Workflow tools for biological applications

When identifying best practices for multistep processes involving data analysis, it is fre- quently the case that the data scientist is asked to wear many hats simultaneouly: developer, programmer, statistician, graphic designer, writer, administrator. Although many scientists address these roles with great success, it is often at the expense of reproducibility, scalability, and organizational knowledge. The process of formalizing each step of the process creates op- portunity to apply lessons learned and proven tools from multiple disciplines to optimize each step of the transformation from raw data to usable output. This modular approach allows organizations to mix off the shelf technical solutions with custom, swap out components for flexibility and minimize rework. The primary focus of this dissertation is to extend the conceptualization of pipeline to include methods drawn from human computer interaction, exploratory data analysis, interactive graphics, and reproducible research. We describe application to three distinct user groups: (1) a general audience of readers (2) biologists involved in metabolomics analysis (3) analysts working in a public sector regulatory environment. The resulting technical tools are implemented in the R packages ggparallel, chromatoplotsGUI, dataFormats, and CVBreports. Our analysis shows that these tools facilitate a positive transformative effect on the quality of communication between stakeholders. Specifically we see that the common angles plot pre- sented in ggparallel reduces the lie factor, chromatoplotsGUI enables display of metabolomic data rapidly and with a level of detail that facilitates development of the underlying analysis en- gine and the methods of dataFormats and CVBreports enable significantly reduced turnaround times for preliminary data assesment

Pretty Picky for a Generalist: Impacts of Toxicity and Nutritional Quality on Mantid Prey Processing

Prey have evolved a number of defenses against predation, and predators have developed means of countering these protective measures. Although caterpillars of the monarch butterfly, Danaus plexippus L., are defended by cardenolides sequestered from their host plants, the Chinese mantid Tenodera sinensis Saussure guts the caterpillar before consuming the rest of the body. We hypothesized that this gutting behavior might be driven by the heterogeneous quality of prey tissue with respect to toxicity and/or nutrients. We conducted behavioral trials in which mantids were offered cardenolide-containing and cardenolide-free D. plexippus caterpillars and butterflies. In addition, we fed mantids starved and unstarved D. plexippus caterpillars from each cardenolide treatment and nontoxic Ostrinia nubilalis Hübner caterpillars. These trials were coupled with elemental analysis of the gut and body tissues of both D. plexippus caterpillars and corn borers. Cardenolides did not affect mantid behavior: mantids gutted both cardenolide-containing and cardenolide-free caterpillars. In contrast, mantids consumed both O. nubilalis and starved D. plexippus caterpillars entirely. Danaus plexippus body tissue has a lower C:N ratio than their gut contents, while O. nubilalis have similar ratios; gutting may reflect the mantid’s ability to regulate nutrient uptake. Our results suggest that post-capture prey processing by mantids is likely driven by a sophisticated assessment of resource quality

Meta-analysis of thyroidectomy with ultrasonic dissector versus conventional clamp and tie

<p>Abstract</p> <p>Background</p> <p>We conducted a systematic review to evaluate the role of Ultrasonic dissector (UAS) versus conventional clamp and tie in thyroidectomy.</p> <p>Materials and methods</p> <p>We searched for all published RCT in into electronic databases. To be included in the analysis, the studies had to compare thyroidectomy with UAS versus conventional vessel ligation and tight (conventional technique = CT). The following outcomes were used to compare the total thyroidectomy group with UAS versus CT group: operative duration, operative blood loss, overall drainage volume during the first 24 hours, transiet laryngeal nerve palsy, permanent laryngeal nerve palsy, transiet hypocalcaemia and permanent hypocalcaemia.</p> <p>Results</p> <p>There are currently 7 RCT on this issue to compare thyroidectomy with UAS versus CT. From the analysis of these studies it was possible to confront 608 cases: 303 undergoing to thyroidectomy with UAS versus 305 that were treated with CT. Actually, it was shown a relevant advantage of cost-effectiveness in patients treated with UAS; there is a statistically significant reduction of the operative duration (weighted mean difference [WMD], -18.74 minutes; 95% confidence interval [CI], (-26.97 to -10.52 minutes) (P = 0.00001), intraoperative blood loss (WMD, -60.10 mL; 95% CI, -117.04 to 3.16 mL) (P = 0.04) and overall drainage volume (WMD, -35.30 mL; 95% CI, -49.24 to 21.36 mL) (P = 0.00001) in the patients underwent thyroidectomy with UAS. Although the analysis showed that the patients who were treated with USA presented more favourable results in incidence of post-operative complications (transient laryngeal nerve palsy: P = 0.11; permanent laryngeal nerve palsy: not estimable; transient hypocalcaemia: P = 0.24; permanent hypocalcaemia: P = 0.45), these data didn't present statistical relevance.</p> <p>Conclusion</p> <p>This meta-analysis shown a relevant advantage only in terms of cost-effectiveness in patients treated with UAS; it is subsequent to statistically significant reduction of operation duration, intraoperative blood loss and of overall drainage volume during the first 24 hours. Although the analysis showed that the patients who were treated with UAS presented more favourable results in incidence of post-operative complications (transiet laryngeal nerve palsy; transiet hypocalcaemia and permanent hypocalcaemia), these data didn't present statistical relevance.</p

Global monitoring data shows grain size controls turbidity current structure

The first detailed measurements from active turbidity currents have been made in the last few years, at multiple sites worldwide. These data allow us to investigate the factors that control the structure of these flows. By analyzing the temporal evolution of the maximum velocity of turbidity currents at different sites, we aim to understand whether there are distinct types of flow, or if a continuum exists between end-members; and to investigate the physical controls on the different types of observed flow. Our results show that the evolution of the maximum velocity of turbidity currents falls between two end-members. Either the events show a rapid peak in velocity followed by an exponential decay or, flows continue at a plateau-like, near constant velocity. Our analysis suggests that rather than triggers or system input type, flow structure is primarily governed by the grain size of the sediment available for incorporation into the flow

Efficacy of a new technique - INtubate-RECruit-SURfactant-Extubate - "IN-REC-SUR-E" - in preterm neonates with respiratory distress syndrome: Study protocol for a randomized controlled trial

Background: Although beneficial in clinical practice, the INtubate-SURfactant-Extubate (IN-SUR-E) method is not successful in all preterm neonates with respiratory distress syndrome, with a reported failure rate ranging from 19 to 69&nbsp;%. One of the possible mechanisms responsible for the unsuccessful IN-SUR-E method, requiring subsequent re-intubation and mechanical ventilation, is the inability of the preterm lung to achieve and maintain an "optimal" functional residual capacity. The importance of lung recruitment before surfactant administration has been demonstrated in animal studies showing that recruitment leads to a more homogeneous surfactant distribution within the lungs. Therefore, the aim of this study is to compare the application of a recruitment maneuver using the high-frequency oscillatory ventilation (HFOV) modality just before the surfactant administration followed by rapid extubation (INtubate-RECruit-SURfactant-Extubate: IN-REC-SUR-E) with IN-SUR-E alone in spontaneously breathing preterm infants requiring nasal continuous positive airway pressure (nCPAP) as initial respiratory support and reaching pre-defined CPAP failure criteria. Methods/design: In this study, 206 spontaneously breathing infants born at 24+0-27+6 weeks' gestation and failing nCPAP during the first 24&nbsp;h of life, will be randomized to receive an HFOV recruitment maneuver (IN-REC-SUR-E) or no recruitment maneuver (IN-SUR-E) just prior to surfactant administration followed by prompt extubation. The primary outcome is the need for mechanical ventilation within the first 3&nbsp;days of life. Infants in both groups will be considered to have reached the primary outcome when they are not extubated within 30&nbsp;min after surfactant administration or when they meet the nCPAP failure criteria after extubation. Discussion: From all available data no definitive evidence exists about a positive effect of recruitment before surfactant instillation, but a rationale exists for testing the following hypothesis: a lung recruitment maneuver performed with a step-by-step Continuous Distending Pressure increase during High-Frequency Oscillatory Ventilation (and not with a sustained inflation) could have a positive effects in terms of improved surfactant distribution and consequent its major efficacy in preterm newborns with respiratory distress syndrome. This represents our challenge. Trial registration: ClinicalTrials.gov identifier: NCT02482766. Registered on 1 June 2015

Pediatric Pulmonology Year in Review 2014: Part 2

Our discipline and our journal cover an extremely broad range of research and scholarly topics related to children’s respiratory disorders. To better meet the needs of our readership for updated perspectives on the rapidly expanding knowledge in our field, we will summarize the past year’s publications in our major topic areas, as well as selected publications in these areas from the core clinical journal literature outside our own pages. A previous review (Part 1) summarized papers published in 2014 relevant to asthma, diagnostic testing/endoscopy, sleep and breathing disorders, respiratory complications of neuromuscular disorders, and rare lung diseases. The current review covers articles on neonatal lung disease, pulmonary physiology, and respiratory infection

Workflow tools for biological applications

When identifying best practices for multistep processes involving data analysis, it is fre- quently the case that the data scientist is asked to wear many hats simultaneouly: developer, programmer, statistician, graphic designer, writer, administrator. Although many scientists address these roles with great success, it is often at the expense of reproducibility, scalability, and organizational knowledge. The process of formalizing each step of the process creates op- portunity to apply lessons learned and proven tools from multiple disciplines to optimize each step of the transformation from raw data to usable output. This modular approach allows organizations to mix off the shelf technical solutions with custom, swap out components for flexibility and minimize rework. The primary focus of this dissertation is to extend the conceptualization of pipeline to include methods drawn from human computer interaction, exploratory data analysis, interactive graphics, and reproducible research. We describe application to three distinct user groups: (1) a general audience of readers (2) biologists involved in metabolomics analysis (3) analysts working in a public sector regulatory environment. The resulting technical tools are implemented in the R packages ggparallel, chromatoplotsGUI, dataFormats, and CVBreports. Our analysis shows that these tools facilitate a positive transformative effect on the quality of communication between stakeholders. Specifically we see that the common angles plot pre- sented in ggparallel reduces the lie factor, chromatoplotsGUI enables display of metabolomic data rapidly and with a level of detail that facilitates development of the underlying analysis en- gine and the methods of dataFormats and CVBreports enable significantly reduced turnaround times for preliminary data assesment.</p

L’AGOASPIRATO DELLA TIROIDE IN CASO DI TIREOPATIA UNI O PLURINODULARE CON FORMAZIONE MAGGIORE O UGUALE A 3 CM

La patologia nodulare tiroidea è estremamente comune ed il suo riscontro è aumentato negli ultimi anni. Attualmente il 4% della popolazione presenta noduli tiroidei clinicamente palpabili. Dalla revisione della letteratura internazionale si evince che la frequenza della patologia nodulare tiroidea cresce con l’avanzare dell’età con percentuali che si avvicinano al 50% in pazienti con età superiore ai 50 anni e ciò è confermato anche dagli studi autoptici(1,2,3,4,5). L’incidenza del tumore della tiroide è in generale bassa ma il suo riscontro è in aumento( 8,7 x 100000 nel 2002) (4). Parallelamente cresce anche il riscontro di lesioni neoplastiche centimetriche. L’utilizzo routinario dell’ecografia ad alta risoluzione in programmi di screening ha permesso di evidenziare anche quella quota di lesioni nodulari tiroidee non palpabili ed asintomatiche (1,2,6,9). Si può affermare che il diametro del nodulo da solo non è un indicatore indipendente di natura(10) ma il reperto di microcalcificazioni, ipoecogenicità, margini irregolari, predominanza della struttura solida, vascolarizzazione intranodale, avvalora il sospetto diagnostico di neoplasia tiroidea (19,22,26,30). Il gold standard per una corretta diagnosi è l’FNA ecoguidato che permettere di definire la cellularità di quei noduli che ecograficamente hanno caratteri di sospetto e che quindi ne indichino l’esecuzione. L’agoaspirato eco guidato è una metodica diagnostica efficiente ed attendibile che detiene una sensibilità diagnostica comprese tra l’89% e 98% e una specificità del 92%(11,13,18,21,28). L’utilizzo routinario dell’FNA permette una corretta diagnosi di natura delle lesioni nodulari tiroidee e ha ridotto la percentuale di interventi chirurgici privi di indicazione. Alcuni Autori (Pinchot, Meko and Norton, Carillo, McCoy) hanno evidenziato una limitazione dell’accuratezza diagnostica dell’agoaspirato nel caso di lesioni di diametro uguale o maggiore ai 3 cm, con percentuali di falsi negativi compresa tra il 13% e il 17% (12,13,15). Tale limitazione ha indotto gli stessi a definire il diametro nodulare uguale o maggiore a 4 cm come fattore indipendente nell’indicazione all’intervento di tiroidectomia (McCoy, Pinchot). D’altro canto Porterfield, Aschcraft and Van Herle and Grant hanno dimostrato una estrema accuratezza nella valutazione citologica delle lesioni nodulari di diametro maggiore o uguale a 3 cm non consigliando una resezione ai fini diagnostici (32,33,34). Considerando che il riscontro di patologia uni o plurinodulare con formazione maggiore di 4 o più cm rappresenta per la nostra scuola una indicazione assoluta alla tiroidectomia, abbiamo condotto uno studio retrospettivo nel quale sono stati inclusi i pazienti sottoposti ad FNA della lesione maggiore (diametro di 3 o più cm), il cui referto citologico aveva deposto per la benignità (THY2) e successivamente ad intervento chirurgico di tiroidectomia. Abbiamo quindi correlato la diagnosi citologica con la diagnosi istologica definitiva allo scopo di valutare l’incidenza dei falsi negativi nella nostra casistica

How do Prey Refuges Affect Predator-Prey Interactions?

While it is well known that predators eat their prey, prey that avoid predation risk can also incur substantial fitness costs through risk-induced changes in survival and reproduction, growth, and morphology. Changes in prey that occur without the predator physically consuming the prey are referred to as ‘non-consumptive effects’. One way to reduce the risk of predation is to use a refuge. While refuge use may reduce predation risk, however, it may also be costly to the prey. These costs may include within-refuge competition for resources, which can alter prey population dynamics, coexistence, and metapopulation dynamics. While these costs may be significant for the affected prey, no one has ever measured how much refuge-mediated avoidance of predation ‘costs’ in terms of prey growth. This experiment uses freshwater snails (Physa acuta) and crayfish (Cambarus bartonii bartonii) as the prey and predator, respectively. Previous research on this predator-prey pair found that the addition of either crayfish cues or crushed snails to snail-containing tanks changed the patterns of snail refuge use and growth, and that the snail responded differently to cues from different predator species. These studies and other demonstrate how complex non-consumptive effects can be, and illustrate the need for further research on how refuges factor into the model. To accomplish this goal, twenty-four ten-gallon tanks are set up to hold fifteen snails each. We cross two factors, predator present/absent with refuge present/absent, for a total of four treatments: predator present/refuge present, predator present/refuge absent, predator absent/refuge present, and predator absent/refuge absent. Each treatment is replicated six times (i.e., six tanks per treatment). The ‘predator present’ treatments have crayfish water and dead conspecifics added to the tanks weekly as a predation risk cue for the snails. Prior to the snails being placed in the tanks, each snail is measured for shell length, diameter, and thickness; the data is averaged on a per-tank basis for analysis. The experiment continues for three weeks. Whether the snails are present in a refuge or outside of the refuge is recorded twice a day. After three weeks, the snails are removed and the same size measurements as were previously taken are recorded. Through this experimental design this study aims to determine whether the presence or absence of a refuge affects how snails respond to cues from a crayfish predator and crushed conspecifics. This tests whether refuges impact the non-consumptive effects of the crayfish on snail growth and behavior, and increases our understanding of how prey use refuges, and how costly it is to use them