bluuebunny/crossref_metadata_2025 huggingface dataset:
Intraspecific plant-soil feedbacks vary under field conditions among species in a tropical tree community
Authors: Eck Jenalle L. , Hassan Lourdes Hernández , Comita Liza S.
Published: October 2023

Premise

Soil microbes can influence patterns of diversity in plant communities via plant-soil feedbacks. Intraspecific plant-soil feedbacks occur when plant genotype causes variation in soil microbial composition, resulting in differences in the performance of seedlings growing near their maternal plants versus seedlings growing near non-maternal conspecific plants. How commonly such intraspecific plant-soil feedbacks occur in natural plant communities is unclear, especially under variable field conditions.

Methods

We conducted an in situ experiment with four native tree species on Barro Colorado Island (BCI), Panama. Seedlings of each species were transplanted beneath their maternal tree or another conspecific tree in the BCI forest. Mortality and growth were assessed at the end of the wet season (∼4 months post-transplant) and at the end of the experiment (∼7 months post-transplant).

Results

Patterns of seedling performance varied among species and were inconsistent over time. Significant effects of field environment were detected for two of the four species: at the end of the wet season,Virola surinamensisseedlings had higher survival beneath their maternal tree than other conspecific trees, while the opposite pattern was found inOrmosia macrocalyx.However, these differences disappeared by the end of the experiment.

Conclusions

Our results suggest that intraspecific plant-soil feedbacks occur inconsistently under field conditions in tropical tree species and may have a limited role in determining seedling performance in tropical tree communities. Future studies are needed to elucidate the environmental and genetic factors that determine the incidence and direction of intraspecific plant-soil feedbacks in plant communities.
HIPSD&R-seq enables scalable genomic copy number and transcriptome profiling
Authors: Lazareva Olga , Mallm Jan-Philipp , Simovic-Lorenz Milena , Philippos George , Sant Pooja , Parekh Urja , Hammann Linda , Li Albert , Yildiz Umut , Marttinen Mikael , Zaugg Judith , Noh Kyung Min , Stegle Oliver , Ernst Aurélie
Published: October 2023

Single-cell DNA-sequencing (scDNA-seq) enables decoding somatic cancer variation. Existing methods are hampered by low throughput or cannot be combined with transcriptome sequencing in the same cell. We propose HIPSD&R-seq (HIgh-throughPutSingle-cellDna andRna-seq), a scalable yet simple assay to profile low-coverage DNA and RNA in thousands of cells in parallel. Our approach builds on an accessible modification of the 10X Genomics platform for scATAC and multiome profiling. In applications to human cell models and primary tissue, we demonstrate the feasibility to detect rare clones and we combine the assay with combinatorial indexing to profile over 16,000 cells.
Structural Insights into the Interaction Between Adenovirus C5 Hexon and Human Lactoferrin
Authors: Dhillon Arun , Persson B. David , Volkov Alexander N. , Sülzen Hagen , Kádek Alan , Pompach Petr , Kereïche Sami , Lepšík Martin , Danskog Katarina , Uetrecht Charlotte , Arnberg Niklas , Zoll Sebastian
Published: October 2023

Adenovirus (AdV) infection of the respiratory epithelium is common, but poorly understood. Human AdV species C types, such as HAdV-C5, utilize the Coxsackie-adenovirus receptor (CAR) for attachment and subsequently integrins for entry. CAR and integrins are however located deep within the tight junctions in the mucosa where they would not be easily accessible. Recently, a model for CAR-independent AdV entry was proposed. In this model, human lactoferrin (hLF), an innate immune protein, aids the viral uptake into epithelial cells by mediating interactions between the major capsid protein, hexon, and yet unknown host cellular receptor(s). However, a detailed understanding of the molecular interactions driving this mechanism is lacking. Here, we present a new cryo-EM structure of HAdV-5C hexon at high resolution alongside a hybrid structure of HAdV-5C hexon complexed with human lactoferrin (hLF). These structures reveal the molecular determinants of the interaction between hLF and HAdV-C5 hexon. hLF engages hexon primarily via its N-terminal lactoferricin (Lfcin) region, interacting with hexon’s hypervariable region 1 (HVR-1). Mutational analyses pinpoint critical Lfcin contacts and also identify additional regions within hLF that critically contribute to hexon binding. Our study sheds more light on the intricate mechanism by which HAdV-C5 utilizes soluble hLF/Lfcin for cellular entry. These findings hold promise for advancing gene therapy applications and inform vaccine development.
Bsp1, a fungal CPI motif protein, regulates actin filament capping in endocytosis and cytokinesis
Authors: Hummel Daniel R. , Hakala Markku , Toret Christopher P. , Kaksonen Marko
Published: October 2023

The capping of barbed filament ends is a fundamental mechanism for actin regulation. Capping protein controls filament growth and actin turnover in cells by binding to the barbed ends of the filaments with high affinity and slow off-rate. The interaction between Capping protein and actin is regulated by capping protein interaction (CPI) motif proteins. We identified a novel CPI motif protein, Bsp1, which is involved in cytokinesis and endocytosis in budding yeast. We demonstrate that Bsp1 is an actin binding protein with a high affinity for capping protein via its CPI motif. In cells, Bsp1 regulates capping protein at endocytic sites and is a major recruiter of capping protein to the cytokinetic actin ring. Lastly, we define Bsp1-related proteins as a distinct fungi-specific CPI protein group. Our results suggest that Bsp1 promotes actin filament capping by the capping protein. This study establishes Bsp1 as a new capping protein regulator and promising candidate to regulate actin networks in fungi.
G protein subunit Gγ13-mediated signaling pathway is critical to the inflammation resolution and functional recovery of severely injured lungs
Authors: Li Yi-Hong , Yang Yi-Sen , Xue Yan-Bo , Lei Hao , Zhang Sai-Sai , Qian Junbin , Yao Yushi , Zhou Ruhong , Huang Liquan
Published: October 2023

Tuft cells are a group of rare epithelial cells that can detect pathogenic microbes and parasites. Many of these cells express signaling proteins initially found in taste buds. It is, however, not well understood how these taste signaling proteins contribute to the response to the invading pathogens or to the recovery of injured tissues. In this study, we conditionally nullified the signaling G protein subunit Gγ13 and found that the number of ectopic tuft cells in the injured lung was reduced following the infection of the influenza virus H1N1. Furthermore, the infected mutant mice exhibited significantly larger areas of lung injury, increased macrophage infiltration, severer pulmonary epithelial leakage, augmented pyroptosis and cell death, greater bodyweight loss, slower recovery, worsened fibrosis and increased fatality. Our data demonstrate that the Gγ13-mediated signal transduction pathway is critical to tuft cells-mediated inflammation resolution and functional repair of the damaged lungs.To our best knowledge, it is the first report indicating subtype-specific contributions of tuft cells to the resolution and recovery.
Visualizing liquid-liquid phase transitions
Authors: Sahoo Bikash R. , Deng Xiexiong , Wong Ee Lin , Clark Nathan , Yang Harry , Subramanian Vivekanandan , Guzman Bryan B. , Harris Sarah E. , Dehury Budheswar , Miyashita Emi , Hoff J. Damon , Kocaman Vojč , Saito Hirohide , Dominguez Daniel , Plavec Janez , Bardwell James C.A.
Published: October 2023

Liquid-liquid phase condensation governs a wide range of protein-protein and protein-RNA interactions in vivo and drives the formation of membrane-less compartments such as the nucleolus and stress granules. We have a broad overview of the importance of multivalency and protein disorder in driving liquid-liquid phase transitions. However, the large and complex nature of key proteins and RNA components involved in forming condensates such as stress granules has inhibited a detailed understanding of how condensates form and the structural interactions that take place within them. In this work, we focused on the small human SERF2 protein. We show here that SERF2 contributes to the formation of stress granules. We also show that SERF2 specifically interacts with non-canonical tetrahelical RNA structures called G-quadruplexes, structures which have previously been linked to stress granule formation. The excellent biophysical amenability of both SERF2 and RNA G4 quadruplexes has allowed us to obtain a high-resolution visualization of the multivalent protein-RNA interactions involved in liquid-liquid phase transitions. Our visualization has enabled us to characterize the role that protein disorder plays in these transitions, identify the specific contacts involved, and describe how these interactions impact the structural dynamics of the components involved in liquid-liquid phase transitions, thus enabling a detailed understanding of the structural transitions involved in early stages of ribonucleoprotein condensate formation.
Emergent Antibiotic Persistence in Cross-Feeding Bacteria in Structured Habitats
Authors: Xiong Xianyi , Othmer Hans G. , Harcombe William R.
Published: October 2023

Antibiotic persistence allows a sub-population of bacteria to survive antibiotic-induced killing and contributes to the evolution of antibiotic resistance. Although bacteria typically live in microbial communities with complex ecological interactions, little is known about how microbial ecology affects antibiotic persistence. Here, we demonstrated that the combination of cross-feeding and community spatial structure can emergently cause high antibiotic persistence in bacteria by increasing the cell-cell heterogeneity in the metabolic state both during growth and antibiotic killing. We tracked the ampicillin-induced death on agar surfaces in a model obligate mutualism ofEscherichia coliandSalmonella enterica. We found thatE. coliformed ∼100-fold more antibiotic persisters in the cross-feeding coculture than in monoculture. This high persistence could not be explained solely by the presence ofS. enterica, the presence of cross-feeding, or the growth rate differences between the mono- and co-cultures. Time-series fluorescent microscopy revealed increased cell-cell variation inE. colilag time in the mutualistic co-culture. Furthermore, we discovered that anE. colicell can survive antibiotic killing if the nearbyS. entericacells on which it relies die first—a mechanism we termed “dynamical loss of access to nutrient.” In conclusion, we showed that the high antibiotic persistence phenotype can be an emergent phenomenon caused by a combination of cross-feeding and spatial structure. Our work highlights the importance of considering spatially-structured interactions during antibiotic treatment and to understand microbial community resilience more broadly.
Proximity proteomics reveals UCH-L1 as an NLRP3 interactor that modulates IL-1β production in human macrophages and microglia
Authors: Liang Zhu , Damianou Andreas , Vendrell Iolanda , Jenkins Edward , Lassen Frederik H. , Washer Sam J , Liu Guihai , Yi Gangshun , Lou Hantao , Cao Fangyuan , Zheng Xiaonan , Fernandes Ricardo A. , Dong Tao , Tate Edward W. , Daniel Elena Di , Kessler Benedikt M
Published: October 2023

Activation of the NACHT, LRR family pyrin domain containing 3 (NLRP3) inflammasome complex is an essential innate immune signalling mechanism. To reveal how human NLRP3 inflammasome assembly and activation are controlled, in particular by components of the ubiquitin system, proximity labelling, affinity purification and RNAi screening approaches were performed. Our study provides an intricate time-resolved molecular map of different phases of NLRP3 inflammasome activation. Also, we show that ubiquitin C-terminal hydrolase 1 (UCH-L1) interacts with the NACHT domain of NLRP3. Downregulation of UCH-L1 decreases pro-IL-1β levels. UCH-L1 chemical inhibition with small molecules interfered with NLRP3 puncta formation and ASC oligomerization, leading to altered IL-1β cleavage and secretion, particularly in microglia cells, which exhibited elevated UCH-L1 expression as compared to monocytes/macrophages. Altogether, we profiled NLRP3 inflammasome activation dynamics and highlight UCH-L1 as an important modulator of NLRP3-mediated IL-1β production, suggesting that a pharmacological inhibitor of UCH-L1 may decrease inflammation-associated pathologies.
A Cell Atlas of Thoracic Aortic Perivascular Adipose Tissue: a focus on mechanotransducers
Authors: Thompson Janice M. , Watts Stephanie W. , Terrian Leah , Contreras G. Andres , Rockwell Cheryl , Rendon C. Javier , Wabel Emma , Lockwood Lizabeth , Bhattacharya Sudin , Nault Rance
Published: October 2023

Perivascular adipose tissue (PVAT) is increasingly recognized for its function in mechanotransduction. To examine the cell-specificity of recognized mechanotransducers we used single nuclei RNA sequencing (snRNAseq) of the thoracic aorta PVAT (taPVAT) from male Dahl SS rats compared to subscapular brown adipose tissue (BAT). Approximately 30,000 nuclei from taPVAT and BAT each were characterized by snRNAseq, identifying 8 major cell types expected and one unexpected (nuclei with oligodendrocyte marker genes). Cell-specific differential gene expression analysis between taPVAT and BAT identified up to 511 genes (adipocytes) with many (≥20%) being unique to individual cell types.Piezo1was the most highly, widely expressed mechanotransducer. Presence of PIEZO1 in the PVAT was confirmed by RNAscope® and IHC; antagonism of PIEZO1 impaired the PVAT’s ability to hold tension. Collectively, the cell compositions of taPVAT and BAT are highly similar, and PIEZO1 is likely a mechanotransducer in taPVAT.
Review of multilevel inverter for high-power applications
Authors: Barnawi Abdulwasa B. , Alfifi Abdull Rahman A. , Elbarbary Z.M.S. , Alqahtani Saad Fahed , Shaik Irshad Mohammad
Published: October 2023

Purpose

Traditional level inverter technology has drawbacks in the aspect of Total harmonic distortion (THD) and switching losses for higher frequencies. Due to these drawbacks, two-level inverters have become unprofitable for high-power applications. Multilevel inverters (MLIs) are used to enhance the output waveform characteristics (i.e. low THD) and to offer various inverter topologies and switching methods.

Design/methodology/approach

MLIs are upgraded versions of two-level inverters that offer more output levels in current and voltage waveforms while lowering the dv/dt and di/dt ratios. This paper aims to review and compare the different topologies of MLI used in high-power applications. Single and multisource MLI's working principal and switching states for each topology are demonstrated and compared. A Simulink model system integrated using detailed circuit simulations in developed in MATLAB®–Simulink program. In this system, a constant voltage source connected to MLI to feed asynchronous motor with squirrel cage rotor type is used to demonstrate the efficacy of the MLI under different varying speed and torque conditions.

Findings

MLI has presented better control and good range of system parameters than two-level inverter. It is suggested that the MLIs like cascade-five-level and NPC-five-level have shown low current harmonics of around 0.43% and 1.87%, respectively, compared to two-level inverter showing 5.82%.

Originality/value

This study is the first of its kind comparing the different topologies of single and multisource MLIs. This study suggests that the MLIs are more suitable for high-power applications.
Does financial market development really drive migrant remittances’ flow in Sub-Saharan Africa?
Authors: Ikpesu Olapeju
Published: October 2023

Purpose

The discussion on international migration has become a significant part of globalization and a topical issue in international relations, especially in developing economies which mostly relies on migrant remittances. The purpose of the study is to examine whether financial market development (equity market development and banking sector development) really drives migrant remittance flow in Sub-Saharan Africa (SSA).

Design/methodology/approach

The study employs the dynamic heterogeneous panel data approach-the pool mean group (PMG) and the mean group (MG) techniques in analyzing the model based on data obtained from 27 SSA countries covering the period 2000–2020.

Findings

The findings of the study revealed that financial market development (equity market development and banking sector development) is a key driver of migrant remittances flows in the SSA region. In addition, the study revealed that the following macroeconomic variables such as real interest rate, unemployment rate, global growth, emigration, and economic growth are also determinants of migrant remittances flows in the SSA region.

Originality/value

The reviewed empirical literature revealed that several studies documents that the macroeconomic determinants of migrant remittances include inflation, GDP, interest rate, exchange rate, population growth, financial sector development and unemployment rate. Most of these studies fail to capture both equity market development and robust banking sector development (financial market development) as critical drivers of migrant remittances flow in SSA. Also, this study uses a robust measure of equity market development and banking sector development, unlike previous studies.

Peer review

The peer review history for this article is available at: https://publons.com/publon/10.1108/IJSE-05-2023-0361
The role of attributes defining intervention concepts in international doctrinal documents on built heritage
Authors: Lin Mi , Nevzgodin Ivan , Pereira Roders Ana , de Jonge Wessel
Published: October 2023

Purpose

Attributes conveying cultural significance play a key role in heritage management, as well as in differentiating interventions in built heritage. However, seldom the relation between interventions and attributes, either tangible or intangible, has been researched systematically. How do both tangible and intangible attributes and interventions relate? What attributes make interventions on built heritage differ?

Design/methodology/approach

This paper conducts a systematic content analysis of forty-one international doctrinal documents—mainly adopted by the Council of Europe, UNESCO and ICOMOS, between 1877 and 2021. The main aim is to reveal and compare the selected eight intervention concepts, namely—restoration (C1), preservation (C2), conservation (C3), adaptation (C4), rehabilitation (C5), relocation (C6), reconstruction (C7) and renewal (C8)—and their definitions, in relation to attributes, both tangible and intangible. The intensity of the relationship between intervention concepts and attributes is determined based on the frequency of the mentioned attributes per intervention.

Findings

There were three key findings. First, although the attention to intangible attributes has increased in the last decades, the relationship between interventions and tangible attributes remains stronger. The highest frequency of referencing the tangible attributes was identified in “relocation” and “preservation,” while the lowest was in “rehabilitation.” Second, certain attributes play contradictory roles, e.g. “material,” “use” and “process,” which creates inconsistent definitions between documents. Third, as attributes often include one another in building layers, they trigger the intervention concepts in hierarchical patterns.

Originality/value

This paper explores and discusses the results of a novel comparative analysis between different intervention concepts and definitions, with a particular focus on the attributes. The results can support further research and practice, clarifying the identified differences and similarities.
From family firm to Japanese OEM in tacit knowledge innovation: a case study of Sin Kwang plastic resources in Malaysia
Authors: Kean Yew Lee
Published: October 2023

Purpose

Although it is a well-known notion that “a family firm does not survive beyond the third generation”, owing to the ineffective tacit knowledge transfer, studies investigating the relationship between generational evolution and knowledge innovation is scarce. Thus, this case study revolving Sin Kwang Plastic Resources Berhad (SKP) seeks to address this gap in literature.

Design/methodology/approach

To assess the development of family business, a longitudinal case study was performed by documenting the entire evolutionary process starting from its establishment until now. The historical profiles for SKP were obtained from the previous annual reports submitted to the government's Companies Commission (SSM). Secondary materials from the Federation of Malaysian Manufacturers (FMM) and the edge newspaper and articles on the company were also gathered. Throughout the in-depth interviews, the author can see how the next generation of this family firm innovates and implements tacit knowledge innovation in original equipment manufacturing (OEM) by adhering to the Japanese industrial standards.

Findings

Findings show that the second generation utilized the company's extensive knowledge in plastic contract manufacturing in SKP for tacit knowledge conversion, triggers the birth of STS Tecnic Berhad, a subsidiary company that manufactures plastic parts for the industrial packaging and automotive industry. To simplify the process of managing the complex business, SKP opted to “prune the family tree” by dividing the business, involving fewer managers and restricting the number of family shareholders.

Practical implications

This case study traces how Gan's family's tacit knowledge in plastic contract manufacturing have been acquired from the experience of contract manufacturing with the Japanese multinational corporations (MNCs) by further commercializing the tacit knowledge into different companies for different plants. SKP promotes tacit knowledge innovation in the learning organization, thus responding to the firm's sustainability.

Originality/value

This study demonstrates that knowledge transformation plays vital roles in product development and gaining competitive advantage. The success of this business is founded by the building of shared values, norms and technical understanding in plastic contract manufacturing among the Japanese MNCs in Malaysia.
Optimal industrial structure and economic growth: a new measurement method and application
Authors: Huang Yunjue , Ye Dezhu , Xu Shulin
Published: October 2023

Purpose

The purpose of this paper is to explore the matching relationship between factor endowment and industrial structure, and its impact on economic growth.

Design/methodology/approach

The assortative matching method is developed to quantitatively measure the matching between factor endowment and industrial structure. A series of empirical tests are then carried out to evaluate the impact on the economic development of the matching.

Findings

1) The matching between factor endowment and industrial structure has a significantly positive impact on economic growth. (2) Economic growth reaches its maximum when the gap between the two sectors narrows to zero. (3) This effect is particularly significant for countries with higher GDP per capita and GNI per capita. (4) The results remain robust after employing a series of tests.

Practical implications

Aggressive industrial policies are not desirable. The optimal industrial structure is the one that complied with the comparative advantage of the given factor endowment in the economy.

Originality/value

So far, there has been a significant lack of an applicable quantitative indicator for measuring the matching between factor endowment and industrial structure, which is essential for conducting empirical tests and providing evidence for related economic theories.
Long‐term predictors of morbidity and mortality in patients following LVAD replacement
Authors: Jimenez Contreras Fabian , Rames Jess David , Schroder Jacob , Russell Stuart D. , Katz Jason , Omer Tariq , Barac Yaron D. , Milano Carmelo
Published: October 2023

Background

As heart transplant guidelines evolve, the clinical indication for 73% of durable left ventricular assist device (LVAD) implants is now destination therapy. Although completely magnetically levitated LVAD devices have demonstrated improved durability relative to previous models, LVAD replacement procedures are still required for a variety of indications. Thus, the population of patients with a replaced LVAD is growing. There is a paucity of data regarding the outcomes and risk factors for those patients receiving first‐time LVAD replacements.

Methods

The study cohort consisted of all consecutive patients between 2006 and 2020 that received a first‐time LVAD replacement at a single institution. Preoperative clinical and laboratory variables were collected retrospectively. The primary endpoint was death or need for an additional LVAD replacement. Data were subjected to Kaplan–Meier, univariate, and multivariate Cox hazard ratio analyses.

Results

In total, 152 patients were included in the study, of which 101 experienced the primary endpoint. On multivariate analysis, patients receiving HeartMate 3 (HM3) LVADs as the replacement device showed superior outcomes (HR 0.15, 95% CI 0.065–0.35, p < 0.0001). Independent risk factors for death or need for additional replacement included preoperative extracorporeal membrane oxygenation (ECMO) (HR 4.44, 95% CI 1.87–14.45, and p = 0.00042), increased number of sternotomies (HR 5.20, 95% CI 1.87–14.45, and p = 0.0016), and preoperative mechanical ventilation (HR 1.98, 95% CI 1.01–3.86, and p = 0.045).

Conclusions

Replacement with HM3 showed superior outcomes compared to all other pump types when controlling for both initial pump type and other independent predictors of death or LVAD replacement. Preoperative ECMO, mechanical ventilation, and multiple sternotomies also increased the odds for death or the need for subsequent replacement.
From the margins to the center: Advancing research on caregiver socialization of emotion in Asia
Authors: Raval Vaishali V.
Published: October 2023

As in other fields of developmental science, emotion socialization research in Asia, where nearly 60% of the world's population lives, has emerged on the margins. Contextualizing this marginalization within colonial foundations of our science, in this article, I discuss the historic dominance of the Global North frameworks of emotion socialization. I also address associated limitations of emotion socialization research in Asia, recent conceptualizations that integrate cultural processes and emerging insights from this research, and the need for a decolonial framework to further advance this literature. A decolonial framework would enable scholars to contextualize emotion socialization within local milieus; use research methods valued by local communities; and interpret emotion‐related beliefs and behaviors in Asia as assets, not deficits. Adopting a decolonial framework can move emotion socialization research in Asia from the margins to the center of emotion socialization literature, generating knowledge to support the well‐being of children in Asia and around the world.
The Bobath Clinical Reasoning Framework for neurodevelopmental conditions: A call for collaboration instead of de‐implementation
Authors: Blomme Sofie
Published: October 2023

This letter to the editor is on the invited review by Mayston et al. on pages 564–572 of this issue.
Laws, Contingencies, Irreversible Divergence, and Physical Geography*
Authors: Phillips Jonathan D.
Published: October 2023

Four critical challenges for physical geography are examined here: deterioration of common cores of knowledge associated with increasing intellectual niche specialization; the need for conceptual thinking and problem‐framing to catch up with measurement and analysis technology; and the need to explicitly incorporate human decision making in analysis of earth surface systems. The future calls for physical geography to embrace and confront the creative tension between nomothetic and interpretive science, and to fruitfully and explicitly integrate these approaches.
GIS, Cartography, and the “Third Culture”: Geographic Imaginations in the Computer Age*
Authors: Sui Daniel Z.
Published: October 2023

Geographic information systems (GIS) and cartography have traditionally been regarded as fields for the study of techniques. Yet the past ten years have witnessed geographers' increasing intellectual engagement with GIS and cartography. This essay recaps the recent intellectual discourses on GIS and cartography and speculates on possible development in the near future. Geocomputation, spatially integrated social sciences, social informatics, information ecology, and humanistic GIScience are identified as five areas of intensive new research, and it is argued that creative imaginations under the milieu of the “third culture” are urgently needed to address the challenging issues in this new technological era. Whether geography will become an intellectually more vibrant discipline hinges on the extent to which we can rekindle geographic imaginations in this computer age via GIScience to address issues of great societal concern.
In the Critical Zone: Geography at the U.S. Geological Survey
Authors: Graf William L.
Published: October 2023

Geography is again becoming an integral part of the premier natural‐science agency of the federal government. Geographic research emphasizes the surface of the earth, a portion of the earth system that the U.S. Geological Survey (USGS) defines as the “critical zone.” Although geography was part of the USGS from the creation of the agency, in recent years geography in the agency has largely been limited to topographic mapping. Recently, the USGS and an advisory committee of the National Research Council (NRC) reviewed the role of geography at the Survey. The committee's report, along with ongoing decision‐making in the federal government, is likely to reshape geography in the USGS. The newly defined USGS has a regional structure and four disciplines: geology, hydrology, biology, and geography. The NRC report emphasizes the need for the creation of a spatial database called the National Map to replace the existing series of paper topographic maps. The report also outlines the need for geographic research in geographic information science (GIScience), nature‐society connections, and bridging of science to decision‐making. The NRC report has been briefed throughout the USGS, in the federal executive branch, and in Congress. The changing role for geography in the USGS requires change in the agency culture, revised budgetary decisions, and the establishment of a long‐term core agenda for research. Academic geographers will need to prepare a new generation of geographers for participation in the USGS and similar agencies.
From Chicago to L.A. and Back Again: A Chicago‐Inspired Quantitative Analysis of Income Distribution in Montreal*
Authors: Shearmur Richard , Charron Mathieu
Published: October 2023

In a recent issue of Urban Geography (2001), a number of key players in the 1960s and 1970s school of quantitative urban geography (called Chicago II in this article) set out some of the approach's key methodological premises and assessed its influence in the wider arena of urban studies. At about the same time, the 1920s and 1930s Chicago School of urban sociology (called the Chicago School in this article) was being reassessed in France (Huet 2000), and deconstructed in Los Angeles (Dear 2001). In this article, we outline a selection of basic models of urban space proposed by the Chicago School and further elaborated by Chicago II. We then consider certain aspects of three important critiques: humanist/aesthetic, Marxist, and postmodern. We argue that none of these invalidates the Chicago II approach to the study of urban areas, and we demonstrate its resilience and usefulness by way of the empirical example of Montreal. Though the results are of interest in their own right, the principal purpose of the analysis is to illustrate the type of insight that a structured quantitative approach provides and the way this approach rests on a theoretical understanding of processes at work in cities. We conclude by arguing that the humanist and Marxist critiques shed important light upon the possibilities and limits of the Chicago II approach, but that the postmodern claim that the spatial development of urban areas is not structured by at least some general processes is inaccurate.
Effect of in ovo feeding of folic acid on Disabled‐1 and gga‐miR‐182‐5p expression in the cerebral cortex of chick embryo
Authors: Heydari Behnaz , Mashayekhi Farhad , Kashani Maryam Haji Ghasem
Published: October 2023

Folate (vitamin B9) has been shown to reduce the prevalence of neural tube defects (NTDs). Many genes comprising Disabled‐1 (DAB1) and miRNAs have been shown to play important role in normal brain development. Reelin‐signalling has been shown to play key role in regulating of neuronal migration during brain development. The aim of this study was to evaluate the effects of in ovo administration of folic acid (FA) on DAB1 and gga‐miR‐182‐5p expression in the cerebral cortex of chick embryo. A total number of 30 hatching eggs were used in this study. The number of 10 eggs were injected into the yolk sac with FA (150 µg/egg), 10 eggs by normal saline (sham group) on embryonic day 11 and 10 eggs were left without injection as control. Then the cerebral cortices were collected on E19 and the expression of DAB1 and gga‐miR‐182‐5p was studied by Real‐Time PCR. The results showed that DAB1 expression in the cerebral cortex of FA‐treated, sham and control were 2.51 ± 0.13, 1.01 ± 0.04 and 1.03 ± 0.04 fold changes, respectively, and this amount for gga‐miR‐182‐5p were 0.54 ± 0.03, 1.09 ± 0.07 and 1.00 ± 0.06‐fold change respectively. Statistical analysis showed that there is a significant increase in DAB1 and a decrease in gga‐miR‐182‐5p expression in FA injected cerebral cortex as compared either with either SHAM or control (p < 0.0001). But, no significant change in DAB1 and gga‐miR‐182‐5p expression was observed between sham and the control group (p = 0.99 and p = 0.57 respectively). It is concluded that in ovo feeding of FA increases DAB1 and decreases gga‐miR‐182‐5p expression in the developing chick cerebral cortex.
In search of public values in performance budgeting studies
Authors: Ho Alfred Tat‐Kei , Shen Chen , Xu Yan
Published: October 2023

Performance budgeting is inevitably linked to policy priorities, and priorities are fundamentally the expression of public values. Through a bibliometric analysis of past studies, this study shows that over time, the performance budgeting literature is linked to more diverse values beyond efficiency and effectiveness concerns. Transparency, democracy, participation, inclusiveness, and other political, legal, social, and sustainability values have been getting more attention in public administration, accounting, and budgeting journals, as well as in various field journals. This study concludes by suggesting a need for more interdisciplinary and comparative research about the normative foundation of performance budgeting and its connection with public value theory in the future.
Locality of relative symplectic cohomology for complete embeddings
Authors: Groman Yoel , Varolgunes Umut
Published: October 2023

A complete embedding is a symplectic embedding $\iota :Y\to M$ of a geometrically bounded symplectic manifold $Y$ into another geometrically bounded symplectic manifold $M$ of the same dimension. When $Y$ satisfies an additional finiteness hypothesis, we prove that the truncated relative symplectic cohomology of a compact subset $K$ inside $Y$ is naturally isomorphic to that of its image $\iota (K)$ inside $M$. Under the assumption that the torsion exponents of $K$ are bounded, we deduce the same result for relative symplectic cohomology. We introduce a technique for constructing complete embeddings using what we refer to as integrable anti-surgery. We apply these to study symplectic topology and mirror symmetry of symplectic cluster manifolds and other examples of symplectic manifolds with singular Lagrangian torus fibrations satisfying certain completeness conditions.
Response to comment of Albarède and colleagues
Authors:   University of Liverpool, Wood Jonathan R. , Ponting Matthew ,   University of Liverpool, Butcher Kevin ,   University of Warwick
Published: October 2023

Our purpose is to better understand the actions and behaviours of people in the past, often with a focus on ancient economies, and we are willing to use tools from any discipline that allow us to explore these issues. This is why it is so important that the limitations of techniques applied to archaeology are presented as explicitly as their utility.
Reduced Order Synchronization of Two Non-Identical Special Class of Strict Feedback Systems Via Back-Stepping Control Technique
Authors: Bora Riddhi Mohan , Sharma Bharat Bhushan
Published: October 2023

This work offers a systematic technique to achieve reduced order synchronization (ROS) between two different order general classes of chaotic systems in a master-slave configuration. In this study, the dynamics of the master and slave systems are assumed to follow a special class of strict-feedback form, namely, the generalized triangular feedback form. The main objective is to design a suitable scalar controller using a Lyapunov theory-based back-stepping approach such that the mth order slave system gets synchronized with the nth order master system. Due to the difference in the order of the systems (m<n and m=(n−1)), it is only possible to achieve the synchronization between m numbers of states of the slave systems with (n−1) numbers of states of the master system, respectively. We cannot conclude on the stability of the nth state of the master system as there is no counterpart (state) available in the slave system to be synchronized with. Adding an additional (m+1)th state dynamics along with a nonlinear feedback controller (U1) to the slave system ensures that the nth state of the master system is synchronized with the (m+1)th state dynamics of the slave system. With the suggested technique proposed in this article, complete state-to-state synchronization can be achieved with only two controllers. The analytical results are successfully validated through numerical simulations presented in the end.
Systematic Review of Accelerometer Responsiveness to Change for Measuring Physical Activity, Sedentary Behavior, or Sleep
Authors: Clevenger Kimberly A. , Montoye Alexander H.K.
Published: October 2023

Measurement of 24-hr movement behaviors is important for assessing adherence to guidelines, participation trends over time, group differences, and whether health-promoting interventions are successful. For a measurement tool to be useful, it must be valid, reliable, and able to detect change, the latter being a measurement property called responsiveness, sensitivity to change, or longitudinal validity. We systematically reviewed literature on the responsiveness of accelerometers to detect change in 24-hr movement behaviors. Databases (PubMed, Scopus, and EBSCOHost) were searched for peer-reviewed papers published in English between 1998 and 2023. Quality/risk of bias was assessed using a customized tool. This study is registered at https://osf.io/qrn8a. Twenty-six papers met the inclusion/exclusion criteria with an overall sample of 1,939 participants. Narrative synthesis was used. Most studies focused on adults (n = 21), and almost half (n = 12) included individuals with specific medical conditions. Studies primarily took place in free-living settings (n = 21) and used research-grade accelerometers (n = 24) worn on the hip (n = 18), thigh (n = 7), or wrist (n = 9). Outcomes included physical activity (n = 19), sedentary time/behavior (n = 12), or sleep (n = 2) and were calculated using proprietary formulas (e.g., Fitbit algorithm), cut points, and/or count-based methods. Most studies calculated responsiveness by comparing before versus after an intervention (n = 16). Six studies included a criterion measure to confirm that changes occurred. Limited research is available on the responsiveness of accelerometers for detecting change in 24-hr movement behaviors, particularly in youth populations, for sleep outcomes, and for commercial and thigh- or wrist-worn devices. Lack of a criterion measure precludes conclusions about the responsiveness even in more frequently studied outcomes/populations.
Optimization of IspS
ib
stability through directed evolution to improve isoprene production
Authors: Li Meijie , Yang Rumeng , Guo Jing , Liu Min , Yang Jianming
Published: October 2023

Enzyme stability is often a limiting factor in the microbial production of high-value-added chemicals and commercial enzymes. A previous study by our research group revealed that the unstable isoprene synthase from
Ipomoea batatas
(IspS
ib
) critically limits isoprene production in engineered
Escherichia coli
. Directed evolution was, therefore, performed in the present study to improve the thermostability of IspS
ib
. First, a tripartite protein folding system designated as lac′-IspS
ib
-′lac, which could couple the stability of IspS
ib
to antibiotic ampicillin resistance, was successfully constructed for the high-throughput screening of variants. Directed evolution of IspS
ib
was then performed through two rounds of random mutation and site-saturation mutation, which produced three variants with higher stability: IspS
ib
N397V A476V
, IspS
ib
N397V A476T
, and IspS
ib
N397V A476C
. The subsequent
in vitro
thermostability test confirmed the increased protein stability. The melting temperatures of the screened variants IspS
ib
N397V A476V
, IspS
ib
N397V A476T
, and IspS
ib
N397V A476C
were 45.1 ± 0.9°C, 46.1 ± 0.7°C, and 47.2 ± 0.3°C, respectively, each of which was higher than the melting temperature of wild-type IspS
ib
(41.5 ± 0.4°C). The production of isoprene at the shake-flask fermentation level was increased by 1.94-folds, to 1,335 mg/L, when using IspS
ib
N397V A476T
. These findings provide insights into the optimization of the thermostability of terpene synthases, which are key enzymes for isoprenoid production in engineered microorganisms. In addition, the present study would serve as a successful example of improving enzyme stability without requiring detailed structural information or catalytic reaction mechanisms.

IMPORTANCE

The poor thermostability of IspS
ib
critically limits isoprene production in engineered
Escherichia coli
. A tripartite protein folding system designated as lac'-IspS
ib
-'lac, which could couple the stability of IspS
ib
to antibiotic ampicillin resistance, was successfully constructed for the first time. In order to improve the enzyme stability of IspS
ib
, the directed evolution of IspS
ib
was performed through error-PCR, and high-throughput screening was realized using the lac'-IspS
ib
-'lac system. Three positive variants with increased thermostability were obtained. The thermostability test and the melting temperature analysis confirmed the increased stability of the enzyme. The production of isoprene was increased by 1.94-folds, to 1,335 mg/L, using IspS
ib
N397V A476T
. The directed evolution process reported here is also applicable to other terpene synthases key to isoprenoid production.
MiR-184 targeting FOXO1 regulates host-cell oxidative stress induced by
Chlamydia psittaci
via the Wnt/β-catenin signaling pathway
Authors: Chen Lili , Huang Qiaoling , Luo Yuchen , Zhou You , Tong Ting , Chen Yuyu , Bai Qinqin , Lu Chunxue , Li Zhongyu
Published: October 2023

Chlamydia psittaci
is a human pathogen that causes atypical pneumonia after zoonotic transmission. We confirmed that
C. psittaci
infection induces oxidative stress in human bronchial epithelial (HBEs) cells and explored how this is regulated through miR-184 and the Wnt/β-catenin signaling pathway. miR-184 mimic, miR-184 inhibitor, FOXO1 siRNA, or negative control sequence was transfected into HBE cells cultured in serum-free medium using Lipofectamine 2000. Then, prior to the cells were infected with
C. psittaci
6BC, and the cells were treated with or without 30 µM Wnt/β-catenin inhibitor ICG-001. Quantification of reactive oxygen species, malondialdehyde (MDA), superoxide dismutase (SOD), and glutathione was carried out according to the manufacturer’s protocol using a corresponding assay kit. The outcome of both protein and gene was measured by western blotting or real-time fluorescence quantitative PCR. In
C. psittaci
-infected HBE cells, miR-184 was upregulated, while one of its target genes,
FOXO1
, was downregulated. ROS and MDA levels increased, while SOD and GSH contents decreased after
C. psittaci
infection. When miR-184 expression was downregulated, the level of oxidative stress caused by
C. psittaci
infection was reduced, and the Wnt/β-catenin signaling pathway was inhibited. The opposite results were seen when miR-184 mimic was used. Transfecting with FOXO1 siRNA reversed the effect of miR-184 inhibitor. Moreover, when the Wnt/β-catenin-specific inhibitor ICG-001 was used, the level of oxidative stress induced by
C. psittaci
infection was significantly suppressed. miR-184 can target FOXO1 to promote oxidative stress in HBE cells following
C. psittaci
infection by activation of the Wnt/β-catenin signaling pathway.
Three small partner proteins facilitate the type VII-dependent secretion of an antibacterial nuclease
Authors: Yang Yaping , Boardman Eleanor , Deme Justin , Alcock Felicity , Lea Susan , Palmer Tracy
Published: October 2023

The type VIIb secretion system (T7SSb) is a multisubunit protein export machine found in Gram-positive Bacillota which plays a key role in interbacterial competition. The T7SSb secretes a variety of toxic effector proteins targeting closely related strains; however, the mechanism of secretion and the roles of numerous conserved genes within T7SSb gene clusters remain unknown. EsaD is a nuclease toxin secreted by the
Staphylococcus aureus
T7SSb, which forms a pre-secretion complex with its cognate immunity protein, EsaG, and chaperone EsaE. Encoded upstream of EsaD are three small secreted proteins of unknown function: EsxB, EsxC, and EsxD. Here, we show that these three proteins bind to EsaD and function as EsaD export factors and we report preliminary structural information for a complete T7SSb substrate pre-secretion complex. Cryo-electron microscopy of the EsaDEG trimer and the EsaDEG-EsxBCD hexamer shows that incorporation of EsxBCD confers an elongated conformation comprising a flexible globular cargo domain attached to a long narrow shaft that is likely to be crucial for efficient toxin export.

IMPORTANCE

Staphylococcus aureus
is an opportunistic human pathogen associated with severe infections and antimicrobial resistance.
S. aureus
strains utilize a type VII secretion system to secrete toxins targeting competitor bacteria, likely facilitating colonization. EsaD is a nuclease toxin secreted by the type VII secretion system in many strains of
S. aureus
as well as other related bacterial species. Here, we identify three small proteins of previously unknown function as export factors, required for efficient secretion of EsaD. We show that these proteins bind to the transport domain of EsaD, forming a complex with a striking cane-like conformation.