bluuebunny/crossref_metadata_2025 huggingface dataset:
Smoking and Risks Contributing to COVID-19 Hospitalization in Washoe County, Nevada, 2020-2021
Authors: Williams Danika M. , Lu Minggen , Weber Ann M. , Cook Daniel M. , Wang Lingchen , Yang Wei
Published: January 2025

Objectives:

To investigate the association between smoking behavior and COVID-19 hospitalization, integrating individual and regional factors such as community resilience and social determinants of health (SDOH), addressing gaps in existing research.

Design:

Retrospective cohort study utilizing multilevel analytical methods to evaluate the effects of individual smoking status and regional SDOH on COVID-19 hospitalization.

Setting:

Washoe County, Nevada, during the first year of the COVID-19 pandemic (March 5, 2020, to April 30, 2021).

Participants:

All reported laboratory-positive COVID-19-infected adult residents of Washoe County collected by the Washoe County Health District through mandated disease surveillance for which smoking status was recorded, totaling 10,215 cases after data cleaning.

Main Outcome Measure:

Hospitalization among those with COVID-19 was the primary outcome measure, analyzed in relation to individual smoking status and zip code tabulation area (ZCTA)-level SDOH variables.

Results:

The analysis found that individuals infected with COVID-19 who currently and formerly smoked had significantly higher odds of hospitalization compared to those who never had smoked, with odds ratios adjusted for demographics and comorbidities. An increased odds of hospitalization among those with COVID-19 were associated with higher local unemployment, a significant ZCTA-level factor.

Conclusions:

Smoking may have increased the odds of hospitalization among those infected with COVID-19, as well as the socioeconomic factor of unemployment. The integration of SDOH into the assessment of health outcomes underscores the need for targeted public health interventions that address both individual behaviors and community-level factors. Future research should continue to explore these factors to inform more effective public health strategies and policy decisions.
Senility-Related Mortality in the United States During the COVID-19 Pandemic
Authors: Soin Sabrina , Mouhaffel Rama , Nhat Pham Hoang , Sainbayar Enkhtsogt , Abdelnabi Mahmoud , Ibrahim Ramzi
Published: January 2025

Context:

Senility has been shown to negatively impact health outcomes. While national stressors have altered death trajectories for numerous diseases, little is known about the impact of the COVID-19 pandemic on senility-related outcomes.

Objective:

To evaluate the impact of the COVID-19 pandemic on senility-related mortality in the United States.

Design, Setting, and Participants:

This is a retrospective analysis of US decedents with documented senility-related death using the CDC WONDER database. We estimated annual trends in senility-related age-adjusted mortality rates (AAMR) from 1999 to 2020 using log-linear regression models. Calculation of excess deaths attributable to the COVID-19 pandemic was completed by comparison of actual 2020 mortality rates and estimated 2020 mortality using average annual percentage changes.

Results:

A total of 510 819 senility-related deaths were identified. AAMR declined by 9.76%, from 7.48 in 1999 to 6.75 deaths per 100 000 in 2020. Year 2020 showed a marked increase in mortality, with 1.13 excess deaths per 100 000 population attributable to the COVID-19 pandemic. The COVID-19 pandemic contributed to an additional burden of mortality across both sexes, resulting in an estimated 1.18 and 0.99 per 100 000 excess deaths among females and males, respectively. The excess death rates per 100 000 for Black, White, Asian/Pacific Islander, and American Indian/Alaska Native populations were 1.84, 1.05, 0.99, and 1.16, respectively. The impact on US census regions was reflected in excess death rates, with the Northeastern, Midwestern, Southern, and Western regions seeing 1.27, 1.27, 1.39, and 0.31 excess deaths per 100 000, respectively.

Conclusions:

These findings suggest that the pandemic had an association with excess senility-related mortality. Further investigation is warranted to identify factors that impact senility-related outcomes.
Recent Advancements and Future Perspectives on Molecular Biomarkers in Adult Lower-Grade Gliomas
Authors: Fleming Jessica L. , Chakravarti Arnab
Published: January 2025

There has been a significant paradigm shift in the clinical management of lower-grade glioma patients given the recent updates to the 2021 World Health Organization classification along with long-term results from randomized phase III clinical trials. As a result, we are now better able to diagnose and assign patients to the most appropriate treatment course. This review provides a comprehensive summary of the most robust and reliable molecular biomarkers for adult lower-grade gliomas and discusses current challenges facing this patient population that future correlative biology studies combined with advancements in technologies could help overcome.
The Impact of International Fellowship on Research Productivity
Authors: James Andrew J. , Dean Yomna E. , Savitz Benjamin L. , Sullivan Lauren E. , Saad Mariam , Torres-Guzman Ricardo A. , Abbott Erin N. , Cornely Ronald M. , Gutama Barite W. , Alter Noah E. , Bhandari Panambur L.
Published: January 2025

International medical graduates (IMGs) represent a significant portion of the US physician workforce, comprising 25% across all specialties with a strong presence in internal medicine and primary care. However, their representation in plastic surgery remains limited at only 10%. Matching into a US plastic surgery residency is highly competitive for both US medical graduates and IMGs. This study aimed to quantify and identify trends in academic contributions from IMGs applicants in a plastic surgery residency program over the past 13 years, hypothesizing that IMG applicants have increasingly contributed to collaborative research projects.

Data from National Resident Matching Program annual reports were analyzed, focusing on publications, research experience, and match status. An analysis of variance revealed significant differences between US MDs and IMGs in terms of publications and research experience. IMGs had a higher number of publications and work experience compared to matched US MDs, while US MDs had more research experiences than IMGs.

The findings underscore the importance of research for IMGs, who often engage in additional research experiences to enhance their competitiveness for residency positions. The study showed that IMGs have a greater research output, contributing significantly to academic publications within the plastic surgery field. This productivity benefits the IMGs in securing residency positions and enriches the academic research environment of the residency programs.

IMGs bring unique perspectives and innovative approaches to research, often collaborating internationally, which enhances the scope and quality of research projects. Their contributions are vital to the advancement of plastic surgery and the broader medical field. As the demand for physicians in the US grows, integrating IMGs into the healthcare system through strategic inclusion in research and clinical training is essential. This study highlights the critical role of IMGs in driving medical research and underscores the need for supportive policies to facilitate their integration into the US healthcare workforce.
Early Cold Stored Platelet Transfusion Following Traumatic Brain Injury
Authors: Neal Matthew D. , Okonkwo David O. , Guyette Francis X. , Luther James F. , Vincent Laura E. , Puccio Ava M. , Harner Ashley M. , Agnone Allison G. , Brubaker Donovan P. , Love Emily T. , Leeper Christine M. , Brown Joshua B. , Forsythe Raquel , Spinella Philip C , Yazer Mark H. , Wisniewski Stephen R. , Sperry Jason L. ,   and the Cold Stored Platelet for Traumatic Brain Injury (CRISP-TBI) study group
Published: January 2025

Objective:

To determine the feasibility, efficacy, and safety of cold stored compared to room temperature platelet transfusion in patients with traumatic brain injury.

Summary Background Data:

Data demonstrating the safety and efficacy of cold stored platelet transfusion are lacking following traumatic brain injury.

Methods:

A phase 2, randomized, open label, clinical trial was performed at a single U.S. trauma center. Traumatic brain injured patients with positive brain imaging and a need for platelet transfusion received up to two apheresis units of cold stored platelets stored out to 14 days versus standard care room temperature platelet transfusion. The primary outcome was feasibility and the principal clinical outcome for efficacy and safety was the 6-month Glasgow Coma Scale-Extended score.

Results:

The 6-month Glasgow Outcome Scale-Extended score distributions were not different across cold stored and room temperature platelet arms (OR-1.58, 95%CI 0.71 to 3.54, P=0.27). A lower rate of neurosurgical craniotomy/craniectomy was found for those receiving cold stored platelets (difference -14.4%, 95%CI -26.5% to -2.3%, P=0.03). Adverse event rates did not differ across groups. The storage age of the cold stored product was not associated with outcome differences.

Conclusions and Relevance:

In brain injured patients requiring platelet transfusion, early cold stored platelet transfusion is feasible, and did not result in improved 6-month Glasgow Coma Scale-Extended scores. Early cold stored platelet transfusion was associated with a lower rate of neurosurgical operative intervention without an increase in adverse events. The storage age of the cold stored platelet product was not associated with outcome differences. Future phase 3 clinical trials are required to determine clinical outcome differences and safety attributable to cold stored platelet transfusion following traumatic brain injury.
Tracking individual seed fate confirms mainly antagonistic interactions between rodents and European beech
Authors: Sachser Frederik , Gratzer Georg , Pesendorfer Mario B. , Konrad Heino , Kempter Iris , Nopp-Mayr Ursula
Published: January 2025

Food-hoarding granivores act as both predators and dispersers of plant seeds, resulting in facultative species interactions along a mutualism–antagonism continuum. The position along this continuum is determined by the positive and negative interactions that vary with the ratio between seed availability and animal abundance, particularly for mast-seeding species with interannual variation and spatial synchrony of seed production. Empirical data on the entire fate of seeds up to germination and the influence of rodents on seed survival is rare, resulting in a lack of consensus on their position along the mutualism–antagonism continuum. Here, we quantified annual seed rain and rodent abundance in an old-growth European beech forest and tracked 639 beechnuts to the seedling stage with 84% of seeds successfully located. Over 4 study years that covered the range of seed-to-rodent ratios, not a single seed successfully germinated after dispersal, illustrating a predominantly antagonistic interaction between rodents and seeds of European beech. Therefore, our findings do not support the predator dispersal hypothesis and partially contradict the predator satiation hypothesis, as the highest number of germinants and intact seeds were found
in situ
after an intermediate seed crop, not a bumper crop. Our results underline the necessity to track seeds up to germination.
Hormetic response to pesticides in diapausing bees
Authors: Amsalem Etya , Derstine Nathan , Murray Cameron
Published: January 2025

Pollinators face declines and diversity loss associated with multiple stressors, particularly pesticides. Most pollination services are provided by annual bees that undergo winter diapause, and many common pesticides are highly soluble in water and move through soil and plants where bees hibernate and feed, yet the effects of pesticides on pollinators’ diapause survival and performance are poorly understood. Pesticides may have complex effects in bees, and some were shown to induce hormetic effects on various traits characterized by high-dose inhibition coupled with low-dose stimulation. Here, we examined the occurrence of hormesis in the responses of bees to imidacloprid. We found that while longevity and reproduction were reduced following exposure to imidacloprid, the survival length of new queens (gynes) was greater. Diapause is a critical period in the life cycle of most bees with profound effects on their health. Exposure to sublethal doses of pesticides may increase bees’ resistance to stress/cold during diapause but may also trade off with reduced reproductive performance later in life. Identifying these trade-offs is crucial to understanding how stressors affect pollinator health and should be accounted for when assessing pesticide risk, designing studies and facilitating conservation and management tools for supporting annual bees during diapause.
A minimal model of cognition based on oscillatory and current-based reinforcement processes
Authors: Gyllingberg Linnéa , Tian Yu , Sumpter David J. T.
Published: January 2025

Building mathematical models of brains is difficult because of the sheer complexity of the problem. One potential starting point is basal cognition, which gives an abstract representation of a range of organisms without central nervous systems, including fungi, slime moulds and bacteria. We propose one such model, demonstrating how a combination of oscillatory and current-based reinforcement processes can be used to couple resources in an efficient manner, mimicking the way these organisms function. A key ingredient in our model, not found in previous basal cognition models, is that we explicitly model oscillations in the number of particles (i.e. the nutrients, chemical signals or similar, which make up the biological system) and the flow of these particles within the modelled organisms. Using this approach, our model builds efficient solutions, provided the environmental oscillations are sufficiently out of phase. We further demonstrate that amplitude differences can promote efficient solutions and that the system is robust to frequency differences. In the context of these findings, we discuss connections between our model and basal cognition in biological systems and slime moulds, in particular, how oscillations might contribute to self-organized problem-solving by these organisms.
Buzz pollination: investigations of pollen expulsion using the discrete element method
Authors: Boucher-Bergstedt Caelen , Jankauski Mark , Johnson Erick
Published: January 2025

Buzz pollination involves the release of pollen from, primarily, poricidal anthers through vibrations generated by certain bee species. Despite previous experimental and numerical studies, the intricacies of pollen dynamics within vibrating anthers remain elusive due to the challenges in observing these small-scale, opaque systems. This research employs the discrete element method to simulate the pollen expulsion process in vibrating anthers. By exploring various frequencies and displacement amplitudes, a correlation between how aggressively the anther shakes and the initial rate of pollen expulsion is observed under translating oscillations. This study highlights that while increasing both the frequency and displacement of vibration enhances pollen release, the rate of release does not grow linearly with their increase. Our findings also reveal the significant role of pollen–pollen interactions, which account for upwards of one-third of the total collisions. Comparisons between two types of anther exits suggest that pore size and shape also influence expulsion rates. This research provides a foundation for more comprehensive models that can incorporate additional factors such as cohesion, adhesion and Coulomb forces, paving the way for deeper insights into the mechanics of buzz pollination and its variability across different anther types and vibration parameters.
Limiting and optimal Strouhal numbers or tip speed ratios for cruising propulsion by fins, flukes, wings and propellers
Authors: Usherwood James R.
Published: January 2025

Swimming and flying animals produce thrust with oscillating fins, flukes or wings. The relationship between frequency
f
, amplitude
A
and forward velocity
U
can be described with a Strouhal number
St
, where
St
= 2
fA
/
U
, where animals are observed to cruise with

S
t
≈
0.2

–0.4. Under these conditions, thrust is produced economically and a reverse von Kármán wake is observed. However, propeller-driven craft produce thrust with steadily revolving blades and a helical wake. Here, the simplified aerodynamic geometry of lift-based thrust production is described, applicable to both oscillating and revolving foils. The same geometric principles apply in both cases: if the foil moves too slowly, it cannot produce thrust; if it moves too fast, it produces thrust with excessive power demand. Effective, economic thrust production by animals is not the result of oscillating foils or cyclic vortex shedding; rather, the selection of amplitude and frequency, and wake vortex structure, are corollaries of driving an efficient foil velocity with finite amplitudes. Observed Strouhal numbers for cruising animals appear too low for optimal mechanical efficiency; however, the deviation from optimal efficiency may be small, and there are physical and physiological advantages to relatively low amplitudes and frequencies for swimming and flapping flight.
Enzymes enabling the biosynthesis of various C
20
polyunsaturated fatty acids in a sea urchin
Hemicentrotus pulcherrimus
Authors: Peng Yingying , Haga Yutaka , Kabeya Naoki
Published: January 2025

Sea urchins, integral to marine ecosystems and valued as a delicacy in Asia and Europe, contain physiologically important long-chain (>C
20
) polyunsaturated fatty acids (PUFA) in their gonads, including arachidonic acid (ARA, 20:4n-6), eicosapentaenoic acid (EPA, 20:5n-3) and unusual non-methylene-interrupted fatty acids (NMI-FA) such as 20:2
Δ5,11
. Although these fatty acids may partially be derived from their diet, such as macroalgae, the present study on
Hemicentrotus pulcherrimus
has uncovered multiple genes encoding enzymes involved in long-chain PUFA biosynthesis. Specifically, 3 fatty acid desaturases (FadsA, FadsC1 and FadsC2) and 13 elongation of very-long-chain fatty acids proteins (Elovl-like, Elovl1/7-like, Elovl2/5-like, Elovl4-like, Elovl8-like and Elovl6-like A–H) were identified in their genome and transcriptomes. Functional analysis showed that FadsA and FadsC2 function as a Δ5 desaturase and a Δ8 desaturase, respectively, enabling the conversion of 18:2n-6 and 18:3n-3 into ARA and EPA, respectively, along with Elovl, particularly Elovl6-like C. Elovl6-like C demonstrates elongase activity towards both C
18
PUFA and monounsaturated fatty acids. Consequently, FadsA and Elovl6-like C enable the synthesis of several NMI-FA, including 20:2
Δ5,11
and 20:3
Δ5,11,14
, from C
18
precursors. This indicates that
H. pulcherrimus
can endogenously synthesize a wide variety of C
20
PUFA and NMI-FA, highlighting active biosynthesis pathways within sea urchins.
The role of KLF4 in human primordial germ cell development
Authors: Lee Sun-Min , Smela Merrick Pierson , Surani M. Azim
Published: January 2025

Primordial germ cells (PGCs) are the founder cells that develop into mature gametes. PGCs emerge during weeks 2–3 of human embryo development. Pluripotency genes are reactivated during PGC specification, including Krüppel-like factor KLF4, but its precise role in PGC development is unclear. Here, we investigated the role of KLF4 in PGC development using our
in vitro
model for human PGC-like cells (hPGCLCs). We demonstrate that the depletion of KLF4 reduces the efficiency of hPGCLC specification, resulting in hPGCLCs with an aberrant transcriptome. Cut-and-run and transcriptomic analyses reveal that KLF4 represses somatic markers involved in neuronal and endodermal differentiation while promoting the expression of genes associated with PGC specification, such as
PAX5
, and epigenetic regulators, including
DNMT3L
and
REST
. KLF4 targets in hPGCLCs showed significant co-enrichment of motifs for SP and STAT factors, which are known to regulate cell cycle and migration genes. KLF4 contributes to human PGC development by activating genes involved in PGC specification and cell cycle regulation, while repressing somatic genes to maintain PGC identity.
Bioinformatic approach to explain how Mg from seawater may be incorporated into coral skeletons
Authors: Bell Tomoko , Iguchi Akira , Ohno Yoshikazu , Sakai Kazuhiko , Yokoyama Yusuke
Published: January 2025

Corals have been used as geochemical proxies since the 1970s, playing a prominent role in paleoceanography. However, it has not been well elucidated how aqueous ions sourced from seawater are transported and precipitated in coral skeletons. There are limited foundational methods to differentiate and quantify biogenic and abiogenic effects during skeletal formation. Especially, Mg in coral skeletons show individual variations suggesting large biogenic effects. Here, we evaluated biological complexity by investigating how coral genes evolved over geologic time scales. We focused on Mg transporter and analysed five species from genus
Acropora
and three species from genus
Porites
. Mg transporter of
Acropora digitifera
,
Acropora hyacinthus
,
Acropora millepora
and
Porites australiensis
showed higher similarity to Mg transporter of vertebrates and were reported to appear on Earth during the Pleistocene. On the other hand,
Acropora palmata
,
Acropora tenui
s and
Porites astreoides
showed lower or no similarity to vertebrates, and they were reported to appear on Earth before the Pleistocene. We suggest such evolutional records can be evidence to demonstrate biological complexity of Mg transport from seawater. This might explain that Mg transport is subject to evolution and why Mg incorporated in coral skeletons tends to show strong biogenic effects compared with other elements.
A new conceptual model for seed germination and seedling tillering of winter wheat in the field
Authors: Chen Jinping , Whalley Peter A. , Li Zhongyang , Zhang Xiaoxian , Hawkesford Malcolm J. , Whalley W. Richard
Published: January 2025

Seed germination is a crucial stage in plant development, intricately regulated by various environmental stimuli. Understanding these interactions is essential for optimizing planting and seedling management but remains challenging due to the trade-off effects of environmental factors on the germination process. We proposed a new conceptual model by viewing seed germination as a dynamic process in a physiological dimension, with the influence of environmental factors and seed heterogeneity characterized by a germination speed and a dispersion coefficient. To validate the model, we conducted field experiments by drilling wheat seeds at different dates to establish a temperature gradient and in different plots to create a soil water content gradient. Comparisons with our experimental data and literature results show the model accurately reproduces all germination patterns and the subsequent seedling tillering, with
R
2
 > 0.95. Our results reveal that within suboptimal temperature range, the seed germination increases asymptotically with temperature, and that as soil water content increases, the germination speed increases initially before decreasing, illustrating the trade-off effect of soil water on bioavailability of water and oxygen. Introducing a physiological dimension enables seed germination and the subsequent tillering process to be modelled as a continuous physiological process, providing deeper insight into plant growth dynamics.
SARS-CoV-2 transmission dynamics in Mozambique and Zimbabwe during the first 3 years of the pandemic
Authors: Kaondera-Shava Roselyn F. , Galanti Marta , Perini Matteo , Suh Jiyeon , Farley Shannon M. , Chicumbe Sergio , Jani Ilesh , Cassy Annette , Macicame Ivalda , Manafe Naisa , El-Sadr Wafaa , Shaman Jeffrey
Published: January 2025

The 2019 emergence of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and its rapid spread created a public health emergency of international concern. However, the impact of the pandemic in Sub-Saharan Africa, as documented in cases, hospitalizations and deaths, appears far lower than in the Americas, Europe and Asia. Characterization of the transmission dynamics is critical for understanding how SARS-CoV-2 spreads and the true scale of the pandemic. Here, to better understand SARS-CoV-2 transmission dynamics in two southern African countries, Mozambique and Zimbabwe, we developed a dynamic model-Bayesian inference system to estimate key epidemiological parameters, namely the transmission and ascertainment rates. Total infection burdens (reported and unreported) during the first 3 years of the pandemic were reconstructed using a model-inference approach. Transmission rates rose with each successive wave, which aligns with observations in other continents. Ascertainment rates were found to be low and consistent with other African countries. Overall, the estimated disease burden was higher than the documented cases, indicating a need for improved reporting and surveillance. These findings aid understanding of COVID-19 disease and respiratory virus transmission dynamics in two African countries little investigated to date and can help guide future public health planning and control strategies.
Maturing conditions of bimetallic nanocomposites as a new factor influencing Au–Ag synergism and impact of Cu(II) and/or Fe(III) on luminescence
Authors: Svačinová Veronika , Pluháček Tomáš , Petr Martin , Siskova Karolina
Published: January 2025

Gold–silver synergism has been well documented in many scientific works dealing with luminescent nanostructures that are exploitable in biomedical and environmental application. Frequently, the ratio of Au : Ag in synthetic mixtures was varied to influence the extent of Au–Ag synergism of the resulting luminescent gold–silver nanoclusters (GSNCs). However, in our approach, a new step, maturing under differing conditions using the same Au : Ag ratio (5 : 1), has been investigated systematically for the very first time. As referent systems, monometallic gold nanoclusters (AuNCs) and protein treated by the conditions of synthesis and maturing were prepared and investigated. The selected types of maturing conditions led to distinct changes in fluorescence characteristics and, consequently, Au–Ag synergism extent (evaluated as the ratio of fluorescence quantum yields of GSNCs versus AuNCs). The best synergism was obtained for GSNCs matured at 37°C for 2.5 h. The stability of luminescent signal of these GSNCs was tested in the presence of an excess (to 20 mM) of Cu(II) and/or Fe(III) ions (crucial cofactors in living systems). The same metallic ion concentration caused different extents of GSNC luminescence quenching, for which a plausible reasoning is suggested.
A competitive learning approach for specialized models: An approach to modelling complex physical systems with distinct functional regimes
Authors: Ukorigho O. F. , Owoyele O. O.
Published: January 2025

Complex systems in science and engineering sometimes exhibit behaviour that changes across different regimes. Traditional global models struggle to capture the full range of this complex behaviour, limiting their ability to accurately represent the system. In response to this challenge, we propose a competitive learning approach for obtaining localized data-based models of physical systems. The primary idea behind the proposed approach is to employ dynamic loss functions for a set of models that are trained concurrently on the data. Each model competes for each observation during training, allowing for the identification of distinct functional regimes within the dataset. To demonstrate the effectiveness of the learning approach, we coupled it with various regression methods that employ gradient-based optimizers for training. The proposed approach was tested on various problems involving model discovery and function approximation, demonstrating its ability to successfully identify functional regimes, discover true governing equations and reduce test errors.
Symplectic contact analysis of a finite-sized horizontally graded magneto-electro-elastic plane
Authors: Chen Lizichen , Chen Weiqiu
Published: January 2025

Material characterization using high-throughput testing (HTT) techniques has shown great promise in expediting the advancement of high-performance materials. A key step in HTT is the adoption of functionally graded specimens, whose material inhomogeneity, however, imposes a great challenge for analytically evaluating its responsive behaviour under external loads. This work establishes the first symplectic framework for contact analysis of a finite-sized magneto-electro-elastic plane with an exponential material gradient along the horizontal direction. The governing equations are first represented in matrix form in a state space, with the full state vector defined and the operator matrix derived. The operator matrix is found to be distinct from the Hamiltonian operator matrix in the case of a homogeneous medium. With all the eigen-solutions obtained, the Hamiltonian mixed energy variational principle is then introduced to derive the coefficients in the symplectic expansion. The developed analytical solution not only exhibits asymmetry properties but also converges rapidly. The analytical results are validated through comparison with the finite element simulations. The analytical platform established here would work as an effective theoretical basis for the subsequent development of quantitative HTT techniques.
A revision of the NeotropicalCostaceae: results from sixty years of taxonomic struggle
Authors: Maas P.J.M. , Maas-van de Kamer H. , André T. , Skinner D. , Valderrama E. , Specht C.D.
Published: January 2025

Here we present a taxonomic revision of all neotropicalCostaceaerepresented by 90 species, distributed in four monophyletic genera,Chamaecostus(9 spp.),Costus(76 spp.),Dimerocostus(5 spp.), andMonocostus(1 sp.). The work resulted in three new combinations, several nomenclatural changes, and four insufficiently known species are mentioned to demonstrate the need for continued and ongoing work on this charismatic yet often cryptic lineage of plants. We highlight the seventeen species ofCostusand one species ofChamaecostusthat were recently described (Maas et al. 2023) based on knowledge that emerged during this complete revisionary work, 60 years in the making. Included in this revision are details concerning the morphology, distribution, ecology, and phylogenetic relationships among the species studied. All currently recognized species are fully described, including notes on taxonomic synonymy, lectotypification, information on distribution and ecology, conservation status (either as evaluated and published in the IUCN Red List of Threatened Species or as estimated for this publication), vernacular names (when given) and short taxonomic notes. For each species, a distribution map is prepared and at least one colour photograph is included to assist in species identification. Dichotomous keys that include all species are provided, as is a list of all (c. 11.000) exsiccatae studied and an index to scientific names.
Natural Anti-NMDAR1 Autoantibodies Associate with Slowed Decline of Cognitive Functions in Alzheimer’s Diseases
Authors: Zhou Xianjin
Published: January 2025

Anti-NMDAR1 autoantibodies can bind NMDA receptors to suppress glutamate excitotoxicity in the brain. Low titers of blood circulating natural anti-NMDAR1 autoantibodies were reported in ∼10% of the general human population. We developed a new method to more accurately quantify these low titers of natural anti-NMDAR1 autoantibodies. After quantifying natural anti-NMDAR1 autoantibodies in the plasma of 324 age– and sex-matched subjects (163 healthy controls; 161 Alzheimer’s disease (AD) patients), I found that AD patients carrying higher levels of natural anti-NMDAR1 autoantibodies have significantly (p value: 0.003) higher scores of Mini-Mental State Examination (MMSE score: 23.5) than AD patients carrying lower levels of natural anti-NMDAR1 autoantibodies (MMSE score: 21.4). No significant differences in MMSE scores were however found between healthy controls with either higher or lower levels of natural anti-NMDAR1 autoantibodies, indicating little harmful effect of the autoantibodies. Consistently, superior cognitive performances were found in AD patients carrying higher levels of natural anti-NMDAR1 autoantibodies in comparison with AD patients carrying lower levels of the autoantibodies. These data suggest that natural anti-NMDAR1 autoantibodies may have neuroprotective effects against cognitive decline in AD patients.
Hard-to-sample species are more sensitive to land-use change: implications for global biodiversity metrics
Authors: Gutiérrez-Arellano Claudia , Newbold Tim , Hodgson Jenny A.
Published: January 2025

Land-use change drives biodiversity loss, but some species suffer more than others. Indicators of global biodiversity change must attempt to summarise these impacts representatively and meaningfully, to guide biodiversity recovery. Yet species that are hard to detect, and thus feature less in relevant databases, might possess traits that make them particularly sensitive to anthropogenic impacts. Using global data for plant, bird, and spider species, we develop a statistical approach to analyse and correct for the impact of excluding hard-to-sample species from global biodiversity indicators. Based on over 4000 species with abundance comparisons available, we found that species with fewer global occurrence records consistently decline more as land-use intensity increases, suggesting that hard-to-sample species are particularly sensitive to land-use differences. When we extrapolate this relationship to all plant, bird and spider species with valid occurrence records (0.27 M species), we obtain a more representative global indicator of overall land-use impacts for these entire taxonomic groups. Our estimates indicate a lower average abundance in anthropogenic land uses compared to results obtained when hard-to-sample species are excluded. For example, intensive agriculture only has 18% of the biodiversity level of primary vegetation, rather than the 47% estimated without extrapolation. We recommend that other existing indicators include an extrapolation solution based on ours, to incorporate the available data as effectively as possible. Using occurrence data to predict species’ sensitivity unlocks many possibilities to improve global biodiversity indicators, without demanding additional data on poorly known species.
Distinct cell types along thick ascending limb express pathways for monovalent and divalent cation transport
Authors: Demirci Hasan , Bahena-Lopez Jessica , Smorodchenko Alina , Su Xiao-Tong , Nelson Jonathan , Yang Chao-Ling , Curry Joshua , Duan Xin-Peng , Wang Wen-Hui , Sharkovska Yuliya , Liu Ruisheng , Yilmaz Duygu Elif , Quintanova Catarina , Emberly Katie , Emery Ben , Himmerkus Nina , Bleich Markus , Ellison David H. , Bachmann Sebastian
Published: January 2025

Kidney thick ascending limb cells reabsorb sodium, potassium, calcium, and magnesium and contribute to urinary concentration. These cells are typically viewed as of a single type that recycles potassium across the apical membrane and generates a lumen-positive transepithelial voltage driving calcium and magnesium reabsorption, although variability in potassium channel expression has been reported. Additionally, recent transcriptomic analyses suggest that different cell types exist along this segment, but classifications have varied and have not led to a new consensus model. We used immunolocalization, electrophysiology and enriched single nucleus RNA-Seq to identify thick ascending limb cell types in rat, mouse and human. We identified three major TAL cell types defined by expression of potassium channels and claudins. One has apical potassium channels, low basolateral potassium conductance, and is bordered by a sodium-permeable claudin. A second lacks apical potassium channels, has high basolateral potassium conductance and is bordered by calcium- and magnesium-permeable claudins. A third type also lacks apical potassium channels and has a high basolateral potassium conductance, but these cells are ringed by sodium-permeable claudins. The recognition of diverse cell types resolves longstanding questions about how solute transport can be modulated selectively and how disruption of these cells leads to human disease.
Effect of aging, endurance training, and denervation on innate immune signaling in skeletal muscle
Authors: Khemraj Priyanka , Kuznyetsova Anastasiya , Hood David A.
Published: January 2025

Skeletal muscle function relies on mitochondria for energy and for mediating its unique adaptive plasticity. The NLRP3 inflammasome complex is an innate immune mechanism that responds to mitochondrial damage-associated molecular patterns (DAMPS), however its activity relative to mitochondrial dysfunction in muscle requires exploration. The purpose of this study was to characterize immune signaling and mitochondrial function in muscle during aging, endurance training, and disuse induced by denervation. Denervation led to decreases in muscle mass, mitochondrial content, and impaired respiration. Protein analyses revealed increases in NF-κB p65 and downstream inflammatory markers including NLRP3, caspase-1, GSDMD-N, STING and IL-1β, along with pro-apoptotic BAX and AIF. When assessing potential DAMPS, denervation led to increased ROS production but no changes in cytosolic mtDNA levels, relative to total mtDNA. Since we hypothesized that inflammasome activation would be increased with age, we studied young (6-8 months) and aged (21-22 months) mice that remained sedentary or underwent a 6-week voluntary running protocol. Aging resulted in marked increases in the expression of multiple pro-inflammatory and pro-apoptotic proteins. Remarkably, training uniformly attenuated age-related increases in BAX, NLRP3, caspase-1, STING, and GSDMD protein expression, and reduced the elevated level of cytosolic mtDNA evident in aged muscle. Training adaptations were evident also in the aged animals by the preservation of muscle mass and improvements in oxygen consumption and endurance performance and were achieved despite a lower training distance than in young animals. Our results strongly implicate endurance training as a promising therapeutic for combatting disuse and age-related inflammation in skeletal muscle.
Pretransplant targeting of TNFRSF25 and CD25 stimulates recipient Tregs in target tissues ameliorating GVHD post-HSCT
Authors: McManus Duneia , Copsel Sabrina N. , Pffeifer Brent J. , Wolf Dietlinde , Barreras Henry , Ma Symon , Khodor Ali , Komai Seitaro , Burgos da Silva Marina , Hazime Hajar , Gallardo Miguel , van den Brink Marcel RM , Abreu Maria T. , Hill Geoffrey R. , Perez Victor L. , Levy Robert B.
Published: January 2025

The current approach to minimize transplant-associated complications, including graft-versus-host disease (GVHD) includes long-term pharmacological immune suppression frequently accompanied by unwanted side effects. Advances in targeted immunotherapies regulating alloantigen responses in the recipient continue to reduce the need for pan-immunosuppression. Here, in vivo targeting of the TNF superfamily receptor 25 (TNFRSF25) and the high affinity IL-2 receptor with a TL1A-Ig fusion protein and low dose IL-2, respectively, was used to pretreat recipient mice prior to allogeneic-HSCT (aHSCT). Pretreatment induced Treg expansion persisting early post-aHSCT leading to diminished GVHD and improved transplant outcomes. Expansion was accompanied by an increase in frequency of stable and functionally active Tregs as evidenced byin vitroassays using cells from major GVHD target tissues including colon, liver, and eye. Importantly, pretreatment supported epithelial cell function/integrity, a diverse microbiome including reduction of pathologic bacteria overgrowth and promotion of butyrate producing bacteria, while maintaining physiologic levels of obligate/facultative anaerobes. Notably, using a sphingosine 1-phosphate receptor agonist to sequester T cells in lymphoid tissues, we found that the increased tissue Treg frequency included resident CD69+CD103+FoxP3+hepatic Tregs. In contrast to infusion of donor Treg cells, the strategy developed here resulted in the presence of immunosuppressive target tissue environments in the recipient prior to the receipt of donor allo-reactive T cells and successful perseveration of GVL responses. We posit strategies that circumvent the need of producing large numbers ofex-vivomanipulated Tregs, may be accomplished throughin vivorecipient Treg expansion, providing translational approaches to improve aHSCT outcomes.

Graphical Abstract
Quantification of the volume of swallowed air in the gut finds low volumes when asleep may reduce aerobic digestion and explain why short dinner to sleep times are associated with nocturnal reflux
Authors: Hurr Thomas
Published: January 2025

It has been previously reported that air swallowing and breathing exercises could reduce the severity of digestive reflux by supplying oxygen directly to the gut lumen and supporting aerobic digestion, however the normal volume of air swallowed over 24 hours has not been determined. To determine the volume of air swallowed over 24 hours, the number of swallows during eating, drinking and snacks (EDS), asleep, at other times awake (OTA) and the volume of air swallowed per bolus were sought from the literature. Four models were developed to determine the volume of air swallowed per bolus, finding volumes between 0 ml and an average maximum pharyngeal volume of 40 ml were possible, with an average and range of values ≈ 11(1.7-32) ml. From a literature search, the number of swallows over 24 hours determined using a microphone, was found to be the most complete set of data to calculate the volumes of air swallowed while EDS, asleep and OTA. There was on average during EDS ≈ 31 ml air swallowed per minute, when asleep ≈ 1 ml air swallowed per minute and at OTA ≈ 4.3 ml air swallowed per minute giving a total air swallow volume of ≈ 6,400(320-47,000) ml air over 24 hours. The volume of the gases contained in swallowed air were also calculated as nitrogen ≈ 5000 ml, oxygen ≈ 1000 ml and noting swallowed air is expired air from the lungs, carbon dioxide ≈ 320 ml over 24 hours. If improved aerobic digestion reduced the probability of digestive reflux and was related to the volume of air swallowed, then digestive reflux would be least likely to occur during EDS, with the highest air swallow rate, followed by OTA and most likely to occur when asleep, when the lowest volume of air is swallowed. The volume of air swallowed over 24 hours was equivalent to only one or two minutes of breathing at ≈ 6,000 ml per minute for an adult at rest. It is still not clear whether luminal oxygen supply from air swallowing, or luminal (and systemic) oxygen supply from breathing, is the major source of oxygen supply to the gut lumen for aerobic digestion, however if air swallowing is the major source of luminal oxygen supply, then air swallowing is likely an important factor for digestive health.

Graphical Abstract

The low volumes of air swallowed during sleep may reduce aerobic digestion and explain why eating, drinking and snacks less than 3 hours before sleep have been associated with an increased probability of gastric /digestive reflux.

The volume of air swallowed per 24 hours is equivalent to only 1-2 minute of breathing at 6,000 ml per minute for an adult at rest.

Air swallowing link to reflux diseases [8], air swallow volume per bolus [9-14], rates of swallowing per 24 hours [16] breathing air volumes [35], increased reflux less than 3 hours dinner to sleep [38].
Zero-Shot, Big-Shot, Active-Shot - How to estimate cell confluence, lazily
Authors: Joas Maximilian , Freund Daniel , Haase Robert , Rahm Erhard , Ewald Jan
Published: January 2025

Mesenchymal stem cell therapy shows promising results for difficult-to-treat diseases, but standardized manufacturing requires robust quality control through automated cell confluence monitoring. While deep learning can automate confluence estimation, research on cost-effective dataset curation and the role of foundation models in this task remains limited. We systematically investigate the most effective strategies for confluence estimation, focusing on active learning-based dataset curation, goal-specific labeling, and leveraging foundation models for zero-shot inference. Here, we show that zero-shot inference with the Segment Anything Model (SAM) achieves excellent confluence estimation without any task-specific training, outperforming fine-tuned smaller models. Further, our findings demonstrate that active learning does not significantly improve model dataset curation compared to random selection in homogeneous cell datasets. We show that goal-specific, simplified labeling strategies perform comparably to precise annotations while substantially reducing annotation effort. These results challenge common assumptions about dataset curation: neither active learning nor extensive fine-tuning provided significant benefits for our specific use case. Instead, we found that leveraging SAM’s zero-shot capabilities and targeted labeling strategies offers the most cost-effective approach to automated confluence estimation. Our work provides practical guidelines for implementing automated cell monitoring in MSC manufacturing, demonstrating that extensive dataset curation may be unnecessary when foundation models can effectively handle the task out of the box.
An accessible metagenomic strategy allows for better characterization of invertebrate bulk samples
Authors: Callens Martijn , Le Berre Guillaume , Van den Bulcke Laure , Lolivier Marianne , Derycke Sofie
Published: January 2025

DNA-based techniques are a popular approach for assessing biodiversity in ecological research, especially for organisms which are difficult to detect or identify morphologically. Metabarcoding, the most established method for determining species composition and relative abundance in bulk samples, can be more sensitive and time- and cost effective than traditional morphological approaches. However, one drawback of this method is PCR bias caused by between-species variation in the amplification efficiency of a marker gene. Metagenomics, bypassing PCR amplification, has been proposed as an alternative to overcome this bias. Several studies have already shown the promising potential of metagenomics, but they all indicate the unavailability of reference genomes for most species in any ecosystem as one of the primary bottlenecks preventing its wider implementation. In this study, we present a strategy that uses unassembled reads of low-coverage whole genome sequencing to construct a genomic reference database, thus circumventing high sequencing costs and intensive bioinformatic processing. We show that this approach is superior to metabarcoding for approximating relative biomass of macrobenthos species from bulk samples. Furthermore, these results can be obtained with a sequencing effort comparable to metabarcoding. The strategy presented here can thus accelerate the implementation of metagenomics in biodiversity assessments, as it should be relatively easy to adopt by laboratories familiar with metabarcoding and can be used as an accessible alternative.