarity awards.
Bur1/Bur2 and the Ctk Complex in Yeast: The Split Personality of Mammalian P-TEFb

Eukaryotic organisms possess a host of factors that regulate transcriptional elongation. In higher eukaryotes, the transcription factor P-TEFbβ not only regulates phosphorylation of the RNA polymerase II C-terminal domain, but it also inhibits the action of transcriptional repressors and is required for the association of several elongation factors with the transcribing polymerase. In the yeast Saccharomyces cerevisiae, the cyclin dependent kinases Bur1/Bur2 and Ctk complex (Ctk1, 2 and 3) are also able to impact several aspects of transcription. Together, these two kinase complexes appear to functionally reconstitute the activity of P-TEFβ in yeast. Recent findings regarding the role of these kinases in histone tail modifications and transcriptional regulation is briefly reviewed below.
Striation Patterns Classification of Tool Marks Based on Extended Fractal Analysis

Currently, optical device, such as microscopes and CCD cameras, are utilized for identification of tool marks in the field of forensic science which mainly depend on the experience of forensic scientists. A new approach using extended fractal analysis technology to classify tool marks such as striation patterns is presented. it computes four directional multi-scale extended fractal parameters and the maximum direction fractal feature, then performs a supervised classification. Experimental results demonstrate that this method provides a classification scheme that performs well than the traditional schemes and is effective for classification of tool marks.
The Cambridge University 2014 BOLT conversational telephone Mandarin Chinese LVCSR system for speech translation

This paper presents the development of the 2014 Cambridge University conversational telephone Mandarin Chinese LVCSR system for the DARPA BOLT speech translation evaluation. A range of advanced modelling techniques were employed to both improve the recognition performance and provide a suitable integration with the translation system. These include an improved system combination technique using frame level acoustic model combination via joint decoding. Sequence trained deep neural network (DNN) based hybrid and tandem systems were combined on-the-fly to produce a consistent decoding output during search. A multi-level paraphrastic recurrent neural network LM (RNNLM) modelling both alternative paraphrase expressions and character sequences while preserving a consistent character to word segmentation was also used. This system gave an overall character error rate (CER) of 29.1% on the BOLT dev14 development set. Index Terms: conversational speech transcription, speech translation, system combination, RNNLM, character LM
Blood pressure and catecholamine responses to 'stress' in normotensive and hypertensive subjects.

A standardized 'stress' was applied to groups of normotensive and hypertensive subjects. Systolic and diastolic blood pressures rose in both groups but were significantly greater in the hypertensive than in the normotensive group. Urinary catecholamines rose with stress to a similar extent in both groups. There was no evidence that patients with sustained hypertension have an increased production of catecholamines either at rest or under 'stress'.
ABCC1 polymorphisms contribute to level and decline of lung function in two population-based cohorts

Objective The ATP-binding cassette transporter ABCC1 [i.e. multidrug resistance-associated protein 1 (MRP1)] is a membrane-bound pump excreting a variety of xenobiotics from the cell, and thus ABCC1 may play an important role in smoking-related lung function loss and development of chronic obstructive pulmonary disease (COPD). We earlier showed that bronchial epithelium of COPD patients have lower ABCC1 expression than that of healthy controls, with even further decrements in more severe COPD stages. In line with these results, we now aimed to assess effects of ABCC1 single nucleotide polymorphisms (SNPs) on both the level and the longitudinal course of lung function in the general population. Methods All 51 prevalent (minor allele frequency >5%) and noncorrelated (r2<0.8) ABCC1 SNPs were analyzed in two independent, prospective, population-based cohorts, that is, Doetinchem (n = 1152) and Vlagtwedde–Vlaardingen (n = 1390) studies (three and seven median lung function measurements, respectively, per patient), using linear regression and linear mixed-effect models. Results SNPs rs4148382 and rs212093 in the 3′-ABCC1 region were significantly associated with a higher and lower forced expiratory volume in 1 s (FEV1), respectively, in both the cohorts. Another rs35621 SNP (intron 14) was significantly associated with a highly excessive FEV1 decline in both cohorts. All replicated associations were additionally confirmed by permutation testing. Conclusion This is the first study showing a significant relationship between ABCC1 SNPs and lung function in two independent cohorts. These SNPs are therefore putative candidates for studies aiming to prevent COPD and investigating pharmacogenetics in established COPD.
SEED DISPERSAL, SEED PREDATION, AND SEEDLING RECRUITMENT OF A NEOTROPICAL MONTANE TREE

Postdispersal fate of seeds from Ocotea endresiana (Lauraceae), a bird-dispersed Neotropical montane tree, was studied in Costa Rica to determine the influence of seed dispersers, seed predators, and microhabitat characteristics on seedling recruitment. Particular emphasis was placed on finding naturally dispersed seeds in order to study the link between dispersal and postdispersal fate of seeds. Four species of birds (Emerald Toucanet, Aulacorhynchus prasinus; Resplendent Quetzal, Pharomachrus mocinno; Three-wattled Bellbird, Procnias tricarunculata; and Mountain Robin, Turdus plebejus) dispersed the seeds by regurgitation, and one species (Black Guan, Chamaepetes unicolor), by defecation. Most seeds (80%) were dispersed within 25 m of parent trees and under high (>92%) canopy cover. Bellbirds deposited 52% of the seeds they dispersed under habitual song perches in standing dead trees on the edges of treefall gaps >25 m from parent trees. In contrast, the other four species dispersed only 6% of the seeds.
Calcium‐activated force responses in fast‐ and slow‐twitch skinned muscle fibres of the rat at different temperatures.

1. Force responses from mechanically skinned fibres of rat skeletal muscles (extensor digitorum longus and soleus) were measured at different temperatures in the range 3‐35 degrees C following sudden changes in Ca2+ concentration in the preparations. 2. At all temperatures there were characteristic differences between the slow‐ and fast‐twitch muscle fibres with respect to the relative steady‐state force‐[Ca2+] relation: such as a lower [Ca2+] threshold for activation and a less steep force‐pCa curve in slow‐twitch muscle fibres. 3. At 3‐5 degrees C the force changes in both types of muscle fibres lagged considerably behind the estimated changes in [Ca2+] within the preparations and this enabled us to perform a comparative analysis of the Ca2+ kinetics in the process of force development in both muscle fibre types. This analysis suggest that two and six Ca2+ ions are involved in the regulatory unit for contraction of slow‐ and fast‐twitch muscle fibres respectively. 4. The rate of relaxation following a sudden decrease in [Ca2+] was much lower in the slow‐twitch than in the fast‐twitch muscle at 5 degrees C, suggesting that properties of the contractile apparatus could play an essential role in determining the rate of relaxation in vivo. 5. There was substantial variation in Ca2+ sensitivity between muscle fibres of the same type from different animals at each temperature. However the steepness of the force‐[Ca2+] relation was essentially the same for all fibres of the same type. 6. A change in temperature from 5 to 25 degrees C had a statistically significant effect on the sensitivity of the fast‐twitch muscle fibres, rendering them less sensitive to Ca2+ by a factor of 2. However a further increase in temperature from 25 to 35 degrees C did not have any statistically significant effect on the force‐[Ca2+] relation in fast‐twitch muscle fibres. 7. The effect of temperature on the Ca2+ sensitivity of slow‐twitch muscle fibres was not statistically significant, mainly because of the large variation in sensitivity amongst these preparations at room temperature. 8. Two types of oscillatory processes not associated with intracellular membranes were observed in the force response of all slow‐twitch muscle fibres when submaximally activated (less than 60% maximum force) at 25 and 35 degrees C, but never at 3‐5 degrees C. The frequency of oscillations increased with temperature. 9. Maximum Ca2+‐activated force in both muscle fibre types was greatly dependent upon temperature over the range 0‐25 degrees C, but increased only slightly above 25 degrees C. 10. Experiments on the rigor state suggest that the number of possible actomyosin interacting sites diminishes considerably as temperature is decreased below 25 degrees C.
Fabrication of the Toroidal Field Superconducting Coils for the EAST Device

EAST (HT-7U) is a large fusion experimental device being built at IPP, Hefei, China. Its superconducting magnet system consists of sixteen Toroidal Field (TF) coils and fourteen Poloidal Field (PF) coils. The TF coil includes the winding pack with a square cable-in-conduit (CIC) type superconductor in NbTi cooled by a force flow of supercritical helium, the welded case structure, the gravity support which is composed of pedestals with flexible plates, the coil joint with low resistance at high current and other components. At present, the production of all TF coils has been finished and all of the TF coils have been installed in the machine. This paper describes mainly the special fabrication processes of the TF coil
MHD Flow, Heat and Mass Transfer about aHorizontal Cylinder in Porous Medium

MHD flow, heat and mass transfer through porous media have seen a tremendous increase in research attention. This rapidly increasing research activity has been due to the increasing number of practical applications on porous media in chemical reactors, the underground spread of pollutant, many modern industries ranging from micro to macro and many other heat transfer processes. The problem of flow, heat and mass transfer about a horizontal circular cylinder in porous medium is considered in this study. Governing boundary layer equations are first transformed into ordinary differential equations and are solved by using Matlab’s built in solver bvp4c. Velocity, temperature and concentration profiles are shown graphically for different values of parameters involved in the dimensionless equations and discussed in detail.
The narrative approach to personalisation

This article describes the narrative approach to personalisation. This novel approach to the generation of personalised adaptive hypermedia experiences employs runtime reconciliation between a personalisation strategy and a number of contextual models (e.g. user and domain). The approach also advocates the late binding of suitable content and services to the generated personalised pathway resulting in an interactive composition that comprises services as well as content. This article provides a detailed definition of the narrative approach to personalisation and showcases the approach through the examination of two use-cases: the personalised digital educational games developed by the ELEKTRA and 80Days projects; and the personalised learning activities realised as part of the AMAS project. These use-cases highlight the general applicability of the narrative approach and how it has been applied to create a diverse range of real-world systems.
A Survey of Stunning Methods Currently Used during Slaughter of Poultry in Commercial Poultry Plants

Abstract The Food Safety and Inspection Service (FSIS) conducted a 1992 telephone/FAX survey of all poultry slaughter establishments in the United States to determine the types and prevalence of stunning practices for each poultry class presently in use by the poultry industry. The survey revealed that electrical stunning was used in slaughtering greater than 90% of all birds except light fowl and geese. Low voltage-type electrical stunning devices (10 to 25 volts) were used in 216 of the 329 poultry slaughter plants, while 63 plants used electrical stunners set at a range of other voltages and amperages with unspecified waveforms and frequencies. Further studies monitoring voltage, amperage, and waveforms of electricity concurrent with somatosensory-evoked potentials are needed to determine the adequacy of electrical stunning as a humane practice.
Internal Deformation Monitoring of Slope Based on BOTDR

To overcome the shortcomings of conventional slope monitoring methods, this paper presented an in-place inclinometer based on BOTDR (Brillouin Optical Time Domain Reflectometer) which was used to obtain the long-term internal deformation in the slope. The installation process of optical fiber sensors and its measuring principle were introduced. The result of analysis indicated that the error in the measured displacement was proportional to the square of the inclinometer length and the precision of the BOTDR instrument, while it was inversely proportional to the diameter of the inclinometer tube. An actual field slope deformation monitoring case was also introduced. The results show that the BOTDR based inclinometer has a good consistency with the traditional inclinometer. It can effectively access the internal deformation of the slope and help to find the position of potential sliding surface accurately. This technology shows a high reliability and practicality in engineering application that will promote deeper research of slope in the future.
Evidence against putrescine and polyamines as endogenous mediators of fever

Endogenous concentrations of putrescine, spermidine, spermine and related biosynthetic enzymes were not affected by the administration of bacterial endotoxin and the subsequent development of fever in rabbits. In addition, the febrile response to endotoxin was unaffected either by the ornithine decarboxylase inhibitor, DL‐α‐difluoromethylornithine or by putrescine. These data indicate polyamines are not involved in the development of fever.
Cloning and Characterization of a Brain-specific Cationic Amino Acid Transporter*

rCAT3 (at ationic mino acid ransporter 3), a cDNA that encodes a novel member of the murine CAT family was isolated. The protein encoded by rCAT3 contained 619 amino acids, 53-58% of which were identical with those of the murine CAT family proteins previously described (mouse CAT1, CAT2a, CAT2b, and rat CAT1). Transient expression of rCAT3 and L-[14C]arginine incorporation experiments in COS7 cells verified a high affinity system y+ transporter activity of rCAT3. First, rCAT3-mediated L-[14C]arginine incorporation was time-dependent and saturable with half-saturation constant (Km) values of 103 ± 12 μM (mean ± S.E., n = 3). Second, the incorporation was specific for cationic amino acids as evidenced from the inhibition by L-arginine, L-lysine, and L-ornithine. Third, neither sodium nor chloride ions in the extracellular medium were required for the activity. Fourth, the incorporation was inhibited by high potassium-induced membrane depolarization. On Northern blot using RNAs from various rat tissues, the expression of rCAT3 mRNA was restricted to the brain. These results indicated a role of rCAT3 in the system y+ transporter activity in the nervous tissue.
Visual Analysis of Volume Ensembles Based on Local Features

Ensemble datasets describe a specific phenomenon (e.g., a simulation scenario or a measurements series) through a large set of individual ensemble members. These individual members typically do not differ too much from each other but rather feature slightly changing characteristics. In many cases, the ensemble members are defined in 3D space, which implies severe challenges when exploring the complete ensembles such as handling occlusions, focus and context or its sheer datasize. In this paper we address these challenges and put our focus on the exploration of local features in 3D volumetric ensemble datasets, not only by visualizing local characteristics, but also by identifying connections to other local features with similar characteristics in the data. We evaluate the variance in the dataset and use the the spatial median (medoid) of the ensemble to visualize the differences in the dataset. This medoid is subsequently used as a representative of the ensemble in 3D. The variance information is used to guide users during the exploration, as regions of high variance also indicate larger changes within the ensemble members. The local characteristics of the regions can be explored by using our proposed 3D probing widgets. These widgets consist of a 3D sphere, which can be positioned at any point in 3D space. While moving a widget, the local data characteristics at the corresponding position are shown in a separate detail view, which depicts the local outliers and their surfaces in comparison to the medoid surface. The 3D probing widgets can also be fixed at a user-defined position of interest. The fixed probing widgets are arranged in a similarity graph to indicate similar local data characteristics. The similarity graph thus allows to explore whether high variances in a certain region are caused by the same dataset members or not. Finally, it is also possible to compare a single member against the rest of the ensemble. We evaluate our technique through two demonstration cases using volumetric multi-label segmentation mask datasets, two from the industrial domain and two from the medical domain.
Interaction between Constant Levels of Low Back Pain and other Psychological Parameters

87 subjects with varying intensities of constant low back pain answered a pain questionnaire which included Graphic Rating Scales and took part in a battery of psychological tests (Eysenck Personality Inventory, the Meta-Contrast Technique, the Separation Test, and the Rod-and-Frame Test). This was done to corroborate the relationship found between subjects with different intensities of pain and their experiences of psychological problems. Comparisons are made between subjects with acute and chronic pain and between past pain experiences and the present level of pain. No statistical significant differences on psychological measures were found between subjects with varying intensities of pain, but differences were found for previous pain experiences. All subjects had significant rates of depression and regression. A difference between acute and chronic pain subjects was noted in that significantly more women had chronic pain than did men.