bluuebunny/crossref_metadata_2025_split huggingface dataset:
Task-dependent vocal adjustments to optimize biosonar-based information acquisition
Authors: Lewanzik Daniel , Goerlitz Holger R. 
Published: August 2020

AbstractAnimals need to acquire adequate and sufficient information to guide movements, yet information acquisition and processing is costly. Animals thus face a trade-off between gathering too little and too much information and, accordingly, actively adapt sensory input through motor control. Echolocating animals provide the unique opportunity to study the dynamics of adaptive sensing in naturally behaving animals, since every change in the outgoing echolocation signal directly affects information acquisition and the perception of the dynamic acoustic scene. Here we investigated the flexibility with which bats dynamically adapt information acquisition depending on a task. We recorded the echolocation signals of wild-caught Western barbastelle bats (Barbastella barbastellus) while flying through an opening, drinking on the wing, landing on a wall, and capturing prey. We show that the echolocation signal sequences during target approach differed in a task-dependent manner; bats started target approach earlier and increased information update rate more when the task became increasingly difficult, and bats also adjusted dynamics of call duration shortening and peak frequency shifts accordingly. These task-specific differences existed from the onset of object approach, implying that bats plan their sensory-motor program for object approach exclusively based on information received from search call echoes. We provide insights into how echolocating animals deal with the constraints they face when sequentially sampling the world through sound by adjusting acoustic information flow from slow to extremely fast in a highly dynamic manner. Our results further highlight the paramount importance of high behavioural flexibility for acquiring information.Summary statementHaving the right information for a specific job is crucial. Echolocating bats flexibly and independently adjust different call parameters to match the sensory-motor challenges of four different tasks.
The microtubule organization in the zebrafish yolk adapts to transgene-mediated phenotypic variations
Authors: Marsal Maria , Bernardello Matteo , Gualda Emilio J. , Loza-Alvarez Pablo 
Published: August 2020

SUMMARYThe organization of microtubule networks in the cells is orchestrated by subcellular structures named microtubule organizing centers (MTOCs). In zebrafish embryos, the yolk is surrounded by a cytoplasmic layer containing a vast network of microtubules. In order to understand how this complex network is organized, we use dclk2-GFP zebrafish embryos, as a microtubule reporter line, and Light Sheet Fluorescence Microscopy. We find that this organization is mediated by a variable number of aster-like MTOCs during epiboly, and that it does not follow a rigid scheme, exemplifying developmental robustness. We characterize asters morphology, dynamics, and their uniform distribution in the yolk sphere. Consistent with their role as MTOCs we find that they contain key molecular machinery for MTs dynamics, amongst which centrin marks the assignation of MTOCs over time. Finally, we demonstrate that merely the overexpression of dclk2-GFP in wild type embryos can induce the formation of asters. We propose dclk2-GFP embryos as a model for the study of the collective behaviour of microtubules in complex systems.
A simulation study of the use of temporal occupancy for identifying core and transient species
Authors: Snell Taylor Sara , Coyle Jessica R. , White Ethan P. , Hurlbert Allen H. 
Published: August 2020

AbstractTransient species, which do not maintain self-sustaining populations in a system where they are observed, are ubiquitous in nature and their presence often impacts the interpretation of ecological patterns and processes. Identifying transient species from temporal occupancy, the proportion of time a species is observed at a given site over a time series, is subject to classification errors as a result of imperfect detection and source-sink dynamics. We use a simulation-based approach to assess how often errors in detection or classification occur in order to validate the use of temporal occupancy as a metric for inferring whether a species is a core or transient member of a community. We found that low detection increases error in the classification of core species, while high habitat heterogeneity and high detection increase error in classification of transient species. These findings confirm that temporal occupancy is a valid metric for inferring whether a species can maintain a self-sustaining population, but imperfect detection, low abundance, and highly heterogeneous landscapes may yield high misclassification rates.
Structure of papain-like protease from SARS-CoV-2 and its complexes with non-covalent inhibitors
Authors: Osipiuk Jerzy , Azizi Saara-Anne , Dvorkin Steve , Endres Michael , Jedrzejczak Robert , Jones Krysten A. , Kang Soowon , Kathayat Rahul S. , Kim Youngchang , Lisnyak Vladislav G. , Maki Samantha L. , Nicolaescu Vlad , Taylor Cooper A. , Tesar Christine , Zhang Yu-An , Zhou Zhiyao , Randall Glenn , Michalska Karolina , Snyder Scott A. , Dickinson Bryan C. , Joachimiak Andrzej 
Published: August 2020

ABSTRACTThe number of new cases world-wide for the COVID-19 disease is increasing dramatically, while efforts to contain Severe Acute Respiratory Syndrome Coronavirus 2 is producing varied results in different countries. There are three key SARS-CoV-2 enzymes potentially targetable with antivirals: papain-like protease (PLpro), main protease (Mpro), and RNA-dependent RNA polymerase. Of these, PLpro is an especially attractive target because it plays an essential role in several viral replication processes, including cleavage and maturation of viral polyproteins, assembly of the replicase-transcriptase complex (RTC), and disruption of host viral response machinery to facilitate viral proliferation and replication. Moreover, this enzyme is conserved across different coronaviruses and promising inhibitors have already been discovered for its SARS-CoV variant. Here we report a substantive body of structural, biochemical, and virus replication studies that identify several inhibitors of the enzyme from SARS-CoV-2 in both wild-type and mutant forms. These efforts include the first structures of wild-type PLpro, the active site C111S mutant, and their complexes with inhibitors, determined at 1.60–2.70 Angstroms. This collection of structures provides fundamental molecular and mechanistic insight to PLpro, and critically, illustrates details for inhibitors recognition and interactions. All presented compounds inhibit the peptidase activity of PLproin vitro, and some molecules block SARS-CoV-2 replication in cell culture assays. These collated findings will accelerate further structure-based drug design efforts targeting PLpro, with the ultimate goal of identifying high-affinity inhibitors of clinical value for SARS-CoV-2.
Modified base-binding EVE and DCD Domains Implicated in the Origins of Programmed Cell Death and the piRNA Pathway
Authors: Bell Ryan T. , Wolf Yuri I. , Koonin Eugene V. 
Published: August 2020

AbstractBackgroundDNA and RNA of most cellular life forms and many viruses contain an expansive repertoire of modified bases. The modified bases play diverse biological roles that include both regulation of transcription and translation, and protection against restriction endonucleases and antibiotics. Modified bases are often recognized by dedicated protein domains. However, the elaborate networks of interactions and processes mediated by modified bases are far from being completely understood.ResultsWe present a comprehensive census and classification of EVE domains that belong to the PUA/ASCH domain superfamily and bind various modified bases in DNA and RNA. Prokaryotes encode two classes of EVE domain proteins, slow-evolving and fast-evolving. The slow-evolving EVE domains in α-proteobacteria are embedded in a conserved operonic context that implies involvement in coupling between translation and respiration, in particular, cytochrome c biogenesis, potentially, via binding 5-methylcytosine in tRNAs. In β and γ-proteobacteria, the conserved associations implicate the EVE domains in the coordination of cell division, biofilm formation, and global transcriptional regulation by non-coding 6S small RNAs, which are potentially modified and bound by the EVE domains. Down-regulation of the EVE-encoding operons might cause dormancy or programmed cell death (PCD). In eukaryotes, the EVE-domain-containing THYN1-like proteins appear to inhibit PCD and regulate the cell cycle, likely, via binding 5-methylcytosine and its derivatives in DNA and/or RNA. Thus, the link between PCD and cytochrome c that appears to be universal in eukaryotes might have been inherited from the α-proteobacterial, proto-mitochondrial endosymbiont and, unexpectedly, could involve modified base recognition by EVE domains. In numerous prokaryotic genomes, fast-evolving EVE domains are embedded in defense contexts, including toxin-antitoxin modules and Type IV restriction systems, all of which can also induce PCD. These EVE domains likely recognize modified bases in invading DNA molecules and target them for restriction. We additionally identified EVE-like prokaryotic Development and Cell Death (DCD) domains that are also implicated in defense functions including PCD. This function was inherited by eukaryotes but, in animals, the DCD proteins apparently were displaced by the extended Tudor family, whose partnership with Piwi-related Argonautes became the centerpiece of the piRNA system.ConclusionsRecognition of modified bases in DNA and RNA by EVE-like domains appears to be an important, but until now, under-appreciated, common denominator in a variety of processes including PCD, cell cycle control, antivirus immunity, stress response and germline development in animals.
An ancient, conserved gene regulatory network led to the rise of oral venom systems
Authors: Barua Agneesh , Mikheyev Alexander S. 
Published: August 2020

AbstractOral venom systems evolved multiple times in numerous vertebrates enabling exploitation of unique predatory niches. Yet how and when they evolved remains poorly understood. Up to now, most research on venom evolution has focussed strictly on the toxins. However, using toxins present in modern day animals to trace the origin of the venom system is difficult, since they tend to evolve rapidly, show complex patterns of expression, and were incorporated into the venom arsenal relatively recently. Here we focus on gene regulatory networks associated with the production of toxins in snakes, rather than the toxins themselves. We found that overall venom gland gene expression was surprisingly well conserved when compared to salivary glands of other amniotes. We characterised the ‘meta-venom’, a network of approximately 3000 non-secreted housekeeping genes that are strongly co-expressed with the toxins, and are primarily involved in protein folding and modification. Conserved across amniotes, this network was co-opted for venom evolution by exaptation of existing members and the recruitment of new toxin genes. For instance, starting from this common molecular foundation,Helodermalizards, shrews, and solenodon, evolved venoms in parallel by overexpression of kallikreins, which were common in ancestral saliva and induce vasodilation when injected, causing circulatory shock. Derived venoms, such as those of snakes, incorporated novel toxins, though still rely on hypotension for prey immobilization. These similarities suggest repeated co-option of shared molecular machinery for the evolution of oral venom in mammals and reptiles, blurring the line between truly venomous animals and their ancestors.
SMARCA4 deficient tumours are vulnerable to KDM6A/UTX and KDM6B/JMJD3 blockade
Authors: Romero Octavio A. , Vilarrubi Andrea , Alburquerque-Bejar Juan J. , Gomez Antonio , Andrades Alvaro , Trastulli Deborah , Pros Eva , Verdura Sara , Farré Lourdes , Martín-Tejera Juan F. , Llabata Paula , Oaknin Ana , Saigi Maria , Piulats Josep M. , Matias-Guiu Xavier , Medina Pedro P. , Vidal August , Villanueva Alberto , Sanchez-Cespedes Montse 
Published: August 2020

SummaryDespite the genetic inactivation ofSMARCA4, a core component of the SWI/SNF-complex commonly found in cancer, there are no therapies that effectively target SMARCA4-deficient tumours. Here, we show that, unlike the cells with activatedMYConcogene, cells withSMARCA4inactivation are refractory to the histone deacetylase inhibitor, SAHA, leading to the aberrant accumulation of H3K27me3. This is associated with impaired transactivation and significantly reduced levels of the histone demethylases KDM6A/UTX and KDM6B/JMJD3, which confer a strong dependency on the KDM6s in theSMARCA4-mutant cells, so that its inhibition compromises cell viability. Administering the KDM6 inhibitor GSK-J4 to mice orthotopically implanted withSMARCA4-mutant lung cancer cells or primary small cell carcinoma of the hypercalcaemic type (SCCOHT) had strong anti-tumour effects. Our results highlight the vulnerability of KDM6 inhibitors as a characteristic that could be exploited for treatingSMARCA4-mutant cancer patients.
Psychedelic substance use in the Reddit psychonaut community. A qualitative study on motives and modalities
Authors: Pestana Jani , Beccaria Franca , Petrilli Enrico 
Published: August 2020

Purpose
The purpose of this paper is to investigate motives and modalities of psychedelic substance use in the psychonaut community that is hosted on the Reddit platform (r/psychonaut). Psychonauts are sometimes described as responsible drug users. Elements of responsible use include sharing stories, advice and experiences, reagent testing substances, proper dosing and education on harm reduction and its practical implication. Investigating psychonauts’ substance use can highlight what responsible use means for them and could inform best practices for psychedelic use.

Design/methodology/approach
Qualitative content analysis of posts and comments on the r/psychonaut subreddit was completed. In total, 350 posts were investigated. A combination of deductive and inductive methods was used to both structure the research and to allow room for novel information. To investigate participant’s motives, this combination was used to both collect and analyse the data. To examine modalities, concepts and keywords were formed out of the collected data and then analysed.

Findings
Motives for use ranged from self-knowledge, self-investigation and self-medication to increasing artistic expression, curiosity and recreation. Concerning modalities, the respondents put a high emphasis on preparation, set and setting, integration, dosage and gathering and sharing information through research, articles and trip reports. These features are identified in the literature as elements of responsible drug use. This investigation can help by unearthing best practices already in use by the community to inform the bourgeoning movement of psychedelic substance use – both in a medical and self-reflexive setting.

Originality/value
This paper is framed in the context of paucity of the academic literature on people taking psychedelic substances in Western society in non-rave and non-medical settings, with findings that indicate important change happening in the psychonaut subculture.
A novel post-processing method for 316L steel specimen generated by SLM using TiN/TiAlN multilayer coating
Authors: Lyu Yueling , Chen Yangzhi , Wan Yulin 
Published: August 2020

Purpose
Selective laser melting (SLM) is an important advanced additive manufacturing technology. The existing SLM printing technology cannot manufacture the mechanical parts that fully meet the requirements of high precision and strength. This paper aims to explore a new post-processing method for SLM 316L specimen, namely, using of the TiN/TiAlN multilayer coating fabricated by multi-arc ion plating on the surface of SLM specimens, for improving the performance of SLM specimens. The other purpose of this paper is compared the performances of the TiAlN/TiN multilayer coating machined specimen and the TiN/TiAlN multilayer coating SLM specimen.

Design/methodology/approach
The TiN/TiAlN multilayer coating is fabricated by multi-arc ion plating on the surface of 316L specimens. The surface morphology and selected mechanical properties of TiN/TiAlN multilayer coating plating on the SLM substrate specimen and the machined substrate specimen were studied in this paper. The analyzed properties included surface topography, micro hardness, the adhesion, the thickness and the wear resistance of TiN/TiAlN multilayer coating plating on the SLM substrate specimen and the machined substrate specimen.

Findings
The electron microscope images reveal that surface morphology of TiN/TiAlN multilayer coating plating on the SLM specimens is relatively flat, and there are some micro-particles in different sizes and pin holes dispersed on them. After TiN/TiAlN multilayer coating, the performances of SLM samples, such as micro hardness, the thickness and the wear resistance, were significantly improved. The micro hardness of TiN/TiAlN multilayer coating machined specimen is higher than that of TiN/TiAlN multilayer coating SLM specimen. However, the adhesion of TiN/TiAlN multilayer coating machined specimen is less than that of TiN/TiAlN multilayer coating SLM specimen.

Originality/value
The study provides a new post-processing method for SLM 316L specimen to improve the performance of SLM specimens and to enable SLM specimens to be applied in the field of precision mechanical transmission.
The impact of eco-innovation on the stock returns of technology-based KIBS: role of eco-innovation type and its degree of novelty
Authors: Szutowski Dawid 
Published: August 2020

PurposeThe purpose of this paper is to determine the role of eco-innovation type and its degree of novelty in increasing the stock returns of technology-based knowledge-intensive business service companies (T-KIBS), to advance the development of the concept of eco-innovation within the literature on the effects of innovation.Design/methodology/approachThe effects of four eco-innovation types were examined across three degrees of novelty involved. The event study methodology was applied to the sample of 238 eco-innovation announcements released during the period of January 2016–June 2019 (inclusive) by European T-KIBS.FindingsWhile the implementation of product and organisational eco-innovation was the most beneficial, the results indicated that a high degree of novelty resulted in larger increase of stock returns in the case of all the four eco-innovation types.Research limitations/implicationsThe eco-innovation announcements were gathered from specialised databases. However, it could be the case that companies may have used different communication channels (e.g. social media) to communicate innovation. Furthermore, a certain amount of bias undoubtedly exists, as the data came only from the European Union. Expanding the spatial scope to include the North American (especially the USA) and Asian economies appears necessary.Practical implicationsThe practical insights into the role that the degree of novelty plays in eco-innovation announcements were formulated, which may be used to increase the market valuation of the firm.Social implicationsStrategies supporting eco-innovation are crucial for business development as the value created for the stakeholders involved transmits in time into the enterprise value.Originality/valueThe paper attempts to fill the research gap concerning the impact of eco-innovation on the stock returns of T-KIBS.
Persistence of extended‐spectrum β‐lactamase plasmids among Enterobacteriaceae in commercial broiler farms
Authors: Yossapol Montira , Suzuki Kasumi , Odoi Justice Opare , Sugiyama Michiyo , Usui Masaru , Asai Tetsuo 
Published: August 2020

AbstractTo clarify the persistence of extended‐spectrum β‐lactamase (ESBL) producers, 13 plasmids from two broiler farms were analyzed. On the farm not using antimicrobials, one plasmid from Klebsiella pneumoniae isolated from a day‐old chick was similar to that from Escherichia coli isolated a year later, with the deletion of two transposons. On the farm using antimicrobials, most circulating plasmids (eight out of nine) in a flock of 40‐days‐old chicks were identical, although one from K. pneumoniae had a deletion of a transposon carrying a class 1 integron containing aadA2 and dfrA12. Thus, ESBL plasmids persisted in the farms with or without antimicrobial agent use.
Survey analysis of computer science, food science, and cybersecurity skills and coursework of undergraduate and graduate students interested in food safety
Authors: Feye K. M. , Lekkala H. , Lee‐Bartlett J. A. , Thompson D. R. , Ricke S. C. 
Published: August 2020

AbstractAutomation is coming and will enable not only the ability to increase poultry processing line speeds, but also the collection of considerable “big data.” These data can be collected en masse, stored, analyzed, and used to improve food safety, quality, enhance traceability, and also be used for risk assessment. However, as this technology is implemented in the poultry industry, computer hackers will emerge to pose a clear and present danger to the poultry industry and the upcoming generation of professionals must be equipped with the knowledge to protect sensitive data. The objective of this study was to quantitate the current computer science (CS) competency, food science exposure and extracurricular activities, and familiarity with cybersecurity topics of students in food science and related fields. Students ranked their CS abilities, 1 through 5, with 1 being the lowest level of competence and 5 representing the highest level of confidence. To assess their knowledge of food safety‐related sciences, participants were asked about their familiarity with the respective fields. The average student was familiar with common avenues of food safety exposure, such as television and the Internet. Students were less familiar with more advanced, and arguably important topics, such as botnet. Finally, the students ranked their familiarity with cybersecurity topics, 1 through 5, with 1 representing being not familiar at all and 5 representing extremely familiar. Therefore, to meet the future technological demands, specific course‐work is required to improve prospective student CS and cybersecurity competency.