Examining the generalizability of research findings from archival data

This initiative examined systematically the extent to which a large set of archival research findings generalizes across contexts. We repeated the key analyses for 29 original strategic management effects in the same context (direct reproduction) as well as in 52 novel time periods and geographies; 45% of the reproductions returned results matching the original reports together with 55% of tests in different spans of years and 40% of tests in novel geographies. Some original findings were associated with multiple new tests. Reproducibility was the best predictor of generalizability—for the findings that proved directly reproducible, 84% emerged in other available time periods and 57% emerged in other geographies. Overall, only limited empirical evidence emerged for context sensitivity. In a forecasting survey, independent scientists were able to anticipate which effects would find support in tests in new samples

Large expert-curated database for benchmarking document similarity detection in biomedical literature search

Document recommendation systems for locating relevant literature have mostly relied on methods developed a decade ago. This is largely due to the lack of a large offline gold-standard benchmark of relevant documents that cover a variety of research fields such that newly developed literature search techniques can be compared, improved and translated into practice. To overcome this bottleneck, we have established the RElevant LIterature SearcH consortium consisting of more than 1500 scientists from 84 countries, who have collectively annotated the relevance of over 180 000 PubMed-listed articles with regard to their respective seed (input) article/s. The majority of annotations were contributed by highly experienced, original authors of the seed articles. The collected data cover 76% of all unique PubMed Medical Subject Headings descriptors. No systematic biases were observed across different experience levels, research fields or time spent on annotations. More importantly, annotations of the same document pairs contributed by different scientists were highly concordant. We further show that the three representative baseline methods used to generate recommended articles for evaluation (Okapi Best Matching 25, Term Frequency-Inverse Document Frequency and PubMed Related Articles) had similar overall performances. Additionally, we found that these methods each tend to produce distinct collections of recommended articles, suggesting that a hybrid method may be required to completely capture all relevant articles. The established database server located at https://relishdb.ict.griffith.edu.au is freely available for the downloading of annotation data and the blind testing of new methods. We expect that this benchmark will be useful for stimulating the development of new powerful techniques for title and title/abstract-based search engines for relevant articles in biomedical research.Peer reviewe

Retrospective evaluation of whole exome and genome mutation calls in 746 cancer samples

Funder: NCI U24CA211006Abstract: The Cancer Genome Atlas (TCGA) and International Cancer Genome Consortium (ICGC) curated consensus somatic mutation calls using whole exome sequencing (WES) and whole genome sequencing (WGS), respectively. Here, as part of the ICGC/TCGA Pan-Cancer Analysis of Whole Genomes (PCAWG) Consortium, which aggregated whole genome sequencing data from 2,658 cancers across 38 tumour types, we compare WES and WGS side-by-side from 746 TCGA samples, finding that ~80% of mutations overlap in covered exonic regions. We estimate that low variant allele fraction (VAF < 15%) and clonal heterogeneity contribute up to 68% of private WGS mutations and 71% of private WES mutations. We observe that ~30% of private WGS mutations trace to mutations identified by a single variant caller in WES consensus efforts. WGS captures both ~50% more variation in exonic regions and un-observed mutations in loci with variable GC-content. Together, our analysis highlights technological divergences between two reproducible somatic variant detection efforts

Thigh-length compression stockings and DVT after stroke

Controversy exists as to whether neoadjuvant chemotherapy improves survival in patients with invasive bladder cancer, despite randomised controlled trials of more than 3000 patients. We undertook a systematic review and meta-analysis to assess the effect of such treatment on survival in patients with this disease

Retrospective evaluation of whole exome and genome mutation calls in 746 cancer samples

The Cancer Genome Atlas (TCGA) and International Cancer Genome Consortium (ICGC) curated consensus somatic mutation calls using whole exome sequencing (WES) and whole genome sequencing (WGS), respectively. Here, as part of the ICGC/TCGA Pan-Cancer Analysis of Whole Genomes (PCAWG) Consortium, which aggregated whole genome sequencing data from 2,658 cancers across 38 tumour types, we compare WES and WGS side-by-side from 746 TCGA samples, finding that ~80% of mutations overlap in covered exonic regions. We estimate that low variant allele fraction (VAF < 15%) and clonal heterogeneity contribute up to 68% of private WGS mutations and 71% of private WES mutations. We observe that ~30% of private WGS mutations trace to mutations identified by a single variant caller in WES consensus efforts. WGS captures both ~50% more variation in exonic regions and un-observed mutations in loci with variable GC-content. Together, our analysis highlights technological divergences between two reproducible somatic variant detection efforts.The Cancer Genome Atlas (TCGA) and International Cancer Genome Consortium (ICGC) curated consensus somatic mutation calls using whole exome sequencing (WES) and whole genome sequencing (WGS), respectively. Here, as part of the ICGC/TCGA Pan-Cancer Analysis of Whole Genomes (PCAWG) Consortium, which aggregated whole genome sequencing data from 2,658 cancers across 38 tumour types, we compare WES and WGS side-by-side from 746 TCGA samples, finding that -80% of mutations overlap in covered exonic regions. We estimate that low variant allele fraction (VAFPeer reviewe

Retrospective evaluation of whole exome and genome mutation calls in 746 cancer samples

Funder: NCI U24CA211006Abstract: The Cancer Genome Atlas (TCGA) and International Cancer Genome Consortium (ICGC) curated consensus somatic mutation calls using whole exome sequencing (WES) and whole genome sequencing (WGS), respectively. Here, as part of the ICGC/TCGA Pan-Cancer Analysis of Whole Genomes (PCAWG) Consortium, which aggregated whole genome sequencing data from 2,658 cancers across 38 tumour types, we compare WES and WGS side-by-side from 746 TCGA samples, finding that ~80% of mutations overlap in covered exonic regions. We estimate that low variant allele fraction (VAF < 15%) and clonal heterogeneity contribute up to 68% of private WGS mutations and 71% of private WES mutations. We observe that ~30% of private WGS mutations trace to mutations identified by a single variant caller in WES consensus efforts. WGS captures both ~50% more variation in exonic regions and un-observed mutations in loci with variable GC-content. Together, our analysis highlights technological divergences between two reproducible somatic variant detection efforts

Search for CP violating top quark couplings in pp collisions at s \sqrt{s} = 13 TeV

International audienceResults are presented from a search for CP violation in top quark pair production, using proton-proton collisions at a center-of-mass energy of 13 TeV. The data used for this analysis consist of final states with two charged leptons collected by the CMS experiment, and correspond to an integrated luminosity of 35.9 fb$^{−1}$. The search uses two observables, $\mathcal{O} _{1}$ and $\mathcal{O} _{3}$, which are Lorentz scalars. The observable $\mathcal{O} _{1}$ is constructed from the four-momenta of the charged leptons and the reconstructed top quarks, while $\mathcal{O} _{3}$ consists of the four-momenta of the charged leptons and the b quarks originating from the top quarks. Asymmetries in these observables are sensitive to CP violation, and their measurement is used to determine the chromoelectric dipole moment of the top quark. The results are consistent with the expectation from the standard model.[graphic not available: see fulltext

Search for light Higgs bosons from supersymmetric cascade decays in pp\text {pp} collisions at s=13 TeV\sqrt{s}=13\,\textrm{TeV}

A search is reported for pairs of light Higgs bosons (${\textrm{H}} _1$) produced in supersymmetric cascade decays in final states with small missing transverse momentum. A data set of LHC $\hbox {pp}$ collisions collected with the CMS detector at $\sqrt{s}=13\,\text {TeV}$ and corresponding to an integrated luminosity of 138$\,\text {fb}^{-1}$ is used. The search targets events where both ${\textrm{H}} _1$ bosons decay into pairs that are reconstructed as large-radius jets using substructure techniques. No evidence is found for an excess of events beyond the background expectations of the standard model (SM). Results from the search are interpreted in the next-to-minimal supersymmetric extension of the SM, where a “singlino” of small mass leads to squark and gluino cascade decays that can predominantly end in a highly Lorentz-boosted singlet-like ${\textrm{H}} _1$ and a singlino-like neutralino of small transverse momentum. Upper limits are set on the product of the squark or gluino pair production cross section and the square of the branching fraction of the ${\textrm{H}} _1$ in a benchmark model containing almost mass-degenerate gluinos and light-flavour squarks. Under the assumption of an SM-like branching fraction, ${\textrm{H}} _1$ bosons with masses in the range 40–120$\,\text {GeV}$ arising from the decays of squarks or gluinos with a mass of 1200–2500$\,\text {GeV}$ are excluded at 95% confidence level

Azimuthal correlations in Z +jets events in proton–proton collisions at s=13 TeV\sqrt{s} = 13\,\text {Te}\hspace{-.08em}\text {V}

The production of Z bosons associated with jets is measured in $\text {p}\text {p}$ collisions at $\sqrt{s}=13\,\text {Te}\hspace{-.08em}\text {V}$ with data recorded with the CMS experiment at the LHC corresponding to an integrated luminosity of 36.3$\,\text {fb}^{-1}$. The multiplicity of jets with transverse momentum $p_{\textrm{T}} > 30\,\text {Ge}\hspace{-.08em}\text {V}$ is measured for different regions of the Z boson’s $p_{\textrm{T}} (\text {Z })$, from lower than 10$\,\text {Ge}\hspace{-.08em}\text {V}$ to higher than 100$\,\text {Ge}\hspace{-.08em}\text {V}$. The azimuthal correlation $\varDelta \phi$ between the Z boson and the leading jet, as well as the correlations between the two leading jets are measured in three regions of $p_{\textrm{T}} (\text {Z })$. The measurements are compared with several predictions at leading and next-to-leading orders, interfaced with parton showers. Predictions based on transverse-momentum dependent parton distributions and corresponding parton showers give a good description of the measurement in the regions where multiple parton interactions and higher jet multiplicities are not important. The effects of multiple parton interactions are shown to be important to correctly describe the measured spectra in the low $p_{\textrm{T}} (\text {Z })$ regions