Spike sorting for large, dense electrode arrays

Developments in microfabrication technology have enabled the production of neural electrode arrays with hundreds of closely spaced recording sites, and electrodes with thousands of sites are under development. These probes in principle allow the simultaneous recording of very large numbers of neurons. However, use of this technology requires the development of techniques for decoding the spike times of the recorded neurons from the raw data captured from the probes. Here we present a set of tools to solve this problem, implemented in a suite of practical, user-friendly, open-source software. We validate these methods on data from the cortex, hippocampus and thalamus of rat, mouse, macaque and marmoset, demonstrating error rates as low as 5%

A fixed-target platform for serial femtosecond crystallography in a hydrated environment.

For serial femtosecond crystallography at X-ray free-electron lasers, which entails collection of single-pulse diffraction patterns from a constantly refreshed supply of microcrystalline sample, delivery of the sample into the X-ray beam path while maintaining low background remains a technical challenge for some experiments, especially where this methodology is applied to relatively low-ordered samples or those difficult to purify and crystallize in large quantities. This work demonstrates a scheme to encapsulate biological samples using polymer thin films and graphene to maintain sample hydration in vacuum conditions. The encapsulated sample is delivered into the X-ray beam on fixed targets for rapid scanning using the Roadrunner fixed-target system towards a long-term goal of low-background measurements on weakly diffracting samples. As a proof of principle, we used microcrystals of the 24 kDa rapid encystment protein (REP24) to provide a benchmark for polymer/graphene sandwich performance. The REP24 microcrystal unit cell obtained from our sandwiched in-vacuum sample was consistent with previously established unit-cell parameters and with those measured by us without encapsulation in humidified helium, indicating that the platform is robust against evaporative losses. While significant scattering from water was observed because of the sample-deposition method, the polymer/graphene sandwich itself was shown to contribute minimally to background scattering

The Impatient May Use Limited Optimism to Minimize Regret

Discounted-sum games provide a formal model for the study of reinforcement learning, where the agent is enticed to get rewards early since later rewards are discounted. When the agent interacts with the environment, she may regret her actions, realizing that a previous choice was suboptimal given the behavior of the environment. The main contribution of this paper is a PSPACE algorithm for computing the minimum possible regret of a given game. To this end, several results of independent interest are shown. (1) We identify a class of regret-minimizing and admissible strategies that first assume that the environment is collaborating, then assume it is adversarial---the precise timing of the switch is key here. (2) Disregarding the computational cost of numerical analysis, we provide an NP algorithm that checks that the regret entailed by a given time-switching strategy exceeds a given value. (3) We show that determining whether a strategy minimizes regret is decidable in PSPACE

Investigating the linkage between mesopic spatial summation and variations in retinal ganglion cell density across the central visual field

PURPOSE: The relationship between perimetric stimulus area and Ricco's area (RA) determines measured thresholds and the sensitivity of perimetry to retinal disease. The nature of this relationship, in addition to effect of retinal ganglion cell (RGC) number on this, is currently unknown for the adaptation conditions of mesopic microperimetry. In this study, achromatic mesopic spatial summation was measured across the central visual field to estimate RA with the number of RGCs underlying RA also being established. METHODS: Achromatic luminance thresholds were measured for six incremental spot stimuli (0.009-2.07 deg2 ) and 190.4 ms duration, at four locations, each at 2.5°, 5° and 10° eccentricity in five healthy observers (mean age 61.4 years) under mesopic conditions (background 1.58 cd/m2 ). RA was estimated using two-phase regression analysis with the number of RGCs underlying RA being calculated using normative histological RGC counts. RESULTS: Ricco's area exhibited a small but statistically insignificant increase between 2.5° and 10° eccentricity. Compared with photopic conditions, RA was larger, with the difference between RA and the Goldmann III stimulus (0.43°) being minimised. RGC number underlying RA was also higher than reported for photopic conditions (median 70 cells, IQR 36-93), with no significant difference being observed across test locations. CONCLUSIONS: Ricco's area and the number of RGCs underlying RA do not vary significantly across the central visual field in mesopic conditions. However, RA is larger and more similar to the standard perimetric Goldmann III stimulus under mesopic compared with photopic adaptation conditions. Further work is required to determine if compensatory enlargements in RA occur in age-related macular degeneration, to establish the optimal stimulus parameters for AMD-specific microperimetry

Culture clash: Appearance concerns in black and minority ethnic groups

Around the world, men and women of all cultures and ethnicities are being exposed to Western appearance ideals. Paired with a lack of representation of black and minority ethnic (BME) men and women in the mainstream media, the public's appreciation of ethnic diversity is being threatened. Nicola Stock examines the growing trend of appearance-altering practice among those from BME communities

Pedogenic pathways and deep weathering controls on soil organic carbon in Pacific Northwest forest soils

Characterizing the distribution and dynamics of organic carbon in soil is critical for quantifying changes in the global carbon cycle. In particular, weathering controls on near-surface and deep (>1 m) soil organic carbon (SOC) dynamics have been proposed but limited data prevents us from predicting SOC over topographically complex landscapes and quantifying how changes in climate and perturbations, such as wildfire or land management, influence SOC stocks. To advance our understanding of how weathering alters soil geochemistry and influences SOC storage, we synthesize previous data with a new analysis of the Siuslaw River soil chronosequence from terraces in the Oregon Coast Range, a region that harbors the richest SOC inventories in the continental US. We analyze how the relationships between soil geochemistry, physical properties, and SOC storage vary with weathering status and pathways across soils that span 0.041 to 990 kyr and vary in depth from 1 m to >10 m. To distinguish the key properties and processes influencing SOC storage at different depths, we break our analysis into three depth intervals: 0–30, 30–100, and >100 cm. Our results suggest that the processes that control SOC stocks vary systematically with time and depth owing to weathering impacts on soil properties and pedogenic development. At 30 kyr we observe a peak in SOC stock in the top 100 cm coincident with a peak in oxalate extractable Al and Fe concentrations, representing secondary poorly crystalline minerals, which is consistent with previous studies. We also observe a decline in shallow SOC stock for >30 kyr soils as poorly crystalline minerals are replaced by more stable crystalline forms and soils become clay dominated. At 120 kyr, SOC below 100 cm starts to contribute significantly to the total SOC profile inventory and by 990 kyr, this fraction composes >40% of the total SOC stock. Taken together, our results indicate that total SOC stock increases with soil age as the increased intensity of bedrock weathering deepens the critical zone, creating accommodation space for deep SOC storage. These findings reveal the intimate link between poorly crystalline minerals and SOC and suggest that systematic analysis of soil development in the critical zone provides a first-order constraint on SOC stocks

Choice biases in no-sample and delay testing in pigeons (Columba livia)

In experimental tasks that involve stimuli that vary along a quantitative continuum, some choice biases are commonly found. Take, for instance, a matching-to-sample task where animals must, following the presentation of sample stimuli (that differ in duration), choose between two or more comparison stimuli. In tests where no sample is presented there is usually a bias towards the comparison that is correct following the shortest sample. To examine some aspects of these choice biases, pigeons were trained in a symbolic matching-to-sample task with two durations of keylight as samples, where key pecking had to be maintained during sample presentation. Firstly, even though animals were required to attend to the sample, a preference for the "short" comparison in no-sample testing was found. This result disproves an account where this effect was hypothesized to happen due to non-programmed learning resulting from the animals failing to attend to some trials. Secondly, even though a bias for "short" was found in both no-sample and delay testing, the extent of the biases differed between tasks, thus suggesting that forgetting the sample presented during a delay does not necessarily land the animal in a state similar to presenting no sample at all to begin with.The present study was supported by the Portuguese Foundation for Science and Technology and the Portuguese Ministry of Science, Technology and Higher Education through national funds. It was also co-financed by the European Regional Development Fund (FEDER)-through COMPETE2020-under the PT2020 Partnership Agreement (POCI-01-0145-FEDER-007653)

Biodiversity Loss and the Taxonomic Bottleneck: Emerging Biodiversity Science

Human domination of the Earth has resulted in dramatic changes to global and local patterns of biodiversity. Biodiversity is critical to human sustainability because it drives the ecosystem services that provide the core of our life-support system. As we, the human species, are the primary factor leading to the decline in biodiversity, we need detailed information about the biodiversity and species composition of specific locations in order to understand how different species contribute to ecosystem services and how humans can sustainably conserve and manage biodiversity. Taxonomy and ecology, two fundamental sciences that generate the knowledge about biodiversity, are associated with a number of limitations that prevent them from providing the information needed to fully understand the relevance of biodiversity in its entirety for human sustainability: (1) biodiversity conservation strategies that tend to be overly focused on research and policy on a global scale with little impact on local biodiversity; (2) the small knowledge base of extant global biodiversity; (3) a lack of much-needed site-specific data on the species composition of communities in human-dominated landscapes, which hinders ecosystem management and biodiversity conservation; (4) biodiversity studies with a lack of taxonomic precision; (5) a lack of taxonomic expertise and trained taxonomists; (6) a taxonomic bottleneck in biodiversity inventory and assessment; and (7) neglect of taxonomic resources and a lack of taxonomic service infrastructure for biodiversity science. These limitations are directly related to contemporary trends in research, conservation strategies, environmental stewardship, environmental education, sustainable development, and local site-specific conservation. Today’s biological knowledge is built on the known global biodiversity, which represents barely 20% of what is currently extant (commonly accepted estimate of 10 million species) on planet Earth. Much remains unexplored and unknown, particularly in hotspots regions of Africa, South Eastern Asia, and South and Central America, including many developing or underdeveloped countries, where localized biodiversity is scarcely studied or described. ‘‘Backyard biodiversity’’, defined as local biodiversity near human habitation, refers to the natural resources and capital for ecosystem services at the grassroots level, which urgently needs to be explored, documented, and conserved as it is the backbone of sustainable economic development in these countries. Beginning with early identification and documentation of local flora and fauna, taxonomy has documented global biodiversity and natural history based on the collection of ‘‘backyard biodiversity’’ specimens worldwide. However, this branch of science suffered a continuous decline in the latter half of the twentieth century, and has now reached a point of potential demise. At present there are very few professional taxonomists and trained local parataxonomists worldwide, while the need for, and demands on, taxonomic services by conservation and resource management communities are rapidly increasing. Systematic collections, the material basis of biodiversity information, have been neglected and abandoned, particularly at institutions of higher learning. Considering the rapid increase in the human population and urbanization, human sustainability requires new conceptual and practical approaches to refocusing and energizing the study of the biodiversity that is the core of natural resources for sustainable development and biotic capital for sustaining our life-support system. In this paper we aim to document and extrapolate the essence of biodiversity, discuss the state and nature of taxonomic demise, the trends of recent biodiversity studies, and suggest reasonable approaches to a biodiversity science to facilitate the expansion of global biodiversity knowledge and to create useful data on backyard biodiversity worldwide towards human sustainability