bluuebunny/crossref_metadata_2025 huggingface dataset:
Mitochondrial network reorganization and transient expansion during oligodendrocyte generation
Authors: Bame Xhoela , Hill Robert A.
Published: December 2023

Oligodendrocyte precursor cells (OPCs) give rise to myelinating oligodendrocytes of the central nervous system. This process persists throughout life and is essential for recovery from neurodegeneration. To better understand the cellular checkpoints that occur during oligodendrogenesis, we determined the mitochondrial distribution and morphometrics across the oligodendrocyte lineage in mouse and human cerebral cortex. During oligodendrocyte generation, mitochondrial content expanded concurrently with a change in subcellular partitioning towards the distal processes. These changes were followed by an abrupt loss of mitochondria in the oligodendrocyte processes and myelin, coinciding with sheath compaction. This reorganization and extensive expansion and depletion took 3 days. Oligodendrocyte mitochondria were stationary over days while OPC mitochondrial motility was modulated by animal arousal state within minutes. Aged OPCs also displayed decreased mitochondrial size, content, and motility. Thus, mitochondrial dynamics are linked to oligodendrocyte generation, dynamically modified by their local microenvironment, and altered in the aging brain.
Population suppression with dominant female-lethal alleles is boosted by homing gene drive
Authors: Zhu Jinyu , Chen Jingheng , Liu Yiran , Xu Xuejiao , Champer Jackson
Published: December 2023

Methods to suppress pest insect populations using genetic constructs and repeated releases of male homozygotes have recently been shown to be an attractive alternative to older sterile insect technique based on radiation. Female-specific lethal alleles have substantially increased power, but still require large, sustained transgenic insect releases. Gene drive alleles bias their own inheritance to spread throughout populations, potentially allowing population suppression with a single, small-size release. However, suppression drives often suffer from efficiency issues, and the most well-studied type, homing drives, tend to spread without limit. In this study, we show that coupling female-specific lethal alleles with homing gene drive allowed substantial improvement in efficiency while still retaining the self-limiting nature (and thus confinement) of a lethal allele strategy. Using a mosquito model, we show the required releases sizes for population elimination in a variety of scenarios, including different density growth curves, with comparisons to other systems. Resistance alleles reduced the power of this method, but these could be overcome by targeting an essential gene with the drive while also providing rescue. A proof-of-principle demonstration of this system inDrosophila melanogasterwas effective in both basing its inheritance and achieving high lethality among females that inherit the construct in the absence of antibiotic. Overall, our study shows that substantial improvements can be achieved in female-specific lethal systems for population suppression by combining them with a gene drive.
A non-conducting role of the Cav1.4 Ca2+channel drives homeostatic plasticity at the cone photoreceptor synapse
Authors: Maddox Wesley , Ordemann Gregory J. , de la Rosa Vázquez Juan , Huang Angie , Gault Christof , Wisner Serena R. , Randall Kate , Futagi Daiki , Salem Nihal A , Mayfield R. Dayne , Zemelman Boris V. , DeVries Steven , Hoon Mrinalini , Lee Amy
Published: December 2023

In congenital stationary night blindness type 2 (CSNB2), a disorder involving the Cav1.4 (L-type) Ca2+ channel, visual impairment is mild considering that Cav1.4 mediates synaptic release from rod and cone photoreceptors. Here, we addressed this conundrum using a Cav1.4 knockout (KO) mouse and a knock-in (G369i KI) mouse expressing a non-conducting Cav1.4. Surprisingly, Cav3 (T-type) Ca2+ currents were detected in cones of G369i KI mice and Cav1.4 KO mice but not in cones of wild-type mouse, ground squirrel, and macaque retina. Whereas Cav1.4 KO mice are blind, G369i KI mice exhibit normal photopic (i.e., cone-mediated) visual behavior. Cone synapses, which fail to form in Cav1.4 KO mice, are present, albeit enlarged, and with some errors in postsynaptic wiring in G369i KI mice. While Cav1.4 KO mice lack evidence of cone synaptic responses, electrophysiological recordings in G369i KI mice revealed nominal transmission from cones to horizontal cells and bipolar cells. In CSNB2, we propose that Cav3 channels maintain cone synaptic output provided that the nonconducting role of Cav1.4 in cone synaptogenesis remains intact. Our findings reveal an unexpected form of homeostatic plasticity that relies on a non-canonical role of an ion channel.
Integrative omics analysis reveals gene regulatory mechanisms distinguishing organoid-derived hepatocytes from primary human hepatocytes
Authors: Wu Haoyu , Yang Annie S. P. , Stelloo Suzan , Roos Floris J. M. , te Morsche René H. M. , Verkerk Anne H. , Luna-Velez Maria V. , Wingens Laura , de Wilt Johannes H. W. , Sauerwein Robert W. , Mulder Klaas W. , van Heeringen Simon J. , Verstegen Monique M. A. , van der Laan Luc J. W. , Marks Hendrik , Bártfai Richárd
Published: December 2023

Background and Aims

Hepatic organoid cultures are considered a powerful model system to study liver development and diseasesin vitro. However, hepatocyte-like cells differentiated from such organoids remain immature compared to primary human hepatocytes. Therefore, a comprehensive understanding of differences in gene regulatory mechanisms between primary human hepatocytes and hepatic organoids is essential to obtain functional hepatocyte-like cellsin vitrofor fundamental and therapeutic applications.

Methods

We obtained primary human hepatocytes at high purity from all zones of the liver lobule using an optimized two-step perfusion protocol. We captured the single-cell transcriptome and chromatin accessibility landscape using scRNA-seq and ATAC-seq, respectively. We identified key transcription factors and compared the gene regulatory mechanisms in primary human hepatocytes and (un)differentiated intrahepatic cholangiocyte organoids. Using siRNA-mediated perturbations, we showed the functional relevance of an organoid-enriched transcription factor duringin vitrodifferentiation of hepatocyte-like cells.

Results

Our integrative omics analysis revealed that Activator Protein 1 (AP-1) family members cooperate with hepatocyte-specific transcription factors, including HNF4A, in maintaining cellular functionality of mature human hepatocytes. Comparative analysis identified distinct transcription factor sets specifically active in human hepatocytes and organoids. Amongst these ELF3 is unique to intrahepatic cholangiocyte organoids and its expression level negatively correlate with expression of hepatic marker genes. Functional analysis of ELF3 furthermore revealed thatELF3depletion optimizes the formation of hepatocyte-like cells from intrahepatic cholangiocyte organoids.

Conclusions

Collectively, our integrative analysis provides insights into the transcriptional regulatory networks of human hepatocytes and hepatic organoids, thereby informing future strategies for better establishment of urgently-needed hepatic model systemsin vitro.
Active Sampling in Primate Vocal Interactions
Authors: Varella Thiago T. , Takahashi Daniel Y. , Ghazanfar Asif A.
Published: December 2023

Active sensing is a behavioral strategy for exploring the environment. In this study, we show that contact vocal behaviors can be an active sensing mechanism that uses sampling to gain information about the social environment, in particular, the vocal behavior of others. With a focus on the real-time vocal interactions of marmoset monkeys, we contrast active sampling to a vocal accommodation framework in which vocalizations are adjusted simply to maximize responses. We conducted simulations of a vocal accommodation and an active sampling policy and compared them with real vocal exchange data. Our findings support active sampling as the best model for marmoset monkey vocal exchanges. In some cases, the active sampling model was even able to predict the distribution of vocal durations for individuals. These results suggest a new function for primate vocal interactions in which they are used by animals to seek information from social environments.

Significance

We found that marmoset monkeys use vocal exchanges with conspecifics in the same way that bats and electric fish use their self-generated signals: to sample the information space. The difference is that, while bats, electric fish and other echolocating animals emit signals and then interpret that signal’s reflection, for vocalizing marmoset monkeys the “reflection” is the vocal response from conspecifics. We show that marmosets produce variable vocalizations as a means to sample the acoustic space in which they can elicit a conspecific response. They are actively sampling--learning about their dyadic partner like a bat learns about its prey.
«Control of the phage defense mechanism by Quorum Sensing (QS) in clinical isolates ofKlebsiella pneumoniae»
Authors: Barrio-Pujante Antonio , Bleriot Inés , Blasco Lucía , Fernández-Garcia Laura , Pacios Olga , Ortiz-Cartagena Concha , López María , Fernández Cuenca Felipe , Oteo-Iglesias Jesús , Tomás María
Published: December 2023

Multidrug resistant (MDR) bacteria and the shortage of new antibiotics are a serious health problem and have increased the interest in bacteriophages, with great potential as antimicrobial agents but they can induce resistance. The objective of the present study was to reduce the development of phage resistance inK. pneumoniaestrains by inhibiting the Quorum Sensing (QS). The QS inhibition by cinnamaldehyde (CAD) was confirmed indirectly by the reduction of biofilm production and directly by a proteomic analysis. Also, the infection assays showed that the phage resistance mechanisms of the bacteria were inhibited when phage-resistantK. pneumoniaestrains were treated with a combination of phages with CAD. Finally, these results were confirmed by proteomic analysis as proteins related to the phage defence such as CBASS (bacterial cyclic oligonucleotide-based anti-phage signalling) and R-M systems as well as tail fiber proteins were present under phage treatment but not with the combination.

GRAPHICAL ABSTRACT
Fertility decline inAedesmosquitoes is associated with reduced maternal transcript deposition and does not depend on female age
Authors: David Olayinka G. , Arce Andrea V. , Costa-da-Silva Andre Luis , Bellantuono Anthony J. , DeGennaro Matthew
Published: December 2023

Female mosquitoes undergo multiple rounds of reproduction known as gonotrophic cycles. A gonotrophic cycle spans the period from bloodmeal intake to egg laying. Nutrients from vertebrate host blood are necessary for completing egg development. During oogenesis, a female pre-packages mRNA into her oocytes, and these maternal transcripts drive the first two hours of embryonic development prior to zygotic genome activation. In this study, we profiled transcriptional changes in 1-2 hours oldAedes aegyptiembryos across two gonotrophic cycles. We found that homeotic genes which are regulators of embryogenesis are downregulated in embryos from the second gonotrophic cycle. Interestingly, embryos produced byAe. aegyptifemales progressively reduced their ability to hatch as the number of gonotrophic cycles increased. We show that this fertility decline is due to increased reproductive output and not the mosquitoes’ age. Moreover, we found a similar decline in fertility and fecundity across three gonotrophic cycles inAe. albopictus. Our results are useful for predicting mosquito population dynamics to inform vector control efforts.
Hybrid Neural Networks of the Olfactory Learning Center in theDrosophilaBrain
Authors: Cheng Li-Shan , Charng Ching-Che , Chen Ruei-Huang , Feng Kuan-Lin , Chiang Ann-Shyn , Lo Chung-Chuan , Lee Ting-Kuo
Published: December 2023

Biological signal encoding is shaped by the underlying neural circuitry. InDrosophila melanogaster, the mushroom body (MB) houses thousands of Kenyon cells (KCs) that process olfactory signals from hundreds of projection neurons (PNs). Previous studies debated the connectivity between PNs and KCs (random vs. structured). Our multiscale analysis of electron microscopic data revealed a hybrid network with diverse synaptic connection preferences and input divergence across different KC classes. Using MB connectome data, our simulation model, validated via functional imaging, accurately predicted distinct chemical sensitivities in the major KC classes. The model suggests that the hybrid network excels in detecting food odors while maintaining precise odor discrimination in different KC classes. These findings underscore the computational advantages of this hybrid network.
Effect of agriculture–tourism integration on in situ urbanization of rural residents: evidence from 1868 counties in China
Authors: Lu Juan , Li He
Published: December 2023

Purpose

This study aims to clarify the impact of agriculture–tourism integration (ATI) on in situ urbanization (ISURB) of rural residents, to highlight the role of industrial integration in the process of China's ISURB and to provide industrial integration suggestions for promoting urbanization quality in Chinese counties.

Design/methodology/approach

By sorting out the panel data of China's 1868 counties, the evaluation index system of ISURB was constructed. Difference in difference (DID) and spatial Durbin-difference in difference (SDM-DID) model is used for estimate the relationship between ATI and ISURB.

Findings

First, ATI can improve ISURB by 11.4% higher than other regions. Second, theoretical analysis model of ATI on ISURB is constructed from four aspects of “drive–push–pull–block.” The results show that ATI can promote ISURB by increasing upgrading of rural industries, rural employment demand and income capacity, whereas ATI may inhibit ISURB by reducing farmland. Third, considering changes in institutional, hard and soft factors, rural collective economy, information infrastructure and digital finance all promote positive impact of ATI on ISURB. Fourth, ATI will produce spillover effects on ISURB in neighboring regions, which is more pronounced in the central and western regions.

Research limitations/implications

This study lacks quantification of ATI, so future studies are encouraged to further quantify ATI at the county level.

Practical implications

This study has policy significance for constructing ATI demonstration counties and promoting ISURB in China's counties.

Social implications

It is of great practical value to promote China's ISURB. By stimulating ATI, it can improve income and employment capacity of rural residents and stimulate ISURB of China.

Originality/value

This study enriches the theoretical and practical research on industrial integration behaviors during the process of ISURB.

Highlights

Use county data to measure in situ urbanization (ISURB)

Agriculture–tourism integration (ATI) can increase ISURB

Constructs a “drive-push-pull-block” model to explain the influence mechanism

Use spatial Durbin-difference in difference (SDM-DID) models

Consider collective economy, rural information infrastructure and digital finance

Graphical abstract
Coincidental brand origins influence persuasion based on need for cognition
Authors: Cheng Yimin , Orazi Davide Christian
Published: December 2023

Purpose

Many brands claim they were born by coincidence, yet the effects and contingencies of this communication strategy are little understood by extant marketing research on unexpected events. This study aims to investigate how consumers react to brand communications portraying a coincidental vs planned origin.

Design/methodology/approach

This research presents five experimental studies embedding coincidental brand origins into different types of marketing communications (i.e. crowdfunding campaigns, visual ads and brand biographies).

Findings

This research finds that coincidental brand origins increase persuasion (measured as money pledged to a crowdfunding campaign, overall brand equity and purchase intention) but only for consumers high in need for cognition (NFC). This effect is mediated by processing enjoyment, as the intrinsic need for thinking that characterizes high NFC consumers is satisfied by the opportunity to process the coincidence. Further to process, the authors show that explicitly providing an explanation for the coincidence makes the effect disappear, as this deprives high-NFC consumers of the opportunity to autonomously engage in and enjoy the cognitive process.

Practical implications

Brand managers able to leverage coincidences in their storytelling efforts should target high-NFC consumers and should not provide an explanation for the coincidences.

Originality/value

This research advances the limited literature on how consumers react to coincidences in a marketing context, the understanding of how brand communication strategies persuade consumers through information processing and the NFC literature.
Do advisory directors increase discretionary accruals?
Authors: Salma Ummya , Bhuiyan Md. Borhan Uddin
Published: December 2023

Purpose

This study aims to examine whether the presence of advisory directors affects firm discretionary accruals (DACC), a widely used proxy for financial reporting quality. The authors argue that the advisory director weakens the board monitoring role and impairs the firm financial reporting quality by increasing DACC.

Design/methodology/approach

The sample consists of listed firms on the Australian Stock Exchange from 2001 to 2015 using 7,649 firm-year observations. The authors perform descriptive statistics, regression and propensity score matching analyses to examine the research hypothesis.

Findings

The research evidence that firms with a higher presence of advisory directors have more DACC, indicating poor financial reporting quality. Furthermore, the authors categorize the DACC and find that the firm has higher income-increasing DACC in the presence of higher advisory directors. The findings are robust concerning endogeneity issues.

Research limitations/implications

The research evidence that firms with a higher presence of advisory directors have more DACC, indicating poor financial reporting quality. Furthermore, the authors categorize the DACC and find that the firm has higher income-increasing DACC in the presence of higher advisory directors. The findings are robust concerning endogeneity issues.

Practical implications

The research contributes valuable insights for regulators and policymakers seeking to comprehend the implications of firms using more advisory directors. Additionally, the authors recognize the potential significance of the findings for the institution of directors, as they can provide a nuanced understanding of the specific roles played by advisory directors in organizational dynamics.

Originality/value

While the extensive body of literature on corporate governance and financial reporting quality has been well-established, a noticeable void exists in academic research delving into the relationship between advisory directors and DACC management. This study seeks to fill this gap, making a distinctive and original contribution to the existing literature on corporate governance.
Assessing the efficacy of a German‐inspired intervention on occupational contact dermatitis in Denmark: A randomised controlled trial with 3‐month follow‐up
Authors: Dietz Jojo Biel‐Nielsen , Simonsen Anne Birgitte N. , Menné Torkil , Ahlstrøm Malin G. , Flyvholm Mari‐Ann , Blomberg Maria H. , Erichsen Christina Y. , Meyer Harald W. , Viskum Sven , Ahrensbøll‐Friis Ulrik , John Swen M. , Johansen Jeanne D.
Published: December 2023

Background

Occupational contact dermatitis (OCD) is a prevalent, often chronic disease that poses a risk for job loss and decreased quality of life. In Germany, a multi‐step prevention programme emphasising early detection and highly specialised multidisciplinary treatment has been implemented with great success.

Objectives

To examine the effectiveness of a Danish‐adapted version of the German prevention effort on OCD severity, quality of life and occupational consequences at 3‐month follow‐up.

Methods

Randomised, controlled trial. Participants were recruited after the first referral from General Practitioner to Dermatologist with suspected OCD. The intervention group (IG) received a Danish‐adapted, multidisciplinary intervention, while the control group (CG) navigated the Danish healthcare system without interference from the study. OCD severity, occupational consequences and quality of life were assessed at 3‐month follow‐up using self‐reported questionnaires.

Results

A statistically significant decrease in the severity of eczema was found at 3‐month follow‐up in the IG compared to the CG. The IG were statistically significantly more likely to have seen a dermatologist at 3‐month follow‐up. Higher treatment level in the IG was indicated by the results but was not statistically significant. No significant difference was found in quality of life or occupational consequences.

Conclusions

These initial findings suggest that early and specialised treatment of OCD improves OCD prognosis.
Quality of evidence supporting the role of hyperbaric oxygen therapy for diabetic foot ulcers
Authors: Jiang Fuxin , Zhang Yalan , Cheng Shijin , Yang Xiaohui , Bai Min , Zhang Ming
Published: December 2023

The goal of this overview of systematic reviews (SRs) and meta‐analyses (MAs) was to methodically gather, evaluate and summarize the data supporting the use of hyperbaric oxygen therapy (HBOT) to treat diabetic foot ulcers (DFUs). The Cochrane Library, Embase, PubMed, Web of Science and Embase were all searched thoroughly to identify SRs/MAs that qualified. AMSTAR‐2 tool, PRISMA checklists and GRADE system were applied by two reviewers independently to assess the methodological quality, reporting and evidence quality of the included SRs/MAs, respectively. Eleven SRs/MAs were enrolled in this overview. According to AMSTAR‐2, a very low methodological quality assessment was given to the included SRs/MAs due to the limitations of items 2, 4 and 7. For the PRISMA, the overall quality of reporting is not satisfactory due to missing reporting on protocol, search, as well as additional analysis. The majority of outcomes had low‐ to moderate‐quality evidence, and no high‐quality evidence was found to support the role of HBOT for DFUs, according to GRADE. To conclude, the potential of HBOT in treating DFUs is supported by evidence of low to moderate quality. More rigorously designed, high‐level studies are needed in the future to determine the evidence for HBOT for DFU, including the timing, frequency and duration of HBOT interventions.
Novel approach for manufacture of single‐grain EuBCO/Ag bulk superconductors via modified single‐direction melt growth
Authors: Antončík Filip , Lojka Michal , Hlásek Tomáš , Sedmidubský David , Baumann Josef , Durrell John H. , Cardwell David A. , Jankovský Ondřej
Published: December 2023

Despite the success of top‐seeded melt growth (TSMG) and TSIG, some key aspects of their manufacture need to be addressed including the presence of microstructural defects, inhomogeneities in trapped field and the difficulty of growing large‐diameter bulk monoliths. Recently, a promising new method single‐direction melt growth (SDMG) appears to address the majority of the shortcomings of TSMG and TSIG. Single‐grain EuBCO/Ag bulk with the highest peritectic temperature to date was grown by modified SDMG. This remarkable achievement was made possible by lowering the peritectic temperature of the precursor composition by the addition of silver and by using single‐grain EuBCO fabricated by TSMG as a seed. The EuBCO/Ag bulk grown by SDMG has demonstrated significant improvements in comparison to a reference TSMG sample. A reduction of approximately 30% in defect area (associated primarily with porosity), as well as a significantly enhanced homogeneity of trapped field and critical temperature, was observed. Furthermore, the critical current density curves exhibit a considerable improvement, particularly in the 2–5 T field range. The SDMG technique has considerable potential for scale‐up for the fabrication of large‐diameter bulk single grains, with only growth along the c‐axis involved during the thermal process.
Association between SPRY1 and TET3 in skin photoaging and natural aging mechanisms
Authors: Qiu Bo , Yang E. , Zheng Yulian , Zhang Hengshu
Published: December 2023

Background

SPRY1 is associated with the invasiveness and prognosis of various tumors, and TET3 affects aging by regulating gene expression.

Aims

We investigated the roles of SPRY1 and TET3 in natural skin aging, replicative aging, and photoaging, along with the effect of UVA on genome‐wide DNA methylation in HaCaT cells.

Methods

TET3 and SPRY1 expression were measured in the skin of patients of different age groups, as well as in vitro human skin, HaCaT cell replicative senescence, and HaCaT and HaCaT‐siTET3 cell photoaging models. Senescence was verified using β‐galactosidase staining, and DNA damage was detected using immunofluorescence staining for γ‐H2A.X. 5‐Methyl cytosine (5‐mC) content in the genome was determined using ELISA.

Results

SPRY1 expression increased with age, whereas TET3 expression decreased. Similarly, SPRY1 was upregulated and TET3 was downregulated with increasing cell passages. TET3‐siRNA upregulated SPRY1 expression in HaCaT cells. UVA irradiation promoted HaCaT cell senescence and induced cellular DNA damage. SPRY1 was upregulated and TET3 was downregulated upon UVA irradiation. Genome‐wide 5‐mC content increased upon TET3 silencing and UVA irradiation, indicating a surge in overall methylation.

Conclusions

SPRY1 and TET3 are natural skin aging‐related genes that counteract to regulate replicative aging and UVA‐induced photoaging in HaCaT cells. The cell photoaging model may limit experimental bias caused by different exposure times of skin model samples.
A review on ESG investing: Investors’ expectations, beliefs and perceptions
Authors: Kräussl Roman , Oladiran Tobi , Stefanova Denitsa
Published: December 2023

This study examines the recent literature on the expectations, beliefs and perceptions of investors who incorporate Environmental, Social, Governance (ESG) considerations in investment decisions with the aim to generate superior performance or make a societal impact. Through the lens of equilibrium models of agents with heterogeneous tastes for ESG investments, green assets are expected to generate lower returns in the long run compared to their non‐ESG counterparts. However, in the short run, ESG investments can outperform non‐ESG investments through various channels. Empirically, results for the relative performance to ESG investment are mixed. We find strong empirical evidence in the literature that investors have a preference for ESG and that their actions can generate positive social impact through engagement. The shift towards more sustainable policies in firms is motivated by the increased market values and the lower cost of capital of green firms driven by investors’ choices.
Printed abutment model to limit residual cement: A dental technique
Authors: Ryser Andrew S. , Sabol Jennifer V. , Handel Steven
Published: December 2023

Preventing retained cement around implant‐retained crowns is crucial for the long‐term health and success of the implant. Residual subgingival cement is strongly associated with peri‐mucositis and can lead to peri‐implantitis. This clinical technique utilizes a 3D printed model of a custom abutment to seat the implant crown on before cementing intra‐orally to extrude excess cement. The technique aims to limit the amount of retained cement at the crown‐abutment margin and also takes into consideration the cement space already designed into the crown‐abutment complex.
Partial Identification of Marginal Treatment Effects with Discrete Instruments and Misreported Treatment*
Authors: Acerenza Santiago
Published: December 2023

This paper provides partial identification results for the marginal treatment effect (MTE) when the binary treatment variable is potentially misreported and the instrumental variable is discrete. Identification results are derived under smoothness assumptions. Bounds for both the case of misreported treatment and the case of no misreported treatment are derived. The identification results are illustrated by identifying the marginal treatment effects of food stamps on health.
Spatial and temporal distribution of hydrocarbon production on the UK continental shelf
Authors: Osah Ukari , Howell John
Published: December 2023

Hydrocarbon production from oil and gas fields is controlled by a variety of interconnected factors with a hierarchy of significance that is, for the most part, difficult to untangle. This article documents and investigates the spatial and temporal distribution of key hydrocarbon field parameters on the UK Continental Shelf. Data have been compiled from publicly available sources for 424 fields. Variables are considered as “descriptive parameters,” “control parameters” and “outcomes”. Descriptive parameters are metadata such as field name, location, etc. Control Parameters include depositional environment, present depth of burial, porosity, permeability, reservoir formation pressure, reservoir temperature, average net‐to‐gross, number of fault populations, hydrocarbon API, field area, bulk rock volume, well density, number of wells (production and injection), well spacing, gas oil ratio, reservoir thickness, fluid saturation, compartmentalization (quantitated by number of observable non‐communicating fault compartments), structural complexity (scaled from 0 to 5), field production strategy, trap type and stratigraphic heterogeneity. Outcomes are used to assess field performance and include final recovery factor (estimated), maximum production rate, and cumulative monthly production. Analysis of the database illustrates a number of empirical observations regarding hydrocarbon production on the UKCS. The Jurassic plays have been the most successful in the region in terms of total volumes produced while the Permian reservoirs of the SNS account for the majority of the gas. Most of the UKCS reservoirs record top depths between 2000 and 4500 m with good reservoir quality. The best reservoir quality is observed in reservoirs that were deposited within deep marine systems. The largest hydrocarbon reserves are found in the Northern North Sea basin in these deep marine (as well as paralic and shallow marine) reservoirs. Using the data from this article and affiliated data, potential exists for extracting insight beyond spatio‐temporal distributions.
São Paulo's Crackland as Urban Impasse: An Ethnographic Account of Mobility, Territory and Viracao as Form of Nomadism
Authors: Fromm Deborah , Blokland Talja
Published: December 2023

Drugs feature in the geography of crime as an economy and as a threat to social order and public health. Spatial and social strategies of crime reduction ascribe agency to the state and to regulated residents of marginalised urban areas. Geographers also discussed anti‐drug policy have a revanchist neoliberal governance. Through the lens of urban territory and urban nomads in the crack‐cocaine‐dominated area Crackland in the centre of São Paulo, we argue that instead of a fixity of homelessness, drug markets and drug users in the geography of crime, one could pay more attention to nomadism, which can be found ethnographically in the journeys of three agents which we discuss. For over 20 years, city authorities have tried to ‘end’ Crackland with social programmes and police actions, or codifying attempts of territorialisation. An urban impasse emerged as these programmes failed to recognise Crackland as mobile territory of viracao. Crackland remains a zone reserved for the city's ‘human waste’ while perfectly integrated in the urban fabric.
Clarifying contemporary conceptualizations of allyship with LGBTQ2S+ groups in the context of health care or health settings: a scoping review protocol
Authors: Handlovsky Ingrid , Marcellus Lenora , Newton Lorelei , Zakher Bernadette , Mussell Jessica
Published: December 2023

Objective:

The objective of this review is to better understand how allyship is defined in the literature from 1970 to the present with regard to lesbian, gay, bisexual, transgender, queer, two-spirit, and other (LGBTQ2S+) groups within health settings where English is the primary spoken language.

Introduction:

LGBTQ2S+ individuals experience health inequities rooted in discrimination. Activism to redress this discrimination in health settings is frequently termed allyship. Definitions of allyship, however, remain ambiguous. A clearer understanding of how allyship is defined and operationalized within health settings is integral to supporting the health of LGBTQ2S+ groups.

Inclusion criteria:

Literature in English from 1970 to the present that utilizes the concept of allyship within health care and/or health settings in relation to LGBTQ2S+ groups in Canada and the United States, Australia, New Zealand, and the United Kingdom will be included.

Methods:

This scoping review will be conducted in accordance with the JBI methodology for scoping reviews. Databases to be searched will include MEDLINE (OVID), CINAHL (EBSCOhost), APA PsycINFO (EBSCOhost), LGBTQ+ Source (EBSCOhost), Scopus, and Web of Science, along with ProQuest Dissertations and Theses for gray literature. Two independent reviewers will screen titles, abstracts, and full-text articles; discrepancies will be resolved by consensus or with a third reviewer. Data will be extracted using an extraction tool developed by the research team. Findings will be presented in tabular/diagram format along with a narrative summary to highlight key themes that relate to contemporary conceptualizations of allyship with LGBTQ2S+ individuals/groups within health care settings and the implications for health professional practice and health outcomes.

Review registration:

Open Science Framework osf.io/2rek9
Chalcogen isotopes reveal limited volatile contribution from late veneer to Earth
Authors: Wang Wenzhong , Walter Michael J. , Brodholt John P. , Huang Shichun , Petaev Michail I.
Published: December 2023

The origin of Earth’s volatile elements is highly debated. Comparing the chalcogen isotope ratios in the bulk silicate Earth (BSE) to those of its possible building blocks, chondritic meteorites, allows constraints on the origin of Earth’s volatiles; however, these comparisons are complicated by potential isotopic fractionation during protoplanetary differentiation, which largely remains poorly understood. Using first-principles calculations, we find that core-mantle differentiation does not notably fractionate selenium and tellurium isotopes, while equilibrium evaporation from early planetesimals would enrich selenium and tellurium in heavy isotopes in the BSE. The sulfur, selenium, and tellurium isotopic signatures of the BSE reveal that protoplanetary differentiation plays a key role in establishing most of Earth’s volatile elements, and a late veneer does not substantially contribute to the BSE’s volatile inventory.
A mechanochemical model recapitulates distinct vertebrate gastrulation modes
Authors: Serra Mattia , Serrano Nájera Guillermo , Chuai Manli , Plum Alex M. , Santhosh Sreejith , Spandan Vamsi , Weijer Cornelis J. , Mahadevan L.
Published: December 2023

During vertebrate gastrulation, an embryo transforms from a layer of epithelial cells into a multilayered gastrula. This process requires the coordinated movements of hundreds to tens of thousands of cells, depending on the organism. In the chick embryo, patterns of actomyosin cables spanning several cells drive coordinated tissue flows. Here, we derive a minimal theoretical framework that couples actomyosin activity to global tissue flows. Our model predicts the onset and development of gastrulation flows in normal and experimentally perturbed chick embryos, mimicking different gastrulation modes as an active stress instability. Varying initial conditions and a parameter associated with active cell ingression, our model recapitulates distinct vertebrate gastrulation morphologies, consistent with recently published experiments in the chick embryo. Altogether, our results show how changes in the patterning of critical cell behaviors associated with different force-generating mechanisms contribute to distinct vertebrate gastrulation modes via a self-organizing mechanochemical process.
Inhibition of ACLY overcomes cancer immunotherapy resistance via polyunsaturated fatty acids peroxidation and cGAS-STING activation
Authors: Xiang Wei , Lv Hongwei , Xing Fuxue , Sun Xiaoyan , Ma Yue , Wu Lu , Lv Guishuai , Zong Qianni , Wang Liang , Wu Zixin , Feng Qiyu , Yang Wen , Wang Hongyang
Published: December 2023

Adenosine 5′-triphosphate citrate lyase (ACLY) is a cytosolic enzyme that converts citrate into acetyl–coenzyme A for fatty acid and cholesterol biosynthesis. ACLY is up-regulated or activated in many cancers, and targeting ACLY by inhibitors holds promise as potential cancer therapy. However, the role of ACLY in cancer immunity regulation remains poorly understood. Here, we show that ACLY inhibition up-regulates PD-L1 immune checkpoint expression in cancer cells and induces T cell dysfunction to drive immunosuppression and compromise its antitumor effect in immunocompetent mice. Mechanistically, ACLY inhibition causes polyunsaturated fatty acid (PUFA) peroxidation and mitochondrial damage, which triggers mitochondrial DNA leakage to activate the cGAS-STING innate immune pathway. Pharmacological and genetic inhibition of ACLY overcomes cancer resistance to anti–PD-L1 therapy in a cGAS-dependent manner. Furthermore, dietary PUFA supplementation mirrors the enhanced efficacy of PD-L1 blockade by ACLY inhibition. These findings reveal an immunomodulatory role of ACLY and provide combinatorial strategies to overcome immunotherapy resistance in tumors.
Tobacco smoke exposure recruits inflammatory airspace monocytes that establish permissive lung niches for
Mycobacterium tuberculosis
Authors: Corleis Björn , Tzouanas Constantine N. , Wadsworth Marc H. , Cho Josalyn L. , Linder Alice H. , Schiff Abigail E. , Zessin Björn , Stei Fabian , Dorhoi Anca , Dickey Amy K. , Medoff Benjamin D. , Shalek Alex K. , Kwon Douglas S.
Published: December 2023

Tobacco smoking doubles the risk of active tuberculosis (TB) and accounts for up to 20% of all active TB cases globally. How smoking promotes lung microenvironments permissive to
Mycobacterium tuberculosis
(
Mtb
) growth remains incompletely understood. We investigated primary bronchoalveolar lavage cells from current and never smokers by performing single-cell RNA sequencing (scRNA-seq), flow cytometry, and functional assays. We observed the enrichment of immature inflammatory monocytes in the lungs of smokers compared with nonsmokers. These monocytes exhibited phenotypes consistent with recent recruitment from blood, ongoing differentiation, increased activation, and states similar to those with chronic obstructive pulmonary disease. Using integrative scRNA-seq and flow cytometry, we identified CD93 as a marker for a subset of these newly recruited smoking-associated lung monocytes and further provided evidence that the recruitment of monocytes into the lung was mediated by CCR2-binding chemokines, including CCL11. We also show that these cells exhibit elevated inflammatory responses upon exposure to
Mtb
and accelerated intracellular growth of
Mtb
compared with mature macrophages. This elevated
Mtb
growth could be inhibited by anti-inflammatory small molecules, providing a connection between smoking-induced pro-inflammatory states and permissiveness to
Mtb
growth. Our findings suggest a model in which smoking leads to the recruitment of immature inflammatory monocytes from the periphery to the lung, which results in the accumulation of these
Mtb
-permissive cells in the airway. This work defines how smoking may lead to increased susceptibility to
Mtb
and identifies host-directed therapies to reduce the burden of TB among those who smoke.
Complete genome sequence of
Methanothermobacter
sp. DP, a hydrogenotrophic and thermophilic methanogen
Authors: Prabhaharan Darsha , Nair Pranav Sasidharan , Park Hyojung , Choi Okkyoung , Sang Byoung-In
Published: December 2023

Here, we report the complete genome sequence of the thermophilic hydrogenotrophic methanogen
Methanothermobacter
sp. DP isolated in South Korea from an anaerobic digester fed with cigarette waste. The genome consists of 1,693,285 bp, with 1,772 protein-coding genes and a GC content of 48.8%.
Host DNA depletion methods and genome-centric metagenomics of bovine hindmilk microbiome
Authors: Duarte Vinícius da Silva , Porcellato Davide
Published: December 2023

Bovine mastitis is a multi-etiological and complex disease, resulting in serious economic consequences for dairy farmers and industry. In recent years, the microbiological evaluation of raw milk has been investigated in-depth using next-generation sequencing approaches such as metataxonomic analysis. Despite this, host DNA is a major concern in the shotgun metagenomic sequencing of microbial communities in milk samples, and it represents a big challenge. In this study, we aimed to evaluate different methods for host DNA depletion and/or microbial DNA enrichment and assess the use of PCR-based whole genome amplification in milk samples with high somatic cell count (SCC) by using short- and long-read sequencing technologies. Our results evidenced that DNA extraction performed differently in terms of host DNA removal, impacting metagenome composition and functional profiles.. Moreover, the ratio of SCC/bacteria ultimately impacts microbial DNA yield, and samples with low SCC (SCC below 100,000 cells/mL) are the most problematic. When milk samples with high SCC (SCC above 200,000 cells/mL) underwent multiple-displacement amplification (MDA), we successfully recovered high-quality metagenome-assembled genomes (MAGs), and long-read sequencing was feasible even for samples with low DNA concentration. By associating MDA and short‐read sequencing, we recovered two times more MAGs than in untreated samples, and an ongoing co‐infection not reported by traditional methods was detected for mastitis pathogen. Overall, this new approach will improve the detection of mastitis-associated microorganisms and make it possible to examine host-microbiome interactions in bovine mastitis.

IMPORTANCE

Next-generation sequencing technologies have been widely used to gain new insights into the diversity of the microbial community of milk samples and dairy products for different purposes such as microbial safety, profiling of starter cultures, and host-microbiome interactions. Milk is a complex food matrix, and additionally, the presence of host nucleic acid sequences is considered a contaminant in untargeted high-throughput sequencing studies. Therefore, genomic‐centric metagenomic studies of milk samples focusing on the health‐disease status in dairy cattle are still scarce, which makes it difficult to evaluate the microbial ecophysiology of bovine hindmilk. This study provides an alternative method for genome-centric metagenome studies applied to hindmilk samples with high somatic cell content, which is indispensable to examining host-microbiome interactions in bovine mastitis.
Construction of an arrayed CRISPRi library as a resource for essential gene function studies in
Streptococcus mutans
Authors: St. Pierre Jackson , Roberts Justin , Alam Mohammad A. , Shields Robert C.
Published: December 2023

Arrayed mutant libraries are important resources that have advanced our understanding of bacterial genetics. Until recently, essential genes which are necessary for bacterial survival, and constitute ~10% of bacterial genes, were not included in arrayed library resources. However, recent advances in clustered regularly interspaced short palindromic repeats interference (CRISPRi) have made it possible to study essential genes with increasing throughput. Here, we constructed an arrayed CRISPRi library in the dental caries pathogen
Streptococcus mutans
, known as SNAP (

S

treptococcus muta
n
s

a
rrayed CRIS
P
Ri). In this library, each strain contains a short guide RNA which selectively targets a single essential gene, and this is controlled through xylose induction. In total, the library can selectively repress >250 essential and growth-supporting genes. Initial characterization showed that SNAP strains grow as expected, and initial proof-of-concept experiments displayed the utility of the library. We anticipate that this library will be of benefit to the research community by allowing for high-throughput characterization of
S. mutans
essential genes.

IMPORTANCE

The construction of arrayed mutant libraries has advanced the field of bacterial genetics by allowing researchers to more efficiently study the exact function and importance of encoded genes. In this study, we constructed an arrayed clustered regularly interspaced short palindromic repeats interference (CRISPRi) library, known as

S

treptococcus muta
n
s

a
rrayed CRIS
P
Ri (SNAP), as a resource to study >250 essential and growth-supporting genes in
Streptococcus mutans
. SNAP will be made available to the research community, and we anticipate that its distribution will lead to high-quality, high-throughput, and reproducible studies of essential genes.
A multichromatic colorimetric detection method for
Vibrio parahaemolyticus
based on Fe
3
O
4
-Zn-Mn nanoenzyme and dual substrates
Authors: Qiao Wenteng , Wang Luliang , Yang Kun , Liu Yushen , Liu Quanwen , Yin Feng
Published: December 2023

A successful development of a dual-substrate colorimetric system for rapid and multicolorimetric semi-quantification of
Vibrio parahaemolyticus (V. parahaemolyticus
) has been achieved. The enzymatic activity of Fe
3
O
4
-Zn-MnO
2
-aptamer (Fe
3
O
4
-Zn-Mn-Apt) catalysts can induce the oxidation of 3,3′,5,5′-tetramethylbenzidine (TMB) to form oxidized TMB (TMB
+
with a bluish green color) and ortho-phenylenediamine (OPD) to form oxidized OPD (with yellow color), resulting in a three-color comparison due to the complementary nature of bluish green and yellow. The absorbance value of TMB
+
at 652 nm is used for the determination of
V. parahaemolyticus
. After optimizing the reaction conditions, the developed dual-substrate colorimetric method exhibits high sensitivity for
V. parahaemolyticus
detection (limit of detection of 1.12 cfu mL
−1
) and a linear range of 0–1 × 10
4
cfu mL
−1
(
R
2
= 0.9934). Additionally, as the concentration of
V. parahaemolyticus
increases, the reaction solution changes from bluish green to green and then to yellow, enabling semi-quantitative detection by visual observation with a visual detection limit of 10 cfu mL
−1
. Furthermore, the developed dual-substrate colorimetric method demonstrates excellent selectivity for
V. parahaemolyticus
detection and satisfactory recovery rates when applied to the determination of
V. parahaemolyticus
in food samples.

IMPORTANCE

The Fe
3
O
4
-Zn-Mn nanomimetic enzyme demonstrates significant importance in dual-substrate colorimetric detection for
V. parahaemolyticus
, owing to its enhanced sensitivity, selectivity, and rapid detection capabilities. Additionally, it offers cost-effectiveness, portability, and the potential for multiplex detection. This innovative approach holds promise for improving the monitoring and control of
V. parahaemolyticus
infections, thereby contributing to advancements in public health and food safety.