Streamlining Sound Speed Profile Pre-Processing: Case Studies and Field Trials

High rate sound speed profiling systems have the potential to maximize the efficiency of multibeam echosounder systems (MBES) by increasing the accuracy at the outer edges of the swath where refraction effects are at their worst. In some cases, high rate sampling on the order of tens of casts per hour is required to capture the spatio-temporal oceanographic variability and this increased sampling rate can challenge the data acquisition workflow if refraction corrections are to be applied in real-time. Common bottlenecks result from sound speed profile (SSP) preprocessing requirements, e.g. file format conversion, cast extension, reduction of the number of points in the cast, filtering, etc. Without the ability to quickly pre-process SSP data, the MBES operator can quickly become overwhelmed with SSP related tasks, potentially to the detriment of their other duties. A series of algorithms are proposed in which SSPs are automatically pre-processed to meet input criteria of MBES acquisition systems, specifically the problems of cast extrapolation and thinning are addressed. The algorithmic performance will be assessed in terms of sounding uncertainty through a series of case studies in a variety of oceanographic conditions and water depths. Results from a field trial in the French Mediterranean will be used to assess the improvement in real-time MBES acquisition workflow and survey accuracy and will also highlight where further improvements can be made in the pre-processing pipeline

The Mixed Marriages Act (1949) : a theological critique based on the investigation of legislative action and church responses to this legislation

Bibliography: pages 208-228.The thesis is concerned with the nature of the interaction between church and state, and more generally between politics and religion, in the matter of so-called mixed marriages, and more particularly the debate surrounding the South African Mixed Marriages Act of 1949. The methodology of the study is interdisciplinary, dealing in detail with historical material as a basis for theological reflection and analysis. In the first chapter, marriage is dealt with generally from a theological viewpoint. Various approaches to marriage are considered, such as those in African society, the Bible, and in the Catholic and Reformation traditions. In contrast with the fertility-lineage, group-oriented ethic detected in the early part of the Old Testament and in many preliterate and patriarchal societies, a personalist and essentially 'sacramental' model of marriage is developed on the basis of New Testament teaching and later Christian theological reflection. The effects of a fertility-lineage and group-oriented ethic of marriage in South Africa are demonstrated in chapter two, which deals with the drive for anti-miscegenation laws in that country, with special reference to the role of the Afrikaans Reformed churches in this regard. The third chapter takes up this historical material, examining the nature of the initial debate on the Mixed Marriages Act in 1949-1950 and the aims of the Nationalist Government in introducing this legislation. The contrasting responses to the Act on the part of the Afrikaans Reformed churches and the more 'liberal', non-racial, mainly English-speaking churches are also considered here. In the fourth chapter the developments in the debate surrounding the Act since 1949 are discussed, with special reference to key points in the changing attitudes of the churches (especially the Afrikaans Reformed churches) to this legislation. This provides the background to the heated debate since the mid-seventies, when the Government began to show apparent signs of favouring a reformulation of apartheid which purportedly aimed at eliminating the most obviously racially biased aspects of that policy. The final chapter examines the theological assumptions of Afrikaans Reformed thought, and attempts to show how its roots in a particular view of Calvinism, Kuyperian Neo-Calvinism and the Bible result in the kind of fertility-lineage ethic which makes support for the Act possible. An effort is made to show the theological inadequacies of this thought from a Christian perspective, and to suggest an alternative, more dynamic theology, which recognizes the importance of individual choice and human rights. The impediments to such a fundamental reorientation are recognised, however, and it is argued that any major changes in position on the miscegenation laws on the part of either reformist government politicians or the Afrikaans Reformed churches in the near future will face major resistance

Effect of an Herbal/Botanical Supplement on Strength, Balance, and Muscle Function Following 12-Weeks of Resistance Training: A Placebo Controlled Study

Background: StemSport (SS; StemTech International, Inc. San Clemente, CA) contains a proprietary blend of the botanical Aphanizomenon flos-aquae and several herbal antioxidant and anti-inflammatory substances. SS has been purported to accelerate tissue repair and restore muscle function following resistance exercise. Here, we examine the effects of SS supplementation on strength adaptations resulting from a 12-week resistance training program in healthy young adults. Methods: Twenty-four young adults (16 males, 8 females, mean age = 20.5 ± 1.9 years, mass = 70.9 ± 11.9 kg, stature = 176.6 ± 9.9 cm) completed the twelve week training program. The study design was a double-blind, placebo controlled parallel group trial. Subjects either received placebo or StemSport supplement (SS; mg/day) during the training. 1-RM bench press, 1-RM leg press, vertical jump height, balance (star excursion and center of mass excursion), isokinetic strength (elbow and knee flexion/extension) and perception of recovery were measured at baseline and following the 12-week training intervention. Results: Resistance training increased 1-RM strength (p \u3c 0.008), vertical jump height (p \u3c 0.03), and isokinetic strength (p \u3c 0.05) in both SS and placebo groups. No significant group-by-time interactions were observed (all p-values \u3e0.10). Conclusions: These data suggest that compared to placebo, the SS herbal/botanical supplement did not enhance training induced adaptations to strength, balance, and muscle function above strength training alone

Effect of an herbal/botanical supplement on strength, balance, and muscle function following 12-weeks of resistance training: a placebo controlled study

Background: StemSport (SS; StemTech International, Inc. San Clemente, CA) contains a proprietary blend of the botanical Aphanizomenon flos-aquae and several herbal antioxidant and anti-inflammatory substances. SS has been purported to accelerate tissue repair and restore muscle function following resistance exercise. Here, we examine the effects of SS supplementation on strength adaptations resulting from a 12-week resistance training program in healthy young adults. Methods: Twenty-four young adults (16 males, 8 females, mean age = 20.5 ± 1.9 years, mass = 70.9 ± 11.9 kg, stature = 176.6 ± 9.9 cm) completed the twelve week training program. The study design was a double-blind, placebo controlled parallel group trial. Subjects either received placebo or StemSport supplement (SS; mg/day) during the training. 1-RM bench press, 1-RM leg press, vertical jump height, balance (star excursion and center of mass excursion), isokinetic strength (elbow and knee flexion/extension) and perception of recovery were measured at baseline and following the 12-week training intervention. Results: Resistance training increased 1-RM strength (p \u3c 0.008), vertical jump height (p \u3c 0.03), and isokinetic strength (p \u3c 0.05) in both SS and placebo groups. No significant group-by-time interactions were observed (all p-values \u3e0.10). Conclusions: These data suggest that compared to placebo, the SS herbal/botanical supplement did not enhance training induced adaptations to strength, balance, and muscle function above strength training alone

Exploiting and assessing multi-source data for supervised biomedical named entity recognition

Motivation: Recognition of biomedical entities from scientific text is a critica l component of natural language processing and automated information extraction platfo rms. Modern named entity recognition approaches rely heavily on supervised machine learning tech niques, which are critically dependent on annotated training corpora. These approaches have been shown to perform well when trained and tested on the same source. However, in such scenario, the performance and evaluation of these models may be optimistic, as such models may not necessarily generalize to in dependent corpora, resulting in potential non-optimal entity recognition for large-scale tagging of widel y diverse articles in databases such as PubMed. Results: Here we aggregated published corpora for the recognition of bio molecular entities (such as genes, RNA, proteins, variants, drugs, and metabolites), identi fied entity class overlap and performed leave-corpus-out cross validation strategy to test the efficiency o f existing models. We demonstrate that accuracies of models trained on individual corpora decre ase substantially for recognition of the same biomolecular entity classes in independent corpora. Thi s behavior is possibly due to limited generalizability of entity-class-related features captured by i ndividual corpora (model “overtraining”) which we investigated further at the orthographic level, as well as potenti al annotation standard differences. We show that the combined use of multi-source training corpora re sults in overall more generalizable models for named entity recognition, while achieving comparab le individual performance. By performing learning-curve-based power analysis we further identified that performance is often not limited by the quantity of the annotated data

Application of a Mathematical Model to Describe the Effects of Chlorpyrifos on Caenorhabditis elegans Development

The nematode Caenorhabditis elegans is being assessed as an alternative model organism as part of an interagency effort to develop better means to test potentially toxic substances. As part of this effort, assays that use the COPAS Biosort flow sorting technology to record optical measurements (time of flight (TOF) and extinction (EXT)) of individual nematodes under various chemical exposure conditions are being developed. A mathematical model has been created that uses Biosort data to quantitatively and qualitatively describe C. elegans growth, and link changes in growth rates to biological events. Chlorpyrifos, an organophosphate pesticide known to cause developmental delays and malformations in mammals, was used as a model toxicant to test the applicability of the growth model for in vivo toxicological testing.L1 larval nematodes were exposed to a range of sub-lethal chlorpyrifos concentrations (0-75 microM) and measured every 12 h. In the absence of toxicant, C. elegans matured from L1s to gravid adults by 60 h. A mathematical model was used to estimate nematode size distributions at various times. Mathematical modeling of the distributions allowed the number of measured nematodes and log(EXT) and log(TOF) growth rates to be estimated. The model revealed three distinct growth phases. The points at which estimated growth rates changed (change points) were constant across the ten chlorpyrifos concentrations. Concentration response curves with respect to several model-estimated quantities (numbers of measured nematodes, mean log(TOF) and log(EXT), growth rates, and time to reach change points) showed a significant decrease in C. elegans growth with increasing chlorpyrifos concentration.Effects of chlorpyrifos on C. elegans growth and development were mathematically modeled. Statistical tests confirmed a significant concentration effect on several model endpoints. This confirmed that chlorpyrifos affects C. elegans development in a concentration dependent manner. The most noticeable effect on growth occurred during early larval stages: L2 and L3. This study supports the utility of the C. elegans growth assay and mathematical modeling in determining the effects of potentially toxic substances in an alternative model organism using high-throughput technologies

The evolutionary history of the stearoyl-CoA desaturase gene family in vertebrates

<p/> <p>Background</p> <p>Stearoyl-CoA desaturases (SCDs) are key enzymes involved in <it>de novo </it>monounsaturated fatty acid synthesis. They catalyze the desaturation of saturated fatty acyl-CoA substrates at the delta-9 position, generating essential components of phospholipids, triglycerides, cholesterol esters and wax esters. Despite being crucial for interpreting SCDs roles across species, the evolutionary history of the SCD gene family in vertebrates has yet to be elucidated, in particular their isoform diversity, origin and function. This work aims to contribute to this fundamental effort.</p> <p>Results</p> <p>We show here, through comparative genomics and phylogenetics that the SCD gene family underwent an unexpectedly complex history of duplication and loss events. Paralogy analysis hints that SCD1 and SCD5 genes emerged as part of the whole genome duplications (2R) that occurred at the stem of the vertebrate lineage. The SCD1 gene family expanded in rodents with the parallel loss of SCD5 in the Muridae family. The SCD1 gene expansion is also observed in the Lagomorpha although without the SCD5 loss. In the amphibian <it>Xenopus tropicalis </it>we find a single SCD1 gene but not SCD5, though this could be due to genome incompleteness. In the analysed teleost species no SCD5 is found, while the surrounding SCD5-less locus is conserved in comparison to tetrapods. In addition, the teleost SCD1 gene repertoire expanded to two copies as a result of the teleost specific genome duplication (3R). Finally, we describe clear orthologues of SCD1 and SCD5 in the chondrichthian, <it>Scyliorhinus canicula</it>, a representative of the oldest extant jawed vertebrate clade. Expression analysis in <it>S. canicula </it>shows that whilst SCD1 is ubiquitous, SCD5 is mainly expressed in the brain, a pattern which might indicate an evolutionary conserved function.</p> <p>Conclusion</p> <p>We conclude that the SCD1 and SCD5 genes emerged as part of the 2R genome duplications. We propose that the evolutionary conserved gene expression between distinct lineages underpins the importance of SCD activity in the brain (and probably the pancreas), in a yet to be defined role. We argue that an expression independent of an external stimulus, such as diet induced activity, emerged as a novel function in vertebrate ancestry allocated to the SCD5 isoform in various tissues (e.g. brain and pancreas), and it was selectively maintained throughout vertebrate evolution.</p

NeuroBench: Advancing Neuromorphic Computing through Collaborative, Fair and Representative Benchmarking

The field of neuromorphic computing holds great promise in terms of advancing computing efficiency and capabilities by following brain-inspired principles. However, the rich diversity of techniques employed in neuromorphic research has resulted in a lack of clear standards for benchmarking, hindering effective evaluation of the advantages and strengths of neuromorphic methods compared to traditional deep-learning-based methods. This paper presents a collaborative effort, bringing together members from academia and the industry, to define benchmarks for neuromorphic computing: NeuroBench. The goals of NeuroBench are to be a collaborative, fair, and representative benchmark suite developed by the community, for the community. In this paper, we discuss the challenges associated with benchmarking neuromorphic solutions, and outline the key features of NeuroBench. We believe that NeuroBench will be a significant step towards defining standards that can unify the goals of neuromorphic computing and drive its technological progress. Please visit neurobench.ai for the latest updates on the benchmark tasks and metrics