pinecone/core-2020-05-10-deduplication huggingface dataset:
Assessment of the Patient, Health System, and Population Effects of Xpert MTB/RIF and Alternative Diagnostics for Tuberculosis in Tanzania: An Integrated Modelling Approach.

Several promising new diagnostic methods and algorithms for tuberculosis have been endorsed by WHO. National tuberculosis programmes now face the decision on which methods to implement and where to place them in the diagnostic algorithm. We used an integrated model to assess the effects of different algorithms of Xpert MTB/RIF and light-emitting diode (LED) fluorescence microscopy in Tanzania. To understand the effects of new diagnostics from the patient, health system, and population perspective, the model incorporated and linked a detailed operational component and a transmission component. The model was designed to represent the operational and epidemiological context of Tanzania and was used to compare the effects and cost-effectiveness of different diagnostic options. Among the diagnostic options considered, we identified three strategies as cost effective in Tanzania. Full scale-up of Xpert would have the greatest population-level effect with the highest incremental cost: 346 000 disability-adjusted life-years (DALYs) averted with an additional cost of US$36·9 million over 10 years. The incremental cost-effectiveness ratio (ICER) of Xpert scale-up ($169 per DALY averted, 95% credible interval [CrI] 104-265) is below the willingness-to-pay threshold ($599) for Tanzania. Same-day LED fluorescence microscopy is the next most effective strategy with an ICER of $45 (95% CrI 25-74), followed by LED fluorescence microscopy with an ICER of $29 (6-59). Compared with same-day LED fluorescence microscopy and Xpert full rollout, targeted use of Xpert in presumptive tuberculosis cases with HIV infection, either as an initial diagnostic test or as a follow-on test to microscopy, would produce DALY gains at a higher incremental cost and therefore is dominated in the context of Tanzania. For Tanzania, this integrated modelling approach predicts that full rollout of Xpert is a cost-effective option for tuberculosis diagnosis and has the potential to substantially reduce the national tuberculosis burden. It also estimates the substantial level of funding that will need to be mobilised to translate this into clinical practice. This approach could be adapted and replicated in other developing countries to inform rational health policy formulation
Redox Signaling by the RNA Polymerase III TFIIB-Related Factor Brf2.

TFIIB-related factor 2 (Brf2) is a member of the family of TFIIB-like core transcription factors. Brf2 recruits RNA polymerase (Pol) III to type III gene-external promoters, including the U6 spliceosomal RNA and selenocysteine tRNA genes. Found only in vertebrates, Brf2 has been linked to tumorigenesis but the underlying mechanisms remain elusive. We have solved crystal structures of a human Brf2-TBP complex bound to natural promoters, obtaining a detailed view of the molecular interactions occurring at Brf2-dependent Pol III promoters and highlighting the general structural and functional conservation of human Pol II and Pol III pre-initiation complexes. Surprisingly, our structural and functional studies unravel a Brf2 redox-sensing module capable of specifically regulating Pol III transcriptional output in living cells. Furthermore, we establish Brf2 as a central redox-sensing transcription factor involved in the oxidative stress pathway and provide a mechanistic model for Brf2 genetic activation in lung and breast cancer
Gene and pathway level analyses of germline DNA-repair gene variants and prostate cancer susceptibility using the iCOGS-genotyping array

Background:  

Germline mutations within DNA-repair genes are implicated in susceptibility to multiple forms of cancer. For prostate cancer (PrCa), rare mutations in BRCA2 and BRCA1 give rise to moderately elevated risk, whereas two of ~100 common, low-penetrance PrCa susceptibility variants identified so far by genome-wide association studies implicate RAD51B and RAD23B.

Methods:  

Genotype data from the iCOGS array were imputed to the 1000 genomes phase 3 reference panel for 21 780 PrCa cases and 21 727 controls from the Prostate Cancer Association Group to Investigate Cancer Associated Alterations in the Genome (PRACTICAL) consortium. We subsequently performed single variant, gene and pathway-level analyses using 81 303 SNPs within 20 Kb of a panel of 179 DNA-repair genes.

Results:  

Single SNP analyses identified only the previously reported association with RAD51B. Gene-level analyses using the SKAT-C test from the SNP-set (Sequence) Kernel Association Test (SKAT) identified a significant association with PrCa for MSH5. Pathway-level analyses suggested a possible role for the translesion synthesis pathway in PrCa risk and Homologous recombination/Fanconi Anaemia pathway for PrCa aggressiveness, even though after adjustment for multiple testing these did not remain significant.

Conclusions:  

MSH5 is a novel candidate gene warranting additional follow-up as a prospective PrCa-risk locus. MSH5 has previously been reported as a pleiotropic susceptibility locus for lung, colorectal and serous ovarian cancers.This is the final version of the article. It first appeared from Nature Publishing Group via http://dx.doi.org/10.1038/bjc.2016.5
Mapping species distributions : A comparison of skilled naturalist and lay citizen science recording

Acknowledgements We are grateful to Elaine O’Mahony, Imogen Pearce, Richard Comont, Anthony McCluskey and other BBCT staff for the many hours of BeeWatch species identification and for all people who submitted sightings to BeeWatch, OPAL, BWARS and the various local recording schemes and societies. We thank the NBN for allowing us to download the bumblebee records without strings attached, and the Essex, Greater London, Cumbria and Sussex based recording centres for providing records upon request. Finally, we are indebted to Tom August and two anonymous reviewers for their valuable critique on an earlier version of this work.Peer reviewedPublisher PD
Search for the standard model Higgs boson decaying to bottom quarks in pp collisions at √s = 7 TeV

A search for the standard model Higgs boson (H) decaying to b[bar over b] when produced in association with weak vector bosons (V) is reported for the following modes: W(μν)H, W(eν)H, Z(μμ)H, Z(ee)H and Z(νν)H. The search is performed in a data sample corresponding to an integrated luminosity of 4.7 fb[superscript −1], recorded by the CMS detector in proton–proton collisions at the LHC with a center-of-mass energy of 7 TeV. No significant excess of events above the expectation from background is observed. Upper limits on the VH production cross section times the H→b[bar over b] branching ratio, with respect to the expectations for a standard model Higgs boson, are derived for a Higgs boson in the mass range 110–135 GeV. In this range, the observed 95% confidence level upper limits vary from 3.4 to 7.5 times the standard model prediction; the corresponding expected limits vary from 2.7 to 6.7 times the standard model prediction.European Organization for Nuclear ResearchUnited States. Dept. of EnergyNational Science Foundation (U.S.)Alfred P. Sloan Foundatio
NNLO QCD corrections to Higgs boson production at large transverse momentum

We derive the second-order QCD corrections to the production of a Higgs boson recoiling against a parton with finite transverse momentum, working in the effective field theory in which the top quark contributions are integrated out. To account for quark mass effects, we supplement the effective field theory result by the full quark mass dependence at leading order. Our calculation is fully differential in the final state kinematics and includes the decay of the Higgs boson to a photon pair. It allows one to make next-to-next-to-leading order (NNLO)-accurate theory predictions for Higgs-plus-jet final states and for the transverse momentum distribution of the Higgs boson, accounting for the experimental definition of the fiducial cross sections. The NNLO QCD corrections are found to be moderate and positive, they lead to a substantial reduction of the theory uncertainty on the predictions. We compare our results to 8 TeV LHC data from ATLAS and CMS. While the shape of the data is well-described for both experiments, we agree on the normalization only for CMS. By normalizing data and theory to the inclusive fiducial cross section for Higgs production, good agreement is found for both experiments, however at the expense of an increased theory uncertainty. We make predictions for Higgs production observables at the 13 TeV LHC, which are in good agreement with recent ATLAS data. At this energy, the leading order mass corrections to the effective field theory prediction become significant at large transverse momenta, and we discuss the resulting uncertainties on the predictions
Measurement of the mass of the top quark in decays with a $J/\psi$ meson in pp collisions at 8 TeV

A first measurement of the top quark mass in the decay channel t → (W → ℓν) (b → J/ψ + X → μ$^{+}$ μ$^{−}$ + X) is presented. The analysis uses events selected from the proton-proton collisions recorded by the CMS detector at the LHC at a center-of-mass energy of 8 TeV. The data correspond to an integrated luminosity of 19.7 fb$^{−1}$, with 666 $ \mathrm{t}\overline{\mathrm{t}} $ and single top quark candidate events containing a reconstructed J/ψ candidate decaying into an oppositely-charged muon pair. The mass of the (J/ψ + ℓ) system, where ℓ is an electron or a muon from W boson decay, is used to extract a top quark mass of 173.5 ± 3.0 (stat) ± 0.9 (syst) GeV
On neutron stars in ƒ (R) theories: Small radii, large masses and large energy emitted in a merger

In the context of ƒ (R) gravity theories, we show that the apparent mass of a neutron star as seen from an observer at infinity is numerically calculable but requires careful matching, first at the star’s edge, between interior and exterior solutions, none of them being totally Schwarzschild-like but presenting instead small oscillations of the curvature scalar R; and second at large radii, where the Newtonian potential is used to identify the mass of the neutron star. We find that for the same equation of state, this mass definition is always larger than its general relativistic counterpart. We exemplify this with quadratic R^2 and Hu-Sawicki-like modifications of the standard General Relativity action. Therefore, the finding of two-solar mass neutron stars basically imposes no constraint on stable ƒ (R) theories. However, star radii are in general smaller than in General Relativity, which can give an observational handle on such classes of models at the astrophysical level. Both larger masses and smaller matter radii are due to much of the apparent effective energy residing in the outer metric for scalar-tensor theories. Finally, because the ƒ (R) neutron star masses can be much larger than General Relativity counterparts, the total energy available for radiating gravitational waves could be of order several solar masses, and thus a merger of these stars constitutes an interesting wave source
Teaching Disciplines "History of Russia" and "Country Studies" to Foreign Students: Problems and Solutions

The present paper is focused on the problem of teaching foreign students such disciplines as "Country studies" and "History of Russia", which appear to be compulsory for the international students, getting higher education in Russia. Studying these disciplines, students meet some difficulties due to various reasons, beginning with poor knowledge of Russian language and ending with ethical problems. A lecturer needs to cross this socio-cultural and linguistic barrier and find solutions in order to give the full information in accordance with the educational working program. The research has an applied character. It is based on the sociological survey conducted among the foreign students of National Research Tomsk Polytechnic University. The aim of the paper is to demonstrate real difficulties of students and lecturers at studying and teaching disciplines "Country studies" and "History of Russia" and to offer solutions for overcoming these problems
Behaviour that underpins non-pathological criminal incapacity and automatism : toward clarity for psychiatric testimony

Psychiatric expert testimony is challenging in cases of violence when the accused person submits a defence that
he or shewas so overwhelmed by emotions triggered by an upsetting event that his or her violent behaviourwas
an uncontrollable consequence of the emotions. This defence is usually presented in terms of an automatismparticularly
not attributed to a mental disorder. Clouding testimony in these cases is the various definitions of both
automatism and mental disorder—definitions by which the jurisprudential distinction is made between a sane
and an insane automatism, or pathological and non-pathological incapacity (NPCI).
To avert testimony that is tainted from the very beginning by the lack of agreed definitions, this article proposes
that psychiatrists focus in their assessment and testimony on particularly the behaviour as being distinct fromthe
jurisprudential concernswhether that behaviour constitutes an automatism andwhether it is (not) attributed to
a mental disorder. This focus on the behaviour affords clarity by which the properties of the behaviour may be
examined theoretically and clinically in terms of behaviour therapy, specifying accordingly its antecedents,
consequences, topography, intensity, latency, duration, frequency, and quality.
So informed, the behaviour that underpins NPCI and automatism is described here as emotionally triggered
involuntary violent behaviour about which testimony may be given distinct from whether the behaviour is
(not) causally attributed to a mental disorder, and from jurisprudential concerns with accountability.A postgraduate bursary by the University
 of Pretoriahttp://www.journals.elsevier.com/international-journal-of-law-and-psychiatryam2017Psychiatr
Antarctic Intermediate Water properties since 400 ka recorded in infaunal (Uvigerina peregrina) and epifaunal (Planulina wuellerstorfi) benthic foraminifera

AbstractReconstruction of intermediate water properties is important for understanding feedbacks within the ocean-climate system, particularly since these water masses are capable of driving high–low latitude teleconnections. Nevertheless, information about intermediate water mass evolution through the late Pleistocene remains limited. This paper examines changes in Antarctic Intermediate Water (AAIW), the most extensive intermediate water mass in the modern ocean through the last 400 kyr using the stable isotopic composition (δ18O and δ13C) and trace element concentration (Mg/Ca and B/Ca) of two benthic foraminiferal species from the same samples: epifaunal Planulina wuellerstorfi and infaunal Uvigerina peregrina. Our results confirm that the most reasonable estimates of AAIW temperature and Δ[CO2−3] are generated by Mg/CaU. peregrina and B/CaP. wuellerstorfi, respectively. We present a 400 kyr record of intermediate water temperature and Δ[CO2−3] from a sediment core from the Southwest Pacific (DSDP site 593; 40°30′S, 167°41′E, 1068 m water depth), which lies within the core of modern AAIW. Our results suggest that a combination of geochemical analyses on both infaunal and epifaunal benthic foraminiferal species yields important information about this critical water mass through the late Pleistocene. When combined with two nearby records of water properties from deeper depths, our data demonstrate that during interglacial stages of the late Pleistocene, AAIW and Circumpolar Deep Water (CPDW) have more similar water mass properties (temperature and δ13C), while glacial stages are typified by dissimilar properties between AAIW and CPDW in the Southwest Pacific. Our new Δ[CO2−3] record shows short time-scale variations, but a lack of coherent glacial–interglacial variability indicating that large quantities of carbon were not stored in intermediate waters during recent glacial periods
Trace-anomaly driven inflation in f(T) gravity and in minimal massive bigravity

AbstractWe explore trace-anomaly driven inflation in modified gravity. It is explicitly shown that in T2 teleparallel gravity, the de Sitter inflation can occur, although quasi de Sitter inflation happens in R2 gravity. Furthermore, we investigate the influence of the trace anomaly on inflation. It is found that in f(T) gravity, the de Sitter inflation can end because it becomes unstable due to the trace anomaly, whereas also in higher derivative gravity, the de Sitter inflation can be realized and it will be over owing to the trace anomaly for smaller parameter regions in comparison with those in teleparallelism. The instability of the de Sitter inflation in T2 gravity and R2 gravity (both with taking account of the trace anomaly) is examined. In addition, we study trace-anomaly driven inflation in minimal massive bigravity, where the contribution from the massive graviton acts as negative cosmological constant. It is demonstrated that the de Sitter inflation can occur and continue for long enough duration
Nurturing Supportive and Engaging Induction Environments for Distance-learning Students

AbstractDistance learning (DL) students typically learn with very limited or no requirements for physical presence and this often means that learning may be perceived as a more isolating or less ‘natural’ experience. Postgraduate (PG) DL students are particularly vulnerable as mature students with working and family commitments who require more support in their transition to a DL PG study, having experienced a longer break in education. This paper presents the main findings of a survey of 82 students and semi-structured interviews with 11 students studying at the Robert Gordon University (Aberdeen, Scotland). The research explored their expectations and challenges encountered in transitioning to a DL PG study across a number of different subject areas. The study found that the online induction process should meet a variety of expectations and needs, focusing primarily on academic and social aspects. DL study can be an isolating experience, which can be made less alienating when there is a chance for students to get to know their peers and teaching staff. An inclusive approach to online induction geared towards flexible support and interactive, engaging content is an important consideration
Firewood, food and human niche construction: the potential role of Mesolithic hunter–gatherers in actively structuring Scotland's woodlands

AbstractOver the past few decades the potential role of Mesolithic hunter–gatherers in actively constructing their own niches, through the management of wild plants, has frequently been discussed. It is probable that Mesolithic hunter–gatherers systematically exploited specific woodland resources for food and fuel and influenced the ‘natural’ abundance or distribution of particular species within Mesolithic environments. Though there has been considerable discussion of the pollen evidence for potential small-scale human-woodland manipulation in Mesolithic Scotland, the archaeobotanical evidence for anthropogenic firewood and food selection has not been discussed in this context. This paper assesses the evidence for the active role of Mesolithic hunter–gatherer communities in systematically exploiting and managing woodlands for food and fuel in Scotland. While taphonomic factors may have impacted on the frequency of specific species in archaeobotanical assemblages, it is suggested that hunter–gatherers in Mesolithic Scotland were systematically using woodland plants, and in particular hazel and oak, for food and fuel. It is argued that the pollen evidence for woodland management is equivocal, but hints at the role of hunter–gatherers in shaping the structure of their environments, through the maintenance or creation of woodland clearings for settlement or as part of vegetation management strategies. It is proposed that Mesolithic hunter–gatherers may have actively contributed to niche construction and that the systematic use of hazel and oak as a fuel may reflect the deliberate pruning of hazel trees to increase nut-yields and the inadvertent – or perhaps deliberate – coppicing of hazel and oak during greenwood collection
Consensus Standards for Acquisition, Measurement, and Reporting of Intravascular Optical Coherence Tomography Studies A Report From the International Working Group for Intravascular Optical Coherence Tomography Standardization and Validation

ObjectivesThe purpose of this document is to make the output of the International Working Group for Intravascular Optical Coherence Tomography (IWG-IVOCT) Standardization and Validation available to medical and scientific communities, through a peer-reviewed publication, in the interest of improving the diagnosis and treatment of patients with atherosclerosis, including coronary artery disease.BackgroundIntravascular optical coherence tomography (IVOCT) is a catheter-based modality that acquires images at a resolution of ∼10 μm, enabling visualization of blood vessel wall microstructure in vivo at an unprecedented level of detail. IVOCT devices are now commercially available worldwide, there is an active user base, and the interest in using this technology is growing. Incorporation of IVOCT in research and daily clinical practice can be facilitated by the development of uniform terminology and consensus-based standards on use of the technology, interpretation of the images, and reporting of IVOCT results.MethodsThe IWG-IVOCT, comprising more than 260 academic and industry members from Asia, Europe, and the United States, formed in 2008 and convened on the topic of IVOCT standardization through a series of 9 national and international meetings.ResultsKnowledge and recommendations from this group on key areas within the IVOCT field were assembled to generate this consensus document, authored by the Writing Committee, composed of academicians who have participated in meetings and/or writing of the text.ConclusionsThis document may be broadly used as a standard reference regarding the current state of the IVOCT imaging modality, intended for researchers and clinicians who use IVOCT and analyze IVOCT data
Radiative and seesaw threshold corrections to the S3 symmetric neutrino mass matrix

AbstractWe systematically analyze the radiative corrections to the S3 symmetric neutrino mass matrix at high energy scale, say the GUT scale, in the charged lepton basis. There are significant corrections to the neutrino parameters both in the Standard Model (SM) and Minimal Supersymmetric Standard Model (MSSM) with large tan⁡β, when the renormalization group evolution (RGE) and seesaw threshold effects are taken into consideration. We find that in the SM all three mixing angles and atmospheric mass squared difference are simultaneously obtained in their current 3σ ranges at the electroweak scale. However, the solar mass squared difference is found to be larger than its allowed 3σ range at the low scale in this case. There are significant contributions to neutrino masses and mixing angles in the MSSM with large tan⁡β from the RGEs even in the absence of seesaw threshold corrections. However, we find that the mass squared differences and the mixing angles are simultaneously obtained in their current 3σ ranges at low energy when the seesaw threshold effects are also taken into account in the MSSM with large tan⁡β