pinecone/core-2020-05-10-deduplication huggingface dataset:
Comparative genomics of Neisseria meningitidis strains: new targets for molecular diagnostics

AbstractIn 2010, Jaton et al. (False-negative PCR result due to gene polymorphism: the example of Neisseria meningitidis. J Clin Microbiol 2010;48:4590–2) reported an isolate of Neisseria meningitidis serogroup B that was not detected by the ctrA quantitative real-time PCR (qRT-PCR) used in our diagnostic laboratory. Sequence analysis of ctrA revealed several single nucleotide polymorphisms responsible for the negative qRT-PCR. Therefore, we sequenced the genome of this isolate and performed comparative genomics to propose new gene targets for the specific detection of N. meningitidis from clinical specimens. We identified 11 genes as specific to N. meningitidis genomes and common to at least 177 (97%) of the 183 genomes available. Among them, three genes (metA, tauE and shlA) were selected to develop new qRT-PCRs for the detection of N. meningitidis DNA. The three qRT-PCRs were highly sensitive and specific, and they exhibited a good reproducibility when tested on plasmidic positive controls and genomic DNA extracted from strains of N. meningitidis and other relevant bacterial species. The clinical sensitivity and specificity of metA and tauE qRT-PCRs were both 100% based on a testing of cerebrospinal fluid samples positive for N. meningitidis or other clinically relevant bacteria. Despite a 100% specificity, the sensitivity of the shlA qRT-PCR was only 70%. We thus recommend using the metA and/or tauE qRT-PCRs developed here. To prevent PCR failure in the presence of new polymorphic strains, the detection of dual targets by duplex qRT-PCR would be more accurate and suitable for the diagnosis of N. meningitidis from clinical specimens
Precision measurement of orthopositronium decay rate using SiO2 powder

AbstractThe intrinsic decay rate of orthopositronium formed in SiO2 powder is measured using the direct 2γ correction method such that the time dependence of the pick-off annihilation rate is precisely determined using high energy-resolution germanium detectors. As a systematic test, two different types of SiO2 powder are used with consistent findings. The intrinsic decay rate of orthopositronium is found to be 7.0396±0.0012(stat)±0.0011(sys) μs−1, which is consistent with previous measurements using SiO2 powder with about twice the accuracy. Results agree well with a recent O(α2) QED prediction, varying 3.8–5.6 experimental standard deviations from other measurements
A Novel Class of MYB Factors Controls Sperm-Cell Formation in Plants

AbstractIn contrast to animals, the plant male germline is established after meiosis in distinctive haploid structures, termed pollen grains. The germline arises by a distinct asymmetric division of the meiotic products [1, 2, 3]. The fates of the resulting vegetative and generative cells are distinct. In contrast to the larger vegetative cell, arrested in the G1 phase of the cell cycle, the smaller generative cell divides once to produce the two male gametes or sperm cells. Sperm cells are delivered to the female gametes by the pollen tube, which develops from the vegetative cell. In spite of recent efforts to understand pollen development [4–8], the molecular pathway controlling sperm-cell ontogenesis is unknown. Here, we present the isolation of DUO1, a novel R2R3 MYB gene of Arabidopsis, as the first gene shown to control male gamete formation in plants. DUO1 is specifically expressed in the male germline, and DUO1 protein accumulates in sperm-cell nuclei. Mutations in DUO1 produce a single larger diploid sperm cell unable to perform fertilization. DUO1 appears to be evolutionarily conserved in several plant species and defines a new subfamily of pollen-specific MYB genes
Type I and new seesaw in left–right symmetric theories

AbstractWe extend the Type I seesaw and suggest a new seesaw mechanism to generate neutrino masses within the left–right symmetric theories where parity is spontaneously broken. We construct a next to minimal left–right symmetric model where neutrino masses are determined irrespective of the B−L breaking scale and call it the new seesaw mechanism. In this scenario B−L scale can be very low. This makes B−L gauge boson and the quasi-Dirac heavy leptons very light. These TeV scale particles could have large impact on lepton flavor and CP violating processes. We also shed light on the phenomenological aspects of the model within the reach of the LHC
The social context of tuberculosis treatment in urban risk groups in the United Kingdom: a qualitative interview study

SummaryObjectivesThere is scant qualitative research into the experiences of tuberculosis (TB) treatment in urban risk groups with complex health and social needs in the UK. This study aimed to describe the social context of adherence to treatment in marginalized groups attending a major TB centre in London.MethodsA qualitative cross-sectional study was performed using semi-structured interviews with patients receiving treatment for TB. Analytical frameworks aimed to reflect the role of broader social structures in shaping individual health actions.ResultsThere were 17 participants; the majority were homeless and had complex medical and social needs, including drug and alcohol use or immigration problems affecting entitlement to social welfare. Participants rarely actively chose not to take their medication, but described a number of social and institutional barriers to adherence and their need for practical support. Many struggled with the physical aspects of taking medication and the side effects. Participants receiving directly observed therapy (DOT) reported both positive and negative experiences, reflecting the type of DOT provider and culture of the organization.ConclusionsThere is a need for integrated care across drug, alcohol, HIV, and homeless services in order to address the complex clinical co-morbidities and social needs that impact on the patient's ability to sustain a course of treatment
Shape coexistence and the role of axial asymmetry in 72Ge

AbstractThe quadrupole collectivity of low-lying states and the anomalous behavior of the 02+ and 23+ levels in 72Ge are investigated via projectile multi-step Coulomb excitation with GRETINA and CHICO-2. A total of forty six E2 and M1 matrix elements connecting fourteen low-lying levels were determined using the least-squares search code, gosia. Evidence for triaxiality and shape coexistence, based on the model-independent shape invariants deduced from the Kumar–Cline sum rule, is presented. These are interpreted using a simple two-state mixing model as well as multi-state mixing calculations carried out within the framework of the triaxial rotor model. The results represent a significant milestone towards the understanding of the unusual structure of this nucleus
Measurement of the longitudinal and transverse cross-section in e+e− annihilation at s=35–44 GeV

AbstractAn investigation of the polar angle distribution of charged hadrons is presented using data taken by the JADE experiment at the PETRA e+e− collider at centre-of-mass energies of 35 and 44 GeV. From fits to the polar angle distribution the longitudinal, σL, and transverse, σT, cross-section relative to the total hadronic are determined at an average energy scale of 36.6 GeV. The results are σLσtot=0.067±0.013, σTσtot=0.933∓0.013, where total errors are given and the results are exactly anticorrelated. Using the next-to-leading order QCD prediction for the longitudinal cross-section, the value αS(36.6GeV)=0.150±0.025 of the strong coupling constant is obtained in agreement with the world average value of αS evolved to an energy scale of 36.6 GeV
International Geosphere–Biosphere Programme and Earth system science: Three decades of co-evolution

AbstractThe maturing of Earth system science as a discipline has underpinned the development of concepts such as the Anthropocene and planetary boundaries. The International Geosphere–Biosphere Programme’s (IGBP) scientific and institutional history is deeply intertwined with the development of the concept of the Earth as a system as well as the discipline of Earth system science. Here we frame the broader programme of IGBP through its core projects and programme-level activities and illustrate this co-evolution. We identify and discuss three phases in the programme’s history. In its first phase beginning in 1986, IGBP focused on building international networks and global databases that were key to understanding Earth system component processes. In the early 2000s IGBP’s first major synthesis and associated activities promoted a more integrated view of the Earth system informed by greater emphasis on interdisciplinarity. Human actions were seen as an integral part of the Earth system and the concept of the Anthropocene came to the fore. In recent years IGBP has increased focus on sustainability and multifaceted engagement with policy processes. IGBP closed at the end of 2015 after three decades of coordinating international research on global change. The programme’s longevity points to its capacity to adapt its scientific and institutional structures to changing scientific and societal realities. Its history may offer lessons for the emerging Future Earth initiative as it seeks to rally international collaborative research around sustainability and solutions
Noncommutative Riemann Integration and Novikov–Shubin Invariants for Open Manifolds

AbstractGiven a C*-algebra A with a semicontinuous semifinite trace τ acting on the Hilbert space H, we define the family AR of bounded Riemann measurable elements w.r.t. τ as a suitable closure, á la Dedekind, of A, in analogy with one of the classical characterizations of Riemann measurable functions, and show that AR is a C*-algebra, and τ extends to a semicontinuous semifinite trace on AR. Then, unbounded Riemann measurable operators are defined as the closed operators on H which are affiliated to A″ and can be approximated in measure by operators in AR, in analogy with unbounded Riemann integration. Unbounded Riemann measurable operators form a τ-a.e. bimodule on AR, denoted by AR, and such a bimodule contains the functional calculi of selfadjoint elements of AR under unbounded Riemann measurable functions. Besides, τ extends to a bimodule trace on AR. Type II1 singular traces for C*-algebras can be defined on the bimodule of unbounded Riemann-measurable operators. Noncommutative Riemann integration and singular traces for C*-algebras are then used to define Novikov–Shubin numbers for amenable open manifolds, to show their invariance under quasi-isometries, and to prove that they are (noncommutative) asymptotic dimensions
Giant magnon solution and dispersion relation in string theory in AdS3×S3×T4 with mixed flux

AbstractWe address the question of the exact form of the dispersion relation for light-cone string excitations in string theory in AdS3×S3×T4 with mixed R–R and NS–NS 3-form fluxes. The analogy with string theory in AdS5×S5 suggests that in addition to the data provided by the perturbative near-BMN expansion and symmetry algebra considerations there is another source of information for the dispersion relation – the semiclassical giant magnon solution. In earlier work in arXiv:1303.1037 and arXiv:1304.4099 we found that the symmetry algebra constraints, which are consistent with a perturbative expansion, do not completely determine the form of the dispersion relation. The aim of the present paper is to fix the dispersion relation by constructing a generalisation of the known dyonic giant magnon soliton on S3 to the presence of a non-zero NS–NS flux described by a WZ term in the string action (with coefficient q). We find that the angular momentum of this soliton gets shifted by a term linear in world-sheet momentum p. We also discuss the symmetry algebra of the string light-cone S-matrix and show that the exact dispersion relation, which should have the correct perturbative BMN and semiclassical giant magnon limits, should also contain such a linear momentum term. The simplicity of the resulting bound-state picture provides a strong argument in favour of this dispersion relation
PeV scale Left–Right symmetry and baryon asymmetry of the Universe

AbstractWe study the cosmology of two versions of supersymmetric Left–Right symmetric model. The scale of the B–L symmetry breaking in these models is naturally low, 104–106 GeV. Spontaneous breakdown of parity is accompanied by a first order phase transition. We simulate the domain walls of the phase transition and show that they provide requisite conditions, specifically, CP violating phase needed for leptogenesis. Additionally soft resonant leptogenesis is conditionally viable in the two models considered. Some of the parameters in the soft supersymmetry breaking terms are shown to be constrained from these considerations. It is argued that the models may be testable in upcoming collider and cosmology experiments
Mutations in DNAH1, which Encodes an Inner Arm Heavy Chain Dynein, Lead to Male Infertility from Multiple Morphological Abnormalities of the Sperm Flagella

Ten to fifteen percent of couples are confronted with infertility and a male factor is involved in approximately half the cases. A genetic etiology is likely in most cases yet only few genes have been formally correlated with male infertility. Homozygosity mapping was carried out on a cohort of 20 North African individuals, including 18 index cases, presenting with primary infertility resulting from impaired sperm motility caused by a mosaic of multiple morphological abnormalities of the flagella (MMAF) including absent, short, coiled, bent, and irregular flagella. Five unrelated subjects out of 18 (28%) carried a homozygous variant in DNAH1, which encodes an inner dynein heavy chain and is expressed in testis. RT-PCR, immunostaining, and electronic microscopy were carried out on samples from one of the subjects with a mutation located on a donor splice site. Neither the transcript nor the protein was observed in this individual, confirming the pathogenicity of this variant. A general axonemal disorganization including mislocalization of the microtubule doublets and loss of the inner dynein arms was observed. Although DNAH1 is also expressed in other ciliated cells, infertility was the only symptom of primary ciliary dyskinesia observed in affected subjects, suggesting that DNAH1 function in cilium is not as critical as in sperm flagellum
Competing particle–hole excitations in 30Na: Constraining state-of-the-art effective interactions

AbstractThe odd–odd nucleus 30Na is studied via a one-proton, one-proton–one-neutron and one-neutron removal reaction using an intermediate-energy 31Mg, 32Mg and 31Na radioactive ion beam, respectively. Combining high-resolution γ-ray spectroscopy with the selectivity of the three reaction mechanisms, we are able to distinguish multiple particle–hole configurations. Negative-parity states in 30Na are observed for the first time, providing an important measure of the excitation of the 1p1h/3p3h configuration and hence the sd–pf shell gap. The extracted band structures and level energies serve as invaluable input for the theoretical refinement of the effective interactions used in this region
The in-plane deformation of a tire carcass: Analysis and measurement

AbstractThe deformation of parts of a tire is the direct result of tire–road interactions, and therefore is of great interest in tire sensor development. This case study focuses on the analysis of the deformation of the tire carcass and investigates its potential for the estimation of the in-plane tire force. The deformation of the tire carcass due to applied steady-state in-plane forces is first analyzed with the flexible ring model and then validated through optical tire sensor measurements. Coupled deformations of the tire carcass in the radial and tangential directions are observed. This reveals a promising method for tire sensing applications in the estimation of the in-plane tire force, which relies only on direct measurements of the radial deformation of the tire carcass. Moreover, indicators are proposed to correlate the radial deformation of the tire carcass with in-plane tire forces
An extension of two-Higgs-doublet model and the excesses of 750 GeV diphoton, muon g-2 and h→μτ

AbstractIn this paper we simultaneously explain the excesses of the 750 GeV diphoton, muon g-2 and h→μτ in an extension of the two-Higgs-doublet model (2HDM) with additional vector-like fermions and a CP-odd scalar singlet (P) which is identified as the 750 GeV resonance. This 750 GeV resonance has a mixing with the CP-odd scalar (A) from a second scalar doublet, which leads to a coupling between P and the SM particles as well as a coupling between A and the vector-like fermions. Such mixing and couplings are strongly constrained by τ→μγ, muon g-2 and the 750 GeV diphoton data. We scan over the parameter space and find that such an extension can simultaneously account for the observed excesses of 750 GeV diphoton, muon g-2 and h→μτ. The 750 GeV resonance decays in exotic modes, such as P→hA, P→HZ, P→HA and P→W±H∓, and its width can be dozens of GeV and is sensitive to the mixing angle
Controlled non-uniform random generation of decomposable structures

AbstractConsider a class of decomposable combinatorial structures, using different types of atoms Z={Z1,…,Z∣Z∣}. We address the random generation of such structures with respect to a size n and a targeted distribution in k of its distinguished atoms. We consider two variations on this problem.In the first alternative, the targeted distribution is given by k real numbers μ1,…,μk such that 0<μi<1 for all i and μ1+⋯+μk≤1. We aim to generate random structures among the whole set of structures of a given size n, in such a way that the expected frequency of any distinguished atom Zi equals μi. We address this problem by weighting the atoms with a k-tuple π of real-valued weights, inducing a weighted distribution over the set of structures of size n. We first adapt the classical recursive random generation scheme into an algorithm taking O(n1+o(1)+mnlogn) arithmetic operations to draw m structures from the π-weighted distribution. Secondly, we address the analytical computation of weights such that the targeted frequencies are achieved asymptotically, i.e. for large values of n. We derive systems of functional equations whose resolution gives an explicit relationship between π and μ1,…,μk. Lastly, we give an algorithm in O(kn4) for the inverse problem, i.e. computing the frequencies associated with a given k-tuple π of weights, and an optimized version in O(kn2) in the case of context-free languages. This allows for a heuristic resolution of the weights/frequencies relationship suitable for complex specifications.In the second alternative, the targeted distribution is given by k natural numbers n1,…,nk such that n1+⋯+nk+r=n where r≥0 is the number of undistinguished atoms. The structures must be generated uniformly among the set of structures of size n that contain exactly ni atoms Zi (1≤i≤k). We give a O(r2∏i=1kni2+mnklogn) algorithm for generating m structures, which simplifies into a O(r∏i=1kni+mn) for regular specifications
Cryopreservation and transplantation of ovarian tissue exclusively to postpone menopause: technically possible but endocrinologically doubtful

AbstractTransplantation of cryopreserved ovarian tissue has been shown to induce pregnancies and puberty successfully. Therefore, using cryopreserved ovarian tissue to postpone menopause (tissue hormone therapy [THT]) seems to be an interesting option to avoid conventional menopause hormone therapy (MHT). Pregnancy induction and replacing MHT by THT, however, are completely different topics as different requirements need to be met. First, MHT requires long-lasting and continuous hormone production. It still needs to be proven if the transplanted tissue is active for at least 5 years with a continuous follicle growth to avoid phases with low oestrogen production, which would otherwise cause menopausal symptoms and could reduce the postulated benefit for women's health. Second, the advantage of a physiological hormone production over a non-physiological MHT is still hypothetical. Third, women who have undergone hysterectomies who do not need progesterone for endometrial protection would only require oestrogens, imposing more health benefits (cardiovascular system, mammary gland) than oestrogen and progesterone production or replacement. Therefore, transplanting ovarian tissue exclusively to postpone menopause is endocrinologically doubtful and should only be carried out within clinical trials
ER stress is associated with reduced ABCA-1 protein levels in macrophages treated with advanced glycated albumin – Reversal by a chemical chaperone

AbstractATP-binding cassette transporter A1 mediates the export of excess cholesterol from macrophages, contributing to the prevention of atherosclerosis. Advanced glycated albumin (AGE-alb) is prevalent in diabetes mellitus and is associated with the development of atherosclerosis. Independently of changes in ABCA-1 mRNA levels, AGE-alb induces oxidative stress and reduces ABCA-1 protein levels, which leads to macrophage lipid accumulation. These metabolic conditions are known to elicit endoplasmic reticulum (ER) stress. We sought to determine if AGE-alb induces ER stress and unfolded protein response (UPR) in macrophages and how disturbances to the ER could affect ABCA-1 content and cholesterol efflux in macrophages. AGE-alb induced a time-dependent increase in ER stress and UPR markers. ABCA-1 content and cellular cholesterol efflux were reduced by 33% and 47%, respectively, in macrophages treated with AGE-alb, and both were restored by treatment with 4-phenyl butyric acid (a chemical chaperone that alleviates ER stress), but not MG132 (a proteasome inhibitor). Tunicamycin, a classical ER stress inductor, also impaired ABCA-1 expression and cholesterol efflux (showing a decrease of 61% and 82%, respectively), confirming the deleterious effect of ER stress in macrophage cholesterol accumulation. Glycoxidation induces macrophage ER stress, which relates to the reduction in ABCA-1 and in reverse cholesterol transport, endorsing the adverse effect of macrophage ER stress in atherosclerosis. Thus, chemical chaperones that alleviate ER stress may represent a useful tool for the prevention and treatment of atherosclerosis in diabetes
Anisotropic flow of charged hadrons, pions and (anti-)protons measured at high transverse momentum in Pb–Pb collisions at sNN=2.76 TeV

AbstractThe elliptic, v2, triangular, v3, and quadrangular, v4, azimuthal anisotropic flow coefficients are measured for unidentified charged particles, pions, and (anti-)protons in Pb–Pb collisions at sNN=2.76 TeV with the ALICE detector at the Large Hadron Collider. Results obtained with the event plane and four-particle cumulant methods are reported for the pseudo-rapidity range |η|<0.8 at different collision centralities and as a function of transverse momentum, pT, out to pT=20 GeV/c. The observed non-zero elliptic and triangular flow depends only weakly on transverse momentum for pT>8 GeV/c. The small pT dependence of the difference between elliptic flow results obtained from the event plane and four-particle cumulant methods suggests a common origin of flow fluctuations up to pT=8 GeV/c. The magnitude of the (anti-)proton elliptic and triangular flow is larger than that of pions out to at least pT=8 GeV/c indicating that the particle type dependence persists out to high pT