bluuebunny/crossref_metadata_2025 huggingface dataset:
Vasovagal syncope with asystole
Authors: Middleton Hayden T. , Bachman Maria J. , Strelow Brittany A.
Published: September 2024

Although vasovagal episodes are a common cause of syncope, vasovagal syncope can be cardioinhibitory in nature, resulting in a severe heart block or asystole. This case report focuses on a young man with a history of seizures and frequent syncopal episodes who required an extensive clinical workup and treatment for cardioinhibitory syncope.
Airway obstruction secondary to vocal cord polyp
Authors: Filarski Carolyn F. , Donald Carrlene B. , Mendez Anthony P. , Lott David G.
Published: September 2024

Patients with vocal cord polyps commonly present with symptoms of hoarseness. Although rare, large polyps can cause shortness of breath and stridor and should be included in the differential for patients with airway obstruction. Dysphonia or hoarseness can be a symptom of underlying disease, such as head and neck cancer. This case illustrates the importance of prompt and accurate diagnosis in a patient with persistent symptoms and a history of smoking. Obtaining a laryngoscopy is crucial to appropriately evaluate the larynx. Proper visualization of the laryngeal structures will help direct patient care toward further diagnostic imaging and medical or surgical intervention if indicated.
PA leadership
Authors: DePalma Sondra M. , Walker Carson S. , Simon Trevor , Walczyk Eric
Published: September 2024

Physician associate/assistant (PA) leaders are essential to healthcare and critical to a healthcare organization's success. In this article, the second of a two-part series on PA leadership, we summarize methods for implementing and sustaining PA leadership opportunities and organizational structures.
Reducing the Cardiovascular Risks Associated With Gout
Authors: Itzkowitz Yaakov , Frishman William H.
Published: September 2024

Gout has increasingly been linked to the development of numerous cardiovascular diseases and cardiac events. The inflammatory processes underlying the pathophysiology of many cardiovascular diseases are similar or identical to those responsible for gout. This article will discuss the pathogenesis of gout, the inflammatory processes that drive it, and the similar process seen in numerous cardiovascular diseases. By viewing gout as a symptom of systemically high levels of inflammation and a possible harbinger of cardiovascular diseases, we can decrease the risk of development of associated cardiovascular conditions and adverse cardiac events. This review will also investigate possible inflammatory markers that can act as drug targets to decrease inflammation, ameliorate symptoms, and reduce the risk of heart disease.
Challenges in professional development of anaesthesiology trainees
Authors: Dow Olivia , Kustura Antonia , Lior Yotam , Berger-Estilita Joana , Morais Diogo , De Hert Stefan , Abramovich Igor
Published: September 2024

BACKGROUND

The coronavirus disease (COVID-19) pandemic disrupted training in anaesthesiology. The global shortage of healthcare workers has also negatively affected training opportunities.

OBJECTIVE

To evaluate the current experiences, challenges and professional development of anaesthesiology trainees across Europe.

DESIGN

An online cross-sectional survey of anaesthesiology trainees.

PARTICIPANTS

Anaesthesiology trainees from the 42 European Society of Anaesthesiology and Intensive Care (ESAIC)-affiliated countries.

MAIN OUTCOME MEASURES

Quality of training supervision and program structure; the impact of COVID-19 on training and practical learning, trainee support systems, financial challenges and professional development, involvement in the ESAIC Exchange Program and career mobility insights.

RESULTS

Seven hundred and seventy-one participants from 35 ESAIC-affiliated European countries highlighted several aspects of anaesthesiology training. Approximately 30.5% of trainees reported being able to independently anaesthetise patients with ASA class 1 and 2 within 3 months, whereas independence for ASA 3 and 4 patients under indirect supervision was achieved by 24.3% between 6 and 9 months. Half of the respondents attained an independent working capacity in the ICU after 1.5 years. Although 51.3% reported receiving adequate training and supervision, only 30.1% received employer financial support for educational activities. The COVID-19 pandemic led to 40.2% being redeployed, primarily to ICUs, with 45.2% experiencing negative training effects. Career-wise, 12.5% engaged in international exchange programs, and 49.1% considered relocating for better career opportunities and work–life balance.

CONCLUSION

The findings provide valuable insights into the current state of anaesthesiology training in Europe, highlighting the need for adaptive strategies in medical education and training to meet evolving challenges and ensure continual professional growth.
Ribs with Anterior Protrusion (Winged Ribs) Treated Using Percutaneous Chondroplasty
Authors: Manzaneda Cipriani Raúl M. , Adrianzen Gerardo A.
Published: September 2024

Background:

Thoracic features play a significant role in determining various plastic surgery techniques. Particularly, the thorax has potential for excessive anterior projection, commonly referred to as winged ribs. This study aimed to describe a treatment method for addressing winged ribs for aesthetic purposes using percutaneous chondral management.

Methods:

Thirty-two female patients underwent FrontXribs from February to March 2023. Two angular measurements were obtained: (1) the angle formed by lines intersecting tangentially to the shoulder and the lower gluteal border; and (2) the angle formed by a line tangential to the greatest anterior projection, intersected by a vertical line on the standing axis. Length measurements were obtained using a tape measure at the position of the greatest thoracic projection. Pulmonary function studies were conducted. All variables were measured before surgery and 6 months postoperatively.

Results:

On average, patients were 25 years old. The average operative time was 51.1 minutes, and all patients underwent general anesthesia. The average increase for angular measurement 1 was 26.1 degrees, whereas that for angular measurement 2 was 3.43 degrees. The average decrease in anterior chest length during the postoperative period was 9.66 cm (P < 0.001). Spirometric tests showed no significant changes 6 months postoperatively.

Conclusions:

The FrontXribs technique for treating winged ribs effectively reduces anterior costal protrusion, as evidenced by the angular variation of projections and the reduction in thoracic length at this level. No adverse effects on respiratory function were observed 6 months postoperatively.
Use of Fascia Lata as Matrix for Subpectoral Breast Reconstruction
Authors: Spyropoulou Georgia-Alexandra , Koukouritaki Zambia , Kokkonis Dimitris
Published: September 2024

Matrices are used with increased frequency to assist with tissue expander or implant-based breast reconstruction. These devices usually have a high cost, especially when they are human-derived. We present the use of fascia lata for implant and expander-based subpectoral reconstruction. According to our review of the literature, this is the first report of the use of a patient’s own fascia lata instead of a matrix.
Learned Symptom-Specific Fear Toward a Visceral Sensation and Its Impact on Perceptual Habituation
Authors: Pattyn Lauren , Zaman Jonas , van de Pavert Iris , Jelinčić Valentina , von Leupoldt Andreas , Van Oudenhove Lukas , Van Diest Ilse
Published: September 2024

Objective

Impaired habituation of bodily sensations has been suggested as a contributing factor to chronic pain. We examined in healthy volunteers the influence of fear learning toward a nonpainful sensation in the esophagus on the perceptual habituation of this sensation.

Methods

In a homoreflexive fear learning paradigm, nonpainful electrical sensations in the esophagus were used as a conditioned stimulus (CS). This sensation was presented 42 times before, during, and after fear learning. In the fear learning group (n = 41), the CS was paired with a painful electrical sensation in the esophagus (unconditioned stimulus [US]). In the control group (n = 41), the CS was not paired with the US. Ratings for CS intensity, US expectancy, startle electromyogram (EMG), skin conductance responses (SCR), and event-related potentials (ERPs) to the CS were assessed.

Results

Compared to the control group, fear learning was observed in the fear learning group as evidenced by potentiated startle responses after the CS relative to ITI (t(1327) = 3.231, p = .001) and higher US expectancy ratings (t(196) = 3.17, p = .002). SCRs did not differ between groups (F
1,817 = 1.241, p = .33). Despite successful fear learning, the fear learning group did not show a distinct pattern of habituation to the visceral CS relative to the control group (intensity ratings: F
1,77.731 = 0.532, p = .47; ERPs: F
1,520.78 = 0.059, p = .94).

Conclusion

Acquired fear to nonpainful esophageal sensations does not affect their perceptual habituation patterns.
Development of a Surgery-Specific Comorbidity Score for Use in Administrative Data
Authors: Chervu Nikhil L. , Balian Jeff , Verma Arjun , Sakowitz Sara , Cho Nam Yong , Mallick Saad , Russell Tara A. , Benharash Peyman
Published: September 2024

Objective:

To create a novel comorbidity score tailored for surgical database research.

Summary Background Data:

Despite their use in surgical research, the Elixhauser (ECI) and Charlson Comorbidity Indices (CCI) were developed nearly four decades ago utilizing primarily non-surgical cohorts.

Methods:

Adults undergoing 62 operations across 14 specialties were queried from the 2019 National Inpatient Sample (NIS) using International Classification of Diseases, 10th Revision (ICD-10) codes. ICD-10 codes for chronic diseases were sorted into Clinical Classifications Software Refined (CCSR) groups. CCSR with non-zero feature importance across four machine learning algorithms predicting in-hospital mortality were used for logistic regression; resultant coefficients were used to calculate the Comorbid Operative Risk Evaluation (CORE) score based on previously validated methodology. Areas under the receiver operating characteristic (AUROC) with 95% Confidence Intervals (CI) were used to compare model performance in predicting in-hospital mortality for the CORE score, ECI, and CCI. Validation was performed using the 2016-2018 NIS, combined 2018-2019 Florida and New York State Inpatient Databases (SID), and 2016-2022 institutional data.

Results:

699,155 records from the 2019 NIS were used for model development. The CORE score better predicted in-hospital mortality compared to the ECI within the NIS (0.90, 95%CI:0.90-0.90 vs. 0.84, 95%CI:0.84-0.84), SID (0.91, 95%CI:0.90-0.91 vs. 0.86, 95%CI:0.86-0.87), and institutional (0.88, 95%CI:0.87-0.89 vs. 0.84, 95%CI:0.83-0.85) databases (all P<0.001). Likewise, it outperformed the CCI for the NIS (0.76, 95%CI:0.76-0.76), SID (0.78, 95%CI:0.77-0.78), and institutional (0.62, 95%CI:0.60-0.64) cohorts (all P<0.001).

Conclusions:

The CORE score may better predict in-hospital mortality after surgery due to comorbid diseases in outcome-based research.
Phylogenomic diversity of archigregarine apicomplexans
Authors: Lax Gordon , Park Eunji , Na Ina , Jacko-Reynolds Victoria , Kwong Waldan K. , House Chloe S. E. , Trznadel Morelia , Wakeman Kevin , Leander Brian S. , Keeling Patrick
Published: September 2024

Gregarines are a large and diverse subgroup of Apicomplexa, a lineage of obligate animal symbionts including pathogens such as
Plasmodium
, the malaria parasite. Unlike
Plasmodium
, however, gregarines are poorly studied, despite the fact that as early-branching apicomplexans they are crucial to our understanding of the origin and evolution of all apicomplexans and their parasitic lifestyle. Exemplifying this, the earliest branch of gregarines, the archigregarines, are particularly poorly studied: around 80 species have been described from marine invertebrates, but almost all of them were assigned to a single genus,
Selenidium
. Most are known only from light micrographs and largely unresolved rDNA phylogenies, where they exhibit a great deal of sequence variation, and fall into four subclades. To resolve the relationships within archigregarines, we sequenced 12 single-cell transcriptomes from species representing all four known subclades, as well as one blastogregarine (which frequently branch with
Selenidium
). A 190-gene phylogenomic tree confirmed four maximally supported individual clades of archigregarines and blastogregarines. These clades are discrete and distantly related, and also correlate with host identity. We propose the establishment of three novel genera of archigregarines to reflect their phylogenetic diversity and host range, and nine novel species isolated from a range of marine invertebrates.
The impact of predators and vegetation on shoaling in wild zebrafish
Authors: Mukherjee Ishani , Bhat Anuradha
Published: September 2024

In their natural habitats, animals experience multiple ecological factors and regulate their social responses accordingly. To unravel the impact of two ecological factors on the immediate behavioural response of groups, we conducted experiments on wild zebrafish shoals in arenas with vegetation, predator cues, and both factors simultaneously or neither (control treatments). Analysis of 297 trials revealed that while shoals formed significantly larger subgroups in the presence of predator cues, their subgroup size was comparable to control treatments when they faced predator cues and vegetation. Shoals were highly polarized in open arenas, in the absence of either ecological factors and in the presence of predator cues (with/without vegetation). The presence of vegetation alone, however, significantly reduced shoal polarization. Furthermore, food intake was significantly reduced when predator cues and/or vegetation were present. Tracking individuals revealed that (i) individuals within shoals receiving predator cues had a significantly higher probability to continue being in a group compared with control treatments and (ii) individuals occupying the front positions deviated less from their median position within a shoal as compared with other individuals regardless of predator cues. The adaptability of animals depends on behavioural responses to changing environments, making this study significant in the context of environmental changes.
Study on the improvement of grouting stone properties in coal mine goafs using combined denitrifying bacteria
Authors: He Hao , Xu Nengxiong , Qin Yan , Xu Tianchi , Guo Yuxi
Published: September 2024

Grouting can effectively reduce residual deformation of coal mine goafs, but fly ash grouting materials suffer from poor flowability and slow early strength development. Microbially -induced calcite precipitation (MICP), with its high environmental compatibility and minimal disturbance to geotechnical bodies, effectively improves the injectability of grouting slurry in goafs. This study combined
Castellaniella denitrificans
and
Sporosarcina pasteurii
to induce calcite precipitation, preparing cement–fly ash slurry with varying water–solid ratios, solid ratios and denitrifying bacteria concentrations. The physical properties of the slurry and the mechanical properties of the grouted stone bodies under sealed curing conditions were measured. Results show that the dual-bacteria MICP improves stone body performance by enhancing cohesive, frictional and interlocking forces, so that the strength of the stone bodies cured by MICP increased rapidly within 7 days, and the strength reached the standard 2.03 MPa at 28 days under conditions of low solid ratio and high water–solid ratio, with the best compressive strength at a denitrifying bacteria concentration with an optical density of 0.8 at 600 nm wavelength. At a water–solid ratio of 1 : 1.2 and a solid ratio of 15%, initial and final setting times were 67.2 and 96 h, respectively, which prolonged the initial setting time and final setting time by nearly 70% and 110% compared with that of the slurry without MICP treatment, indicating that MICP enhances slurry fluidity, providing more time for grouting construction in goafs.
Female African elephant rumbles differ between populations and sympatric social groups
Authors: Pardo Michael A. , Lolchuragi David S. , Poole Joyce , Granli Petter , Moss Cynthia , Douglas-Hamilton Iain , Wittemyer George
Published: September 2024

Vocalizations often vary in structure within a species, from the individual to population level. Vocal differences among social groups and populations can provide insight into biological processes such as vocal learning and evolutionary divergence, with important conservation implications. As vocal learners of conservation concern, intraspecific vocal variation is of particular interest in elephants. We recorded calls from individuals in multiple, wild elephant social groups in two distinct Kenyan populations. We used machine learning to investigate vocal differentiation among individual callers, core groups, bond groups (collections of core groups) and populations. We found clear evidence for vocal distinctiveness at the individual and population level, and evidence for much subtler vocal differences among social groups. Social group membership was a better predictor of call similarity than genetic relatedness, suggesting that subtle vocal differences among social groups may be learned. Vocal divergence among populations and social groups has conservation implications for the effects of social disruption and translocation of elephants.
Fitness consequences of anthropogenic subsidies for a partially migratory wading bird
Authors: Picardi Simona , Frederick Peter , Basille Mathieu
Published: September 2024

Human activities are forcing wildlife to confront selective pressures different from those under which they evolved. In seasonal environments, migration evolved as an adaptation to fluctuating resource availability. Anthropogenic subsidies modify resource dynamics by providing a steady food source that is not subject to seasonality. Globally, many migratory populations are becoming increasingly resident in response to food supplementation. While these population-level shifts are assumed to arise from changing fitness consequences of individual behaviour in response to resource dynamics, these mechanisms are often difficult to quantify and disentangle. Here, we quantified fitness consequences of responses to anthropogenic subsidies in partially migratory wood storks (Mycteria americana) in the heavily urbanized southeastern United States. First, we tested whether individual migratory behaviour is linked to different responses to anthropogenic subsidies. Second, we quantified fitness consequences of these behavioural responses. We found that, in our system, migration and residency are alternative behavioural tactics associated with different responses to food supplementation. In turn, the use of anthropogenic resources alters a fitness component by enhancing nest survival. These results provide a mechanistic examination of how animals may respond to human-modified resource dynamics and how fitness consequences of individual tactics may translate into behavioural shifts at the population level.
Utilizing citizen science data to rapidly assess changing associations between wild birds and avian influenza outbreaks in poultry
Authors: Vickers Stephen H. , Raghwani Jayna , Banyard Ashley C. , Brown Ian H. , Fournie Guillaume , Hill Sarah C.
Published: September 2024

High pathogenicity avian influenza virus (HPAIV) is a rapidly evolving virus causing significant economic and environmental harm. Wild birds are a key viral reservoir and an important source of viral incursions into animal populations, including poultry. However, we lack a thorough understanding of which species drive incursions and whether this changes over time. We explored associations between the abundances of 152 avian species and outbreaks of highly pathogenic avian influenza (HPAI) in poultry premises across Great Britain between October 2021 and January 2023. Spatial generalized additive models were used, with species abundance distributions sourced from eBird. Associations were investigated at the species-specific level and across species aggregations. During autumn/winter, associations were generally strongest with waterbirds such as ducks and geese; however, we also found significant associations in groups such as non-native gamebirds and rapid change in species-specific associations over time. Our results demonstrate the value of citizen science to rapidly explore wild species as potential facilitators of disease incursions into well-monitored populations, especially in regions where viral surveillance in wild species is limited. This can be a critical step towards prioritizing targeted surveillance that could inform species-specific biosecurity measures; particularly for HPAIV, which has undergone sudden shifts in host range and continues to rapidly evolve.
Association Analysis ofPAEP,KRT10 andBMP7 Genes SNPs with Reproductive Traits in Kele Pigs
Authors: Zhao Yong , Wang Chunyuan , Wu Yan , Xiang Jin , Zhang Yiyu
Published: September 2024

The aims of this study were to investigate the effects of single nucleotide polymorphisms (SNPs) in progestogen-associated endometrial protein (PAEP), keratin 10 (KRT10), and bone morphogenetic protein 7 (BMP7) genes on reproductive traits (total number of piglets born, number of piglets born alive, litter birth weight, number of piglets weaned and litter weight weaned) in Kele pigs. We used a total of 255 multiparous Kele sow (2-4 parities) as research materials. SNPs were identified by PCR amplification instrument and sequence alignment software DANMAN. The population genetic characteristics of SNPs were analyzed using the SHEsis online software. Bioinformatics analysis of SNPs were conducted using RNAfold, SOPMA, SWISS-MODEL, and Swiss-PdbViewer programs. The associations between the SNPs and reproductive traits in Kele pigs were analyzed through SPSS 22.0 software. In this study, nine SNPs were identified in the three genes: g.1884992 T>C (exon 4), g.1885152 G>C (intron 4) and g.1887834 G>A (intron 4) inPAEP, g.21643703 C>T (intron 4), g.21643714 G>A (intron 4) and g.21643741 G>A (exon 5) inKRT10, and g.57647887 G>A (intron 3), g.57647990 C>T (intron 3) and g.57648145 C>G (intron 3) inBMP7. In SNPs g.1884992 T>C ofPAEP,missense mutation eventuated structural changes in mRNA and proteins secondary structure. In SNPs g.21643741 G>A ofKRT10, synonymous mutation led to alteration in mRNA secondary structure. ForPAEP,the CC genotype in SNPs g.1885152 G>C and the AA genotype in SNPs g.1887834 G>A showed significantly higher values than other genotypes in all reproduction traits except for litter birth weight, preliminarily identified as favorable genotypes. ForKRT10, the GG genotype in SNPs g.21648641 G>A showed significant superiority than AA genotype (P<0.05) in all aspects except for litter birth weight, and notably surpassed the GA genotype in total number of piglets born (P<0.05), preliminarily recognized as a favorable genotype. RegardingBMP7, the GA genotype in SNPs g.57647887 G>A and the CT genotype in SNPs g.57647990 C>T exhibited significantly higher number of piglets born alive and number of piglets born alive compared to other genotypes (P<0.05). And the GG genotype in SNPs g.57648145 C>G was significantly associated with higher litter birth weight (P<0.05). The result of diplotype analyses indicated that the H3H3 (CCGGGG) ofPAEPand H3H3 (CCGGAA) ofKRT10 had a significant effect on the five traits. ForBMP7, the H4H4 (AATTGG) diplotype showed a significant influence on all genotypes except litter birth weight.
Next-generation snow leopard population assessment tool: multiplex-PCR SNP panel for individual identification from feces
Authors: Solari Katherine A. , Ahmad Shakeel , Armstrong Ellie E. , Campana Michael G. , Ali Hussain , Hameed Shoaib , Ullah Jami , Khan Barkat Ullah , Nawaz Muhammad A. , Petrov Dmitri A.
Published: September 2024

Snow leopards,Panthera uncia, are under threat from numerous pressures and are the focus of a great deal of conservation efforts. However, their elusive nature makes it difficult to estimate population sizes. Current methods used to monitor local population sizes include visually identifying individuals from camera trap photos and genetically identifying individuals from fecal samples using microsatellite loci. Here, we present a new method for identifying snow leopard individuals from fecal samples using a multiplex PCR single nucleotide polymorphism (SNP) panel method. The SNP panel we present consists of 144 SNPs and utilizes next-generation sequencing technology, making it cheaper and easier than current microsatellite methods. We validate our SNP panel with paired tissue and fecal samples from zoo individuals, showing a minimum of 96.7% accuracy in allele calls per run. We then generate SNP data from 235 field-collected fecal samples from across Pakistan to show that the panel can reliably identify individuals from low-quality fecal samples of unknown age and is robust to contamination. We also show that our SNP panel has the capability to identify first-order relatives and provides insights into the geographic origin of samples. This SNP panel will empower the snow leopard research community in their efforts to assess local and global snow leopard population sizes. More broadly, we present a method for developing a SNP panel that utilizes open source software for SNP selection and primer design, Illumina sequencing technology, and a streamlined lab and bioinformatics protocol which can be used to create similar SNP panels for any species of interest for which adequate genomic reference data is available.
BiMultiNetPlot: An R package for visualizing ecological bipartite multilayer networks
Authors: Li Hai-Dong
Published: September 2024

With the increasing study of ecological multilayer bipartite networks, the visualization of these networks has become more important. However, tools for visualizing multilayer networks are still lacking.

I present BiMultiNetPlot, an R package designed for visualizing ecological bipartite multilayer networks.

I demonstrate how to use BiMultiNetPlot through a series of examples that represent the most common types of ecological multilayer networks.

BiMultiNetPlot is an open-source, flexible package within the ggplot2 environment, helping ecologists better understand the multilayer nature of ecological networks.
Achieving Single Cell Acoustic Localisation with Deactivation Super Resolution
Authors: Smith Cameron A. B. , Duan Mengtong , Yan Jipeng , Taylor Laura , Shapiro Mikhail G. , Tang Meng-Xing
Published: September 2024

Super-resolution optical microscopy enables optical imaging of cells, molecules and other biological structures beyond the diffraction limit. However, no similar method exists to super-resolve specific cells with ultrasound. Here we introduce Deactivation Super Resolution (DSR), an ultrasound imaging method that uses the acoustic deactivation of genetically encodable contrast agents to super-resolve individual cells with ultrasound as they navigate through structures that cannot be resolved by conventional imaging methods. DSR takes advantage of gas vesicles, which are air-filled sub-micron protein particles that can be expressed in genetically engineered cells to produce ultrasound contrast. Our experimental results show that DSR can distinguish sub-wavelength microstructures that standard B-mode ultrasound images fail to resolve by super- localizing individual mammalian cells. This study provides a proof of concept for the potential of DSR to serve as a super- resolution ultrasound technique for individual cell localization, opening new horizons in the field.
Hyperspectral imaging has a limited ability to remotely sense the onset of beech bark disease
Authors: Tougas Guillaume , Wallis Christine I. B. , Laliberté Etienne , Vellend Mark
Published: September 2024

Insect and pathogen outbreaks have a major impact on northern forest ecosystems. Even for pathogens that have been present in a region for decades, such as beech bark disease (BBD), new waves of mortality are expected in host populations. Hence, there is a need for innovative approaches to monitor their advancement extensively in real-time. Here we test whether airborne hyperspectral imaging – involving data from 344 wavelengths in the visible, near infrared (NIR) and short-wave infrared (SWIR) – can be used to assess beech bark disease severity in southern Quebec, Canada. Field data on disease severity were linked to the airborne hyperspectral data for individual beech crowns. Partial least-squares regression (PLSR) models using airborne imaging spectroscopy data predicted a small proportion of the variance in beech bark disease severity: the best model had an R2of only 0.10. Wavelengths with the strongest contributions were from the NIR (∼719 nm) and the SWIR (∼1287 nm), which may suggest mediation by canopy greenness, water content and canopy architecture. Similar models using hyperspectral data taken directly on individual leaves had no explanatory power (R2= 0). In addition, airborne and leaf-level hyperspectral datasets were uncorrelated. The failure of leaf-level models suggests that canopy structure was likely responsible for the limited predictive ability of the airborne model. Somewhat better performance in predicting disease severity was found using common band ratios for canopy greenness assessment (the Green Normalized Difference Vegetation Index, gNDVI, the Red-edge Inflexion Point, REIP, and the Normalized Phaeophytinization Index, NPQI); these variables explained up to 19% of the variation in disease severity. Overall, we argue that the complexity of hyperspectral data is not necessary for assessing BBD spread and that spectral data in general may not provide an efficient means of improving BBD monitoring on a larger scale.
Ancient inversion polymorphisms are locally adaptive in a widespread butterfly species
Authors: Seixas Fernando , Dendy Sarah , Guan Shuzhe , Rosser Neil , Grishin Nick , Davies Neil , Gilbert Lawrence E. , Owen McMillan W. , Mallet James
Published: September 2024

Wide-ranging species are subject to varying biotic and abiotic selection pressures across their distribution. While local adaptation does not manifest in obvious morphological changes, population genomic studies can reveal cryptic diversity and provide insights into local adaptive processes. In this study, we investigated the biogeographic history and genomic diversity across the range of the zebra longwing butterflyHeliconius charithonia,a species with a widespread distribution in the Neotropics, but which is phenotypically homogenous across its range. We examined whole genome sequence data from 55 individuals from the eight described subspecies. We infer that there were at least two distinct colonization events of the Caribbean islands from the mainland. The second colonization wave occurred relatively recently, accounting for the genetic homogeneity observed across the species’ range. Despite low divergence across most of the genome, two large non-recombining genomic regions showed deeply divergent haplotypes that correspond to chromosomal inversions. Phylogenetic analyses indicate ancient origins of these inversion polymorphisms, and there is no evidence that they were introgressed from another extant lineage ofHeliconius. These ancient polymorphisms are likely maintained by heterogeneous selection across the landscape, with the inversion on chromosome 19 likely playing a role in local adaptation to cold and desiccation. Our findings underscore the importance of genomic analysis in uncovering hidden diversity and adaptation in phenotypically homogenous species and highlight the significant role of chromosomal inversions in driving local adaptation.
Cognition-Associated Protein Structural Changes in a Rat Model of Aging are Related to Reduced Refolding Capacity
Authors: Tarbox Haley E. , Branch Audrey , Fried Stephen D.
Published: September 2024

Cognitive decline during aging represents a major societal burden, causing both personal and economic hardship in an increasingly aging population. There are a few well-known proteins that can misfold and aggregate in an age-dependent manner, such as amyloid β and α-synuclein. However, many studies have found that the proteostasis network, which functions to keep proteins properly folded, is impaired with age, suggesting that there may be many more proteins that incur structural alterations with age. Here, we used limited-proteolysis mass spectrometry (LiP-MS), a structural proteomic method, to globally interrogate protein conformational changes in a rat model of cognitive aging. Specifically, we compared soluble hippocampal proteins from aged rats with preserved cognition to those from aged rats with impaired cognition. We identified several hundred proteins as having undergone cognition-associated structural changes (CASCs). We report that CASC proteins are substantially more likely to be nonrefoldable than non-CASC proteins, meaning they typically cannot spontaneously refold to their native conformations after being chemically denatured. The potentially cofounding variable of post-translational modifications is systematically addressed, and we find that oxidation and phosphorylation cannot significantly explain the limited proteolysis signal. These findings suggest that noncovalent, conformational alterations may be general features in cognitive decline, and more broadly, that proteins need not form amyloids for their misfolded states to be relevant to age-related deterioration in cognitive abilities.

TEASER

Up to 10% of rat hippocampal proteins can undergo structural changes that associate with age-related decline in spatial learning.
Limited population structure but signals of recent selection in introduced African Fig Fly(Zaprionus indianus) in North America
Authors: Erickson Priscilla A. , Bangerter Alyssa , Gunter Ansleigh , Polizos Nikolaos T. , Bergland Alan O.
Published: September 2024

Invasive species have devastating consequences for human health, food security, and the environment. Many invasive species adapt to new ecological niches following invasion, but little is known about the early steps of adaptation. Here we examine population genomics of a recently introduced drosophilid in North America, the African Fig Fly,Zaprionus indianus. This species is likely intolerant of subfreezing temperatures and recolonizes temperate environments yearly. We generated a new chromosome-level genome assembly forZ. indianus. Using resequencing of over 200 North American individuals collected over four years in temperate Virginia, plus a single collection from subtropical Florida, we tested for signatures of recolonization, population structure, and adaptation within invasive populations. We show founding populations are sometimes small and contain close genetic relatives, yet temporal population structure and differentiation of populations is mostly absent across recurrent recolonization events. Although we find limited signals of genome-wide spatial or temporal population structure, we identify haplotypes on the X chromosome that are repeatedly differentiated between Virginia and Florida populations. These haplotypes show signatures of natural selection and are not found in African populations. We also find evidence for several large structural polymorphisms segregating within North America populations and show X chromosome evolution in invasive populations is strikingly different from the autosomes. These results show that despite limited population structure, populations may rapidly evolve genetic differences early in an invasion. Further uncovering how these genomic regions influence invasive potential and success in new environments will advance our understanding of how organisms evolve in changing environments.

Article Summary

Invasive species (organisms that have been moved outside their natural range by human activities) can cause problems for both humans and the environment. We studied the genomes of over 200 individuals of a newly invasive fruit fly in North America, the African Fig Fly. We found genetic evidence that these recently introduced flies may be evolving in their new environments, which could make them stronger competitors and more likely to become pests.
Small mammals and their burrows shape the distribution ofCoccidioidesin soils: a long-term ecological experiment
Authors: Head Jennifer R. , Camponuri Simon K. , Weaver Amanda K. , Montoya Lilliam , Lee Erika , Radosevich Molly , Jones Isabel , Wagner Robert , Bhattachan Abinash , Campbell Grace , Keeney Nicole , Collender Philip A. , Heaney Alexandra K. , Couper Lisa , Colvin Kate A. , Larios Loralee , Bean William T. , Taylor John , Remais Justin V.
Published: September 2024

Background

For nearly all human fungal pathogens, the environmental constraints on their distributions remain poorly understood, hindering disease management. Here, we investigated the role of zoonotic host presence, soil conditions, and their interaction on the presence ofCoccidioides immitis– an emerging fungal pathogen and causative agent of coccidioidomycosis.

Methods

A long-term experimental study initiated in 2007 in the Carrizo Plain National Monument, California excluded rodents from certain areas (20 by 20-meter exclosures; n = 20) via the installation of submerged mesh fences, leaving emptied burrows intact. We collected 1,988 soil samples over four sampling periods spanning April 2021 to April 2022 using a factorial design that crossed burrows and surface soils (i.e., top 10 cm of soil) with exclosures (i.e., rodent absence) and non-exclosures (i.e., rodent presence). We measuredin situsoil moisture, temperature, and vegetation, and analyzed soils forC. immitisDNA.

Results

The proportion of samples containingC. immitiswas significantly higher (p <0.0001) in burrow samples taken from outside rodent exclosures (i.e., rodents present; 28.5% positive) compared to burrow samples taken from within exclosures (i.e., rodents absent; 19.7%), surface soils outside of exclosures (3.6%) and surface soils within exclosures (0.5%). In generalized linear mixed models adjusting for soil conditions, rodent presence, and sample type (burrow vs. surface soil), we estimated that the odds of detectingC. immitiswere 19.2 (95% CI: 11.3 – 36.7, p < 0.0001) times higher in soils taken from burrows compared to surface soils, and 2.6 (95% CI: 1.0 – 5.6, p = 0.049) times higher in soils where rodents were present compared to absent. Soil moisture was the only abiotic factor associated withC. immitisdetection (odds ratio per 1% increase in water content: 0.83, 95% CI: 0.70 – 0.89, p = 0.0002). In mediation analyses, we estimated that 73.7% (95% CI: 68.9, 78.5) of the total association between rodents andCoccidioidesdetection effect was attributable to rodent creation of burrows.

Conclusions

Rodent creation and occupation of burrows substantially increasesC. immitisdetection. Synergy between reservoir host presence and environmental conditions may exist for other human fungal pathogens.
Multi-material volumetric bioprinting and plug-and-play suspension bath biofabrication via bioresin molecular weight tuning and multiwavelength optics
Authors: Ribezzi Davide , Zegwaart Jan-Philip , van Gansbeke Thomas , Tejo-Otero Aitor , Florczak Sammy , Aerts Joska , Delrot Paul , Hierholzer Andreas , Fussenegger Martin , Malda Jos , Olijve Jos , Levato Riccardo
Published: September 2024

Volumetric Bioprinting (VBP), enables to rapidly build complex, cell-laden hydrogel constructs for tissue engineering and regenerative medicine. Light-based tomographic manufacturing enables spatial-selective polymerization of a bioresin, resulting in higher throughput and resolution than what achieved using traditional techniques. However, methods for multi-material printing are needed for a broad VBP adoption and applicability. Although converging VBP with extrusion bioprinting in support baths offers a novel, promising solution, further knowledge on the engineering of hydrogels as light-responsive, volumetrically printable baths is needed. Therefore, this study investigates the tuning of gelatin macromers, in particular leveraging the effect of molecular weight and degree of modification, to overcome these challenges, creating a library of materials for VBP and Embedded extrusion Volumetric Printing (EmVP). Bioresins with tunable printability and mechanical properties are produced, and a novel subset of gelatins and GelMA exhibiting stable shear-yielding behavior offers a new, single-component, ready-to-use suspension medium for in-bath printing, which is stable over multiple hours without needing temperature control. As proof-of-concept biological application, bioprinted gels are tested with insulin-producing pancreatic cell lines for 21 days of culture. Leveraging a multi-color printer, complex multi-material and multi-cellular geometries are produced, enhancing the accessibility of volumetric printing for advanced tissue models.
Organellular imagingin vivoreveals a depletion of endoplasmic reticular calcium during post-ictal cortical spreading depolarization
Authors: Stern Matthew A. , Cole Eric R. , Gutekunst Claire-Anne , Yang Jenny J. , Berglund Ken , Gross Robert E.
Published: September 2024

Abstract

During cortical spreading depolarization (CSD), neurons exhibit a dramatic increase in cytosolic calcium, which may be integral to CSD-mediated seizure termination. This calcium increase greatly exceeds that during seizures, suggesting the calcium source may not be solely extracellular. Thus, we sought to determine if the endoplasmic reticulum (ER), the largest intracellular calcium store, is involved. We developed a two-photon calcium imaging paradigm to simultaneously record the cytosol and ER during seizures in awake mice. Paired with direct current recording, we reveal that CSD can manifest as a slow post-ictal cytosolic calcium wave with a concomitant depletion of ER calcium that is spatiotemporally consistent with a calcium-induced calcium release. Importantly, we observed both naturally occurring and electrically induced CSD suppressed post-ictal epileptiform activity. Collectively, this work links ER dynamics to CSD, which serves as an innate process for seizure suppression and a potential mechanism underlying therapeutic electrical stimulation for epilepsy.
Direct and ultrasensitive bioluminescent detection of intact respiratory viruses
Authors: Gräwe Alexander , van der Veer Harm , Jongkees Seino A.K. , Flipse Jacky , Rossey Iebe , de Vries Robert P. , Saelens Xavier , Merkx Maarten
Published: September 2024

Respiratory viruses such as SARS-CoV-2, influenza, and respiratory syncytial virus (RSV) represent pressing health risks. Rapid diagnostic tests for these viruses detect single antigens or nucleic acids, which do not necessarily correlate with the amount of intact virus. Instead, specific detection of intact respiratory virus particles may better assess the contagiousness of a patient. Here, we report GLOVID, a modular biosensor platform to detect intact virions against a background of ‘free’ viral proteins in solution. Our approach harnesses the multivalent display of distinct proteins on the surface of a viral particle to template the reconstitution of a split luciferase, allowing specific, single-step detection of intact influenza A and RSV virions corresponding to 0.1 - 0.3 fM of genomic units. The protein ligation system used to assemble GLOVID sensors is compatible with a broad range of binding domains, including nanobodies, scFv fragments and cyclic peptides, which allows straightforward adjustment of the sensor platform to target different viruses.
Comprehensive annotations of alternative splicing, lncRNAs, and circRNAs in seven species of flowering plants
Authors: Gabel Alexander , Schuster Christoph , Drost Hajk-Georg , Meyerowitz Elliot M. , Grosse Ivo
Published: September 2024

The successful occupation of terrestrial habitats by early plants was catalyzed by the adaptive evolution of new organs able to supply water and compensate for the gravitational impact under changing land conditions. Because plants are sessile, it has been proposed that the capacity of plants to innovate specialized organs is driven by a complex interplay between developmental gene expression and regulatory RNAs such as lncRNAs and circRNAs, evolving through sequence polymorphisms, genomic rearrangements, and expression divergence. Despite the importance of alternative and noncoding transcripts for enabling plant life, their accurate quantification causes major challenges as many of them are expressed at low levels and tissue-specific. Here, we describe the re-annotation of seven land plant genomes based on deep, organ-specific, ribo-depleted developmental RNA-Seq data. Using this comparative resource, we uncover 5,000 new lncRNAs and 2,000 new circular RNAs that are promising candidates for further functional investigation. Our annotation will become a reference catalog for studies on plant organ evolution and for uncovering tissue-specific patterns of transcript emergence.
Global diversity of soil-transmitted helminths reveals population-biased genetic variation that impacts diagnostic targets
Authors: Papaiakovou Marina , Waeschenbach Andrea , Ajibola Olumide , Ajjampur Sitara SR , Anderson Roy M , Bailey Robin , Benjamin-Chung Jade , Cambra-Pellejà Maria , Caro Nicolas R , Chaima David , Cimino Ruben O , Cools Piet , Cossa Anélsio , Dunn Julia , Galagan Sean , Gandasegui Javier , Grau-Pujol Berta , Houlder Emma L , Ibikounlé Moudachirou , Jenkins Timothy P , Kalua Khumbo , Kjetland Eyrun F , Krolewiecki Alejandro J , Levecke Bruno , Luty Adrian , MacDonald Andrew , Mandomando Inácio , Manuel Malathi , Martínez-Valladares Maria , Mejia Rojelio , Mekonnen Zeleke , Messa Augusto , Mpairwe Harriet , Muchisse Osvaldo , Muñoz Jose , Mwinzi Pauline , Novela Valdemiro , Odiere Maurice R , Sacoor Charfudin , Walson Judd L , Williams Steven A , Witek-McManus Stefan , Littlewood D. Timothy J. , Cantacessi Cinzia , Doyle Stephen R
Published: September 2024

Soil-transmitted helminths (STHs) are intestinal pathogens affecting over a billion people worldwide. STH control relies on microsopy-based diagnostics to monitor parasite prevalence and enable post-treatment surveillance, however, molecular diagnostics are rapidly being developed due to increased sensitivity, particularly in low-STH-prevalence settings. The genetic diversity of helminths and its potential impact on molecular diagnostics remains unclear. Using low-coverage genome sequencing, we assessed the presence of STHs in worm, faecal and purified egg samples from 27 countries, identifying differences in the genetic connectivity and diversity of STH-positive samples across regions and cryptic diversity between closely related human- and pig-infective species. We defined substancial copy number and sequence variants in current diagnostic targets and validated the impact of genetic variants on qPCR diagnostics usingin vitroassays. Our study provides insights into the diversity and genomic epidemiology of STHs, highlighting challenges and opportunities for developing molecular diagnostics needed to support STH control efforts.