bluuebunny/crossref_metadata_2025 huggingface dataset:
Forecasting of a complex microbial community using meta-omics
Authors: Delogu F. , Kunath B. J. , Queirós P. M. , Halder R. , Lebrun L. A. , Pope P. B. , May P. , Widder S. , Muller E. E. L. , Wilmes P.
Published: October 2022

Microbial communities are complex assemblages whose dynamics are shaped by abiotic and biotic factors. A major challenge concerns correctly forecasting the community behaviour in the future. In this context, communities in biological wastewater treatment plants (BWWTPs) represent excellent model systems, because forecasting them is required to ultimately control and operate the plants in a sustainable manner. Here, we forecast the microbial community from the water-air interface of the anaerobic tank of a BWWTP via longitudinal meta-omics (metagenomics, metatranscriptomics and metaproteomics) data covering 14 months at weekly intervals. We extracted all the available time-dependent information, summarised it in 17 temporal signals (explaining 91.1% of the temporal variance) and linked them over time to rebuild the sequence of ecological phenomena behind the community dynamics. We forecasted the signals over the following five years and tested the predictions with 21 extra samples. We were able to correctly forecast five signals accounting for 22.5% of the time-dependent information in the system and generate mechanistic predictions on the ecological events in the community (e.g. a predation cycle involving bacteria, viruses and amoebas). Through the forecasting of the 17 signals and the environmental variables readings we reconstructed the gene abundance and expression for the following 5 years, showing a nearly perfect trend prediction (coefficient of determination ≥ 0.97) for the first 2 years. The study demonstrates the maturity of microbial ecology to forecast composition and gene expression of open microbial ecosystems using year-spanning interactions between community cycles and environmental parameters.
Engineered synthetic one-carbon fixation exceeds yield of the Calvin Cycle
Authors: Dronsella Beau , Orsi Enrico , Benito-Vaquerizo Sara , Glatter Timo , Bar-Even Arren , Erb Tobias. J. , Claassens Nico J.
Published: October 2022

One-carbon (C1) feedstocks derived from CO2and renewable electricity, such as formate, are promising substrates for sustainable production of chemicals, food and fuels. Energetically more efficient, engineered C1-fixation pathways were proposed to increase biomass yields above their natural counterparts, but have so far not been shown to achieve this. Here, we replace the native ‘energy-inefficient’ Calvin-Benson-Bassham (CBB) cycle inCupriavidus necatorby genomic integration of the synthetic reductive glycine pathway for growth on formate. Our final engineered strain reaches a higher biomass yield than the CBB-cycle-utilizing wild type, showing for the first time that efficiencies found in natural metabolism can be exceeded via a synthetic pathway. This yield increase demonstrates the potential of synthetic metabolism and is an important step towards realizing truly sustainable, economically feasible bio-based production.
Structure of human TRPM8 channel
Authors: Palchevskyi Sergii , Czarnocki-Cieciura Mariusz , Vistoli Giulio , Gervasoni Silvia , Nowak Elżbieta , Beccari Andrea R. , Nowotny Marcin , Talarico Carmine
Published: October 2022

TRPM8 is a calcium ion channel that is activated by multiple factors, such as temperature, voltage, pressure, and osmolality. It is a therapeutic target for anticancer drug development, and its modulators can be utilized for several pathological conditions. Here, we present a cryo-electron microscopy structure of a human TRPM8 channel in the closed state that was solved at 2.7 Å resolution. Based on our reconstruction, we built the most complete model of the N-terminal pre-melastatin homology region. We also visualized several ligands that are bound by the protein and modeled how the human channel interacts with icilin. Analyses of pore helices showed that all available TRPM8 structures can be grouped into closed and desensitized states based on the register of pore helix S6 and the resulting positioning of particular amino acid residues at the channel constriction.
Broadly neutralizing SARS-CoV-2 antibodies through epitope-based selection from convalescent patients
Authors: Rouet Romain , Henry Jake Y. , Johansen Matt D. , Sobti Meghna , Balachandran Harikrishnan , Langley David B. , Walker Gregory , Lenthall Helen , Jackson Jennifer , Ubiparipovic Stephanie , Mazigi Ohan , Schofield Peter , Burnett Deborah L. , Brown Simon H. J. , Martinello Marianne , Hudson Bernard , Gilroy Nicole , Post Jeffrey J. , Kelleher Anthony , Jäck Hans-Martin , Goodnow Christopher C. , Turville Stuart G. , Rawlinson William D. , Bull Rowena A. , Stewart Alastair G. , Hansbro Philip M. , Christ Daniel
Published: October 2022

Emerging variants of concern (VOCs) are threatening to limit the effectiveness of SARS-CoV-2 monoclonal antibodies and vaccines currently used in clinical practice; broadly neutralizing antibodies and strategies for their identification are therefore urgently required. Here we demonstrate that broadly neutralizing antibodies can be isolated from peripheral blood mononuclear cells (PBMCs) of convalescent patients using SARS-CoV-2 receptor binding domains (RBDs) carrying epitope-specific mutations. This is exemplified by two human antibodies, GAR05, binding to epitope class 1, and GAR12, binding to a new epitope class 6 (located between class 3 and class 5). Both antibodies broadly neutralize VOCs, exceeding the potency of the clinical monoclonal sotrovimab (mAb S309) by orders of magnitude. They also provide potent prophylactic and therapeuticin vivoprotection of hACE2 mice against viral challenge. Our results indicate that exposure to Wuhan SARS-CoV-2 induces antibodies that maintain potent and broad neutralization against emerging VOCs using two unique strategies: either by targeting the divergent class 1 epitope in a manner resistant to VOCs (ACE2 mimicry, as illustrated by GAR05 and mAbs P2C-1F11/S2K14); or alternatively, by targeting rare and highly conserved epitopes, such as the new class 6 epitope identified here (as illustrated by GAR12). Our results provide guidance for next generation monoclonal antibody development and vaccine design.
Glycogen degrading activities of catalytic domains of α-amylase and α-amylase-pullulanase enzymes conserved inGardnerellaspp. from the vaginal microbiome
Authors: Bhandari Pashupati , Tingley Jeffrey , Abbott D. Wade , Hill Janet E.
Published: October 2022

Gardnerellaspp. are associated with bacterial vaginosis, in which normally dominant lactobacilli are replaced with facultative and anaerobic bacteria includingGardnerellaspp. Co-occurrence of multiple species ofGardnerellais common in the vagina and competition for nutrients such as glycogen likely contributes to the differential abundances ofGardnerellaspp. Glycogen must be digested into smaller components for uptake; a process that depends on the combined action of glycogen degrading enzymes. In this study, the ability of culture supernatants of 15 isolates ofGardnerellaspp. to produce glucose, maltose, maltotriose and maltotetraose from glycogen was demonstrated. Carbohydrate active enzymes were identified bioinformatically inGardnerellaproteomes using dbCAN2. Identified proteins included a single domain α-amylase (EC 3.2.1.1) (encoded by all 15 isolates) and an α-amylase-pullulanase (EC 3.2.1.41) containing amylase, carbohydrate binding modules and pullulanase domains (14/15 isolates). To verify the sequence-based functional predictions, the amylase and pullulanase domains of the α-amylase-pullulanase, and the single domain α-amylase were each produced inE. coli. The α-amylase domain from the α-amylase-pullulanase released maltose, maltotriose and maltotetraose from glycogen, and the pullulanase domain released maltotriose from pullulan and maltose from glycogen, demonstrating that theGardnerellaα-amylase-pullulanase is capable of hydrolyzing α-1,4 and α-1,6 glycosidic bonds. Similarly, the single domain α-amylase protein also produced maltose, maltotriose and maltotetraose from glycogen. Our findings show thatGardnerellaspp. produce extracellular amylase enzymes as ‘public goods’ that can digest glycogen into maltose, maltotriose and maltotetraose that can be used by the vaginal microbiota.

Importance

Increased abundance ofGardnerellaspp. is a diagnostic characteristic of bacterial vaginosis, an imbalance in the human vaginal microbiome associated with troubling symptoms, and negative reproductive health outcomes, including increased transmission of sexually transmitted infections and preterm birth. Competition for nutrients is likely an important factor in causing dramatic shifts in the vaginal microbial community but little is known about the contribution of bacterial enzymes to the metabolism of glycogen, a major food source available to vaginal bacteria. The significance of our research is characterizing the activity of enzymes conserved inGardnerellaspecies that contribute to the ability of these bacteria to utilize glycogen.
“Staphylococcus aureusSigS induces expression of a regulatory protein pair that modulate its mRNA stability”
Authors: Ali Amer Al , Alsulami Jamilah , Aubee Joseph I , Idowu Ayotimofe , Tomlinson Brooke R. , Felton Emily A. , Jackson Jessica K. , Shaw Lindsey , Thompson Karl M
Published: October 2022

SigS is the sole extracytoplasmic function sigma inS. aureusand is necessary for virulence, immune evasion, as well as surviving exposure to toxic chemicals and environmental stressors. Despite the contribution of SigS to a myriad of critical phenotypes, the downstream effectors of the SigS-dependentS. aureuspathogenesis, immune evasion, and stress response remain elusive. To address this knowledge gap, we analyzed theS. aureustranscriptome following transient over-expression of SigS. We identified a bi-cistronic transcript, up-regulated by 1000-fold, containing two mid-sized genes each containing single domains of unknown function (DUF). We renamed these genessroA(SigSregulatedorfA) andsroB(SigSregulatedorfB). We demonstrated that the SigS regulation of thesroABoperon is direct using in vitro transcription analysis. Using northern blot analysis, we also demonstrated that SroA and SroB have opposing auto- regulatory functions on the transcriptional architecture of thesigSlocus; with SroA stimulated SigS mRNA levels and SroB stimulating s750 (SigS antisense) levels. We hypothesized that these this opposing regulatory effects were due to a direct interaction. We demonstrated an interaction between SroA and SroB using an in-vivo surrogate genetics approach via Bacterial Two Hybrid. We demonstrated that the SroA effect on SigS is at the post-transcriptional level of mRNA stability, highlighting a mechanism likely used byS. aureusto tightly control SigS levels. Finally, we demonstrate that thesroABlocus promotes virulence in a female murine pneumonia model of infection.
Pseudomonas aeruginosaincreases the susceptibility ofCandida albicansto amphotericin B in dual species biofilms
Authors: Alam Farhana , Blackburn Sarah , Correia Joao , Blair Jessica , Hall Rebecca A
Published: October 2022

Biofilms are the leading cause of nosocomial infections, and are hard to eradicate due to their inherent antimicrobial resistance.Candida albicansis the leading cause of nosocomial fungal infections, and is frequently co-isolated with the bacteriumPseudomonas aeruginosafrom biofilms in the Cystic Fibrosis lung and severe burn wounds. The presence ofC. albicansin multi-species biofilms is associated with enhanced antibacterial resistance, which is largely mediated through fungal extracellular carbohydrates sequestering the antibiotics. However, significantly less is known regarding the impact of polymicrobial biofilms on antifungal resistance. Here we show that, in dual species biofilms,P. aeruginosaenhances the sensitivity ofC. albicansto amphotericin B, an effect that was biofilm specific. Transcriptional analysis combined with gene ontology enrichment analysis identified severalC. albicansprocesses associated with oxidative stress to be differentially regulated in dual species biofilms, suggesting thatP. aeruginosaexerts oxidative stress onC. albicans, likely through the actions of secreted phenazines. However, the mitochondrial superoxide dismutaseSOD2was significantly downregulated in the presence ofP. aeruginosa.Monospecies biofilms of thesod2Δ mutant were more susceptible to amphotericin B, and the susceptibility of these biofilms was further enhanced by the addition of exogenous phenazines. Therefore, we propose that in dual species biofilms,P. aeruginosasimultaneously induces mitochondrial oxidative stress, whilst downregulating key detoxification enzymes, which preventC. albicansmounting an appropriate oxidative stress response to amphotericin B, leading to fungal cell death. This work highlights the importance of understanding the impact of polymicrobial interactions on antimicrobial susceptibility.

Importance

Biofilms are aggregates of cells encased in an extracellular matrix, and are responsible for the majority of infections in hospitals. The Gram-negative bacteriumPseudomonas aeruginosa, and the fungal pathogenCandida albicansare frequently co-isolated from biofilms in the Cystic Fibrosis lung, and in burn wounds. Here we show that in these biofilms,P. aeruginosasecreted phenazines induce mitochondrial reactive oxygen species stress, which enhances the sensitivity ofC. albicansto the antifungal amphotericin B. This work highlights the importance of understanding the impact of polymicrobial interactions on antimicrobial susceptibility.
High-throughput transposon mutagenesis in the family Enterobacteriaceae reveals core essential genes and rapid turnover of essentiality
Authors: Ghomi Fatemeh A. , Langridge Gemma C. , Cain Amy K. , Boinett Christine , Abd El Ghany Moataz , Pickard Derek J. , Kingsley Robert A. , Thomson Nicholas R. , Parkhill Julian , Gardner Paul P. , Barquist Lars
Published: October 2022

The Enterobacteriaceae are a scientifically and medically important clade of bacteria, containing the gut commensal and model organismEscherichia coli, as well as several major human pathogens including multiple serovars ofSalmonella entericaandKlebsiella pneumoniae. Essential gene sets have been determined for several members of the Enterobacteriaceae, with theE. coliKeio single-gene deletion library often regarded as a gold standard for gene essentiality studies. However, it remains unclear how gene essentiality varies between related strains and species. To investigate this, we have assembled a collection of thirteen sequenced high-density transposon mutant libraries from five genera within the Enterobacteriaceae. We first benchmark a number of gene essentiality prediction approaches, investigate the effects of transposon density on essentiality prediction, and identify biases in transposon insertion sequencing data. Based on these investigations we develop a new classifier for gene essentiality. Using this new classifier, we define a core essential genome in the Enterobacteriaceae of 201 universally essential genes, and reconstruct an ancestral essential gene set of 296 genes. Despite the presence of a large cohort of variably essential genes, surprisingly we find an absence of evidence for genus-specific essential genes. A clear example of this sporadic essentiality is given by the set of genes regulating the σEextracytoplasmic stress response, which appears to have independently become essential multiple times in the Enterobacteriaceae. Finally, we compare our essential gene sets to the natural experiment of gene loss in obligate insect endosymbionts that have emerged from within the Enterobacteriaceae. This isolates a remarkably small set of genes absolutely required for survival, and uncovers several instances of essential stress responses masked by redundancy in free-living bacteria.
Modifications in the piperazine ring of nucleozin affects anti-influenza activity
Authors: Correa-Padilla Erick , Hernández-Cano Alejandro , Cuevas Gabriel , Acevedo-Betancur Yunuen , Esquivel-Guadarrama Fernando , Madariaga-Mazon Abraham , Martinez-Mayorga Karina
Published: October 2022

The infection caused by influenza virus is a latent tret, to contribute on the advancement of the discovery and design of nucleozin analogs, a molecule with antiinfluenza activity, we analyzed nucleozin analogs with modifications in the piperazine system, which leads to molecules with larger conformational freedom. Following a new nucleozin synthetic strategy, we obtained three new nucleozin analogs, and two of them were biologically evaluatedin vitroand were less active than nucleozin. The loss of activity in the more flexible molecules highlights the need for the piperazine ring to maintain the activity of nucleozin analogues. Interestingly, this coincides with a QSAR model developed here for the prediction of the anti-influenza activity. The proposed model, along with the synthetic route, will be useful for further development of nucleozin analogues with antiviral activity.
De novodesign of anti-variant COVID-19 Vaccine
Authors: Goswami Arpita , Kumar S. Madan , Ullah Samee , Gore Milind M.
Published: October 2022

Recent studies have shown the efficacy of hybrid SARS-COV-2 vaccines using wild-type nucleocapsid (N) and Spike (S) protein. We upgraded this strategy one step further using clinically proven spike protein by considering the delta and post-delta omicron variant of concern (VOC) mutations and nucleocapsid peptides conferring T-cell immunity. Nucleocapsid peptides are considered much better immunological replacement of nucleocapsid proteins. Hence, peptide linking strategy is applied which is more economic for cellular biosynthesis than whole proteins. An envelope peptide with potent T-cell immune response is also selected. All these peptides are clustered in this hybrid spike’s designed cytoplasmic region separated by non-immunogenic helical linkers. The resulting domain is more folded in the construct devoid of transmembrane domain after AlphaFold analysis. Alongside, we also propose the idea of introduction of any T-cell peptide like other Human Corona Viruses (HuCoV) in these linker regions whenever required. In addition to SARS-COV-2, the same approach can be applied for any emergency or even long-term unsolved outbreaks of Influenza, Dengue and West Nile Virus etc. In this era of novelty as presented by subunit and nucleic acid vaccines, multiepitope strategies like this can help to combat multiple diseases successfully in real time to give hope for better future.
Identifying Genetic Regulatory Variants that Affect Transcription Factor Activity
Authors: Li Xiaoting , Lappalainen Tuuli , Bussemaker Harmen J.
Published: October 2022

Assessing the functional impact of genetic variants across the human genome is essential for understanding the molecular mechanisms underlying complex traits and disease risk. Genetic variation that causes changes in gene expression can analyzed through parallel genotyping and functional genomics assays across sets of individuals. Trans-acting variants are of particular interest, but more challenging to identify than cis-acting variants. Here, to map variants that impact the expression of many genes simultaneously through a shared transcription factor (TF), we use an approach in which the protein-level regulatory activity of the TF is inferred from genome-wide expression data and then genetically mapped as a quantitative trait. To analyze RNA-seq profiles from the Genotype Tissue Expression (GTEx) project, we developed a generalized linear model (GLM) to estimate TF activity levels in an individual-specific manner. A key feature is that we fit a beta-binomial GLM at the level of pairs of neighboring genes in order to control for variation in local chromatin structure along the genome and other confounding effects. As a predictor in our model we use differential gene expression signatures from TF perturbation experiments. We estimated genotype-specific activities for 55 TFs across 49 tissues and performed genome-wide association analysis on the virtual TF activity trait. This revealed hundreds of TF activity quantitative trait loci, or aQTLs. Altogether, the set of tools we introduce here highlights the potential of genetic association studies for cellular endophenotypes based on a network-based multi-omic approach.
The comparative advantages in the wooden furniture industry: does the export price matter?
Authors: Topcu Yunus Emre
Published: October 2022

Purpose

The purpose of this paper is to evaluate the global competitiveness of the top ten wooden furniture exporting countries with several approaches and to test the effect of export prices (EXPRs) on the global competition.

Design/methodology/approach

Countries' competitiveness levels were measured with revealed comparative advantage (RCA), normalised RCA (NRCA), revealed symmetric comparative advantage (RSCA) and trade balance index. Furthermore, panel regression analysis techniques were used to test the effects of EXPR on RCA, NRCA and RSCA in the wooden furniture industry (WFI).

Findings

Although the comparative advantage approaches give different results, the global competitiveness of Poland and Vietnam is at a high level in all approaches. Canada has been the country with the weakest global competitiveness in all approaches. According to the results of the analysis, EXPRs positively affect all the competitive advantage indexes. As a result, the competitiveness of the WFI is affected by the non-price factors instead of the EXPR.

Research limitations/implications

The framework allows us to measure and illustrate the export competitiveness of the WFI and permits a global comparison. Similar analyses can be made for different labour-intensive sectors. In addition, analysis can be made to identify non-price factors for the WFI sector. Thus, more specific inferences can be made.

Practical implications

This study is useful for policymakers, government officials, the industry associations and the company executives to assess their export competitiveness in the WFI. Thus, they can determine whether to shift scarce resources to this industry or other industries. In addition, this study may affect the price competition policy of the sector representatives in the global market.

Originality/value

This study deals with the competitiveness of the WFI with different approaches. And this study determines the importance of price for global competition in this sector.
Family incivility and workplace bullying: mediating and moderating model of psychological safety, optimism and organization-based self-esteem
Authors: Paul Vincent Maria Tresita , P.M. Nimmi , Jose Geetha , John Anjali , Kuriakose Vijay
Published: October 2022

Purpose

This study aims to explore how family incivility is linked to workplace bullying among employees. This study examines the role of psychological safety as an explanatory mechanism linking both. This paper also looks into the moderating roles of optimism between family incivility and psychological safety and organization-based self-esteem (OBSE) between psychological safety and workplace bullying.

Design/methodology/approach

Drawing from the conservation of resources theory and work home resources model, this study developed various hypotheses. The proposed relationships were tested using responses gathered from 260 teaching faculty across the universities in India. This study used Warp-PLS for data analysis.

Findings

The findings suggest that psychological safety mediated the relationship between experienced family incivility and workplace bullying. This study also found support for the mediating role of psychological safety. Further, this study has proved that trait optimism and OBSE are boundary conditions influencing the outcomes of family incivility.

Practical implications

The findings have practical implications for teachers, educational institution leaders and policymakers. This study augments the importance of cultivating optimism and OBSE to combat conflicting situations. Employees who practice optimism on a daily basis are high in psychological safety and when supported with OBSE by the institution, the impact of family incivility and its adverse effects in the workplace is reduced, curbing the instances of workplace bullying.

Originality/value

To the best of the authors’ knowledge, this is one of the first studies to establish the role of “organizational resource,” OBSE, as a coping mechanism in tackling the adverse effects of family incivility. From a resource perspective, this study is one of the first to look into the enablers and inhibitors of resource creation in an individual while experiencing family incivility.
Determination of health workers' perceptions of the disaster management process and gender inequality: the case of a state hospital in Turkey
Authors: Çoban Büşra Nur , İnal Önal Ebru
Published: October 2022

Purpose

This study aims to identify levels of gender perception specific to disaster management process and gender-related factors among the health workers employed at Çan State Hospital, Turkey.

Design/methodology/approach

The study was carried out with a survey form consisting of 41 questions created by researchers with 207 health workers working at Çan State Hospital and by means of face-to-face interview technique. SPSS ver. 19.0 statistics software package was used in the research for analysis of data.

Findings

Of the participants, 70.24% had experienced a disaster before; 88.03% reported that women and men were equally affected by disasters and 72.94% reported that women and men were equally affected by the COVID-19 pandemic. The majority of the participants (70.29%) reported that the COVID-19 pandemic affected health workers of both genders equally. The health workers who consider that the disaster legislation is gender-sensitive, who have attended any disaster response training and who consider that women are included in the fragile/vulnerable group in disaster response activities have been found out to have significantly higher gender perception scores specific to disaster management process (p < 0.05). Most of the participants stated that both genders were affected equally by the disasters they experienced, which manifests that they adopted an egalitarian approach.

Practical implications

This study revealed the importance of providing disaster training for health workers to improve the gender perceptions. It is of high significance to integrate gender into the disaster trainings.

Originality/value

This study identifies and evaluates health workers' disaster-specific perceptions of gender, and necessary response activities can be performed accordingly.
SARS-CoV-2 seroprevalence study after the first wave among persons living and working in an overcrowded Swiss prison
Authors: Gétaz Laurent , Wolff Hans , Gonçalves Leonel , Togni Giuseppe , Stringhini Silvia , Chacowry Pala Komal , Iten Anne , Guessous Idris , Kaiser Laurent , Chappuis Francois , Baggio Stéphanie
Published: October 2022

Purpose

Prisons can be epicentres of infectious diseases. However, empirical evidence on the impact of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemic in prison is still scarce. This study aims to estimate the seroprevalence rates of anti-SARS-CoV-2 in the largest and most crowded Swiss prison and compare them with the seroprevalence rate in the general population.

Design/methodology/approach

A cross-sectional study was conducted in June 2020, one month after the first wave of SARS-CoV-2 in Switzerland. Groups included: people living in detention (PLDs) detained before the beginning of the pandemic (n = 116), PLDs incarcerated after the beginning of the pandemic (n = 61), prison staff and prison healthcare workers (n = 227) and a sample from the general population in the same time period (n = 3,404). The authors assessed anti-SARS-CoV-2 IgG antibodies.

Findings

PLDs who were incarcerated before the beginning of the pandemic had a significantly lower seroprevalence rate [0.9%, confidence interval (CI)95%: 0.1%–5.9%] compared to the general population (6.3%, CI 95%: 5.6–7.3%) (p = 0.041). The differences between PLDs who were incarcerated before and other groups were marginally significant (PLDs incarcerated after the beginning of the pandemic: 6.6%, CI 95%: 2.5%–16.6%, p = 0.063; prison staff CI 95%: 4.8%, 2.7%–8.6%, p = 0.093). The seroprevalence of prison staff was only slightly and non-significantly lower than that of the general population.

Originality/value

During the first wave, despite overcrowding and interaction with the community, the prison was not a hotspot of SARS-CoV-2 infection. Preventive measures probably helped avoiding clusters of infection. The authors suggest that preventive measures that impact social welfare could be relaxed when overall circulation in the community is low to prevent the negative impact of isolation.
SNS use reduction: a two-facet privacy concern perspective
Authors: Neves Joana , Turel Ofir , Oliveira Tiago
Published: October 2022

Purpose

While social networking sites (SNS) have many positive aspects, they can have several adverse outcomes, among which privacy violations are a vital concern. The authors first posit that concerns regarding privacy violations can drive attempts to reduce SNS use. Next, the authors note that these violations can have two sources: peers and the social media provider. Thus, there is a need to understand how this complex system of privacy concerns affects use reduction decisions. To do so, this paper aims to examine the separate and joint roles of institutional and peer privacy concerns in driving SNS use reduction.

Design/methodology/approach

Based on privacy calculus theory, the authors propose a theoretical model to explain SNS use reduction, with institutional and peer privacy concerns as independent variables. The authors empirically examine the research model using a sample of 258 SNS users.

Findings

This study reveals that institutional and peer privacy concerns independently increase one's intention to reduce SNS use and that institutional privacy concern strengthen the relation between peer privacy concern and the intention to reduce SNS use.

Originality/value

Research thus far has not examined how the two facets of privacy work in tandem to affect 'users' decisions to change their behaviors on SNS platforms. Considering the unique and joint effect of these facets can thus provide a more precise and realistic perspective. This paper informs theories and models of privacy and online user behavior change.
Searching for Swedish LGBTQI fiction: challenges and solutions
Authors: Golub Koraljka , Bergenmar Jenny , Humlesjö Siska
Published: October 2022

Purpose

The purpose of this study is to investigate the needs of potential end-users of a database dedicated to Swedish lesbian, gay, bisexual, transgender, queer, and intersex (LGBTQI) literature (e.g. prose, poetry, drama, graphic novels/comics, and illustrated books), in order to inform the development of a database, search interface functionalities, and an LGBTQI thesaurus for fiction.

Design/methodology/approach

A web questionnaire was distributed in autumn 2021 to potential end-users. The questions covered people's reasons for reading LGBTQI fiction, ways of finding LGBTQI fiction, experience of searching for LGBTQI fiction, usual search elements applied, latest search for LGBTQI fiction, desired subjects to search for, and ideal search functionalities.

Findings

The 101 completed questionnaires showed that most respondents found relevant literature through social media or friends and that most obtained copies of literature from a library. Regarding desirable search functionalities, most respondents would like to see suggestions for related terms to support broader search results (i.e. higher recall). Many also wanted search support that would enable retrieving more specific results based on narrower terms when too many results are retrieved (i.e. higher precision). Over half would also appreciate the option to browse by hierarchically arranged subjects.

Originality/value

This study is the first to show how readers of LGBTQI fiction in Sweden search for and obtain relevant literature. The authors have identified end-user needs that can inform the development of a new database and a thesaurus dedicated to LGBTQI fiction.
Understanding the relationship between IT capabilities and operational agility: a multi-method approach
Authors: Mao Hongyi , Gong Yeming , Titah Ryad
Published: October 2022

Purpose

The system of information technology (IT)-oriented resources and processes that organizations need to develop to achieve operational agility remains unclear. The study research seeks to extend existing competency literature by incorporating the unique contextual nuances of the relationship between IT capabilities and operational agility.

Design/methodology/approach

Using a multi-method approach, this paper presents a theoretical framework of IT-enabled operations strategy that conceptualizes the role of IT capability in leveraging resources and processes for operational agility. Drawing on operations and information systems research, the authors advance that IT enables operational agility through two dimensions. From the perspective of a resource-based operations strategy, the authors explore the role of IT in resource-leveraging activities by investigating the nonlinear relationship between IT infrastructure and IT reconfiguration. From the perspective of a process-oriented operations strategy, the authors explore the role of IT in process-enhancing activities by investigating the nonlinear relationship between IT coordination and IT integration.

Findings

The study results, based on a sample of 113 organizations in Europe, Asia and North America, show that the interaction between IT infrastructure and IT reconfiguration positively influences operational agility, hence showing complementarity between the two constructs, while the interaction between IT coordination and IT integration negatively affects operational agility, hence indicating substitutability between the two constructs. A series of 62 interviews and a case study of Carrefour were further conducted to validate the field survey's results and to provide a finer grained explanation of the research model and quantitative findings.

Originality/value

The study findings offer an alternative explanation of the inconsistent relationship between IT capability and operational agility.
Evidence for divergence in phenology over morphology in response to limiting similarity in montane communities of Rhododendron
Authors: Li Qin , Wang Ji , Fuller Ryan , Xing Yaowu , Liu Jianquan , Ree Richard H.
Published: October 2022

The coexistence of closely related species is key to understanding the nature of biodiversity hotspots where in situ diversification has yielded rich communities of close relatives. Limiting similarity predicts that co‐occurring species are differentiated in their niches; identifying the axes of differentiation in sympatric close relatives can thus help reveal the eco‐evolutionary dynamics of community assembly. For flowering plants, these axes may be temporal (related to reproductive phenology) or morphological (related to functional traits).

We collected fine‐scale data on abundance, morphology and phenology over a flowering season for 34 species of Rhododendron (Ericaceae) spanning a 2700 m elevation gradient in a nature reserve in the eastern Hengduan Mountains, China. We used null models to test for patterns of clustering versus overdispersion in species' abundances, phylogenetic relatedness and functional traits across sites, and applied joint distribution models to examine the correlates of pairwise associations.

We found that species tended to be spatially aggregated, indicating that communities are not strongly structured by competitive exclusion. At higher elevation sites, species tended to be vegetatively more similar (clustered) and closely related. Environmental variables, including climate and topography, were strong predictors of species' ranges. No evidence of niche differentiation was detected along spatial or morphological (functional) axes, but along the temporal axis, the phenology of co‐occurring species showed significant divergence, and was less phylogenetically conserved compared to morphological traits.

Synthesis. Local communities of Rhododendron in its centre of diversity are structured by environmental filtering and the effects of limiting similarity. Evidence for the latter is apparent in the pervasive phenological divergence of co‐occurring species, likely driven by reproductive interference from shared pollinators. The evolutionary lability of flowering time appears to render it the quickest path to coexistence for recently diverged species that experience secondary contact in this biodiversity hotspot.
Increased recovery in coarse‐root secondary growth improves resilience to drought in transition forests
Authors: Acuña‐Míguez Belén , Olano Jose Miguel , Valladares Fernando , García‐Hidalgo Miguel , Bravo‐Oviedo Andrés
Published: October 2022

Interaction of global change drivers affects forest resilience. Land‐use changes (land abandonment) and climate change (a higher frequency and intensity of droughts) are interacting in the Mediterranean Region. Components of resilience in secondary stem growth have been widely studied but, despite the importance of root systems in forest functionality and resilience, non‐previous studies have assessed them in coarse roots.

In this study, we use Juniperus thurifera tree‐ring chronologies in coarse roots and stems to assess biomass allometry and tree resilience to drought events comparing two stages of a forest expansion gradient (mature forests and transition zone) in Alto Tajo Natural Park. We extracted cores of stems and coarse roots in 48 trees distributed in different developmental stages and calculated cross‐sectional area increments, root‐stem allometric relationship and resilience components for both organs in each individual for two drought events (2005 and 2012).

Stem and root growth as well as its allometric exponent were higher in the transition zone than in mature forests. Both organs exhibited a trade‐off between resistance and recovery in mature forests but maintenance of higher values in the transition zone. Resilience did not show differences between organs being higher in the transition zone than in mature forests. However, relative resilience in roots in the transition zone was higher than in mature forests, without differences in stems between stages. Finally, the 2012 drought event showed a higher impact on the components of resilience than the 2005 drought event.

Synthesis. This study extends the knowledge of root response to drought events and highlights the potential of land‐use legacies to reduce the negative impact of climate change by promoting increased root recovery after drought events in trees established in past agricultural lands.
Poleward increase in feeding efficiency of leafminer Stigmella lapponica (Lepidoptera: Nepticulidae) in a latitudinal gradient crossing a boreal forest zone
Authors: Kozlov Mikhail V. , Zverev Vitali , Sandner Tobias M. , van Nieukerken Erik J. , Zvereva Elena L.
Published: October 2022

Damage to plant communities imposed by insect herbivores generally decreases from low to high latitudes. This decrease is routinely attributed to declines in herbivore abundance and/or diversity, whereas latitudinal changes in per capita food consumption remain virtually unknown. Here, we tested the hypothesis that the lifetime food consumption by a herbivore individual decreases from low to high latitudes due to a temperature‐driven decrease in metabolic expenses. From 2016 to 2019, we explored latitudinal changes in multiple characteristics of linear (gallery) mines made by larvae of the pygmy moth, Stigmella lapponica, in leaves of downy birch, Betula pubescens. The mined leaves were larger than intact leaves at the southern end of our latitudinal gradient (at 60°N) but smaller than intact leaves at its northern end (at 69°N), suggesting that female oviposition preference changes with latitude. No latitudinal changes were observed in larval size, mine length or area, and in per capita food consumption, but the larval feeding efficiency (quantified as the ratio between larval size and mine size) increased with latitude. Consequently, S. lapponica larvae consumed less foliar biomass at higher latitudes than at lower latitudes to reach the same size. Based on space‐for‐time substitution, we suggest that climate warming will increase metabolic expenses of insect herbivores with uncertain consequences for plant–herbivore interactions.
Lung ultrasound in neonates – An underused tool
Authors: Thakur Anup , Fursule Anurag
Published: October 2022

Point of care lung ultrasound (USG) can help in the diagnosis and management of critically sick neonates. It is based on seven simple principles that are comprehensive enough to diagnose all major lung pathologies. A compact small machine and a micro‐convex or linear probe are the basic requirements to perform lung USG. In contrast to traditional USG principles, USG of the lung is based on artefacts. Some of the terminologies that are used to characterize normal lung include the pleural line, A‐line, bat sign, lung sliding and seashore sign. Air/fluid mixture in varying ratios helps in diagnosis of normal lung, pneumothorax, interstitial syndrome (transient tachypnoea of newborn, respiratory distress syndrome, bronchopulmonary dysplasia), lung consolidation and pleural effusion.
Application of several machine learning algorithms for the prediction of afatinib treatment outcome in advanced‐stage EGFR‐mutated non‐small‐cell lung cancer
Authors: Kim Taeyun , Lee Sang Jin , Jang Tae‐Won
Published: October 2022

Background

The present study aimed to evaluate the performance of several machine learning (ML) algorithms in predicting 1‐year afatinib continuation and 2‐year survival after afatinib initiation and to identify the differences in survival outcomes between ML‐classified strata.

Methods

Data that were also used in the RESET study were retrospectively collected from 16 hospitals in South Korea. A stratified random sampling method was applied to split the data into training and test sets (70:30 split ratio). Clinical information, such as age, sex, tumor stage, smoking, performance status, metastasis, type of metastasis, dose adjustment, and pathologic information on EGFR mutations were inputted. Training was performed using eight ML algorithms: logistic regression, decision tree, deep neural network, random forest, support vector machine, boosting, bagging, and the naïve Bayes classifier. The model performance was assessed based on sensitivity, specificity, and accuracy. Area under the receiver operator characteristic curve (AUC) was calculated and compared between the ML models using DeLong's test. A Kaplan–Meier (KM) curve was used to visualize the identified strata obtained from the ML models.

Results

No significant differences in the input variables were observed between the training and test datasets. The best‐performing models were support vector machine in predicting 1‐year afatinib continuation (AUC 0.626) and decision tree in 2‐year survival after afatinib start (AUC 0.644), although the performances of the ML models were comparable and did not display any predictive roles. KM analysis and log‐rank test revealed significant differences between the strata identified from the ML model (p < 0.001) in terms of both time‐on‐treatment (TOT) and overall survival (OS).

Conclusion

The performances of ML models in our study found no discernible roles in predicting afatinib‐related outcomes, although the identified strata revealed different TOT and OS in the KM analysis. This implies the strength of ML in predicting the survival outcome, as well as the limitation of electronic medical record‐based variables in ML algorithms. Careful consideration of variable inclusion is likely to improve the general model performance.
Why agricultural insurance may slow down agricultural development
Authors: Bulte Erwin , Lensink Robert
Published: October 2022

How does agricultural insurance affect the modernization of farming in low income countries? We focus on institutional contexts without formal contract enforcement, where smallholders cannot access modern inputs via markets. Instead, farmers can engage in relational contracting with traders to sell their crop and gain access to inputs (as an advance in‐kind payment). Although conventional theory assumes that insurance “crowds in” modern inputs by attenuating investment risk, we demonstrate that insurance reduces the number of farmers receiving modern inputs from traders. Insurance also reduces the quantity of inputs that traders provide to farmers who remain in a relationship. Insurance may impede the uptake of modern inputs when institutions are imperfect.
PDCL2 is essential for sperm acrosome formation and male fertility in mice
Authors: Fujihara Yoshitaka , Kobayashi Kiyonori , Abbasi Ferheen , Endo Tsutomu , Yu Zhifeng , Ikawa Masahito , Matzuk Martin M.
Published: October 2022

Background

Each year, infertility affects 15% of couples worldwide, with 50% of cases attributed to men. Globozoospermia is an uncommon cause of male factor infertility, characterized by defects in sperm acrosome formation, leading to round‐headed spermatozoa.

Objective

We generated Pdcl2 knockout mice to investigate the essential roles of PDCL2 in mammalian reproduction.

Materials and methods

We used reverse transcription‐polymerase chain reaction to demonstrate that PDCL2 was expressed exclusively in the male reproductive tract in mice and humans. We created Pdcl2 knockout mice using the CRISPR‐Cas9 system and analyzed their fertility. Pdcl2 null spermatozoa underwent further evaluation using computer‐assisted sperm analysis, light microscopy, and ultrastructural microscopy. We used immunoblot analysis and immunofluorescence to elucidate relationships between PDCL2 and other acrosomal proteins.

Results

The PDC family is highly conserved in eukaryotes. Mouse and human PDCL2 are testis enriched and localized to the testicular endoplasmic reticulum. Loss of the protein causes sterility because of abnormal acrosome biogenesis during spermiogenesis and immotility. Furthermore, Pdcl2 null spermatozoa have rounded heads, similar to globozoospermia in humans. Observation of the knockout testis shows a lack of acrosomal cap formation, aberrant localization of mitochondria in the sperm head, and misshapen nuclei.

Conclusion

PDCL2 is essential for sperm acrosome development and male fertility in mice and is a putative contraceptive target in men.
Internet‐based interventions for parents with children 0–5 years: A scoping review
Authors: Størksen Hege Therese , Haga Silje Marie , Hammerstrøm Karianne Thune , Jacobsen Heidi , Drozd Filip
Published: October 2022

Aim

This study aims to review the existing literature on Internet‐based health interventions directed to support parents of children aged 0–5 years.

Methods

We systematically searched electronic databases between January 2000 and 2018. The search consisted of terms describing eHealth, intervention and families and/or children.

Results

Internet‐based parent support interventions were most often directed at rehabilitation and selective prevention, and we identified more studies on mental health (57%) than somatic health (41%). Developmental disorders were the most frequently studied mental health condition (n = 33), while interventions for obesity (15%) were the most studied somatic health condition. Forty‐four percent of mental health studies were RCTs and 65% of interventions were theory driven. Interventions most often used a behavioural approach, included guidance and delivered content via text‐based information.

Conclusion

Several significant gaps were identified such as the need for more research outside of English‐speaking countries, more systematic reviews and effect studies. This review also elucidates the need for researchers to improve reporting on the theoretical approaches employed in interventions, and to focus on determining the importance of guidance. Finally, program developers should consider using more audio‐visual technology to avoid reinforcing social inequalities in access to healthcare.