Search

In an effort to characterise the various dimensions of activity within the biodiversity informatics landscape, we developed a framework to survey these dimensions for ten major organisations*1 relative to both their current activities and long-term strategic ambitions. This survey assessed the contact between these infrastructure organisations by capturing the breadth of activities for each infrastructure across five categories (data, standards, software, hardware and policy), for nine types of data (specimens, collection descriptions, opportunistic observations, systematic observations, taxonomies, traits, geological data, molecular data, and literature), and for seven phases of activity (creation, aggregation, access, annotation, interlinkage, analysis, and synthesis). This generated a dataset of 6,300 verified observations, which have been scored and validated by leading members of each infrastructure organisation. In this analysis of the resulting data, we address a set of high-level questions about the overall biodiversity informatics landscape, looking at the greatest gaps, overlap and possible rate-limiting steps. Across the infrastructure organisations, we also explore how far each is in relation to achieving its ambitions and the extent of its niche relative to other organisations. Our results show that when viewed by scope, most infrastructures occupy a relatively narrow niche in the overall landscape of activity, with the notable exception of the Global Biodiversity Information Facility (GBIF) and possibly LifeWatch. Niches associated with molecular data and biological taxonomy are very well filled, suggesting there is still considerable room for growth in other areas, with the Distributed System of Scientific Collections (DiSSCo) and the Integrated European Long-Term Ecosystem Research Infrastructure (eLTER RI) showing the highest levels of difference between their current activities and stated ambitions, potentially reflecting the relative youth of these organisations. iNaturalist, the Biodiversity Heritage Library and Catalogue of Life all occupy narrow and tightly circumscribed niches. These organisations are also amongst the closest to achieving their stated ambitions within their respective areas of activity. The largest gaps in infrastructure activity relate to the development of hardware and standards, with many gaps set to be addressed if the stated ambitions of those surveyed come to fruition. Nevertheless, some gaps persist, outlining a potential role for this survey as a planning tool to help coordinate and align investment in future biodiversity informatics activities. GBIF and LifeWatch are the two infrastructures where there is the most similarity in ambition with DiSSCo, with the greatest overlap concentrated on activities related to data/content, specimen data and their shared ambition to interlink information. While overlap appears intense, the analysis is limited by the resolution of the survey framework and ignores existing collaborations between infrastructures. In addition to presenting the results of this survey, we outline our plans to publish this work and a proposal to develop the methodology as an interactive web-based tool. This would allow other projects and infrastructures to self-score their activities and visualise their niche within the current landscape, encouraging better global alignment of activities. For example, our results should make it easier for initiatives to strengthen collaboration and differentiate work when their activities overlap. Likewise, this approach would be useful for funding agencies when targeting gaps in the informatics landscape or increasing the technical maturity of certain critical activities, e.g., to improve immature data standards. While no framework is perfect, we hope to encourage a dialogue on the potential for taking an algorithmic approach to community alignment and see this as a means of strengthening community cooperation when addressing problems that require global cooperation.

Palatable food can trigger appetitive responses, such as salivation and approach tendencies. Though evolutionarily functional, these conditioned responses can encourage overeating and obesity when food is abundant. The current study examines the neural correlates of ‘denovo’ Pavlovian appetitive conditioning, pairing one class of unknown objects (conditioned stimuli, CS) with their sweet taste (unconditioned stimulus, US) during a single trial. To do so, 23 participants consumed unknown (marzipan) objects of one particular color (CS+) while only interacting with control stimuli of different color and shape (CS-). After this single-trial conditioning procedure, participants viewed and rated images of the marzipan figures and the control objects during functional magnetic resonance imaging (fMRI). Relative to the CS-, the CS+ elicited stronger activation in the dorsal striatum, a brain region associated with cue-reward coupling. Furthermore, conditioning effects in subjective ‘craving’, defined as increased palatability and desire to eat, were observed, and these were positively related to conditioning effects in the amygdala, a brain region associated with the need-dependent value of a reward. Thus, the study identified reward-related brain regions involved in single-trial appetitive learning, thereby providing a potential mechanism that contributes to the etiology of food craving. These findings might help to understand clinically relevant food cravings in individuals with eating or weight related concerns and might support the development of extinction based treatments.

In serial visual search we shift attention successively from location to location in search for the target. Although such search has been investigated using fMRI, overt attention (i.e., eye movements) was usually neglected or discouraged. As a result, it is unclear what happens in the instant when our gaze falls upon a target as compared to a distractor. In the present experiment, we used a multiple target search task that required eye movements and employed an analysis based on fixations as events of interest to investigate differences between target and distractor processing. Twenty young healthy adults indicated the number of targets (0-3) among distractors in a 20-item display. Compared to distractor fixations, we found that target fixations gave rise to wide-spread activation in the dorsal attention system, as well as in the visual cortex. Targets that were found later during the search activated the left inferior frontal gyrus and the left supramarginal gyrus more strongly than those that were found earlier. Finally, areas associated with visual and verbal working memory showed increased activation with a larger number of targets in the display.

Objectives The United States National Institute for Occupational Safety and Health (NIOSH) is developing a protocol to assess the containment performance of closed system transfer devices (CSTDs) when used for drug preparation (task 1) and administration (task 2) and published a draft protocol in September 2016. Nine possible surrogates were proposed by NIOSH for use in the testing. The objectives of this study were to: (A) select the most appropriate surrogate; (B) validate the NIOSH protocol using this surrogate; and (C) determine the containment performance of four commercial CSTDs as compared with an open system of needle and syringe using the validated NIOSH protocol. Methods 2-Phenoxyethanol (2-POE) was selected as a surrogate based on its water solubility, Henry’s volatility constant, detectability by mass spectrometry, and non-toxicity. Standard analytical validation methods including system suitability, limit of detection (LOD), and limit of quantitation (LOQ) as well as system cleaning validation were performed. The amount of 2-POE released when the CSTDs were manipulated according to two tasks defined by NIOSH was determined using mass spectrometry coupled to thermal desorption and gas chromatography. This approach allows sensitivity of detection below 1 part per billion (ppb). Equashield, Tevadaptor (OnGuard), PhaSeal, and ChemoClave were assessed according to manufacturers’ instructions for use. Results 2-POE was tested and validated for suitability of use within the NIOSH protocol. A simple and efficient cleaning protocol achieved consistently low background values, with an average value, based on 85 measurements, of 0.12 ppb with a 95% confidence interval (CI) of ±0.16 ppb. This gives an LOD for the tests of 0.35 ppb and an LOQ of 0.88 ppb. The Equashield, Tevadaptor (OnGuard), and PhaSeal devices all showed average releases, based on 10 measurements from five tests, that were less than the LOQ (i.e. < 0.88 ppb), while the ChemoClave Vial Shield with Spinning Spiros showed average releases of 2.9±2.3 ppb and 7.5±17.9 ppb for NIOSH tasks 1 and 2 respectively at the 95% confidence level. The open system of needle and syringe showed releases, based on two measurements from a single test, of 4.2±2.2 ppb and 5.1±1.7 ppb for NIOSH tasks 1 and 2 respectively at the 95% confidence level. Conclusions 2-POE proved to be an ideal surrogate for testing of CSTDs using the NIOSH protocol. We propose that a CSTD can be qualified using the NIOSH testing approach if the experimental LOQ is less than 1 ppb and the release values are below the LOQ. Equashield, Tevadaptor (OnGuard), and PhaSeal meet these acceptance criteria and can therefore all be qualified as CSTDs, but the ChemoClave system does not and so would not qualify as a CSTD.

Urinary stone disease is the third most common condition affecting the urinary tract. It contributes to a great deal of morbidity for both men and women, and cost the United States (US) over 5.3 billion dollars in 2000 alone. Moreover, it is associated with systemic diseases such as hypertension, diabetes, and other components of the metabolic syndrome. Reciprocally, these systemic diseases may be contributing to the rising incidence in urinary stone disease. Previously described mechanisms of stone formation attribute stone development and growth to the urinary milieu. While this may partly influence the process, it cannot account for the associations between systemic diseases and stones observed in large community-based studies. Here we present a review of the evidence demonstrating a link between urinary stone disease and components of the metabolic syndrome. We believe a vascular etiology for the initiation of urinary stones may tie these processes together.

The Eromanga Basin is a large Mesozoic sedimentary basin in Central and Northern Australia. It covers an area of 1,000,000 km2 and is the location of important onshore petroleum and natural gas deposits in Australia including the nation's largest onshore oilfield at Jackson. We performed a pre-stack time migration and later on a pre-stack depth migration sequence on a 300sqkm block in the basin with the objective to map out intricate formations for detection of areas with high potential for gas hydrocarbon. The basin contains an ancient meteorite crater (astrobleme) which distorts seismic images, and is made of sandstone, siltstone, mudstone, coal and shale. The oil and gas producing interval is located around 1,200m below the surface. Vibroseis seismic data was processed through an amplitude-preserved and surface-consistent sequence followed by offset-class regularisation and pre-stack migration. Refraction and residual statics were applied to correct for near surface time distortions. The time migrated data illustrates high signal-to-noise ratio with generally flat rock beddings with some noticeably complicated formations at known horizons, forming strong velocity boundaries. These formation oddities generally appear from Cadna-Owie ( C ) Formation and deeper; the Top C horizon is of significance for exploration as the top of the unit approximates a distinctive seismic reflector and is mappable over the entire basin. During depth-velocity modelling it was revealed that there are significant velocity variations (~500m/s) at Top C and other boundaries. Time imaging was not able to image these intervals properly. Depth migration improved seismic image quality especially in fault shadow zones, and areas with complex seismo-geological settings. The benefits of depth imaging on the Eromanga Basin data were demonstrated by significant uplift in structural conformity and increased confidence in interpretation results.

Obesity is a strong risk factor for nephrolithiasis, but the role of physical activity and caloric intake remains poorly understood. We evaluated this relationship in84,225 womenwith no history of stones as part of the Women's Health Initiative Observational Study, a longitudinal, prospective cohort of postmenopausal women enrolled from 1993 to 1998 with 8 years' median follow-up. The independent association of physical activity (metabolic equivalents [METs]/wk), calibrated dietary energy intake, and body mass index (BMI) with incident kidney stone development was evaluated after adjustment for nephrolithiasis risk factors. Activity intensity was evaluated in stratified analyses. Compared with the risk in inactive women, the risk of incident stones decreased by 16% in women with the lowest physical activity level (adjusted hazard ratio [aHR], 0.84; 95% confidence interval [95% CI], 0.74 to 0.97). As activity increased, the risk of incident stones continued to decline until plateauing at a decrease of approximately 31% for activity levels ≥10 METs/wk (a HR, 0.69; 95% CI, 0.60 to 0.79). Intensity of activity was not associated with stone formation. As dietary energy intake increased, the risk ofincident stones increased by up to 42% (a HR, 1.42; 95% CI, 1.02 to 1.98). However, intake < 1800 kcal/d did not protect against stone formation. Higher BMI category was associated with increased risk of incident stones. In summary, physical activity may reduce the risk of incident kidney stones in postmenopausal women independent of caloric intake and BMI, primarily because of the amount of activity rather than exercise intensity. Higher caloric intake further increases the risk of incident stones. Copyright © 2014 by the American Society of Nephrology.

UNLABELLED Transesophageal echocardiography (TEE) may improve intraoperative decision-making and patient outcome if it is performed and interpreted correctly. After revising our TEE examination to fulfill the published guidelines for basic TEE practitioners, we prospectively evaluated the ability of our cardiac anesthesiologists (all very experienced with TEE) to record and interpret this revised examination. Educational aids and regular TEE performance feedback were provided to the anesthesiologists. Their interpretations were compared with the independently determined results of experts. Compared with their own historical controls (42% recording rate), all anesthesiologists showed significant improvement in their ability to record a basic intraoperative TEE examination resulting in 81% (P < 0.0001) of all required images being recorded: 88% before cardiopulmonary bypass, 77% immediately after bypass, and 64% after chest closure. Seventy-nine percent of the images recorded at baseline were correctly interpreted, 6% were incorrectly interpreted, and 15% were not evaluated. Our attempt to assess compliance with published guidelines for basic intraoperative TEE resulted in a marked improvement in our intraoperative TEE practice. Most, but not all, standard cross-sections are recorded or interpreted correctly, even by highly experienced and motivated practitioners. IMPLICATIONS Experienced cardiac anesthesiologists can obtain and correctly interpret most basic intraoperative transesophageal echocardiograms.

Purpose: The limitations imposed by human clinical studies and mammalian models of nephrolithiasis have hampered the development of effective medical treatments and preventive measures for decades. The simple but elegant Drosophila melanogaster is emerging as a powerful translational model of human disease, including nephrolithiasis. It may provide important information essential to our understanding of stone formation. We present the current state of research using D. melanogaster as a model of human nephrolithiasis. Materials and Methods: We comprehensively reviewed the English language literature using PubMed-. When necessary, authoritative texts on relevant subtopics were consulted. Results: The genetic composition, anatomical structure and physiological function of Drosophila malpighian tubules are remarkably similar to those of the human nephron. The direct effects of dietary manipulation, environmental alteration and genetic variation on stone formation can be observed and quantified in a matter of days. Several Drosophila models of human nephrolithiasis have been developed, including genetically linked and environmentally induced stones. A model of calcium oxalate stone formation is among the most recent fly models of human nephrolithiasis. Conclusions: The ability to readily manipulate and quantify stone formation in D. melanogaster models of human nephrolithiasis presents the urological community with a unique opportunity to increase our understanding of this enigmatic disease. © 2013 by AMERICAN UROLOGICAL ASSOCIATION EDUCATION AND RESEARCH, INC.

Background —The ability to predict the rate of hemodynamic progression in an individual patient with valvular aortic stenosis has been elusive. The purpose of the present study was to evaluate whether the rate of change in aortic valve area (AVA) measured during the ejection phase of a cardiac cycle predicts the rate of hemodynamic progression in patients with asymptomatic aortic stenosis. Methods and Results —In 84 adults with initially asymptomatic aortic stenosis and a baseline AVA of ≥0.9 cm 2 , annual echocardiographic data were obtained prospectively (mean follow-up 2.8±1.3 years). With the initial echocardiogram, the ratio of AVA measured at mid-acceleration and mid-deceleration to the AVA at peak velocity was calculated. The primary outcome variable was the annual rate of change in AVA (rate of progression), with rate of progression classified as rapid (a reduction in AVA of ≥0.2 cm 2 /y) or slow (2 /y). Rapid progression was significantly associated with an AVA ratio of ≥1.25 ( P =0.004, risk ratio 3.1, 95% CI 1.2 to 7.9). The sensitivity, specificity, and positive predictive value of AVA ratio of ≥1.25 for the prediction of rapid progression of valvar aortic stenosis was 64%, 72%, and 80% respectively. The decrease in ejection fraction measured from the initial to final echocardiogram was small but greater for patients with an AVA ratio of ≥1.25 (−4±7% versus +2±7%, P Conclusions —A flow-dependent change in AVA can be measured during a routine transthoracic echocardiographic study. The rate of change in AVA is an additional measure of disease severity and may be used to predict an individual’s risk for subsequent rapid disease progression.

Purpose: Calyceal selection for percutaneous renal access is critical for safe, effective performance of percutaneous nephrolithotomy. Available anatomical evidence is contradictory and incomplete. We present detailed renal calyceal anatomy obtained from in vivo 3-dimentional computerized tomography renderings. Materials and Methods: A total of 60 computerized tomography urograms were randomly selected. The renal collecting system was isolated and 3-dimensional renderings were constructed. The primary plane of each calyceal group of 100 kidneys was determined. A coronal maximum intensity projection was used for simulated percutaneous access. The most inferior calyx was designated calyx 1. Moving superiorly, the subsequent calyces were designated calyx 2 and, when present, calyx 3. The surface rendering was rotated to assess the primary plane of the calyceal group and the orientation of the select calyx. Results: The primary plane of the upper pole calyceal group was mediolateral in 95% of kidneys and the primary plane of the lower pole calyceal group was anteroposterior in 95%. Calyx 2 was chosen in 90 of 97 simulations and it was appropriate in 92%. Calyx 3 was chosen in 7 simulations but it was appropriate in only 57%. Calyx 1 was not selected in any simulation and it was anteriorly oriented in 75% of kidneys. Conclusions: Appropriate lower pole calyceal access can be reliably accomplished with an understanding of the anatomical relationship between individual calyceal orientation and the primary plane of the calyceal group. Calyx 2 is most often appropriate for accessing the anteroposterior primary plane of the lower pole. Calyx 1 is most commonly oriented anterior. © 2013 American Urological Association Education and Research, Inc.

Purpose: Strontium has chemical similarity to calcium, which enables the replacement of calcium by strontium in biomineralization processes. Incorporating strontium into human bone and teeth has been studied extensively but little research has been performed of the incorporation of strontium into urinary calculi. We used synchrotron based x-ray fluorescence and x-ray absorption techniques to examine the presence of strontium in different types of human kidney stones. Materials and Methods: Multiple unique human stone samples were obtained via consecutive percutaneous nephrolithotomies/ureteroscopies. A portion of each stone was sent for standard laboratory analysis and a portion was retained for x-ray fluorescence and x-ray absorption measurements. X-ray fluorescence and x-ray absorption measurements determined the presence, spatial distribution and speciation of strontium in each stone sample. Results: Traditional kidney stone analyses identified calcium oxalate, calcium phosphate, uric acid and cystine stones. X-ray fluorescence measurements identified strontium in all stone types except pure cystine. X-ray fluorescence elemental mapping of the samples revealed co-localization of calcium and strontium. X-ray absorption measurements of the calcium phosphate stone showed strontium predominately present as strontium apatite. Conclusions: Advanced x-ray fluorescence imaging identified strontium in all calcium based stones, present as strontium apatite. This finding may be critical since apatite is thought to be the initial nidus for calcium stone formation. Strontium is not identified by standard laboratory stone analyses. Its substitution for calcium can be reliably identified in stones from multiple calcium based stone formers, which may offer opportunities to gain insight into early events in lithogenesis. © 2013 American Urological Association Education and Research, Inc.

The pathophysiology of the various forms of urinary stone disease remains a complex topic. Epidemiologic research and the study of urine and serum chemistries have created an abundance of data to help drive the formulation of pathophysiologic theories. This article addresses the associations of urinary stone disease with hypertension, cardiovascular disease, atherosclerosis, obesity, dyslipidemia, diabetes, and other disease states. Findings regarding the impact of dietary calcium and the formation of Randall's plaques are also explored and their implications discussed. Finally, further avenues of research are explored, including genetic analyses and the use of animal models of urinary stone disease. © 2013.

J Miller, TH TarterSouthern Illinois University School of Medicine, Department of Surgery, Springfield, IL, USAAbstract: Benign prostatic hyperplasia (BPH) is a frequent cause of lower urinary symptoms, with a prevalence of 50% by the sixth decade of life. Hyperplasia of stromal and epithelial prostatic elements that surround the urethra cause lower urinary tract symptoms (LUTS), urinary tract infection and acute urinary retention. Medical treatments of symptomatic BPH include; 1) the 5α-reductase inhibitors, 2) the α1-adrenergic antagonists, and 3) the combination of a 5α-reductase inhibitor and a α1-adrenergic antagonist. Selective α1-adrenergic antagonists relax the smooth muscle of the prostate and bladder neck without affecting the detrussor muscle of the bladder wall, thus decreasing the resistance to urine flow without compromising bladder contractility. Clinical trials have shown that α1-adrenergic antagonists decrease LUTS and increase urinary flow rates in men with symptomatic BPH, but do not reduce the long-term risk of urinary retention or need for surgical intervention. Inhibitors of 5α-reductase decrease production of dihydrotestosterone within the prostate resulting in decreased prostate volumes, increased peak urinary flow rates, improvement of symptoms, and decreased risk of acute urinary retention and need for surgical intervention. Interim results of the ongoing Combination of Avodart and Tamsulosin (CombAt) study have shown combination therapy with the 5α-reductase inhibitor dutasteride and the α1-adrenergic antagonist tamsulosin offer significant improvements from baseline compared with either drug alone.Keywords: prostatic hyperplasia, 5α-reductase, dutasteride, tamsulosin

© 2015 Chi et al. Ectopic calcification is a driving force for a variety of diseases, including kidney stones and atherosclerosis, but initiating factors remain largely unknown. Given its importance in seemingly divergent disease processes, identifying fundamental principal actors for ectopic calcification may have broad translational significance. Here we establish a Drosophila melanogaster model for ectopic calcification by inhibiting xanthine dehydrogenase whose deficiency leads to kidney stones in humans and dogs. Micro X-ray absorption near edge spectroscopy (μXANES) synchrotron analyses revealed high enrichment of zinc in the Drosophila equivalent of kidney stones, which was also observed in human kidney stones and Randall's plaques (early calcifications seen in human kidneys thought to be the precursor for renal stones). To further test the role of zinc in driving mineralization, we inhibited zinc transporter genes in the ZnT family and observed suppression of Drosophila stone formation. Taken together, genetic, dietary, and pharmacologic interventions to lower zinc confirm a critical role for zinc in driving the process of heterogeneous nucleation that eventually leads to stone formation. Our findings open a novel perspective on the etiology of urinary stones and related diseases, which may lead to the identification of new preventive and therapeutic approaches.

A 42-year-old male soldier in the Air National Guard presented to our hospital with a 2-month history of increasing dyspnea on exertion, orthopnea, paroxysmal nocturnal dyspnea, and lower extremity edema, and presented to our hospital. Complete blood …

Mitral regurgitation (MR) is a major determinant of outcome in cardiac surgery. The location and mechanism of mitral lesions determine the approach to various repairs and their feasibility. Because of incomplete evaluations or change in patient condition, detailed intraoperative transesophageal echocardiography (TEE) examination of the mitral valve may be required. We hypothesized that a systematic TEE mitral valve examination would allow precise identification of the anatomic location and mechanism of MR in patients undergoing mitral surgery. We designed a systematic mitral valve examination consisting of six views: fivechamber, four-chamber, two-chamber anterior, twochamber mid, two-chamber posterior and short-axis. We used this examination prospectively in 13 patients undergoing mitral valve surgery for severe MR and compared the results with the surgical findings. We then retrospectively interpreted 11 similar patients who had undergone intraoperative TEE studies before this examination. TEE correctly diagnosed the mechanism and precise location of pathology in 12 of 13 patients in the prospective group, but in only 6 of 10 patients in the retrospective group. TEE also correctly identified 75 of 78 mitral segments (96%) as being normal or abnormal. In the retrospective group, only 42 of 60 segments (70%) were correctly identified (P , 0.001). We conclude that this systematic TEE mitral valve examination improves identification of mitral segments and precise localization of pathologies and may also improve the diagnosis of the mechanism of MR. Implications: In this article, we describe how a systematic examination of the mitral valve by using transesophageal echocardiography allows identification of the different segments of the mitral valve, precise localization of pathology, and helps to diagnose the mechanism of mitral regurgitation. This is important in determining an approach to mitral valve repair and its feasibility. (Anesth Analg 1999;88:1205‐12)

A novel, minimally invasive measurement technique has been developed for the detection of drugs in the anterior chamber of the eye. Presently there is no satisfactory, real-time detection method available to the ophthalmic community. Accurate determination of drug concentrations in the eye would be of great value and assistance to researchers and manufacturers of ophthalmic drugs and ocular implants, to enable a better understanding of intraocular pharmacokinetics. At present researchers use techniques of direct sampling of the aqueous humor from laboratory animal eyes into which the drug has been introduced topically or systemically. Rabbit eyes are frequently used in this context. Sampling via paracentesis is invasive, and does not yield a continuous measurement. Our approach to addressing this measurement requirement is, in effect, to turn the eye into a cuvette and use optical absorbance spectroscopy measurements to detect drug concentrations. A novel contact lens has been designed using commercial, off-the-shelf, optical design software. The lenses have been optimized to direct light across the anterior chamber of a rabbit's eye. Practical demonstration and characterization of light propagation across the eye have been undertaken and are reported. Preliminary results of the identification of drug compounds introduced into model eyes are also reported.