bluuebunny/crossref_metadata_2025 huggingface dataset:
Chitosan-coated carboxylic acids show antimicrobial activity against antibiotic-resistant Gram-negative and positive pathogens
Authors: Cogan Tristan , James-Meyer Lynn
Published: September 2022

Antibiotic resistance in bacteria is suggested to be the greatest risk to human health, but new agents are not being brought to market as the rapid evolution of resistance to them means that drug development costs cannot be recouped. Fatty acids have been proposed as a new generation of antibiotics, but toxicity and poor absorption has meant that their use has been impractical in the past. Chitosan has been used to encapsulate other agents as nanoparticles, but has not been used with fatty acids. Here we show that chitosan can be modified to direct fatty acids towards Gram-positive or negative bacteria so that they exert antimicrobial effects. We show that fatty acids work as effective antibiotics in vitro and in vivo, with activity against extremely drug resistant pathogens. Bacteria exposed to them do not develop resistance to these agents, and they are not toxic to mammalian cells. Activity was seen against salmonellosis andC. difficileinfection in animal models. Our results demonstrate that fatty acids formulated as chitosan nanoparticles are effective antibiotics, and can be used for a long period of time without resistance developing. This suggests that the usage of fatty acids coated in this manner could be sold in sufficient quantities to recoup its development costs, overcoming this barrier. These agents would form a new class of antibiotics, with the novel property of lack of bacterial resistance.
Environmental feedback drives oxidative stress response heterogeneity in bacterial populations
Authors: Choudhary Divya , Lagage Valentine , Foster Kevin , Uphoff Stephan
Published: September 2022

Induction of phenotypic heterogeneity is a ubiquitous consequence of bacterial stress responses. It is commonly postulated that isogenic cells exploit stochastic molecular fluctuations to generate phenotypic heterogeneity as a population survival strategy (termed bet-hedging). However, it is also possible that each cell attempts to maximise its own chances of survival. In that case, the apparent heterogeneity could either be caused by inevitable molecular noise or by underlying deterministic mechanisms which have escaped observation. Here, we investigated the sources and consequences of gene expression heterogeneity in the response of Escherichia coli cells to hydrogen peroxide (H2O2) stress. A machine-learning model accurately predicted the variable responses of individual cells growing in structured populations, indicating that the phenotypic heterogeneity has a deterministic origin. The model further showed that spatio-temporal dynamics in H2O2 concentration were dictated by the H2O2 scavenging capacity and morphology of cells in the local environment. Hence, oxidative stress response fluctuations were in fact the result of a precise and rapid feedback between each cell and its immediate environment. Although single cells optimise their individual responses, the formation of short-range H2O2 gradients by their scavenging activities increases stress tolerance at the population level and leads to spatial variation in mutation rates.
Targeted insertion and reporter transgene activity at a gene safe harbor of the human blood fluke,Schistosoma mansoni
Authors: Ittiprasert Wannaporn , Moescheid Max F. , Chaparro Cristian , Mann Victoria H. , Quack Thomas , Rodpai Rutchanee , Miller André , Wistiphongpun Prapakorn , Buakaew Watunyoo , Mentink-Kane Margaret , Schmid Sarah , Popratiloff Anastas , Grevelding Christoph G. , Grunau Christoph , Brindley Paul J.
Published: September 2022

The identification and characterization of genomic safe harbor sites (GSH) aims to facilitate consistent transgene activity without disruption to the host cell genome. We combined genome annotation and chromatin structure analysis by computational approach to predict the location of four GSHs in the human blood fluke,Schistosoma mansoni, a major infectious pathogen of the tropics. Introduction of a transgene into the egg of the parasite was accomplished using CRISPR/Cas-assisted homology-directed repair and overlapping guide RNAs. Gene editing efficiencies of 24% and transgene-encoded fluorescence of 75% of gene-edited schistosome eggs were observed. These outcomes advance functional genomics for schistosomes by providing a tractable path towards transgenic helminths using homology directed repair-catalyzed transgene insertion. This approach should be adaptable to helminths generally.

Motivation

Functional genomics methods are needed in the arena of the Neglected Tropical Diseases, especially for helminth parasites, to facilitate basic and transformational studies to improve global public health. Gain-of-function phenotypes would be valuable in this context. Hence, the motivation for this investigation was to identify a genome safe harbor (GSH) site in the chromosomes of the human blood fluke,Schistosoma mansoniand, in a pilot approach, and to develop methods for transgene insertion and methods to characterize transgene performance following homology directed insertion at the schistosome GSH. The progress reported here can be expected to advance functional genomics for species of the Platyhelminthes – including model, free living species of planarians, and should be adaptable to helminths generally.
The spatiotemporal dynamics of semantic integration in the human brain
Authors: Murphy Elliot , Forseth Kiefer J. , Donos Cristian , Rollo Patrick S. , Tandon Nitin
Published: September 2022

Language depends critically on the integration of lexical information to derive semantic concepts. The neurobiology of this fundamental aspect of human cognition remains mostly unknown. Limitations of spatiotemporal resolution have previously rendered it difficult to disentangle processes involved in semantic integration from independent computations such as tracking word meaning and establishing referents. We utilized intracranial recordings (n = 58) during the presentation of orthographic descriptions that were either referential or non-referential to a common object. Referential contexts enabled high frequency broadband gamma activation (70–150 Hz) of a distributed network including the inferior frontal sulcus (IFS), medial parietal cortex (MPC) and medial temporal lobe (MTL) in the left, language-dominant hemisphere. Components of this network (IFS, MPC), alongside posterior superior temporal sulcus, showed greater engagement for trials that did not progressively isolate a limited set of referents, relative to trials that did. IFS and posterior middle temporal gyrus activity was modulated by semantic coherence, regardless of whether the sentence picked out a common object. Centered around IFS and spreading out dorsally towards middle frontal gyrus and ventrally towards anterior/posterior inferior frontal gyrus, we uncovered a cortical mosaic of functional specialization for reference, coherence and semantic narrowing. Early processing windows implicated IFS in all aspects of semantics, and in later windows sub-portions of IFS exposed a clearer functional tessellation with some remaining overlap. This work unveils how lateral fronto-temporal regions make distinctly rich semantic contributions and are involved jointly in semantic integration and conflict resolution, depending on the sub-region and processing stage.
Immuno-targeting of Gram-positive Pathogens via a Cell Wall Binding Tick Antifreeze Protein
Authors: Dalesandro Brianna E. , Pires Marcos M.
Published: September 2022

The human immune system employs several mechanisms to defend against pathogenic bacteria. However, pathogenic bacterial cells have evolved means to counter these responses, rendering our immune system less effective. Immunological agents that supplement or modulate the host immune response have proven to have powerful therapeutic potential, although this modality is less explored against bacterial pathogens. We describe the application of a bacterial binding protein to re-engage the immune system towards pathogenic bacteria. More specifically, a hapten was conjugated to a protein expressed by Ixodes scapularis ticks, called Ixodes scapularis antifreeze glycoprotein (IAFGP), that has high affinity for the D-alanine residue on the peptidoglycan of the bacterial cell wall. We showed that a fragment of this protein retained high surface binding affinity. Moreover, when conjugated to a hapten this conjugate led to the display of haptens on the cell surface of vancomycin-resistant Enterococcus faecalis. Hapten display then induced the recruitment of antibodies and promoted immune-cell mediated uptake of bacterial pathogens. These results demonstrate the feasibility in using cell wall binding agents as the basis of a class of bacterial immunotherapies against bacterial pathogens.
Diversity and ecology of Caudoviricetes phages with genome terminal repeats in fecal metagenomes from four Dutch cohorts
Authors: Gulyaeva Anastasia , Garmaeva Sanzhima , Kurilshikov Alexander , Vich Vila Arnau , Riksen Niels P. , Netea Mihai G. , Weersma Rinse K. , Fu Jingyuan , Zhernakova Alexandra
Published: September 2022

The human gut harbors numerous viruses infecting the human host, microbes and other inhabitants of the gastrointestinal tract. Most of these viruses remain undiscovered, and their influence on human health is unknown. Here we characterize viral genomes in gut metagenomic data from 1,950 individuals from four population and patient cohorts. We focus on a subset of viruses that is highly abundant in the gut, remains largely uncharacterized, and allows confident complete genome identification – phages that belong to the class Caudoviricetes and possess genome terminal repeats. We detect 1,899 species-level units belonging to this subset, 19% of which do not have complete representative genomes in major public gut virome databases. These units display diverse genomic features, are predicted to infect a wide range of microbial hosts, and on average account for < 1% of metagenomic reads. Analysis of longitudinal data from 338 individuals shows that the composition of this fraction of the virome remained relatively stable over a period of 4 years. We also demonstrate that 54 species-level units are highly prevalent (detected in > 5% of individuals in a cohort). Finally, we find 34 associations between highly prevalent phages and human phenotypes, 24 of which can be explained by the relative abundance of potential hosts.
The mitochondrial ferredoxin-like is essential for the formation of complex I-containing respiratory supercomplexes in Arabidopsis thaliana
Authors: Röhricht Helene , Przybyla-Toscano Jonathan , Forner Joachim , Boussardon Clément , Keech Olivier , Rouhier Nicolas , Meyer Etienne H.
Published: September 2022

In eukaryotes, mitochondrial ATP is mainly produced by the oxidative phosphorylation (OXPHOS) system, which is composed of five multiprotein complexes (complexes I to V). Analyses of the OXPHOS system by native gel electrophoresis revealed an organization of OXPHOS complexes in supercomplexes, but their roles and assembly pathways remain unclear. In this study, we characterized an atypical mitochondrial ferredoxin (mFDX-like). This protein was previously found associated with complex I, being part of the bridge domain linking the matrix and membrane arms of the complex. A phylogenetic analysis suggests that the Arabidopsis thaliana mFDX-like evolved from classical mitochondrial ferredoxin, but it lost one of the cysteines required for the coordination of the iron-sulfur (Fe-S) cluster essential for the electron transfer function of ferredoxins. Accordingly, our biochemical study shows that AtmFDX-like does not bind an Fe-S cluster, and is therefore unlikely to be involved in electron transfer reactions. To study the function of mFDX-like, we created deletion lines in Arabidopsis using a CRISPR/Cas9 approach. These lines do not show any growth phenotype under standard growth condition. However, the characterization of the OXPHOS system demonstrates that mFDX-like is important for the assembly of complex I, and essential for the formation of complex I-containing supercomplexes. We propose that mFDX-like and the bridge domain are required for the correct conformation of the membrane arm of complex I that is essential for the association of complex I with complex III to form supercomplexes.
Global mapping of RNA-chromatin contacts reveals a proximity-dominated connectivity model for ncRNA-gene interactions
Authors: Limouse Charles , Smith Owen K. , Jukam David , Fryer Kelsey A. , Greenleaf William J. , Straight Aaron F.
Published: September 2022

Non-coding RNAs (ncRNAs) are transcribed throughout the genome and provide regulatory inputs to gene expression through their interaction with chromatin. Yet, the genomic targets and functions of most ncRNAs are unknown. Here we use chromatin-associated RNA sequencing (ChAR-seq) to map the global network of ncRNA interactions with chromatin in human embryonic stem cells, and the dynamic changes in interactions during differentiation into definitive endoderm. We uncover general principles governing the organization of the RNA- chromatin interactome, demonstrating that nearly all ncRNAs exclusively interact with genes in close three-dimensional proximity to their locus, and provide a model predicting the interactome. We uncover RNAs that interact with many loci across the genome, and unveil thousands of unannotated RNAs that dynamically interact with chromatin. By relating the dynamics of the interactome to changes in gene expression, we demonstrate that activation or repression of individual genes is unlikely to be controlled by a single ncRNA.
Distinguishing Signal from Noise: Understanding Patterns of Non-Detections to Inform Accurate Quantitative Metabarcoding
Authors: Gold Zachary , Shelton Andrew Olaf , Casendino Helen R. , Duprey Joe , Gallego Ramón , Van Cise Amy , Fisher Mary , Jensen Alexander J. , D’Agnese Erin , Allan Elizabeth Andruszkiewicz , Ramón-Laca Ana , Garber-Yonts Maya , Labare Michaela , Parsons Kim M. , Kelly Ryan P.
Published: September 2022

Correcting for amplification biases in genetic metabarcoding data can yield quantitative estimates of template DNA concentrations. However, a major source of uncertainty in metabarcoding data is the presence of non-detections, where a technical PCR replicate fails to detect a species observed in other replicates. Such non-detections are an important special case of variability among technical replicates in metabarcoding data, particularly in environmental samples. While many sampling and amplification processes underlie observed variation in metabarcoding data, understanding the causes of non-detections is an important step in distinguishing signal from noise in metabarcoding studies. Here, we use both simulated and empirical data to 1) develop a qualitative understanding of how non-detections arise in metabarcoding data, 2) outline steps to recognize uninformative data in practice, and 3) identify the conditions under which amplicon sequence data can reliably detect underlying biological signals. We show in both simulations and empirical data that, for a given species, the rate of non-detections among technical replicates is a function of both the template DNA concentration and species-specific amplification efficiency. Consequently, we conclude metabarcoding datasets are strongly affected by (1) deterministic amplification biases during PCR and (2) stochastic sampling of amplicons during sequencing — both of which we can model — but also by (3) stochastic sampling of rare molecules prior to PCR, which remains a frontier for quantitative metabarcoding. Our results highlight the importance of estimating species-specific amplification efficiencies and critically evaluating patterns of non-detection in metabarcoding datasets to better distinguish environmental signal from the noise inherent in molecular detections of rare targets.
Plant production of high affinity nanobodies that block SARS-CoV-2 spike protein binding with its receptor, human angiotensin converting enzyme
Authors: Pitino Marco , Fleites Laura A. , Shrum Lauren , Heck Michelle , Shatters Robert G.
Published: September 2022

Nanobodies® (VHH antibodies), are small peptides that represent the antigen binding domain, VHH of unique single domain antibodies (heavy chain only antibodies, HcAb) derived from camelids. Here, we demonstrate production of VHH nanobodies against the SARS-CoV-2 spike proteins in the solanaceous plant Nicotiana benthamiana through transient expression and their subsequent detection verified through western blot. We demonstrate that these nanobodies competitively inhibit binding between the SARS-CoV-2 spike protein receptor binding domain and its human receptor protein, angiotensin converting enzyme 2 (ACE2). We present plant production of nanobodies as an economical and scalable alternative to rapidly respond to therapeutic needs for emerging pathogens in human medicine and agriculture.
Comparative analysis of military heritage in Slovakia, Slovenia and Poland with emphasis on its use in tourism
Authors: Drobňák Martin , Turik Radoslav , Šenková Anna , Ratnayake Kaščáková Dagmara , Derco Jan
Published: September 2022

Purpose

The paper deals with battlefield tourism and war monuments in the Slovak Republic, Slovenia and Poland. The care of these monuments and their use in tourism today takes place separately and it is interesting to see how the same potential can be used in different ways. One of the aims of the paper is to draw attention to this fact and at the same time to present the possibilities of how to improve the use of this heritage by mutual cooperation.

Design/methodology/approach

It is based on field research of the care of military-historical monuments. At the same time, it presents, in the form of retrospective studies, basic experiences from abroad – specifically the construction of thematic trails in Slovakia, Slovenia (The Walk of the Peace) and Poland (The First World War's Eastern Front Trail).

Findings

The paper points out aspects such as the care of battlefield tourism sites, cross-border cooperation in the creation of tourism products, the creation of a strategic conceptual framework for the protection of World War I monuments, their presentation to tourists, cooperation between the state, local government and the third sector.

Originality/value

There was no systematic research in this area in Central and Eastern Europe.
Will winning always encourage risk-taking? The effects of winning–losing perception on consumers’ risk preference
Authors: Wen Beixi , Chang En-Chung
Published: September 2022

Purpose

This research examines the effects of winning–losing perception, generated from success and failure results, on consumers’ risk preference.

Design/methodology/approach

Using different manipulations of success and failure and different measurements of risk preference tendency, the authors conducted five experiments to carry out the research.

Findings

Using different manipulations of success and failure and different measurements of risk preference tendency, five experiments were conducted to demonstrate that a clear success increases consumer’ sense of power, which in turn raises their subsequent risk preference; a clear failure, however, decreases consumers’ sense of power, which in turn reduces their subsequent risk preference. Furthermore, a close result can moderate this effect; that is, the difference between narrow-winners and narrow-losers’ risk preferences is weakened.

Originality/value

This study further enriches the research on the impact of winning–losing perception on individuals’ behavior and provides suggestions on how to use the results of online and offline competitions to carry out marketing activities.
Wrinkles in a CSR story: mismatched agendas in fast fashion service brands' CSR reputation
Authors: Mickelsson Jacob , van Haren Joep J.G.M. , Lemmink Jos G.A.M.
Published: September 2022

Purpose

Corporate social responsibility (CSR) is an increasingly important issue for service brands in fast fashion retailing, as consumers' negative impressions about retailers' CSR activities influence brand experience. Consumers' impressions of CSR efforts arise based on agendas communicated through many channels from different sources. The paper unravels the ‘wrinkles’, i.e. possible mismatches in CSR communication around service brands by studying differences between the three main sources of fast fashion brand-related CSR agendas: Autonomous company communication, news media and social media postings by consumers.

Design/methodology/approach

The authors use structural topic modeling (STM) to analyze a corpus of texts focusing on the CSR efforts of three major fast fashion service brands over three years. The texts included 89 items of company communication (CSR reports and press releases), 5,351 news media articles about the brands' CSR efforts and 57,377 consumer generated tweets about the brands.

Findings

The STM analysis extracted 26 different CRS-related topics from the texts. Results showed differences in how much the three sources emphasized topics. The brands' own communication puts emphasis on environmental responsibility. News media tended to report on economic issues, treatment of employees and specific CSR-related events. Twitter showed more activity in discussing incident-based and emotionally charged topics.

Research limitations/implications

The results feed into the ongoing discussion about how companies' CSR communication relates to communication in the press and among consumers. The authors highlight themes in the individual topics that are emphasized by the three sources, and discuss how CSR themes emerge in the overall transformative agenda.

Practical implications

The paper highlights how fast fashion service brands can identify and understand different CSR agendas arising around their brand. Insight into such agendas can be used to tailor the brands' communication strategies.

Originality/value

The paper contributes to the understanding of the factors behind fashion service brands' CSR reputation, highlighting how the three main sources of CSR reputation (company reports, news and social media) emphasize different types of agendas.
Implementation and evaluation of the school's COVID-19 prevention website
Authors: Chang Jui-Hung , Wang Chi-Jane , Zhong Hua-Xu , Chen Pei-Wen , Pan Ai-Jou , Chiu Po-Sheng
Published: September 2022

Purpose

The purpose of this study is to investigate the effects of the Perceptions of coronavirus 2019 (COVID-19) questionnaire and the Information System Success Questionnaire on students when using the school's COVID-19 epidemic prevention website. The study is aimed toward analyzing both questionnaires as well as evaluating an epidemic prevention website.

Design/methodology/approach

The school's COVID-19 prevention website and two questionnaires (Perceptions of COVID-19 and the Information System Success Questionnaire) are examined in order to investigate 73 students' COVID-19 perceptions. An open-ended question was used as the qualitative data to support quantitative data and evaluate a university's COVID-19 epidemic prevention website from a southern university in Taiwan.

Findings

The findings indicated that most students evaluated the school's COVID-19 website positively and were satisfied. In the open-ended questions, the majority of students rated the quality of the system positively and the need to fix some defects. Students have different COVID-19 perceptions and social distance compliance based on their current situations.

Practical implications

This study provides researchers and website developers a broader understanding of the construction of the school's COVID-19 prevention website and a better understanding of student's COVID-19 perceptions.

Originality/value

To the best of the authors' knowledge, this is the first study examining a school's epidemic prevention website, which is measured by the Information Success Questionnaire and the Perceptions of COVID-19 Questionnaire for college students.
Profiling employee psychological responses during restructuring and downsizing in the public sector: “Flourishers”, “Recoverers” and “Ambivalents”
Authors: Edwards Martin R. , Clinton Michael
Published: September 2022

Purpose

This study aims to examine configurations of person-centered psychological change during organizational restructuring and downsizing in a public sector setting. Drawing on a social cognitive framework of organizational change the authors explore and identify the existence of different groups of employees who demonstrate varied responses (on commitment, engagement and anxiety) to restructuring and downsizing.

Design/methodology/approach

Surveys were collected from employees in three longitudinal waves (Time 1 N = 253; Time 2 N = 107; Time 3 N = 93, twelve months apart) at a UK public sector organization shortly before, during and after restructuring and downsizing.

Findings

Three classes of response emerged based on levels of and change in anxiety, organizational commitment and work engagement: a positive “Flourishers” profile was identified along with two relatively negative response profiles, labeled as “Recoverers” and “Ambivalents”. Higher levels of job control accounted for membership of the more positive response profile; higher structural uncertainty predicted membership of the most negative response group.

Practical implications

Using a person-centered approach, the authors form an understanding of different types of employee responses to downsizing; along with potential factors that help explain why groups of employees may exhibit certain psychological response patterns and may need to be managed differently during change. Thus, this approach provides greater understanding to researchers and managers of the varied impact that restructuring/downsizing has on the workforce.

Originality/value

To date there has been little research exploring employee responses to organizational restructuring and downsizing that has attempted to take a person-centered approach, which assumes population heterogeneity. Unlike variable centered approaches, this unique approach helps identify different patterns of employee responses to restructuring and downsizing.
What innovations would enable the tourism and hospitality industry in Guyana to re-build?
Authors: Sinclair Donald , Ishmael Camille Allison
Published: September 2022

Purpose

The purpose of this paper is to provide answers to the following questions: How was the tourism and hospitality industry in Guyana impacted by the COVID-19 pandemic? What recovery strategies have been designed? What are the prospects for the successful implementation of those strategies?

Design/methodology/approach

The paper is based upon a qualitative analysis of the recommendations and formal proposals that were issued from a variety of sources within government, private sector and academia during the 2019–2021 period of the pandemic.

Findings

The main findings of this paper are that an industry consensus exists regarding the severity of the impact of the pandemic and the need for a collaborative strategy to be designed and innovative measures implemented in order to accelerate industry recovery. This recovery entails attracting to Destination Guyana both a new wave of health-aware travellers as well as visitors from traditional markets and the diaspora. Analysis suggests that there is a broad consensus and convergence of objectives that embrace both government and private sector.

Originality/value

The COVID-19 pandemic has given rise to a significant quantity of literature and has seen a conspicuous incorporation of scientific medical data into tourism analysis. This is only to be expected in the circumstance of a global health emergency that has devastated the global tourism industry. The value of this article lies principally in its proposal of innovative methods and strategies that are critical to tourism recovery.
Climate change and tourism: a paradigm for enhancing tourism resilience in SIDS
Authors: Pedapalli Sarath Chandra Kanth , Gupta Bharti , Mahajan Prachi
Published: September 2022

Purpose

The purpose of this paper is to examine how the changing pattern of climatic conditions is likely to impact tourism in Small island developing states (SIDS). Further, the study suggests appropriate management practices that could help in tackling the consequences of climate change on the tourism sector in SIDS.

Design/methodology/approach

Recently published articles and reports are analysed in relation to the effects of climate change on the tourism sector, and approaches to improve the resilience of tourism in SIDS.

Findings

The study has discovered the likely effects of climate change on the tourism business and found a high possibility of a decline in the tourism-based economy as an outcome. Furthermore, the study found that the absence of institutional alliances, government backing, resilient policy and advanced technological mechanisms are driving the associated risks of climate change in tourism.

Practical implications

The framework presented can assist tourism stakeholders to plan, prepare, mitigate and build resilience against the effects of climate variability on the tourism business in SIDS.

Originality/value

This study presents some practical measures for tourism stakeholders to enable them to reduce the effects of climate change on tourism activities in Small island developing states (SIDS).
Hydrothermal conditions determine soil potential net N mineralization rates in arid and semi‐arid grasslands
Authors: Hu Shuya , Wang Changhui , Risch Anita C. , Liu Yuan , Li Yang , Li Lei , Xu Xiaohui , He Nianpeng , Han Xingguo , Huang Jianhui
Published: September 2022

Soil net nitrogen (N) mineralization is a key biogeochemical process influencing plant available N and net primary productivity in terrestrial ecosystems. However, the spatial variations and controlling factors of soil net N mineralization (RPNM) in arid and semi‐arid grasslands are less studied and unclear.

In this study, we investigated the soil RPNM by performing a laboratory incubation experiment. Soil samples were collected from 30 sites in three east–west transects on the Inner Mongolia Plateau (MP), Loess Plateau (LP) and Tibetan Plateau (TP) along a 3200 km arid and semi‐arid grassland gradient, with each transect containing three different grassland types (meadow steppe [MS], typical steppe [TS] and desert steppe [DS], respectively).

Results showed that the average RPNM values ranged from −0.37 to 1.29 mg N kg−1 day−1, with a significantly lower RPNM found in the DS (0.08 ± 0.01 mg N kg−1 day−1) compared with those in the MS (0.30 ± 0.03 mg N kg−1 day−1) and in the TS (0.33 ± 0.03 mg N kg−1 day−1) in the MP and LP transects (p < 0.05). This difference could be explained by variations in climatic and soil factors, such as hydrothermal index (HT), the soil pH, soil organic matter (SOM) and precipitation. However, no significant differences in RPNM were found among different grassland types in the TP transect, possibly due to the similarly low microbial activity, as indicated by the microbial biomass carbon values. Across all three grassland transects, HT, SOM and microbial variables were the major factors controlling RPNM, which together explained 20.7% of the variation in RPNM. Further structural equation model analysis indicated HT was an integral predictor of RPNM, directly or indirectly via SOM, under different conditions of precipitation and temperature.

Our findings provide field evidence and parameters for biogeochemical cycling to better predict future N transformation processes under changing precipitation and temperature regimes across a wide range of arid and semi‐arid grassland ecosystems.

Read the free Plain Language Summary for this article on the Journal blog.
Niche differences, not fitness differences, explain predicted coexistence across ecological groups
Authors: Buche Lisa , Spaak Jurg W. , Jarillo Javier , De Laender Frederik
Published: September 2022

Understanding the drivers of species coexistence is essential in ecology. Niche and fitness differences (i.e. how species limit themselves compared to others and species' differences in competitive ability, respectively) permit studying the consequences of species interactions. Yet, the multitude of methods to compute niche and fitness differences hampers cross‐community comparisons. Such shortcoming leaves a gap in our understanding of the natural drivers of species coexistence and whether niche or/and fitness differences capture them.

Here, we standardised niche and fitness differences across 953 species pairs to investigate species coexistence across ecological groups and methodological settings (experimental setup, natural co‐occurrence, population model used and growth method). Using data gathered from 29 empirical papers, we asked whether large niche differences, small fitness differences or both explain predicted coexistence. Moreover, we performed an automated clustering algorithm to understand whether different underlying mechanisms drive species interactions. Finally, we tested whether any ecological or/and methodological settings drive these clusters.

Species pairs predicted to coexist have larger niche differences but not smaller fitness differences than species pairs predicted not to coexist. Also, species pairs group into two clear clusters along the niche difference axis: those predicted to coexist and those that are not. Surprisingly, ecological or methodological settings do not drive these clusters.

Synthesis. Overall, our results show that species coexistence is mainly influenced by mechanisms acting on niche differences, highlighting the importance of sustaining mechanisms that promote niche differences to maintain species coexistence. In addition, our results provide evidence that communities predicted to coexist differ from those that are not in ways that transcend their ecological grouping.
Treatment planning computed tomography radiomics for predicting treatment outcomes and haematological toxicities in locally advanced cervical cancer treated with radiotherapy: A retrospective cohort study
Authors: Ren Kang , Shen Lin , Qiu Jianfeng , Sun Kui , Chen Tingyin , Xuan Long , Yang Minwu , She Hao‐Yuan , Shen Liangfang , Zhu Hong , Deng Lan , Jing Di , Shi Liting
Published: September 2022

Objective

We evaluated whether radiomic features extracted from planning computed tomography (CT) scans predict clinical end points in patients with locally advanced cervical cancer (LACC) undergoing intensity‐modulated radiation therapy and brachytherapy.

Design

A retrospective cohort study.

Setting

Xiangya Hospital of Central South University, Changsha, Hunan, China.

Population

Two hundred and fifty‐seven LACC patients who were treated with intensity‐modulated radiotherapy from 2014 to 2017.

Methods

Patients were allocated into the training/validation sets (3:1 ratio) using proportional random sampling, resulting in the same proportion of groups in the two sets. We extracted 254 radiomic features from each of the gross target volume, pelvis and sacral vertebrae. The sequentially backward elimination support vector machine algorithm was used for feature selection and end point prediction.

Main outcomes and measures

Clinical end points include tumour complete response (CR), 5‐year overall survival (OS), anaemia, and leucopenia.

Results

A combination of ten clinicopathological parameters and 34 radiomic features performed best for predicting CR (validation balanced accuracy: 80.8%). The validation balanced accuracy of 54 radiomic features was 85.8% for OS, and their scores can stratify patients into the low‐risk and high‐risk groups (5‐year OS: 95.5% versus 36.4%, p < 0.001). The clinical and radiomic models were also predictive of anaemia and leucopenia (validation balanced accuracies: 71.0% and 69.9%).

Conclusion

This study demonstrated that combining clinicopathological parameters with CT‐based radiomics may have value for predicting clinical end points in LACC. If validated, this model may guide therapeutic strategy to optimise the effectiveness and minimise toxicity or treatment for LACC.
Multiple endocrine factors regulate nutrient mobilization and storage inAedes aegyptiduring a gonadotrophic cycle
Authors: Dou Xiaoyi , Chen Kangkang , Brown Mark R. , Strand Michael R.
Published: September 2022

Anautogenous mosquitoes must blood feed on a vertebrate host to produce eggs. Each gonadotrophic cycle is subdivided into a sugar‐feeding previtellogenic phase that produces primary follicles and a blood meal‐activated vitellogenic phase in which large numbers of eggs synchronously mature and are laid. Multiple endocrine factors including juvenile hormone (JH), insulin‐like peptides (ILPs), ovary ecdysteroidogenic hormone (OEH), and 20‐hydroxyecdysone (20E) coordinate each gonadotrophic cycle. Egg formation also requires nutrients from feeding that are stored in the fat body. Regulation of egg formation is best understood inAedes aegyptibut the role different endocrine factors play in regulating nutrient mobilization and storage remains unclear. In this study, we report that adult femaleAe. aegyptimaintained triacylglycerol (TAG) stores during the previtellogenic phase of the first gonadotrophic cycle while glycogen stores declined. In contrast, TAG and glycogen stores were rapidly mobilized during the vitellogenic phase and then replenishment. Several genes encoding enzymes with functions in TAG and glycogen metabolism were differentially expressed in the fat body, which suggested regulation was mediated in part at the transcriptional level. Gain of function assays indicated that stored nutrients were primarily mobilized by adipokinetic hormone (AKH) while juvenoids and OEH regulated replenishment. ILP3 further showed evidence of negatively regulating certain lipolytic enzymes. Loss of function assays indicated AKH depends on the AKH receptor (AKHR) for function. Altogether, our results indicate that the opposing activities of different hormones regulate nutrient stores during a gonadotrophic cycle inAe. aegypti.
A novel odor stimulation system in freely moving, behaving animals
Authors: GUO Xinsong , LI Shan , YU Xuejie , WU Tingting , LIU Penglai , SHAO Yufeng , LI Anan
Published: September 2022

Precise and reliable presentation of odorants to animals is crucial for olfactory studies. Although odor stimulation systems in anesthetized or awake, head‐fixed animals are well established, temporally precise odor presentation in awake, freely moving animals remains a challenge. Here, we describe a new odor stimulation system which presents odors directly to the nostrils of freely moving mice. The system comprises 3 modules: an odor‐delivery module, an odor‐generation module, and a control module. The new system is precise and temporally reliable, and odor stimulation can be triggered by specific sniffing phases or other events. Moreover, the system can be combined with neural recordings, such as electrophysiology, and olfactory behavioral tests to investigate how neurons in the brain represent odor information during individual olfactory behaviors. This innovative odor stimulation system may replace traditional stimulation systems: It will enable precise odor presentation in a wide range of olfactory studies in freely moving animals.
Temperature determines the shift of thermal neutral zone and influences thermogenic capacity in striped hamsters
Authors: LIAO Shasha , TAN Song , JIANG Meizhi , WEN Jing , LIU Jinsong , CAO Jing , LI Ming , ZHAO Zhijun
Published: September 2022

The thermoneutral zone (TNZ) reflects the adaptation of mammals to their natural habitat. However, it remains unclear how TNZ shifts in response to variations in ambient temperature. To test the hypothesis that ambient temperature plays a key role in determining TNZ variations between seasons, we measured metabolic rate, body temperature, and cytochrome c oxidase (COX) activity of several visceral organs in striped hamsters (Cricetulus barabensis) either acclimated to semi‐natural conditions over a year, or subjected to a gradual decrease in mean temperature from 30 ± 1°C to −15 ± 1°C. The TNZ range in striped hamsters differed seasonally, with a wider TNZ and a lower lower‐critical temperature in winter compared to summer. The hamsters showed a considerable leftward shift of lower‐critical temperature from 30°C to 20°C after the ambient temperature of acclimation from 30°C down to −15°C, whereas the upper‐critical temperature of TNZ remained fixed at 32.5°C. The resting metabolic rate in thermoneutral zone (RMRt), nonshivering thermogenesis (NST), and COX activity of brown adipose tissue, liver, skeletal muscle, brain, and kidneys, increased significantly in hamsters acclimated at lower ambient temperatures. Following acute exposure to 5°C and −15°C, hamsters acclimated to 32.5°C had significantly lower maximal NST and lower serum thyroid tri‐iodothyronine (T3) levels compared to those kept at 23°C. These findings suggest that acclimation to the upper‐critical temperature of TNZ impairs the hamsters’ thermogenic capacity to cope with extreme cold temperature. Reduced ambient temperature was mainly responsible for the leftward shift of TNZ in striped hamsters, which reflects the adaptation to cold environments.
Machine Learning Assisted Reservoir Operation Model for Long‐Term Water Management Simulation
Authors: Gangrade Sudershan , Lu Dan , Kao Shih‐Chieh , Painter Scott L.
Published: September 2022

This study explores strategies for long‐term reservoir simulations by combining generic rule‐based reservoir management model (RMM) and machine learning (ML) models for two major multipurpose reservoirs — Allatoona Lake and Lake Sidney Lanier in the southeastern United States. First, a standalone RMM is developed to simulate daily release and storage during Water Year 1981–2015. Next, using Long‐Short Term Memory (LSTM) as the ML technique, a standalone LSTM model is trained based on reservoir inflow and meteorological observations to simulate reservoir release and estimate reservoir storage through water balance calculation. Three hybrid modeling strategies are developed, one using RMM output as an additional LSTM input (H1), another using LSTM as the initial release estimate in RMM (H2), and the third combining the first two strategies (H3). The Nash–Sutcliffe efficiency (NSE) for release (NSE‐r), storage (NSE‐s), and their mean (NSE‐avg) are used for model evaluation. Overall, H1 improves NSE‐r to 0.65 and 0.54 for Allatoona and Lanier, respectively, compared to standalone RMM (0.44 and 0.21); however, its storage trajectory did not produce a physically feasible solution, similar to LSTM. H2 and especially H3 show that they can retain the best features from RMM and LSTM, with H3 NSE‐avg being 0.695 and 0.55 for Allatoona and Lanier outperforming RMM (0.615 and 0.29). The findings suggest a robust simulation capacity for large‐scale water management in future studies.
A root auto tracing and analysis (ARATA): An automatic analysis software for detecting fine roots in images from flatbed optical scanners
Authors: Yabuki Arata , Ikeno Hidetoshi , Dannoura Masako
Published: September 2022

Buried scanners are often used to study fine root dynamics by continuously observing them from the images taken at a fixed point. Accordingly, software have been developed to support operators to quantitatively analyse fine roots from scanned images. However, image processing is still time‐consuming work.

Deep learning has achieved impressive results as a method for recognising objects in pixel units. In this study, we attempted to automate the image analysis of fine roots using convolutional neural network.

Using a root auto tracing and analysis (ARATA), we succeeded in extracting fine roots from scanned images and calculated projected area of fine roots for long‐term dynamics.

Our software enables the automatic processing of scanned images acquired at various study sites and accelerates the study of fine root dynamics over extended time periods.
Extending isolation by resistance to predict genetic connectivity
Authors: Fletcher Robert J. , Sefair Jorge A. , Kortessis Nicholas , Jaffe Roldolfo , Holt Robert D. , Robertson Ellen P. , Duncan Sarah I. , Marx Andrew J. , Austin James D.
Published: September 2022

Genetic connectivity lies at the heart of evolutionary theory, and landscape genetics has rapidly advanced to understand how gene flow can be impacted by the environment. Isolation by landscape resistance, often inferred through the use of circuit theory, is increasingly identified as being critical for predicting genetic connectivity across complex landscapes. Yet landscape impediments to migration can arise from fundamentally different processes, such as landscape gradients causing directional migration and mortality during migration, which can be challenging to address. Spatial absorbing Markov chains (SAMC) have been introduced to understand and predict these (and other) processes affecting connectivity in ecological settings, but the relationship of this framework to landscape genetics remains unclear.

Here, we relate the SAMC to population genetics theory, provide simulations to interpret the extent to which the SAMC can predict genetic metrics and demonstrate how the SAMC can be applied to genomic data using an example with an endangered species, the Panama City crayfishProcambarus econfinae, where directional migration is hypothesized to occur.

The use of the SAMC for landscape genetics can be justified based on similar grounds to using circuit theory, as we show how circuit theory is a special case of this framework. The SAMC can extend circuit‐theoretic connectivity modelling by quantifying both directional resistance to migration and acknowledging the difference between migration mortality and resistance to migration. Our empirical example highlights that the SAMC better predicts population structure than circuit theory and least‐cost analysis by acknowledging asymmetric environmental gradients (i.e. slope) and migration mortality in this species.

These results provide a foundation for applying the SAMC to landscape genetics. This framework extends isolation‐by‐resistance modelling to account for some common processes that can impact gene flow, which can improve predicting genetic connectivity across complex landscapes.
Incidence of conversion to general anaesthesia and need for intravenous supplementation in parturients undergoing caesarean section under spinal anaesthesia: A retrospective observational study
Authors: Stav Michael , Matatov Yuri , Hoffmann Dana , Heesen Philip , Gliesche Vincent , Binyamin Yair , Ioscovich Alexander , Eidelman Leonid A. , Orbach‐Zinger Sharon
Published: September 2022

Background

Conversion from spinal anaesthesia to general anaesthesia (GA) was shown to be associated with more complications. It has been postulated that spinal injection of a low dose of local anaesthetic is a risk factor. We aimed to discover the rate of conversion from spinal anaesthesia to GA in women who received at least 10 mg heavy bupivacaine and opioids and assess its risk factors.

Methods

All women that underwent spinal anaesthesia for caesarean section from 1 January 2017 to 31 December 2020 were included in this analysis. Spinal anaesthesia was performed according to department protocol using heavy bupivacaine 0.5% 10–13 mg, fentanyl 20 μg, and morphine 0.1 mg. We examined rate of conversion from spinal anaesthesia to GA and rate of need for analgesia/sedation.

Results

There were 1.7% of women that required conversion to GA. Bupivacaine dose (OR 0.54 [95% CI 0.38 to 0.75], p < 0.001), surgery time (OR 1.03 [95% CI 1.02 to 1.04], p < 0.001), emergency caesarean section (OR 1.06 [95% CI 1.16 to 3.76], p = 0.015), and postpartum haemorrhage (OR 5.96 [95% CI 1.09 to 25.18], p = 0.025) were independent predictors of need for conversion to GA. Of the women who had CS under spinal anaesthesia, 4.1% of parturients required intraoperative analgesics/sedatives and 9.1% required anxiolysis.

Conclusions

A small proportion of women required conversion to GA. This conversion occurred especially with emergency caesarean section and when low spinal bupivacaine doses were used.