Conceptual-level workflow modeling of scientific experiments using NMR as a case study

Background  

Scientific workflows improve the process of scientific experiments by making computations explicit, underscoring data flow, and emphasizing the participation of humans in the process when intuition and human reasoning are required. Workflows for experiments also highlight transitions among experimental phases, allowing intermediate results to be verified and supporting the proper handling of semantic mismatches and different file formats among the various tools used in the scientific process. Thus, scientific workflows are important for the modeling and subsequent capture of bioinformatics-related data. While much research has been conducted on the implementation of scientific workflows, the initial process of actually designing and generating the workflow at the conceptual level has received little consideration.     

Sexual development of dairy bulls in the Mexican tropics

Sexual development and pubertal traits were studied in Holstein Frisian (Ho) and Brown Swiss (BS) bulls born and maintained under tropical conditions. Characteristics evaluated every 2 weeks, from 27 to 63 weeks of age, included live weight, scrotal circumference, testicular diameter, semen quality and sexual behavior. Puberty was defined as the age at which a bull first produced an ejaculate containing at least 50 x 106 spermatozoa, with a minimum of 10% progressive motility. Testicular growth was linear in Ho bulls and quadratic in BS bulls. There was no breed difference in age at puberty (Ho, 333 +/- 15.8 days; BS, 311 +/- 10.5 days). However, at puberty, live weight and scrotal circumference tended to be greater in Ho (276 +/- 16.9 kg and 28.4 +/- 1 cm, respectively) than in BS bulls (233 +/- 11.3 kg and 25.9 +/- 0.7 cm, respectively), and testicular diameter was larger for Ho (5.5 +/- 0.24 cm) than for BS bulls (4.8 +/- 0.16 cm). Pooled data for all bulls for semen characteristics at puberty were: volume, 6.3 +/- 0.6 ml; progressive motility, 26.8 +/- 4.4%; sperm concentration, 58.5 +/- 13.9 x 10(6) spermatozoa/ml, and 351.5 +/- 91.2 x 10(6) spermatozoa/ejaculate. These values improved until at least 18 weeks after puberty. Eighty-five percent of bulls mounted heifers by 206 days of age, but only a few bulls had mounts with ejaculation during the study. It was concluded that reproductive development was similar between Ho and BS bulls, but slower than that reported for dairy bulls in temperate areas. Variation in some characteristics, such as scrotal circumference, was observed among bulls within each breed group, which might be of benefit for genetic selection.     

Ammonia volatilization in a Mexican bat cave ecosystem

Direct measurements of gaseous ammonia in the atmosphere of a dry bat cave containing several million insectivorous bats revealed a peak concentration of 1779 ppm (0.96 mg/dm³). Observations indicate that the origin of the gaseous ammonia is rapid microbial decomposition of bat urea, not chitinous guano. Modelling of ammonia distribution and diffusion indicates that ammonia production at the Cueva del Tigre is 257 g NH₃/day, equivalent to the decomposition of 454 g urea/day. Ammonia production is also characterized by significant isotopic fractionation favoring isotopically light (¹⁵N depleted) ammonia.     

Hibernation in the tropics: lessons from a primate

The Malagasy primate Cheirogaleus medius hibernates in tree holes for 7 months, although ambient temperatures during hibernation rise above 30°C in their natural environment. In a field study we show that during hibernation the body temperature of most lemurs fluctuates between about 10°C and 30°C, closely tracking the diurnal fluctuations of ambient temperature passively. These lemurs do not interrupt hibernation by spontaneous arousals, previously thought to be obligatory for all mammalian hibernators. However, some lemurs hibernate in large trees, which provide better thermal insulation. Their body temperature fluctuates only little around 25°C, but they show regular arousals, as known from temperate and arctic hibernators. The results from this study demonstrate that maximum body temperature is a key factor necessitating the occurrence of arousals. Furthermore, we show that hibernation is not necessarily coupled to low body temperature and, therefore, low body temperature should no longer be included in the definition of hibernation.     

COVID-19 and “natural” experiments arising from physical distancing: a hypothetical case study from chronobiology

ABSTRACT

With countless “natural” experiments triggered by the COVID-19-associated physical distancing, one key question comes from chronobiology: “When confined to homes, how does the reduced exposure to natural daylight arising from the interruption of usual outdoor activities plus lost temporal organization ordinarily provided from workplaces and schools affect the circadian timing system (the internal 24 h clock) and, consequently, health of children and adults of all ages?” Herein, we discuss some ethical and scientific facets of exploring such natural experiments by offering a hypothetical case study of circadian biology.     

Dendrochronology in the dry tropics: the Ethiopian case

Dendrochronology is developing outside temperate and boreal regions. Over the past decade substantial progress has been made in Mediterranean and wet tropical regions. However, research in dry tropical regions, notably those of sub-Saharan Africa, has remained fragmentary. Here, we try to identify the unique challenges and opportunities of dendrochronology in the dry tropics. First, we briefly review the status of dendrochronology outside temperate and boreal regions with an emphasis on sub-Saharan Africa. Subsequently, we focus upon one of those areas where dendrochronology in the dry tropics is at the forefront of scientific advance: Ethiopia. A detailed review of tree ring studies in the lowlands and highlands highlights the complexity of ring formation and made us identify four major types of growth ring expression: anatomically not distinct rings, multiple rings per year, annual rings and multiple missing rings. This complex tree growth behaviour is associated with large-scale variations in precipitation regime (unimodal to multimodal) and relatively small-scale variations in tree sensitivity to water availability. Literature results are used to develop a scheme that can be used to predict differences in growth ring formation along gradients in these two factors. Because of the exceptional growth sensitivity of and the importance of local site conditions (topography, biological factors, etc.) for most trees sampled, those growing at the limits of their ecological amplitude are prone to possess multiple rings per year or multiple missing rings. In such circumstances, site selection should not always take place at the limits of the ecological amplitude of a species, but may sometimes have to be diverted to more mesic environments. Successful studies are now appearing, such as those reporting correlations between tree ring chronologies and Blue Nile river flows.     

A case study of a shared/buy-in computing ecosystem

Many research institutions are deploying computing clusters based on a shared/buy-in paradigm. Such clusters combine shared computers, which are free to be used by all users, and buy-in computers, which are computers purchased by users for semi-exclusive use. The purpose of this paper is to characterize the typical behavior and performance of a shared/buy-in computing cluster, using data traces from the Shared Computing Cluster (SCC) at Boston University that runs under this paradigm as a case study. Among our main findings, we show that the semi-exclusive policy, which allows any SCC user to use idle buy-in resources for a limited time, increases the utilization of buy-in resources by 17.4%, thus significantly improving the performance of the system as a whole. We find that jobs allowed to run on idle buy-in resources arrive more frequently and run for a shorter time than other jobs. Finally, we identify the run time limit (i.e., the maximum time during which a job is allowed to use resources) and the type of parallel environment as two factors that have a significant impact on the different performance experienced by shared and buy-in jobs.     

Approaches to assessing and managing cumulative ecosystem change,with the Bay of Quinte as a case study: an essay

Rising concern for the future of humans and the earth's ecosystems provides the backdrop for an essay on approaches to assessing and managing ecosystem health. A review and critique of two rival metaphors of human health, illness and wellness, provide the staring point for evaluation of parallel approaches to the assessment and management of ecosystems. The limitations of the metaphors are noted for humans and ecosystems. The impact assessment and ecosystem approach concepts of ecosystem assessment and management are contrasted. As a case history, the nature and pace of change in the Bay of Quinte ecosystem are reviewed, spanning from colonization by the Empire Loyalists at the end of the 18th century through the current development of a remedial action plan for the ecosystem. The review includes the long-term scientific study of the Bay's response to point-source phosphorus control (Project Quinte) and the recent efforts to develop and implement a coordinated clean-up program (Remedial Action Plan). From the lessons of the Quinte experience, a framework is derived, combining the illness and wellness approaches to health. The framework deals with five topics: uncertainty and the precautionary principle; an ecosystem health scale; indicators of ecosystem health; maximum allowable change; and, regulation and planning. Uncertainty should not be used to justify inaction. A precautionary principle assumes that impacts will occur and places the burden of proof on the proponents of ecosystem disturbance. An ecosystem health scale is defined using current, original, and potential conditions. Restoration to the original condition is unlikely but provides a justifiable direction for actions to establish sustainability. Indicators of ecosystem health with sustainable ranges are preferred over end-points and thresholds. The concept of maximum allowable change is promoted with a tentative suggestion that a fifty percent rule might be used. Finally, an argument for the combined use of regulation and planning. Regulatory approaches tend to perpetuate confrontation. Planning can be used to lengthen the time-horizon from quarterly reports to generations and identify self-regulating codes of behaviour. The framework is briefly discussed and placed in a broader context linking humans and ecosystem, illness and wellness.Based on the text of a talk presented at the Cumulative Impact Assessment Workshop held in Toronto, Ontario, December 1992, and sponsored by the North Central Division of the American Fisheries Society.     

Testing the island rule: primates as a case study

The island rule states that after island colonization, larger animals tend to evolve reduced body sizes and smaller animals increased sizes. Recently, there has been disagreement about how often, if ever, this rule applies in nature, and much of this disagreement stems from differences in the statistical tests employed. This study shows, how different tests of the island rule assume different null hypotheses, and that these rely on quite different biological assumptions. Analysis and simulation are then used to quantify the biases in the tests. Many widely used tests are shown to yield false support for the island rule when island and mainland evolution are indistinguishable, and so a Monte Carlo permutation test is introduced that avoids this problem. It is further shown that tests based on independent contrasts lack power to detect the island rule under certain conditions. Finally, a complete reanalysis is presented of recent data from primates. When head-body length is used as the measure of body size, reports of the island rule are shown to stem from methodological artefacts. But when skull length or body mass are used, all tests agree that the island rule does hold in primates.     

Serum monitoring of IgG and IgM Babesia bigemina (Haemosporidia: Babesiidae) antibodies in calves from the Mexican tropics

Antibody dynamics (IgG and IgM) against Babesia bigemina was studied on 41 under 15 days of age from three ranches (R1, R2 and R3) in Yucatan, Mexico. Blood samples were collected every 30 days, for eight months. Sera were tested by the indirect fluorescent antibody method to detect IgG and IgM. Overall IgM seroprevalence during the calves first eight months of life was 17.1% without relation to age. Overall IgG seroprevalence was 66.8%, increasing with age. Seroprevalence in R1, R2 and R3 were 87.5%, 77.1% and 31.8% respectively. Ranches 1 and 2 were in enzootic stability. In Yucatan, the modification of management factors in ranches with enzootic instability, could increase the risk of clinical babesiosis. Cattle mobilization from ranches with enzootic instability must be strictly controlled.     

Monitoring plant physiological characteristics to evaluate mine site revegetation: A case study from the wet-dry tropics of northern Australia

Biologically driven markers or monitors were used to evaluate plant and ecosystem health of uranium-mining affected sites. Plant water, nitrogen (N) and phosphorus (P) status were used to measure physiological characteristics of tree and shrub species at sites perturbed by mining activities (waste rock dumps: WRD 1, WRD 2; mine wastewater irrigated woodland) and of species at undisturbed woodland (tropical savanna). Plant water status was evaluated by measuring leaf relative water content (RWC) and carbon isotope discrimination (δ¹³C). Leaf RWC varied significantly (P<0.0001) between wet and dry season in species at the woodland sites with higher RWC in the wet season compared to the dry season. No seasonal differences were observed in RWC in species at the WRDs. Leaf δ¹³C was similar in species at woodland sites and WRD 2 (−28.8 to −28.1‰) but was significantly (P<0.05) lower in species at WRD 1 (−27.6‰). This suggests that species at WRD 1 had a lower water availability and/or lower water use compared to species at all other sites. WRD substrate had an up to 4-orders of magnitude greater availability of inorganic phosphate (Pi) compared to woodland soil as determined using in situ ion exchange resin. Pi concentrations in xylem sap of species at WRDs were 2- to 3-fold higher compared to species at woodland sites. Plant nitrate reductase (NR) activity was low in most species at woodland and WRD 1. In contrast, Eucalyptus and Acacia species had high NR activities of up to 300–700 pkat g^-1 fw at WRD 2 indicating that these species had greater nitrate use than species at all other sites. Nitrate availability in the top five cm of the profile, as determined using in situ ion exchange resins, increased at all sites in the wet season, but no significant differences were observed between sites using this method. However, traditional soil analysis revealed that WRD substrate had a 2-times higher nitrate content (0 to 1000 mm depth) compared to woodland soil. Thus, it is likely that plants at WRD2 accessed nitrate from deeper parts of the profile. Proline, an indicator of plant stress, was found in appreciable quantities in leaves of herbaceous species but not in woody species. Soil and leaf δ¹⁵N were measured to investigate N-cycling and the contribution of diazotrophic N₂ fixation to plant N nutrition. Soil δ¹⁵N values were highest and most variable at WRD 2 (6.2‰) compared to all other sites (irrigated woodland 3.1‰, undisturbed woodland 2.5‰, WRD 1 0.9‰). This may indicate that N-turnover and nitrification was greatest at WRD 2 leading to greater ¹⁵N enrichment of soil N. At all sites, Acacia species were nodulated and putatively fixing N₂. With the exception of WRD 2 where leaf δ¹⁵N of Acacia species averaged 0.9‰, Acacia species had ¹⁵N depleted values characteristic of species that receive N derived from N₂ fixation (−0.8 to −0.6‰). Eucalyptus species at the woodland also had ¹⁵N depleted values (average −0.4‰) but ¹⁵N enriched values (0.3 to 1.8‰) at the three mining affected sites. The results show that for the plants studied foliar δ¹⁵N could not be used as an unequivocal measure of plant N sources. The results suggest that biomonitoring of plant and ecosystem health has potential in evaluating performance of mine site revegetation. This revised version was published online in June 2006 with corrections to the Cover Date.     

Fish species richness evaluation in Mexican coastal lagoons: a case study in the Gulf of Mexico

We analyze the origin of knowledge about fish species richness in the Tuxpan-Tampamachoco estuarine system, in Veracuz, México. A complete inventory of the fish species known to date for this system (N = 179) was elaborated from published lists and from sampling seagrass meadows of Tampamachoco Lagoon, which yielded 14 previously unknown species. When compared, the different lists showed a low similarity that may reflect differences in sampling methods and collecting strategies. Current data suggest that fish species richness in Mexican coastal lagoons (Gulf of Mexico) is not related with lagoon surface area, as has been suggested, but with the number of inventories available for each lagoon, being these a reflection of the sampling effort. A sampling design for the assessment of fish species richness in estuarine systems should consider: a) using the highest possible variety of sampling fishing gears, b) collecting in all microhabitat types and c) the preference of bimonthly or quarterly samplings for two or more years over monthly samplings in a single year.     

Cultivable microscopic fungi from an underground chemosynthesis-based ecosystem: a preliminary study

Movile Cave, a unique groundwater ecosystem in southern Romania, was discovered in 1986. This chemoautotrophic cave contains an abundant and diverse fauna with terrestrial and aquatic invertebrate communities, including 33 endemic species. Since its discovery, studies have focused mainly on cave chemoautotrophic bacteria, while the microfungal community has been largely neglected. In this study, we determined the microfungal species living on various substrates in Movile Cave and compared this spectrum with the mycobiota detected outside the cave (outside air-borne and soil-borne microfungi). To investigate all of the niches, we collected samples for two consecutive years from the dry part of the cave (cave air and sediment, corroded limestone walls, isopod feces, and isopod and spider cadavers) and from the post-siphon part of the cave, i.e., Airbell II (sediment and floating microbial mat). A total of 123 microfungal species were identified from among several hundred isolates. Of these, 96 species were only detected in the cave environment and not outside of the cave, while 90 species were from the dry part of the cave and 28 were from Airbell II. The most diverse genera were Penicillium (at least 18 species) and Aspergillus (14 species), followed by Cladosporium (9 species). Surprisingly, high CFU counts of air-borne microfungi were found inside the cave; they were even higher than outside the cave during the first year of investigation.