Many odontocetes produce frequency modulated tonal calls known as whistles. The ability to automatically determine time × frequency tracks corresponding to these vocalizations has numerous applications including species description, identification, and density estimation. This work develops and compares two algorithms on a common corpus of nearly one hour of data collected in the Southern California Bight and at Palmyra Atoll. The corpus contains over 3000 whistles from bottlenose dolphins, long- and short-beaked common dolphins, spinner dolphins, and melon-headed whales that have been annotated by a human, and released to the Moby Sound archive. Both algorithms use a common signal processing front end to determine time × frequency peaks from a spectrogram. In the first method, a particle filter performs Bayesian filtering, estimating the contour from the noisy spectral peaks. The second method uses an adaptive polynomial prediction to connect peaks into a graph, merging graphs when they cross. Whistle contours are extracted from graphs using information from both sides of crossings. The particle filter was able to retrieve 71.5% (recall) of the human annotated tonals with 60.8% of the detections being valid (precision). The graph algorithm's recall rate was 80.0% with a precision of 76.9%.

The NIH Common Fund Stimulating Peripheral Activity to Relieve Conditions (SPARC) initiative is a large-scale program that seeks to accelerate the development of therapeutic devices that modulate electrical activity in nerves to improve organ function. Integral to the SPARC program are the rich anatomical and functional datasets produced by investigators across the SPARC consortium that provide key details about organ-specific circuitry, including structural and functional connectivity, mapping of cell types and molecular profiling. These datasets are provided to the research community through an open data platform, the SPARC Portal. To ensure SPARC datasets are Findable, Accessible, Interoperable and Reusable (FAIR), they are all submitted to the SPARC portal following a standard scheme established by the SPARC Curation Team, called the SPARC Data Structure (SDS). Inspired by the Brain Imaging Data Structure (BIDS), the SDS has been designed to capture the large variety of data generated by SPARC investigators who are coming from all fields of biomedical research. Here we present the rationale and design of the SDS, including a description of the SPARC curation process and the automated tools for complying with the SDS, including the SDS validator and Software to Organize Data Automatically (SODA) for SPARC. The objective is to provide detailed guidelines for anyone desiring to comply with the SDS. Since the SDS are suitable for any type of biomedical research data, it can be adopted by any group desiring to follow the FAIR data principles for managing their data, even outside of the SPARC consortium. Finally, this manuscript provides a foundational framework that can be used by any organization desiring to either adapt the SDS to suit the specific needs of their data or simply desiring to design their own FAIR data sharing scheme from scratch.

Air-grown cells of the marine diatom Phaeodactylum tricornutum showed only 10% of the carbonic-anhydrase activity of air-grown Chlamydomonas reinhardtii. Measurement of carbonic-anhydrase activity using intact cells and cell extracts showed all activity was intracellular in Phaeodactylum. Photosynthetic oxygen evolution at constant inorganic-carbon concentration but varying pH showed that exogenous CO2 was poorly utilized by the cells. Sodium ions increased the affinity of Phaeodactylum for HCO 3 (-) and even at high HCO 3 (-) concentrations sodium ions enhanced HCO 3 (-) utilization. The internal inorganic-carbon pool (HCO 3 (-) +CO2] was measured using a silicone-oil-layer centrifugal filtering technique. The internal [HCO 3 (-) +CO2] concentration never exceeded 15% of the external [HCO 3 (-) +CO2] concentration even at the lowest external concentrations tested. It is concluded that an internal accumulation of inorganic carbon relative to the external medium does not occur in P. tricornutum.

Air-grown cells of Porphyridium purpurem contain appreciable carbonic-anhydrase activity, comparable to that in air-grown Chlamydomonas reinhardtii, but activity is repressed in CO2-grown cells. Assay of carbonic-anhydrase activity in intact cells and cell extracts shows all activity to be intracellular in Porphyridium. Measurement of inorganic-carbon-dependent photosynthetic O2 evolution shows that sodium ions increase the affinity of Porphyridium cells for HCO 3 (-) . Acetazolamide and ethoxyzolamide were potent inhibitors of carbonic anhydrase in cell extracts but at pH 5.0 both acetazolamide and ethoxyzolamide had little effect upon the concentration of inorganic carbon required for the half-maximal rate of photosynthetic O2 evolution (K0.5[CO2]). At pH 8.0, where HCO 3 (-) is the predominant species of inorganic carbon, the K0.5 (CO2) was increased from 50 μM to 950 μM in the presence of ethoxyzolamide. It is concluded that in air-grown cells of Porphyridium. HCO 3 (-) is transported across the plasmalemma and intracellular carbonic anhydrase increases the steady-state flux of CO2 from inside the plasmalemma to ribulose-1,5-bisphosphate carboxylase-oxygenase by catalysing the interconversion of HCO 3 (-) and CO2 within the cell.

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