Miracle-dz/UniFAR-FTUs huggingface dataset:
Optical Quantal Analysis Using Ca2+ Indicators: A Robust Method for Assessing Transmitter Release Probability at Excitatory Synapses by Imaging Single Glutamate Release Events

Despite evidence that presynaptic efficacy and plasticity influence circuit function and behavior in vivo, studies of presynaptic function remain challenging owing to the difficulty of assessing transmitter release in intact tissue. Electrophysiological analyses of transmitter release are indirect and cannot readily resolve basic presynaptic parameters, most notably transmitter release probability (pr), at single synapses. These issues can be circumvented by optical quantal analysis, which uses the all-or-none optical detection of transmitter release in order to calculate pr. Over the past two decades, we and others have successfully demonstrated that Ca2+ indicators can be strategically implemented to perform optical quantal analysis at single glutamatergic synapses in ex vivo and in vitro preparations. We have found that high affinity Ca2+ indicators can reliably detect spine Ca2+ influx generated by single quanta of glutamate, thereby enabling precise calculation of pr at single synapses. Importantly, we have shown this method to be robust to changes in postsynaptic efficacy, and to be sensitive to activity-dependent presynaptic changes at central synapses following the induction of long-term potentiation (LTP) and long-term depression (LTD). In this report, we describe how to use Ca2+-sensitive dyes to perform optical quantal analysis at single synapses in hippocampal slice preparations. The general technique we describe here can be applied to other glutamatergic synapses and can be used with other reporters of glutamate release, including recently improved genetically encoded Ca2+ and glutamate sensors. With ongoing developments in imaging techniques and genetically encoded probes, optical quantal analysis is a promising strategy for assessing presynaptic function and plasticity in vivo.
Assistance Method for Merging by Increasing Clarity of Decision Making

Merging into the flow of high-speed traffic on roadways, such as expressways, is a demanding driving task for non-expert drivers. The difficulty of merging is thought to arise from the difficulty of judging the location where the drivers should merge. In this paper, we propose a mathematical model of driver decision-making that can predict the location where the driver will merge. In addition, we demonstrate that the entropy of the judgment introduced based on the proposed model has the ability to describe the differences in skills of judgment in merging position as well as the difficulty of decision-making in a given situation. Furthermore, we propose a driver assistance method to decrease the difficulty of decision-making with respect to the merging position during the preparation phase based on the proposed decision-making model when the difficulty is judged as being higher than a given threshold. The proposed method recommends acceleration or deceleration to increase the clarity of judgment. Driving simulator experiments demonstrate that the proposed method reduces the difficulty of decision-making for merging and increases the ease of judgment at the early stages of merging preparation. In addition, the proposed method decreases mental demand without leading to an increase in the overall workload, that is, the weighted workload of NASA-TLX.
Impact of Substance Use Disorder Pharmacotherapy on Executive Function: A Narrative Review

Substance use disorders are chronic, relapsing, and harmful conditions characterized by executive dysfunction. While there are currently no approved pharmacotherapy options for stimulant and cannabis use disorders, there are several evidence-based options available to help reduce symptoms during detoxification and aid long-term cessation for those with tobacco, alcohol and opioid use disorders. While these medication options have shown clinical efficacy, less is known regarding their potential to enhance executive function. This narrative review aims to provide a brief overview of research that has investigated whether commonly used pharmacotherapies for these substance use disorders (nicotine, bupropion, varenicline, disulfiram, acamprosate, nalmefene, naltrexone, methadone, buprenorphine, and lofexidine) effect three core executive function components (working memory, inhibitory control and cognitive flexibility). While pharmacotherapy-induced enhancement of executive function may improve cessation outcomes in dependent populations, there are limited and inconsistent findings regarding the effects of these medications on executive function. We discuss possible reasons for the mixed findings and suggest some future avenues of work that may enhance the understanding of addiction pharmacotherapy and cognitive training interventions and lead to improved patient outcomes.
Structure-Based Peptide Inhibitor Design of Amyloid-β Aggregation

Many human neurodegenerative diseases are associated with amyloid fibril formation. Inhibition of amyloid formation is of importance for therapeutics of the related diseases. However, the development of selective potent amyloid inhibitors remains challenging. Here based on the structures of amyloid β (Aβ) fibrils and their amyloid-forming segments, we designed a series of peptide inhibitors using RosettaDesign. We further utilized a chemical scaffold to constrain the designed peptides into β-strand conformation, which significantly improves the potency of the inhibitors against Aβ aggregation and toxicity. Furthermore, we show that by targeting different Aβ segments, the designed peptide inhibitors can selectively recognize different species of Aβ. Our study developed an approach that combines the structure-based rational design with chemical modification for the development of amyloid inhibitors, which could be applied to the development of therapeutics for different amyloid-related diseases.
GeoTxt: A scalable geoparsing system for unstructured text geolocation

In this article we present GeoTxt, a scalable geoparsing system for the recognition and geolocation of place names in unstructured text. GeoTxt offers six named entity recognition (NER) algorithms for place name recognition, and utilizes an enterprise search engine for the indexing, ranking, and retrieval of toponyms, enabling scalable geoparsing for streaming text. GeoTxt offers a flexible application programming interface (API), allowing for customized attribute and/or spatial ranking of retrieved toponyms. We evaluate the system on a corpus of manually geo‐annotated tweets. First, we benchmark the performance of the six NERs that GeoTxt provides access to. Second, we assess GeoTxt toponym resolution accuracy incrementally, demonstrating improvements in toponym resolution achieved (or not achieved) by adding specific heuristics and disambiguation methods. Compared to using the GeoNames web service, GeoTxt's toponym resolution demonstrates a 20% accuracy gain. Our results show that places mentioned in the same tweet do not tend to be geographically proximate.
Characterizing the Biology of Lytic Bacteriophage vB_EaeM_φEap-3 Infecting Multidrug-Resistant Enterobacter aerogenes

Carbapenem-resistant Enterobacter aerogenes strains are a major clinical problem because of the lack of effective alternative antibiotics. However, viruses that lyze bacteria, called bacteriophages, have potential therapeutic applications in the control of antibiotic-resistant bacteria. In the present study, a lytic bacteriophage specific for E. aerogenes isolates, designated vB_EaeM_φEap-3, was characterized. Based on transmission electron microscopy analysis, phage vB_EaeM_φEap-3 was classified as a member of the family Myoviridae (order, Caudovirales). Host range determination revealed that vB_EaeM_φEap-3 lyzed 18 of the 28 E. aerogenes strains tested, while a one-step growth curve showed a short latent period and a moderate burst size. The stability of vB_EaeM_φEap-3 at various temperatures and pH levels was also examined. Genomic sequencing and bioinformatics analysis revealed that vB_EaeM_φEap-3 has a 175,814-bp double-stranded DNA genome that does not contain any genes considered undesirable for the development of therapeutics (e.g., antibiotic resistance genes, toxin-encoding genes, integrase). The phage genome contained 278 putative protein-coding genes and one tRNA gene, tRNA-Met (AUG). Phylogenetic analysis based on large terminase subunit and major capsid protein sequences suggested that vB_EaeM_φEap-3 belongs to novel genus “Kp15 virus” within the T4-like virus subfamily. Based on host range, genomic, and physiological parameters, we propose that phage vB_EaeM_φEap-3 is a suitable candidate for phage therapy applications.
Little Evidence of Benthic Community Resilience to Bottom Trawling on Seamounts After 15 Years

The resilience and recovery dynamics of deep-sea habitats impacted by bottom trawling are poorly known. This paper reports on a fishing impact recovery comparison based on four towed camera surveys over a 15-year period (2001-2015) on a group of small seamounts on the Chatham Rise, east of New Zealand, on which pre-disturbance benthic communities are dominated by thicket-forming scleractinian corals. The six seamounts studied encompass a range of trawl histories, including one with high and persistent levels of trawling throughout the survey period, two with intermittent and intermediate levels of trawling, two which were low/untrawled, and one, ‘Morgue’, which was closed to trawling in 2001, having been heavily trawled up to that point. Still photographs from all surveys were analysed for the identification and abundance of all visible benthic fauna with effort made to ensure consistency of data among surveys. Because increases in image resolution and quality over time resulted in a persistent trend of increasing abundances, analyses were concentrated on comparisons among seamounts within surveys and how these relationships changed with time. The abundance, species richness, and diversity of benthic communities were higher on low/untrawled seamounts than on those that had been trawled. Multivariate community structure showed similar patterns at each survey point, the low/untrawled seamounts being strongly dissimilar to the persistently trawled seamount, with the others ranged between these extremes, broadly in accordance with their cumulative trawl histories. Community structure on the persistently trawled seamount was less variable than on the other seamounts throughout the study period, possibly because of regular ‘re-setting’ of the community by disturbance from trawling. Although there was some variability in results between whole seamount and summit sector analyses, in general communities on Morgue remained similar to those on the persistently trawled seamount, showing no indication of steps towards recovery to its pre-disturbance state following its closure. These results indicate low resilience of benthic communities on the seamounts to the effects of bottom trawling.
Polyamines and Gut Microbiota

The microbiota of gut is the community of microbes living in an individual’s gastrointestinal tract. Several bacterial genera and species act in a concerted manner to establish metabolic interactions with the host (1). Although there is a general high interest in the study of metabolite flow across the microbe-host, at present, only some studies are targeting specificmetabolites produced by intestinal microbiota such as polyamines (PAs) (2).
Inhibition of COX2/PGD2-Related Autophagy Is Involved in the Mechanism of Brain Injury in T2DM Rat

The present study was designed to observe the effect of COX2/PGD2-related autophagy on brain injury in type 2 diabetes rats. The histopathology was detected by haematoxylin–eosin staining. The learning and memory functions were evaluated by Morris water maze. The levels of insulin and PGD2 were measured by enzyme-linked immunosorbent assay. The expressions of COX2, p-AKT(S473), p-AMPK(T172), Aβ, Beclin1, LC3BII, and p62 were measured by immunohistochemistry and Western blotting. In model rats, we found that the body weight was significantly decreased, the blood glucose levels were significantly increased, the plasma insulin content was significantly decreased, the learning and memory functions were impaired and the cortex and hippocampus neurons showed significant nuclear pyknosis. The levels of COX2, p-AKT(S473), PGD2, Aβ, Beclin1 and p62 were significantly increased, whereas the expression of p-AMPK(T172) and LC3BII was significantly decreased in the cortex and hippocampus of model rats. In meloxicam-treated rats, the body weight, blood glucose and the content of plasma insulin did not significantly change, the learning and memory functions were improved and nuclear pyknosis was improved in the cortex and hippocampus neurons. The expression of p-AMPK(T172), Beclin1 and LC3BII was significantly increased, and the levels of COX2, p-AKT(S473), PGD2, Aβ, and p62 were significantly decreased in the cortex and hippocampus of meloxicam-treated rats. Our results suggested that the inhibition of COX2/PGD2-related autophagy was involved in the mechanism of brain injury caused by type 2 diabetes in rats.
Product-Form Solution for Cascade Networks With Intermittent Energy

The power needs of digital devices, their installation in locations where it is difficult to connect them to the power grid and the difficulty of frequently replacing batteries, create the need to operate digital systems with harvested energy. In such cases, local storage batteries must overcome the intermittent nature of the energy supply. System performance then depends on the intermittent energy supply, possible energy leakage, and system workload. Queueing networks with product-form solution (PFS) are standard tools for analyzing the performance of interconnected systems, and predicting relevant performance metrics including job queue lengths, throughput, and system turnaround times and delays. However, existing queueing network models assume unlimited energy availability, whereas intermittently harvested energy can affect system performance due to insufficient energy supply. Thus, this paper develops a new PFS for the joint probability distribution of energy availability, and job queue length for an N-node tandem system. Such models can represent production lines in manufacturing systems, supply chains, cascaded repeaters for optical links, or a data link with multiple input data ports that feeds into a switch or server. Our result enables the rigorous computation of the relevant performance metrics of such systems operating with intermittent energy.
Sexual Transcription Differences in Brachymeria lasus (Hymenoptera: Chalcididae), a Pupal Parasitoid Species of Lymantria dispar (Lepidoptera: Lymantriidae)

Sex differences in gene expression have been extensively documented, but little is known about these differences in parasitoid species that are widely applied to control pests. Brachymeria lasus is a solitary parasitoid species and has been evaluated as a potential candidate for release to control Lymantria dispar. In this study, gender differences in B. lasus were investigated using Illumina-based transcriptomic analysis. The resulting 37,453 unigene annotations provided a large amount of useful data for molecular studies of B. lasus. A total of 1416 differentially expressed genes were identified between females and males, and the majority of the sex-biased genes were female biased. Gene Ontology (GO) and Pathway enrichment analyses showed that (1) the functional categories DNA replication, fatty acid biosynthesis, and metabolism were enhanced in females and that (2) the only pathway enriched in males was phototransduction, while the GO subcategories enriched in males were those involved in membrane and ion transport. In addition, thirteen genes involving transient receptor potential (TRP) channels were annotated in B. lasus. We further explored and discussed the functions of TRPs in sensory signaling of light and temperature. In general, this study provides new molecular insights into the biological and sexually dimorphic traits of parasitoids, which may improve the application of these insects to the biological control of pests.
Identification of Bacterial Composition in Freeze-Dried Agaricus bisporus During Storage and the Resultant Odor Deterioration

Moisture absorption and bacterial growth are critical factors for quality deterioration of freeze-dried Agaricus bisporus. In order to explore the bacterial composition and the resultant odor changes in freeze-dried A. bisporus during storage under three typical conditions (RT: 25°C, 55% RH; HT: 37°C, 85% RH; AT: ambient temperature), bacterial diversity and communities were analyzed using metagenomics. Moreover, volatile compounds were determined using SPME-GC-MS. The results demonstrated that the bacterial composition in freeze-dried A. bisporus was dominated by Pseudomonas, followed by Rhizobium and Pedobacter. In addition, Mucilaginibacter, Flavobacterium, and Thermus were a few other genera more dominant in HT samples, Chryseobacterium was the other genera more dominant in AT samples, while, Sphingobacterium and Chryseobacterium were a few other genera more dominant in RT samples. Furthermore, the increase of benzaldehyde content in HT samples may have been induced by the growth of Pseudomonads and the esters production in RT and AT samples might have been induced by Chryseobacterium. This study provided comprehensive information on exogenous bacterial composition and the resultant odor in freeze-dried A. bisporus. These results may be a theoretical basis for quality control and quick quality detection based on volatiles of freeze-dried A. bisporus.
On Social-Aware Content Caching for D2D-Enabled Cellular Networks With Matching Theory

In this paper, the problem of content caching in 5G cellular networks relying on social-aware device-to-device communications (DTD) is investigated. Our focus is on how to efficiently select important users (IUs) and how to allocate content files to the storage of these selected IUs to form a distributed caching system. We aim at proposing a novel approach for minimizing the downloading latency and maximizing the social welfare simultaneously. In particular, we first model the problem of maximizing the social welfare as a many-to-one matching game based on the social property of mobile users. We study this game by exploiting users’ social properties to generate the utility functions of the two-side players, i.e., content providers (CPs) and IUs. Then we model the problem of minimizing the downloading latency as a many-to-many matching problem. For solving these games, we design a many-to-one IU selection (MOIS) matching algorithm and a many-to-many file allocation (MMFA) matching algorithm, respectively. Simulation and analytical results show that the proposed mechanisms are stable, and are capable of offering a better performance than other benchmarks in terms of social welfare and network downloading latency.
Is Classroom Noise Always Bad for Children? The Contribution of Age and Selective Attention to Creative Performance in Noise

Creativity is considered an important skill in learning but little is known about the environmental factors affecting it in classroom settings. Extending adult findings, this study assessed whether moderate multi-talker noise promotes children’s creativity, and whether this is modulated by children’s age, working memory, and selective attention. Forty-four elementary school children between 5 and 11 years of age, divided into younger and older age groups, participated in this within-subjects’ study. The children completed two idea generation tasks; each participant performed the task both in silence and in moderate (64 dB) classroom noise. Selective attention skills, verbal and visuospatial working memory were assessed with behavioral tasks. Results showed that there were no conditions in which classroom noise promoted children’s creativity whilst some negative effects of noise were observed. Younger children (between 5 and 8 years of age) with low selective attention skills were especially at risk: they gave fewer ideas in the presence of noise, and these ideas were rated as less original. Children with good selective attention skills were globally protected against the effects of noise, performing, similarly, in silence and noise. Future studies about children’s specific creative strategies might help shed light on the mechanisms underlying these effects.
Transcriptomic and Proteomic Analysis of Shaan2A Cytoplasmic Male Sterility and Its Maintainer Line in Brassica napus

Cytoplasmic male sterility (CMS) lines are widely used for hybrid production in Brassica napus. The Shaan2A CMS system is one of the most important in China and has been used for decades; however, the male sterility mechanism underlying Shaan2A CMS remains unknown. Here, we performed transcriptomic and proteomic analysis, combined with additional morphological observation, in the Shaan2A CMS. Sporogenous cells, endothecium, middle layer, and tapetum could not be clearly distinguished in Shaan2A anthers. Furthermore, Shaan2A anther chloroplasts contained fewer starch grains than those in Shaan2B (a near-isogenic line of Shaan2A), and the lamella structure of chloroplasts in Shaan2A anther wall cells was obviously aberrant. Transcriptomic analysis revealed differentially expressed genes (DEGs) mainly related to carbon metabolism, lipid and flavonoid metabolism, and the mitochondrial electron transport/ATP synthesis pathway. Proteomic results showed that differentially expressed proteins were mainly associated with carbohydrate metabolism, energy metabolism, and genetic information processing pathways. Importantly, nine gene ontology categories associated with anther and pollen development were enriched among down-regulated DEGs at the young bud (YB) stage, including microsporogenesis, sporopollenin biosynthetic process, and tapetal layer development. Additionally, 464 down-regulated transcription factor (TF) genes were identified at the YB stage, including some related to early anther differentiation such as SPOROCYTELESS (SPL, also named NOZZLE, NZZ), DYSFUNCTIONAL TAPETUM 1 (DYT1), MYB80 (formerly named MYB103), and ABORTED MICROSPORES (AMS). These results suggested that the sterility gene in the Shaan2A mitochondrion might suppress expression of these TF genes in the nucleus, affecting early anther development. Finally, we constructed an interaction network of candidate proteins based on integrative analysis. The present study provides new insights into the molecular mechanism of Shaan2A CMS in B. napus.