A text-mining system for extracting metabolic reactions from full-text articles

Background: Increasingly biological text mining research is focusing on the extraction of complex relationships relevant to the construction and curation of biological networks and pathways. However, one important category of pathway—metabolic pathways—has been largely neglected. Here we present a relatively simple method for extracting metabolic reaction information from free text that scores different permutations of assigned entities (enzymes and metabolites) within a given sentence based on the presence and location of stemmed keywords. This method extends an approach that has proved effective in the context of the extraction of protein–protein interactions. Results: When evaluated on a set of manually-curated metabolic pathways using standard performance criteria, our method performs surprisingly well. Precision and recall rates are comparable to those previously achieved for the well-known protein-protein interaction extraction task. Conclusions: We conclude that automated metabolic pathway construction is more tractable than has often been assumed, and that (as in the case of protein–protein interaction extraction) relatively simple text-mining approaches can prove surprisingly effective. It is hoped that these results will provide an impetus to further research and act as a useful benchmark for judging the performance of more sophisticated methods that are yet to be developed

Modelling the cost-effectiveness of a newborn hearing screening programme:Usability and pitfalls

Objective: The EUSCREEN project concerns the study of European vision and hearing screening programmes. Part of the project was the development of a cost-effectiveness model to analyse such programmes. We describe the development and usability of an online tool to enable stakeholders to design, analyse or modify a newborn hearing screening (NHS) programme. Design: Data from literature, from existing NHS programmes, and observations by users were used to develop and refine the tool. Required inputs include prevalence of the hearing impairment, test sequence and its timing, attendance, sensitivity, and specificity of each screening step. Outputs include the number of cases detected and the costs of screening and diagnostics. Study sample: Eleven NHS programmes with reliable data. Results: Three analyses are presented, exploring the effect of low attendance, number of screening steps, testing in the maternity ward, or screening at a later age, on the benefits and costs of the programme. Knowledge of the epidemiology of a staged screening programme is crucial when using the tool. Conclusions: This study presents a tool intended to aid stakeholders to design a new or analyse an existing hearing screening programme in terms of benefits and costs.</p

Complete breeding failures in ivory gull following unusual rainy storms in North Greenland

Natural catastrophic events such as heavy rainfall and windstorms may induce drastic decreases in breeding success of animal populations. We report the impacts of summer rainfalls on the reproductive success of ivory gull (Pagophila eburnea) in north-east Greenland. On two occasions, at Amdrup Land in July 2009 and at Station Nord in July 2011, we observed massive ivory gull breeding failures following violent rainfall and windstorms that hit the colonies. In each colony, all of the breeding birds abandoned their eggs or chicks during the storm. Juvenile mortality was close to 100% at Amdrup Land in 2009 and 100% at Station Nord in 2011. Our results show that strong winds associated with heavy rain directly affected the reproductive success of some Arctic bird species. Such extreme weather events may become more common with climate change and represent a new potential factor affecting ivory gull breeding success in the High Arctic

Ultrasonographic and laparoscopic evaluation of the reproductive tract in older captive female cheetahs (Acinonyx jubatus)

The study uniquely described the clinical value of transabdominal ultrasonography for monitoring features characterizing the estrous cycle in female cheetahs (Acinonyx jubatus). The reproductive tracts of 21 female, nulliparous, and relatively aged (median: 11 and interquartile range: 9.25–14 years) captive cheetahs resident on two sites in Namibia were assessed by transabdominal ultrasound. Subsequently, the ovarian findings on ultrasound were compared with direct visualization while performing laparoscopic sterilization. A combination of these observations supported by concurrent sampling for vaginal cytology and serum progesterone concentrations defined the estrous status of individual animals. At one site, six cheetahs had been implanted with the GnRH agonist, deslorelin as a contraceptive at least once within the preceding 11 years. On ultrasound, 31 uterine horns and 35 ovaries with discernible structures on 28 (86%) were visualized in the 21 cheetahs. The uterine body was difficult to visualize because of its intrapelvic location. Eleven of 19 uteri (58%) visualized showed endometrial edema suggestive of estrogenization. The uteri of four cheetahs (19%) showed evidence of mild cystic endometrial hyperplasia. Paraovarian cysts were seen on ultrasound (n ¼ 21) and laparoscopy (n ¼ 26) in 16 (76.2%) and 18 (85.7%) cheetahs, respectively. Ovarian volumes obtained from ultrasonographically determined dimensions predicted cyclic activity. Laparoscopy showed that 19 ovaries had discernible follicular structures. In the study population, 10 (47.6%) cheetahswere in proestrus or estrus; none in the luteal phase; and 11 (52.4%) in anestrus. Transabdominal ultrasound, in combination with serum progesterone concentrations and vaginal cytology, was used with acceptable accuracy to assess cyclic ovarian activity in captive cheetahs. A considerable proportion of this aged population showed ovarian activity and the prevalence of paraovarian cysts was notable. A history of prior deslorelin treatment was not associated with either reproductive activity or uterine pathology.AfriCat Foundation and CCF in Namibia.http://www.theriojournal.com2016-12-31hb2015ab201

Impact of CARDIOrespiratory FITness on Arrhythmia Recurrence in Obese Individuals With Atrial Fibrillation The CARDIO-FIT Study

AbstractBackgroundObesity begets atrial fibrillation (AF). Although cardiorespiratory fitness is protective against incident AF in obese individuals, its effect on AF recurrence or the benefit of cardiorespiratory fitness gain is unknown.ObjectivesThis study sought to evaluate the role of cardiorespiratory fitness and the incremental benefit of cardiorespiratory fitness improvement on rhythm control in obese individuals with AF.MethodsOf 1,415 consecutive patients with AF, 825 had a body mass index ≥27 kg/m2 and were offered risk factor management and participation in a tailored exercise program. After exclusions, 308 patients were included in the analysis. Patients underwent exercise stress testing to determine peak metabolic equivalents (METs). To determine a dose response, cardiorespiratory fitness was categorized as: low (<85%), adequate (86% to 100%), and high (>100%). Impact of cardiorespiratory fitness gain was ascertained by the objective gain in fitness at final follow-up (≥2 METs vs. <2 METs). AF rhythm control was determined using 7-day Holter monitoring and AF severity scale questionnaire.ResultsThere were no differences in baseline characteristics or follow-up duration between the groups defined by cardiorespiratory fitness. Arrhythmia-free survival with and without rhythm control strategies was greatest in patients with high cardiorespiratory fitness compared to adequate or low cardiorespiratory fitness (p < 0.001 for both). AF burden and symptom severity decreased significantly in the group with cardiorespiratory fitness gain ≥2 METs as compared to <2 METs group (p < 0.001 for all). Arrhythmia-free survival with and without rhythm control strategies was greatest in those with METs gain ≥2 compared to those with METs gain <2 in cardiorespiratory fitness (p < 0.001 for both).ConclusionsCardiorespiratory fitness predicts arrhythmia recurrence in obese individuals with symptomatic AF. Improvement in cardiorespiratory fitness augments the beneficial effects of weight loss. (Evaluating the Impact of a Weight Loss on the Burden of Atrial Fibrillation [AF] in Obese Patients; ACTRN12614001123639

Defects and impurities in jarosite: A computer simulation study

Computer modelling techniques involving a rigid ion model have been used to investigate the defect structure and impurity site preferences in end-member K-jarosite. Calculated intrinsic vacancy energies show that the K2SO4 neutral cluster, with an energy per species of 1.34 eV, will be the most common defect in the pure phase. Defect reactions leading to vacancies on the Fe site have high energies, in excess of 4.0 eV per species, and are thus unlikely to occur in great numbers. However, the calculations show that divalent metal cations can be incorporated onto the Fe site via solution reactions with oxides leading to the formation of goethite. Calculated solution reactions are exothermic and thus predicted to be highly favourable. At K sites substitutions occur in the order Cd > Zn > Cu, but will be limited due to endothermic solution energies and structural considerations

Cosmological parameters from SDSS and WMAP

We measure cosmological parameters using the three-dimensional power spectrum P(k) from over 200,000 galaxies in the Sloan Digital Sky Survey (SDSS) in combination with WMAP and other data. Our results are consistent with a ``vanilla'' flat adiabatic Lambda-CDM model without tilt (n=1), running tilt, tensor modes or massive neutrinos. Adding SDSS information more than halves the WMAP-only error bars on some parameters, tightening 1 sigma constraints on the Hubble parameter from h~0.74+0.18-0.07 to h~0.70+0.04-0.03, on the matter density from Omega_m~0.25+/-0.10 to Omega_m~0.30+/-0.04 (1 sigma) and on neutrino masses from <11 eV to <0.6 eV (95%). SDSS helps even more when dropping prior assumptions about curvature, neutrinos, tensor modes and the equation of state. Our results are in substantial agreement with the joint analysis of WMAP and the 2dF Galaxy Redshift Survey, which is an impressive consistency check with independent redshift survey data and analysis techniques. In this paper, we place particular emphasis on clarifying the physical origin of the constraints, i.e., what we do and do not know when using different data sets and prior assumptions. For instance, dropping the assumption that space is perfectly flat, the WMAP-only constraint on the measured age of the Universe tightens from t0~16.3+2.3-1.8 Gyr to t0~14.1+1.0-0.9 Gyr by adding SDSS and SN Ia data. Including tensors, running tilt, neutrino mass and equation of state in the list of free parameters, many constraints are still quite weak, but future cosmological measurements from SDSS and other sources should allow these to be substantially tightened.Comment: Minor revisions to match accepted PRD version. SDSS data and ppt figures available at http://www.hep.upenn.edu/~max/sdsspars.htm

INNODIA Master Protocol for the evaluation of investigational medicinal products in children, adolescents and adults with newly diagnosed type 1 diabetes

Background The INNODIA consortium has established a pan-European infrastructure using validated centres to prospectively evaluate clinical data from individuals with newly diagnosed type 1 diabetes combined with centralised collection of clinical samples to determine rates of decline in beta-cell function and identify novel biomarkers, which could be used for future stratification of phase 2 clinical trials. Methods In this context, we have developed a Master Protocol, based on the “backbone” of the INNODIA natural history study, which we believe could improve the delivery of phase 2 studies exploring the use of single or combinations of Investigational Medicinal Products (IMPs), designed to prevent or reverse declines in beta-cell function in individuals with newly diagnosed type 1 diabetes. Although many IMPs have demonstrated potential efficacy in phase 2 studies, few subsequent phase 3 studies have confirmed these benefits. Currently, phase 2 drug development for this indication is limited by poor evaluation of drug dosage and lack of mechanistic data to understand variable responses to the IMPs. Identification of biomarkers which might permit more robust stratification of participants at baseline has been slow. Discussion The Master Protocol provides (1) standardised assessment of efficacy and safety, (2) comparable collection of mechanistic data, (3) the opportunity to include adaptive designs and the use of shared control groups in the evaluation of combination therapies, and (4) benefits of greater understanding of endpoint variation to ensure more robust sample size calculations and future baseline stratification using existing and novel biomarkers

3D reconstructions of resin dental fillings based on en face OCT images

Optical tomographic techniques are of particular importance in the medical imaging field, because these techniques can provide non-invasive diagnostic images. In the present study, en-face optical coherence tomography (efOCT) was used as a non-invasive high resolution imaging method for supplying the necessary information on the quality of dental hard tissues and coronal composite resin fillings. Teeth after being subject to several treatment methods are imaged in order to asses the material defects and micro-leakage of tooth-filling interface as well as to evaluate the quality of dental hard tissue. C-scan and B-scan OCT images are acquired from a large range of samples. Based on such images, 3D reconstructions were assembled, which lead to a better view of the investigated areas. Cracks and voids in the dental structures as well as material defects and gaps at the interfaces are clearly exposed. The advantages of the OCT imaging method consist in non-invasiveness and high resolution. The en-face OCT offers the user the possibility of rapidly acquiring sequential B-scans and C-scans by switching the instrument between the two regimes. Sequential and rapid switching between the en-face regime and the cross-section regime, specific for the en-face OCT systems, represent a significant advantage in the process of non-invasive imaging, as images with different orientations can be obtained using the same system, during the same imaging event. 3D reconstructions of volumes allow evaluation and localization of defects in the samples. By importing such data into numerical simulation software can provide answers on the behavior of the investigated structures