bluuebunny/crossref_metadata_2025_split huggingface dataset:
TweetyNet: A neural network that enables high-throughput, automated annotation of birdsong
Authors: Cohen Yarden , Nicholson David , Sanchioni Alexa , Mallaber Emily K. , Skidanova Viktoriya , Gardner Timothy J. 
Published: August 2020

AbstractSongbirds have long been studied as a model system of sensory-motor learning. Many analyses of birdsong require time-consuming manual annotation of the individual elements of song, known as syllables or notes. Here we describe the first automated algorithm for birdsong annotation that is applicable to complex song such as canary song. We developed a neural network architecture, “TweetyNet”, that is trained with a small amount of hand-labeled data using supervised learning methods. We first show TweetyNet achieves significantly lower error on Bengalese finch song than a similar method, using less training data, and maintains low error rates across days. Applied to canary song, TweetyNet achieves fully automated annotation of canary song, accurately capturing the complex statistical structure previously discovered in a manually annotated dataset. We conclude that TweetyNet will make it possible to ask a wide range of new questions focused on complex songs where manual annotation was impractical.
FRETboard: semi-supervised classification of fret traces
Authors: de Lannoy Carlos , Filius Mike , Kim Sung Hyun , Joo Chirlmin , de Ridder Dick 
Published: August 2020

AbstractFörster resonance energy transfer (FRET) is a useful phenomenon in biomolecular investigations, as it can be leveraged for nano-scale measurements. The optical signals produced by such experiments can be analyzed by fitting a statistical model. Several software tools exist to fit such models in an unsupervised manner, but their operating system-dependent installation requirements and lack of flexibility impede wide-spread adoption. Here we propose to fit such models more efficiently and intuitively by adopting a semi-supervised approach, in which the user interactively guides the model to fit a given dataset, and introduce FRETboard, a web tool that allows users to provide such guidance. We show that our approach is able to closely reproduce ground truth FRET statistics in a wide range of simulated single-molecule scenarios, and correctly estimate parameters for up to eleven states. Onin vitrodata we retrieve parameters identical to those obtained by laborious manual classification in a fraction of the required time. Moreover, we designed FRETboard to be easily extendable to other models, allowing it to adapt to future developments in FRET measurement and analysis.Availabilitysource code is available athttps://github.com/cvdelannoy/FRETboard. The FRETboard classification tool is also available as a browser application athttps://www.bioinformatics.nl/FRETboard.
PrkC modulates MreB filament density and cellular growth rate by monitoring cell wall precursors
Authors: Sun Yingjie , Garner Ethan 
Published: August 2020

AbstractHow bacteria link their rate of growth to the external nutrient conditions is not known. To explore howBacillus subtilismodulates the rate cells expand their encapsulating cell wall, we compared the single-cell growth rate to the density of moving MreB filaments under different conditions. MreB filament density scales with the growth rate, and is modulated by themurgenes that create the cell wall precursor lipid II. Lipid II is sensed by the serine/threonine kinase PrkC, which, among other proteins, phosphorylates RodZ. Phosphorylated RodZ then increases MreB filament density, increasing growth. Strikingly, increasing the activity of this pathway results in cells elongating far faster than wild type in nutrient-poor media, indicating slow-growing bacteria contain spare growth capacity. Overall, this work reveals that PrkC functions as a cellular rheostat, tuning the activities of cellular processes in response to lipid II, allowing cells to grow robustly across a broad range of nutrient conditions.One-sentence summaryThe serine/threonine kinase PrkC modulates both MreB filament density and cellular growth rate by sensing lipid II inBacillus subtilis.
A single immunization with spike-functionalized ferritin vaccines elicits neutralizing antibody responses against SARS-CoV-2 in mice
Authors: Powell Abigail E. , Zhang Kaiming , Sanyal Mrinmoy , Tang Shaogeng , Weidenbacher Payton A. , Li Shanshan , Pham Tho D. , Pak John E. , Chiu Wah , Kim Peter S. 
Published: August 2020

AbstractDevelopment of a safe and effective SARS-CoV-2 vaccine is a public health priority. We designed subunit vaccine candidates using self-assembling ferritin nanoparticles displaying one of two multimerized SARS-CoV-2 spikes: full-length ectodomain (S-Fer) or a C-terminal 70 amino-acid deletion (SΔC-Fer). Ferritin is an attractive nanoparticle platform for production of vaccines and ferritin-based vaccines have been investigated in humans in two separate clinical trials. We confirmed proper folding and antigenicity of spike on the surface of ferritin by cryo-EM and binding to conformation-specific monoclonal antibodies. After a single immunization of mice with either of the two spike ferritin particles, a lentiviral SARS-CoV-2 pseudovirus assay revealed mean neutralizing antibody titers at least 2-fold greater than those in convalescent plasma from COVID-19 patients. Additionally, a single dose of SΔC-Fer elicited significantly higher neutralizing responses as compared to immunization with the spike receptor binding domain (RBD) monomer or spike ectodomain trimer alone. After a second dose, mice immunized with SΔC-Fer exhibited higher neutralizing titers than all other groups. Taken together, these results demonstrate that multivalent presentation of SARS-CoV-2 spike on ferritin can notably enhance elicitation of neutralizing antibodies, thus constituting a viable strategy for single-dose vaccination against COVID-19.
ß2-Arrestin germline knockout does not attenuate opioid respiratory depression
Authors: Bachmutsky Iris , Durand Adelae , Yackle Kevin 
Published: August 2020

AbstractOpioids are perhaps the most effective analgesics in medicine. However, from 1999 to 2018, they also killed more than 400,000 people in the United States by suppressing breathing, a common side-effect known as opioid induced respiratory depression. This doubled-edged sword has inspired the dream of developing novel therapeutics that provide opioid-like analgesia without respiratory depression. One such approach has been to develop so-called ‘biased agonists’ that activate some, but not all pathways downstream of the µ-opioid receptor (MOR), the target of morphine and other opioid analgesics. This hypothesis stems from a study suggesting that MOR-mediated activation of ß2-Arrestin is the downstream signaling pathway responsible for respiratory depression, whereas inhibition of adenylyl cyclase produces analgesia. To further verify this model, which represents the motivation for the biased agonist approach, we examined respiratory behavior in mice lacking the gene for ß2-Arrestin. Contrary to previous findings, we find no correlation between ß2-Arrestin function and opioid-induced respiratory depression, suggesting that any effect of biased agonists must be mediated through an as-yet to be identified signaling mechanism.
The relationship between multisensory associative learning and multisensory integration
Authors: Lauzon Sébastien Á. , Abraham Arin. E. , Curcin Kristina , Stevenson Ryan A. 
Published: August 2020

AbstractOur perception of the world around us is inherently multisensory, and integrating sensory information from multiple modalities leads to more precise and efficient perception and behaviour. Determining which sensory information from different modalities should be perceptually bound is a key component of multisensory integration. To accomplish this feat, our sensory systems rely on both low-level stimulus features, as well as multisensory associations learned throughout development based on the statistics of our environment. The present study explored the relationship between multisensory associative learning and multisensory integration using encephalography (EEG) and behavioural measures. Sixty-one participants completed a three-phase study. First, participants were exposed to novel pairings audiovisual shape-tone pairings with frequent and infrequent stimulus pairings and complete a target detection task. EEG recordings of the mismatch negativity (MMN) and P3 were calculated as neural indices of multisensory associative learning. Next, the same learned stimulus pairs presented in audiovisual as well as unisensory auditory and visual modalities while both early (<120 ms) and late neural indices of multisensory integration were recorded. Finally, participants completed an analogous behavioural speeded-response task, with behavioural indices of multisensory gain calculated using the race model. Significant relationships were found in fronto-central and occipital areas between neural measures of associative learning and both early and late indices of multisensory integration in frontal and centro-parietal areas, respectively. Participants who showed stronger indices of associative learning also exhibited stronger indices of multisensory integration of the stimuli they learned to associate. Furthermore, a significant relationship was found between neural index of early multisensory integration and behavioural indices of multisensory gain. These results provide insight into the neural underpinnings of how higher-order processes such as associative learning guide multisensory integration.
Genome-wide analysis of in vivo CcpA binding with and without its key co-factor HPr in the major human pathogen group AStreptococcus
Authors: DebRoy Sruti , Tobar Victor Aliaga , Galvez Gabriel , Arora Srishtee , Liang Xiaowen , Horstmann Nicola , Maracaja-Coutinho Vinicius , Latorre Mauricio , Hook Magnus , Flores Anthony R. , Shelburne Samuel A. 
Published: August 2020

SummaryCatabolite control protein A (CcpA) is a master regulator of carbon source utilization and contributes to the virulence of numerous medically important Gram-positive bacteria. Most functional assessments of CcpA, including interaction with its key co-factor HPr, have been performed in non-pathogenic bacteria. In this study we aimed to identify the in vivo DNA binding profile of CcpA and assess the extent to which HPr is required for CcpA-mediated regulation and DNA binding in the major human pathogen group AStreptococcus(GAS). Using a combination RNAseq/ChIPseq approach, we found that CcpA affects transcript levels of 514 of 1667 GAS genes (31%) whereas direct DNA binding was identified for 105 GAS genes. Three of the directly regulated genes encode the key GAS virulence factors Streptolysin S, PrtS (IL-8 degrading proteinase), and SpeB (cysteine protease). Mutating CcpA Val301 to Ala (strain 2221-CcpA-V301A) abolished interaction between CcpA and HPr and impacted the transcript levels of 205 genes (40%) in the total CcpA regulon. By ChIPseq analysis, CcpAV301A bound to DNA from 74% of genes bound by wild-type CcpA, but generally with lower affinity. These data delineate the direct CcpA regulon and clarify the HPr-dependent and independent activities of CcpA in a key pathogenic bacterium.Data sharing and data availabilityThe data that support the findings of this study are available from the corresponding author upon reasonable request.
ORP1L regulates dynein clustering on endolysosmal membranes in response to cholesterol levels
Authors: Thakur Shreyasi , Relich Peter K. , Sorokina Elena M. , Gyparaki Melina T. , Lakadamyali Melike 
Published: August 2020

AbstractThe sub-cellular positioning of endolysosomes is crucial for regulating their function. Particularly, the positioning of endolysosomes between the cell periphery versus the peri-nuclear region impacts autophagy, mTOR (mechanistic target of rapamycin) signaling and other processes. The mechanisms that regulate the positioning of endolysosomes at these two locations are still being uncovered. Here, using super-resolution microscopy, we show that the retrograde motor dynein forms nano-clusters on endolysosomal membranes containing 1-2 dyneins, with an average of ~3 nanoclusters per endolysosome. These data suggest that a very small number of dynein motors (1-6) drive endolysosome motility. Surprisingly, dynein nano-clusters are slightly larger on peripheral endolysosomes having higher cholesterol levels compared to peri-nuclear ones. By perturbing endolysosomal membrane cholesterol levels, we show that dynein copy number within nano-clusters is influenced by the amount of endolysosomal cholesterol while the total number of nano-clusters per endolysosome is independent of cholesterol. Finally, we show that the dynein adapter protein ORP1L (Oxysterol Binding Protein Homologue) regulates the number of dynein motors within nano-clusters in response to cholesterol levels. We propose a new model by which endolysosomal transport and positioning is influenced by the cholesterol sensing adapter protein ORP1L, which influences dynein’s copy number within nano-clusters.
Diversity analysis of gut microbiota between healthy controls and those with atopic dermatitis in a Chinese population
Authors: Ye Siqi , Yan Fenggen , Wang Haiyan , Mo Xiumei , Liu Junfeng , Zhang Yu , Li Hongyi , Chen Dacan 
Published: August 2020

AbstractAn increasing body of evidence suggests that gut microbiota is involved in atopic dermatitis (AD). We aimed to use high‐throughput sequencing to characterize the differences in the composition of the gut microbiota between healthy controls and patients with AD. Fecal samples from 93 volunteers were analyzed using 16S rRNA sequencing, including 44 patients with AD and 49 healthy control subjects, aged 6–22 years. Our data show that the operational taxonomic unit composition in patients with AD had greater component similarity than the healthy controls. Patients with AD had a lower alpha diversity than healthy control subjects. The relative abundance ofPorphyromonadaceae,Blautia,Parabacteroides,Bacteroides ovatus,Bacteroides uniformisandPrevotella stercoreawas significantly higher (P < 0.05) in patients with AD than healthy control subjects.ClostridiumandP. stercoreawere higher (P < 0.05) in healthy control subjects compared with patients with AD. The results of linear discriminant analysis effect size show thatBacteroidaceaeandPorphyromonadaceaecan act as possible biomarkers associated with diagnosis of AD. However, this needs further experimental verification. Taken together, these results demonstrate the changes in microbiota composition in AD compared with a healthy control group, opening the way to future diagnosis or intervention studies.
Functional traits of avian frugivores have shifted following species extinction and introduction in the Hawaiian Islands
Authors: Case Samuel B. , Tarwater Corey E. 
Published: August 2020

Abstract

The extinction and introduction of species can alter ecological processes owing to the loss or gain of species roles. In vertebrate‐dependent seed dispersal, mutualisms between frugivores and fruiting plants depend, in part, on matching of functional traits. High species turnover of frugivores has occurred on the Hawaiian Islands, owing to both the loss of native frugivores and the introduction of a new suite of frugivores. How this turnover has altered the functional traits of frugivores and the potential impacts on seed dispersal remain unclear.

We investigated how avian frugivore traits differed between historic and modern assemblages of the Hawaiian Islands. We also tested how traits shifted within foraging guilds (ground vs. arboreal) to distinguish potential impacts on plants within low versus high forest strata.

Compared to historic frugivores, the modern assemblage is smaller in gape width and body mass in both ground and arboreal guilds. Wing shape did not significantly change between assemblages. From the results, we postulate that changes in the frugivore community have likely altered seed dispersal processes by reducing (a) the size of seeds consumed, (b) frugivory rates per animal and (c) seed dispersal distances.

Owing to seed size placing strong constraints on consumption, we reviewed recent studies on frugivory by modern birds in the Hawaiian Islands and compared the size of seeds consumed versus seeds available. We found that larger‐seeded plants (>8.1 mm seed width) were not consumed by modern birds and were more likely to be of conservation risk compared to smaller‐seeded plants. Consequently, dispersal limitation may threaten Hawaiian plant communities, with larger‐seeded plants at greatest risk of extinction.

Broadly, we show that extensive turnover within assemblages may lead to significant changes in functional traits, with potential knock‐on effects for mutualistic interactions and communities.

A free Plain Language Summary can be found within the Supporting Information of this article.
Negative effect of turbidity on prey capture for both visual and non‐visual aquatic predators
Authors: Ortega Jean C. G. , Figueiredo Bruno R. S. , da Graça Weferson J. , Agostinho Angelo A. , Bini Luis M. 
Published: August 2020

Abstract

Turbidity plays an important role in aquatic predator–prey interactions. Increases in turbidity are expected to reduce prey capture rates, especially for visually oriented predators. However, there is also evidence indicating that turbidity may have little or no effect on predation rates.

Here, we conducted a systematic review and meta‐analysis of the relationship between turbidity and capture rate. We explored possible sources of heterogeneity in the effect sizes (capture strategy, predator's body size, relative eye size and turbidity range in the experiments) while controlling for the dependence among effects sizes and phylogenetic relationships among predator species.

We found a consistent negative effect of turbidity on prey capture and that turbidity range (manipulated in the experiments) was the main factor accounting for between‐study variation in effect sizes. Also, capture rates of both visually and non‐visually oriented predators decreased with an increase in turbidity. In addition, for visually oriented fish predators, the relative eye size did not influence the effect sizes.

Despite the paucity of studies for some groups of aquatic predators (mainly in tropical regions), we provide corroborative evidence that turbidity is a critical environmental factor controlling predator–prey interactions. This result is especially relevant considering that changes in turbidity is a human‐induced pervasive environmental alteration resulted from, among other mechanisms, runoff after deforestation, eutrophication or oligotrophication in reservoir cascades, which imply changes in predator–prey interactions.
Temperature drives caste‐specific morphological clines in ants
Authors: Brassard François , Francoeur André , Lessard Jean‐Philippe 
Published: August 2020

Abstract

The morphology of organisms relates to most aspects of their life history and autecology. As such, elucidating the drivers of morphological variation along environmental gradients might give insight into processes limiting species distributions. In eusocial organisms, the concept of morphology is more complex than in solitary organisms. Eusocial insects such as ants exhibit drastic morphological differences between reproductive and worker castes. How environmental selection operates on the morphology of each caste, and whether caste‐specific selection has fitness consequences is largely unknown, but is potentially crucial to understand what limits ant species' distributions.

Here we aimed to examine whether ant shape and body size covaries with climate at the scale of an entire continent, and whether such relationship might be caste specific.

We used 26,472 georeferenced morphometric measurements from 2,206 individual ants belonging to 32 closely related North American species in the genus Formica to assess how ant morphology relates to geographic variation in the abiotic environment.

Although precipitation and seasonality explained some of the geographic variation in morphology, temperature was the best predictor. Specifically, geographic variation in body size was positively related to temperature, meaning that ants are smaller in cold than in warm environments. Moreover, the strength of the relationship between size and temperature was stronger for the reproductive castes (i.e. queens and males) than for the worker caste. The shape of workers and males also varied along these large‐scale abiotic gradients. Specifically, the relative length of workers' legs, thoraxes and antennae positively related to temperature, meaning that they had shorter appendages in cold environments. In contrast, males had smaller heads, but larger thoraxes in more seasonal environments.

Overall, our results suggest that geographic variation in ambient temperature influences the morphology of ants, but that the strength of this effect is caste specific. In conclusion, whereas ant ecology has traditionally focused on workers, our study shows that considering the ecology of the reproductive castes is imperative to move forward in this field.
Response surface optimization of the water immersion extraction and macroporous resin purification processes of anhydrosafflor yellow B from Carthamus tinctorius L.
Authors: Zhou Peng , Fangma Yijia , Jin Weifeng , Jin Zhan , Li Xiaohong , He Yu 
Published: August 2020

AbstractIn this study,based on a developed high performance liquid chromatographic quantitative method, the suitable extraction and purification conditions of anhydrosafflor yellow B (AHSYB) from safflower were determined by response surface methodology. The optimal water immersion extraction parameters were as follows: liquid to solid ratio of 22:1; extraction temperature of 75 °C; extraction time of 35 min. Under these conditions, the maximum extraction yield of AHSYB reached 0.465%. The aqueous extract was further purified by HPD‐300 macroporous resin. The optimum adsorption conditions were: pH 2.8; adsorption flow rate of 1.9 mL/min; solution concentration of 0.06 g/mL. The optimum desorption conditions were: ethanol concentrations of 74%; desorption flow rate of 1.6 mL/min; elution volume of 4.4 BV. Under these conditions, the maximum adsorption ratio and desorption ratio reached 1.095 and 0.906 mg/g, respectively. The content of AHSYB reached 6.83%, which was 2.91 times higher than that before purification.Practical ApplicationThe suitable conditions for water immersion extraction and macroporous resin purification of AHSYB are first determined, which facilitates the further utilization of AHSYB as a food and drug.
r3PG – Anrpackage for simulating forest growth using the 3‐PG process‐based model
Authors: Trotsiuk Volodymyr , Hartig Florian , Forrester David I. 
Published: August 2020

AbstractProcess‐based forest models (PBMs) are important tools for quantifying forest growth and vulnerability, particularly under climate change. The 3‐PG model (Physiological Processes Predicting Growth) is one of the most widely used forest growth simulators for this purpose worldwide.Here, we presentr3PG, a newFortranimplementation of 3‐PG, wrapped into anrpackage.r3PGcan simulate monospecific as well as mixtures of evergreen and deciduous tree species in even‐aged or uneven‐aged stands.The combination ofFortranfunctions with anrinterface makes the model extremely fast. This facilitates the use ofr3PGfor extensive computer experiments and sensitivity analysis. We demonstrate this in a case study including (a) single model runs; (b) a sensitivity analysis and a full Bayesian calibration of the model and (c) spatial simulations of forest growth across Switzerland.r3PGis faster and easier to use than previous implementations of 3‐PG in visual basic. We believe that this will make 3‐PG even more useful and popular for ecologists and climate change scientists.