Intelligent modelling of bioprocesses: A comparison of structured and unstructured approaches

This contribution moves in the direction of answering some general questions about the most effective and useful ways of modelling bioprocesses. We investigate the characteristics of models that are good at extrapolating. We trained 3 fully predictive models with different representational structures (diff eqns, inheritance of rates, network of reactions) on Saccharopolyspora erythraea shake flask fermentation data using genetic programming. The models were then tested on unseen data outside the range of the training data and the resulting performances compared. It was found that constrained models with mathematical forms analogous to internal mass balancing and stoichiometric were superior to flexible unconstrained models even though no A priori knowledge of this fermentation was used

Take only photographs, leave only footprints: novel applications of non-invasive survey methods for rapid detection of small, arboreal animals

This is the final version of the article. Available from the publisher via the DOI in this record.The development of appropriate wildlife survey techniques is essential to promote effective and efficient monitoring of species of conservation concern. Here, we demonstrate the utility of two rapid-assessment, non-invasive methods to detect the presence of elusive, small, arboreal animals. We use the hazel dormouse, Muscardinus avellanarius, a rodent of conservation concern, as our focal species. Prevailing hazel dormouse survey methods are prolonged (often taking months to years to detect dormice), dependent on season and habitat, and/or have low detection rates. Alternatives would be of great use to ecologists who undertake dormouse surveys, especially those assessing the need for mitigation measures, as legally required for building development projects. Camera traps and footprint tracking are well-established tools for monitoring elusive large terrestrial mammals, but are rarely used for small species such as rodents, or in arboreal habitats. In trials of these adapted methods, hazel dormice visited bait stations and were successfully detected by both camera traps and tracking equipment at each of two woodland study sites, within days to weeks of installation. Camera trap images and footprints were of adequate quality to allow discrimination between two sympatric small mammal species (hazel dormouse and wood mouse, Apodemus sylvaticus). We discuss the relative merits of these methods with respect to research aims, funds, time available and habitat.The work in this study was undertaken as part of a self-funded PhD and the authors have no support or funding to report for the work outlined in this manuscript

Axial and transverse deep‐water sediment supply to syn‐rift fault terraces: insights from the West Xylokastro Fault Block, Gulf of Corinth, Greece

Deep‐water syn‐rift systems develop in partially‐ or transiently‐linked depocentres to form complicated depositional architectures, which are characterised by short transport distances, coarse grain sizes, and a wide range of sedimentary processes. Exhumed systems that can help to constrain the tectono‐stratigraphic evolution of such systems are rare or complicated by inversion tectonics. Here, we document a mid‐Pleistocene deep‐water syn‐rift system fed by Gilbert‐type fan deltas in the hangingwall of a rift margin fault bounding the West Xylokastro Horst block, on the southern margin of the Gulf of Corinth, Greece. Structural and stratigraphic mapping combined with digital outcrop models permit observations along this syn‐rift depositional system from hinterland source to deep‐water sink. The West Xylokastro Fault hangingwall is filled by two distinct sediment systems; an axial system fed by coarse‐grained sediment gravity flows derived from fault‐tip Gilbert‐type fan deltas and a lateral system dominated by mass transport deposits fed from an evolving fault‐scarp apron. Abrupt changes in stratigraphic architecture across the axial system are interpreted to record changes in relative base level, sediment supply and tectonics. Locally, depositional topography and intra‐basinal structures controlled sediment dispersal patterns, from bed‐scale infilling of local rugose topography above mass transport complexes, to basin‐scale confinement from the fault scarp apron. These acted to generate a temporally and spatially variable, heterogeneous stratigraphic architecture throughout the basin‐fill. The transition of the locus of sedimentation from a rift margin to a fault terrace through the syn‐sedimentary growth of a basinward fault produced regressive surfaces updip, which manifest themselves as channels in the deep‐water realm and acted to prograde the system. We present a new conceptual model that recognises coeval axial and transverse systems based on the stratigraphic architecture around the West Xylokastro fault block that emphasises the lateral and vertical heterogeneity of rift basin‐fills with multiple entry points

Distribution and habitat use of a cryptic small cetacean, the Burmeister's porpoise, monitored from a small-scale fishery platform

This is the final version. Available from Frontiers Media via the DOI in this record. There is widespread evidence that small-scale fisheries (SSF) bycatch threatens many populations of small cetaceans, yet conservation efforts are often limited by a lack of basic knowledge regarding their abundance, distribution, and habitat use. Here, we used passive acoustic monitoring from an SSF platform-of-opportunity to better characterize the distribution and habitat use of small cetaceans in northern Peru, focussing on the little-known Burmeister's porpoise Phocoena spinipinnis. From 2009 to 2012, acoustic click detectors (C-PODs) were attached to fishing nets for the duration of 116 fishing sets (30 fishing trips). Dolphins (unspecified delphinids) and porpoises were recorded around 71 and 22% of fishing sets, respectively. The probability of occurrence and buzzing behavior (a proxy for foraging), and time spent, were linked to both static and dynamic environmental variables to examine the drivers of habitat use. Dolphin activity was spread evenly throughout the fishing area and was not linked to any habitat variables. In contrast, porpoises were detected in neritic waters, and habitat models performed well, identifying preferences for shallow (< 200 m depth) and cooler (17-18°C) waters, close (< 50 km) to shore. The high bycatch rate of small cetaceans in Peruvian SSF gave us the unique opportunity to investigate the link between bycatch and cetacean activity around vessels. We found a positive relationship between the likelihood of a bycatch event and acoustic presence for both dolphins and porpoises, however as we did not know the timing of entanglement, we could not link vocalization rates to mortality events. Nonetheless, as small cetaceans (particularly dolphins) frequently encounter fishing boats, the likelihood of entanglements may be reduced through effective efforts to alert animals to the presence of the net, either acoustically (using acoustic alarms) or visually. This study demonstrates that passive acoustic monitoring from a fisheries platform can provide insights into the distribution and habitat use of small cetaceans at relatively low cost, and is likely to be suitable in regions with low monitoring effort and high fishing pressure.Natural Environment Research CouncilEuropean UnionDarwin Initiativ

Quantifying faulting and base level controls on syn-rift sedimentation using stratigraphic architectures of coeval, adjacent Early-Middle Pleistocene fan deltas in Lake Corinth, Greece

Quantification of allogenic controls in rift basin‐fills requires analysis of multiple depositional systems because of marked along‐strike changes in depositional architecture. Here, we compare two coeval Early‐Middle Pleistocene syn‐rift fan deltas that sit 6 km apart in the hangingwall of the Pirgaki‐Mamoussia Fault, along the southern margin of the Gulf of Corinth, Greece. The Selinous fan delta is located near the fault tip and the Kerinitis fan delta towards the fault centre. Selinous and Kerinitis have comparable overall aggradational stacking patterns. Selinous comprises 15 cyclic stratal units (ca. 25 m thick), whereas at Kerinitis 11 (ca. 60 m thick) are present. Eight facies associations are identified. Fluvial and shallow water facies dominate the major stratal units in the topset region, with shelfal fine‐grained facies constituting ca. 2 m thick intervals between major topset units and thick conglomeratic foresets building down‐dip. It is possible to quantify delta build times (Selinous: 615 kyr; Kerinitis: >450 kyr) and average subsidence and equivalent sedimentation rates (Selinous: 0.65 m/kyr; Kerinitis: >1.77 m/kyr). The presence of sequence boundaries at Selinous, but their absence at Kerinitis, enables sensitivity analysis of the most uncertain variables using a numerical model, ‘Syn‐Strat’, supported by an independent unit thickness extrapolation method. Our study has three broad outcomes: (a) the first estimate of lake level change amplitude in Lake Corinth for the Early‐Middle Pleistocene (10–15 m), which can aid regional palaeoclimate studies and inform broader climate‐system models; (b) demonstration of two complementary methods to quantify faulting and base level signals in the stratigraphic record—forward modelling with Syn‐Strat and a unit thickness extrapolation—which can be applied to other rift basin‐fills; and (c) a quantitative approach to the analysis of stacking patterns and key surfaces that could be applied to stratigraphic pinch‐out assessment and cross‐hole correlations in reservoir analysis

Big catch, little sharks: Insight into Peruvian small-scale longline fisheries.

PublishedJournal ArticleThis is the final version of the article. Available from Wiley Open Access via the DOI in this record.Shark take, driven by vast demand for meat and fins, is increasing. We set out to gain insights into the impact of small-scale longline fisheries in Peru. Onboard observers were used to document catch from 145 longline fishing trips (1668 fishing days) originating from Ilo, southern Peru. Fishing effort is divided into two seasons: targeting dolphinfish (Coryphaena hippurus; December to February) and sharks (March to November). A total of 16,610 sharks were observed caught, with 11,166 identified to species level. Of these, 70.6% were blue sharks (Prionace glauca), 28.4% short-fin mako sharks (Isurus oxyrinchus), and 1% were other species (including thresher (Alopias vulpinus), hammerhead (Sphyrna zygaena), porbeagle (Lamnus nasus), and other Carcharhinidae species (Carcharhinus brachyurus, Carcharhinus falciformis, Galeorhinus galeus). Mean ± SD catch per unit effort of 33.6 ± 10.9 sharks per 1000 hooks was calculated for the shark season and 1.9 ± 3.1 sharks per 1000 hooks were caught in the dolphinfish season. An average of 83.7% of sharks caught (74.7% blue sharks; 93.3% mako sharks) were deemed sexually immature and under the legal minimum landing size, which for species exhibiting k-selected life history traits can result in susceptibility to over exploitation. As these growing fisheries operate along the entire Peruvian coast and may catch millions of sharks per annum, we conclude that their continued expansion, along with ineffective legislative approaches resulting in removal of immature individuals, has the potential to threaten the sustainability of the fishery, its target species, and ecosystem. There is a need for additional monitoring and research to inform novel management strategies for sharks while maintaining fisher livelihoods.We would like to thank the members of the fishing communities who participated in this study, in particular the fishers who were willing to have an observer onboard. We acknowledge Pro Delphinus staff: Bernedo, Cuentas, Lopez, and Mamani, for their help in data collection. We are thankful also to Pro Delphinus staff Natalia Ortiz and Nadia Balducci for support in data entry. This study was conducted in conjunction with and funded by the Darwin Initiative Sustainable Artisanal Fisheries Initiative in Peru and an initial grant from the Oak Foundation through Duke University. MJW was funded by PRIMaRE. JAS and JCM received support from ORSAS and University of Exeter, respectively

Detecting green shoots of recovery: The importance of long-term individual-based monitoring of marine turtles

This is the author accepted manuscript. The final version is available from Wiley via the DOI in this recordPopulation monitoring is an essential part of evaluating the effectiveness of management interventions for conservation. Coastal breeding aggregations of marine vertebrate species that come ashore to pup or nest provide an opportunistic window of observation into otherwise widely dispersed populations. Green turtle (Chelonia mydas) nesting on the north and west coasts of northern Cyprus has been monitored consistently and exhaustively since 1993, with an intensive saturation tagging programme running at one key site for the same duration. This historically depleted nesting population is showing signs of recovery, possibly in response to nest protection approaching two decades, with increasing nest numbers and rising levels of recruitment. Strong correlation between year-to-year magnitude of nesting and the proportion of new breeders in the nesting cohort implies that recruitment of new individuals to the breeding population is an important driver of this recovery trend. Recent changes in fishing activities may be impacting the local juvenile neritic stage, however, which may hinder this potential recovery. Individuals returning to breed after two years laid fewer clutches than those returning after three or four years, demonstrating a trade-off between remigration interval and breeding output. Average clutch frequencies have remained stable around a median of three clutches a year per female despite the demographic shift towards new nesters, which typically lay fewer clutches in their first season. We show that where local fecundity has been adequately assessed, the use of average clutch frequencies can be a reliable method for deriving nester abundance from nest counts. Index sites where individual-based monitoring is possible will be important in monitoring long-term climate driven changes in reproductive rates.European Social Fun

Spatial variability in depositional reservoir quality of deep-water channel-fill and lobe deposits

Initial porosity and permeability in deep-water systems are controlled by primary sedimentary texture and mineralogy. Therefore, understanding the sedimentary processes that control changes in primary texture is critical for improved reservoir quality predictions. A well-constrained, exhumed submarine lobe in the Jaca Basin, and a submarine channel-fill element in the Aínsa Basin, northern Spain, were studied to characterize the depositional reservoir quality in axial to marginal/fringe positions. Construction of architectural panels and strategic sampling enabled analysis of the spatial changes in textural properties, and their relationship to reservoir quality distribution. Samples were analyzed in thin-section to establish how depositional processes inferred from outcrop observations affect textural properties. Results show that high-density turbidites are concentrated in lobe- and channel-axis positions and exhibit good depositional reservoir quality. Lobe off-axis deposits contain high- and low-density turbidites and have moderate depositional reservoir quality. Conversely, low-density turbidites dominate lobe fringe and channel-margin positions and have relatively poor depositional reservoir quality. There is a sharp decrease in depositional reservoir quality between the lobe off-axis and lobe fringe due to: 1) an abrupt increase in matrix content; 2) an abrupt decrease in sandstone amalgamation; and 3) a decrease in grain-size. There is an abrupt increase in depositional reservoir quality from channel margin to channel axis corresponding to: 1) an increase in total sandstone thickness and amalgamation; 2) an increase in grain-size, 3) a decrease in matrix content. Rates of change of key properties are up to two orders of magnitude greater between channel-fill sub-environments compared to lobe sub-environments. Spatial variability in properties of discrete architectural elements, and rates of changes, provides input to reservoir models during exploration, appraisal, and development phases of hydrocarbon fields

Ultrasonic partial glossectomy

This is an Open Access article distributed under the terms of the Creative Commons Attribution Licens

Resection of the liver for colorectal carcinoma metastases - A multi-institutional study of long-term survivors

In this review of a collected series of patients undergoing hepatic resection for colorectal metastases, 100 patients were found to have survived greater than five years from the time of resection. Of these 100 long-term survivors, 71 remain disease-free through the last follow-up, 19 recurred prior to five years, and ten recurred after five years. Patient characteristics that may have contributed to survival were examined. Procedures performed included five trisegmentectomies, 32 lobectomies, 16 left lateral segmentectomies, and 45 wedge resections. The margin of resection was recorded in 27 patients, one of whom had a positive margin, nine of whom had a less than or equal to 1-cm margin, and 17 of whom had a greater than 1-cm margin. Eighty-one patients had a solitary metastasis to the liver, 11 patients had two metastases, one patient had three metastases, and four patients had four metastases. Thirty patients had Stage C primary carcinoma, 40 had Stage B primary carcinoma, and one had Stage A primarycarcinoma. The disease-free interval from the time of colon resection to the time of liver resection was less than one year in 65 patients, and greater than one year in 34 patients. Three patients had bilobar metastases. Four of the patients had extrahepatic disease resected simultaneously with the liver resection. Though several contraindications to hepatic resection have been proposed in the past, five-year survival has been found in patients with extrahepatic disease resected simultaneously, patients with bilobar metastases, patients with multiple metastases, and patients with positive margins. Five-year disease-free survivors are also present in each of these subsets. It is concluded that five-year survival is possible in the presence of reported contraindications to resection, and therefore that the decision to resect the liver must be individualized. © 1988 American Society of Colon and Rectal Surgeons