Developmental control of hypoxia during bud burst in grapevine

Dormant or quiescent buds of woody perennials are often dense, and in the case of grapevine (Vitis vinifera L.) have a low tissue oxygen status. The precise timing of the decision to resume growth is difficult to predict, but once committed the increase in tissue oxygen status is rapid and developmentally regulated. Here we show that more than a third of the grapevine homologues of widely conserved hypoxia-responsive genes, and nearly a fifth of all grapevine genes possessing a plant hypoxia-responsive promoter element were differentially regulated during bud burst, in apparent harmony with resumption of meristem identity and cell-cycle gene regulation. We then investigated the molecular and biochemical properties of the grapevine ERF-VII homologues, which in other species are oxygen labile and function in transcriptional regulation of hypoxia-responsive genes. Each of the three VvERF-VIIs were substrates for oxygen-dependent proteolysis in vitro, as a function of the N-terminal cysteine. Collectively these data support an important developmental function of oxygen-dependent signalling in determining the timing and effective coordination bud burst in grapevine. In addition, novel regulators, including GASA-, TCP-, MYB3R-, PLT- and WUS-like transcription factors, were identified as hallmarks of the orderly and functional resumption of growth following quiescence in buds

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

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

Physiological parameters for Prognosis in Abdominal Sepsis (PIPAS) Study : a WSES observational study

BackgroundTiming and adequacy of peritoneal source control are the most important pillars in the management of patients with acute peritonitis. Therefore, early prognostic evaluation of acute peritonitis is paramount to assess the severity and establish a prompt and appropriate treatment. The objectives of this study were to identify clinical and laboratory predictors for in-hospital mortality in patients with acute peritonitis and to develop a warning score system, based on easily recognizable and assessable variables, globally accepted.MethodsThis worldwide multicentre observational study included 153 surgical departments across 56 countries over a 4-month study period between February 1, 2018, and May 31, 2018.ResultsA total of 3137 patients were included, with 1815 (57.9%) men and 1322 (42.1%) women, with a median age of 47years (interquartile range [IQR] 28-66). The overall in-hospital mortality rate was 8.9%, with a median length of stay of 6days (IQR 4-10). Using multivariable logistic regression, independent variables associated with in-hospital mortality were identified: age > 80years, malignancy, severe cardiovascular disease, severe chronic kidney disease, respiratory rate >= 22 breaths/min, systolic blood pressure 4mmol/l. These variables were used to create the PIPAS Severity Score, a bedside early warning score for patients with acute peritonitis. The overall mortality was 2.9% for patients who had scores of 0-1, 22.7% for those who had scores of 2-3, 46.8% for those who had scores of 4-5, and 86.7% for those who have scores of 7-8.ConclusionsThe simple PIPAS Severity Score can be used on a global level and can help clinicians to identify patients at high risk for treatment failure and mortality.Peer reviewe

X -ray scattering studies of maquette peptide monolayers

We have applied x-ray scattering techniques to characterize the structure of Langmuir and Langmuir-Blodgett monolayers containing maquette peptides. These small, soluble, synthetic, de novo designed peptides were developed as test systems for studying electron transfer in proteins, but may also be useful as a new class of thin film materials for endowing surfaces with functionalities. In the family of maquettes under consideraton, the 31-mer unit synthesized forms an amphipathic α-helix with a flexible [special characters omitted] tether at the N-terminus. In solution, pairs of such units associate and dimerize covalently via a disulfide bond between the cysteine residues, and then further associate into 4-helix bundles. Each dihelix forms a pair of bis-His sites for binding prosthetic groups. We studied the prototype peptide of this family, H10H24, and a derivative, BBC16, palmitoylated at the N-terminus. Both peptides form monolayers at the air/water interface with a plateau in their isotherms. The more amphiphilic BBC16 forms more stable Langmuir monolayers that could be studied via synchrotron-based x-ray reflectivity at surface pressures above and below the plateau, while H10H24 could only be studied below the plateau. The data, analyzed by slab-model fitting and a model-independent refinement procedure, demonstrate that BBC16 undergoes an orientational transition as pressure increases. At low pressures, both peptides exist as dihelices parallel to the plane of the air/water interface, but at high pressure BBC16\u27s helices are approximately normal to the interface. The addition of free DLPE to BBC16 monolayers increased their stability sufficiently to allow collection of off-specular inplane scattering for long periods. The difference signal between a 2:1 DLPE:BBC16 and a pure DLPE monolayer indicates that the upright helices form a 2-dimensional glass. X-ray interferometry demonstrates that BBC16 monolayers LB deposited onto alkylated solid supports can maintain the perpendicular orientation that the peptide has in the precursor Langmuir film. H10H24 monolayers LB deposited at low pressure onto a thiol surface also have the peptide oriented perpendicular to the plane of the support, indicating that rearrangement of the molecules must occur during or after deposition. The suitability of these systems for future electrochemical and neutron scattering studies is discussed