Search for top quark decays t → qH, with H → γγ, in s=13 TeV pp collisions using the ATLAS detector

This article presents a search for flavour-changing neutral currents in the decay of a top quark into an up-type (q = c, u) quark and a Higgs boson, where the Higgs boson decays into two photons. The proton-proton collision data set analysed amounts to 36.1 fb−1 at s=13 TeV collected by the ATLAS experiment at the LHC. Top quark pair events are searched for, where one top quark decays into qH and the other decays into bW . Both the hadronic and leptonic decay modes of the W boson are used. No significant excess is observed and an upper limit is set on the t → cH branching ratio of 2.2 × 10−3 at the 95% confidence level, while the expected limit in the absence of signal is 1.6 × 10−3. The corresponding limit on the tcH coupling is 0.090 at the 95% confidence level. The observed upper limit on the t → uH branching ratio is 2.4 × 10−3

Analysis of the Wtb vertex from the measurement of triple-differential angular decay rates of single top quarks produced in the t-channel at s=8 TeV with the ATLAS detector

The electroweak production and subsequent decay of single top quarks in the t-channel is determined by the properties of the Wtb vertex, which can be described by the complex parameters of an effective Lagrangian. An analysis of a triple-differential decay rate in t-channel production is used to simultaneously determine five generalised helicity fractions and phases, as well as the polarisation of the produced top quark. The complex parameters are then constrained. This analysis is based on 20.2 fb−1 of proton-proton collision data at a centre-of-mass energy of 8 TeV collected with the ATLAS detector at the LHC. The fraction of decays containing transversely polarised W bosons is measured to be f1 = 0.30 ± 0.05. The phase between amplitudes for transversely and longitudinally polarised W bosons recoiling against left-handed b-quarks is measured to be δ− = 0.002π+ 0.017π+ 0.016π, giving no indication of CP violation. The fractions of longitudinal or transverse W bosons accompanied by right-handed b-quarks are also constrained. Based on these measurements, limits are placed at 95% CL on the ratio of the complex coupling parameters Re [gR/VL ∈ [−0.12, 0.17] and Im [gR/VL ∈ [−0.07, 0.06]. Constraints are also placed on the ratios |VR/VL| and |gL/VL|. In addition, the polarisation of single top quarks in the t-channel is constrained to be P > 0.72 (95% CL). None of the above measurements make assumptions about the value of any of the other parameters or couplings and all of them are in agreement with the Standard Model

Measurement of jet fragmentation in Pb+Pb and pp collisions at √sNN = 2.76 TeV with the ATLAS detector at the LHC

The distributions of transverse momentum and longitudinal momentum fraction of charged particles in jets are measured in Pb+Pb and pp collisions with the ATLAS detector at the LHC. The distributions are measured as a function of jet transverse momentum and rapidity. The analysis utilises an integrated luminosity of 0.14 nb-1 of Pb+Pb data and 4.0 pb-1 of pp data collected in 2011 and 2013, respectively, at the same centre-of-mass energy of 2.76 TeV per colliding nucleon pair. The distributions measured in pp collisions are used as a reference for those measured in Pb+Pb collisions in order to evaluate the impact on the internal structure of jets from the jet energy loss of fast partons propagating through the hot, dense medium created in heavy-ion collisions. Modest but significant centrality-dependent modifications of fragmentation functions in Pb+Pb collisions with respect to those in pp collisions are seen. No significant dependence of modifications on jet pT and rapidity selections is observed except for the fragments with the highest transverse momenta for which some reduction of yields is observed for more forward jets

Searches for the Zγ decay mode of the Higgs boson and for new high-mass resonances in pp collisions at s=13 TeV with the ATLAS detector

AbstractThis article presents searches for the Zγ decay of the Higgs boson and for narrow high-mass resonances decaying to Zγ, exploiting Z boson decays to pairs of electrons or muons. The data analysis uses 36.1 fb−1 of pp collisions at s=13 recorded by the ATLAS detector at the CERN Large Hadron Collider. The data are found to be consistent with the expected Standard Model background. The observed (expected — assuming Standard Model pp → H → Zγ production and decay) upper limit on the production cross section times the branching ratio for pp → H → Zγ is 6.6. (5.2) times the Standard Model prediction at the 95% confidence level for a Higgs boson mass of 125.09 GeV. In addition, upper limits are set on the production cross section times the branching ratio as a function of the mass of a narrow resonance between 250 GeV and 2.4 TeV, assuming spin-0 resonances produced via gluon-gluon fusion, and spin-2 resonances produced via gluon-gluon or quark-antiquark initial states. For high-mass spin-0 resonances, the observed (expected) limits vary between 88 fb (61 fb) and 2.8 fb (2.7 fb) for the mass range from 250 GeV to 2.4 TeV at the 95% confidence level

Multi-targeted priming for genome-wide gene expression assays

<p>Abstract</p> <p>Background</p> <p>Complementary approaches to assaying global gene expression are needed to assess gene expression in regions that are poorly assayed by current methodologies. A key component of nearly all gene expression assays is the reverse transcription of transcribed sequences that has traditionally been performed by priming the poly-A tails on many of the transcribed genes in eukaryotes with oligo-dT, or by priming RNA indiscriminately with random hexamers. We designed an algorithm to find common sequence motifs that were present within most protein-coding genes of <it>Saccharomyces cerevisiae </it>and of <it>Neurospora crassa</it>, but that were not present within their ribosomal RNA or transfer RNA genes. We then experimentally tested whether degenerately priming these motifs with multi-targeted primers improved the accuracy and completeness of transcriptomic assays.</p> <p>Results</p> <p>We discovered two multi-targeted primers that would prime a preponderance of genes in the genomes of <it>Saccharomyces cerevisiae </it>and <it>Neurospora crassa </it>while avoiding priming ribosomal RNA or transfer RNA. Examining the response of <it>Saccharomyces cerevisiae </it>to nitrogen deficiency and profiling <it>Neurospora crassa </it>early sexual development, we demonstrated that using multi-targeted primers in reverse transcription led to superior performance of microarray profiling and next-generation RNA tag sequencing. Priming with multi-targeted primers in addition to oligo-dT resulted in higher sensitivity, a larger number of well-measured genes and greater power to detect differences in gene expression.</p> <p>Conclusions</p> <p>Our results provide the most complete and detailed expression profiles of the yeast nitrogen starvation response and <it>N. crassa </it>early sexual development to date. Furthermore, our multi-targeting priming methodology for genome-wide gene expression assays provides selective targeting of multiple sequences and counter-selection against undesirable sequences, facilitating a more complete and precise assay of the transcribed sequences within the genome.</p

Menstrual mood disorders are associated with blunted sympathetic reactivity to stress

AbstractObjectiveFew studies have directly compared women with a menstrually related mood disorder (MRMD) with women who have suffered from depression for stress reactivity phenotypes. It is unclear whether blunted responses to stress in women with a MRMD reflect a unique phenotype of MRMDs or may be explained by a history of depression.MethodsWe assessed cardiovascular reactivity to stress in four groups: 1) Women with a MRMD without a history of depression (n=37); 2) women with a MRMD plus a history of depression (n=26); 3) women without a MRMD and without a history of depression (n=43); and 4) women without a MRMD but with a history of depression (n=20).ResultsWomen with a MRMD showed blunted myocardial (heart rate and cardiac index) reactivity to mental stress compared to non-MRMD women, irrespective of histories of depression. Hypo-reactivity to stress predicted greater premenstrual symptom severity in the entire sample. Women with a MRMD showed blunted norepinephrine and diastolic blood pressure stress reactivity relative to women with no MRMD, but only when no history of depression was present. Both MRMD women and women with depression histories reported greater negative subjective responses to stress relative to their non-MRMD and never depressed counterparts.ConclusionOur findings support the assertion that a blunted stress reactivity profile represents a unique phenotype of MRMDs and also underscore the importance of psychiatric histories to stress reactivity. Furthermore, our results emphasize the clinical relevance of myocardial hypo-reactivity to stress, since it predicts heightened premenstrual symptom severity

First records of Phytophthora spp. based on DNA analysis in Lithuania

The assessment of alien invasive species of Phytophthora genus causing serious forest tree species diseases was carried out in Lithuania. The presence of Phytophthora DNA was recorded for the first time using real-time PCR analysis on 23 DNA samples. The sampling includes wood from diseased trees, leaves from shrubs, leaves baited in water, and soil samples taken around diseased plants. Extracted DNA from soil and plant tissues was tested for the presence of Phytophthora. All analysed samples were positively recognized by Phytophthora-specific probe during real-time PCR which proves the presence of pathogens in environmental samples.Przemysław Szmi

Surgical site infection after gastrointestinal surgery in high-income, middle-income, and low-income countries: a prospective, international, multicentre cohort study

Background: Surgical site infection (SSI) is one of the most common infections associated with health care, but its importance as a global health priority is not fully understood. We quantified the burden of SSI after gastrointestinal surgery in countries in all parts of the world. Methods: This international, prospective, multicentre cohort study included consecutive patients undergoing elective or emergency gastrointestinal resection within 2-week time periods at any health-care facility in any country. Countries with participating centres were stratified into high-income, middle-income, and low-income groups according to the UN's Human Development Index (HDI). Data variables from the GlobalSurg 1 study and other studies that have been found to affect the likelihood of SSI were entered into risk adjustment models. The primary outcome measure was the 30-day SSI incidence (defined by US Centers for Disease Control and Prevention criteria for superficial and deep incisional SSI). Relationships with explanatory variables were examined using Bayesian multilevel logistic regression models. This trial is registered with ClinicalTrials.gov, number NCT02662231. Findings: Between Jan 4, 2016, and July 31, 2016, 13 265 records were submitted for analysis. 12 539 patients from 343 hospitals in 66 countries were included. 7339 (58·5%) patient were from high-HDI countries (193 hospitals in 30 countries), 3918 (31·2%) patients were from middle-HDI countries (82 hospitals in 18 countries), and 1282 (10·2%) patients were from low-HDI countries (68 hospitals in 18 countries). In total, 1538 (12·3%) patients had SSI within 30 days of surgery. The incidence of SSI varied between countries with high (691 [9·4%] of 7339 patients), middle (549 [14·0%] of 3918 patients), and low (298 [23·2%] of 1282) HDI (p < 0·001). The highest SSI incidence in each HDI group was after dirty surgery (102 [17·8%] of 574 patients in high-HDI countries; 74 [31·4%] of 236 patients in middle-HDI countries; 72 [39·8%] of 181 patients in low-HDI countries). Following risk factor adjustment, patients in low-HDI countries were at greatest risk of SSI (adjusted odds ratio 1·60, 95% credible interval 1·05–2·37; p=0·030). 132 (21·6%) of 610 patients with an SSI and a microbiology culture result had an infection that was resistant to the prophylactic antibiotic used. Resistant infections were detected in 49 (16·6%) of 295 patients in high-HDI countries, in 37 (19·8%) of 187 patients in middle-HDI countries, and in 46 (35·9%) of 128 patients in low-HDI countries (p < 0·001). Interpretation: Countries with a low HDI carry a disproportionately greater burden of SSI than countries with a middle or high HDI and might have higher rates of antibiotic resistance. In view of WHO recommendations on SSI prevention that highlight the absence of high-quality interventional research, urgent, pragmatic, randomised trials based in LMICs are needed to assess measures aiming to reduce this preventable complication

Harmonized NDVI time-series from Landsat and Sentinel-2 reveal phenological patterns of diverse, small-scale cropping systems in East Africa

Capturing the phenological responses of crops in diverse, small-scale agricultural systems is one of the most notable remote sensing research gaps in Eastern Africa. Because of the heterogeneous and complex agricultural environments, remote sensing methodologies successfully implemented elsewhere yield poor results in Eastern Africa. The reliance on local rainfall and dry spells can lead to alterations in planting patterns, impacting growing season timing and yield, underscoring the importance of high temporal resolution for capturing crop phenology. We generated a high-resolution land use/land cover (LULC) classification map of 10 m using Sentinel-1 and Sentinel-2 imagery together with a large set of reference data acquired in situ in 2022. The LULC classification yielded an overall accuracy of 87.9% and Cohen's kappa value of 0.83. Based on the LULC map, we investigated the phenological metrics of the most important crops in the Kamuli district of Eastern Uganda by combining a multi-sensor harmonization approach, thresholding method, and cloud computing. Previously unavailable Landsat 9 band adjustment coefficients were derived. By harmonizing Landsat (LS) 7 Enhanced Thematic Mapper Plus (ETM+), Landsat 8 and 9 Operational Land Imager (OLI), with Sentinel-2 Multispectral Instrument (MSI), the phenological patterns during the March to May growing season were captured using a dense temporal Normalized Difference Vegetation Index (NDVI) time series. The seasonal onset for most crop types was in the end of March to middle of April while the end of the growing season occurred from the end of June to middle of July. Investigation of the 13 crop types using a high-resolution LULC map and dense, harmonized NDVI time series signifies the first field-level phenological metrics estimation of smallholder farming systems in Eastern Africa. Future research should focus on expanding the methodology in space and time to provide insights into past and current growing season development