The chromatin-remodeling factor CHD4 coordinates signaling and repair after DNA damage

The CHD4 helicase is identified as a new component of the genome surveillance machinery in a proteomic screen for factors enriched on chromatin after ionizing radiation (see also related paper by Smeenk et al. in this issue)

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

Late Holocene natural and man induced environmental changes in the Western Iberian coast: acessing forcing factors

The Western coast of the Iberian Peninsula stands as an interface between both the Atlantic and Mediterranean climatic influences and marine / fluvial conditions. The paper aims to assess the environmental changes in the last ca 6000 years (both natural and anthropogenic induced) using multiproxy analysis (geomorphological and sedimentological data, elemental and stable isotope content, microfossil assemblages, radiocarbon dating, and historical records) applied to an embayed coast. The results showed the prevalence of marine environment until 6272-6000 cal BP, but with fluvial infilling of the inner embayment, even before present sea level was reached (ca 4500-4000 cal BP). The influx of sediments was probably the result of the four recorded wet episodes (at modelled age cal BP (2σ): E1 – 6067-4770, E2 – 5806-4409, E3 – 5383-4088, and E4 – 4086-3905). These great sediment influxes along the previous 3000 years continues until 2110-1962 cal BP triggering the downstream migration of the river mouth, the development of a sand barrier coast and of a sheltered lagoon inside the palaeo-embayment. Afterwards the sedimentation rate (SR) reached high values (0.19-0.48 cmyr-1), as the result of Roman intervention in the drainage basin where pastures and local fires are recorded, together with an increasing dryness. A major disturbance is recorded in the Pollen Assemblages Zones (between PAZ II and PAZ III) and in the sediments around 1863-1706 cal BP (2σ), in the transition from the Roman Age to the Muslim invasion period, probably reflecting a hiatus in the sedimentary record. Onwards, SR reached 0.21-0.57 cmyr-1. Two major hydro marine episodes may have contributed to this fact: the latter is the Lisbon tsunami (1755 AD) while the former may reflect the 16th Century tsunamis or a great marine storm episode. An aeolian environment prevailed since then and the embayment was transformed into a dune field interrupted only by the narrow channel of the river whose mouth is often closed.info:eu-repo/semantics/publishedVersio

Management and 1-Year Outcomes of Patients With Newly Diagnosed Atrial Fibrillation and Chronic Kidney Disease: Results From the Prospective GARFIELD-AF Registry

Background-Using data from the GARFIELD-AF (Global Anticoagulant Registry in the FIELD-Atrial Fibrillation), we evaluated the impact of chronic kidney disease (CKD) stage on clinical outcomes in patients with newly diagnosed atrial fibrillation (AF)