pinecone/core-2020-05-10-deduplication huggingface dataset:
A tripartite of immune-, epithelial-, and nervous-systems in the homeostatic regulation of the gut

Various cell types in the intestinal mucosa are constantly exposed to complex signals
emanating from the lumen, including the microbiota and its metabolites. How these bilateral
interactions in turn influences intestinal homeostasis is an important question in order to
understand microbiota-host interactions. This thesis has attempted to address this question in
the following papers. Deletion of the diet- and microbiota-regulated aryl hydrocarbon
receptor in CD11c+ cells was found to result in aberrant intestinal epithelium morphogenesis
and increased susceptibility of these mice to chemically induced colitis (Paper I). Our data
highlight a possible gateway of communication between the host and its environment,
through the AhR in intestinal antigen presenting cells, consequently regulating intestinal
epithelial cell biology and function. 



In the second paper, we studied the impact of the microbiota on the development of the
enteric nervous system (ENS). The ENS controls many aspects of gut physiology, including
mucosal immunity. The major cellular component of the ENS is the enteric glia cell (EGC).
Our data showcased that the migration and expansion of EGC networks in the lamina propria
towards the lumen are under the influence of the microbiota. The postnatal expansion of
mucosal EGC networks was found to coincide with the same period where the microbiota
increases in number and diversity. Moreover, this microbiota-driven mechanism is an active
process that can be impaired following the exposure to antibiotics, which abrogate signalling
pathways mediating the host-microbe cross talk. 



In the final manuscript, we developed a co-culture model system to study EGC functions
further, in relation to intestinal epithelial barrier functions. Using genetic labeling techniques
and live cell imaging, we observed close associations of EGCs with co-cultured intestinal
epithelial organoids ex vivo, reminiscent of the contacts reported between these two cell types
in vivo. 



In conclusion, this thesis open more questions than answers especially as it addresses the
issue of cross communication between different biological systems required for the
development of complex organisms. The new player here is the microbiome and how it
constantly affects the response of different cell types, including cell-to-cell communications,
important for cellular adaptation to environmental cues. Future work will address the precise
molecular and cellular mechanisms underlying the interplay between the microbiota and hosttissues
to establish and maintain intestinal homeostasis
Measurements of differential production cross sections for a Z boson in
  association with jets in pp collisions at sqrt(s) = 8 TeV

Cross sections for the production of a Z boson in association with jets in
proton-proton collisions at a centre-of-mass energy of sqrt(s) = 8 TeV are
measured using a data sample collected by the CMS experiment at the LHC
corresponding to 19.6 inverse femtobarns. Differential cross sections are
presented as functions of up to three observables that describe the jet
kinematics and the jet activity. Correlations between the azimuthal directions
and the rapidities of the jets and the Z boson are studied in detail. The
predictions of a number of multileg generators with leading or next-to-leading
order accuracy are compared with the measurements. The comparison shows the
importance of including multi-parton contributions in the matrix elements and
the improvement in the predictions when next-to-leading order terms are
included.Comment: Replaced with the published version. Added the journal reference and
  DOI. All the figures and tables can be found at
  http://cms-results.web.cern.ch/cms-results/public-results/publications/SMP-14-013/index.htm
Dynamic range in the C. elegans brain network

© 2016 AIP Publishing LLC. We study external electrical perturbations and their responses in the brain dynamic network of the Caenorhabditis elegans soil worm, given by the connectome of its large somatic nervous system. Our analysis is inspired by a realistic experiment where one stimulates externally specific parts of the brain and studies the persistent neural activity triggered in other cortical regions. In this work, we perturb groups of neurons that form communities, identified by the walktrap community detection method, by trains of stereotypical electrical Poissonian impulses and study the propagation of neural activity to other communities by measuring the corresponding dynamic ranges and Steven law exponents. We show that when one perturbs specific communities, keeping the rest unperturbed, the external stimulations are able to propagate to some of them but not to all. There are also perturbations that do not trigger any response. We found that this depends on the initially perturbed community. Finally, we relate our findings for the former cases with low neural synchronization, self-criticality, and large information flow capacity, and interpret them as the ability of the brain network to respond to external perturbations when it works at criticality and its information flow capacity becomes maximal
Patients' willingness and ability to participate actively in the reduction of clinical errors: a systematic literature review

This systematic review identifies the factors that both support and deter patients from being willing and able to participate actively in reducing clinical errors. Specifically, we add to our understanding of the safety culture in healthcare by engaging with the call for more focus on the relational and subjective factors which enable patients' participation (Iedema, Jorm, & Lum, 2009; Ovretveit, 2009). A systematic search of six databases, ten journals and seven healthcare organisations' web sites resulted in the identification of 2714 studies of which 68 were included in the review. These studies investigated initiatives involving patients in safety or studies of patients' perspectives of being actively involved in the safety of their care. The factors explored varied considerably depending on the scope, setting and context of the study. Using thematic analysis we synthesized the data to build an explanation of why, when and how patients are likely to engage actively in helping to reduce clinical errors. The findings show that the main factors for engaging patients in their own safety can be summarised in four categories: illness; individual cognitive characteristics; the clinician-patient relationship; and organisational factors. We conclude that illness and patients' perceptions of their role and status as subordinate to that of clinicians are the most important barriers to their involvement in error reduction. In sum, patients' fear of being labelled "difficult" and a consequent desire for clinicians' approbation may cause them to assume a passive role as a means of actively protecting their personal safety
Vestibular receptors contribute to the cortical auditory evoked potentials

Abstract:\ud
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Acoustic sensitivity of the vestibular apparatus is well-established, but the contribution of vestibular receptors to the late auditory evoked potentials of cortical origin is unknown. Evoked potentials from 500 Hz tone pips were recorded using 70 channel EEG at several intensities below and above the vestibular acoustic threshold, as determined by vestibular evoked myogenic potentials (VEMPs). In healthy subjects both auditory mid- and long-latency auditory evoked potentials (AEPs), consisting of Na, Pa, N1 and P2 waves, were observed in the sub-threshold conditions. However, in passing through the vestibular threshold, systematic changes were observed in the morphology of the potentials and in the intensity dependence of their amplitude and latency. These changes were absent in a patient without functioning vestibular receptors. In particular, for the healthy subjects there was a fronto-central negativity, which appeared at about 42 ms, referred to as an N42, prior to the AEP N1. Source analysis of both the N42 and N1 indicated involvement of cingulate cortex, as well as bilateral superior temporal cortex. Our findings are best explained by vestibular receptors contributing to what were hitherto considered as purely auditory evoked potentials and in addition tentatively identify a new component that appears to be primarily of vestibular origin
Application of whole genome and RNA sequencing to investigate the genomic landscape of common variable immunodeficiency disorders.

Common Variable Immunodeficiency Disorders (CVIDs) are the most prevalent cause of primary antibody failure. CVIDs are highly variable and a genetic causes have been identified in <5% of patients. Here, we performed whole genome sequencing (WGS) of 34 CVID patients (94% sporadic) and combined them with transcriptomic profiling (RNA-sequencing of B cells) from three patients and three healthy controls. We identified variants in CVID disease genes TNFRSF13B, TNFRSF13C, LRBA and NLRP12 and enrichment of variants in known and novel disease pathways. The pathways identified include B-cell receptor signalling, non-homologous end-joining, regulation of apoptosis, T cell regulation and ICOS signalling. Our data confirm the polygenic nature of CVID and suggest individual-specific aetiologies in many cases. Together our data show that WGS in combination with RNA-sequencing allows for a better understanding of CVIDs and the identification of novel disease associated pathways
UK prescribing practices as proxy markers of unmet need in allergic rhinitis : a retrospective observational study

Acknowledgements We thank Ruth B Murray for reviewing and editing this manuscript. We thank Joan B Soriano for his critical review and constructive comments. We thank Helga Mikkelsen and Alessandra Cifra for their assistance with manuscript editing and revision. Finally, we thank the Journal blind peer reviewers, whose suggestions and critical appraisal significantly improved our original submission. FUNDING This study was funded by Meda, Solna, Sweden. Data acquisition and analyses were funded by Meda. The study was conducted by Research in Real Life as an independent research organisation; Meda had no role in the conduct or reporting of the study.Peer reviewedPublisher PD
A novel facility for reduced-gravity testing: A setup for studying low-velocity collisions into granular surfaces

This work presents an experimental design for studying low-velocity collisions into granular surfaces in low-gravity. In the experiment apparatus, reduced-gravity is simulated by releasing a free-falling projectile into a surface container with a downward acceleration less than that of Earth’s gravity. The acceleration of the surface is controlled through the use of an Atwood machine, or a system of pulleys and counterweights. The starting height of the surface container and the initial separation distance between the projectile and surface are variable and chosen to accommodate collision velocities up to 20 cm/s and effective accelerations of ∼0.1 to 1.0 m/s2. Accelerometers, placed on the surface container and inside the projectile, provide acceleration data, while high-speed cameras capture the collision and act as secondary data sources. The experiment is built into an existing 5.5 m drop tower frame and requires the custom design of all components, including the projectile, surface sample container, release mechanism, and deceleration system. Data from calibration tests verify the efficiency of the experiment’s deceleration system and provide a quantitative understanding of the performance of the Atwood system
The consequences of understanding expert probability reporting as a decision

In this paper we reiterate that the personalist interpretation of probability is inevitable and as least as informed as any other allegedly more ‘objective’ definition of probability. We also argue that the problem faced by forensic scientists, the reporting on imperfect personal knowledge, in terms of probabilities, can be reconstructed as a decision problem. Tackling this problem through a rigorous decision theoretic analy- sis provides further argument in support of the view that optimal probability reporting is in terms of single numbers, not intervals
Angular coefficients of Z bosons produced in pp collisions at √s=8 TeV and decaying to μ+μ- as a function of transverse momentum and rapidity

Measurements of the five most significant angular coefficients, A0 through A4, for Z bosons produced in pp collisions at √s=8 TeV and decaying to μ+μ- are presented as a function of the transverse momentum and rapidity of the Z boson. The integrated luminosity of the dataset collected with the CMS detector at the LHC corresponds to 19.7 fb-1. These measurements provide comprehensive information about the Z boson production mechanisms, and are compared to the QCD predictions at leading order, next-to-leading order, and next-to-next-to-leading order in perturbation theoryWe acknowledge the computing centers and
personnel of the Worldwide LHC Computing Grid for delivering so
effectively the computing infrastructure essential to our analyses.
Finally, we acknowledge the enduring support for the construction
and operation of the LHC and the CMS detector provided by
the following funding agencies: BMWFW and FWF (Austria); FNRS
and FWO (Belgium); CNPq, CAPES, FAPERJ, and FAPESP (Brazil);
MES (Bulgaria); CERN; CAS, MOST, and NSFC (China); COLCIENCIAS
(Colombia); MSES and CSF (Croatia); RPF (Cyprus); MoER, ERC IUT
and ERDF (Estonia); Academy of Finland, MEC, and HIP (Finland);
CEA and CNRS/IN2P3 (France); BMBF, DFG, and HGF (Germany);
GSRT (Greece); OTKA and NIH (Hungary); DAE and DST (India);
IPM (Iran); SFI (Ireland); INFN (Italy); MSIP and NRF (Republic
of Korea); LAS (Lithuania); MOE and UM (Malaysia); CINVESTAV,
CONACYT, SEP, and UASLP-FAI (Mexico); MBIE (New Zealand); PAEC
(Pakistan); MSHE and NSC (Poland); FCT (Portugal); JINR (Dubna);
MON, RosAtom, RAS and RFBR (Russia); MESTD (Serbia); SEIDI and
CPAN (Spain); Swiss Funding Agencies (Switzerland); MST (Taipei);
ThEPCenter, IPST, STAR and NSTDA (Thailand); TUBITAK and TAEK
(Turkey); NASU and SFFR (Ukraine); STFC (United Kingdom); DOE
and NSF (USA).
Individuals have received support from the Marie-Curie program
and the European Research Council and EPLANET (European
Union); the Leventis Foundation; the A.P. Sloan Foundation; the
Alexander von Humboldt Foundation; the Belgian Federal Science
Policy Office; the Fonds pour la Formation à la Recherche dans
l’Industrie et dans l’Agriculture (FRIA-Belgium); the Agentschap
voor Innovatie door Wetenschap en Technologie (IWT-Belgium);
the Ministry of Education, Youth and Sports (MEYS) of the Czech
Republic; the Council of Scientific and Industrial Research, India;
the HOMING PLUS program of the Foundation for Polish Science,
cofinanced from European Union, Regional Development Fund; the
Compagnia di San Paolo (Torino); the Consorzio per la Fisica (Trieste);
MIUR project 20108T4XTM (Italy); the Thalis and Aristeia
programs cofinanced by EU-ESF and the Greek NSRF; and the
National Priorities Research Program by Qatar National Research
Fun
Grasp planning under uncertainty

Advanced robots such as mobile manipulators offer nowadays great opportunities for realistic manipulators. Physical interaction with the environment is an essential capability for service robots when acting in unstructured environments such as homes. Thus, manipulation and grasping under uncertainty has become a critical research area within robotics research.
This thesis explores techniques for a robot to plan grasps in presence of uncertainty in knowledge about objects such as their pose and shape. First, the question how much information about the graspable object the robot can perceive from a single tactile exploration attempt is considered. Next, a tactile-based probabilistic approach for grasping which aims to maximize the probability of a successful grasp is presented. The approach is further extended to include information gathering actions based on maximal entropy reduction. The combined framework unifies ideas behind planning for maximally stable grasps, the possibilities of sensor-based grasping and exploration.
Another line of research is focused on grasping familiar object belonging to a specific category. Moreover, the task is also included in the planning process as in many applications the resulting grasp should be not only stable but task compatible. The vision-based framework takes the idea of maximizing grasp stability in the novel context to cover shape uncertainty. Finally, the RGB-D vision-based probabilistic approach is extended to include tactile sensor feedback in the control loop to incrementally improve estimates about object shape and pose and then generate more stable task compatible grasps.
The results of the studies demonstrate the benefits of applying probabilistic models and using different sensor measurements in grasp planning and prove that this is a promising direction of study and research. Development of such approaches, first of all, contributes to the rapidly developing area of household applications and service robotics
T-odd quarks at the large hadron collider: 2010–2012

AbstractWe study the potential of the current Large Hadron Collider (LHC) 7 TeV run to search for heavy, colored vector-like fermions, which are assumed to carry a conserved Z2 quantum number forcing them to be pair-produced. Each fermion is assumed to decay directly into a Standard Model quark and an invisible stable particle. T-odd quarks and the lightest T-odd particle (LTP) of the Littlest Higgs model with T-parity provide an example of this setup. We estimate the bounds based on the published CMS search for events with jets and missing transverse energy in the 35 pb−1 data set collected in the 2010 run. We find that T-odd quark masses below about 450 GeV are ruled out for the LTP mass about 100 GeV. This bound is somewhat stronger than the published Tevatron constraint. We also estimate the reach with higher integrated luminosities expected in the 2011–2012 run. If no deviation from the SM is observed, we expect that a bound on the T-odd quark mass of about 650 GeV, for the LTP mass of 300 GeV and below, can be achieved with 1 fb−1 of data. We comment on the possibility of using initial-state radiation jets to constrain the region with nearly-degenerate T-odd quark and LTP
Divergent evolution of vitamin B9 binding underlies Juno-mediated adhesion of mammalian gametes

SummaryThe interaction between egg and sperm is the first necessary step of fertilization in all sexually reproducing organisms. A decade-long search for a protein pair mediating this event in mammals culminated in the identification of the glycosylphosphatidylinositol (GPI)-anchored glycoprotein Juno as the egg plasma membrane receptor of sperm Izumo1 [1,2]. The Juno–Izumo1 interaction was shown to be essential for fertilization since mice lacking either gene exhibit sex-specific sterility, making these proteins promising non-hormonal contraceptive targets [1,3]. No structural information is available on how gamete membranes interact at fertilization, and it is unclear how Juno — which was previously named folate receptor (FR) 4, based on sequence similarity considerations — triggers membrane adhesion by binding Izumo1. Here, we report the crystal structure of Juno and find that the overall fold is similar to that of FRα and FRβ but with significant flexibility within the area that corresponds to the rigid ligand-binding site of these bona fide folate receptors. This explains both the inability of Juno to bind vitamin B9/folic acid [1], and why mutations within the flexible region can either abolish or change the species specificity of this interaction. Furthermore, structural similarity between Juno and the cholesterol-binding Niemann-Pick disease type C1 protein (NPC1) suggests how the modified binding surface of Juno may recognize the helical structure of the amino-terminal domain of Izumo1. As Juno appears to be a mammalian innovation, our study indicates that a key evolutionary event in mammalian reproduction originated from the neofunctionalization of the vitamin B9-binding pocket of an ancestral folate receptor molecule
N=4 scattering amplitudes and the deformed Graßmannian

AbstractSome time ago the general tree-level scattering amplitudes of N=4 Super Yang–Mills theory were expressed as certain Graßmannian contour integrals. These remarkable formulas allow to clearly expose the super-conformal, dual super-conformal, and Yangian symmetries of the amplitudes. Using ideas from integrability it was recently shown that the building blocks of the amplitudes permit a natural multi-parameter deformation. However, this approach had been criticized by the observation that it seemed impossible to reassemble the building blocks into Yangian-invariant deformed non-MHV amplitudes. In this note we demonstrate that the deformations may be succinctly summarized by a simple modification of the measure of the Graßmannian integrals, leading to a Yangian-invariant deformation of the general tree-level amplitudes. Interestingly, the deformed building blocks appear as residues of poles in the spectral parameter planes. Given that the contour integrals also contain information on the amplitudes at loop-level, we expect the deformations to be useful there as well. In particular, applying meromorphicity arguments, they may be expected to regulate all notorious infrared divergences. We also point out relations to Gelfand hypergeometric functions and the quantum Knizhnik–Zamolodchikov equations
Universality of the Collins–Soper–Sterman nonperturbative function in vector boson production

AbstractWe revise the b∗ model for the Collins–Soper–Sterman resummed form factor to improve description of the leading-power contribution at nearly nonperturbative impact parameters. This revision leads to excellent agreement of the transverse momentum resummation with the data in a global analysis of Drell–Yan lepton pair and Z boson production. The nonperturbative contributions are found to follow universal quasi-linear dependence on the logarithm of the heavy boson invariant mass, which closely agrees with an estimate from the infrared renormalon analysis
Universal Bethe ansatz solution for the Temperley–Lieb spin chain

AbstractWe consider the Temperley–Lieb (TL) open quantum spin chain with “free” boundary conditions associated with the spin-s representation of quantum-deformed sl(2). We construct the transfer matrix, and determine its eigenvalues and the corresponding Bethe equations using analytical Bethe ansatz. We show that the transfer matrix has quantum group symmetry, and we propose explicit formulas for the number of solutions of the Bethe equations and the degeneracies of the transfer-matrix eigenvalues. We propose an algebraic Bethe ansatz construction of the off-shell Bethe states, and we conjecture that the on-shell Bethe states are highest-weight states of the quantum group. We also propose a determinant formula for the scalar product between an off-shell Bethe state and its on-shell dual, as well as for the square of the norm. We find that all of these results, except for the degeneracies and a constant factor in the scalar product, are universal in the sense that they do not depend on the value of the spin. In an appendix, we briefly consider the closed TL spin chain with periodic boundary conditions, and show how a previously-proposed solution can be improved so as to obtain the complete (albeit non-universal) spectrum