bluuebunny/crossref_metadata_2025 huggingface dataset:
Impact of radiative feedback on the initial mass function of metal-poor stars
Authors: Chon Sunmyon , Hosokawa Takashi , Omukai Kazuyuki , Schneider Raffaella
Published: April 2024

The stellar initial mass function (IMF) in the early universe is essential to understand the formation of ancient galaxies. To this end, we conduct a series of long-term radiation hydrodynamic simulations following star cluster formation, varying the metallicity from Z/Z⊙ = 10−4 to 1. We particularly consider the effects of protostellar radiative feedback, which modify the exact shape of the IMF and determine the star formation efficiency (SFE), i.e. the ratio between the mass in stars and the initial gas mass in the parental cloud. Our results show that the IMF changes from a Salpeter-type to a top-heavy function as the metallicity decreases. When Z/Z⊙ ≲ 10−2, the IMF becomes log-flat and distinct from a Salpeter-like IMF. Stellar feedback is effective in shaping both the low- and high-mass ends of the IMF. Heating of dust grains by stellar radiation suppresses small-scale fragmentation and reduces the number of low-mass stars with M* ≲ 1 M⊙ at all metallicities. The ionizing radiation hinders the growth of massive stars, steepening the slope of the IMF at the high-mass end. The resulting feedback is more effective at lower metallicity, and star formation is regulated by stellar radiative feedback, with the SFE decreasing with decreasing metallicity. We suggest that the unexpectedly large number of UV-bright galaxies at z > 10 reported by JWST observations can be explained by considering star cluster formation at Z/Z⊙ ∼ 10−2 or 10−3, where the IMF is top-heavy, but the SFE is not too low due to stellar feedback.
Using ZDI maps to determine magnetic forces and torques at the photospheres of early-type stars
Authors: MacDonald James , Natan Tali , Petit Véronique , Kochukhov Oleg , Shultz Matthew E
Published: April 2024

We use the magnetic field components measured by Zeeman Doppler imaging (ZDI) to calculate the stellar surface force and torque due to magnetic stresses for the fast rotators σ Ori E, 36 Lyn, and CU Vir, and the slow rotator τ Sco. If we assume the stars have spherical photospheres, the estimated torques give spin-down time-scales no larger than 7 × 105 yr. For σ Ori E, the predicted spin-down time-scale, ≃ 6000 yr, is much less than the observationally measured time-scale of ≃ 106 yr. However, for CU Vir, we find that the spin-down time-scale from its ZDI map is 7 × 105 yr in good agreement with its average rate of spin-down from 1960 to 2010.

With the exception of τ Sco, the net force due to magnetic stresses at the stellar surface are large compared to the surface-integrated pressure. We discuss possible reasons for the large values of the forces (and torques), and suggest that the likely explanation is that rotation and the magnetic stresses create significant departures from spherical symmetry.
The metallicity gradients of star-forming regions store information of the assembly history of galaxies
Authors: Jara-Ferreira F , Tissera P B , Sillero E , Rosas-Guevara Y , Pedrosa S E , De Rossi M E , Theuns T , Bignone L
Published: April 2024

The variations in metallicity and spatial patterns within star-forming regions of galaxies result from diverse physical processes unfolding throughout their evolutionary history, with a particular emphasis on recent events. Analysing MaNGA and EAGLE galaxies, we discovered an additional dependence of the mass–metallicity relation (MZR) on metallicity gradients (∇(O/H)). Two regimes emerged for low- and high-stellar mass galaxies, distinctly separated at approximately M⋆ > 109.75$\rm{M}_{\odot}$. Low-mass galaxies with strong positive ∇(O/H) appear less enriched than the MZR median, while those with strong negative gradients are consistently more enriched in both simulated and observed samples. Interestingly, low-mass galaxies with strong negative ∇(O/H) exhibit high star-forming activity, regardless of stellar surface density or ∇(O/H). In contrast, a discrepancy arises for massive galaxies between MaNGA and EAGLE data sets. The latter exhibit a notable anticorrelation between specific star formation rate and stellar surface density, independent of ∇(O/H), while MaNGA galaxies show this trend mainly for strong positive ∇(O/H). Further investigation indicates that galaxies with strong negative gradients tend to host smaller central black holes in observed data sets, a trend not replicated in simulations. These findings suggest disparities in metallicity recycling and mixing history between observations and simulations, particularly in massive galaxies with varying metallicity gradients. These distinctions could contribute to a more comprehensive understanding of the underlying physics.
Dynamics of cold circumstellar gas in debris discs
Authors: Cui Can , Marino Sebastian , Kral Quentin , Latter Henrik
Published: April 2024

Mounting observational evidence indicates that cold circumstellar gas is present in debris disc systems. This work focuses on various dynamical processes that debris disc gas may undergo. We review five mechanisms that can transport angular momentum and their applications to debris discs. These include molecular viscosity, hydrodynamic turbulence, magnetohydrodynamic (MHD) turbulence, magnetized disc winds, and laminar magnetic stress. We find that molecular viscosity can result in α as high as ≲0.1 for sufficiently low densities, while the Rossby wave instability is a possible source of hydrodynamic turbulence and structure formation. We argue that the vertical shear instability is unlikely due to the long cooling times. The onset of the magnetorotational instability (MRI) is dichotomous: for low-density discs the MRI can be excited at the mid-plane, while for high-mass discs it may only be operating at z > 2 − 3H, if at all. The MHD wind and laminar magnetic stress mechanisms rely on the configuration and strength of any background large-scale magnetic field, the existence of which is uncertain and possibly unlikely. We conclude that the dominant mechanism and its efficiency in transporting angular momentum vary from one system to the other, depending especially closely on the gas density. More detailed analyses shall be performed in the future focusing on representative, nearby debris discs.
Changes in U.S. Adolescent Nicotine Vaping Prevalence From 2022 to 2023: The Role of Reduced Initiation Three Years Earlier During the Onset of the Pandemic
Authors: Miech Richard
Published: April 2024

Introduction

The prevalence of adolescent nicotine vaping declined substantially after the COVID-19 pandemic onset in the United States during the Spring of 2020. This study examines whether the decline continued from 2022 to 2023, and the extent to which any decline reflects the lasting influence of lowered levels of initiation 3 years earlier, at the onset of the pandemic.

Aims and Methods

Data for this study come from nationally representative, cross-sectional surveys of U.S. 12th-grade (n = 9854) and 10th-grade (n = 14 663) students administered in the Spring of 2022 and 2023. The main outcomes are past 12-month nicotine vaping and grade first ever vaped nicotine.

Results

From 2022 to 2023 prevalence of past 12-month nicotine vaping declined a relative 20% for 12th-grade students, from 24.3% to 19.1%, and for 10th-grade students by a relative 16%, from 17.8% to 15.1%. Among 12th-grade students who vaped nicotine in the past 12 months, a significant decline in prevalence took place only among those who first ever vaped nicotine in ninth grade, and not among those who first ever vaped nicotine in any other grade. Among 10th grade students who vaped nicotine in the past 12 months, a significant decline in prevalence took place only among those who first ever vaped nicotine in seventh grade, and not among those who first ever vaped nicotine in any other grade.

Conclusions

These results contribute national-level evidence that forestalled initiation of nicotine use for 1 year may have a lasting effect that continues to lower adolescents’ levels of use many years afterward.

Implications

These findings caution against looking to contemporaneous policy for explanations of the large, 1-year decline in nicotine vaping from 2022 to 2023. It can be tempting to interpret the decline as a victory for current efforts to restrict adolescent access to vaping products, or current education/media campaigns that warn adolescents of the dangers of vaping. The findings of this study suggest, instead, that the 1-year vaping declines primarily result from declines in initiation that were set into place 3 years ago during the pandemic onset, more so than the immediate result of contemporaneous policy.
Cohort Effects on Tobacco Consumption and Its Genetic and Environmental Variance Among Finnish Adults Born Between 1880 and 1957
Authors: Zellers Stephanie , Maes Hermine H M , Latvala Antti , Kaprio Jaakko
Published: April 2024

Introduction

Population research indicates that smoking behaviors in Finland have varied over time by sex and birth cohort. Smoking behaviors are influenced by genes and the environment; like the behaviors themselves, these underlying influences are not necessarily stable over time and may be modifiable by national drug policy.

Aims and Methods

We utilized longitudinal mixed-effects models and causal–common–contingent twin models to evaluate sex and cohort effects on tobacco consumption and the underlying genetic and environmental variance components in a birth cohort sample of same-sex twins born in Finland between 1880 and 1957, assessed in 1975, 1981, 1990, and 2011.

Results

We identified significant main effects of age, sex, and cohort on quantity of cigarette consumption, as well as significant age × cohort and sex × cohort interactions. We also identified sex and cohort effects on the liability to initiate regular smoking and the magnitude of variation underlying quantity of cigarette consumption. That said, heritability and environmental contributions to both traits were not different between the four sex × cohort groups.

Conclusions

Our results indicate sex and cohort effects on the prevalence of smoking and its underlying variation. Our results on changing prevalence mirror existing population-level research in Finnish samples, but we did not identify differences in heritability found in other studies of cohort effects in tobacco use, potentially due to power issues. These results highlight the importance of considering age, cohort, and timing of policy changes when evaluating changes in substance consumption across time.

Implications

This study identifies sex and cohort effects influencing tobacco consumption in a sample of Finnish adult twins born between 1880 and 1957. Our results are in line with other population-level research in Finland and research on cohort effects influencing alcohol use in the same sample. Our results highlight the intertwining effects of age, cohort, sex, and substance policies on substance use.
Are People More Likely to Vape or Smoke Indoors? A Population Survey of Adults in England
Authors: Tattan-Birch Harry , Jackson Sarah E , Shahab Lion , Brown Jamie
Published: April 2024

Background

Increasingly, people smoke cigarettes outdoors and avoid exposing bystanders to harm. People may not have the same motivation to vape outdoors since e-cigarettes, unlike cigarettes, do not create side stream emissions and exhaled aerosol contains fewer toxicants than secondhand smoke. This study aims to estimate the prevalence and correlates of vaping and smoking indoors among adults in England.

Aims and Methods

Data came from the Health Survey for England 2019, a cross-sectional household survey. Adults who vape or smoke (N = 1530) were asked whether they had vaped or smoked indoors inside the home, car, or other places within the past 7 days. Logistic regression was used to estimate prevalence and key correlates of indoor use, including age, sex, presence of adults/children in home, housing tenure, and nicotine dependence.

Results

People who exclusively vaped were much more likely to use their product indoors than those who exclusively smoked (87.0% vs. 52.0%; odds ratio [OR] = 6.16, 95% confidence interval [CI] = 4.09 to 9.28). Similarly, people who dual used had higher odds of vaping than smoking indoors (62.1% vs. 44.3%; OR = 3.76, 95% CI = 2.06 to 6.84). The preference for vaping over smoking indoors was found across different locations, including at home and in cars. Those who were older, highly dependent on nicotine, and lived alone were most prone to use any product indoors. While housing tenure was not strongly associated with vaping indoors, those living in social housing were much more likely to smoke indoors than homeowners.

Conclusions

Adults in England are much more likely to vape than smoke indoors. Age, nicotine dependence, and living alone are strongly associated with both behaviors.

Implications

Our results show that people have a strong preference for vaping over smoking indoors, including in the home. Given the high prevalence of vaping indoors, policy makers, landlords, and businesses must weigh up the ethics, benefits, and harms of extending smoke-free laws to include e-cigarettes.
Geochemical Evidence of Plume Sources for High-MgO Lavas in the Western Kunlun Orogenic Belt
Authors: Cheng Zhiguo , Zhang Zhaochong , Lang Mingde , Santosh M , Xu Lijuan , Liu Jingao
Published: April 2024

Plume-derived high-MgO lavas provide important information on the lithological, thermal and chemical variations of Earth’s deep mantle. Here we present results from detailed field, mineralogical and geochemical studies of Late Permian–Late Triassic high-MgO lavas near the Chalukou area in the Western Kunlun (WK) orogenic belt, NW China. The major element compositions of the lavas show extremely high MgO contents (26.6–33.8 wt %) in accordance with olivine accumulation. The parental magma is inferred to be picritic in composition with MgO of 17.2 ± 0.9 wt %. Olivine Zn/Fe and Mn/Zn ratios suggest a peridotite-dominated source with a minor fraction of pyroxenite. The temperature and oxygen fugacity estimates based on multi-methods including olivine-melt Mg–Fe equilibria, Al-in-olivine and olivine–spinel thermometry and oxybarometer yield a mantle potential temperature of 1522–1556 °C and high oxygen fugacity of FMQ (fayalite-magnetite-quartz) + 0.93. The H2O contents in the picrite flows are estimated as 3.67 ± 1.0 wt %, indicating the volatile-rich nature of parental magma and its mantle source. The immobile trace element features show that the WK picrites are OIB (oceanic island basalt)-like, with the enrichment in light rare earth elements and positive Nb, Ta, Zr and Hf anomalies. Furthermore, the Nd–O–Os isotopes display typical mantle values without involvement of recycled materials. Our results suggest the high-MgO volcanism in the WK orogenic belt originated from a volatile-rich plume source.
The Elusive Gains from Nationally Oriented Monetary Policy
Authors: Bodenstein Martin , Corsetti Giancarlo , Guerrieri Luca
Published: April 2024

The gains from monetary policy cooperation depend on real and financial distortions in the economy and evolve dynamically with prevailing economic conditions. We show that, with international trade in assets, these gains are driven by asymmetric cross-border developments in productivity and savings, and can reach multiples of the cost of economic fluctuations. When financial flows are restricted to nonstate-contingent bonds, the gains from cooperation grow with the size of global imbalances, i.e. net-foreign-asset positions.
The Use of Mobility-Focused Outcome Measures for Young Adults With Cancer Undergoing Chemotherapy
Authors: Edward Holly , Nayiga Brenda , Nicolau Daniel , Darsot Faheemah , Smith-Turchyn Jenna
Published: April 2024

Background:

Young adults living with cancer face many unique challenges during treatment and throughout survivorship. Chemotherapy is a standard anticancer treatment that has been known to lead to negative side effects on health including loss of muscle mass, strength, and physical function (ie, physical mobility). This scoping review aimed to explore what, how, and when mobility-focused outcome measures are being used during chemotherapy treatments for young adults living with cancer to examine changes in physical mobility.

Methods:

Five databases were searched. To be included in this review, studies must have included young adults (age 18-40) living with cancer, who were receiving chemotherapy treatment and used any form of physical mobility measurement during treatment. Duplicates were removed, and all screening and data extraction were performed by 2 or more independent reviewers.

Results:

A total of 1734 studies were screened, and four studies were included in this review. Three studies included a self-reported activity log. All studies assessed physical mobility using types of performance-based outcome measures such as accelerometers, muscle strength tests, cycle ergometer testing, or the 6- minute walk test. Assessments were conducted in person by study personnel in 2 studies. Outcomes were assessed throughout the chemotherapy cycle, including preadministration, over the first 7 days, weekly, and months into treatment.

Conclusion:

Although a scarcity of available literature exists, this review highlights the potential for screening and monitoring changes in mobility for young adults with cancer. Clinical application of the measures highlighted in this review shows promise in guiding appropriate interventions and informing changes in treatment dosage. Future research should build upon existing work to address the limited availability of mobility measures validated in this population.
Timely Completion of Direct Access Colonoscopy Is Noninferior to Office Scheduled for Screening and Surveillance
Authors: White Mary , Israilevich Rachel , Lam Sophia , McCarthy Michael , Mico Vasil , Chipkin Benjamin , Abrams Eric , Moore Kelly , Kastenberg David
Published: April 2024

Goals:

We aimed to evaluate whether direct access colonoscopy (DAC) is noninferior to office-scheduled colonoscopy (OSC) for achieving successful colonoscopy.

Background:

DAC may improve access to colonoscopy. We developed an algorithm assessing eligibility, risk for inadequate preparation, and need for nursing/navigator assistance.

Study:

This was a retrospective, single-center study of DAC and OSC patients from June 5, 2018, to July 31, 2019. Patients were 45 to 75 years old with an indication of screening or surveillance. A successful colonoscopy met 3 criteria: complete colonoscopy (cecum, anastomosis, or ileum), adequate preparation (Boston Score ≥2/segment), and performed <90 days from initial patient contact. Unsuccessful colonoscopy did not meet ≥1 criteria. Secondary end points included days to successful colonoscopy, preparation quality, polyp detection, and 10-year recall rate. Noninferiority against risk ratio value of 0.85 was tested using 1-sided alpha of 0.05.

Results:

A total of 1823 DAC and 828 OSC patients were eligible. DAC patients were younger, with a greater proportion of black patients and screening indications. For the outcome of successful colonoscopy, DAC was noninferior to OSC (DAC vs. OSC: 62.7% vs. 57.1%, RR 1.16, 95% LCL 1.09, P=0.001). For DAC, days to colonoscopy were fewer, and likelihood of 10-year recall after negative screening greater. Boston Score and polyp detection were similar for groups. Black patients were less likely to achieve successful colonoscopy; otherwise, groups were similar. For unsuccessful colonoscopies, proportionally more DAC patients canceled or no-showed while more OSC patients scheduled >90 days. DAC remained noninferior to OSC at 180 days.

Conclusions:

DAC was noninferior to OSC for achieving successful colonoscopy, comparing similarly in quality and efficiency outcomes.
Protocol for a Randomized Controlled Trial to Evaluate a Permissive Blood Pressure Target Versus Usual Care in Critically Ill Children with Hypotension (PRESSURE)
Authors: Darnell Robert , Brown Alanna , Laing Emma , Edwards Julia , Harrison David A. , Manning Joseph C. , Peters Mark J. , Ramnarayan Padmanabhan , Ray Samiran , Sadique Zia , Scholefield Barnaby R. , Shortt Dermot , Lampro Lamprini , Au Carly , Rowan Kathy M. , Mouncey Paul , Inwald David P. ,   Protocolised Evaluation of Permissive Blood Pressure Targets Versus Usual Care (PRESSURE) Trial Investigators on behalf of the U.K. Paediatric Critical Care Society Study Group (PCCS-SG)
Published: April 2024

OBJECTIVES:

Management of hypotension is a fundamental part of pediatric critical care, with cardiovascular support in the form of fluids or vasoactive drugs offered to every hypotensive child. However, optimal blood pressure (BP) targets are unknown. The PRotocolised Evaluation of PermiSSive BP Targets Versus Usual CaRE (PRESSURE) trial aims to evaluate the clinical and cost-effectiveness of a permissive mean arterial pressure (MAP) target of greater than a fifth centile for age compared with usual care.

DESIGN:

Pragmatic, open, multicenter, parallel-group randomized control trial (RCT) with integrated economic evaluation.

SETTING:

Eighteen PICUs across the United Kingdom.

PATIENTS:

Infants and children older than 37 weeks corrected gestational age to 16 years accepted to a participating PICU, on mechanical ventilation and receiving vasoactive drugs for hypotension.

INTERVENTIONS:

Adjustment of hemodynamic support to achieve a permissive MAP target greater than fifth centile for age during invasive mechanical ventilation.

MEASUREMENTS AND MAIN RESULTS:

Randomization is 1:1 to a permissive MAP target or usual care, stratified by site and age group. Due to the emergency nature of the treatment, approaching patients for written informed consent will be deferred until after randomization. The primary clinical outcome is a composite of death and days of ventilatory support at 30 days. Baseline demographics and clinical status will be recorded as well as daily measures of BP and organ support, and discharge outcomes. This RCT received Health Research Authority approval (reference 289545), and a favorable ethical opinion from the East of England—Cambridge South Research Ethics Committee on May 10, 2021 (reference number 21/EE/0084). The trial is registered and has an International Standard RCT Number (reference 20609635).

CONCLUSIONS:

Trial findings will be disseminated in U.K. national and international conferences and in peer-reviewed journals.
Outcomes of an Emergency Department Program to Identify and Link Patients at Increased Risk for Acquiring HIV Infection to Outpatient HIV Prevention Services: The HIV PreventED Program
Authors: White Douglas AE , Godoy Ashley , Jewett Montana , Burns Molly , Pinto Cinthya Mujica , Packel Laura J , Garcia-Chinn Maria , Anderson Erik S , McCoy Sandra I
Published: April 2024

Background:

Emergency departments (ED) provide care to patients at increased risk for acquiring HIV and for many of them, the ED serves as their sole point of entry into the healthcare system. We implemented the HIV PreventED Program to increase access to HIV prevention services for ED patients.

Setting:

Emergency department in Oakland, CA with an annual census of 57,000 visits.

Methods:

This cross-sectional study evaluated the first 9 months of the HIV PreventED Program. In this program, a navigator surveyed adult HIV negative ED patients to determine their risk for acquiring HIV infection, incorporating HIV prevention counseling into their assessments. Patients at higher risk for acquiring HIV were referred to outpatient prevention services, if interested. The primary outcome measure was the number and proportion of ED patients at higher risk for acquiring HIV that followed up for outpatient prevention services.

Results:

There were 1,233 HIV negative patients assessed by the navigator and who received ED-based HIV prevention counseling. Of these, 193 (15.7%) were identified at higher risk and offered an outpatient referral for prevention services, of which 104 accepted (53.9%), 23 (11.9%) attended the referral, and 13 (6.7%) were prescribed pre-exposure prophylaxis (PrEP). The median time to linkage was 28 days (interquartile range 15 to 41 days).

Conclusion:

A navigator focused on providing ED-based HIV prevention counseling and linkage to outpatient services is feasible. Strategies to more efficiently identify ED patients at higher risk for HIV acquisition, such as automated identification of risk data from the electronic health record, and policies to improve follow up and the receipt of PrEP, such as same-day PrEP initiation, should be prospectively evaluated.
In vivo
mechanical characterization of arterial wall using an inverse analysis procedure: application on an animal model of intracranial aneurysm
Authors: Raviol J. , Plet G. , Langlois J. B. , Si-Mohamed S. , Magoariec H. , Pailler-Mattei C.
Published: April 2024

Intracranial aneurysm is a pathology related to the deterioration of the arterial wall. This work is an essential part of a large-scale project aimed at providing clinicians with a non-invasive patient-specific decision support tool to facilitate the rupture risk assessment. It will lean on the link between the aneurysm shape clinically observed and a database derived from the
in vivo
mechanical characterization of aneurysms. To supply this database, a deformation device prototype of the arterial wall was developed. Its use coupled with medical imaging (spectral photon-counting computed tomography providing a spatial resolution down to 250 μm) is used to determine the
in vivo
mechanical properties of the wall based on the inverse analysis of the quantification of the wall deformation observed experimentally. This study presents the
in vivo
application of this original procedure to an animal model of aneurysm. The mechanical properties of the aneurysm wall identified were consistent with the literature, and the errors between the numerical and experimental results were less than 10%. Based on these parameters, this study allows the assessment of the aneurysm stress state for a known solicitation and points towards the definition of a rupture criterion.
Deciphering the interaction surface between the West Nile virus NS3 and NS5 proteins
Authors: Brand Carolin , Geiss Brian , Bisaillon Martin
Published: April 2024

West Nile virus (WNV) is the most prevalent mosquito-borne disease and the leading cause of viral encephalitis in the continental United States. It belongs to the Flavivirus family which includes other important human pathogens such as dengue virus (DENV), Japanese encephalitis virus (JEV), and Zika viruses (ZIKV). Despite several decades of research, no specific antiviral drugs are available to treat Flavivirus infections. The present study characterizes the interaction between the WNV NS3 and NS5 proteins for the purpose of identifying hotspots in the protein-protein interaction which could be targeted for the development of antiviral therapeutics. We previously developed an interaction model in silico based on data available in the literature. Here, potential interacting residues on NS3 and NS5 were mutated in a WNV replicon, and seven mutations in the NS3 protein were found to drastically reduce viral replication. In addition to being well conserved among mosquito-borne Flaviviruses, these residues are located on the protein’s surface in two clusters which might be interesting new targets for future drug development.
Enhancement of growth media for extreme iron-limitation in Escherichia coli

Authors: Southwell James W , Wilson Keith S , Thomas Gavin H , Duhme-Klair Anne-Kathrin
Published: April 2024

Iron is an essential nutrient for microbial growth and bacteria have evolved numerous routes to solubilise and scavenge this biometal, which is often present at very low concentrations in host tissue. We recently used a MOPS-based medium to induce iron limitation in Escherichia coli  K-12 during the characterisation of novel siderophore conjugated antibiotics. In this study we confirm that growth media derived from commercially-available M9 salts are unsuitable for studies of iron-limited growth, likely through the contamination of the sodium phosphate buffer components with over 100 µM iron. In contrast, MOPS-based media that are treated with metal-binding Chelex® resin, allow the free iron concentration to be reduced to growth-limiting levels. Despite these measures a small amount of E. coli growth is still observed in these iron-depleted media. By growing E. coli in conditions that theoretically increase the demand for iron-dependent enzymes, namely by replacing the glucose carbon source for acetate and by switching to a microaerobic atmosphere, we can reduce background growth even further. Finally, we demonstrate that by adding an exogeneous siderophore to the growth media which is poorly used by E. coli, we can completely prevent growth, perhaps mimicking situation in host tissue. In conclusion, this short study provides practical experimental insight into low iron media and how to augment the growth conditions of E. coli for extreme iron-limited growth.
An Evaluation of ChatGPT and Bard (Gemini) in the Context of Biological Knowledge Retrieval
Authors: Caspi Ron , Karp Peter D.
Published: April 2024

ChatGPT and Bard (now called Gemini), two conversational AI models developed by OpenAI and Google AI, respectively, have garnered considerable attention for their ability to engage in natural language conversations and perform various language-related tasks. While the versatility of these chatbots in generating text and simulating human-like conversations is undeniable, we wanted to evaluate their effectiveness in retrieving biological knowledge for curation and research purposes. To do so we asked each chatbot a series of questions and scored their answers based on their quality.  Out of a maximal score of 24, ChatGPT scored 5 and Bard scored 13. The encountered issues included missing information, incorrect answers, and instances where responses combine accurate and inaccurate details. Notably, both tools tend to fabricate references to scientific papers, undermining their usability.
In light of these findings, we recommend that biologists continue to rely on traditional sources while periodically assessing the reliability of ChatGPT and Bard. As ChatGPT aptly suggested, for specific and up-to-date scientific information, established scientific journals, databases, and subject-matter experts remain the preferred avenues for trustworthy data.
Multiomics analyses decipher intricate changes in the cellular and metabolic landscape of steatotic livers upon dietary restriction and sleeve gastrectomy
Authors: Chen Shuai , Zeng Qinghe , Cai Xiurong , Xue Jiaming , Song Peng , Tang Liming , Klein Christophe , Tacke Frank , Guillot Adrien , Liu Hanyang
Published: April 2024

Metabolic dysfunction-associated steatotic liver disease (MASLD) is a chronic, progressive liver disease that encompasses a spectrum of steatosis, steatohepatitis (or MASH), and fibrosis. Evidence suggests that dietary restriction (DR) and sleeve gastrectomy (SG) can lead to remission of hepatic steatosis and inflammation through weight loss, but it is unclear whether these procedures induce distinct metabolic or immunological changes in MASLD livers. This study aims to elucidate the intricate hepatic changes following DR, SG or sham surgery in rats fed a high-fat diet as a model of obesity-related MASLD, in comparison to a clinical cohort of patients undergoing SG. Single-cell and single-nuclei transcriptome analysis, spatial metabolomics, and immunohistochemistry revealed the liver landscape, while circulating biomarkers were measured in serum samples. Artificial intelligence (AI)-assisted image analysis characterized the spatial distribution of hepatocytes, myeloid cells and lymphocytes. In patients and experimental MASLD rats, SG improved BMI, circulating liver injury biomarkers and triglyceride levels. Both DR and SG attenuated liver steatosis and fibrosis in rats. Metabolism-related genes (Ppara,Cyp2e1andCyp7a1) were upregulated in hepatocytes upon DR and SG, while SG broadly upregulated lipid metabolism on cholangiocytes, monocytes, macrophages, and neutrophils. Furthermore, SG promoted myeloid cell accumulation in the liver not only ameliorating inflammation but activating liver repair processes. Regions with potent myeloid infiltration were marked with enhanced metabolic capacities upon SG. Additionally, a disruption of periportal hepatocyte functions was observed upon DR. In conclusion, this study indicates a dynamic cellular crosstalk in steatotic livers undergoing SG. Notably, PPARα- and gut-liver axis-related processes, and metabolically-active myeloid cell infiltration indicate intervention-related mechanisms supporting SG for the treatment of MASLD.
β-glucan induced trained immunity enhances antibody levels in a vaccination model in mice
Authors: Ajit Jainu , Chen Qing , Ung Trevor , Rosenberger Matthew , Kim Jeremiah , Solanki Ani , Shen Jingjing , Esser Kahn Aaron P.
Published: April 2024

Trained immunity improves disease resistance by strengthening our first line of defense, the innate immune system. Innate immune cells, predominantly macrophages, are epigenetically and metabolically rewired by β-glucan, a fungal cell wall component, to induce trained immunity. These trained macrophages exhibit increased co-stimulatory marker expression and altered cytokine production. Signaling changes from antigen-presenting cells, including macrophages, polarize T-cell responses. Recent work has shown that trained immunity can generally enhance protection against infection, and some work has shown increased protection with specific vaccines. It has been hypothesized that the trained cells themselves potentially modulate adaptive immunity in the context of vaccines. However, the mechanistic link between trained immunity on subsequent vaccinations to enhance antibody levels has not yet been identified. We report that trained immunity induced by a single dose of β-glucan increased antigen presentation in bone-marrow-derived macrophages (BMDMs) and CD4+T cell proliferationin-vitro. Mice trained with a single dose of β-glucan a week before vaccination elicited higher antigen-specific antibody levels than untrained mice. Further experiments validate that macrophages mediate this increase. This effect persisted even after vaccinations with 100 times less antigen in trained mice. We report β-glucan training as a novel prophylactic method to enhance the effect of subsequent vaccines.
Harnessing full-text publications for deep insights intoC. elegansandDrosophilaconnectomes
Authors: Arulprakasam Karthick Raja , Toh Janelle Wing Shan , Foo Herman , Kumar Mani R , Kutevska An-Nikol , Davey Emilia Emmanuelle , Mutwil Marek , Thibault Guillaume
Published: April 2024

In the rapidly expanding domain of scientific research, tracking and synthesizing information from the rapidly increasing volume of publications pose significant challenges. To address this, we introduce a novel high-throughput pipeline that employs ChatGPT to systematically extract and analyze connectivity information from the full-texts and abstracts of 24,237 and 150,538 research publications concerningCaenorhabditis elegansandDrosophila melanogaster, respectively. This approach has effectively identified 200,219 and 1,194,587 interactions within theC. elegansandDrosophilaconnectomes, respectively. Utilizing Cytoscape Web, we have developed comprehensive, searchable online connectomes that link relevant keywords to their corresponding PubMed IDs, thus providing seamless access to an extensive knowledge network encompassingC. elegansandDrosophila. Our work highlights the transformative potential of integrating artificial intelligence with bioinformatics to deepen our understanding of complex biological systems. By revealing the intricate web of relationships among key entities inC. elegansandDrosophila, we offer invaluable insights that promise to propel advancements in genetics, developmental biology, neuroscience, longevity, and beyond. We also provide details and discuss significant nodes within both connectomes, including the insulin/IGF-1 signaling (IIS) and the notch pathways. Our innovative methodology sets a robust foundation for future research aimed at unravelling complex biological networks across diverse organisms.
Effects of abiotic and biotic drivers on tadpoles in seasonal rock pools of Western Ghats rock outcrops, India
Authors: Jithin Vijayan , Naniwadekar Rohit
Published: April 2024

We assessed the influence of abiotic (pool size, monsoon progression) and biotic (predator abundances) factors on occurrence and abundance of three species of tadpoles by periodically monitoring rock pools in lateritic plateaus. Tadpole responses were positively associated with rock pool size and monsoon progression negatively, but not with predator abundance.
Microsaccade Selectivity as Discriminative Feature for Object Decoding
Authors: Nouri Salar , Tehrani Amirali Soltani , Faridani Niloufar , Toosi Ramin , Noroozi Jalaledin , Dehaqani Mohammad-Reza A.
Published: April 2024

Microsaccades, a form of fixational eye movements, maintain visual stability during stationary observations. Previous studies have provided valuable insights into the relationship between microsaccade characteristics and external stimuli. However, the dynamic nature of microsaccades provides an opportunity to explore the mechanisms of information processing, particularly object decoding. This study examines the modulation of microsaccadic rates by different stimulus categories. Our experimental approach involves an analysis of microsaccade characteristics in monkeys and human subjects engaged in a passive viewing task. The stimulus categories comprised four primary categories: human, animal, natural, and man-made. We identified distinct microsaccade patterns across different stimulus categories, successfully decoding the stimulus category based on the microsaccade rate post-stimulus distribution. Our experiments demonstrate that stimulus categories can be classified with an average accuracy and recall of up to 85%. Our study found that microsaccade rates are independent of pupil size changes. Neural data showed that category classification in the inferior temporal (IT) cortex peaks earlier than microsaccade rates, suggesting a feedback mechanism from the IT cortex that influences eye movements after stimulus discrimination. These results exhibit potential for advancing neurobiological models, developing more effective human-machine interfaces, optimizing visual stimuli in experimental designs, and expanding our understanding of the capability of microsaccades as a feature for object decoding.
Influence of advanced footwear technology spikes on middle- and long-distance running performance measures in trained runners
Authors: Rodrigo-Carranza Víctor , Muñoz de la Cruz Violeta , Hoogkamer Wouter
Published: April 2024

Two types of track spikes are commonly used, recently: spikes with a compliant and resilient midsole foam (e.g., PEBA), and spikes that combine such modern foam with a carbon fiber plate. Here we evaluated the effect of these different spike technologies on running performance measures for middle- and long-distance track events in trained runners. Fourteen females performed a single visit with six 200m trials at self-perceived 800m race pace in three different spike conditions (Control, PEBA and PEBA+Plate) twice in a mirrored order. Sixteen males completed four visits. During the first three visits they performed six 200m trials at self-perceived 800m race pace, twice in each condition. Subsequently, they performed a 3,000m time trial in one of the three spike conditions. During visit four, participants completed six 4-minute running economy trials at 5 m/s, twice in each condition. At 800m race pace females ran faster in PEBA (2.1%) and PEBA+Plate (2.0%) compared to Control. Males ran faster in PEBA (1.4%) and PEBA+Plate (2.4%) compared to Control, and in PEBA+Plate compared to PEBA (1.1%). Similarly, males ran the 3,000m time trial faster in PEBA (1.0%) and PEBA+Plate (2.4%) than in Control. Running economy was better in PEBA (5.1%) and PEBA+Plate (4.0%) than in Control. Performance benefits from modern foam spikes with and without a plate are equivalent for female middle-distance running, and for male long-distance running, but larger from modern foam spikes with a plate for male middle-distance running.
T follicular helper cell profiles differ by malaria antigen and for children compared to adults
Authors: Forconi Catherine S. , Nixon Christina , Wu Hannah W. , Odwar Boaz , Pond-Tor Sunthorn , Ong’echa John M. , Kurtis Jonathan , Moormann Ann M.
Published: April 2024

Background

Circulating T-follicular helper (cTFH) cells have the potential to provide an additional correlate of protection againstPlasmodium falciparum(Pf)as they are essential to promote B-cell production of long-lasting antibodies. Assessing the specificity of cTFHsubsets to individual malaria antigens is vital to understanding the variation observed in antibody responses and identifying promising malaria vaccine candidates.

Methods

Using spectral flow cytometry and unbiased clustering analysis, we assessed antigen-specific cTFHcell recall responsesin vitroto malaria vaccine candidatesPf-schizont egress antigen-1 (PfSEA-1A) andPf-glutamic acid-rich protein (PfGARP) within a cross-section of children and adults living in a malaria-holoendemic region of western Kenya.

Findings

In children, a broad array of cTFHsubsets (defined by cytokine and transcription factor expression) were reactive to both malaria antigens,PfSEA-1A andPfGARP, while adults had a narrow profile centering on cTFH17- and cTFH1/17-like subsets following stimulation withPfGARP only.

Interpretation

Because TFH17 cells are involved in the maintenance of memory antibody responses within the context of parasitic infections, our results suggest thatPfGARP might generate longer-lived antibody responses compared toPfSEA-1A. These findings have intriguing implications for evaluating malaria vaccine candidates as they highlight the importance of including cTFHprofiles when assessing interdependent correlates of protective immunity.
Label-free structural imaging of plant roots and microbes using third-harmonic generation microscopy
Authors: Pan Daisong , Rivera Jose A. , Kim Peter , Miao Max , Tyml Tomáš , Rodríguez Cristina , Wang Bing , Yoshikuni Yasuo , Elisabeth Nathalie H. , Northen Trent , Vogel John P. , Ji Na
Published: April 2024

Root biology is pivotal in addressing global challenges including sustainable agriculture and climate change. However, roots have been relatively understudied among plant organs, partly due to the difficulties in imaging root structures in their natural environment. Here we used microfabricated ecosystems (EcoFABs) to establish growing environments with optical access and employed nonlinear multimodal microscopy of third-harmonic generation (THG) and three-photon fluorescence (3PF) to achieve label-free,in situimaging of live roots and microbes at high spatiotemporal resolution. THG enabled us to observe key plant root structures including the vasculature, Casparian strips, dividing meristematic cells, and root cap cells, as well as subcellular features including nuclear envelopes, nucleoli, starch granules, and putative stress granules. THG from the cell walls of bacteria and fungi also provides label-free contrast for visualizing these microbes in the root rhizosphere. With simultaneously recorded 3PF fluorescence signal, we demonstrated our ability to investigate root-microbe interactions by achieving single-bacterium tracking and subcellular imaging of fungal spores and hyphae in the rhizosphere.
A transcriptome atlas of zygotic and somatic embryogenesis in Norway spruce
Authors: Stojkovič Katja , Canovi Camilla , Le Kim-Cuong , Delhomme Nicolas , Egertsdotter Ulrika , Street Nathaniel R.
Published: April 2024

Somatic embryogenesis (SE) is a powerful model system for studying embryo development and an important method for scaling up availability of elite and climate-adapted genetic material of Norway spruce (Picea abiesL. Karst). However, there are several steps during the development of the somatic embryo (Sem) that are suboptimal compared to zygotic embryo (Zem) development. These differences are poorly understood and result in substantial yield losses during plant production, which limits cost-effective large-scale production of SE plants. This study presents a comprehensive data resource profiling gene expression during zygotic and somatic embryo development to support studies aiming to advance understanding of gene regulatory programmes controlling embryo development. Transcriptome expression patterns were analysed during zygotic embryogenesis (ZE) in Norway spruce, including separated samples of the female gametophytes and Zem and at multiple stages during SE. Expression data from eight developmental stages of SE, starting with pro-embryogenic masses (PEMs) up until germination, revealed extensive modulation of the transcriptome between the early and mid-stage maturing embryos and at the transition of desiccated embryos to germination. Comparative analysis of ZE and SE identified differences in timing relative to SE development and functional enrichment of these provided insight into the associated biological processes. Orthologs of transcription factors known to regulate embryo development in angiosperms were differentially expressed during Zem and Sem development and in the different zygotic embryo tissues, providing clues to the differences in development observed between Zem and Sem. This resource represents the most comprehensive dataset available for exploring embryo development in conifers.

Significance Statement

Somatic embryogenesis is used as a model system to study embryo development, however detailed information to verify similarities and explain differences between somatic and zygotic embryogenesis is largely missing for conifers. This data resource provides sequential mRNA transcriptome data from nine stages of conifer zygotic embryo and female gametophyte development, and eight stages of somatic embryo development, to enable exploration of biological questions and comparisons of the two developmental processes.
Elucidating human gut microbiota interactions that robustly inhibit diverse Clostridioides difficile strains across different nutrient landscapes
Authors: Sulaiman Jordy , Thompson Jaron , Qian Yili , Vivas Eugenio , Diener Christian , Gibbons Sean M , Safdar Nasia , Venturelli Ophelia S
Published: April 2024

The human gut pathogen Clostridioides difficile displays extreme genetic variability and confronts a changeable nutrient landscape in the gut. We mapped gut microbiota inter-species interactions impacting the growth and toxin production of diverse C. difficile strains in different nutrient environments. Although negative interactions impacting C. difficile are prevalent in environments promoting resource competition, they are sparse in an environment containing C. difficile-preferred carbohydrates. C. difficile strains display differences in interactions with Clostridium scindens and the ability to compete for proline. C. difficile toxin production displays substantial community-context dependent variation and does not trend with growth-mediated inter-species interactions. C. difficile shows substantial differences in transcriptional profiles in the presence of the closely related species C. hiranonis or C. scindens. In co-culture with C. hiranonis, C. difficile exhibits massive alterations in metabolism and other cellular processes, consistent with their high metabolic overlap. Further, Clostridium hiranonis inhibits the growth and toxin production of diverse C. difficile strains across different nutrient environments and ameliorates the disease severity of a C. difficile challenge in a murine model. In sum, strain-level variability and nutrient environments are major variables shaping gut microbiota interactions with C. difficile.