Allele specific repair of splicing mutations in cystic fibrosis through AsCas12a genome editing.

Funder: Fondazione Fibrosi Cistica - FFC#1/2017Cystic fibrosis (CF) is an autosomal recessive disease caused by mutations in the CFTR gene. The 3272-26A>G and 3849+10kbC>T CFTR mutations alter the correct splicing of the CFTR gene, generating new acceptor and donor splice sites respectively. Here we develop a genome editing approach to permanently correct these genetic defects, using a single crRNA and the Acidaminococcus sp. BV3L6, AsCas12a. This genetic repair strategy is highly precise, showing very strong discrimination between the wild-type and mutant sequence and a complete absence of detectable off-targets. The efficacy of this gene correction strategy is verified in intestinal organoids and airway epithelial cells derived from CF patients carrying the 3272-26A>G or 3849+10kbC>T mutations, showing efficient repair and complete functional recovery of the CFTR channel. These results demonstrate that allele-specific genome editing with AsCas12a can correct aberrant CFTR splicing mutations, paving the way for a permanent splicing correction in genetic diseases

Measurement of the top quark mass using the matrix element technique in dilepton final states

We present a measurement of the top quark mass in pp¯ collisions at a center-of-mass energy of 1.96 TeV at the Fermilab Tevatron collider. The data were collected by the D0 experiment corresponding to an integrated luminosity of 9.7  fb−1. The matrix element technique is applied to tt¯ events in the final state containing leptons (electrons or muons) with high transverse momenta and at least two jets. The calibration of the jet energy scale determined in the lepton+jets final state of tt¯ decays is applied to jet energies. This correction provides a substantial reduction in systematic uncertainties. We obtain a top quark mass of mt=173.93±1.84  GeV

Antigenic, Immunologic and Genetic Characterization of Rough Strains B.abortus RB51, B.melitensis B115 and B.melitensis B18

The lipopolysaccharide (LPS) is considered the major virulent factor in Brucella spp. Several genes have been identified involved in the synthesis of the three LPS components: lipid A, core and O-PS. Usually, Brucella strains devoid of O-PS (rough mutants) are less virulent than the wild type and do not induce undesirable interfering antibodies. Such of them proved to be protective against brucellosis in mice. Because of these favorable features, rough strains have been considered potential brucellosis vaccines. In this study, we evaluated the antigenic, immunologic and genetic characteristics of rough strains B.abortus RB51, B.melitensis B115 and B.melitensis B18. RB51 derived from B.abortus 2308 virulent strain and B115 is a natural rough strain in which the O-PS is present in the cytoplasm. B18 is a rough rifampin-resistan mutant isolated in our laboratory

Spatial distribution and risk factors of Brucellosis in Iberian wild ungulates

<p>Abstract</p> <p>Background</p> <p>The role of wildlife as a brucellosis reservoir for humans and domestic livestock remains to be properly established. The aim of this work was to determine the aetiology, apparent prevalence, spatial distribution and risk factors for brucellosis transmission in several Iberian wild ungulates.</p> <p>Methods</p> <p>A multi-species indirect immunosorbent assay (iELISA) using <it>Brucella </it>S-LPS antigen was developed. In several regions having brucellosis in livestock, individual serum samples were taken between 1999 and 2009 from 2,579 wild bovids, 6,448 wild cervids and4,454 Eurasian wild boar (<it>Sus scrofa</it>), and tested to assess brucellosis apparent prevalence. Strains isolated from wild boar were characterized to identify the presence of markers shared with the strains isolated from domestic pigs.</p> <p>Results</p> <p>Mean apparent prevalence below 0.5% was identified in chamois (<it>Rupicapra pyrenaica</it>), Iberian wild goat (<it>Capra pyrenaica</it>), and red deer (<it>Cervus elaphus</it>). Roe deer (<it>Capreolus capreolus</it>), fallow deer (<it>Dama dama</it>), mouflon (<it>Ovis aries</it>) and Barbary sheep (<it>Ammotragus lervia</it>) tested were seronegative. Only one red deer and one Iberian wild goat resulted positive in culture, isolating <it>B. abortus </it>biovar 1 and <it>B. melitensis </it>biovar 1, respectively. Apparent prevalence in wild boar ranged from 25% to 46% in the different regions studied, with the highest figures detected in South-Central Spain. The probability of wild boar being positive in the iELISA was also affected by age, age-by-sex interaction, sampling month, and the density of outdoor domestic pigs. A total of 104 bacterial isolates were obtained from wild boar, being all identified as <it>B. suis </it>biovar 2. DNA polymorphisms were similar to those found in domestic pigs.</p> <p>Conclusions</p> <p>In conclusion, brucellosis in wild boar is widespread in the Iberian Peninsula, thus representing an important threat for domestic pigs. By contrast, wild ruminants were not identified as a significant brucellosis reservoir for livestock.</p

Feasibility of a walking virtual reality system for rehabilitation: objective and subjective parameters

[EN] Background: Even though virtual reality (VR) is increasingly used in rehabilitation, the implementation of walking navigation in VR still poses a technological challenge for current motion tracking systems. Different metaphors simulate locomotion without involving real gait kinematics, which can affect presence, orientation, spatial memory and cognition, and even performance. All these factors can dissuade their use in rehabilitation. We hypothesize that a marker-based head tracking solution would allow walking in VR with high sense of presence and without causing sickness. The objectives of this study were to determine the accuracy, the jitter, and the lag of the tracking system and its elicited sickness and presence in comparison of a CAVE system. Methods: The accuracy and the jitter around the working area at three different heights and the lag of the head tracking system were analyzed. In addition, 47 healthy subjects completed a search task that involved navigation in the walking VR system and in the CAVE system. Navigation was enabled by natural locomotion in the walking VR system and through a specific device in the CAVE system. An HMD was used as display in the walking VR system. After interacting with each system, subjects rated their sickness in a seven-point scale and their presence in the Slater-Usoh-Steed Questionnaire and a modified version of the Presence Questionnaire. Results: Better performance was registered at higher heights, where accuracy was less than 0.6 cm and the jitter was about 6 mm. The lag of the system was 120 ms. Participants reported that both systems caused similar low levels of sickness (about 2.4 over 7). However, ratings showed that the walking VR system elicited higher sense of presence than the CAVE system in both the Slater-Usoh-Steed Questionnaire (17.6 +/- 0.3 vs 14.6 +/- 0.6 over 21, respectively) and the modified Presence Questionnaire (107.4 +/- 2.0 vs 93.5 +/- 3.2 over 147, respectively). Conclusions: The marker-based solution provided accurate, robust, and fast head tracking to allow navigation in the VR system by walking without causing relevant sickness and promoting higher sense of presence than CAVE systems, thus enabling natural walking in full-scale environments, which can enhance the ecological validity of VR-based rehabilitation applications.The authors wish to thank the staff of LabHuman for their support in this project, especially José Miguel Martínez and José Roda for their assistance. This study was funded in part by Ministerio de Economia y Competitividad of Spain (Project NeuroVR, TIN2013-44741-R and Project REACT, TIN2014-61975-EXP), by Ministerio de Educacion y Ciencia of Spain (Project Consolider-C, SEJ2006-14301/PSIC), and by Universitat Politecnica de Valencia (Grant PAID-10-14).Borrego, A.; Latorre Grau, J.; Llorens Rodríguez, R.; Alcañiz Raya, ML.; Noé, E. (2016). Feasibility of a walking virtual reality system for rehabilitation: objective and subjective parameters. Journal of NeuroEngineering and Rehabilitation. 13:1-9. https://doi.org/10.1186/s12984-016-0174-1S1913Lee KM. Presence. Explicated Communication Theory. 2004;14(1):27–50.Riva G. Is presence a technology issue? Some insights from cognitive sciences. Virtual Reality. 2009;13(3):159–69.Banos RM, et al. Immersion and emotion: their impact on the sense of presence. Cyberpsychol Behav. 2004;7(6):734–41.Llorens R, et al. Tracking systems for virtual rehabilitation: objective performance vs. subjective experience. A practical scenario. Sensors (Basel). 2015;15(3):6586–606.Navarro MD, et al. Validation of a low-cost virtual reality system for training street-crossing. A comparative study in healthy, neglected and non-neglected stroke individuals. Neuropsychol Rehabil. 2013;23(4):597–618.Parsons TD. Virtual reality for enhanced ecological validity and experimental control in the clinical, affective and social neurosciences. Front Hum Neurosci. 2015;9:660.Cameirao MS, et al. Neurorehabilitation using the virtual reality based Rehabilitation Gaming System: methodology, design, psychometrics, usability and validation. J Neuroeng Rehabil. 2010;7:48.Llorens R, et al. Improvement in balance using a virtual reality-based stepping exercise: a randomized controlled trial involving individuals with chronic stroke. Clin Rehabil. 2015;29(3):261–8.Llorens R, et al. Videogame-based group therapy to improve self-awareness and social skills after traumatic brain injury. J Neuroeng Rehabil. 2015;12:37.Fong KN, et al. Usability of a virtual reality environment simulating an automated teller machine for assessing and training persons with acquired brain injury. J Neuroeng Rehabil. 2010;7:19.Levin MF, Weiss PL, Keshner EA. Emergence of virtual reality as a tool for upper limb rehabilitation: incorporation of motor control and motor learning principles. Phys Ther. 2015;95(3):415–25.Llorens R, et al. Effectiveness, usability, and cost-benefit of a virtual reality-based telerehabilitation program for balance recovery after stroke: a randomized controlled trial. Arch Phys Med Rehabil. 2015;96(3):418–25. e2.Cruz-Neira C, et al. Scientists in wonderland: A report on visualization applications in the CAVE virtual reality environment. In: 1993. Proceedings IEEE 1993 Symposium on Research Frontiers in Virtual Reality. 1993.Juan MC, Perez D. Comparison of the levels of presence and anxiety in an acrophobic environment viewed via HMD or CAVE. Presence. 2009;18(3):232–48.Yang YR, et al. Virtual reality-based training improves community ambulation in individuals with stroke: a randomized controlled trial. Gait Posture. 2008;28(2):201–6.Cho KH, Lee WH. Virtual walking training program using a real-world video recording for patients with chronic stroke: a pilot study. Am J Phys Med Rehabil. 2013;92(5):371–84.Darter BJ, Wilken JM. Gait training with virtual reality-based real-time feedback: improving gait performance following transfemoral amputation. Phys Ther. 2011;91(9):1385–94.Yang S, et al. Improving balance skills in patients who had stroke through virtual reality treadmill training. Am J Phys Med Rehabil. 2011;90(12):969–78.Walker ML, et al. Virtual reality-enhanced partial body weight-supported treadmill training poststroke: feasibility and effectiveness in 6 subjects. Arch Phys Med Rehabil. 2010;91(1):115–22.Riley PO, et al. A kinematic and kinetic comparison of overground and treadmill walking in healthy subjects. Gait Posture. 2007;26(1):17–24.Alton F, et al. A kinematic comparison of overground and treadmill walking. Clin Biomech. 1998;13(6):434–40.Lee SJ, Hidler J. Biomechanics of overground vs. treadmill walking in healthy individuals. J Appl Physiol. 2008;104(3).Slater M. Measuring presence: a response to the witmer and Singer presence questionnaire. Presence. 1999;8(5):560–5.Viau A, et al. Reaching in reality and virtual reality: a comparison of movement kinematics in healthy subjects and in adults with hemiparesis. J Neuroeng Rehabil. 2004;1(1):11.Parsons TD, et al. The potential of function-led virtual environments for ecologically valid measures of executive function in experimental and clinical neuropsychology. Neuropsychol Rehabil. 2015;11:1–31. doi: 10.1080/09602011.2015.1109524 .Aravind G, Lamontagne A. Perceptual and locomotor factors affect obstacle avoidance in persons with visuospatial neglect. J Neuroeng Rehabil. 2014;11:38.Darekar A, Lamontagne A, Fung J. Dynamic clearance measure to evaluate locomotor and perceptuo-motor strategies used for obstacle circumvention in a virtual environment. Hum Mov Sci. 2015;40:359–71.Whittle MW. Chapter 4 - Methods of gait analysis. In: Whittle MW, editor. Gait analysis. Edinburgh: Butterworth-Heinemann; 2007. p. 137–75.Hodgson E, et al. WeaVR: a self-contained and wearable immersive virtual environment simulation system. Behav Res Methods. 2015;47(1):296–307.Akizuki H, et al. Effects of immersion in virtual reality on postural control. Neurosci Lett. 2005;379(1):23–6.Thies SB, et al. Comparison of linear accelerations from three measurement systems during "reach & grasp". Med Eng Phys. 2007;29(9):967–72.Fiala M. Designing highly reliable fiducial markers. IEEE Trans Pattern Anal Mach Intell. 2010;32(7):1317–24.Garrido-Jurado S, et al. Automatic generation and detection of highly reliable fiducial markers under occlusion. Pattern Recognition. 2014;47(6):2280–92.Kim K, et al. Effects of virtual environment platforms on emotional responses. Comput Methods Programs Biomed. 2014;113(3):882–93.Slater M, Steed A. A virtual presence counter. Presence. 2000;9(5):413–34.Witmer BG, Singer MJ. Measuring presence in virtual environments: a presence questionnaire. Presence Teleop Virt. 1998;7(3):225–40.Martín-Gutiérrez J, et al. Design and validation of an augmented book for spatial abilities development in engineering students. Comput Graph. 2010;34(1):77–91.Lopez-Mir F, et al. Design and validation of an augmented reality system for laparoscopic surgery in a real environment. Biomed Res Int. 2013;2013:758491.Abawi DF, Bienwald J, Dorner R. Accuracy in optical tracking with fiducial markers: an accuracy function for ARToolKit. In: Third IEEE and ACM International symposium on mixed and augmented reality, ISMAR 2004. 2004.Malbezin P, Piekarski W, Thomas BH. Measuring ARTootKit accuracy in long distance tracking experiments. In: The first IEEE International workshop augmented reality toolkit. 2002.Paquette C, Paquet N, Fung J. Aging affects coordination of rapid head motions with trunk and pelvis movements during standing and walking. Gait Posture. 2006;24(1):62–9.Graham JE, et al. Walking speed threshold for classifying walking independence in hospitalized older adults. Phys Ther. 2010;90(11):1591–7.Gorea A. A refresher of the original Bloch’s Law paper (bloch, july 1885). i-Perception. 2015;6:4.Moss JD, Muth ER. Characteristics of head-mounted displays and their effects on Simulator sickness. Hum Factors. 2011;53(3):308–19.Draper MH, et al. Effects of image scale and system time delay on Simulator sickness within head-coupled virtual environments. Hum Factors. 2001;43(1):129–46.Fujisaki W. Effects of delayed visual feedback on grooved pegboard test performance. Front Psychol. 2012;3:61.Keshner EA, et al. Augmenting sensory-motor conflict promotes adaptation of postural behaviors in a virtual environment. Conf Proc IEEE Eng Med Biol Soc. 2011;2011:1379–82.Slaboda JC, Keshner EA. Reorientation to vertical modulated by combined support surface tilt and virtual visual flow in healthy elders and adults with stroke. J Neurol. 2012;259(12):2664–72.Tossavainen T. Comparison of CAVE and HMD for visual stimulation in postural control research. Stud Health Technol Inform. 2004;98:385–7.Akiduki H, et al. Visual-vestibular conflict induced by virtual reality in humans. Neurosci Lett. 2003;340(3):197–200.Duh HBL, et al. Effects of field of view on balance in an immersive environment. In: Virtual Reality, 2001. Proceedings. IEEE. 2001.Krijn M, et al. Treatment of acrophobia in virtual reality: the role of immersion and presence. Behav Res Ther. 2004;42(2):229–39.Mania K, Chalmers A. The effects of levels of immersion on memory and presence in virtual environments: a reality centered approach. Cyberpsychol Behav. 2001;4(2):247–64.Gorini A, et al. The role of immersion and narrative in mediated presence: the virtual hospital experience. Cyberpsychol Behav Soc Netw. 2011;14(3):99–105.Fromberger P, et al. Virtual viewing time: the relationship between presence and sexual interest in androphilic and gynephilic Men. PLoS One. 2015;10(5), e0127156.Slater M, et al. Visual realism enhances realistic response in an immersive virtual environment. IEEE Comput Graph Appl. 2009;29(3):76–84.Nir-Hadad SY, et al. A virtual shopping task for the assessment of executive functions: Validity for people with stroke. Neuropsychol Rehabil. 2015;11:1–26. doi: 10.1080/09602011.2015.1109523 .Vasilyeva M, Lourenco SF. Development of spatial cognition. Wiley Interdiscip Rev Cogn Sci. 2012;3(3):349–62.Banakou D, Groten R, Slater M. Illusory ownership of a virtual child body causes overestimation of object sizes and implicit attitude changes. Proc Natl Acad Sci U S A. 2013;110(31):12846–51.Yee N, Bailenson JN, Ducheneaut N. The proteus effect: implications of transformed digital self-representation on online and offline behavior. Commun Res. 2009;36(2):285–312.Baylor AL. Promoting motivation with virtual agents and avatars: role of visual presence and appearance. Philos Trans R Soc Lond B Biol Sci. 2009;364(1535):3559–65.Clemente M, et al. Assessment of the influence of navigation control and screen size on the sense of presence in virtual reality using EEG. Expert Sys App. 2014;41(4, Part 2):1584–92.Clemente M, et al. An fMRI study to analyze neural correlates of presence during virtual reality experiences. 2013. Interacting with Computers

Studies of X(3872) and ψ(2S) production in p\bar{p}over-bar collisions at 1.96 TeV

We present various properties of the production of the X (3872) and ψ(2S) states based on 10.4fb‾¹ collected by the D0 experiment in Tevatron p\bar{p} collisions at \sqrt{s} = 1.96 TeV. For both states, we measure the nonprompt fraction fNP of the inclusive production rate due to decays of b-flavored hadrons. We find the fNP values systematically below those obtained at the LHC. The fNP fraction for ψ(2S) increases with transverse momentum, whereas for the X(3872) it is constant within large uncertainties, in agreement with the LHC results. The ratio of prompt to nonprompt ψ(2S) production, (1 - fNP)/fNP, decreases only slightly going from the Tevatron to the LHC, but for the X(3872), this ratio decreases by a factor of about 3. We test the soft-pion signature of the X(3872) modeled as a weakly bound charm-meson pair by studying the production of the X(3872) as a function of the kinetic energy of the X(3872) and the pion in the X(3872) π center-of-mass frame. For a subsample consistent with prompt production, the results are incompatible with a strong enhancement in the production of the X(3872) at the small kinetic energy of the X(3872) and the π in the X(3872)π center-of-mass frame expected for the X + soft-pion production mechanism. For events consistent with being due to decays of hadrons, there is no significant evidence for the soft-pion effect, but its presence at the level expected for the binding energy of 0.17 MeV and the momentum scale Λ = M(π) is not ruled out

Properties of Z±c(3900) produced in pp¯ collisions

We study the production of the exotic charged charmoniumlike state Z ± c ( 3900 ) in p ¯ p collisions through the sequential process ψ ( 4260 ) → Z ± c ( 3900 ) π ∓ , Z ± c ( 3900 ) → J / ψ π ± . Using the subsample of candidates originating from semi-inclusive weak decays of b -flavored hadrons, we measure the invariant mass and natural width to be M = 3902.6 + 5.2 − 5.0 ( stat ) + 3.3 − 1.4 ( syst )     MeV and Γ = 3 2 + 28 − 21 ( stat ) + 26 − 7 ( syst )     MeV , respectively. We search for prompt production of the Z ± c ( 3900 ) through the same sequential process. No significant signal is observed, and we set an upper limit of 0.70 at the 95% credibility level on the ratio of prompt production to the production via b -hadron decays. The study is based on 10.4     f b − 1 of p ¯ p collision data collected by the D0 experiment at the Fermilab Tevatron collider

Combined Tevatron upper limit on gg->H->W+W- and constraints on the Higgs boson mass in fourth-generation fermion models

Report number: FERMILAB-PUB-10-125-EWe combine results from searches by the CDF and D0 collaborations for a standard model Higgs boson (H) in the process gg->H->W+W- in p=pbar collisions at the Fermilab Tevatron Collider at sqrt{s}=1.96 TeV. With 4.8 fb-1 of integrated luminosity analyzed at CDF and 5.4 fb-1 at D0, the 95% Confidence Level upper limit on \sigma(gg->H) x B(H->W+W-) is 1.75 pb at m_H=120 GeV, 0.38 pb at m_H=165 GeV, and 0.83 pb at m_H=200 GeV. Assuming the presence of a fourth sequential generation of fermions with large masses, we exclude at the 95% Confidence Level a standard-model-like Higgs boson with a mass between 131 and 204 GeV.We combine results from searches by the CDF and D0 collaborations for a standard model Higgs boson (H) in the process gg→H→W+W- in pp̅ collisions at the Fermilab Tevatron Collider at √s=1.96  TeV. With 4.8  fb-1 of integrated luminosity analyzed at CDF and 5.4  fb-1 at D0, the 95% confidence level upper limit on σ(gg→H)×B(H→W+W-) is 1.75 pb at mH=120  GeV, 0.38 pb at mH=165  GeV, and 0.83 pb at mH=200  GeV. Assuming the presence of a fourth sequential generation of fermions with large masses, we exclude at the 95% confidence level a standard-model-like Higgs boson with a mass between 131 and 204 GeV.Peer reviewe