Database resources of the National Center for Biotechnology Information.

The National Center for Biotechnology Information (NCBI) provides online information resources for biology, including the GenBank® nucleic acid sequence database and the PubMed® database of citations and abstracts published in life science journals. NCBI provides search and retrieval operations for most of these data from 35 distinct databases. The E-utilities serve as the programming interface for most of these databases. Resources receiving significant updates in the past year include PubMed, PMC, Bookshelf, SciENcv, the NIH Comparative Genomics Resource (CGR), NCBI Virus, SRA, RefSeq, foreign contamination screening tools, Taxonomy, iCn3D, ClinVar, GTR, MedGen, dbSNP, ALFA, ClinicalTrials.gov, Pathogen Detection, antimicrobial resistance resources, and PubChem. These resources can be accessed through the NCBI home page at https://www.ncbi.nlm.nih.gov.

Predicting Bordeaux red wine origins and vintages from raw gas chromatograms.

Connecting chemical properties to various wine characteristics is of great interest to the science of olfaction as well as the wine industry. We explored whether Bordeaux wine chemical identities and vintages (harvest year) can be inferred from a common and affordable chemical analysis, namely, a combination of gas chromatography (GC) and electron ionization mass spectrometry. Using 12 vintages (within the 1990-2007 range) from 7 estates of the Bordeaux region, we report that, remarkably, nonlinear dimensionality reduction techniques applied to raw gas chromatograms recover the geography of the Bordeaux region. Using machine learning, we found that we can not only recover the estate perfectly from gas chromatograms, but also the vintage with up to 50% accuracy. Interestingly, we observed that the entire chromatogram is informative with respect to geographic location and age, thus suggesting that the chemical identity of a wine is not defined by just a few molecules but is distributed over a large chemical spectrum. This study demonstrates the remarkable potential of GC analysis to explore fundamental questions about the origin and age of wine.

Markov blankets and Bayesian territories.

Bruineberg et al. argue that one ought not confuse the map (model) for the territory (reality) and delineate a distinction between innocuous Pearl blankets and metaphysically laden Friston blankets. I argue that all we have are models, all knowledge is conditional, and that if there is a Pearl/Friston distinction, it is a matter of the domain of application: latents or observations. This suggests that, if anything, Friston blankets may inherit philosophical significance previously assigned to observations.

Small All-Range Lidar for Asteroid and Comet Core Missions.

We report the development of a new type of space lidar specifically designed for missions to small planetary bodies for both topographic mapping and support of sample collection or landing. The instrument is designed to have a wide dynamic range with several operation modes for different mission phases. The laser transmitter consists of a fiber laser that is intensity modulated with a return-to-zero pseudo-noise (RZPN) code. The receiver detects the coded pulse-train by correlating the detected signal with the RZPN kernel. Unlike regular pseudo noise (PN) lidars, the RZPN kernel is set to zero outside laser firing windows, which removes most of the background noise over the receiver integration time. This technique enables the use of low peak-power but high pulse-rate lasers, such as fiber lasers, for long-distance ranging without aliasing. The laser power and the internal gain of the detector can both be adjusted to give a wide measurement dynamic range. The laser modulation code pattern can also be reconfigured in orbit to optimize measurements to different measurement environments. The receiver uses a multi-pixel linear mode photon-counting HgCdTe avalanche photodiode (APD) array with near quantum limited sensitivity at near to mid infrared wavelengths where many fiber lasers and diode lasers operate. The instrument is modular and versatile and can be built mostly with components developed by the optical communication industry.

Database resources of the National Center for Biotechnology Information.

The National Center for Biotechnology Information (NCBI) provides a large suite of online resources for biological information and data, including the GenBank® nucleic acid sequence database and the PubMed database of citations and abstracts published in life science journals. The Entrez system provides search and retrieval operations for most of these data from 35 distinct databases. The E-utilities serve as the programming interface for the Entrez system. Custom implementations of the BLAST program provide sequence-based searching of many specialized datasets. New resources released in the past year include a new PubMed interface, a sequence database search and a gene orthologs page. Additional resources that were updated in the past year include PMC, Bookshelf, My Bibliography, Assembly, RefSeq, viral genomes, the prokaryotic genome annotation pipeline, Genome Workbench, dbSNP, BLAST, Primer-BLAST, IgBLAST and PubChem. All of these resources can be accessed through the NCBI home page at www.ncbi.nlm.nih.gov.

Probabilistic inferential decision-making under time pressure in rhesus macaques (Macaca mulatta).

Decisions often involve the consideration of multiple cues, each of which may inform selection on the basis of learned probabilities. Our ability to use probabilistic inference for decisions is bounded by uncertainty and constraints such as time pressure. Previous work showed that when humans choose between visual objects in a multiple-cue, probabilistic task, they cope with time pressure by discounting the least informative cues, an example of satisficing or "good enough" decision-making. We tested two rhesus macaques (Macaca mulatta) on a similar task to assess their capacity for probabilistic inference and satisficing in comparison with humans. In each trial, a monkey viewed two compound stimuli consisting of four cue dimensions. Each dimension (e.g., color) had two possible states (e.g., red or blue) with different probabilistic weights. Selecting the stimulus with highest total weight yielded higher odds of receiving reward. Both monkeys learned the assigned weights at high accuracy. Under time pressure, both monkeys were less accurate as a result of decreased use of cue information. One monkey adopted the same satisficing strategy used by humans, ignoring the least informative cue dimension. Both monkeys, however, exhibited a strategy not reported for humans, a "group-the-best" strategy in which the top two cues were used similarly despite their different assigned weights. The results validate macaques as an animal model of probabilistic decision-making, establishing their capacity to discriminate between objects using at least four visual dimensions simultaneously. The time pressure data suggest caution, however, in using macaques as models of human satisficing. (PsycINFO Database Record (c) 2019 APA, all rights reserved).

Striatal fast-spiking interneurons selectively modulate circuit output and are required for habitual behavior.

Habit formation is a behavioral adaptation that automates routine actions. Habitual behavior correlates with broad reconfigurations of dorsolateral striatal (DLS) circuit properties that increase gain and shift pathway timing. The mechanism(s) for these circuit adaptations are unknown and could be responsible for habitual behavior. Here we find that a single class of interneuron, fast-spiking interneurons (FSIs), modulates all of these habit-predictive properties. Consistent with a role in habits, FSIs are more excitable in habitual mice compared to goal-directed and acute chemogenetic inhibition of FSIs in DLS prevents the expression of habitual lever pressing. In vivo recordings further reveal a previously unappreciated selective modulation of SPNs based on their firing patterns; FSIs inhibit most SPNs but paradoxically promote the activity of a subset displaying high fractions of gamma-frequency spiking. These results establish a microcircuit mechanism for habits and provide a new example of how interneurons mediate experience-dependent behavior.

A probabilistic approach to demixing odors.

The olfactory system faces a hard problem: on the basis of noisy information from olfactory receptor neurons (the neurons that transduce chemicals to neural activity), it must figure out which odors are present in the world. Odors almost never occur in isolation, and different odors excite overlapping populations of olfactory receptor neurons, so the central challenge of the olfactory system is to demix its input. Because of noise and the large number of possible odors, demixing is fundamentally a probabilistic inference task. We propose that the early olfactory system uses approximate Bayesian inference to solve it. The computations involve a dynamical loop between the olfactory bulb and the piriform cortex, with cortex explaining incoming activity from the olfactory receptor neurons in terms of a mixture of odors. The model is compatible with known anatomy and physiology, including pattern decorrelation, and it performs better than other models at demixing odors.