bluuebunny/crossref_metadata_2025_split huggingface dataset:
Phenology and ecological role of Aerobic Anoxygenic Phototrophs in fresh waters
Authors: Villena-Alemany Cristian , Mujakić Izabela , Fecskeová Livia K. , Woodhouse Jason , Auladell Adrià , Dean Jason , Hanusova Martina , Socha Magdalena , Gazulla Carlota R. , Ruscheweyh Hans-Joachim , Sunagawa Shinichi , Kavagutti Vinicius , Andrei Adrian-Ştefan , Grossart Hans-Peter , Ghai Rohit , Koblížek Michal , Piwosz Kasia 
Published: November 2023

AbstractAerobic anoxygenic phototrophic (AAP) bacteria are heterotrophic bacteria that supply their metabolism with light energy harvested by bacteriochlorophyll-a-containing reaction centres. Despite their substantial contribution to bacterial biomass, microbial food webs and carbon cycle, their phenology in freshwater lakes remains unknown. Hence, we investigated seasonal variations of AAP abundance and community composition biweekly across three years in a temperate, meso-oligotrophic freshwater lake. AAP bacteria displayed a clear seasonal trend with a spring maximum following the bloom of phytoplankton and a secondary maximum in autumn. As the AAP bacteria represent a highly diverse assemblage of species, we followed their seasonal succession using the amplicon sequencing of thepufM marker gene. To enhance the accuracy of the taxonomic assignment, we developed newpufM primers that generate longer amplicons and compiled the currently largest database ofpufM gene, comprising 3633 reference sequences spanning all phyla known to contain AAP species. With this novel resource we demonstrated recurrent and dynamic seasonal succession of the AAP community. The majority of the species appeared during specific phases of the seasonal cycle, with less than 2% of AAP species detected during the whole year. Our results document the indigenous freshwater nature of the AAP community, characterized by high resilience and heterogenic adaptations to varying conditions of the freshwater environment. By integrating this information with the indicator of primary production (Chlorophyll-a) and existing ecological models, we show that AAP bacteria play a pivotal role in the recycling of dissolved organic matter released during spring phytoplankton bloom, contributing significantly to the ecological dynamics of lakes.
Enhancing Ligand-Based Virtual Screening with 3D Shape Similarity via a Distance-Aware Transformer Model
Authors: Sellner Manuel S. , Mahmoud Amr H. , Lill Markus A. 
Published: November 2023

AbstractFollowing the assumption that chemically similar molecules exhibit similar biologcial properties, ligand-based virtual screening can be a valuable starting point in drug discovery projects. While 2D-based similarity metrics generally focus on similar scaffolds or substructures, 3D-based methods can capture the shape of a molecule, allowing for the identification of compounds with different scaffolds. We recently published a proof-of-concept study which demonstrated how a Transformer model can be adapted to preserve 2D similarities in latent space in the form of Euclidean distances. In this work, we extend this research and prove that the approach can be adapted to 3D similarities. We use pharmacophore-based shape similarity as 3D similarity measure. We show that the model is able to enrich the predicted most similar hits with compounds with different scaffolds that are indeed similar in 3D space. Whereas classical pharmacophore- or shape-based 3D similarity methods rely on expensive alignment processes, in our approach, we identify similar compounds directly by the Euclidean distances in latent space. This enables for the first time the 3D screening of ultra-large databases with high efficiency.
Chromosomal Integrons are Genetically and Functionally Isolated Units of Genomes
Authors: Blanco Paula , da Roza Filipa Trig , Toribio-Celestino Laura , García-Pastor Lucía , Caselli Niccolò , Ojeda Francisco , Darracq Baptiste , Vergara Ester , Millán Álvaro San , Skovgaard Ole , Mazel Didier , Loot Céline , Escudero José Antonio 
Published: November 2023

ABSTRACTIntegrons are genetic elements that increase the evolvability of bacteria by capturing new genes and stockpiling them in arrays. Sedentary chromosomal integrons (SCIs), can be massive and highly stabilized structures encoding hundreds of genes, whose function remains generally unknown. SCIs have co-evolved with the host for aeons and are highly intertwined with their physiology from a mechanistic point of view. But, paradoxically, other aspects, like their variable content and location within the genome, suggest a high genetic and functional independence. In this work, we have explored the connection of SCIs to their host genome using as a model the Superintegron (SI), a 179-cassette long SCI in the genome ofVibrio choleraeN16961. We have relocated and deleted the SI using SeqDelTA, a novel method that allows to counteract the strong stabilization conferred by toxin-antitoxin systems within the array. We have characterized in depth the impact inV. cholerae’sphysiology, measuring fitness, chromosome replication dynamics, persistence, transcriptomics, phenomics and virulence. The deletion of the SI did not produce detectable effects in any condition, proving that -despite millions of years of co-evolution-, SCIs are genetically and functionally isolated units of genomes.
Neutrophil subsets play dual roles in tuberculosis by producing inflammasome dependent-IL-1β or suppressing T-cells via PD-L1
Authors: Doz-Deblauwe Emilie , Bounab Badreddine , Carreras Florence , Silveira-Fahel Julia , Oliveira Sergio C. , Lamkanfi Mohamed , Vern Yves Le , Germon Pierre , Pichon Julien , Kempf Florent , Paget Christophe , Remot Aude , Winter Nathalie 
Published: November 2023

AbstractNeutrophils can be beneficial or deleterious during tuberculosis (TB). Based on the expression of MHC-II and programmed death ligand 1 (PD-L1), we distinguished two functionally and transcriptionally distinct neutrophil subsets in the lungs of mice infected with mycobacteria. Inflammatory [MHC-II-, PD-L1lo] neutrophils produced inflammasome-dependent IL-1β in the lungs in response to virulent mycobacteria and “accelerated” deleterious inflammation, which was highly exacerbated in IFN-γR-/-mice. Regulatory [MHC-II+, PD-L1hi] neutrophils “brake” inflammation by suppressing T-cell proliferation and IFN-γ production. Such beneficial regulation, which depends on PD-L1, is controlled by IFN-γR signaling in neutrophils. The hypervirulent HN878 strain from the Beijing genotype curbed PD-L1 expression by regulatory neutrophils, abolishing the braking function and driving deleterious hyper-inflammation in the lungs. These findings add a layer of complexity to the roles played by neutrophils in TB and may explain the reactivation of this disease observed in cancer patients treated with anti-PD-L1.One Sentence SummaryRegulatory and inflammatory neutrophil subsets play inverse roles in tuberculosis.
Evidence that the Isc Iron-Sulfur Cluster Biogenesis Machinery Delivers Iron for [NiFe]-Cofactor Biosynthesis inEscherichia coli
Authors: Haase Alexander , Arlt Christian , Sinz Andrea , Sawers R. Gary 
Published: November 2023

Abstract[NiFe]-hydrogenases have a bimetallic NiFe(CN)2CO cofactor in their large, catalytic subunit. The 136 Da Fe(CN)2CO group of this cofactor is assembled on a distinct HypC-HypD scaffold complex prior to delivery to the apo-catalytic subunit, but the intracellular source of the iron ion is unresolved. Native mass spectrometric (native MS) analysis of HypCD complexes defined the [4Fe-4S] cluster associated with HypD and identified +26 - 28 Da and +136 Da modifications specifically associated with HypC. A HypCC2Avariant dissociated from its complex with native HypD lacked all modifications. HypC dissociated from HypCD complexes isolated fromEscherichia colistrains deleted for theiscSoriscUgenes, encoding core components of the Isc iron-sulfur cluster biogenesis machinery, specifically lacked the +136 Da modification; however, it was retained on HypC isolated fromsufmutants. The presence or absence of the +136 Da modification on the HypCD complex correlated with the hydrogenase enzyme activity profiles of the respective mutant strains. Notably, the [4Fe-4S] cluster on HypD was identified in all HypCD complexes analyzed. These results suggest that the iron of the Fe(CN)2CO group on HypCD derives from the Isc machinery, while either the Isc or the Suf machinery can deliver the [4Fe-4S] cluster to HypD.
Viscoelastic Deformability Cytometry: Ultra-high Throughput Platform for Mechanical Phenotyping of Cells in Liquid and Solid Biopsies
Authors: Asghari Mohammad , Ivetich Sarah Duclos , Aslan Mahmut Kamil , Aramesh Morteza , Oleksandr Melkonyan , Meng Yingchao , Xu Rong , Colombo Monica , Weiss Tobias , Balabanov Stefan , Stavrakis Stavros , deMello Andew J. 
Published: November 2023

AbstractDue to the differences in mechanical properties between cancer cells and their benign counterparts, the mechanical characteristics of cells have emerged as a significant feature in diagnosing cancer. Consequently, measuring cell deformability as a means of mechanical phenotyping is promising for both the detection and classification of the disease. However, performing high-throughput single-cell deformability measurements on liquid or solid tissue biopsies remains a significant challenge within a clinical setting. Herein, we introduce an ultra-high throughput viscoelastic-based microfluidic platform to measure the cell mechanical properties at rates of up to 100,000 cells/s. Thanks to the viscoelastic property of the fluid, cells are focused and deformed within the same platform obviating the need for any sheath fluid. We used the presented platform for cell phenotyping in both liquid and solid tumor biopsies, such as identification of malignant lymphocytes in peripheral blood samples and glioblastoma-type cell classification from solid tumor samples. The presented platform has the potential to open new opportunities in the assessment of cancer, enable precise mechanical profiling of rare cells, and facilitate sensitive diagnostic applications.
Information seeking and personal information management behaviors as scaffolding during life transitions: the case of early-career researchers
Authors: Alon Lilach 
Published: November 2023

PurposeThe study investigates the information-related challenges as well as the practices adopted by early-career researchers during transitions between roles and institutions. Its primary goal is to delve into how information behaviors serve as scaffolding during significant life shifts. Moreover, the research aims to provide actionable insights based on this scaffolding concept for individuals navigating transitions.Design/methodology/approachThis preliminary and exploratory study took a phenomenological approach to examine the role of information seeking and personal information management (PIM) behaviors during life transitions. In-depth semi-structured interviews were held with 15 early-career researchers from various disciplines, who were about to finish their PhDs or had recently graduated.FindingsBy employing information seeking and PIM practices, participants were able to address three main information challenges that arose during the transition process: the timing of information behavior, the nature of information and the social components of the transition. The use of networked and independent information seeking/validation practices enabled to establish a sustainable network of transition-related information, reducing uncertainty. PIM practices helped planning the transition, maintaining information over the long-term and gaining control over personal information.Originality/valueThis study underscores the significance of information behaviors, encompassing both information seeking and PIM, as scaffolding mechanisms during crucial life transitions. It offers essential insights that can guide the creation of impactful interventions and resources. Additionally, the research illuminates the pressing demand for more in-depth exploration in this domain.
An investigation into knowledge management adoption and sustainable competitive advantage in an emerging market economy
Authors: Almalki Mohammed , Al-Shammari Minwir 
Published: November 2023

Purpose
Organizations sustain competitiveness by improving product or service quality, performing efficiently or innovating. This paper aims to investigate the relationship between knowledge management (KM) and sustainable competitive advantage (SCA) in business organizations in the Kingdom of Bahrain. The KM initiatives are categorized into knowledge creation, knowledge storage, knowledge transfer and knowledge application. Employees’ attitudes toward workplace knowledge resources are derived from their perceptions of their importance, usefulness and ease of use.

Design/methodology/approach
This paper adopts a cross-sectional survey design. Data is collected via an electronic questionnaire developed using Google Forms. Purposive sampling used a list of 122 business organizations. Ninety responses were received and taken into consideration for data analysis.

Findings
Spearman correlation analysis and partial least square structural equation modeling revealed a positive association between KM and SCA. This study reflected a positive association between employees’ attitudes toward knowledge resources and sustaining organizations’ competitive advantages.

Originality/value
In Bahrain, empirical studies still need to be developed to explore KM in business organizations and investigate its association with SCA. This study aims to fill this gap by examining the relationship between KM and the sustainability of quality, efficiency and innovation-based competitive advantages in business organizations in an emerging economy context.
Financial development and renewable energy deployment in sub-Saharan African countries
Authors: Diallo Souleymane , Ouoba Youmanli 
Published: November 2023

Purpose
The underdevelopment of the financial sector could be one of the barriers to the deployment of renewable energies in developing countries. The purpose of this paper is therefore to analyse the effect of financial development in the deployment of renewable energies in sub-Saharan African countries.

Design/methodology/approach
The empirical analysis is based on a production approach and a cross-sectionally augmented autoregressive distributive lag error correction model estimate for 25 sub-Saharan African countries over the period 1990–2018. The augmented mean group (AMG) and common correlated effects mean group (CCEMG) estimators were used for the robustness analysis.

Findings
Two results emerge: financial development contributes positively to renewable energy deployment in sub-Saharan African countries in the short and long run; and fossil fuel dependence impedes significantly renewable energy deployment in the short and long run. The robustness analyses using the AMG and CCEMG methods confirm these results.

Practical implications
These results suggest the need for policies to support and strengthen the development of the financial sector to improve its ability to effectively finance investments in renewable energy technologies.

Originality
The originality of this paper lies in the fact that the analysis is based on a renewable energy production approach. Indeed, the level of renewable energy deployment is measured by the production and not the consumption of renewable energy, unlike other previous work. In addition, this research uses recent econometric estimation techniques that overcome the problems of cross-sectional dependence and slope heterogeneity.
The Indonesian national family planning program: progress and remaining challenges in implementing a rights-based approach
Authors: Utomo Budi , Rahayu Sukma , Liyanto Elvira , Romadlona Nohan Arum , Nuryana Dewi , Aryanty Riznawaty Imma , Hidayat Melania , Sariastuti Anggraini , Gayatri Maria , Magnani Robert 
Published: November 2023

Purpose
Indonesia subscribes to rights-based principles of family planning. However, a chasm between principles and practice has long been noted on a global basis, and progress has not been well-documented. This paper aims to assess the extent to which the Indonesian national family planning program has evolved in a manner that is consistent with rights-based principles.

Design/methodology/approach
The primary source of data was five Indonesian Demographic Health Surveys undertaken from 1997 to 2017. The analyses were organized around three major categories of family planning-related human rights. Trend analysis and logistic regression were used in analyzing the data.

Findings
Indonesian women have considerable autonomy in family planning decision, reporting that family planning decisions were mainly made by themselves or jointly with their spouse. Although contraceptive method awareness and demand for family planning are high, Indonesia fares poorly with regard to informed choice in contraceptive method selection. Access to family planning services is comparatively high as judged by contraceptive prevalence, family planning demand satisfaction and unmet need for family planning. However, significant geographic and socioeconomic inequity were observed on many indicators, with eastern Indonesian provinces consistently lagging behind.

Research limitations/implications
This paper focuses on married couple, as Indonesia has a restrictive policy to limiting access and information of family planning for other groups, unmarried youth in particular.

Originality/value
This paper makes an important contribution to document how effectively the prohuman rights policy orientation toward family planning has been translated into services.
How job autonomy influences life satisfaction: the role of work-family enrichment and segmentation preference
Authors: Ma The-Ngan , Vu Hong Van 
Published: November 2023

Purpose
Drawing on conservation of resources theory, this study aims to develop and test a model of moderated mediation in the relationship between job autonomy and employee life satisfaction, focusing on the mediating role of work–family enrichment (WFE) and the moderating role of segmentation preference.

Design/methodology/approach
Using a time-lagged research design, data were collected from 314 employees representing various organisations in Vietnam. The PROCESS macro in SPSS 20.0 was used to analyse the relationships.

Findings
The results indicate a positive relationship between job autonomy and employees’ life satisfaction, mediated by WFE. Additionally, the indirect effect of job autonomy on life satisfaction via WFE was weaker when employees preferred high work–family segmentation.

Practical implications
The study suggests that organisations can enhance employee life satisfaction by increasing job autonomy and promoting WFE. Organisations can establish a more supportive and engaging work environment that promotes well-being by tailoring these interventions to suit employees’ segmentation preferences.

Originality/value
This study contributes to the literature by shedding light on how organisational factors influence employee life satisfaction. It provides the first empirical evidence of a relationship between job autonomy and life satisfaction. It also explores the potential mediation effect of WFE and the moderating effect of segmentation preference.
Remittance flows and welfare implications: the Nigerian experience
Authors: Nwodo Ikenna Paulinus , Omeje Ambrose Nnaemeka , Okereke Chukwu Ugwu 
Published: November 2023

PurposeIn Africa, recent data show that Nigeria is the second top remittance recipient behind Egypt, but welfare seems deteriorating. Most related reviewed literature is micro-based with surveys, giving credence to the dearth of macro-based literature whose gap this study attempted to fill. Thus, the main purpose of this study is to examine remittance flows and its welfare implications in Nigeria.Design/methodology/approachThe study used quarterly data (1980Q1–2020Q4) from World Development Indicators (2020) and applied the dynamic ordinary least squares (DOLS) model.FindingsRemittance flows were found to be significantly improving the welfare of Nigerians by about 0.04% for a percentage remittance increase. Financial sector development results show that while loans decrease welfare per individual significantly by 0.25% given a 1% increase in the loans accessible by the private sector, a percentage increase in broad money supply in circulation raises welfare per individual significantly by about 0.43%.Practical implicationsSince remittance is found to improve welfare, the study recommends that relevant stakeholders should endeavor to eliminate all form of bottlenecks (payment delays, remitting costs, transfer delays, poor policies and policy inconsistencies) inherent in remitting funds back to Nigeria. The implication of this is that if the impediments are minimized, remittances are bound to rise which will ultimately lead to improved welfare.Originality/valueThe existing literature revealed that there exists very limited or no macro-based study in this context, hence this novelty study.
Tribological performance of maintenance-free Cu-Sn-Ni-MoS2 composites over a wide temperature range
Authors: Zhao Yingxiang , Guo Junde , Yan Xiaoni , Du Shan , Gong Min , Sun Biao , Shi Junwen , Deng Wen 
Published: November 2023

Purpose
The purpose of this paper is to investigate the friction and wear mechanisms in copper-based self-lubricating composites with MoS2 as the lubricating phase, which provides a theoretical basis for subsequent research on high-performance copper-based self-lubricating materials.

Design/methodology/approach
Friction tests were performed at a speed of 100 r/min, a load of 10 N, a friction radius of 5 mm and a sliding speed of 30 min. Friction experiments were carried out at RT-500°C. The phase composition of the samples was characterized by X-ray diffraction of Cu Ka radiation, and the microstructure, morphology and elemental distribution were characterized by scanning electron microscopy and energy dispersive spectroscopy. Reactants and valences formed during the wear process were analyzed by X-ray photoelectron spectroscopy.

Findings
The addition of MoS2 can effectively improve friction-reducing and anti-wear action of the matrix, which is beneficial to form a lubricating film on the sliding track. After analyzing different changing mechanism of the sliding tracks, the oxides and sulfides of MoS2, MoO2, Cu2O, CuO and Ni(OH)2 were detected to form a synergetic lubricating film on the sliding track, which is responsible for the excellent tribological properties from room to elevated temperature.

Research limitations/implications
For self-lubrication Cu–Sn–Ni–MoS2 material in engineering field, there are still few available references on high-temperature application.

Practical implications
This paper provides a theoretical basis for the following research on copper-based self-lubricating materials with high performance.

Originality/value
With this statement, the authors hereby certify that the manuscript is the results of their own effort and ability. They have indicated all quotes, citations and references. Furthermore, the authors have not submitted any essay, paper or thesis with similar content elsewhere. No conflict of interest exits in the submission of this manuscript.