bluuebunny/crossref_metadata_2025_split huggingface dataset:
Basolateral Amygdala Represents and Remembers Ethological Events
Authors: Mazuski Cristina , O’Keefe John 
Published: August 2021

AbstractThe basolateral amygdala plays a crucial role in memory consolidation yet the general neural mechanism remains elusive. Basolateral amygdala neurons were recorded from freely-moving rats as they interacted with different ethological stimuli: male or female rats, a moving toy and food. Over 20% of neurons showed highly tuned event-specific responses to a single class of stimuli. Firing persisted in 30% of these responsive cells for minutes after the removal of the eliciting stimulus. Neural information flowed directionally from event-specific neurons to less specific neurons with changes in connection strength after removal of the stimulus. We propose that the basolateral amygdala identifies specific ethological events, with circuit-wide activity driven by the event-specific neurons during and after the termination of those events likely facilitating active short-term memory consolidation.
Genetic coupling of life-history and aerobic performance in Atlantic salmon
Authors: Prokkola Jenni M. , Åsheim Eirik R. , Morozov Sergey , Bangura Paul , Erkinaro Jaakko , Ruokolainen Annukka , Primmer Craig R. , Aykanat Tutku 
Published: August 2021

AbstractA better understanding of the genetic and phenotypic architecture underlying life-history variation is a longstanding aim in biology. Theories suggest energy metabolism determines life-history variation by modulating resource acquisition and allocation trade-offs, but the genetic underpinnings of the relationship and its dependence on ecological conditions have rarely been demonstrated. The strong genetic determination of age-at-maturity by two unlinked genomic regions (vgll3andsix6) makes Atlantic salmon (Salmo salar) an ideal model to address these questions. Using more than 250 juveniles in common garden conditions, we quantified the covariation between metabolic phenotypes –standard and maximum metabolic rates (SMR and MMR), and aerobic scope (AS) – and the life-history genomic regions and tested if food availability modulates the relationships. We found that the early maturation genotype invgll3was associated with higher MMR and consequently AS. Additionally, MMR exhibited physiological epistasis; it was decreased when late maturation genotypes co-occurred in both genomic regions. Contrary to our expectation, the life-history genotypes had no effects on SMR. Further, food availability had no effect on the genetic covariation, suggesting a lack of genotype-by-environment interactions. Our results provide insights on the key organismal processes that link energy use at the juvenile-stage to age-at-maturity, indicating potential mechanisms by which metabolism and life-history can coevolve.
proovframe: frameshift-correction for long-read (meta)genomics
Authors: Hackl Thomas , Trigodet Florian , Eren A. Murat , Biller Steven J. , Eppley John M. , Luo Elaine , Burger Andrew , DeLong Edward F. , Fischer Matthias G. 
Published: August 2021

AbstractLong-read sequencing technologies hold big promises for the genomic analysis of complex samples such as microbial communities. Yet, despite improving accuracy, basic gene prediction on long-read data is still often impaired by frameshifts resulting from small indels. Consensus polishing using either complementary short reads or to a lesser extent the long reads themselves can mitigate this effect but requires universally high sequencing depth, which is difficult to achieve in complex samples where the majority of community members are rare. Here we present proovframe, a software implementing an alternative approach to overcome frameshift errors in long-read assemblies and raw long reads. We utilize protein-to-nucleotide alignments against reference databases to pinpoint indels in contigs or reads and correct them by deleting or inserting 1-2 bases, thereby conservatively restoring reading-frame fidelity in aligned regions. Using simulated and real-world benchmark data we show that proovframe performs comparably to short-read-based polishing on assembled data, works well with remote protein homologs, and can even be applied to raw reads directly. Together, our results demonstrate that protein-guided frameshift correction significantly improves the analyzability of long-read data both in combination with and as an alternative to common polishing strategies. Proovframe is available from https://github.com/thackl/proovframe.
Cargo genes of Tn7-like transposons comprise an enormous diversity of defense systems, mobile genetic elements and antibiotic resistance genes
Authors: Benler Sean , Faure Guilhem , Tran Han-Altae , Shmakov Sergey , Zheng Feng , Koonin Eugene 
Published: August 2021

AbstractTransposition is a major mechanism of horizontal gene mobility in prokaryotes. However, exploration of the genes mobilized by transposons (cargo) is hampered by the difficulty in delineating integrated transposons from their surrounding genetic context. Here, we present a computational approach that allowed us to identify the boundaries of 6,549 Tn7-like transposons at base pair resolution. We found that 96% of these transposons carry at least one cargo gene. Delineation of distinct communities in a gene-sharing network demonstrates how transposons function as a conduit of genes between phylogenetically distant hosts. Comparative analysis of the cargo genes reveals significant enrichment of mobile genetic elements (MGEs) nested within Tn7-like transposons, such as insertion sequences and toxin-antitoxin modules, genes involved in recombination and anti-MGE defense, and in antibiotic resistance. More unexpectedly, cargo also includes genes encoding central carbon metabolism enzymes. Twenty- two Tn7-like transposons carry both an anti-MGE defense system and antibiotic resistance genes, illustrating how bacteria can overcome these combined pressures upon acquisition of a single transposon. This work substantially expands the distribution of Tn7-like transposons, defines their evolutionary relationships and provides a large-scale functional classification of prokaryotic genes mobilized by transposition.SignificanceTransposons are major vehicles of horizontal gene transfer that, in addition to genes directly involved in transposition, carry cargo genes. However, characterization of these genes is hampered by the difficulty of identification of transposon boundaries. We developed a computational approach for detecting transposon ends and applied it to perform a comprehensive census of the cargo genes of Tn7-like transposons, a large class of bacterial mobile genetic elements (MGE), many of which employ a unique, CRISPR-mediated mechanism of site- specific transposition. The cargo genes encompass a striking diversity of MGE, defense and antibiotic resistance systems. Unexpectedly, we also identified cargo genes encoding metabolic enzymes. Thus, Tn7-like transposons mobilize a vast repertoire of genes that can have multiple effects on the host bacteria.
OXPHOS deficiencies affect peroxisome proliferation by downregulating genes controlled by the SNF1 signaling pathway
Authors: Farré Jean-Claude , Carolino Krypton , Devanneaux Lou , Subramani Suresh 
Published: August 2021

SummaryHow environmental cues influence peroxisome proliferation, particularly through other organelles, remains largely unknown. Yeast peroxisomes metabolize all fatty acids (FA), and methylotrophic yeasts also metabolize methanol. NADH and acetyl-CoA, the products of these pathways enter mitochondria for ATP production, and for anabolic reactions. During the metabolism of FA and/or methanol, the mitochondrial oxidative phosphorylation (OXPHOS) pathway accepts NADH for ATP production and maintains cellular redox balance. Remarkably, peroxisome proliferation inPichia pastoriswas abolished in NADH shuttling and OXPHOS mutants affecting complex I or III, or by the mitochondrial uncoupler, 2,4-dinitrophenol (DNP), indicating ATP depletion causes the phenotype. We show that mitochondrial OXPHOS deficiency inhibits the expression of several peroxisomal proteins implicated in FA and methanol metabolism, as well as in peroxisome division and proliferation. These genes are regulated by the Snf1 complex (SNF1), a pathway generally activated by high AMP and low ATP. Consistent with this mechanism, in OXPHOS mutants, Snf1 is activated by phosphorylation, but Gal83, its interacting subunit, fails to translocate to the nucleus. Phenotypic defects in peroxisome proliferation observed in the OXPHOS mutants, and phenocopied by theΔgal83mutant, were rescued by deletion of three transcriptional repressor genes (MIG1,MIG2andNRG1) controlled by SNF1 signaling. We uncovered here the mechanism by which peroxisomal and mitochondrial metabolites influence redox and energy metabolism, while also influencing peroxisome biogenesis and proliferation, thereby exemplifying interorganellar communication and interplay involving peroxisomes, mitochondria, cytosol and the nucleus. We discuss the physiological relevance of this work in view of human OXPHOS deficiencies.
Deep immune profiling of the maternal-fetal interface with mild SARS-CoV-2 infection
Authors: Sureshchandra Suhas , Zulu Michael Z , Doratt Brianna , Jankeel Allen , Tifrea Delia , Edwards Robert , Rincon Monica , Marshall Nicole E. , Messaoudi Ilhem 
Published: August 2021

ABSTRACTPregnant women are an at-risk group for severe COVID-19, though the majority experience mild/asymptomatic disease. Although severe COVID-19 has been shown to be associated with immune activation at the maternal-fetal interface even in the absence of active viral replication, the immune response to asymptomatic/mild COVID-19 remains unknown. Here, we assessed immunological adaptations in both blood and term decidua from 9 SARS-exposed pregnant women with asymptomatic/mild disease and 15 pregnant SARS-naive women. In addition to selective loss of tissue-resident decidual macrophages, we report attenuation of antigen presentation and type I IFN signaling but upregulation of inflammatory cytokines and chemokines in blood monocyte derived decidual macrophages. On the other hand, infection was associated with remodeling of the T cell compartment with increased frequencies of activated CD69+ tissue-resident T cells and decreased abundance of Tregs. Interestingly, frequencies of cytotoxic CD4 and CD8 T cells increased only in the blood, while CD8 effector memory T cells were expanded in the decidua. In contrast to decidual macrophages, signatures of type I IFN signaling were increased in decidual T cells. Finally, T cell receptor diversity was significantly reduced with infection in both compartments, albeit to a much greater extent in the blood. The resulting aberrant immune activation in the placenta, even with asymptomatic disease may alter the exquisitely sensitive developing fetal immune system, leading to long-term adverse outcomes for offspring.
Water Pollution and Administrative Division Adjustments: A Quasi-natural Experiment in Chaohu Lake of China
Authors: Li Jing , Liu Di , Cai Mengyuan 
Published: August 2021

AbstractThe adjustment of administrative divisions introduces a series of uncertain impacts on the social and economic development in the administrative region. Previous studies focused more on the economic effects of the adjustment of administrative divisions, while, in this paper, we also take environmental effects into consideration. The administrative division adjustment for Chaohu Lake is used as a quasi-natural experiment to explore the influence of the adjustment on pollution control. The synthetic control method is used in this study to access the effect of administrative division adjustment on the water quality indicators of Chaohu Lake and its internal mechanism. Some conclusions are as follows. First, after the administrative division adjustment, some water quality indicators, such as ammonia nitrogen, have indeed been alleviated; however, other major pollution indicators, such as chemical oxygen demand and dissolved oxygen, have deteriorated to varying degrees. Second, the results also reveal that improper development ideas, industrial excessive expansion, and the swing of economic growth and environmental goals are problems after the adjustment. Returning to the original intention of adjustment, rationalizing the Chaohu Lake management system and designing a sound and feasible accountability mechanism are fundamental measures to reduce pollution.
Structure-based design of antisense oligonucleotides that inhibit SARS-CoV-2 replication
Authors: Li Yan , Garcia Gustavo , Arumugaswami Vaithilingaraja , Guo Feng 
Published: August 2021

ABSTRACTAntisense oligonucleotides (ASOs) are an emerging class of drugs that target RNAs. Current ASO designs strictly follow the rule of Watson-Crick base pairing along target sequences. However, RNAs often fold into structures that interfere with ASO hybridization. Here we developed a structure-based ASO design method and applied it to target severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Our method makes sure that ASO binding is compatible with target structures in three-dimensional (3D) space by employing structural design templates. These 3D-ASOs recognize the shapes and hydrogen bonding patterns of targets via tertiary interactions, achieving enhanced affinity and specificity. We designed 3D-ASOs that bind to the frameshift stimulation element and transcription regulatory sequence of SARS-CoV-2 and identified lead ASOs that strongly inhibit viral replication in human cells. We further optimized the lead sequences and characterized structure-activity relationship. The 3D-ASO technology helps fight coronavirus disease-2019 and is broadly applicable to ASO drug development.
Development of cost-effective shock tube based on experimental and numerical analysis
Authors: Thaloor Ramesh Praveenkumar , Kengaiah Vijayaraja , Gutema Endalkachew Mosisa , Velusamy Prabu , Balamoorthy Dhivya 
Published: August 2021

Purpose
The purpose of the study is to design economical shock tube. It is an instrument used for experimental investigations not only related to shock phenomena but also for the behavior of the material when it is subjected to high-speed flow. The material used here in this shock tube is stainless steel ss304 and aluminum. A shock tube consists of two sections, namely, the driver and the driven. The gas in the driven and driver is filled with atmospheric air and nitrogen, respectively, under the predominant condition.

Design/methodology/approach
The focus of the study is on the design and fabrication of shock tubes. a shock tube is a research tool to make an aerodynamic test in the presence of high pressure and temperature by generating moving normal shock waves under controlled conditions.

Findings
The main necessity for instrumentation in the shock tube experiment is to know the velocity of the moving shock wave from which the other parameters can be calculated. the pressure transducers are located in the shock tube in various locations to measure aerodynamic parameters in terms of pressure.

Originality/value
The main objective of this project work is to make an experimental setup to produce supersonic velocity with the readily available material in the market in a highly safe manner.
A fast radiometric correction method for Sentinel-2 satellite images
Authors: Moradi Elahe , Sharifi Alireza 
Published: August 2021

Purpose
Radiometric calibration is a method that estimates the reflection of the target from the measured input radiation. The purpose of this study is to radiometrically calibrate three spectral bands of Sentinel-2A, including green, red and infrared. For this purpose, Landsat-8 OLI data are used. Because they have bands with the same wavelength range and they have the same structure. As a result, Landsat-8 OLI is appropriate for relative radiometric calibration.

Design/methodology/approach
The method used in this study is radiometric calibration uncorrected data from a sensor with corrected data from another sensor. Also, another aim of this study is a comparison between radiometric correction data and data that, in addition to radiometric correction, has been sharpened with panchromatic data. In this method, both of them have been used for radiometric calibration. Calibration coefficients have been obtained using the first-order polynomial equation.

Findings
This study showed that the corrected data has more valid answers than corrected and sharpened data. This method studied three land-cover types, including soil, water and vegetation, which it obtained the most accurate coefficients of calibration for soil class because R-square in all three bands was above 88%, and the root mean square error in all three bands was below 0.01. In the case of water and vegetation classes, only results of red and infrared bands were suitable.

Originality/value
For validating this method, the radiometric correction module of SNAP software was used. According to the results, the coefficient of radiometric calibration of the Landsat-8 sensor was very close to the coefficients obtained from the corrected data by SNAP.
The mediating effect of work engagement on innovative work behavior and the role of psychological well-being in the job demands–resources (JD-R) model
Authors: Koroglu Şennur , Ozmen Omur 
Published: August 2021

PurposeThis study revisits the role of work engagement (WE) on innovative work behavior (IWB) in conjunction with the job demands–resources (JD-R) model, specifically examining its mediating role between antecedent variables of psychological well-being (PWB), interpersonal conflict (IPC) and perceived organizational support (POS).Design/methodology/approachThe study was conducted within five different sectors and 416 work settings in Turkey. A cross-sectional, correlational research design was used, and structural equation modeling (SEM) was applied to test the mediating effect of WE.FindingsThe results of the SEM provided partial support for eight hypotheses. The results of this study demonstrate a positive relationship between PWB, POS, WE and IWB. This indicates that resources are vital in increasing both WE and IWB. As expected, the correlation of IPC and IWB resulted in a negative relationship. The findings demonstrate a positive relationship between PWB and WE and IWB.Research limitations/implicationsExtending the model, future research could incorporate the antecedents as mediators and utilize them to further explore the mechanisms of employee engagement (EE) and the IWB link. It would also be beneficial to include other variables such as personal differences, trust, personal environment fit, fairness in the workplace, recognition and organizational culture and employee value proposition as moderators of EE and IWB.Practical implicationsThe findings offer the suggestion of few practical applications such as the need to encourage organizations to enhance PWB to foster positive feelings in the work environment. This includes increasing employees' effort and dedication by utilizing POS in the workplace and considering employee's well-being. Additionally, EE should be an important organizational strategy to positively influence employee creativity within the workplace.Social implicationsThis research was conducted within the Turkish business context; it would be worthwhile to validate the findings of this study in a multicultural context that did not share similar basic characteristics as those in Turkey. There could be a comparative study of EE between Turkey and other countries as a cross-cultural investigation.Originality/valueThe results of data analysis have revealed an enhanced understanding of the role of the mediation effect of WE on IWBs. This study also expands the concept that psychological well-being can enhance WE, which in turn corresponds to more IWB in the context of the JD-R model. The findings indicate that in order to better comprehend its function, IPC needs to be further examined with other antecedents.
Integrating risk management's best practices to estimate deep excavation projects’ time and cost
Authors: Heravi Gholamreza , Taherkhani Amir Hosein , Sobhkhiz Soroush , Hassandokht Mashhadi Ali , Zahiri-Hashemi Rouzbeh 
Published: August 2021

PurposeThis study provides an integrated risk-based cost and time estimation approach for deep excavation projects. The purpose is to identify the best practices in recent advances of excavation risk analysis (RA) and integrate them with traditional cost and time estimation methods.Design/methodology/approachThe implemented best practices in this research are as follows: (1) fault-tree analysis (FTA) for risk identification (RI); (2) Bayesian belief networks (BBNs), fuzzy comprehensive analysis and Monte Carlo simulation (MCS) for risk analysis; and (3) sensitivity analysis and root-cause analysis (RCA) for risk response planning (RRP). The proposed approach is applied in an actual deep excavation project in Tehran, Iran.FindingsThe results show that the framework proposes a practical approach for integrating the risk management (RM) best practices in the domain of excavation projects with traditional cost and time estimation approaches. The proposed approach can consider the interrelationships between risk events and identify their root causes. Further, the approach engages different stakeholders in the process of RM, which is beneficial for determining risk owners and responsibilities.Originality/valueThis research contributes to the project management body of knowledge by integrating recent RM best practices in deep excavation projects for probabilistic estimation of project time and cost.
Be zhongyong and be ethical: dual leadership in promoting employees’ thriving at work
Authors: Guo Shenghao , Hu Qianqian 
Published: August 2021

Purpose
The roles that one single leadership style plays on motivating employees have been studied. However, in reality, an individual may exhibit more than one type of leadership style. This study aims to reveal how zhongyong leadership can lead to employees’ thriving at work in China, with a glance at ethical leadership as a moderator. The intrinsic motivation of employees is also considered as a mediator to show the specific path that bridges employees’ perceived leadership styles and their thriving at work.

Design/methodology/approach
Using three-period data from a sample of 346 employees working in Chinese companies, this study performs regression and bootstrap analyzes in PROCESS macro to test the hypotheses. By adopting the Johnson-Neyman technique, this study further identifies the specific moderating range within which ethical leadership makes a difference.

Findings
The positive correlation between zhongyong leadership and employees’ thriving at work only withstand scrutiny when the level of ethical leadership is sufficiently high and employees’ intrinsic motivation plays a mediating role. Specifically, when the ethical leadership level is higher than 6.022 (on a seven-point scale), zhongyong leadership can significantly increase the intrinsic motivation of employees and their thriving at work will be stronger as a result. On the contrary, when ethical leadership is lower than 1.089 (on a seven-point scale), this mediated relationship will head exactly in the opposite direction.

Originality/value
This study focuses on investigating the effects of multiple positive leadership behaviors on promoting employees’ thriving at work. The resultant findings provide compelling evidence for the integration of different leadership styles in practice and consolidate the theoretical underpinnings of related research on thriving at work.