bluuebunny/crossref_metadata_2025 huggingface dataset:
Ehrlichia
Wnt SLiM ligand mimic deactivates the Hippo pathway to engage the anti-apoptotic Yap-GLUT1-BCL-xL axis
Authors: Byerly Caitlan D. , Patterson LaNisha L. , Pittner Nicholas A. , Solomon Regina N. , Patel Jignesh G. , Rogan Madison R. , McBride Jere W.
Published: August 2023

Ehrlichia chaffeensis
TRP120 effector has evolved short linear motif (SLiM) ligand mimicry to repurpose multiple evolutionarily conserved cellular signaling pathways, including Wnt, Notch, and Hedgehog. In this investigation, we demonstrate that
E. chaffeensis
and recombinant TRP120 deactivate Hippo signaling, resulting in the activation of Hippo transcription coactivator Yes-associated protein (Yap). Moreover, a homologous 6 amino acid (QDVASH) SLiM shared by TRP120 and Wnt3a/5a ligands phenocopied Yap and β-catenin activation induced by
E. chaffeensis,
rTRP120, and Wnt5a. Similar Hippo gene expression profiles were also stimulated by
E. chaffeensis
, rTRP120, SLiM, and Wnt5a. Single siRNA knockdown of Hippo transcription co-activator/factors, Yap, and transcriptional enhanced associate domain (TEAD) significantly decreased
E. chaffeensis
infection. Yap activation was abolished in THP-1 Wnt Frizzled-5 (Fzd5) receptor knockout cells (KO), demonstrating Fzd5 receptor dependence. In addition, the TRP120-Wnt-SLiM antibody blocked Hippo deactivation (Yap activation). Expression of anti-apoptotic Hippo target gene
SLC2A1
(encodes glucose transporter 1; GLUT1) was upregulated by
E. chaffeensis
and corresponded to increased levels of GLUT1. Conversely, siRNA knockdown of
SLC2A1
significantly inhibited infection. Higher GLUT1 levels correlated with increased B cell lymphoma-extra large (BCL-xL) and decreased BCL2-associated X, apoptosis regulator (Bax) levels. Moreover, blocking Yap activation with the inhibitor Verteporfin induced apoptosis that corresponded to significant reductions in GLUT1 and BCL-xL levels and activation of Bax and Caspase-3 and -9. This study identifies a novel shared Wnt/Hippo SLiM ligand mimic and demonstrates that
E. chaffeensis
deactivates the Hippo pathway to engage the anti-apoptotic Yap-GLUT1-BCL-xL axis.
The largest HIV-1-infected T cell clones in children on long-term combination antiretroviral therapy contain solo LTRs
Authors: Botha Johannes C. , Demirov Dimiter , Gordijn Carli , Katusiime Mary Grace , Bale Michael J. , Wu Xiaolin , Wells Daria , Hughes Stephen H. , Cotton Mark F. , Mellors John W. , Kearney Mary F. , van Zyl Gert U.
Published: August 2023

Combination antiretroviral therapy (cART) suppresses viral replication but does not cure HIV infection because a reservoir of infectious (intact) HIV proviruses persists in long-lived CD4+T cells. However, a large majority (>95%) of HIV-infected cells that persist on effective cART carry defective (non-infectious) proviruses. Defective proviruses consisting of only a single LTR (solo long terminal repeat) are commonly found as endogenous retroviruses in many animal species, but the frequency of solo-LTR HIV proviruses has not been well defined. Here we show that, in five pediatric donors whose viremia was suppressed on cART for at least 5 years, the proviruses in the nine largest clones of HIV-infected cells were solo LTRs. The sizes of five of these clones were assayed longitudinally by integration site-specific quantitative PCR. Minor waxing and waning of the clones was observed, suggesting that these clones are generally stable over time. Our findings show that solo LTRs comprise a large fraction of the proviruses in infected cell clones that persist in children on long-term cART.

IMPORTANCE

This work highlights that severely deleted HIV-1 proviruses comprise a significant proportion of the proviral landscape and are often overlooked.
A modular plasmid toolkit applied in marine bacteria reveals functional insights during bacteria-stimulated metamorphosis
Authors: Alker Amanda T. , Farrell Morgan V. , Aspiras Alpher E. , Dunbar Tiffany L. , Fedoriouk Andriy , Jones Jeffrey E. , Mikhail Sama R. , Salcedo Gabriella Y. , Moore Bradley S. , Shikuma Nicholas J.
Published: August 2023

A conspicuous roadblock to studying marine bacteria for fundamental research and biotechnology is a lack of modular synthetic biology tools for their genetic manipulation. Here, we applied, and generated new parts for, a modular plasmid toolkit to study marine bacteria in the context of symbioses and host-microbe interactions. To demonstrate the utility of this plasmid system, we genetically manipulated the marine bacterium
Pseudoalteromonas luteoviolacea
, which stimulates the metamorphosis of the model tubeworm,
Hydroides elegans
. Using these tools, we quantified constitutive and native promoter expression, developed reporter strains that enable the imaging of host-bacteria interactions, and used CRISPR interference (CRISPRi) to knock down a secondary metabolite and a host-associated gene. We demonstrate the broader utility of this modular system for testing the genetic tractability of marine bacteria that are known to be associated with diverse host-microbe symbioses. These efforts resulted in the successful conjugation of 12 marine strains from the Alphaproteobacteria and Gammaproteobacteria classes. Altogether, the present study demonstrates how synthetic biology strategies enable the investigation of marine microbes and marine host-microbe symbioses with potential implications for environmental restoration and biotechnology.

IMPORTANCE

Marine Proteobacteria are attractive targets for genetic engineering due to their ability to produce a diversity of bioactive metabolites and their involvement in host-microbe symbioses. Modular cloning toolkits have become a standard for engineering model microbes, such as
Escherichia coli
, because they enable innumerable mix-and-match DNA assembly and engineering options. However, such modular tools have not yet been applied to most marine bacterial species. In this work, we adapt a modular plasmid toolkit for use in a set of 12 marine bacteria from the Gammaproteobacteria and Alphaproteobacteria classes. We demonstrate the utility of this genetic toolkit by engineering a marine
Pseudoalteromonas
bacterium to study their association with its host animal
Hydroides elegans
. This work provides a proof of concept that modular genetic tools can be applied to diverse marine bacteria to address basic science questions and for biotechnology innovations.
Draft genome of the
Ogataea polymorpha
type strain CBS 4732
Authors: Collins Joseph H. , Young Eric M.
Published: August 2023

The methylotrophic yeast
Ogataea polymorpha
is of significant biotechnological interest, particularly in high-temperature fermentations and for recombinant protein production. Here, we present a high-quality genome assembly for the
O. polymorpha
type strain CBS 4732.
Exceptional age constraint on a fossiliferous sedimentary succession preceding the Cretaceous Thermal Maximum
Authors: Tucker Ryan T. , Crowley James L. , Mohr Michael T. , Renaut Ray K. , Makovicky Peter J. , Zanno Lindsay E.
Published: August 2023

Understanding the effects of climatic upheavals during the Early to Late Cretaceous transition is essential for characterizing the tempo of tectonically driven landscape modification and biological interchange; yet, current chronostratigraphic frameworks are too imprecise, even on regional scales, to address many outstanding questions. This includes the Mussentuchit Member of the uppermost Cedar Mountain Formation, central Utah (southwestern United States), which could provide crucial insights into these impacts within the Western Interior Basin of North America yet remains imprecisely constrained. Here, we present high-precision U-Pb zircon dates from four primary ash beds distributed across ~50 km in central Utah that better constrain the timing of deposition of the Mussentuchit Member and the age of entombed fossils. Ages for ash beds are interpreted through a combination of Bayesian depositional age estimation and stratigraphic age modeling, resulting in posterior ages from 99.490 + 0.057/–0.050 to 98.905 + 0.158/–0.183 Ma. The age model predicts probabilistic ages for fossil localities between the ashes, including new ages for Moros intrepidus, Siats meekerorum, and several undescribed ornithischian dinosaur species of key interest for understanding the timing of faunal turnover in western North America. This new geochronology for the Mussentuchit Member offers unprecedented temporal insights into a volatile interval in Earth’s history.
Out-of-hospital multimodal seizure detection: a pilot study
Authors: Nielsen Jonas Munch , Kristinsdóttir Ástrós Eir , Zibrandtsen Ivan Chrilles , Masulli Paolo , Ballegaard Martin , Andersen Tobias Søren , Kjær Troels Wesenberg
Published: August 2023

Background

Out-of-hospital seizure detection aims to provide clinicians and patients with objective seizure documentation in efforts to improve the clinical management of epilepsy. In-patient studies have found that combining different modalities helps improve the seizure detection accuracy. In this study, the objective was to evaluate the viability of out-of-hospital seizure detection using wearable ECG, accelerometry and behind-the-ear electroencephalography (EEG). Furthermore, we examined the signal quality of out-of-hospital EEG recordings.

Methods

Seventeen patients were monitored for up to 5 days. A support vector machine based seizure detection algorithm was applied using both in-patient seizures and out-of-hospital electrographic seizures in one patient. To assess the content of noise in the EEG signal, we compared the root-mean-square (RMS) of the recordings to a reference threshold derived from manually categorised segments of EEG recordings.

Results

In total 1427 hours of continuous EEG was recorded. In one patient, we identified 15 electrographic focal impaired awareness seizures with a motor component. After training our algorithm on in-patient data, we found a sensitivity of 91% and a false alarm rate (FAR) of 18/24 hours for the detection of out-of-hospital seizures using a combination of EEG and ECG recordings. We estimated that 30.1% of the recorded EEG signal was physiological EEG, with an RMS value within the reference threshold.

Conclusion

We found that detection of out-of-hospital focal impaired awareness seizures with a motor component is possible and that applying multiple modalities improves the diagnostic accuracy compared with unimodal EEG. However, significant challenges remain regarding a high FAR and that only 30.1% of the EEG data represented usable signal.
Antitetanus toxoid antibodies in mothers and neonates: a single-centre study from Uganda
Authors: Mugagga Nicholas , Bagaya Bernard Ssentalo , Nantongo Mary , Muwanda Fahad , Mukunya David , Musaba Milton W , Nakimuli Annette Olivia , Musooko Moses , Sekikubo Musa
Published: August 2023

Background

Neonatal mortality due to tetanus persists in Uganda despite the mandatory vaccination of pregnant mothers. Maternal antibodies wane within a year. Uganda’s maternal vaccination guidelines do not specify the timing or frequency of tetanus shots, contributing to suboptimal transfer of tetanus antibodies to neonates. We aimed to determine the prevalence and factors associated with protective tetanus antibodies among newborns at Kawempe National Referral Hospital.

Methods

We conducted a cross-sectional study among 293 mother-newborn pairs. At delivery, neonatal cord and maternal venous blood were collected and titred for antitetanus antibodies using a quantitative ELISA kit. The primary outcome of the study was the proportion of newborn babies with tetanus antibodies ≥0.1 IU/mL. Associated factors were determined using generalised linear models for the Poisson family with a log link and robust variance estimation.

Results

A total of 258/293 (88.1%) newborns had protective antibody titres. Factors associated with adequate protective antibodies in the newborn included: high (≥0.1 IU/mL) maternal antibody titres, first antenatal visit ≥12 weeks of gestation and receiving a tetanus toxoid (TT) shot ≥28 weeks of gestation. However, number of doses received before current pregnancy was not associated with adequate protective antibody titres.

Conclusion

There is a high prevalence of adequate protective levels of antibodies among TT-vaccinated mothers. Maternal titres and a third trimester TT dose correlate with adequate levels of protective anti-TT antibodies among newborns. A third trimester TT dose is recommended.
Deep learning with test-time augmentation for radial endobronchial ultrasound image differentiation: a multicentre verification study
Authors: Yu Kai-Lun , Tseng Yi-Shiuan , Yang Han-Ching , Liu Chia-Jung , Kuo Po-Chih , Lee Meng-Rui , Huang Chun-Ta , Kuo Lu-Cheng , Wang Jann-Yuan , Ho Chao-Chi , Shih Jin-Yuan , Yu Chong-Jen
Published: August 2023

Purpose

Despite the importance of radial endobronchial ultrasound (rEBUS) in transbronchial biopsy, researchers have yet to apply artificial intelligence to the analysis of rEBUS images.

Materials and methods

This study developed a convolutional neural network (CNN) to differentiate between malignant and benign tumours in rEBUS images. This study retrospectively collected rEBUS images from medical centres in Taiwan, including 769 from National Taiwan University Hospital Hsin-Chu Branch, Hsinchu Hospital for model training (615 images) and internal validation (154 images) as well as 300 from National Taiwan University Hospital (NTUH-TPE) and 92 images were obtained from National Taiwan University Hospital Hsin-Chu Branch, Biomedical Park Hospital (NTUH-BIO) for external validation. Further assessments of the model were performed using image augmentation in the training phase and test-time augmentation (TTA).

Results

Using the internal validation dataset, the results were as follows: area under the curve (AUC) (0.88 (95% CI 0.83 to 0.92)), sensitivity (0.80 (95% CI 0.73 to 0.88)), specificity (0.75 (95% CI 0.66 to 0.83)). Using the NTUH-TPE external validation dataset, the results were as follows: AUC (0.76 (95% CI 0.71 to 0.80)), sensitivity (0.58 (95% CI 0.50 to 0.65)), specificity (0.92 (95% CI 0.88 to 0.97)). Using the NTUH-BIO external validation dataset, the results were as follows: AUC (0.72 (95% CI 0.64 to 0.82)), sensitivity (0.71 (95% CI 0.55 to 0.86)), specificity (0.76 (95% CI 0.64 to 0.87)). After fine-tuning, the AUC values for the external validation cohorts were as follows: NTUH-TPE (0.78) and NTUH-BIO (0.82). Our findings also demonstrated the feasibility of the model in differentiating between lung cancer subtypes, as indicated by the following AUC values: adenocarcinoma (0.70; 95% CI 0.64 to 0.76), squamous cell carcinoma (0.64; 95% CI 0.54 to 0.74) and small cell lung cancer (0.52; 95% CI 0.32 to 0.72).

Conclusions

Our results demonstrate the feasibility of the proposed CNN-based algorithm in differentiating between malignant and benign lesions in rEBUS images.
Health systems research in burn care: an evidence gap map
Authors: Keshri Vikash Ranjan , Peden Margaret , Singh Pratishtha , Norton Robyn , Abimbola Seye , Jagnoor Jagnoor
Published: August 2023

Background

Burn injury is associated with significant mortality and disability. Resilient and responsive health systems are needed for optimal response and care for people who sustain burn injuries. However, the extent of health systems research (HSR) in burn care is unknown. This review aimed to systematically map the global HSR related to burn care.

Methods

An evidence gap map (EGM) was developed based on the World Health Organization health systems framework. All major medical, health and injury databases were searched. A standard method was used to develop the EGM.

Results

A total of 6586 articles were screened, and the full text of 206 articles was reviewed, of which 106 met the inclusion criteria. Most included studies were cross-sectional (61%) and were conducted in hospitals (71%) with patients (48%) or healthcare providers (29%) as participants. Most studies were conducted in high-income countries, while only 13% were conducted in low-and middle-income countries, accounting for 60% of burns mortality burden globally. The most common health systems areas of focus were service delivery (53%), health workforce (33%) and technology (19%). Studies on health policy, governance and leadership were absent, and there were only 14 qualitative studies.

Conclusions

Major evidence gaps exist for an integrated health systems response to burns care. There is an inequity between the burden of burn injuries and HSR. Strengthening research capacity will facilitate evidence-informed health systems and policy reforms to sustainably improve access to affordable, equitable and optimal burn care and outcomes.
Bans on tobacco display, advertising and vending machines in the Netherlands: impact on visibility of tobacco and compliance of retailers
Authors: Borowiecki Mateusz , van Deelen Tessa R D , van den Putte Bas , Kunst Anton E , Kuipers Mirte A G
Published: August 2023

Introduction

Visibility of tobacco products at retail tobacco outlets is associated with smoking initiation. To address this, across 2020–2022 the Netherlands banned tobacco product displays, advertisements and vending machines in the retail environment. Tobacco/vape specialist shops were exempted. This study assessed the impact of these policies on tobacco visibility in the retail environment and retailer compliance.

Methods

We conducted observational audits of all tobacco outlets in four Dutch cities (Amsterdam, Haarlem, Eindhoven and Zwolle) between 2019 and 2022 (before and after policy implementation), assessing visibility of tobacco products and advertisements, compliance and remaining sources of tobacco visibility (after implementation). We described results by location and outlet type.

Results

The number of tobacco outlets with any tobacco advertising or product visibility declined from 530 to 267 (−50%). Among outlets not exempt from the ban, the number with visibility declined from 449 to 172 (−62%), with lower postban visibility in petrol stations (12%) and supermarkets (6%) than small shops (47%). Visibility among tobacco/vape shops increased by 17%. Tobacco product displays remained the main source of visibility. 93% of tobacco vending machines were removed. Maps showed that non-compliance is concentrated in Amsterdam’s city centre and more evenly distributed in other cities.

Conclusion

The bans on tobacco display and tobacco advertising halved the visibility of tobacco in the retail environment, and the vending machine ban practically eradicated vending machines. To further reduce tobacco visibility, violations in small shops should be addressed and tobacco visibility should be regulated in currently exempt tobacco specialist shops.
Feeding graded levels of camelina expeller meal up to 20% of dietary dry matter decreases feed intake and milk production but enhances concentration in milk fat of n-3 fatty acids in dairy cows
Authors: Mutsvangwa Timothy , Thomas Sarah , Newkirk Rex
Published: August 2023

Eight Holstein cows were used in a replicated 4 × 4 Latin square design study to determine the effects of feeding 0%, 10%, 15%, and 20% camelina expeller meal (CEM) on production and milk fatty acid profiles. Dry matter intake (DMI) and milk fat content decreased linearly, whereas milk yield decreased quadratically, as CEM increased. Concentrations in milk fat of C18:2n-6 and cis-9, trans-11 C18:2 increased linearly, whereas those of C18:3n-3 and trans-10, cis-12 C18:2 increased quadratically as CEM increased. Results show that CEM levels up to 20% decrease DMI and milk yield but increase concentrations in milk fat of desirable n-3 fatty acids.
Managing exploitation of freshwater species and aggregates to protect and restore freshwater biodiversity
Authors: Cooke Steven J. , Piczak Morgan L. , Nyboer Elizabeth A. , Michalski Fernanda , Bennett Abigail , Koning Aaron A. , Hughes Kathy A. , Chen Yushun , Wu Jinming , Cowx Ian G. , Koehnken Lois , Raghavan Rajeev , Pompeu Paulo S. , Phang Sui , Valbo-Jørgensen John , Bendixen Mette , Torres Aurora , Getahun Abebe , Kondolf G. Mathias , Acreman Michael C. , Song Andrew M. , Taylor William W.
Published: August 2023

For millennia humans have extracted biological and physical resources from the planet to sustain societies and enable the development of technology and infrastructure. Growth in the human population and changing consumption patterns have increased the human footprint on ecosystems and their biodiversity, including in fresh waters. Freshwater ecosystems and biodiversity face many threats and it is now widely accepted that we are in a biodiversity crisis. One means of protecting and restoring freshwater biodiversity is to better manage the exploitation of freshwater biota and aggregate resources (e.g., sand, gravel, and boulders). Here we outline the threats arising from such exploitation and identify response options to ensure that methods and levels of extraction are sustainable and allow recovery of over-exploited freshwater biodiversity and ecosystems. The guidance we provide will enable practitioners, policy-makers, and resource stewards to embrace effective, sustainable, and evidence-based approaches to resource extraction. Response options for managing species exploitation include strengthening assessment and reporting, using science-based approaches to reduce overexploitation and support recovery, embracing community engagement, and building or tightening legislation. Response options for managing exploitation of freshwater aggregate resources include reducing demand for harvest, strengthening governance, reporting, and monitoring of environmental impacts, and promoting the restoration of degraded ecosystems or compensating for losses. Diverse case studies highlight examples of where various management actions have been implemented in an effort to consider how they can be scaled up and adapted to other contexts. Managing exploitation will be a key aspect of broader initiatives needed to protect and restore freshwater biodiversity around the globe.
Overspinning a rotating black hole in semiclassical gravity with type-A trace anomaly
Authors: Jiang Jie , Zhang Ming
Published: August 2023

Recently, Fernandes discovered an analytic solution for rotating black holes in semiclassical gravity induced by the trace anomaly. These solutions exhibit some distinctive characteristics, including a non-spherically symmetric event horizon, the absence of circularity conditions, and violations of the Kerr bound. As a crucial assumption to uphold causality in spacetime, we investigate the validity of the weak cosmic censorship conjecture (WCCC) within this class of solutions with type-A trace anomaly by introducing a test particle on the equatorial plane. Our study reveals three distinct mechanisms that can potentially destroy the event horizon, leading to a violation of the WCCC. Our findings indicate that, with the exception of extremal Kerr, static extremal, and static singular black holes, the WCCC may be violated under the first-order perturbation of the test particle. These results suggest the need for further exploration of modifications to the behavior of the test particle under quantum effects in order to address the violation of the WCCC in this system.
Chicoric Acid Presented NLRP3-Mediated Pyroptosis through Mitochondrial Damage by PDPK1 Ubiquitination in an Acute Lung Injury Model
Authors: Zhang Weiwei , Zhao Min , Pu Zhichen , Yin Qin , Shui Yinping
Published: August 2023

Chicoric acid (CA), a functional food ingredient, is a caffeic acid derivative that is mainly found in lettuce, pulsatilla, and other natural plants. However, the anti-inflammatory effects of CA in acute lung injury (ALI) remain poorly understood. This study was conducted to investigate potential drug usage of CA for ALI and the underlying molecular mechanisms of inflammation. C57BL/6 mice were given injections of liposaccharide (LPS) to establish the in vivo model. Meanwhile, BMDM cells were stimulated with LPS+ATP to build the in vitro model. CA significantly alleviated inflammation and oxidative stress in both the in vivo and in vitro models of ALI through the inhibition of NLR family pyrin domain-containing 3 (NLRP3)-mediated pyroptosis. In addition, CA attenuated mitochondrial damage to suppress NLRP3-mediated pyroptosis in the in vivo and in vitro models of ALI by suppressing the production of reactive oxygen species (ROS) via inhibiting the Akt/nuclear factor erythroid 2-related factor 2 (Nrf2) pathway. CA inhibited the interaction between Akt at T308 and phosphoinositide-dependent kinase-1 (PDPK1) at S549, thus promoting the phosphorylation of the Akt protein. Furthermore, CA directly targeted the PDPK1 protein and accelerated PDPK1 ubiquitination, indicating that 91-GLY, 111-LYS, 126-TYR, 162-ALA, 205-ASP, and 223-ASP might be responsible for the interaction between PDPK1 and CA. In conclusion, CA from Lettuce alleviated NLRP3-mediated pyroptosis in the ALI model through ROS-induced mitochondrial damage by activating Akt/Nrf2 pathway via PDPK1 ubiquitination. The present study suggests that CA might be a potential therapeutic drug to treat or prevent ALI in pneumonia or COVID-19.
Coptis chinensis-Induced Changes in Metabolomics and Gut Microbiota in Rats
Authors: Wang Yong-Xiang , Zhang Jin-Ying , Cao Yu-Min , Liu Tong , Zhang Zhen-Kai , Zhang Bing-Xian , Feng Wei-Sheng , Li Kai , Zheng Xiao-Ke , Zhou Ning
Published: August 2023

Rhizoma coptidis (CR) is traditionally used for treating gastrointestinal diseases. Wine-processed CR (wCR), zingiber-processed CR (zCR), and evodia-processed CR (eCR) are its major processed products. However, the related study of their specific mechanisms is very limited, and they need to be further clarified. The aim of this study is to compare the intervening mechanism of wCR/zCR/eCR on rats via faecal metabolomics and 16S rDNA gene sequencing analysis. First, faecal samples were collected from the control and CR/wCR/zCR/eCR groups. Then, a metabolomics analysis was performed using UHPLC-Q/TOF-MS to obtain the metabolic profile and significantly altered metabolites. The 16S rDNA gene sequencing analysis was carried out to analyze the composition of gut microbiota and screen out the significantly altered microbiota at the genus level. Finally, a pathway enrichment analysis of the significantly altered metabolites via the KEGG database and a functional prediction of relevant gut microbes based on PICRUSt2 software were performed in combination. Together with the correlation analysis between metabolites and gut microbiota, the potential intervening mechanism of wCR/zCR/eCR was explored. The results suggested that wCR played a good role in maintaining immune homeostasis, promoting glycolysis, and reducing cholesterol; zCR had a better effect on protecting the integrity of the intestinal mucus barrier, preventing gastric ulcers, and reducing body cholesterol; eCR was good at protecting the integrity of the intestinal mucus barrier and promoting glycolysis. This study scientifically elucidated the intervening mechanism of wCR/zCR/eCR from the perspective of faecal metabolites and gut microbiota, providing a new insight into the processing mechanism research of Chinese herbs.
Skyrmions at finite density
Authors: Canfora Fabrizio , Rebolledo-Caceres Scarlett C.
Published: August 2023

In this paper, we will describe recent advances in analytical methods to construct exact solutions of the Skyrme model (and its generalizations) representing inhomogeneous Hadronic condensates living at finite Baryon density. Such novel analytical tools are based on the idea to generalize the well-known spherical hedgehog ansatz to situations (relevant for the analysis of finite density effects) in which there is no spherical symmetry anymore. Besides the intrinsic mathematical interest to find exact solutions with nonvanishing Baryonic charge confined to a finite volume, this framework opens the possibility to compute important physical quantities which would be difficult to compute otherwise.
The coefficients of the Jones polynomial
Authors: Manathunga V. A.
Published: August 2023

It has been known that the coefficients of the series expansion of the Jones polynomial evaluated at [Formula: see text] are rational-valued Vassiliev invariants. In this paper, we calculate minimal multiplying factor, [Formula: see text], needed for these rational-valued invariants to become integer-valued Vassiliev invariants. By doing that, we obtain a set of integer-valued Vassiliev invariants.
AN ANALOGICAL METHOD ON FRACTAL DIMENSION FOR THREE-DIMENSIONAL FRACTURE TORTUOSITY IN COAL BASED ON CT SCANNING
Authors: LIU GAOFENG , ZHANG ZHEN , CAO YUNXING , WANG XIAOMING , LIU HUAN , LI BAOLIN , SI NIAN , GUAN WENBO
Published: August 2023

In this work, we have given an analogical method for estimating the fractal dimension for three-dimensional fracture tortuosity (3D-FT). The comparison and error analysis of analogical and rigorous methods on fractal dimension for 3D-FT were carried out in this work. The fractal dimension [Formula: see text] for 3D-FT from the proposed analogical method is the function of 3D fracture average tortuosity ([Formula: see text] and average fracture length ([Formula: see text]. The analogical method for estimating fractal dimension ([Formula: see text] with high accuracy indicates good consistency with the rigorous method ([Formula: see text]. The fractal dimension ([Formula: see text] from the rigorous method is the embodiment of the physical meaning of [Formula: see text]. The fractal dimension ([Formula: see text] from the analogical method is relatively convenient for calculating the premise of ensuring accuracy.
Productivity Growth Effects of FDI Spillovers: Evidence from the Türkiye Manufacturing Industries
Authors: Waqar Shahid Mahmood , Abdu Musa
Published: August 2023

This study explores the productivity growth effects of horizontal, backward, and forward FDI spillovers in the Türkiye manufacturing sector using industry-level data for the period 2008–2018. While controlling for capital intensity and human capital as proxies for the absorption capacity, we apply system GMM and bootstrapped LSDV estimator to estimate the models. Our findings reveal that backward linkages significantly hamper industrial productivity due to the rudimentary nature of the products in the downstream sector or lack of absorption capacity. While horizontal spillovers retard the productivity growth; forward linkages enhance the growth, though all insignificant. The results depict that all the interactions with capital intensity strongly promote industrial productivity growth.
Exploring natural hydrogen hotspots: a review and soil-gas survey design for identifying seepage
Authors: Langhi Laurent , Strand Julian
Published: August 2023

Exploration for natural hydrogen seepages has grown rapidly, with surface seepages being seen as a primary indication of an underlying resource. While soil gas sampling has proven successful in detecting hydrogen in the soil, current understanding of hydrogen in the subsurface remains incomplete, with various potential sources of origin.

This paper presents a selected review of published hydrogen hotspots around the world, examining their distribution with respect to two main features commonly associated with natural seepages: sub-circular depressions (SCD) and fault zones. Based on the findings, the paper proposes a conceptual soil-gas survey design for efficiently identifying potential hydrogen hotspots. The proposed scheme is tested on a SCD and a fault zone located in Western Australia. The study findings near the Perth Basin and the Yilgarn Craton highlight the presence of anthropogenic artifacts in hydrogen measurement, necessitating further investigation to constrain the possible sources of hydrogen generation.

The study of the SCD in the Perth Basin supports the development of a statistical understanding of hydrogen distribution around surface features associated with hydrogen hotspots. Such a framework can guide soil-gas surveys and target areas with a higher likelihood of detecting natural hydrogen seepage. By addressing these points, prospective areas for natural hydrogen seepage can be better identified and evaluated, ultimately contributing to the development of hydrogen as a sustainable energy resource.

Thematic collection:
This article is part of the Hydrogen as a future energy source collection available at:
https://www.lyellcollection.org/topic/collections/hydrogen
Accountable Bench-to-Bedside Data-Sharing Mechanism for Researchers
Authors: Seneviratne Oshani , Adams Kacy , McGuinness Deborah L.
Published: August 2023

We present a trustworthy mechanism for sharing, reusing, and repurposing data to address the challenge of the costly and time-consuming effort needed to bring an innovative idea from the bench (basic research) to the bedside (clinical level). Even though researchers may generate a solution on their own, other aspects of research, including peer review and dissemination of data/results, have an inherent social component. Compared with the centralized mechanisms of data-sharing (and the subsequent reuse and repurposing), many, if not all, aspects of these processes can be decentralized by using blockchain (for full decentralized and autonomous control), coupled with provenance (to ascertain how and where the resources have been leveraged) and incentive semantics (for characterizing how researchers would be rewarded for their contributions). By capturing metadata details at each step of the workflow, data will be easier to audit, verify, and merge with related datasets. It is common in settings where data is either sensitive or valuable (or both) to have formal data use agreements or sometimes less formal rules for reuse, which we have captured in smart contracts. A key innovative aspect of this work is the departure from the traditional natural language–based data use agreements to make these agreements more computable, resulting in enhanced usability and interoperability by a broader community. We have developed the Data Sharing Ontology, a structured vocabulary to guide various incentive mechanisms and criteria used in the decentralized protocol we introduced with smart contracts. Our solution can track data reuse, provide peer reviews on accountable data reuse, and report any violations, thus providing metrics for measuring data producers’ impact on reward structures and research measures. We introduce the
SCIENCE-index
designed to incentivize data-sharing in scientific research, which builds upon prior indices used in academic research, such as the h-index and the data-index. The
SCIENCE-index
is publicly available and automatically calculated by a smart contract based on an individual’s data sharing, reuse, and responsible stewardship activities. By incentivizing fair and honest data-related activities, the
SCIENCE-index
can help improve the speed, cost, and quality of scientific research. As an example application of this decentralized data-sharing framework, we demonstrate how this approach could radically improve the quality and the efficiency of scientific output in the setting of COVID-19 research data-sharing from the National COVID Cohort Collaborative (N3C).
miR-122-5p is involved in posttranscriptional regulation of the mitochondrial thiamin pyrophosphate transporter (SLC25A19) in pancreatic acinar cells
Authors: Ramamoorthy Kalidas , Sabui Subrata , Manzon Kameron I. , Balamurugan Appakalai N. , Said Hamid M.
Published: August 2023

This study shows that the expression and function of mitochondrial TPP transporter (MTPPT) are subject to posttranscriptional regulation by miRNA-122-5p in pancreatic acinar cells.
Effects of Dietary Medlar (Mespilus germanica L.) Extract on Growth Performance, Innate Immune Characteristics, Antioxidant Status, and Responses to Crowding Stress in Rainbow Trout (Oncorhynchus mykiss)
Authors: Patra Indrajit , Dewi Afiska Prima , Fawzi Mohammed , Hussam Fadhil , Obayes Israa K. , Jamal Mohammed Ahmed , Hammoodi Hayder A. , Abbass Zainab R. , Dadras Mahnaz , Narimanizad Fariborz
Published: August 2023

High stocking density is a stress factor that potentially affects physiological and immune responses. In this study, the effects of medlar (Mespilus germanica) extract (ME) supplementation on growth performance, antioxidant, immune status, and stress responses in rainbow trout (Oncorhynchus mykiss) were studied. Six hundred fish (40.19 ± 1.09 g; average fish weight ± standard error) were distributed randomly into five experimental groups (assayed in triplicates). The experimental diets were formulated as follows: 0 (T1, control), 0.5% (T2), 1% (T3), 1.5% (T4), and 2% (T4). After 60 days feeding trial, the fish were confined, and the density increased (60 kg/m3) for further 14 days. Results showed significant increases in final weight (FW), weight gain (WG), specific growth rate, and feed intake in the T4 compared to the control (

P
<
0.05

). The feed conversion ratio (FCR) in T4 significantly decreased compared to the control (

P
<
0.05

). Also, the treated groups showed significant improvements in catalase (CAT), superoxide dismutase (SOD), glutathione peroxidase (GPx), lysozyme (LYZ), total immunoglobulin (total Ig), respiratory burst activity (RBA), total protein, and phagocytosis (PHA) (

P
<
0.05

). Moreover, compared with the control group, supplementation could significantly decrease glucose (GLU) and cortisol (CORT), alanine transaminase (ALT), lactate dehydrogenase (LDH), aspartate transaminase (AST), and alkaline phosphatase (ALP) (

P
<
0.05

). After the challenge, FW and WG in all treated challenge groups were significantly improved compared to the control group (

P
<
0.05

). FCR showed a significant decrease in all treated challenged groups compared to the control group (

P
<
0.05

). However, malondialdehyde, CAT, GPx, SOD, LYZ, complement activity (C3 and C4), total Ig, RBA, peroxidase, and PHA in challenged treated groups were significantly increased compared to the control group (

P
<
0.05

). All treated challenged groups showed lower ALT, LDH, AST, ALP, GLU, and CORT levels than the control group (

P
<
0.05

). The experiment herein successfully demonstrated that dietary ME stimulated fish growth, antioxidant status, and immune responses in crowding conditions and can be recommended as beneficial feed additives for rainbow trout.
Open-Label Observational Study of a Topical Formulation of Calcium Spirulan Contained in a Defined Extract of the Microalga Spirulina platensis in the Treatment of Children with Molluscum Contagiosum
Authors: Jungclaus Karoline , Mascarenhas Rosa , Tellechea Oscar , Reich Jeremias L. K. , Reich Kristian
Published: August 2023

Background. Molluscum contagiosum (MC) is a common viral skin infection primarily affecting children which is difficult to treat using available therapeutic approaches. The sulfated polysaccharide named calcium spirulan (Ca-SP) has demonstrated antiviral effects against herpes simplex virus in keratinocytes in vitro, and a cream containing 1.5% Ca-SP and 1% of a defined microalgae extract (Spiralin®) effectively prevented herpes labialis in a trial with susceptible individuals. This observational study aimed to show antiviral effects of a similar formulation (Spirularin® VS) against MC in children. Methods. Children with active MC lesions were treated with Spirularin® VS cream twice daily on affected skin over several months and asked to return for follow-up visits after 1 to 3 months. Clinical status of MC infection was documented at baseline and follow-up visits. Results. Of the 31 children enrolled in the study, 26 completed treatment and returned for control visits. Spirularin® VS cream was applied twice daily over a period of 1 to 9 months (mean treatment duration 3.9 months). 19/26 (73.1%) children achieved complete clearance of MC lesions with no clinical evidence of bacterial skin infection during treatment. No irritative skin reactions or unpleasant symptoms were observed or reported. Conclusion. This open-label observational study suggests that a cream formulation containing 1.5% Ca-SP and 1% Spiralin® may be an effective and safe treatment option for children with active MC lesions. The high rate of complete clearance of MC lesions and lack of adverse reactions warrant further investigation in larger, controlled trials.
The Polyherbal Functional Ingredient Containing Ginger, Chinese Date, and Wood Ear Mushroom Protects against Dementia following Metabolic Syndrome
Authors: Nakyam Thuntiva , Wattanathorn Jintanaporn , Thukham-mee Wipawee , Muchimapura Supaporn
Published: August 2023

The anti‐dementia effect following ischemic stroke with metabolic syndrome (MetS) of the polyherbal functional ingredient comprising ginger, Chinese date, and wood ear mushroom (GCJ) was hypothesized due to its neuroprotective effect against stroke. This study was performed to test this hypothesis and to explore the underlying mechanism. Male Wistar rats weighing 180‐220 g were induced metabolic syndrome (MetS) with a 16‐week high‐carbohydrate high‐fat diet (HCHF) feeding. The rats with MetS characteristics were orally administered GCJ at various doses (GCJ100, GCJ200, and GCJ300 mg kg-1 BW) 21 days pre‐induction and 21 days post‐induction of reperfusion injury (I/R) at the right middle cerebral artery (MCAO). Memory was evaluated every 7 days during the study period. At the end of the study, neuron density, AChE activity, and the expressions of eNOS, BDNF, and pERK/ERK in the prefrontal cortex, and hippocampus were also determined. MetS rats with GCJ treatment improved memory impairment, enhanced neuron density, and increased the expressions of eNOS, BDNF, and pERK/ERK but suppressed AChE in both areas. Therefore, the anti‐dementia effect following ischemic stroke with metabolic syndrome of GCJ may involve the improvement of AChE, eNOS, BDNF, pERK/ERK, and neural plasticity. However, this required confirmation by clinical study.
Designing for Digital Wellbeing: From Theory to Practice a Scoping Review
Authors: Al-Mansoori Reem S. , Al-Thani Dena , Ali Raian
Published: August 2023

In a world that is highly dependent on digital connectivity, technology use is becoming unavoidable, intense, and possibly harmful. The pervasiveness of technology which has been in tandem with the increasing number of reported cases of harmful usage styles, with some exhibiting symptoms of behavioural addiction, raised concerns around users’ psychological health and well-being. Digital Wellbeing is a new facet of human well-being that has recently emerged. While the term is yet to have a commonly agreed definition, it typically denotes a technology that promotes positivity, personal growth, and a usage that is balanced and healthy. In this paper, we aim to examine the extent, range, and nature of Digital Wellbeing research activity in human-computer interaction- (HCI-) related literature. We conducted a scoping review analysing 87 articles that researched Digital Wellbeing and its interrelation with technology design. Our analysis identified different meanings and constructs of the Digital Wellbeing concept, research trends, and a gap related to incorporating it in the design process. Accordingly, we recommend that an agreed-on definition for Digital Wellbeing and validated tools and frameworks are needed to ensure its integration in the digital design process. We also recommend that a wider research direction for HCI researchers and practitioners interested in Digital Wellbeing is needed to include the role of designers and societal institutions in the digital design process to ensure a design that is inclusive and well-being sensitive.
Supplementary Table S2 from Characteristics of Cancer Epidemiology Studies That Employ Metabolomics: A Scoping Review
Authors: Yu Catherine T. , Farhat Zeinab , Livinski Alicia A. , Loftfield Erikka , Zanetti Krista A.
Published: August 2023

Supplementary Table S2 shows additional study design and analysis characteristics of population-based cancer metabolomics studies.
Supplementary Figure S6 from Characteristics of Cancer Epidemiology Studies That Employ Metabolomics: A Scoping Review
Authors: Yu Catherine T. , Farhat Zeinab , Livinski Alicia A. , Loftfield Erikka , Zanetti Krista A.
Published: August 2023

Supplementary Figure S6 shows pie chart displaying breakdown of studies that used an LC-MS semi-targeted approach.
Figure S1 from Associations between Ambient Air Pollutants and Clonal Hematopoiesis of Indeterminate Potential
Authors: Leiser Claire L. , Whitsel Eric A. , Reiner Alexander , Rich Stephen S. , Rotter Jerome I. , Taylor Kent D. , Tracy Russel P. , Kooperberg Charles , Smith Albert Vernon , Manson JoAnn E. , Mychaleckyj Josyf C. , Bick Alexander G. , Szpiro Adam A. , Kaufman Joel D.
Published: August 2023

Figure S1 shows the sample selection for the WHI and MESA cohorts in TOPMed.
Supplementary Table 4 from Patterns of Evidence-Based Care for the Diagnosis, Staging, and First-line Treatment of Breast Cancer by Race–Ethnicity: A SEER-Medicare Study
Authors: Herbach Emma L. , Nash Sarah H. , Lizarraga Ingrid M. , Carnahan Ryan M. , Wang Kai , Ogilvie Amy C. , Curran Michaela , Charlton Mary E.
Published: August 2023

Supplementary Table 4 shows a sensitivity analysis: rate ratios for all outcomes adjusted for all covariates except marital status and low-income subsidy.
Data from Socioeconomic Status at Birth and Breast Tissue Composition in Adolescence and Adulthood
Authors: Kehm Rebecca D. , Lilge Lothar , Walter E. Jane , White Melissa , Herbstman Julie B. , Perera Frederica P. , Miller Rachel L. , Terry Mary Beth , Tehranifar Parisa
Published: August 2023

AbstractBackground:
Socioeconomic status (SES) at birth is associated with breast cancer risk. Whether this association is driven by changes in breast tissue composition (BTC) prior to adulthood remains unclear.
Methods:
We used multivariable linear regression models to examine whether SES at birth is associated with BTC in adolescence and adulthood using data from a New York City cohort of daughters (n = 165, 11–20 years) and mothers (n = 160, 29–55 years). We used maternal-reported data on daughters’ household income and maternal education at birth, analyzed individually and in combination (SES index). Women also reported their own mothers’ education at birth. We used optical spectroscopy to evaluate BTC measures that positively (water content, collagen content, optical index) and negatively (lipid content) correlate with mammographic breast density, a recognized breast cancer risk factor.
Results:
Being in the highest versus lowest category of the SES index was associated with lower lipid content [βadjusted (βadj) = −0.80; 95% confidence interval (CI), −1.30 to –0.31] and higher collagen content (βadj = 0.54; 95% CI, 0.09–0.99) in adolescence. In women with a body mass index (BMI) <30 kg/m2, higher maternal education at birth (≥ vs. < high school degree) was associated with lower lipid content (βadj = −0.57; 95% CI, −0.97 to −0.17), higher water content (βadj = 0.70; 95% CI, 0.26–1.14), and higher optical index (βadj = 0.53; 95% CI, 0.10–0.95).
Conclusions:
This study supports that SES at birth is associated with BTC in adolescence and adulthood, although the latter association may depend on adult BMI.
Impact:
Further research is needed to identify the socially patterned early life factors influencing BTC.