Ex Situ Conservation Of Holstein-Friesian Cattle - Comparing The Dutch, French And USA Germplasm Collections

The establishment of gene banks using cryopreservation to secure the genetic diversity of farm breeds have been widely assessed. France, the Netherlands and the USA were among the first countries to organize national cryobanks and these banks are now 10 to 20 years old. All three countries have started Holstein-Friesian (HF) collections to conserve as much genetic diversity as possible for this globally important breed. In order better understand the diversity captured in these collections, the genetic variability of HF collections within and between countries was assessed, and genetic variability of germplasm collections were compared with active bulls in each country. The overall aim of the project was to determine the breed’s security and to guide future collection activities

Snowex 2017 Community Snow Depth Measurements: A Quality-Controlled, Georeferenced Product

Snow depth was one of the core ground measurements required to validate remotely-sensed data collected during SnowEx Year 1, which occurred in Colorado. The use of a single, common protocol was fundamental to produce a community reference dataset of high quality. Most of the nearly 100 Grand Mesa and Senator Beck Basin SnowEx ground crew participants contributed to this crucial dataset during 6-25 February 2017. Snow depths were measured along ~300 m transects, whose locations were determined according to a random-stratified approach using snowfall and tree-density gradients. Two-person teams used snowmobiles, skis, or snowshoes to travel to staked transect locations and to conduct measurements. Depths were measured with a 1-cm incremented probe every 3 meters along transects. In shallow areas of Grand Mesa, depth measurements were also collected with GPS snow-depth probes (a.k.a. MagnaProbes) at ~1-m intervals. During summer 2017, all reference stake positions were surveyed with <10 cm accuracy to improve overall snow depth location accuracy. During the campaign, 193 transects were measured over three weeks at Grand Mesa and 40 were collected over two weeks in Senator Beck Basin, representing more than 27,000 depth values. Each day of the campaign depth measurements were written in waterproof field books and photographed by National Snow and Ice Data Center (NSIDC) participants. The data were later transcribed and prepared for extensive quality assessment and control. Common issues such as protocol errors (e.g., survey in reverse direction), notebook image issues (e.g., halo in the center of digitized picture), and data-entry errors (sloppy writing and transcription errors) were identified and fixed on a point-by-point basis. In addition, we strove to produce a georeferenced product of fine quality, so we calculated and interpolated coordinates for every depth measurement based on surveyed stakes and the number of measurements made per transect. The product has been submitted to NSIDC in csv format. To educate data users, we present the study design and processing steps that have improved the quality and usability of this product. Also, we will address measurement and design uncertainties, which are different in open vs. forest areas

Comparing Rule-based, Feature-based and Deep Neural Methods for De-identification of Dutch Medical Records

Unstructured information in electronic health records provide an invaluable resource for medical research. To protect the confidentiality of patients and to conform to privacy regulations, de-identification methods automatically remove personally identifying information from these medical records. However, due to the unavailability of labeled data, most existing research is constrained to English medical text and little is known about the generalizability of de-identification methods across languages and domains. In this study, we construct a varied dataset consisting of the medical records of 1260 patients by sampling data from 9 institutes and three domains of Dutch healthcare. We test the generalizability of three de-identification methods across languages and domains. Our experiments show that an existing rule-based method specifically developed for the Dutch language fails to generalize to this new data. Furthermore, a state-of-the-art neural architecture performs strongly across languages and domains, even with limited training data. Compared to feature-based and rule-based methods the neural method requires significantly less configuration effort and domain-knowledge. We make all code and pre-trained de-identification models available to the research community, allowing practitioners to apply them to their datasets and to enable future benchmarks.Comment: Proceedings of the 1st ACM WSDM Health Search and Data Mining Workshop (HSDM2020), 202

Архівна Евристика: практичні аспекти

Для молодої генерації сучасних дослідників здійснення ефективного пошуку інформації для вирішення конкретних завдань набуває надзвичайної ваги та актуальності. Вміння грамотно і професійно шукати достовірну та актуальну інформацію, робити висновки та приймати правильні рішення спонукає фахівця-інтелектуала опановувати спеціальні евристичні методи

Towards Uniform Gene Bank Documentation In Europe – The Experience From The EFABISnet Project

In the EFABISnet project, a collaborative effort of EAAP, FAO and partners from 14 European countries, in cooperation with the European Regional Focal Point for Animal Genetic Resources (ERFP), national information systems for monitoring the animal genetic resources on breed level were established in Austria, Cyprus, Estonia, Georgia, Iceland, Ireland, Italy, Netherlands, Slovakia, Slovenia, Switzerland, and United Kingdom. The network was soon extended beyond the project plans, with the establishment of EFABIS databases in Finland, Greece, and Hungary. The network was then complemented by a set of inventories of national gene bank collections to strengthen the documentation of ex situ conservation programmes. These documentation systems were established by the National Focal Points for management of farm animal genetic resources. Here we present the experience gained in establishment of these national inventories of gene banks and their relevance to the Strategic Priority Areas of the Global Plan of Action which could be useful for other areas in the world

Assessing the reactive surface area of soils and the association of soil organic carbon with natural oxide nanoparticles using ferrihydrite as proxy

Assessment of the surface reactivity of natural metal-(hydr)oxide nanoparticles is necessary for predicting ion adsorption phenomena in soils using surface complexation modeling. Here, we describe how the equilibrium concentrations of PO4, obtained with 0.5 M NaHCO3 extractions at different solution-to-soil ratios, can be interpreted with a state-of-the-art ion adsorption model for ferrihydrite to assess the reactive surface area (RSA) of agricultural top soils. Simultaneously, the method reveals the fraction of reversibly adsorbed soil PO4 (R-PO4). The applied ion-probing methodology shows that ferrihydrite is a better proxy than goethite for consistently assessing RSA and R-PO4. The R-PO4 pool agrees well with ammonium oxalate (AO)-extractable phosphorus, but only if measured as orthophosphate. The RSA varied between ∼2 and 20 m2/g soil. The corresponding specific surface area (SSA) of the natural metal-(hydr)oxide fraction is ∼350–1400 m2/g, illustrating that this property is highly variable and cannot be represented by a single value based on the AO-extractable oxide content. The soil organic carbon (SOC) content of our top soils increases linearly not only with the increase in RSA but remarkably also with the increase in mean particle size (1.5–5 nm). To explain these observations, we present a structural model for organo-mineral associations based on the coordination of SOC particles to metal-(hydr)oxide cores.Universidad de Costa Rica/[]/UCR/Costa RicaUCR::Vicerrectoría de Investigación::Unidades de Investigación::Ciencias Agroalimentarias::Centro de Investigaciones Agronómicas (CIA

Tomography of photon-number resolving continuous-output detectors

We report a comprehensive approach to analysing continuous-output photon detectors. We employ principal component analysis to maximise the information extracted, followed by a novel noise-tolerant parameterised approach to the tomography of PNRDs. We further propose a measure for rigorously quantifying a detector's photon-number-resolving capability. Our approach applies to all detectors with continuous-output signals. We illustrate our methods by applying them to experimental data obtained from a transition-edge sensor (TES) detector.Comment: 5 pages, 3 figures, also includes supplementary informatio

Clinical Examination for the Prediction of Mortality in the Critically Ill : The Simple Intensive Care Studies-I

Objectives: Caregivers use clinical examination to timely recognize deterioration of a patient, yet data on the prognostic value of clinical examination are inconsistent. In the Simple Intensive Care Studies-I, we evaluated the association of clinical examination findings with 90-day mortality in critically ill patients. Design: Prospective single-center cohort study. Setting: ICU of a single tertiary care level hospital between March 27, 2015, and July 22, 2017. Patients: All consecutive adults acutely admitted to the ICU and expected to stay for at least 24 hours. Interventions: A protocolized clinical examination of 19 clinical signs conducted within 24 hours of admission. Measurements Main Results: Independent predictors of 90-day mortality were identified using multivariable logistic regression analyses. Model performance was compared with established prognostic risk scores using area under the receiver operating characteristic curves. Robustness of our findings was tested by internal bootstrap validation and adjustment of the threshold for statistical significance. A total of 1,075 patients were included, of whom 298 patients (28%) had died at 90-day follow-up. Multivariable analyses adjusted for age and norepinephrine infusion rate demonstrated that the combination of higher respiratory rate, higher systolic blood pressure, lower central temperature, altered consciousness, and decreased urine output was independently associated with 90-day mortality (area under the receiver operating characteristic curves = 0.74; 95% CI, 0.71-0.78). Clinical examination had a similar discriminative value as compared with the Simplified Acute Physiology Score-II (area under the receiver operating characteristic curves = 0.76; 95% CI, 0.73-0.79; p = 0.29) and Acute Physiology and Chronic Health Evaluation-IV (using area under the receiver operating characteristic curves = 0.77; 95% CI, 0.74-0.80; p = 0.16) and was significantly better than the Sequential Organ Failure Assessment (using area under the receiver operating characteristic curves = 0.67; 95% CI, 0.64-0.71; p <0.001). Conclusions: Clinical examination has reasonable discriminative value for assessing 90-day mortality in acutely admitted ICU patients. In our study population, a single, protocolized clinical examination had similar prognostic abilities compared with the Simplified Acute Physiology Score-II and Acute Physiology and Chronic Health Evaluation-IV and outperformed the Sequential Organ Failure Assessment score.Peer reviewe