pinecone/core-2020-05-10-deduplication huggingface dataset:
Convergence of Genes and Cellular Pathways Dysregulated in Autism Spectrum Disorders

Rare copy-number variation (CNV) is an important source of risk for autism spectrum disorders (ASDs). We analyzed 2,446 ASD-affected families and confirmed an excess of genic deletions and duplications in affected versus control groups (1.41-fold, p = 1.0 × 10−5) and an increase in affected subjects carrying exonic pathogenic CNVs overlapping known loci associated with dominant or X-linked ASD and intellectual disability (odds ratio = 12.62, p = 2.7 × 10−15, ∼3% of ASD subjects). Pathogenic CNVs, often showing variable expressivity, included rare de novo and inherited events at 36 loci, implicating ASD-associated genes (CHD2, HDAC4, and GDI1) previously linked to other neurodevelopmental disorders, as well as other genes such as SETD5, MIR137, and HDAC9. Consistent with hypothesized gender-specific modulators, females with ASD were more likely to have highly penetrant CNVs (p = 0.017) and were also overrepresented among subjects with fragile X syndrome protein targets (p = 0.02). Genes affected by de novo CNVs and/or loss-of-function single-nucleotide variants converged on networks related to neuronal signaling and development, synapse function, and chromatin regulation
Vacuum energy of the Bukhvostov–Lipatov model

AbstractBukhvostov and Lipatov have shown that weakly interacting instantons and anti-instantons in the O(3) non-linear sigma model in two dimensions are described by an exactly soluble model containing two coupled Dirac fermions. We propose an exact formula for the vacuum energy of the model for twisted boundary conditions, expressing it through a special solution of the classical sinh-Gordon equation. The formula perfectly matches predictions of the standard renormalized perturbation theory at weak couplings as well as the conformal perturbation theory at short distances. Our results also agree with the Bethe ansatz solution of the model. A complete proof the proposed expression for the vacuum energy based on a combination of the Bethe ansatz techniques and the classical inverse scattering transform method is presented in the second part of this work [42]
The structure relation for Askey–Wilson polynomials

AbstractAn explicit structure relation for Askey–Wilson polynomials is given. This involves a divided q-difference operator which is skew symmetric with respect to the Askey–Wilson inner product and which sends polynomials of degree n to polynomials of degree n+1. By specialization of parameters and by taking limits, similar structure relations, as well as lowering and raising relations, can be obtained for other families in the q-Askey scheme and the Askey scheme. This is explicitly discussed for Jacobi polynomials, continuous q-Jacobi polynomials, continuous q-ultraspherical polynomials, and for big q-Jacobi polynomials. An already known structure relation for this last family can be obtained from the new structure relation by using the three-term recurrence relation and the second order q-difference formula. The results are also put in the framework of a more general theory. Their relationship with earlier work by Zhedanov and Bangerezako is discussed. There is also a connection with the string equation in discrete matrix models and with the Sklyanin algebra
B-cell O-galactosyltransferase activity, and expression of O-glycosylation genes in bone marrow in IgA nephropathy

In IgA nephropathy (IgAN), pathogenic IgA1 is likely derived from bone marrow (BM) cells and exhibits reduced O-galactosylation. Defective O-galactosylation may arise from the compromised expression or function of the enzyme β-galactosyltransferase and/or its molecular chaperone (Cosmc). We measured B-cell O-galactosylation activity and the relative gene expression of β-galactosyltransferase and Cosmc in peripheral blood and BM taken from patients with IgAN and controls. O-galactosylation activity was measured in peripheral and BM B cells by the incorporation of radiolabeled galactose into an asialo-mucin acceptor. Gene expression of β-galactosyltransferase and Cosmc was measured by real-time PCR and related to that of the enzyme GalNAc-T2 (UDP-N-acetyl-α-D-galactosamine:polypeptide N-acetylgalactosaminyltransferase-2), which synthesizes the core O-glycan. Neither the B-cell O-galactosylation activity nor the gene expression of the enzyme or chaperone was different between patients and controls. However, the relationships between the O-glycosylation of serum IgA1, galactosylation activity, and β-galactosyltransferase gene expression showed different patterns in IgAN and controls. In IgAN, O-galactosylation activity correlated with β-galactosyltransferase gene expression, but not with IgA1 O-glycosylation, suggesting that factors other than the availability of β-galactosyltransferase or Cosmc are responsible for altered IgA1 O-glycosylation
Origin and function of the stalk-cell vacuole in Dictyostelium

AbstractLarge vacuoles are characteristic of plant and fungal cells, and their origin has long attracted interest. The cellular slime mould provides a unique opportunity to study the de novo formation of vacuoles because, in its life cycle, a subset of the highly motile animal-like cells (prestalk cells) rapidly develops a single large vacuole and cellulosic cell wall to become plant-like cells (stalk cells). Here we describe the origin and process of vacuole formation using live-imaging of Dictyostelium cells expressing GFP-tagged ammonium transporter A (AmtA-GFP), which was found to reside on the membrane of stalk-cell vacuoles. We show that stalk-cell vacuoles originate from acidic vesicles and autophagosomes, which fuse to form autolysosomes. Their repeated fusion and expansion accompanied by concomitant cell wall formation enable the stalk cells to rapidly develop turgor pressure necessary to make the rigid stalk to hold the spores aloft. Contractile vacuoles, which are rich in H+-ATPase as in plant vacuoles, remained separate from these vacuoles. We further argue that AmtA may play an important role in the control of stalk-cell differentiation by modulating the pH of autolysosomes
Multi-scale modeling of the mechanical behavior of polycrystalline ice under transient creep

AbstractIce is a challenging material for understanding the overall behavior of polycrystalline materials and more specifically the coupling between elastic and viscous e_ects during transient creep. At the single crystal level, ice is an hexagonal material with a rather weak elastic anisotropy but with a strong viscoplastic anisotropy. The strain-stress curve of ice single crystals shows a softening behavior depending on the strain-rate. The strong viscous anisotropy of ice gives rise to the progressive development of intergranular and intragranular strain heterogeneities and to stress concentrations which play an important role in the understanding of the creep behavior of ice polycrystals. The single crystal constitutive relations of Castelnau et al [1] are slightly modified here for a better evolution of the reference resolved shear stress on the slip systems and to account for kinematic hardening at the single crystal level. These constitutive relations are then used in a full-field simulation performed by an elasto-viscoplastic FFT-based method. The material parameters of the model are determined by comparison with experimental data available for single crystals as well as for polycrystals
Correlation or not Correlation? This is the Question in Modelling Residential Water Demand Pulses

AbstractThis paper presents a comparison of two different modelling approaches for the generation of residential water demand pulses as Poisson processes. Both approaches are able to preserve the mean value of daily water demand. The main difference lies in the fact that the first considers the correlation between pulse durations and intensities whereas the second neglects it. Overall, the results of the applications aimed at reproducing the measured pulses in two households show that the increase in parameterization burden associated with taking correlation into account delivers a considerable improvement in the quality of model predictions
Palaeolimnological evidence for an east–west climate see-saw in the Mediterranean since AD 900

AbstractDuring the period of instrumental records, the North Atlantic Oscillation (NAO) has strongly influenced inter-annual precipitation variations in the western Mediterranean, while some eastern parts of the basin have shown an anti-phase relationship in precipitation and atmospheric pressure. Here we explore how the NAO and other atmospheric circulation modes operated over the longer timescales of the Medieval Climate Anomaly (MCA) and Little Ice Age (LIA). High-resolution palaeolimnological evidence from opposite ends of the Mediterranean basin, supplemented by other palaeoclimate data, is used to track shifts in regional hydro-climatic conditions. Multiple geochemical, sedimentological, isotopic and palaeoecological proxies from Estanya and Montcortés lakes in northeast Spain and Nar lake in central Turkey have been cross-correlated at decadal time intervals since AD 900. These dryland lakes capture sensitively changes in precipitation/evaporation (P/E) balance by adjustments in water level and salinity, and are especially valuable for reconstructing variability over decadal–centennial timescales. Iberian lakes show lower water levels and higher salinities during the 11th to 13th centuries synchronous with the MCA and generally more humid conditions during the ‘LIA’ (15th–19th centuries). This pattern is also clearly evident in tree-ring records from Morocco and from marine cores in the western Mediterranean Sea. In the eastern Mediterranean, palaeoclimatic records from Turkey, Greece and the Levant show generally drier hydro-climatic conditions during the LIA and a wetter phase during the MCA. This implies that a bipolar climate see-saw has operated in the Mediterranean for the last 1100years. However, while western Mediterranean aridity appears consistent with persistent positive NAO state during the MCA, the pattern is less clear in the eastern Mediterranean. Here the strongest evidence for higher winter season precipitation during the MCA comes from central Turkey in the northeastern sector of the Mediterranean basin. This in turn implies that the LIA/MCA hydro-climatic pattern in the Mediterranean was determined by a combination of different climate modes along with major physical geographical controls, and not by NAO forcing alone, or that the character of the NAO and its teleconnections have been non-stationary
Toric Sasaki–Einstein metrics on S2×S3

AbstractWe show that by taking a certain scaling limit of a Euclideanised form of the Plebanski–Demianski metrics one obtains a family of local toric Kähler–Einstein metrics. These can be used to construct local Sasaki–Einstein metrics in five dimensions which are generalisations of the Yp,q manifolds. In fact, we find that these metrics are diffeomorphic to those recently found by Cvetic, Lu, Page and Pope. We argue that the corresponding family of smooth Sasaki–Einstein manifolds all have topology S2×S3. We conclude by setting up the equations describing the warped version of the Calabi–Yau cones, supporting (2,1) three-form flux
Environmental and Financial Life Cycle Assessment of ‘Open-renovation-systems’: Methodology and Case Study

AbstractThe emphasis in this research is on affordable and innovative semi-prefabricated ‘open-renovation-systems’ for extending residential buildings. Based on an existing LCA (life cycle assessment) and LCC (life cycle costing) methodology, two methodological issues in evaluating renovation interventions are assessed: (1) the allocation of the environmental impact of the existing structures and materials to the life cycle before and after renovation and (2) the energy calculation method. An existing semi-prefabricated ‘open-renovation-system’ for a rooftop extension is assessed both on element and building level from an environmental and financial life cycle perspective
Measurement of transverse momentum relative to dijet systems in PbPb and pp collisions at sqrt(s[NN]) = 2.76 TeV

An analysis of dijet events in PbPb and pp collisions is performed to explore the properties of energy loss by partons traveling in a quark-gluon plasma. Data are collected at a nucleon-nucleon center-of-mass energy of 2.76 TeV at the LHC. The distribution of transverse momentum (pT) surrounding dijet systems is measured by selecting charged particles in different ranges of pT and at different angular cones of pseudorapidity and azimuth. The measurement is performed as a function of centrality of the PbPb collisions, the pT asymmetry of the jets in the dijet pair, and the distance parameter R used in the anti-kt jet clustering algorithm. In events with unbalanced dijets, PbPb collisions show an enhanced multiplicity in the hemisphere of the subleading jet, with the pT imbalance compensated by an excess of low-pT particles at large angles from the jet axes
A search for high-mass resonances decaying to τ +τ − in pp collisions at √s = 8 TeV with the ATLAS detector

Journal of High Energy Physics 2015.7 (2015): 157 reproduced by permission of Scuola Internazionale Superiore di Studi Avanzati (SISSA)Artículo escrito por muchos autores, sólo se referencian el que aparece en primer lugar, el nombre del grupo de colaboración y los autores que firman como pertenecientes a la UAMA search for high-mass resonances decaying into τ+τ− final states using proton-proton collisions at √s = 8 TeV produced by the Large Hadron Collider is presented. The data were recorded with the ATLAS detector and correspond to an integrated luminosity of 19.5–20.3 fb−1. No statistically significant excess above the Standard Model expectation is
 observed; 95% credibility upper limits are set on the cross section times branching fraction
 of Z' resonances decaying into τ+τ− pairs as a function of the resonance mass. As a
 result, Z' bosons of the Sequential Standard Model with masses less than 2.02 TeV are
 excluded at 95% credibility. The impact of the fermionic couplings on the Z' acceptance
 is investigated and limits are also placed on a Z' model that exhibits enhanced couplings
 to third-generation fermionsWe acknowledge the support of ANPCyT, Argentina; YerPhI, Armenia; ARC, Australia;
BMWFW and FWF, Austria; ANAS, Azerbaijan; SSTC, Belarus; CNPq and FAPESP, Brazil; NSERC, NRC and CFI, Canada; CERN; CONICYT, Chile; CAS, MOST and NSFC, China; COLCIENCIAS, Colombia; MSMT CR, MPO CR and VSC CR, Czech Republic; DNRF, DNSRC and Lundbeck Foundation, Denmark; EPLANET, ERC and NSRF, European Union; IN2P3-CNRS, CEA-DSM/IRFU, France; GNSF, Georgia; BMBF, DFG, HGF, MPG and AvH Foundation, Germany; GSRT and NSRF, Greece; RGC, Hong Kong SAR, China; ISF, MINERVA, GIF, I-CORE and Benoziyo Center, Israel; INFN, Italy; MEXT and JSPS, Japan; CNRST, Morocco; FOM and NWO, Netherlands; BRF and RCN, Norway; MNiSW and NCN, Poland; GRICES and FCT, Portugal; MNE/IFA, Romania; MES of Russia and NRC KI, Russian Federation; JINR; MSTD, Serbia; MSSR, Slovakia; ARRS and MIZS, Slovenia; DST/NRF, South Africa; MINECO, Spain; SRC and Wallenberg Foundation, Sweden; SER, SNSF and Cantons of Bern and Geneva, Switzerland; NSC, Taiwan; TAEK, Turkey; STFC, the Royal Society and Leverhulme Trust, United Kingdom; DOE and NSF, United States of Americ
The impact of quality assurance certification on Australian software developers

[Abstract]: This paper draws on existing literature and research on software development process improvement, and related fields, to explore the impact of  quality assurance (QA) certification on the Australian software development industry.  Recently, many developers have committed resources to achieve certification in response to government purchasing policies favouring standards-certified suppliers, but cynics suggest the ‘piece of paper’ does little to improve the processes and subsequent product.  This paper details a research project undertaken to assess the extent of Australian software developers’ adoption of QA certification, their capability maturity and perceptions regarding certification costs and benefits
The inverse problem for the Gross-Pitaevskii equation

Two different methods are proposed for the generation of wide classes of exact solutions to the stationary Gross-Pitaevskii equation (GPE). The first method, suggested by the work by Kondrat'ev and Miller (1966), applies to one-dimensional GPE. It is based on the similarity between the GPE and the integrable Gardner equation, all solutions of the latter equation (both stationary and nonstationary ones) generating exact solutions to the GPE. The second method is based on the 'inverse problem' for the GPE,\ud
i.e. construction of a potential function which provides a desirable solution to the equation. Systematic results are presented for one- and two-dimensional cases. Both methods are illustrated by a variety of localized solutions, including solitary vortices, for both attractive and repulsive nonlinearity in the GPE. The stability of the one-dimensional solutions is tested by direct simulations of the time-dependent GPE
Counter-intuitive influence of Himalayan river morphodynamics on Indus Civilisation urban settlements.

Urbanism in the Bronze-age Indus Civilisation (~4.6–3.9 thousand years before the present, ka) has been linked to water resources provided by large Himalayan river systems, although the largest concentrations of urban-scale Indus settlements are located far from extant Himalayan rivers. Here we analyse the sedimentary architecture, chronology and provenance of a major palaeochannel associated with many of these settlements. We show that the palaeochannel is a former course of the Sutlej River, the third largest of the present-day Himalayan rivers. Using optically stimulated luminescence dating of sand grains, we demonstrate that flow of the Sutlej in this course terminated considerably earlier than Indus occupation, with diversion to its present course complete shortly after ~8 ka. Indus urban settlements thus developed along an abandoned river valley rather than an active Himalayan river. Confinement of the Sutlej to its present incised course after ~8 ka likely reduced its propensity to re-route frequently thus enabling long-term stability for Indus settlements sited along the relict palaeochannel
Igneous sills record far-field and near-field stress interactions during volcano construction : Isle of Mull, Scotland.

Sill emplacement is typically associated with horizontally mechanically layered host rocks in a near-hydrostatic far-field stress state, where contrasting mechanical properties across the layers promote transitions from dykes, or inclined sheets, to sills. We used detailed field observations from the Loch Scridain Sill Complex (Isle of Mull, UK), and mechanical models to show that layering is not always the dominant control on sill emplacement. The studied sills have consistently shallow dips (1°–25°) and cut vertically bedded and foliated metamorphic basement rocks, and horizontally bedded cover sedimentary rocks and lavas. Horizontal and shallowly-dipping fractures in the host rock were intruded with vertical opening in all cases, whilst steeply-dipping discontinuities within the sequence (i.e. vertical fractures and foliation in the basement, and vertical polygonal joints in the lavas) were not intruded during sill emplacement. Mechanical models of slip tendency, dilation tendency, and fracture susceptibility for local and overall sill geometry data, support a radial horizontal compression during sill emplacement. Our models show that dykes and sills across Mull were emplaced during NW–SE horizontal shortening, related to a far-field tectonic stress state. The dykes generally accommodated phases of NE–SW horizontal tectonic extension, whereas the sills record the superposition of the far-field stress with a near-field stress state, imposed by emplacement of the Mull Central Volcano. We show that through detailed geometric characterisation coupled with mechanical modelling, sills may be used as an indication of fluctuations in the paleostress state
Incoherent majorities: the McGarvey problem in judgement aggregation

`Judgement aggregation' is a model of social choice where the space of social alternatives is the set of consistent truth-valuations (`judgements') on a family of logically interconnected propositions. It is well-known that propositionwise majority voting can yield logically inconsistent judgements.  We show that, for a variety of spaces, propositionwise majority voting can yield any possible judgement.  By considering the geometry of sub-polytopes of the Hamming cube, we also estimate the number of voters required to achieve all possible judgements.  These results generalize the classic results of McGarvey (1953) and Stearns (1959).
Mechanism Design for eliciting probabilistic estimates from multiple suppliers with unknown costs and limited precision

This paper reports on the design of a novel two-stage mechanism, based on strictly proper scoring rules, that allows a centre to acquire a costly probabilistic estimate of some unknown parameter, by eliciting and fusing estimates from multiple suppliers. Each of these suppliers is capable of producing a probabilistic estimate of any precision, up to a privately known maximum, and by fusing several low precision estimates together the centre is able to obtain a single estimate with a speciﬁed minimum precision.  Speciﬁcally, in the mechanism’s ﬁrst stage M from N agents are pre-selected by eliciting their privately known costs. In the second stage, these M agents are sequentially approached in a random order and their private maximum precision is elicited. A payment rule, based on a strictly proper scoring rule, then incentivises them to make and truthfully report an estimate of this maximum precision, which the centre fuses with others until it achieves its speciﬁed precision. We formally prove that the mechanism is incentive compatible regarding the costs, maximum precisions and estimates, and that it is individually rational. We present empirical results showing that our mechanism describes a family of possible ways to perform the pre-selection in the ﬁrst stage, and formally prove that there is one that dominates all others.
Improving compliance with hospital antibiotic guidelines: a time-series intervention analysis

Objectives: This study investigated the impact of a combined intervention strategy to improve antimicrobial prescribing at University Hospital Groningen. For the intervention, the antimicrobial treatment guidelines were updated and disseminated in paperback and electronic format. The credibility of the guidelines was improved by consultation with users. In a second phase, academic detailing (AD) was used to improve specific areas of low compliance with the guidelines. Materials and methods: Prescribing data were prospectively collected for 2869 patients receiving 7471 prescriptions for an antimicrobial for an infection covered by the guidelines between July 2001 and September 2003. After collection of baseline data, the guidelines were actively disseminated in February 2002. Next, after a 5 month interval, a second intervention, i.e. an AD approach, addressed suboptimal prescribing of ciprofloxacin and co-amoxiclav. Segmented regression analysis was used to analyse the interrupted time-series data. Results: At baseline, compliance with the drug choice guidelines was 67%. The first intervention showed a significant change in the level of compliance of +15.5% (95% CI: 8%; 23%). AD did not lead to statistically significant additional changes in already high levels +12.5% (95% CI:-3%; 28%) of compliance. Post-intervention compliance was stable at 86%. Conclusions: Updating the guidelines in close collaboration with the specialists involved followed by active dissemination proved to be an efficient way to improve compliance with guideline recommendations. An 86% compliance level was achieved in this study without compulsory measures. A ceiling effect may have limited the added value of AD