bluuebunny/crossref_metadata_2025 huggingface dataset:
A Joint Trauma System Clinical Practice Guideline: Traumatic Brain Injury Management and Basic Neurosurgery in the Deployed Environment
Authors: Dengler Bradley , McCafferty Randall , Neal Christopher , Bell Randy , Sonka Brian J , Jensen Shane , Tadlock Matthew D , Van Gent Jan-Michael , How Remealle A , Gurney Jennifer
Published: June 2024

Management of the patient with moderate to severe brain injury in any environment can be time consuming and resource intensive. These challenges are magnified while forward deployed in austere or hostile environments. This Joint Trauma System Clinical Practice Guideline provides recommendations for the treatment and medical management of casualties with moderate to severe head injuries in an environment where personnel, resources, and follow-on care are limited. These guidelines have been developed by acknowledging commonly recognized recommendations for neurosurgical and neuro-critical care patients and augmenting those evaluations and interventions based on the experience of neurosurgeons, trauma surgeons, and intensivists who have delivered care during recent coalition conflicts.
Distributed Maritime Operations and the Medical Challenge: How a Medical Common Operating Picture Can Help Bridge the Gap
Authors: Cole Jacob H , Hughey Scott , Kotler Joshua , de Geus John , Brust Adam , Checchi Kyle , Lin Andrew
Published: June 2024

This work explores the challenges of delivering medical care in the geographically dispersed and resource-constrained environment of Distributed Maritime Operations (DMO) and Expeditionary Advanced Base Operations (EABO). Traditional medical planning approaches may struggle to adapt to the vast operational space, extended evacuation times, and limited medical force present in these scenarios. The concept of a Medical Common Operating Picture (COP) emerges as a potential solution. By providing a shared view of the medical situation across the theater, encompassing logistics, personnel, and patient data, a medical COP has the potential to facilitate medical command and control (MED C2) in DMO/EABO. The implementation of a medical COP has the potential to optimize resource allocation, enhance situational awareness, streamline medical evacuation, and reduce healthcare provider moral injury in large-scale combat operations. A medical COP will allow medical planners to make informed decisions on triage, resupply, and evacuation, ensuring the best use of limited medical resources. This is done by leveraging a comprehensive understanding of the medical landscape, enabling informed clinical and operational decision-making by humanitarian and combat personnel respectively. A fully realized medical COP system will enable a dynamic theater evacuation policy, balancing the conflicting needs of patient care at higher echelons with the operational expediency of returning servicemembers to their operational units, thereby maximizing evacuation effectiveness. It will further enable medical personnel to perform dynamic casualty triage based on operational realities, mitigating potential ethical dilemmas. Implementing such a medical COP system will require overcoming communication limitations to facilitate data exchange and potentially integrating clinical decision support tools for real-time data analysis and recommendations. It will also require the rapid adoption of modernized operational medicine documentation solutions by medical assets within the operational forces. Ultimately, this work suggests that a medical COP has the potential to bridge the gap between traditional medical planning and the unique demands of DMO/EABO, ultimately optimizing casualty care, maximizing resource efficiency, and preserving the fighting force.
Candida auris: Outbreak, surveillance and epidemiological monitoring in Northern Greece
Authors: Poulopoulou Aikaterina , Sidiropoulou Anna , Sarmourli Theopisti , Zachrou Evaggelia , Michailidou Chrysi , Zarras Charalampos , Vagdatli Eleni , Massa Eleni , Mouloudi Eleni , Pyrpasopoulou Athina , Meletis Georgios , Protonotariou Efthymia , Skoura Lemonia , Metallidis Simeon , Karampatakis Theodoros , Katsifa Eleni , Nikopoulou Anna , Louka Alexandra , Rizou Artemisia , Arvaniti Kostoula , Kouvelis Vassili , Borman Andrew , Roilides Emmanuel , Vyzantiadis Timoleon-Achilleas
Published: June 2024

Candida auris is an emerging fungal pathogen associated with multi-drug resistance rates and widespread outbreaks in hospitals and healthcare units worldwide. Sequencing studies have revealed that different clonal lineages of the fungus seem to be prevalent among distinct geographical sites. The first case of C. auris in Northern Greece was reported in Thessaloniki in October 2022, almost 2 years after the first isolation in Greece (Athens 2019). The Mycology Laboratory of the Medical School of Aristotle University of Thessaloniki stands as the reference laboratory for fungal diseases in Northern Greece and a meticulous search for the yeast, in plenty of suspicious samples, has been run since 2019 in the Lab as well as a retrospective analysis of all its yeasts’ collection, back to 2008, with negative results for the presence of C. auris. Here, are presented the findings concerning the outbreak and surveillance of C. auris in Northern Greece, mainly the region of Thessaloniki and the broader area of Macedonia, from October 2022 until August 2023. The isolates from Northern Greece continue to fall in Clade I and present with an almost equal and stable sensitivity profile until now.
Results of a long-term optical variability study of 11 quasars and VRI photometry of comparison stars
Authors: Minev Milen , Trifonov Trifon , Ivanov Valentin D , Ovcharov Evgeni , Bozhilov Vladimir , Valcheva Antoniya , Kostov Andon , Nedialkov Petko
Published: June 2024

We present the results of a 15-yr long-term optical monitoring of 11 quasars conducted with the 2-m Ritchey–Chretien–Coude and the 50/70 cm Schmidt telescopes at the Rozhen National Astronomical Observatory, Bulgaria. Our observations are performed with standard Johnson-Cousins $VRI$ band filters and for each quasar we present a set of comparison standard stars that can be used for monitoring of objects in these fields (including finding charts for the stars identification). The variability and periodicity of each quasar are analysed individually and discussed. The physical properties of each quasar, such as their classification, redshift, and radio structures, are also discussed based on previous literature. Damped random walk model shows the best or the second best fit to the light curves of all objects. However, in six cases periodic models provide comparably good fits and make these six objects a valuable addition to the growing sample of quasars with periodic flux variation. They will be suitable for further investigation of the hitherto unclear mechanisms that give rise to this variability pattern. Our results provide important insights into the long-term variability and physical properties of quasars, which can further deepen our understanding of the nature and evolution of active galaxy nuclei.
Unveiling the (in)consistencies among the galaxy stellar mass function, star formation histories, satellite abundances, and intracluster light from a semi-empirical perspective
Authors: Fu Hao , Shankar Francesco , Ayromlou Mohammadreza , Koutsouridou Ioanna , Cattaneo Andrea , Bertemes Caroline , Bellstedt Sabine , Martín-Navarro Ignacio , Leja Joel , Allevato Viola , Bernardi Mariangela , Boco Lumen , Dimauro Paola , Gruppioni Carlotta , Lapi Andrea , Menci Nicola , Rodríguez Iván Muñoz , Puglisi Annagrazia , Alonso-Tetilla Alba V
Published: June 2024

In a hierarchical, dark matter-dominated Universe, stellar mass functions (SMFs), galaxy merger rates, star formation histories (SFHs), satellite abundances, and intracluster light (ICL), should all be intimately connected observables. However, the systematics affecting observations still prevent universal and uniform measurements of, for example, the SMF and the SFHs, inevitably preventing theoretical models to compare with multiple data sets robustly and simultaneously. We here present our holistic semi-empirical model decode (Discrete statistical sEmi-empiriCal mODEl) that converts via abundance matching dark matter merger trees into galaxy assembly histories, using different SMFs in input and predicting all other observables in output in a fully data-driven and self-consistent fashion with minimal assumptions. We find that: (1) weakly evolving or nearly constant SMFs below the knee ($M_\star \lesssim 10^{11} \, \mathrm{M}_\odot$) are the best suited to generate SFHs aligned with those inferred from MaNGA, SDSS, GAMA, and, more recently, JWST; (2) the evolution of satellites after infall only affects the satellite abundances and SFHs of massive central galaxies but not their merger histories; (3) the resulting SFR–$M_\star$ relation is lower in normalization by a factor of $\sim 2$ with respect to observations, with a flattening at high masses more pronounced in the presence of mergers; (4) the latest data on ICL can be reproduced if mass-loss from mergers is included in the models. Our findings are pivotal in acting as pathfinder to test the self-consistency of the high-quality data from, e.g. JWST and Euclid.
Past orbital evolution and its effects on the surface of (162173) Ryugu
Authors: Guimarães M C , Araujo R A N , Winter O C
Published: June 2024

The Japanese probe Hayabusa 2 recently visited the NEA (162173) Ryugu. This mission provided valuable information about the asteroid, including in situ images and a surface sample brought back to the Earth. The data suggests that Ryugu has likely been affected by space weathering, but the underlying cause of the surface modification remains unclear. This paper aims to shed light on the problem by providing new information about the possible past orbital path of Ryugu. We used a procedure to estimate how Ryugu has dynamically evolved since it entered the NEAs’ region and whether this can explain the observed data. We have conducted numerical integrations of the N-body gravitational problem. The system comprises the Sun, the Solar system’s eight planets, and a group of 29 000 test particles initially placed in the main asteroidal belt (MAB) near the ν6 secular resonance. We then tracked the particles that left the MAB and eventually arrived close to Ryugu’s current orbit. Our analysis showed that out of 307 clones of Ryugu, only three came very close to the Sun at a distance of less than 0.1 au. Consequently, it is unlikely that Ryugu has undergone significant surface temperature variations. We also computed that ∼70 per cent of the clones have spent more than 5 Myr at an equivalent distance of 1 au from the Sun. This result suggests that Ryugu has been exposed to significant amounts of solar radiation over a long period, which may have resulted in space weathering effects on its surface.
Germline susceptibility from broad genomic profiling of pediatric brain cancers
Authors: Mardis Elaine R , Potter Samara L , Schieffer Kathleen M , Varga Elizabeth A , Mathew Mariam T , Costello Heather M , Wheeler Gregory , Kelly Benjamin J , Miller Katherine E , Garfinkle Elizabeth A R , Wilson Richard K , Cottrell Catherine E
Published: June 2024

Background

Identifying germline predisposition in CNS malignancies is of increasing clinical importance, as it contributes to diagnosis and prognosis, and determines aspects of treatment. The inclusion of germline testing has historically been limited due to challenges surrounding access to genetic counseling, complexity in acquiring a germline comparator specimen, concerns about the impact of findings, or cost considerations. These limitations were further defined by the breadth and scope of clinical testing to precisely identify complex variants as well as concerns regarding the clinical interpretation of variants including those of uncertain significance.

Methods

In the course of conducting an IRB-approved protocol that performed genomic, transcriptomic and methylation-based characterization of pediatric CNS malignancies, we cataloged germline predisposition to cancer based on paired exome capture sequencing, coupled with computational analyses to identify variants in known cancer predisposition genes and interpret them relative to established clinical guidelines.

Results

In certain cases, these findings refined diagnosis or prognosis or provided important information for treatment planning.

Conclusions

We outline our aggregate findings on cancer predisposition within this cohort which identified 16% of individuals (27 of 168) harboring a variant predicting cancer susceptibility and contextualize the impact of these results in terms of treatment-related aspects of precision oncology.
Spike N354 glycosylation augments SARS-CoV-2 fitness for human adaptation through structural plasticity
Authors: Liu Pan , Yue Can , Meng Bo , Xiao Tianhe , Yang Sijie , Liu Shuo , Jian Fanchong , Zhu Qianhui , Yu Yuanling , Ren Yanyan , Wang Peng , Li Yixin , Wang Jinyue , Mao Xin , Shao Fei , Wang Youchun , Gupta Ravindra Kumar , Cao Yunlong , Wang Xiangxi
Published: June 2024

Selective pressures have given rise to a number of SARS-CoV-2 variants during the prolonged course of the COVID-19 pandemic. Recently evolved variants differ from ancestors in additional glycosylation within the spike protein receptor-binding domain (RBD). Details of how the acquisition of glycosylation impacts viral fitness and human adaptation are not clearly understood. Here, we dissected the role of N354-linked glycosylation, acquired by BA.2.86 sub-lineages, as a RBD conformational control element in attenuating viral infectivity. The reduced infectivity is recovered in the presence of heparin sulfate, which targets the ‘N354 pocket’ to ease restrictions of conformational transition resulting in a ‘RBD-up’ state, thereby conferring an adjustable infectivity. Furthermore, N354 glycosylation improved spike cleavage and cell–cell fusion, and in particular escaped one subset of ADCC antibodies. Together with reduced immunogenicity in hybrid immunity background, these indicate a single spike amino acid glycosylation event provides selective advantage in humans through multiple mechanisms.
Immobile polyanionic backbone enables a 900-μm-thick electrode for compact energy storage with unprecedented areal capacitance
Authors: Li Haoran , Wu Zhitan , Liu Xiaochen , Lu Haotian , Zhang Weichao , Li Fangbing , Yu Hongyuan , Yu Jinyang , Zhang Boya , Xiong Zhenxin , Tao Ying , Yang Quan-Hong
Published: June 2024

Thickening of electrodes is crucial for maximizing the proportion of active components and thus improving the energy density of practical energy storage cells. Nevertheless, trade-offs between electrode thickness and electrochemical performance persist because of the considerably increased ion transport resistance of thick electrodes. Herein, we propose accelerating ion transport through thick and dense electrodes by establishing an immobile polyanionic backbone within the electrode pores; and as a proof of concept, gel polyacrylic electrolytes as such a backbone are in situ synthesized for supercapacitors. During charge and discharge, protons rapidly hop among RCOO− sites for oriented transport, fundamentally reducing the effects of electrode tortuosity and polarization resulting from concentration gradients. Consequently, nearly constant ion transport resistance per unit thickness is achieved, even in the case of a 900-μm-thick dense electrode, leading to unprecedented areal capacitances of 14.85 F cm−2 at 1 mA cm−2 and 4.26 F cm−2 at 100 mA cm−2. This study provides an efficient method for accelerating ion transport through thick and dense electrodes, indicating a significant solution for achieving high energy density in energy storage devices, including but not limited to supercapacitors.
Missed Opportunities: A Narrative Review on Why Nonoccupational Postexposure Prophylaxis for HIV Is Underutilized
Authors: Allan-Blitz Lao-Tzu , Mayer Kenneth H
Published: June 2024

Postexposure prophylaxis (PEP) is an important tool for preventing HIV infection but remains underutilized. In this narrative review, we aim to summarize the frequency of missed opportunities for prescribing PEP among studies from around the world, discuss the complexities of the challenges facing PEP provision, and describe possible solutions. We identified 20 studies published in the last 10 years among 43 832 individuals, of whom an estimated 41 477 were eligible for PEP. Of those eligible for PEP, PEP was prescribed among 27 705 (66.8%). There was a significant difference in PEP prescriptions in acute compared with non–acute care settings (63.5% vs 94.5%; P < .001). Emergent themes contributing to PEP underutilization included lack of provider and patient awareness, reduced PEP acceptability, HIV stigma and homophobia, lack of access (either to care or to medication), and stigmatizing policies. Each of those issues should be the focus of future PEP implementation efforts.
In situ forest with lycopsid trees bearing lobed rhizomorphs from the Upper Devonian of Lincheng, China
Authors: Qin Min , Wang Deming , Liu Le , Liu Lu , Zhou Yi
Published: June 2024

The earliest forests in the Devonian were reported from only four localities worldwide. The tree lycopsids, sometimes as the primary elements of Devonian forests, had evolved several types of rooting systems. In recent years, we found and excavated a Late Devonian (Famennian, 374–359 Ma) lycopsid forest from Zhejiang Province, China. The fossil forest occurs at seven locations of Lincheng Town of Changxing County and mainly consists of in situ small tree lycopsid (Heliodendron longshanense gen. et sp. nov.) stems usually connected to lobed cormose rhizomorphs. The four short lobes of each rhizomorph often branch once and bear roots arranged radially. Allometry is observed between the trunk diameter of Heliodendron and the length of its rhizomorphic lobes, indicating that the trunk develops later than the rhizomorph in tree lycopsid plants. The Devonian witnessed the transformation from clastic nonlycopsid dominated forests to Carboniferous swampy forests dominated by giant lycopsid trees. These trees form a multigenerational community, as shown by the in situ preserved stems at various levels within the same area due to frequent sedimentation events.
The role of retinal irradiance estimates in melanopsin-driven retinal responsivity: a reanalysis of the post-illumination pupil response in seasonal affective disorder
Authors: Klevens Alison M , Taylor Maddison L , Wescott Delainey L , Gamlin Paul D , Franzen Peter L , Hasler Brant P , Siegle Greg , Roecklein Kathryn A
Published: June 2024

To isolate melanopsin contributions to retinal sensitivity measured by the post-illumination pupil response (PIPR), controlling for individual differences in non-melanopsin contributions including retinal irradiance is required. When methodologies to negate such differences present barriers, statistical controls have included age, baseline diameter, iris pigmentation, and circadian time of testing. Alternatively, the pupil light reflex (PLR) and calculations estimating retinal irradiance both reflect retinal irradiance, while the PLR also reflects downstream pathways. We reanalyzed data from an observational, correlational study comparing the PIPR across seasons in seasonal affective disorder (SAD) and controls. The PIPR was measured in 47 adults in Pittsburgh, Pennsylvania (25 SAD) over 50 seconds after 1 second of red and blue stimuli of 15.3 log photons/cm2/s. The PLR was within 1 second while PIPR was averaged over 10–40 seconds post-stimulus. Two raters ranked iris pigmentation using a published scale. We evaluated model fit using Akaike’s Information Criterion (AIC) across different covariate sets. The best-fitting models included either estimated retinal irradiance or PLR, and circadian time of testing. The PLR is collected contemporaneously in PIPR studies and is an individually specific measure of nonspecific effects, while being minimally burdensome. This work extends the prior publication by introducing theoretically grounded covariates that improved analytic model fits based on AIC specific to the present methods and sample. Such quantitative methods could be helpful in studies which must balance participant and researcher burden against tighter methodological controls of individual differences in retinal irradiance.
An engineering biology approach to automated workflow and biodesign
Authors: Casas Alexis , Bultelle Matthieu , Kitney Richard
Published: June 2024

The paper addresses the application of engineering biology strategies and techniques to the automation of laboratory workflow—primarily in the context of biofoundries and biodesign applications based on the Design, Build, Test and Learn paradigm. The trend toward greater automation comes with its own set of challenges. On the one hand, automation is associated with higher throughput and higher replicability. On the other hand, the implementation of an automated workflow requires an instruction set that is far more extensive than that required for a manual workflow. Automated tasks must also be conducted in the order specified in the workflow, with the right logic, utilizing suitable biofoundry resources, and at scale—while simultaneously collecting measurements and associated data. The paper describes an approach to an automated workflow that is being trialed at the London Biofoundry at SynbiCITE. The solution represents workflows with directed graphs, uses orchestrators for their execution, and relies on existing standards. The approach is highly flexible and applies to not only workflow automation in single locations but also distributed workflows (e.g. for biomanufacturing). The final section presents an overview of the implementation—using the simple example of an assay based on a dilution, measurement, and data analysis workflow.
A meta-regression analysis to evaluate the effects of narasin on grow-finish pig performance
Authors: Becker Larissa L , Gebhardt Jordan T , Tokach Mike D , Arentson Roger A , Shields Michael , Woodworth Jason C , Goodband Robert D , DeRouchey Joel M , Seltzer Jenna A , Puls Christopher L
Published: June 2024

Ionophores are feed additives that decrease gram-positive microbial populations by disrupting the ion transfer across cell membranes resulting in improved growth performance. Narasin (Skycis; Elanco Animal Health, Greenfield, IN) is an FDA-approved ionophore utilized for increased rate of weight gain and improved feed efficiency in growing-finishing pigs. A meta-regression analysis was conducted to evaluate the effects of added narasin in growing-finishing pig diets to predict its influence on average daily gain (ADG), feed efficiency (G:F), and carcass yield. A database was developed containing 21 technical reports, abstracts, and refereed papers from 2012 to 2021 representing 35 observations for growth performance data in studies ranging from 35 to 116 d in length (overall data). In addition, within these 35 observations, individual period data were evaluated (143 observations) using weekly, bi-weekly, or monthly performance intervals (period data). Regression model equations were developed, and predictor variables were assessed with a stepwise manual forward selection procedure. The ADG model using the overall data included ADG, ADFI, and G:F of the control group, added narasin dose, and narasin feeding duration categorized as longer or shorter than 65 d. Predictor variables included in the G:F model using overall data were ADG, ADFI, and G:F of the control group and added narasin dose. For carcass yield, the final model included ADFI and G:F of the control group, added narasin dose, and narasin feeding duration of longer than 65 d. In the period model for ADG, the predictors included ADG, ADFI, and G:F of the control group, added narasin dose, and average BW of the control group categorized into greater than or less than 105 kg. For period data for G:F, the model selected ADG, ADFI, and G:F of the control group and added narasin dose. Based on the results, the overall response to added narasin for ADG and G:F was quadratic and tended to decrease as ADG and G:F increased. A similar quadratic response was observed for the individual period data. In summary, using median values from the database for predictor variables, this meta-analysis demonstrated narasin would be expected to improve ADG between 1.06% and 1.65%, G:F between 0.71% and 1.71%, and carcass yield by 0.31% when fed continuously for longer than 65 d.
Assessing Outcome Measurements and Impact of Simulation in Neurocritical Care Training: A Systematic Review
Authors: Yousef Khalil M. , Alananzeh Ibrahim , Beegom Shameena , Chavez Jose , Hatahet Sarah , Khalil Heba , Krom Zachary , Svetlov Olena
Published: June 2024

AIM: The use of simulation training in neurocritical care is increasing. Yet, the pooled impact on patient and trainee outcomes remains unclear. This systematic review aims to determine the outcome measurements used after simulation training in neurocritical care and to synthesize the current evidence about the impact of simulation training on these outcomes. METHODS: A 3-step search was conducted in CINAHL, Cochrane, MEDLINE, PsychINFO, and Scopus. The inclusion criteria were composed of studies exploring simulation training in neurocritical care, published in English between 2000 and 2023. Two reviewers independently conducted screening, critical appraisal, and data extraction, using standardized Joanna Briggs Institute tools. Meta-analysis was precluded because of clinical, methodological, and statistical heterogeneity. RESULTS: Nine relevant studies were found: 1 quality improvement project and 8 quasi-experimental studies. The overall quality of the relevant studies was moderate to high (61.1%–77.8%). Three types of outcome measurements for simulation in neurocritical care were identified: knowledge and clinical performance; confidence and comfort; and teamwork, communication, and leadership skills. Simulation training was associated with a significant improvement in knowledge and clinical performance, and confidence and comfort, but not in communication and leadership skills. CONCLUSION: Significant improvement in trainees' outcomes was observed. The current literature includes significant heterogeneity in the methods of evaluating simulation outcomes, although no patient outcomes were observed. Investigating the effect of simulation in neurocritical care training on patient outcomes in future studies is warranted.
Primary leiomyosarcoma of the colon: a report of two cases and review of literature
Authors: Doan Tu Trong , Pham Duong The
Published: June 2024

Introduction

Primary leiomyosarcoma (LMS) of the colon is a rare neoplasm and constitutes less than 0.1% of all colon malignancies. These tumors are more aggressive and have poorer prognoses than other gastrointestinal tumors, including gastrointestinal stromal tumors (GIST) or adenocarcinomas. The authors herein report two cases and review the literature to highlight the epidemiology, diagnosis, treatment and prognosis of this uncommon malignancy.

Case report

The authors reported two very rare cases of LMS of left colon, which referred to our institution with symptoms of abdominal pain. After the initial investigations, patients were diagnosed with primary colonic leiomyosarcoma that underwent laparotomy. In both cases pathological examination revealed a spindle cell tumor growing circumferentially and transmurally in the colon. Final immunohistochemistry were positive with SMA, CK and desmin without the expression of GIST markers (CD117, CD34 and DOG1) that confirmed leiomyosarcoma. One patient was diagnosed with diffused peritoneal metastasis at 6 months postoperatively and he died after 2 months of paliative care, another one is still on active surveillance.

Discussion

LMS of the colon is a really rare entity and is only presented in clinical case reports. LMS has non-specific symptoms and is commonly diagnosed when it reaches a large size. Surgery is a mainstay treatment option. Nowadays, there is no clear evidence for the effectiveness of chemotherapy and radiation therapy.

Conclusion

LMS is a rare neoplasm of colon. For the time being, there is no guidelines for treatment, but surgery still plays a fundamental role.
Comparative genomics of parasitoid lifestyle as exemplified by Mermithidae and Nematomorpha
Authors: Kirangwa Joseph , Bednarski Viktoria , Guiglielmoni Nadège , Poulin Robert , Dowle Eddy , Schiffer Philipp H. , Holovachov Oleksandr
Published: June 2024

Mermithidae and Nematomorpha are parasitoids united by the commonalities in their lifestyle – immature stages infect arthropod hosts, species from both phyla can manipulate their host to induce a similar water-seeking behaviour, and both have a final free-living non-feeding adult reproductive stage, often killing their host upon emergence. Some of these species are of great economic importance, being evaluated as biological control agents against mosquito vectors responsible for diseases like malaria, and other insect pests, but with scarce genomic resources currently available. Nematomorpha, despite being closely related to Nematoda, received insufficient attention in genomic research, leading to gaps in our understanding of their diverse genetic makeup. This study aimed to investigate the genetic features encoded in the genomes of both parasitoid taxa to identify similarities and parallels linked to their ecological lifestyles. We performed a comparative analysis of 12 genomes, comprising parasitoid, parasitic and free-living worms. The investigation revealed genomic signatures unique to parasitoid species, including expanded gene families enriched in neural transmission modulation, likely linked to the known host manipulation that both mermithids and nematomorphs exert on their hosts. The analysis also uncovered a diverse array of conserved transposable element superfamilies across both lineages. The findings from this study provide valuable insights into the potential genomic adaptations associated with parasitoidism in nematode and nematomorph worms. The identification of expanded gene families and conserved transposable element superfamilies sheds light on the molecular underpinnings of their unique biological traits. Additionally, the core set of orthologs specific to parasitoid worms offers new avenues for understanding the evolution of parasitism within these groups of organisms.
Evolutionary diversification of ancestral genes across vertebrates and insects
Authors: Mantica Federica , Irimia Manuel
Published: June 2024

Background

Vertebrates and insects diverged approximately 700 million years ago, and yet they retain a large core of conserved genes from their last common ancestor. These ancient genes present strong evolutionary constraints, which limit their overall sequence and expression divergence. However, these constraints can greatly vary across ancestral gene families and, in at least some cases, sequence and expression changes can have functional consequences. Importantly, overall patterns of sequence and expression divergence and their potential functional outcomes have never been explored in a genome-wide manner across large animal evolutionary distances.

Results

We focused on approximately 7,000 highly conserved genes shared between vertebrates and insects, and we investigated global patterns of molecular diversification driven by changes in sequence and gene expression. We identified molecular features generally linked to higher or lower diversification rates, together with gene groups with similar diversification profiles in both clades. Moreover, we discovered that specific sets of genes underwent differential diversification during vertebrate and insect evolution, potentially contributing to the emergence of unique phenotypes in each clade.

Conclusions

We generated a comprehensive resource of measures of sequence and expression divergence across vertebrates and insects, which revealed a continuous spectrum of evolutionary constraints among highly conserved genes. These constraints are normally consistent between these two clades and associated with specific molecular features, but in some cases we also identified cases of lineage-specific diversification likely linked to functional evolution.
Enhanced Cell Tracking Using A GAN-based Super-Resolution Video-to-Video Time-Lapse Microscopy Generative Model
Authors: Zargari Abolfazl , Mashhadi Najmeh , Shariati S. Ali
Published: June 2024

Cells are among the most dynamic entities, constantly undergoing various processes such as growth, division, movement, and interaction with other cells as well as the environment. Time-lapse microscopy is central to capturing these dynamic behaviors, providing detailed temporal and spatial information that allows biologists to observe and analyze cellular activities in real-time. The analysis of time-lapse microscopy data relies on two fundamental tasks: cell segmentation and cell tracking. Integrating deep learning into bioimage analysis has revolutionized cell segmentation, producing models with high precision across a wide range of biological images. However, developing generalizable deep-learning models for tracking cells over time remains challenging due to the scarcity of large, diverse annotated datasets of time-lapse movies of cells. To address this bottleneck, we propose a GAN-based time-lapse microscopy generator, termed tGAN, designed to significantly enhance the quality and diversity of synthetic annotated time-lapse microscopy data. Our model features a dual-resolution architecture that adeptly synthesizes both low and high-resolution images, uniquely capturing the intricate dynamics of cellular processes essential for accurate tracking. We demonstrate the performance of tGAN in generating high-quality, realistic, annotated time-lapse videos. Our findings indicate that tGAN decreases dependency on extensive manual annotation to enhance the precision of cell tracking models for time-lapse microscopy.
Estimating population size with repeated observations of non-invasive sampling in presence of misidentification
Authors: Fraysse Rémi , Choquet Rémi , Pradel Roger
Published: June 2024

Although non-invasive sampling is increasingly used in capture-recapture (CR) experiments, it carries a risk of misidentification that, if ignored, causes an overestimation of population size. Models that deal with misidentification have been proposed. However, these models assume that only one sample can be collected per individual at one occasion. This is not true for several experiments based on DNA, for example for those that extract the DNA from faecal samples. The models do not take repeated observations into account, leading to biased estimates.

In this paper, we develop an approach that extends the latent multinomial model (LMM) of Link et al., 2010 using a Poisson distribution to account for simultaneous multiple sampling of the same individual. We then conduct simulations to test how our new model performs. As an illustration, we applied the new Poisson model to a collection of Eurasian otter faeces Lampa et al., 2015.

Our findings indicate that repeated observations can be modelled without bias. The application on otters shows that our model is necessary to estimate properly the population size in presence of misidentification and repeated observations.
Comparative RNA profiling identifies stage-specific phasiRNAs and co-expressedArgonautegenes in Bambusoideae and Pooideae species
Authors: Bélanger Sébastien , Zhan Junpeng , Yu Yunqing , Meyers Blake C.
Published: June 2024

PhasiRNAs (phased, small interfering RNAs) play a crucial role in supporting male fertility in grasses. Earlier work in maize (Zea mays) and rice (Oryza sativa) – and subsequently many other plant species – identified premeiotic 21-nt and meiotic 24-nt phasiRNAs. More recently, a group of premeiotic 24-nt phasiRNAs were discovered in the anthers of two Pooideae species, barley (Hordeum vulgare) and bread wheat (Triticum aestivum). The conservation of premeiotic 24-nt phasiRNAs and other classes of reproductive phasiRNAs across Pooideae species remains unclear. We conducted a comparative RNA profiling of three anther stages in six Pooideae species and one Bambusoideae species. We observed complex temporal accumulation patterns of 21-nt and 24-nt phasiRNAs in Pooideae and Bambusoideae grasses. In Bambusoideae, 21-nt phasiRNAs accumulated during meiosis, whereas 24-nt phasiRNAs were present in both premeiotic and postmeiotic stages. We identified premeiotic 24-nt phasiRNAs in all seven species examined. These phasiRNAs exhibit distinct biogenesis mechanisms and potential Argonaute effectors compared to meiotic 24-nt phasiRNAs. We show that specificArgonautegenes co-expressed with stage-specific phasiRNAs are conserved across Bambusoideae and Pooideae species. Our degradome analysis identified a set of conserved miRNA target genes across species, while 21-nt phasiRNAs targets were species-specific. Cleavage of few targets was observed for 24-nt phasiRNAs.
Repeated evolution of reduced visual investment at the onset of ecological speciation in high-altitudeHeliconiusbutterflies
Authors: Rivas-Sánchez David F , Salazar Camilo , Pardo-Diaz Carolina , Merrill Richard M , Montgomery Stephen H
Published: June 2024

Colonisation of new habitats is typically followed by divergent selection acting on traits that are immediately important for fitness in the new habitat. For example, shifting sensory environments are often associated with variation in sensory traits critical for navigation and foraging. However, the extent to which the initial response to novel sensory conditions is mediated by phenotypic plasticity, and its contribution to early species divergence remains unclear. We took advantage of repeated cases of speciation inHeliconiusbutterflies with independent allopatric distributions in the west of the Colombian and Ecuadorian Andes. Using volumetric brain measurements, we analysed patterns of investment in sensory processing in brain components across different localities and habitats. We find that a higher-altitude species,H. chestertonii, differs in levels of investment in visual and olfactory brain centres compared to its lower altitude relativeH. erato venus, mainly attributable to heritable variation as inferred from comparisons between wild and common-garden reared individuals. We compared these shifts with those reported for another high-altitude species,H. himera, and its parapatric lowland counterpart,H. erato cyrbia, and demonstrate parallel reductions in the size of specific optic lobe neuropils. Conversely, for the antennal lobe, we detected disparate trait shifts inH. himeraandH. chestertoniiin respect to their lowlanderatoneighbours. Overall, our findings add weight to the adaptive potential for neuroanatomical divergence related to sensory processing during early species formation.

Lay summary

Repeated associations between trait variation and environmental shifts may indicate adaptation to local sources of natural selection. For instance, in fish, the presence of certain morphological traits in specific ecological conditions across independent populations is well documented, suggesting equivalent phenotypic responses to shared sources of natural selection. We compared independent cases of ecological divergence inHeliconiusbutterflies distributed along altitude gradients from sea level to mid mountain in the west of the Colombian and Ecuadorian Andes. Shifts in altitude involve repeated, abrupt transitions from wet, large-leaved, warm forests to higher dry, open, cold scrubs. We tested hypotheses about the role of these ecological shifts in driving adaptive evolution in neuroanatomical traits during early speciation. We showed that inHeliconius, independent changes in forest-type have been accompanied by heritable parallel patterns of divergence in sensory investment in visual processing in the brain. We propose these differences likely facilitate species divergence in the face of ongoing geneflow.
Combining quantitative proteomics and interactomics for a deeper insight into molecular differences between human cell lines
Authors: Bakhtina Anna A. , Wippel Helisa H. , Chavez Juan D. , Bruce James E.
Published: June 2024

Cellular functional pathways have evolved through selection based on fitness benefits conferred through protein intra- and inter-molecular interactions that comprise all protein conformational features and protein-protein interactions, collectively referred to as the interactome. While the interactome is regulated by proteome levels, it is also regulated independently by, post translational modification, co-factor, and ligand levels, as well as local protein environmental factors, such as osmolyte concentration, pH, ionic strength, temperature and others. In modern biomedical research, cultivatable cell lines have become an indispensable tool, with selection of optimal cell lines that exhibit specific functional profiles being critical for success in many cases. While it is clear that cell lines derived from different cell types have differential proteome levels, increased understanding of large-scale functional differences requires additional information beyond abundance level measurements, including how protein conformations and interactions are altered in certain cell types to shape functional landscapes. Here, we employed quantitativein vivoprotein cross-linking coupled to mass spectrometry to probe large-scale protein conformational and interaction changes among three commonly employed human cell lines, HEK293, MCF-7, and HeLa cells. Isobaric quantitative Protein Interaction Reporter (iqPIR) technologies were used to obtain quantitative values of cross-linked peptides across three cell lines. These data illustrated highly reproducible (R2values larger than 0.8 for all biological replicates) quantitative interactome levels across multiple biological replicates. We also measured protein abundance levels in these cells using data independent acquisition quantitative proteomics methods. Combining quantitative interactome and proteomics information allowed visualization of cell type- specific interactome changes mediated by proteome level adaptations as well as independently regulated interactome changes to gain deeper insight into possible drivers of these changes. Among the biggest detected alterations in protein interactions and conformations are changes in cytoskeletal proteins, RNA-binding proteins, chromatin remodeling complexes, mitochondrial proteins, and others. Overall, these data demonstrate the utility and reproducibility of quantitative cross-linking to study systems-level interactome variations. Moreover, these results illustrate how combined quantitative interactomics and proteomics can provide unique insight on cellular functional landscapes.

GRAPHICAL ABSTRACT
PFS alleviates bone destruction in collagen-induced arthritis mice associated with macrophage polarization
Authors: Sun Guangchen , Bao Chunmei , Sun Xin , Liu Yingqin
Published: June 2024

Periploca forrestii Schltr is a clinical traditional Chinese medicine for the treatment of Rheumatoid arthritis (RA). This study aimed to investigate effects of Periploca forrestii Schltr saponin (PFS) on bone destruction and macrophage polarization in arthritis model mice and to explore its possible mechanism. Arthritis was induced in two species, BALB/c and C57BL/6 mice, by immunization with type II chicken collagen. The arthritic mice were administered PFS for four weeks. The hindfeet, blood and spleen were harvested. Molecular expression was determined by ELISA, RT-PCR and immunoblotting. PFS treatment resulted in a significant reduction in paw swelling in both species of mice. PFS also reduced cartilage destruction and infiltration of osteoclasts in BALB/c mice. Furthermore, it decreased the levels of M1 macrophage cytokines while increasing the levels of M2 macrophage cytokines in the paw and plasma. Micro-CT results in C57BL/6 mice showed that PFS attenuated microstructural damage in bone tissue. PFS inhibited CD68 and affected the expression of M1 macrophage factors such as CCL-2, TLR4, and IL-1β in the mouse paw. In addition, PFS treatment increased the M2 macrophage factor CD206 and CD163. PFS inhibits the activation of ERK, JNK, and p38 and the expression of transcription factors, including STAT3, p65, and c-Fos. PFS may modulate pleiotropic macrophage polarization and thus play an ameliorative role in bone damage, therefore PFS may be an effective alternative drug for the treatment of RA.
Early IKKβ-dependent anabolic signature governs vascular smooth muscle cells fate and abdominal aortic aneurysm development
Authors: Doyon Priscilla , Kizilay-Mancini Ozge , Dô Florence , Huynh David , Mayer Gaétan , Lehoux Stéphanie , Ong Huy , Batardière Maelle , Quoc-Huy Vincent , Marleau Sylvie , Gravel Simon-Pierre , Servant Marc J
Published: June 2024

Background

Abdominal aortic aneurysm (AAA) is a detrimental disease with no effective pharmacological therapy. While inflammation is recognized as one of the key regulators of AAA, targeting inflammatory pathways once the disease is established does not impact the outcomes. However, understanding the earliest molecular indicators could shed light on the precise biological targets and prognostic markers for AAA.

Methods

Using apolipoprotein E (ApoE)-deficient mice fed with a standard diet and infused with Angiotensin II (Ang II), we conducted bulk RNA-sequencing (RNA-Seq) analysis on suprarenal (SRA) regions obtained from both unchallenged and challenged WT mice, specifically examining responses 24 hours after Ang II infusion to capture the initial phases of aortic stress response. We further created a unique model of hyperlipidemic mice in which the expression of the inhibitor of nuclear factor kappa B kinase subunit beta (IKKβ) can be conditionally (via tamoxifen injection) suppressed in vascular smooth muscle cells (VSMC). The development of AAA was evaluated using in situ examination and quantified using RT-qPCR, immunohistochemistry and fluorescence microscopy. Cultured VSMC were exposed to the selective IKKβ inhibitor MLN120b and the expression levels of phenotypic markers kruppel like factor 4 (KLF4), β-Catenin and cellular communication network factor 2 (CCN2) were addressed using cellular extracts and immunoblot analysis.

Results

RNA-Seq data support the presence of early anabolic events in SRA regions detailing activation of the mammalian target of rapamycin complex 1 (mTORC1) pathway, which paralleled cellular anabolic processes including mitochondria, ribosome and sterol biosynthesis, the Unfolded Protein Response (UPR) and fibrogenesis. Conditional deletion of theIkbkbgene in VSMC significantly reduces the incidence of SRA lesions as well as the rate of aneurysm ruptures in mice exposed to Ang II.In situanalysis further demonstrated that the protection conferred by the lack of IKKβ expression in VSMC is associated with reduced inflammatory response, the preservation of the contractile over the degradative VSMC phenotypes, and the absence of an anabolic signature.

Conclusion

Our results not only reinforce the major roles played by VSMC in the rapid adaptation leading to the deleterious remodeling of the vascular wall and aortic lesions but also support a paradigm aiming at repositioning the efforts focusing on anabolic rather than inflammatory events.