scholarly journals Functional synapse types via characterization of short-term synaptic plasticity

2019 ◽  
Author(s):  
Jung Hoon Lee ◽  
Luke Campagnola ◽  
Stephanie C. Seeman ◽  
Tim Jarsky ◽  
Stefan Mihalas
Keyword(s):  
Large Scale ◽  
Short Term ◽  
Brain Science ◽  
Short Term Plasticity ◽  
Synaptic Physiology ◽  
History Of ◽  
Experimental Protocols ◽  
Network Simulations ◽  
Underlying Mechanisms

AbstractThe strengths of synaptic connections dynamically change depending on the history of synaptic events, which is referred to as short-term plasticity (STP). While STP’s underlying mechanisms are well researched, its exact functions remain poorly understood. This is in part due to the diverse patterns of STP experimentally reported. Recently, the Allen Institute for Brain Science has launched the synaptic physiology pipeline to characterize the diverse properties of synapses. Since this pipeline generates a large-scale survey of synapses in mouse primary visual cortex using highly standardized experimental protocols, it provides a unique opportunity to study diverse patterns of STP. Here, we develop an end-to-end workflow that can characterize STP from the Allen Institute for Brain Science pipeline data and conduct network simulations to infer STP’s functions. Employing this workflow, we find 1) that diverse patterns of STP exist even in the same synapse classes and 2) that postsynaptic neurons’ responses have distinct characteristics depending on STP.

scholarly journals A model of order-selectivity based on dynamic changes in the balance of excitation and inhibition produced by short-term synaptic plasticity

2015 ◽  
Vol 113 (2) ◽  
pp. 509-523 ◽  
Author(s):  
Vishwa Goudar ◽  
Dean V. Buonomano
Keyword(s):  
Synaptic Plasticity ◽  
Computational Models ◽  
Experimental Studies ◽  
Inhibitory Synapses ◽  
Speech Discrimination ◽  
Short Term ◽  
Dynamic Changes ◽  
Short Term Plasticity ◽  
Underlying Mechanisms ◽  
Parametric Analyses

Determining the order of sensory events separated by a few hundred milliseconds is critical to many forms of sensory processing, including vocalization and speech discrimination. Although many experimental studies have recorded from auditory order-sensitive and order-selective neurons, the underlying mechanisms are poorly understood. Here we demonstrate that universal properties of cortical synapses—short-term synaptic plasticity of excitatory and inhibitory synapses—are well suited for the generation of order-selective neural responses. Using computational models of canonical disynaptic circuits, we show that the dynamic changes in the balance of excitation and inhibition imposed by short-term plasticity lead to the generation of order-selective responses. Parametric analyses predict that among the forms of short-term plasticity expressed at excitatory-to-excitatory, excitatory-to-inhibitory, and inhibitory-to-excitatory synapses, the single most important contributor to order-selectivity is the paired-pulse depression of inhibitory postsynaptic potentials (IPSPs). A topographic model of the auditory cortex that incorporates short-term plasticity accounts for both context-dependent suppression and enhancement in response to paired tones. Together these results provide a framework to account for an important computational problem based on ubiquitous synaptic properties that did not yet have a clearly established computational function. Additionally, these studies suggest that disynaptic circuits represent a fundamental computational unit that is capable of processing both spatial and temporal information.

scholarly journals Shedding new light on opsin evolution

2011 ◽  
Vol 279 (1726) ◽  
pp. 3-14 ◽  
Author(s):  
Megan L. Porter ◽  
Joseph R. Blasic ◽  
Michael J. Bok ◽  
Evan G. Cameron ◽  
Thomas Pringle ◽  
...  
Keyword(s):  
Evolutionary History ◽  
Large Scale ◽  
Current Model ◽  
Expression Patterns ◽  
Model Organisms ◽  
Biological Functions ◽  
Site Specific ◽  
History Of ◽  
Functional Features

Opsin proteins are essential molecules in mediating the ability of animals to detect and use light for diverse biological functions. Therefore, understanding the evolutionary history of opsins is key to understanding the evolution of light detection and photoreception in animals. As genomic data have appeared and rapidly expanded in quantity, it has become possible to analyse opsins that functionally and histologically are less well characterized, and thus to examine opsin evolution strictly from a genetic perspective. We have incorporated these new data into a large-scale, genome-based analysis of opsin evolution. We use an extensive phylogeny of currently known opsin sequence diversity as a foundation for examining the evolutionary distributions of key functional features within the opsin clade. This new analysis illustrates the lability of opsin protein-expression patterns, site-specific functionality (i.e. counterion position) and G-protein binding interactions. Further, it demonstrates the limitations of current model organisms, and highlights the need for further characterization of many of the opsin sequence groups with unknown function.

scholarly journals Virulence Characterization of Puccinia striiformis f. sp. tritici Using a New Set of Yr Single-Gene Line Differentials in the United States in 2010

Plant Disease ◽  
2014 ◽  
Vol 98 (11) ◽  
pp. 1534-1542 ◽  
Author(s):  
Anmin Wan ◽  
Xianming Chen
Keyword(s):  
United States ◽  
Stripe Rust ◽  
Large Scale ◽  
Puccinia Striiformis ◽  
Yellow Rust ◽  
Single Gene ◽  
The United States ◽  
The Past ◽  
History Of

Puccinia striiformis f. sp. tritici causes stripe rust (yellow rust) of wheat and is highly variable in virulence toward wheat with race-specific resistance. During 2010, wheat stripe rust was the most widespread in the recorded history of the United States, resulting in large-scale application of fungicides and substantial yield loss. A new differential set with 18 yellow rust (Yr) single-gene lines was established and used to differentiate races of P. striiformis f. sp. tritici, which were named as race PSTv in distinction from the PST races identified in the past. An octal system was used to describe the virulence and avirulence patterns of the PSTv races. From 348 viable P. striiformis f. sp. tritici isolates recovered from a total of 381 wheat and grass stripe rust samples collected in 24 states, 41 races, named PSTv-1 to PSTv-41, were identified using the new set of 18 Yr single-gene differentials, and their equivalent PST race names were determined on the previous set of 20 wheat cultivar differentials. The frequencies and distributions of the races and their virulences were determined. The five most predominant races were PSTv-37 (34.5%), PSTv-11 (17.5%), PSTv-14 (7.2%), PSTv-36 (5.2%), and PSTv-34 (4.9%). PSTv-37 was distributed throughout the country while PSTv-11 and PSTv-14 were almost restricted to states west of the Rocky Mountains. The races had virulence to 0 to 13 of the 18 Yr genes. Frequencies of virulences toward resistance genes Yr6, Yr7, Yr8, Yr9, Yr17, Yr27, Yr43, Yr44, YrTr1, and YrExp2 were high (67.0 to 93.7%); those to Yr1 (32.8%) and YrTye (31.3%) were moderate; and those to Yr10, Yr24, Yr32, and YrSP were low (3.4 to 5.7%). All of the isolates were avirulent to Yr5 and Yr15.

scholarly journals HISTORY OF THE CHANNEL SYSTEMS REORGANIZATION OF THE KAMA-KELTMA LOWLAND IN THE LATE PLEISTOCENE – HOLOCENE

2020 ◽  
pp. 6-17
Author(s):  
Nikolai N. Nazarov ◽  
◽  
Sergei V. Kopytov ◽  
Keyword(s):  
Late Pleistocene ◽  
Radiocarbon Dating ◽  
Large Scale ◽  
Bottom Relief ◽  
Short Term ◽  
Second Stage ◽  
The Third ◽  
Third Stage ◽  
History Of ◽  
Channel Systems

The analysis of the actual data on the age and stages of the channel systems formation in the Kama-Keltma lowland was based on the altitudinal differentiation of different stages of the relief and the results of radiocarbon dating of organics from the channel and floodplain facies. Late Pleistocene lake terrace is the highest level in the Upper Kama depression and Keltma hollow. The research into the geomorphological structure and age of deposited materials, with a particular focus on separate elements of the Kama-Keltma lowland erosive and accumulative relief, indicates the existence of six stages of the channel systems formation (reorganization). The first stage (end of the Kalinin stadial) is the Chepets hollow formation. The hollow was preserved after large-scale changes in the bottom relief of the Upper Kama depression. The second stage (Mologa-Sheksna interstadial) is the first Kama terrace formation. The third stage (Ostashkov stadial, 20-18 ka) is the period of the runoff hollow formation (including the ‘large terrace hollow’), which actively dissected the surface of aeolian landforms. The fourth stage (LGM, 18-10 ka) is the formation of the macromeanders of the South Keltma, Pilva, and Timsher, as well as the multi-arm channel of the Kama during alternating periods of relatively short-term warming and cooling. The fifth stage is the wide Kama floodplain formation in the Preboreal – Subboreal, represented by segmental generations. The sixth stage (modern) is characterized by the ‘straightening’ of the Kama channel – the formation of a relatively straight channel throughout the Kama-Keltma lowland.

scholarly journals Comprehensive Census and Complete Characterization of Nearby Debris Disk Stars

2015 ◽  
Vol 10 (S314) ◽  
pp. 179-182
Author(s):  
Tara H. Cotten ◽  
Inseok Song
Keyword(s):  
Large Scale ◽  
Complete Characterization ◽  
High Resolution Spectroscopy ◽  
Debris Disks ◽  
Infrared Excess ◽  
History Of ◽  
Debris Disk ◽  
Host Stars ◽  
Comprehensive Study

AbstractDebris disks are intimately linked to planetary system evolution since the rocky material surrounding the host stars is believed to be due to secondary generation from the collisions of planetesimals. With the conclusion and lack of future large scale infrared excess survey missions, it is time to summarize the history of using excess emission in the infrared as a tracer of debris and exploit all available data as well as provide a comprehensive study of the parameters of these important objects. We have compiled a catalog of infrared excess stars from peer-reviewed articles and performed an extensive search for new debris disks by cross-correlating the Tycho-2 and AllWISE catalogs. This study will conclude following the thorough examination of each debris disk star's parameters obtained through high-resolution spectroscopy at various facilities which is currently ongoing. We will maintain a webpage (www.debrisdisks.org) devoted to these infrared excess sources and provide various resources related to our catalog creation, SED fitting, and data reduction.

Fashion informatics and the network of fashion knockoffs

First Monday ◽  
2019 ◽  
Author(s):  
Lauren Copeland ◽  
Giovanni Luca Ciampaglia ◽  
Li Zhao
Keyword(s):  
Knowledge Discovery ◽  
Large Scale ◽  
Multimedia Data ◽  
Fashion Industry ◽  
Structure And Dynamics ◽  
Computer Scientists ◽  
History Of ◽  
Fashion Apparel ◽  
Use Of Knowledge

Knowledge discovery techniques have a long history of application to fields of practice such as marketing and business intelligence. Fashion and other manufacturing compartments have comparably enjoyed little attention from computer scientists. With the increasing availability of multimedia data from the Web and social media, our understanding of the fashion apparel industry could be significantly enhanced through the use of knowledge discovery methods and of large scale datasets obtained from places such as Twitter and Instagram. Here, we are interested in one of the issues at the center of the contemporary structure and dynamics of the fashion industry: the practice of knockoffs. We combine Web scraping and network science techniques to give a preliminary characterization of how brands knock designs off each other. Such a study could be one of the first examples of an emergent field, which we refer to and define as “fashion informatics.”

scholarly journals Reconstruction of ancient microbial genomes from the human gut

Nature ◽  
2021 ◽  
Author(s):  
Marsha C. Wibowo ◽  
Zhen Yang ◽  
Maxime Borry ◽  
Alexander Hübner ◽  
Kun D. Huang ◽  
...  
Keyword(s):  
Gut Microbiome ◽  
Large Scale ◽  
De Novo ◽  
Human Gut ◽  
Microbial Genomes ◽  
Functional Profiling ◽  
History Of ◽  
Southwestern Usa ◽  
Gut Microorganisms

AbstractLoss of gut microbial diversity1–6 in industrial populations is associated with chronic diseases7, underscoring the importance of studying our ancestral gut microbiome. However, relatively little is known about the composition of pre-industrial gut microbiomes. Here we performed a large-scale de novo assembly of microbial genomes from palaeofaeces. From eight authenticated human palaeofaeces samples (1,000–2,000 years old) with well-preserved DNA from southwestern USA and Mexico, we reconstructed 498 medium- and high-quality microbial genomes. Among the 181 genomes with the strongest evidence of being ancient and of human gut origin, 39% represent previously undescribed species-level genome bins. Tip dating suggests an approximate diversification timeline for the key human symbiont Methanobrevibacter smithii. In comparison to 789 present-day human gut microbiome samples from eight countries, the palaeofaeces samples are more similar to non-industrialized than industrialized human gut microbiomes. Functional profiling of the palaeofaeces samples reveals a markedly lower abundance of antibiotic-resistance and mucin-degrading genes, as well as enrichment of mobile genetic elements relative to industrial gut microbiomes. This study facilitates the discovery and characterization of previously undescribed gut microorganisms from ancient microbiomes and the investigation of the evolutionary history of the human gut microbiota through genome reconstruction from palaeofaeces.

scholarly journals Progress in managing the transition from the RS92 to the Vaisala RS41 as the operational radiosonde within the GCOS Reference Upper-Air Network

2019 ◽  
Author(s):  
Ruud J. Dirksen ◽  
Greg E. Bodeker ◽  
Peter W. Thorne ◽  
Andrea Merlone ◽  
Tony Reale ◽  
...  
Keyword(s):  
Measurement Errors ◽  
Large Scale ◽  
Integrated Approach ◽  
Burden Sharing ◽  
Ancillary Data ◽  
Laboratory Characterization ◽  
History Of ◽  
Large Scale Change

Abstract. This paper describes the GRUAN-wide approach to manage the transition from the Vaisala RS92 to the Vaisala RS41 as the operational radiosonde. The goal of the GCOS Reference Upper-Air Network (GRUAN) is to provide long-term high-quality reference observations of upper air Essential Climate Variables (ECVs) such as temperature and water vapor. With GRUAN data being used for climate monitoring, it is vital that the change of measurement system does not introduce inhomogeneities in to the data record. The majority of the 27 GRUAN sites were launching the RS92 as their operational radiosonde, and following the end of production of the RS92 in the last quarter of 2017, most of these sites have now switched to the RS41. Such a large-scale change in instrumentation is unprecedented in the history of GRUAN and poses a challenge for the network. Several measurement programmes have been initiated to characterize differences in biases, uncertainties and noise between the two radiosonde types. These include laboratory characterization of measurement errors, extensive twin sounding studies with RS92 and RS41 on the same balloon, and comparison with ancillary data. This integrated approach is commensurate with the GRUAN principles of traceability and deliberate redundancy. A two-year period of regular twin soundings is recommended, and for sites that are not able to implement this burden sharing is employed, such that measurements at a certain site are considered representative of other sites with similar climatological characteristics. All data relevant to the RS92-RS41 transition are archived in a database that will be accessible to the scientific community for external scrutiny. Furthermore, the knowledge and experience gained about GRUAN's RS92-RS41 transition will be extensively documented to ensure traceability of the process. This documentation will benefit other networks in managing changes in their operational radiosonde systems. Preliminary analysis of the laboratory experiments indicates that the manufacturer's calibration of the RS41's temperature and humidity sensors is more accurate than for the RS92; with uncertainties of

scholarly journals Towards biologically constrained attractor models of schizophrenia

2021 ◽  
Author(s):  
Heike Stein ◽  
Joao Barbosa ◽  
Albert Compte
Keyword(s):  
Working Memory ◽  
Synaptic Transmission ◽  
Firing Rate ◽  
Experimental Evidence ◽  
Cognitive Deficits ◽  
Critical Points ◽  
Network Models ◽  
Short Term ◽  
Short Term Plasticity ◽  
Network Simulations

Alterations in neuromodulation or synaptic transmission in biophysical attractor network models, as proposed by the dominant dopaminergic and glutamatergic theories of schizophrenia, successfully mimic working memory (WM) deficits in people with schizophrenia (PSZ). Yet, multiple, often opposing circuit mechanisms can lead to the same behavioral patterns in these network models. Here, we critically revise the computational and experimental literature that links NMDAR hypofunction to WM precision loss in PSZ. We show in network simulations that currently available experimental evidence cannot set apart competing mechanistic accounts, and critical points to resolve are firing rate tuning and shared noise modulations by E/I ratio alterations through NMDAR blockade, and possible concomitant deficits in short-term plasticity. We argue that these concerted experimental and computational efforts will lead to a better understanding of the neurobiology underlying cognitive deficits in PSZ.

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