bluuebunny/crossref_metadata_2025 huggingface dataset:
Comparison of Transepidermal Water Loss in Preterm Newborns Treated with Two Different Types of Phototherapies
Authors: Aydin Meryem , Balci Serap
Published: November 2024

Objective

To compare transepidermal water loss (TEWL) in preterm newborns treated with two different types of phototherapies.

Methods

In this experimental randomized controlled study, participants were 60 preterm infants aged 30 to 36 weeks’ gestation who were admitted to the neonatal ICU of Duzce University Research and Application Center from December 2015 to May 2016. Researchers randomly assigned the newborns to two phototherapy groups: light-emitting diode (LED) and fluorescent phototherapy. Each group included 30 participants. Data were collected using a demographic information form and an evaporimeter to measure TEWL levels.

Results

Prior to phototherapy, the anterior region TEWL values were 11.99 ± 3.04 and 11.56 ± 3.99 g/m2 per hour in the fluorescent and LED groups, respectively, and the posterior region TEWL values were 12.82 ± 3.94 and 12.42 ± 4.24 g/m2 per hour in the fluorescent and LED groups, respectively. Prior to phototherapy, anterior and posterior TEWL measurements did not differ either within or between groups. However, in comparison with fluorescent group participants, participants in the LED group experienced significantly less water loss at 30 minutes and 1, 3, 6, 12, and 24 hours after the start of phototherapy (P < .001).

Conclusions

Fluorescent phototherapy causes more water loss than LED phototherapy in preterm infants, and TEWL values are similar in both anterior and posterior measurements.
Platelet-Rich Plasma in the Treatment of Diabetic Foot Ulcers
Authors: Gomez Paul T. , Andrews Karen L. , Arthurs Jennifer R. , Bruce Alison J. , Wyles Saranya P.
Published: November 2024

BACKGROUND

Chronic nonhealing neuropathic foot ulcers affect approximately 15% to 30% of patients with diabetes mellitus and are associated with significant morbidity and mortality. Although current strategies to address these chronic wounds include a multifactorial approach, clinical outcomes remain poor and warrant improvement. Platelet-rich plasma (PRP), derived from autologous or allogeneic blood, is an emerging regenerative product that aims to serve as an adjuvant to standard diabetic foot ulcer (DFU) treatment.

OBJECTIVE

To examine controlled clinical trials investigating the efficacy of platelet-rich therapies in promoting healing of chronic DFUs.

DATA SOURCES

The PubMed/MEDLINE database.

STUDY SELECTION

Researchers selected 11 controlled clinical trials published between 2011 and 2021 that investigated the efficacy of PRP treatments for chronic DFUs.

DATA EXTRACTION

Extracted data included study type and size, participant sex and age, duration of diabetes, glycated hemoglobin levels, baseline ulcer area, wound duration, healing parameters, PRP preparation approach, and application type.

DATA SYNTHESIS

Randomized prospective studies (n = 8), prospective controlled studies (n = 2), and a double-blind, randomized controlled study (n = 1) were included in the review. In general, PRP plus standard of care provided superior wound healing, in both percentage of wound closure and healing rate, compared with standard of care alone.

CONCLUSIONS

Use of PRP as an adjuvant for healing chronic DFUs appears to improve wound healing. Further research on optimizing PRP preparation and exploring combinatorial approaches will be important in advancing this avenue for chronic wound healing.
Midazolam Boosting With Cobicistat in a Patient With Drug-Resistant Epilepsy and Focal Status Epilepticus
Authors: Born-Bondt van den Tessa , Westra Niels , Krzywicka Katarzyna , Moes Harmen R. , Schuls-Fouchier Manon , Touw Daan J. , Thijs H Oude Munnink
Published: November 2024

Background:

This report presents the case of a patient with drug-resistant epilepsy. Despite treatment with 4 antiepileptic drugs, the patient experienced an increasing frequency of focal seizures, necessitating hospitalization, and continuous intravenous midazolam infusion.

Methods:

Cobicistat was introduced as a pharmacokinetic booster to decrease the metabolic clearance of midazolam, leading to increased exposure and an extended half-life.

Results:

Cobicistat boosting allowed the switch from intravenous to oral midazolam, and the patient was discharged on an oral midazolam regimen.

Conclusions:

Cobicistat can be effectively used to boost midazolam exposure pharmacokinetically in patients with drug-resistant epilepsy who require stable midazolam blood concentrations.
Pre-declaration Fetal Dose Assignment and Predictive Full term Fetal Dose at Medical Facilities
Authors: Underwood James Kyle , Sturchio Glenn M.
Published: November 2024

Many medical facilities across the United States use ionizing-radiation-producing machines and radioactive materials for diagnostic and therapeutic purposes on a regular basis. While institutions are required to ensure full-term fetal doses are below the regulatory limit, clear guidance on how pre-declaration fetal doses should be estimated is not available. This paper provides a process that can be used to estimate the pre-declaration fetal dose and provides a predictive screening tool for licensees to use to recommend workload adjustments prior to actual fetal dosimetry results that could exceed the institutions derived investigation levels. The evaluation process presented herein serves as a guide for medical licensees when performing fetal dose evaluations for declared pregnant workers.
Medical Cases and Its Role in TCM Pedagogy: A Narrative Analysis
Authors: Zhao Yunfan , Tan Xinyi , Chen Xiaoyun
Published: November 2024

Narrative medicine has gained significant attention in recent decades. The similarities between "parallel charts" and "medical cases" in traditional Chinese medicine (TCM) primarily lie in their authenticity. However, they differ in structure and narrative methods. Furthermore, medical case teaching is a prevalent pedagogical approach in TCM education that practitioners must master. This study explores the connection between TCM medical case teaching and narrative medicine, and concludes that the evolution of modern TCM case teaching aligns with the international standards of narrative medicine while integrating key TCM characteristics to enhance its value. This approach is essential for fostering humanistic sentiments, empathy, and reflective capabilities among future well-rounded TCM practitioners.
Diffusion-Weighted Imaging–Based Radiomics Features and Machine Learning Method to Predict the 90-Day Prognosis in Patients With Acute Ischemic Stroke
Authors: Li Guirui , Zhang Yueling , Tang Jian , Chen Shijian , Liu Qianqian , Zhang Jian , Shi Shengliang
Published: November 2024

Objectives:

The evaluation of the prognosis of patients with acute ischemic stroke (AIS) is of great significance in clinical practice. We aim to evaluate the feasibility and effectiveness of diffusion-weighted imaging (DWI) image-based radiomics features and machine learning methods in predicting 90-day prognosis among patients with AIS.

Patients and Methods:

We enrolled a total of 171 patients with AIS in this study, including 134 patients with a good prognosis and 37 patients with a poor prognosis, and collected the patients’ clinical and DWI image data. Radiomics features from manually sketched ischemic lesions were extracted using the Pyradiomics package of Python, and the best radiomics features were selected by a t test and the least absolute shrinkage and selection operator. The radiomics model and clinical model were constructed using support vector machine and logistic regression, respectively, and the predictive performance of each model was evaluated.

Results:

We selected 9 features from a total of 851 radiomics features to build the final radiomics model. For predicting the poor prognosis of patients with AIS, the area under the curves, accuracy, sensitivity and specificity of the clinical model, radiomics model in the training set and radiomics model in the testing set were 0.865, 0.930 and 0.906, 81.3%, 92.0% and 90.0%, 81.1%, 76.0% and 75.0%, and 81.3%, 97.0% and 95.0%, respectively.

Conclusions:

DWI image-based radiomics features and machine learning methods can accurately predict the 90-day prognosis of patients with AIS, and the radiomics model is superior to the clinical model in predicting prognosis.
Developing international scope and standards for high-quality home-based nursing practice
Authors: Narayan Mary Curry , Hinck Susan , Harris Marilyn D.
Published: November 2024

The scope and standards of professional nursing practice define and guide high-quality nursing care. This article describes the collaboration between the International Home Care Nurses Organization and the American Nurses Association to develop evidence-based scope and standards of practice relevant to home-based nursing around the world.
A Unique Cause of Chronic Right Hip Pain and Unilateral Leg Swelling 10 Years Following Total Hip Arthroplasty
Authors: Banks Evan , Gharib Mahmood
Published: November 2024

Patient is a 64-year-old female with a history of right total hip arthroplasty (THA) who presented with progressive painful right lower extremity edema and chronic groin pain for 2 years. A CT scan from October 2021 revealed an expanding, large iliopsoas bursal fluid collection that caused compression of the right common femoral artery and vein in June 2023. Further workup excluded deep venous thrombosis or infectious causes. Iliopsoas fluid collections can result from various conditions such as a rare complication of THA. This is likely due to mechanical irritation from the prosthetic components and was confirmed with resolution of symptoms after undergoing revision of THA in 2024. This case highlights iliopsoas hematoma as a rare but important consideration in patients with unilateral lower extremity edema following THA.
Dermatological manifestations during Dengue, Chikungunya, and Zika infections
Authors: Sonego Benedetta , Schettini Antonio , Talhari Sinesio , Maciel Luiz , Massone Cesare
Published: November 2024

Purpose of review

Arboviral infections caused by Dengue, Zika, and Chikungunya viruses continue to pose a significant global health threat, particularly in endemic regions. This review is timely because of the increasing prevalence of these infections, driven by factors such as urbanization and climate change. Dermatological manifestations of these viruses are crucial for early diagnosis, especially given the overlap in symptoms, which can complicate differential diagnosis.

Recent findings

Recent studies emphasize the importance of mucocutaneous symptoms in diagnosing arboviral infections. In Dengue, distinctive rashes like the ‘islands of white in a sea of red’ and hemorrhagic skin manifestations have been key diagnostic features. Zika is marked by a pruritic maculopapular rash and nonpurulent conjunctivitis, whereas Chikungunya often results in persistent rashes, desquamation, and hyperpigmentation, particularly on the face. Emerging research highlights the skin's role as both a primary infection site and an immune mediator in these viral diseases, offering new insights into their pathophysiology and potential therapeutic targets.

The unique dermatological profiles of Dengue, Zika, and Chikungunya are critical for guiding clinical diagnosis and treatment, especially in resource-limited settings. Understanding these cutaneous manifestations can improve early recognition, particularly in differentiating between these viruses in co-endemic areas. Future research may uncover novel therapeutic strategies by focusing on the interaction between these viruses and the skin's immune responses.
Can 3 Stages Forehead Flap Provide Longer Flap Length?
Authors: Horoz Ugur , Tellioglu Ali Teoman
Published: November 2024

This article discusses the use of the forehead flap technique in nasal reconstruction, specifically examining the effect of the 3-stage forehead flap procedure in providing longer flap length. Traditionally performed in 2 stages, the forehead flap technique often requires additional operations due to the thickness of the forehead skin. The 3-stage procedure, however, allows for better control of the flap thickness and improved reconstruction of nasal subunits. In this study, 17 patients who underwent this procedure for nasal defect repair were evaluated. Despite minor complications such as bleeding and venous congestion in some patients, the overall outcomes were successful. The 3-stage forehead flap is highlighted as an effective method for achieving both functional and aesthetic results in nasal reconstruction. This technique is particularly beneficial for addressing complex nasal defects and achieving optimal tissue matching between the flap and the recipient site.
The significance of social interactions in synchronized swarming flight in a termite
Authors: Mizumoto Nobuaki , Nozaki Tomonari
Published: November 2024

In social insects, individuals of working caste coordinate their actions to manage various collective tasks. Such collective behaviours exist not only in workers but also in winged reproductives (alates). During certain seasons, newly emerged alates fly from the nest to disperse and find mating partners in a synchronized manner. This ‘swarming’ behaviour is one of the collective behaviours that involve the greatest number of individuals in social insects. However, such synchronization is considered to be caused by the response to specific environmental cues rather than behavioural coordination among colony members. Here, we show that a termite
Reticulitermes kanmonensis
shows synchronized dispersal flight among alates within the same colony even under the constant temperature environment. Under the semi-field environment with fluctuating temperatures, alates within the same colony synchronized their dispersal flight under higher temperatures, while flight was suppressed under lower temperatures. We observed that termites synchronized their dispersal flights even under constant temperature conditions in the laboratory (20℃), indicating that environmental cues are not always necessary for synchronization. In either case, higher synchronization happened with a larger number of alates. These results suggest that social factors interplay with environmental cues to enable the synchronized swarming flight of social insects.
Experimentally measured assembly indices are required to determine the threshold for life
Authors: Walker Sara I. , Mathis Cole , Marshall Stuart , Cronin Leroy
Published: November 2024

Assembly theory (AT) aims to distinguish living from non-living systems by explaining and quantifying selection and evolution. The theory proposes that the degree of assembly depends on the number of complex objects, with complexity measured using a combination of the object’s assembly index (AI) and its abundance. We previously provided experimental evidence supporting AT’s predictive power, finding that abiotic systems do not randomly produce organic molecules with an AI greater than approximately 15 in detectable amounts. Hazen
et al
. (Hazen
et al
. 2024
J. R. Soc. Interface
21
, 20230632. (doi:10.1098/rsif.2023.0632)) proposed inorganic molecules that theoretically have AIs greater than 15, suggesting similar complexity to biological molecules. However, our AIs are experimentally measured for organic, covalently bonded molecules, whereas Hazen’s are theoretical, derived from crystal structures of charged units that are not isolable in solution. This distinction underscores the challenge in experimentally validating theoretical AIs.
Data-driven Huntington’s disease progression modelling and estimation of societal cost in the UK
Authors: Pollard Andrew , Greetham Danica , Myatt James , Rickards Hugh , Stanley Cath , Dungate Dave
Published: November 2024

We develop a Huntington’s disease (HD) progression model and integrate this with a novel economic model, accounting for the major factors of the HD’s societal cost. Data from the Enroll-HD observational study were used to fit a continuous-time hidden Markov disease progression model, which identified five distinct states. The number of disease states was determined using a cross-validated maximum likelihood approach. A novel data augmentation method was used to correct the biased life expectancy of the progression model. Multiple sources of cost data were then mapped to Enroll-HD variables using expert experience. A simulation of a synthetic patient population was used to show the feasibility of the approach in estimating population costs and the impact of hypothetical intervention scenarios. Our results confirm that early cognitive decline, which is not captured by the total functional capacity score currently used by clinicians but flagged up in HD integrated staging system, can be quantified from participants’ visits. Finally, the results of the UK cost modelling show that indirect costs of HD such as state benefits and lost gross domestic product contribution could be the driving factors for the societal cost, over and above health and social care costs.
Turns around periodic spatial boundaries facilitate increasing event segmentation over time
Authors: Ross Tyler Wayne , Slater Benjamin , Easton Alexander
Published: November 2024

Event segmentation is a neurocognitive process bridging perception and episodic memory. To our knowledge, almost all segmentation work is framed towards humans, yet evolutionarily conserved mechanisms in event cognition exist across species. Here, we addressed segmentation in a way that is applicable to humans and non-human animals, inspired by research in rats; specifically, the fragmentation of grid-cell spatial representations following the insertion of boundaries into an environment (forming a corridor maze). Participants indicated when they felt a meaningful unit of activity ended and another began, while watching an agent traverse from a first-person perspective. A virtual corridor maze (experiment 1) and two other mazes were used (experiment 2), with participants viewing/segmenting the same stimuli twice. We found that people segmented more during turns relative to corridors, with elevated segmentation occurring in discrete moments around turns. Interestingly, we also found that boundaries of the corridor maze facilitated an increase in segmentation within and across viewings. These results suggest that segmentation can be driven by recognized repeating activity that can become more meaningful over time, highlighting an important link between event segmentation and pattern separation that is relevant to many species in their formation of episodic-(like) memory.
Hummingbirds rapidly respond to the removal of visible light and control a sequence of rate-commanded escape manoeuvres in milliseconds
Authors: Anwar Md Zafar , Tobalske Bret W. , Agrawal Suyash , Mongeau Jean-Michel , Luo Haoxiang , Cheng Bo
Published: November 2024

Hummingbirds routinely execute a variety of stunning aerobatic feats, which continue to challenge current notions of aerial agility and controlled stability in biological systems. Indeed, the control of these amazing manoeuvres is not well understood. Here, we examined how hummingbirds control a sequence of manoeuvres within milliseconds, and tested whether and when they use vision during this rapid process. We repeatedly elicited escape flights in calliope hummingbirds, removed visible light during each manoeuvre at various instants and quantified their flight kinematics and responses. We show that the escape manoeuvres were composed of rapidly controlled sequential modules including evasion, reorientation, nose-down dive, forward flight and nose-up to hover. The hummingbirds did not respond to the light removal during evasion and reorientation until a critical light-removal time; afterwards, they showed two categories of luminance-based responses that rapidly altered manoeuvring modules to terminate the escape. We also show that hummingbird manoeuvres were rate-commanded and required no active braking (i.e. their body angular velocities were proportional to the change of wing motion patterns, a trait that probably alleviates the computational demand on flight control). This work uncovers key traits of hummingbird agility, which can also inform and inspire designs for next-generation agile aerial systems.
Colouration of the uropygial secretion in starling nestlings: a possible role of bacteria in parent-offspring communication
Authors: Martínez-Renau Ester , Martín-Platero Antonio M. , Barón María Dolores , García-Núñez Antonio José , Martínez-Bueno Manuel , Ruiz-Castellano Cristina , Tomás Gustavo , Soler Juan José
Published: November 2024

The use of cosmetic substances in communication is widespread in animals. Birds, for instance, use their uropygial secretion as a cosmetic in scenarios of sexual selection and parent-offspring communication. This secretion harbours symbiotic bacteria that could mediate the synthesis of pigments for cosmetic colouration. Here, we investigate the association between bacteria and the conspicuous yellow secretion used by spotless starling (
Sturnus unicolor
) nestlings to stain their mouths, and hypothesize a possible role of bacteria in the colour production. We also experimentally explore how nestling oxidizing condition influences the microbiota, suggesting that the possible bacterial-mediated coloured secretion acts as a reliable honest signal. An antioxidant supplementation experiment, previously known to affect secretion and mouth colouration, was conducted to assess its impact on the microbial community of secretions from control and experimental siblings. Antioxidant supplementation increased richness and phylogenetic diversity of the secretion’s microbiota. Moreover, the microbiota’s alpha and beta diversity, and the abundance of two bacterial genera (
Parabacteroides
and
Pseudogracilibacillus
), correlated with secretion colour. These findings demonstrate that antioxidant condition influences the gland microbiota of starling nestlings, and suggest a link between bacteria and the colouration of their cosmetic secretion. Alternative explanations for the detected links between bacteria and colouration are discussed.
Shift in diet composition of a riparian predator along a stream pollution gradient
Authors: Huszarik Maike , Roodt Alexis P. , Wernicke Teagan , Link Moritz , Lima-Fernandes Eva , Åhlén David , Schreiner Verena C. , Schulz Ralf , Hambäck Peter , Entling Martin H.
Published: November 2024

Terrestrial insectivores in riparian areas, such as spiders, can depend on emergent aquatic insects as high-quality prey. However, chemical pollution entering streams from agricultural and urban sources can alter the dynamics and composition of aquatic insect emergence, which may also affect the riparian food web. Few studies have examined the effects of stressor-induced alterations in aquatic insect emergence on spiders, especially in terms of chemical pollution and diet composition. We used DNA metabarcoding of gut content to describe the diet of
Tetragnatha montana
spiders collected from 10 forested streams with differing levels of pesticide and wastewater pollution. We found that spiders consumed more
Chironomidae
and fewer other aquatic Diptera, including Tipulidae, Ptychopteridae and Culicidae, at more polluted streams. Pollution-related effects were mainly observed in the spider diet, and were not significant for the number nor composition of flying insects trapped at each site. Our results indicate that the composition of riparian spider diets is sensitive to stream pollution, even in the absence of a change in the overall proportion of aquatic prey consumed. A high reliance on aquatic prey at polluted streams may give spiders an increased risk of dietary exposure to chemical pollutants retained by emergent insects.
Experimental comparison of mowing and mulching on snail communities in wet meadows
Authors: Farkas Roland , Bán Miklós , Oláh Gergő , Dudás György , Barta Zoltán
Published: November 2024

The condition of wet meadows nowadays depends mainly on human activities; the biodiversity and productivity of these habitats can only be maintained by appropriate management methods. Mowing and grazing are well-known traditional methods, but a new method, regular mulching – the fragmentation of plant material and its deposition in the area - is also increasingly used. The ecological impact of traditional management is still not fully known, and we know almost nothing about the effects of mulching. To better understand the impact of these methods we directly compared their effects on snails, an invertebrate taxon common in these habitats and known as good bioindicators. We experimentally manipulated management methods on two wet meadows in Northern Hungary, Europe, and surveyed their snail communities immediately before and one year after treatments. Our results showed that mowing had a detectable negative effect on the snail communities. On the other hand, mulching did not alter their characteristics. Therefore, mulching may be a more desirable method for short-term interventions on wet meadows, whilst at the same time also preserving their biodiversity.
Neurostructural and cognitive signatures of novel polygenic risk scores for molecular brain aging
Authors: Clifford Kevan P. , Dos Santos Fernanda , Abdelhack Mohamed , Felsky Daniel , Sibille Etienne , Nikolova Yuliya S.
Published: November 2024

The world population is shifting sharply toward an older-age demographic. To navigate the escalating burden of physical and cognitive decline common to aging, and heightened risk of neurodegenerative and neuropsychiatric disease, we require advances in treatment and prevention interventions. These advances are predicated on attaining a deeper understanding of the molecular processes underlying brain aging. Here, we employed novel GWAS and cis-eQTL-based polygenic risk scores (GWASAGE-PRS andcis-eQTLAGE-PRS) indexing genetic risk for accelerated molecular brain aging, and examined their associations with cortical thickness and performance in age-sensitive cognitive domains in 31 384 participants (16 392 women, age 64.1±7.65) from the UK Biobank. WhileGWASAGE-PRS was nominally associated with lower cortical thickness in frontotemporal regions,cis-eQTLAGE-PRS displayed robust associations with greater cortical thickness in age-sensitive frontal, temporal, and parietal regions, including the left and right precentral (pFDR<0.0001, pFDR=0.05), left insula (pFDR=0.05), as well as the right supramarginal (pFDR=0.05) and precuneus (pFDR=0.05) regions. Similar pFDR trending associations occurred bilaterally in the caudal middle frontal (pFDR=0.052, pFDR=0.078) and right insula (pFDR=0.071). These structural findings co-occurred alongside increased executive function performance on the Trail Making Test B (pFDR=0.035), suggesting a potential neurostructural and cognitive reserve phenotype. This resilience profile may reflect previously uncharacterized pathways of brain reserve in age-related pathology, informing future translational research identifying novel treatment and prevention targets.
Towards optimizing diversifying base editors for high-throughput studies of single- nucleotide variants
Authors: Schwartz Carley I , Abell Nathan S , Li Amy , Aradhana  , Tycko Josh , Truong Alisa , Montgomery Stephen B , Hess Gaelen T
Published: November 2024

Determining the phenotypic effects of single nucleotide variants is critical for understanding the genome and interpreting clinical sequencing results. Base editors, including diversifying base editors that create C>N mutations, are potent tools for installing point mutations in mammalian genomes and studying their effect on cellular function. Numerous base editor options are available for such studies, but little information exists on how the composition of the editor (deaminase, recruitment method, and fusion architecture) affects editing. To address this knowledge gap, the effect of various design features, such as deaminase recruitment and delivery method (electroporation or lentiviral transduction), on editing was assessed across ∼200 synthetic target sites. The direct fusion of a hyperactive variant of activation-induced cytidine deaminase to the N-terminus of dCas9 (DivA-BE) produced the highest editing efficiency, ∼4-fold better than the previous CRISPR-X method. Additionally, DivA-BE mutagenized the DNA strand that anneals to the targeting sgRNA to create G>N mutations, which were absent when the deaminase was fused to the C-terminus of dCas9. The DivA-BE editors efficiently diversified their target sites, an ideal characteristic for discovering functional variants. These and other findings provide a comprehensive analysis of how design features influence the activity of several popular base editors.
Low levels of neutralizing antibodies against SARS-CoV-2 KP.3.1.1 and XEC in serum from seniors in May 2024
Authors: Fossum Even , Vikse Elisabeth Lea , Robertson Anna Hayman , Wolf Asia-Sophia , Rohringer Andreas , Trogstad Lill , Mjaaland Siri , Hungnes Olav , Bragstad Karoline
Published: November 2024

New immune evasive variants of SARS-CoV-2 may increase infections and hospitalizations in risk groups, such as the elderly. In this study we evaluated neutralizing antibodies against KP.3.1.1 and XEC, virus variants that are either widely distributed or on the rise globally, in sera from a cohort of seniors aged 68 - 82 years from April/May 2024. Neutralizing responses were low against both KP.3.1.1 and XEC, supporting the recommendation of an updated covid-19 vaccine booster in this age group.
In silicoanalysis of the evolution of root phenotypes during maize domestication in Neolithic soils of Tehuacán
Authors: Lopez-Valdivia Ivan , Vallebueno-Estrada Miguel , Rangarajan Harini , Swarts Kelly , Benz Bruce F. , Blake Michael , Sidhu Jagdeep Singh , Perez-Limon Sergio , Sawers Ruairidh J. H. , Schneider Hannah , Lynch Jonathan P.
Published: November 2024

Roots are essential for plant adaptation to changing environments, yet the role of roots in crop domestication remains unclear. This study examines the evolution of root phenotypes from teosinte to maize, a transition resulting in reduced nodal root number (NRN), multiseriate cortical sclerenchyma (MCS), and increased seminal root number (SRN). We reconstructed the root phenotypes of maize and teosinte, as well as the environments of the Tehuacan Valley over the last 18,000 years using a combination of ancient DNA, paleobotany, and functional-structural modeling. Our models reveal that increasing Holocene atmospheric CO2concentrations favored the appearance of reduced NRN and MCS between 12000 to 8000 years before present (yBP), promoting deeper root systems. The advent of irrigation by 6000 yBP switched nitrogen distribution from topsoil to subsoil domains, a change which increased the utility of reduced NRN and MCS. Comparison of allelic frequencies among ancient samples ranging from 5500 to 500 yBP suggest that increased SRN may have appeared around 3500 yBP, coinciding with a period of increased human population, agricultural intensification, and soil degradation. Our results suggest that root phenotypes that enhance plant performance under nitrogen stress were important for maize adaptation to changing agricultural practices in the Tehuacan Valley.

Classification

Physiology & Development
Mycobacterial lipoarabinomannan negatively interferes with macrophage responses toAspergillus fumigatus in-vitro
Authors: Gonzales-Huerta LE , Williams TJ , Aljohani R , Robertson B , Evans CA , Armstrong-James DPH
Published: November 2024

Introduction

Over 1 million people have chronic pulmonary aspergillosis (CPA) secondary to pulmonary tuberculosis. Additionally,Aspergillus fumigatus(Af) has been reported as one of the most common pathogens associated with mycobacteria in patients with cystic fibrosis. Mycobacterial virulence factors, like lipoarabinomannan, have been shown to interfere with host’s intracellular pathways required for an effective immune response, however, the immunological basis for mycobacterial-fungal coinfection is still unknown. We therefore investigated the effect of lipoarabinomannan on macrophage responses againstAf.

Methods

Bone marrow-derived macrophages (BMDMs) were stimulated with non-mannose-capped lipoarabinomannan (LAM) fromMycobacterium smegmatisor mannose-capped lipoarabinomannan (ManLAM) fromMycobacterium tuberculosisfor 2 hours and then infected with swollenAfconidia. Cell death was assessed by lactate dehydrogenase release. Cytokine release was measured in supernatant using Enzyme Linked Immuno-Sorbent Assay (ELISA). Colony forming units counting and time-lapse fluorescence microscopy was performed for studying conidia killing by macrophages.

Results

BMDMs stimulated with LAM showed increased cell death and inflammatory cytokine release in a dose-dependent manner, characterised by a significant increase of IL-1β release. Time-lapse fluorescence microscopy and CFUs revealed that both LAM and ManLAM significantly decrease the capacity of macrophages to killAfconidia within the first 6 hours of infection.

Conclusions

The mycobacterial virulence factor, lipoarabinomannan, disrupts macrophage capacity to efficiently clearAfat early stages of infectionin-vitro.
Deleterious mutations can contribute to the evolution of recombination suppression between sex chromosomes
Authors: Jay Paul , Véber Amandine , Giraud Tatiana
Published: November 2024

Many organisms have sex chromosomes with large non-recombining regions that expand in a stepwise manner, although the underlying reasons remain poorly understood. Recently, we proposed that recombination suppression may evolve in sex chromosomes simply because of the presence of recessive deleterious mutations within genomes. Specifically, we demonstrated that chromosomal inversions suppressing recombination and carrying by chance fewer deleterious mutations than average have a selective advantage. In addition, we showed that the permanent heterozygosity of Y-like sex chromosomes facilitates the fixation of these less-loaded inversions by a sheltering effect, i.e., by preventing the expression of recessive deleterious mutations in a homozygous state when they increase in frequency. In contrast, similar less-loaded inversions in autosomes suffer from a disadvantage in the homozygous state as their frequency increases, preventing their fixation. However, the methodology and significance of our previous study have been questioned. Here, we present new analyses that further reinforce our original claims, demonstrating that the lower-load advantage and the sheltering effect can explain the fixation of inversions on sex chromosomes over a broad range of parameter values. We show that these mechanisms promote the fixation of inversions on Y-like chromosomes at rates exceeding those expected under drift alone. We used, as a control, autosomes with a similar population size as the Y chromosome, which, we argue, provides the appropriate neutral control for the sheltering effect. We also address criticisms regarding our focus on inversions surviving the first 20 generations in a figure of our previous study, and show that these criticisms stemmed from a misunderstanding of what this figure was intended to illustrate. Including all inversions, even those that went extinct within 20 generations, does not alter our conclusions. Overall, the present study offers new support for our theory based on the combination of lower-load advantage and sheltering effect, and addresses the questions about its significance and range of applicability.
GLOBAL BIOGEOGRAPHY AND EVOLUTIONARY DRIVERS OF FERNS WITH CHLOROPHYLLOUS SPORES
Authors: Mellado-Mansilla Daniela , Weigelt Patrick , Kessler Michael , Craven Dylan , Zotz Gerhard , Kreft Holger
Published: November 2024

About 14% of all fern species have chlorophyllous spores. Unlike their counterparts, chlorophyllous spores lack dormancy and have a shorter viability (i.e. only a few days in some species). Such spores should limit long-distance dispersal and be more susceptible to harsher climatic conditions raising questions about the evolutionary and ecological advantages of this trait. This study aims to assess the global biogeography of chlorophyllous-spored ferns evaluating their underlying environmental and evolutionary drivers. We studied the global distribution of 10,995 fern taxa across 556 geographical regions, and assessed the association of the proportional representation of 1387 chlorophyllous-spored species (CSS) with environmental variables using generalized linear mixed models. To assess the influence of phylogenetic relationships on the distribution of this trait across the phylogeny and across geographic regions, we calculated the phylogenetic signal and phylogenetic distances among species in different assemblages. Species richness of chlorophyllous-spored ferns peaked in the tropics while their proportional representation was highest in temperate and island floras. The proportion of CSS was positively influenced by water availability, but negatively by variables associated with temperature. Spore type was strongly conserved phylogenetically, and CSS assemblages were phylogenetically clustered towards higher latitudes. Our study provides strong evidence that chlorophyllous spores do not limit the geographical distribution of fern species. Their latitudinal distribution patterns can be explained both for environmental and phylogenetic drives.
Integrated Ising Model with global inhibition for decision making
Authors: Tapinova Olga , Finkelman Tal , Reitich-Stolero Tamar , Paz Rony , Tal Assaf , Gov Nir S.
Published: November 2024

Humans and other organisms make decisions choosing between different options, with the aim to maximize the reward and minimize the cost. The main theoretical framework for modeling the decision-making process has been based on the highly successful drift-diffusion model, which is a simple tool for explaining many aspects of this process. However, new observations challenge this model. Recently, it was found that inhibitory tone increases during high cognitive load and situations of uncertainty, but the origin of this phenomenon is not understood. Motivated by this observation, we extend a recently developed model for decision making while animals move towards targets in real space. We introduce an integrated Ising-type model, that includes global inhibition, and use it to explore its role in decision-making. This model can explain how the brain may utilize inhibition to improve its decision-making accuracy. Compared to experimental results, this model suggests that the regime of the brain’s decision-making activity is in proximity to a critical transition line between the ordered and disordered. Within the model, the critical region near the transition line has the advantageous property of enabling a significant decrease in error with a small increase in inhibition and also exhibits unique properties with respect to learning and memory decay.
The taxonomic status ofFarlowella colombiensisRetzer & Page 1997 with comments on species of theF. acusspecies group (Loricariidae: Loricariinae)
Authors: Melo-Ortiz Omar Eduardo , Retzer Michael E. , Prada-Pedreros Saúl , Ballen Gustavo A.
Published: November 2024

The genusFarlowellahas been historically challenging, in part due to the difficulty in defining diagnostic characters which allow to clearly set apart and identify the species.Farlowella colombiensisRetzer & Page 1997 is one of such examples, whose diagnostic characters were based on caudal-fin colour pattern, body cover ventral pattern, and details of the head. We herein reassess the taxonomic status of this species against congeners of theF. acusspecies group (F. acus,F. martini,F. mitoupibo,F. venezuelensis, andF. vittata). We found no significant differences betweenF. colombiensisandF. acusin morphometric, meristic, and discrete characters, therefore renderingFarlowella colombiensisa junior synonym ofFarlowella acus. We provide remarks on different species of theF. acusgroup in Colombia, as well as description of sexual dimorphism in the genital papilla for the first time in the subfamily. We also provide a key to the species of theF. acusspecies group in Colombia.
Direct thin-layer agar for bedaquiline-susceptibility testing ofMycobacterium tuberculosisat BSL2 level yields high accuracy in 15 days from sputum processing
Authors: Martin I. Cuella , Runyambo D. , De Bock S. , Diels M. , Niyompano H. , Hakizayezu F. , Keysers J. , De Rijk W.B. , Habimana Y. M. , Gahamanyi N. , Ardizzoni E. , Muvunyi C.M. , de Jong B.C. , Ngabonziza J.C.S. , Rigouts L.
Published: November 2024

This study evaluated thin-layer agar (TLA) as a faster alternative for both indirect MIC determination of bedaquiline (BDQ) from culture isolates and direct drug-susceptibility testing (DST) from sputum samples. Indirect BDQ-MIC results from TLA were compared to the established 7H11 solid DST. Direct-TLA-DST performance was assessed using 143 baseline sputum samples from rifampicin-resistant TB cases. Direct-TLA tested susceptibility to rifampicin, isoniazid, levofloxacin, and BDQ, with results compared to Löwenstein-Jensen (LJ) and MGIT.

For indirect BDQ-MIC determination, TLA demonstrated high accuracy, with MIC values for H37Rv falling within the WHO control range (0.015-0.12μg/ml). The incubation conditions (5-10% CO2, standard) and reading time (day 7, 14) significantly affected results, with D7 readings in standard incubator providing optimal accuracy. Direct-TLA-DST detected MTB in 53.8% of samples, compared to 55.9% on LJ and 69.4% in MGIT. Uninterpretable results due to contamination or medium drying were low (4.9%). Median time to result was 15 days for smear-positive and 22 days for smear-negative samples, faster than WHO endorsed methods. Sensitivity was 100% for rifampicin and 87.8% for isoniazid, with a specificity of 100% for all drugs except isoniazid (96.2%). No BDQ nor levofloxacin resistance was detected, thus direct TLA sensitivity could not be assessed.

In conclusion, direct-TLA-DST offers a reliable and faster alternative to conventional DST methods for BDQ and other anti-TB drugs. Essentially, this technique can be operated at BioSafety Level 2, allowing decentralization of pDST for managing drug-resistant TB in settings with limited laboratory infrastructure.

Importance

This paper addresses the critical need for faster direct drug-susceptibility testing (DST) on sputum, especially for bedaquiline (BDQ), which is a key drug in treating drug-resistant TB. Currently, there is a lack of rapid, reliable methods for direct BDQ testing from sputum samples, limiting timely and accurate treatment decisions and monitoring. By demonstrating the potential of thin-layer agar (TLA) for direct BDQ-MIC determination, this study offers a promising solution that could significantly improve patient care.
Activation of IL1A/IRAK1 axis and downstream proinflammatory signaling in healthy adult and neonatal African American skin
Authors: Trubetskoy Dimitri , Grudzien Patrick , Klopot Anna , Tsoi Lam C , Kundu Roopal V , White Bethany E Perez , Budunova Irina
Published: November 2024

Differences in prevalence of inflammatory skin diseases including atopic dermatitis and psoriasis in African American (AA) versus White Non-Hispanic (WNH) population are well recognized. However, the underlying mechanisms are largely unknown. We previously observed significant differences in healthy AA skin transcriptome with differentially expressed genes (DEG) enriched for inflammation and cornification processes. Here we analyzed proteome in skin biopsies from healthy AA and WNH volunteers usingOlink®Explore Inflammation384 biomarker panel. Among proteins with higher expression in AA skin were IRAK1, IL1A, IL4, IL22RA1. IL1A binding to IL1R1 receptor is known to result in recruitment of adapter molecules such as IRAK1, and activation of downstream NF-κB and MAPK signaling. We confirmed NF-κB and ERK1/2 activation in AA skin by Western blot analysis of their phosphorylation at specific activating sites. Importantly, we observed similar differences between AA and WNH neonatal foreskin and between AA and WNH 3D skin organoids. Further analysis of DEG promoters by Gene Transcription Regulation Database (GTRD) pointed to NF-κB and AP1 as key transcription factors involved in AA DEG regulation. Overall, proinflammatory signaling in healthy AA skin starting early in childhood may contribute to the increased risk of certain inflammatory skin diseases within the AA population.
Whole-Genome Sequencing of the Wild Barley Diversity Collection: A Resource for Identifying and Exploiting Genetic Variation for Cultivated Barley Improvement
Authors: Sallam Ahmad H. , Guo Yu , Jayakodi Murukarthick , Himmelbach Axel , Fiebig Anne , Simmons Jamie , Bethke Gerit , Lee Yoonjung , Spanner Rebecca , Badea Ana , Baum Michael , Belzile François , Ben-David Roi , Brueggeman Robert , Case Austin , Cattivelli Luigi , Davis Michael , Dockter Christoph , Doležel Jaroslav , Dreiseitl Antonin , Gavin Ryan , Glick Lior , Greiner Stephan , Hamilton Ruth , Hayes Patrick M. , Heisel Scott , Henson Cynthia , Kilian Benjamin , Komatsuda Takao , Li Chengdao , Liu Cheng , Mahalingam Ramamurthy , Maruschewski Maren , Matny Oadi , Maurer Andreas , Mayer Klaus F. X. , Mayrose Itay , Morrell Peter , Moscou Matthew , Muehlbauer Gary J. , Oono Youko , Ordon Frank , Özkan Hakan , Pecinka Ales , Perovic Dragan , Pillen Klaus , Pourkheirandish Mohammad , Russell Joanne , Šafář Jan , Salvi Silvio , Sanchez-Garcia Miguel , Sato Kazuhiro , Schmutzer Thomas , Scholz Uwe , Scott Jeness , Brar Gurcharn Singh , Smith Kevin P. , Sorrells Mark E. , Spannagl Manuel , Stein Nils , Tondelli Alessandro , Tuberosa Roberto , Tucker James , Turkington Thomas , Valkoun Jan , Verma Ramesh Pal Singh , Vinje Marcus A. , von Korff Schmising Maria , Walling Jason G. , Waugh Robbie , Wise Roger P. , Wulff Brande B. H. , Yang Shengming , Zhang Guoping , Mascher Martin , Steffenson Brian J.
Published: November 2024

To exploit allelic variation inHordeum vulgaresubsp.spontaneum, the Wild Barley Diversity Collection was evaluated for several agronomic traits and subjected to paired-end Illumina sequencing at ∼9X depth, generating 109.5 million single nucleotide polymorphisms after alignment to the Morex V3 assembly. A genome-wide association study of lemma color identified one marker-trait association (MTA) on chromosome 1HL close toHvBlp, the cloned gene controlling black lemma. Four MTAs were identified for stem rust resistance: one co-locating to the complex RMRL1-RMRL2 locus on 5HL, and three novel loci on 1HS, 1HL, and 5HL. Six MTAs for days to heading (DTH) on vernalized plants were identified on all chromosomes except 1H and 6H. Two MTAs for DTH on non-vernalized plants were identified on chromosomes 1HL and 2HS. All MTAs for DTH were novel. The whole genome sequence data described herein will facilitate the identification and utilization of new alleles for barley improvement.