bluuebunny/crossref_metadata_2025 huggingface dataset:
Prevalence, pain trajectories, and presurgical predictors for chronic postsurgical pain in a pediatric sample in Spain with a 24-month follow-up
Authors: Ceniza-Bordallo Guillermo , Gómez Fraile Andrés , Martín-Casas Patricia , Rabbitts Jennifer A. , Li Rui , Palermo Tonya M. , López-de-Uralde-Villanueva Ibai
Published: July 2024

Pediatric chronic pain, particularly chronic postsurgical pain (CPSP), poses a significant public health challenge, impacting 20% of pediatric populations. While several presurgical predictors have been identified, there is a scarcity of data on long-term outcomes, especially beyond 1 to 2 years postsurgery. Previous research primarily focuses on North American children, creating gaps in understanding CPSP outcomes in diverse health systems, such as in Spain. This study, registered as NCT04735211, investigates CPSP in 159 children and adolescents (mean age = 12.4 years, 37.1% girls, retention rate = 65%) undergoing various surgeries in Spain. The objectives include examining CPSP prevalence (Numerical Rating Scale ≥ 4) at 3, 6, 12, and 24 months, exploring postsurgical pain trajectories through group-based trajectory modeling, and identifying potential presurgical predictors for CPSP (pain intensity, pain catastrophizing, pain anxiety, fear of pain, kinesiophobia, health-related quality of life, pain interference, and physical activity), using multiple logistic regressions. Results show a CPSP prevalence of 41% at 3 months, decreasing to 14% at 24 months. Presurgical factors including pain intensity (adjusted odds ratio [aOR] = 1.25, 95% confidence interval [CI] = 1.02-1.53), pain catastrophizing (aOR = 1.06, 95% CI = 1.00-1.13), and pain anxiety (aOR = 1.06, 95% CI = 1.02-1.11) were associated with CPSP at 3 months. Group-based trajectory modeling revealed 3 postsurgical pain trajectories: Low Pain with Rapid Recovery Group (30.2%), Moderate Pain with Recovery Group (53.5%), and High Pain with Slow Recovery Group (16.3%), with group differences in presurgical predictors, excluding physical activity. This study contributes valuable insights into CPSP, emphasizing the need for long-term follow-up. The findings could inform the implementation of preventive programs for CPSP into diverse health systems.
Construction of a Risk Prediction Model for the Occurrence of Acute Skin Failure in Critically Ill Patients: A Prospective Study
Authors: ZHU Li-Hong , SHEN Yan-Fei , REN Qi , LIN Juan
Published: July 2024

Background

The risk factors for acute skin failure (ASF), a serious complication of the skin, are not fully understood.

Purpose

This study was designed to explore the risk factors for ASF in critically ill patients and construct a clinical prediction model.

Methods

Intensive care unit patients were prospectively observed and assigned into two groups: with and without ASF. A logistic regression model was constructed, and its predictive power and clinical utility were evaluated.

Results

Of the 204 eligible patients enrolled as participants, 58 (28.43%) developed ASF. Sepsis, vasoactive drugs, and age were shown to be risk factors for ASF, whereas peripheral perfusion index ratio and albumin level were shown to be protective factors. The area under the receiver operating characteristic curve was 0.83. The maximum Youden index of the model was 0.39 (specificity: 0.87, sensitivity: 0.77). The Hosmer–Lemeshow test (p = .20) and calibration curve showed good fitness and predictive utility with respect to the model.

Conclusions

The developed model effectively predicts ASF risk, allowing for the early identification of high-risk patients. Identifying risk factors such as sepsis, vasoactive drugs, and age and considering protective factors such as peripheral perfusion index and albumin levels may help optimize care plans. Clinical staff should pay special attention to these factors and their impact on skin health in critically ill patients.
Rapid alleviation of perioperative airway obstruction through positional adjustments in a patient with a giant anterior mediastinal mass: A case report
Authors: Qian Liu , Chen Lingmin , Lin Yanjun
Published: July 2024

Rationale:

This case describes the rapid resolution of acute airway obstruction after anesthesia induction in a young man with a massive 12.7 × 9 × 12 cm anterior mediastinal tumor. It emphasizes the remarkable effectiveness of positional adjustments in immediately alleviating airway compression caused by large mediastinal masses. The crisis was resolved quickly and without invasive measures through only positional tactics, without the need for emergency invasive interventions. This highlights the decisive role of strategic patient positioning as a primary technique for perioperative management of mediastinal masses, ensuring adequate ventilation and preventing catastrophic outcomes.

Patient concerns:

Due to the unique anatomical location of mediastinal tumors, the anesthesia risks for patients with mediastinal tumors are very high. These tumors can cause airway compression, leading to severe cardiovascular dysfunction and even mortality during general anesthesia.

Diagnoses:

Combining the patient’s medical history, symptoms and signs, fiberoptic bronchoscopy and excluding other causes, it was confirmed that the tumor compressed the airway and blocked the airway.

Interventions:

Ventilation was rapidly improved by adjusting the patient’s position, ultimately to the left lateral decubitus position with head-up tilt.

Outcomes:

Through positional adjustment, the patient’s airway obstruction symptoms rapidly improved. Airway pressure decreased significantly, end-tidal carbon dioxide returned to 40 mm Hg, and oxygen saturation increased to 95%. The mediastinal tumor was ultimately successfully resected. The surgical procedure went smoothly with successful extubation on the first postoperative day. The patient had a smooth recovery and was discharged on the seventh postoperative day without any lingering postoperative complications.

Lessons:

This case provides an important educational illustration of how mediastinal mass patients can develop sudden catastrophic airway obstruction after induction despite being asymptomatic preoperatively. It demonstrates an effective crisis rescue technique through positioning that may help inform management of similar high-risk cases.
Disaster preparedness for people with kidney disease and kidney healthcare providers
Authors: Sever Mehmet Şükrü , Vanholder Raymond , Lameire Norbert
Published: July 2024

Purpose of review

Man-made and natural disasters become more frequent and provoke significant morbidity and mortality, particularly among vulnerable people such as patients with underlying kidney diseases. This review summarizes strategies to minimize the risks associated with mass disasters among kidney healthcare providers and patients affected by kidney disease.

Recent findings

Considering patients, in advance displacement or evacuation are the only options to avoid harmful consequences of predictable disasters such as hurricanes. Following unpredictable catastrophes, one can only rely upon educational initiatives for disaster risk mitigation. Preparatory initiatives before disasters such as training courses should target minimizing hazards in order to decrease morbidity and mortality by effective interventions during and early after disasters. Retrospective evaluation of previous interventions is essential to identify adverse consequences of disaster-related health risks and to assess the efficacy of the medical response. However, preparations and subsequent responses are always open for ameliorations, even in well developed countries that are aware of disaster risks, and even after predictable disasters.

Adverse consequences of disasters in patients with kidney diseases and kidney healthcare providers can be mitigated by predisaster preparedness and by applying action plans and pragmatic interventions during and after disasters. Preparing clear, practical and concise recommendations and algorithms in various languages is mandatory.
New insights of glycoprotein Ib-IX-V complex organization and glycoprotein Ibα in platelet biogenesis
Authors: Huang Lulu , Shao Bojing
Published: July 2024

Purpose of review

Glycoprotein (GP) Ib-IX-V, a platelet surface receptor that plays a critical role in platelet adhesion and platelet-mediated immune responses, consists of GPIbα, GPIbβ, GPIX, and GPV in a stoichiometry of 2 : 4 : 2 : 1. Forming a complex is essential for GPIb-IX-V to function. GPIb-IX-V also plays an important role in platelet biogenesis by regulating the number and size of platelets. Yet how GPIb-IX-V regulates platelet biogenesis remains elusive. This review will summarize recent findings in the complex organization of GPIb-IX-V and its role in platelet biogenesis.

Recent findings

Proteomics studies suggest that GPIbα, GPIbβ, GPIX, and GPV form the complex in a ratio of 1 : 2 : 1 : 1, which is supported by analysis of molecular weight of GPIb-IX-V and GPIb-IX and the structure of entire GPIb-IX-V. To activate platelets, GPIbα requires binding of CLEC-2 to trigger signals. Furthermore, disrupting the GPIbα anchorage to filamin A causes defects in platelet budding away from proplatelets leading to giant platelets and a low platelet count.

New studies challenge the traditional model for the organization of GPIb-IX-V as a complex and indicate the role of GPIb-IX-V in platelet production. Those studies provide insights for GPIb-IX-V in the regulation of platelet activation and platelet biogenesis.
Classic ear moulding technique for a lop ear deformity: case report
Authors: Touzri Wissal , Tahiri Alaoui Mohamed El Arbi , Bentahar Oussama
Published: July 2024

Introduction and importance:

Lop ear is a congenital auricular deformity (CAD) detected at birth. It can negatively impact aesthetic appearance and the mental health of both the parents and the infant. Therefore, a treatment initiated at an early age is imperative.

Case presentation:

A male newborn patient on his 11th week of his life presented with his mother to the Maxillofacial Prosthodontic Unit. The extraoral examination showed a pendulous upper part of the auricle covering the antihelix with no deficiencies. The newborn’s hearing function was normal and no associated syndrome was identified. The patient was diagnosed with congenital unilateral lop ear (Tanzer grade II constricted ear). A non-surgical correction with a classic ear moulding device was attempted at the 11th week after birth to reshape the abnormal ear.

Clinical discussion:

CADs are traditionally managed by an otoplasty at age 6. Unfortunately, this option can cause many unpredictable complications, such as anaesthesia risks and under-correction. Therefore, the classic non-surgical correction of congenital auricular deformities is a non-surgical and earlier alternative to otoplasty. Moreover, many patients present at an older age; an auricular moulding device can still be a successful treatment option for these older patients.

Conclusion:

Classic ear moulding is an early non-surgical alternative to otoplasty for managing congenital ear abnormalities. It can be initiated as early as 6 weeks after birth. Including an ear examination as a routine in every child’s immediate post-birth physical examination is crucial for early diagnosis and better outcomes.
Challenges in diagnosing and managing hyper-IgE syndrome in a resource-limited setting: a case report
Authors: Adhikari Pratik , Regmi Rabin , Yadav Pramodman Singh , Kafle Sujan
Published: July 2024

Introduction and importance:

Hyper-IgE syndrome (HIES), also known as Job syndrome, is a rare immunodeficiency disorder characterized by elevated immunoglobulin E levels and recurrent infections. Diagnosing and managing HIES in resource-limited settings is challenging due to the lack of advanced diagnostic tools. This report highlights the necessity of clinical evaluation and basic laboratory investigations for diagnosing HIES.

Case presentation:

A 3-year-old male presented with fever, cough, and widespread pustular lesions. He had a history of recurrent respiratory infections and otitis media. Physical examination revealed characteristic facial features, skin findings, and laboratory investigations showed elevated immunoglobulin E levels (>3000 IU/ml) and leukocytosis. A clinical diagnosis of HIES was made, and the patient responded well to antibiotics, antihistamines, and topical steroids.

Clinical discussion:

HIES is caused by genetic mutations affecting immune function, primarily involving STAT3 and DOCK8 genes. Diagnosis in resource-limited settings relies on clinical features and basic investigations. Challenges include the unavailability of genetic testing. Management includes antibiotics and symptomatic relief adapted to available resources.

Conclusion:

Diagnosing and managing HIES in resource-limited settings requires adaptation of clinical approaches to available resources. This case underscores the importance of clinical vigilance and basic diagnostic tools in diagnosing rare immunodeficiencies.
Implementing a Halo Gravity Traction Program
Authors: Stuedemann Anne , Huston Michon , Saddler Nicolette , Schwend Richard M. , Anderson John , Pierce Elizabeth , Koivuniemi-Berg Tiffany , Fryatt Jamie , Herman Katrina
Published: July 2024

Halo gravity traction (HGT) is a preoperative modality for children with severe spinal deformity used to optimize spine flexibility and balance while decreasing the likelihood of neurologic injury. HGT is a dependable solution for these challenging spinal deformities. Aligning treatment guidelines and providing resources, education, and training for staff are key components for a successful HGT program. The HGT program at Children’s Mercy Hospital was then developed with a systems approach with the holistic goal of multidisciplinary collaboration with physical/occupational therapy, hospital medicine, pulmonology, psychology, nutrition, child life, and complex care management. Education, research, and national collaboration to standardize this therapy should improve patient safety and support quality improvement.
Understanding the biopsychosocial knee osteoarthritis pain experience: an ecological momentary assessment
Authors: Overton Mark , Swain Nicola , Falling Carrie , Gwynne-Jones David , Fillingim Roger , Mani Ramakrishnan
Published: July 2024

Introduction:

Psychological, social, and lifestyle factors contribute to the knee osteoarthritis (OA) pain experience. These factors could be measured more accurately using smartphone ecological momentary assessment (EMA).

Objectives:

The objective of this study was to characterise the pain experiences of those with knee OA by a smartphone EMA survey and explain how momentary psychological and social states influence knee OA pain experiences.

Methods:

A smartphone EMA survey was designed and piloted. Eligible participants completed smartphone EMA assessing the knee OA pain experience 3 times daily for 2 weeks. Descriptive statistics were used to characterise factors involved in knee OA pain followed by the development of mixed-effects location scale models to explore heterogeneity and relationships between symptoms involved in the knee OA pain experience.

Results:

Eighty-six community-dwelling volunteers with knee OA were recruited. Pain, psychosocial, and lifestyle factors involved in knee OA pain experience were heterogeneous and variable. Those with greater variability in pain, fatigue, negative affect, and stress had worse levels of these symptoms overall. In addition, fatigue, negative affect, stress, anxiety, loneliness, and joint stiffness demonstrated within-person relationships with knee OA pain outcomes.

Conclusions:

Knee OA pain is a heterogeneous biopsychosocial condition. Momentary experiences of psychological, social, fatigue, and joint stiffness explain individual and between-individual differences in momentary knee OA pain experiences. Addressing these momentary factors could improve pain and functional outcomes in those with knee OA. Validation studies, including individuals with more severe knee OA presentations, are required to support findings and guide clinical interventions to improve outcomes for those with knee OA.
What’s New in Cleft Palate and Velopharyngeal Dysfunction Management: An Update
Authors: Smetona John T. , Naran Sanjay , Ford Matthew , Losee Joseph E.
Published: July 2024

Learning Objectives:

After studying this article, the participant should be able to: (1) Describe the pathology of velopharyngeal dysfunction (VPD) as it relates to patients with a cleft palate. (2) Use the perceptual speech assessment and objective diagnostic tools to determine the presence or absence of VPD. (3) Describe the surgical options available for the treatment of patients with VPD. (4) Develop an evidence-based, customized treatment plan for VPD founded on objective considerations.

To treat patients with cleft palate effectively, the surgeon must understand the diagnosis and surgical management of cleft-associated velopharyngeal dysfunction. The authors review diagnostic modalities including perceptual speech assessment, video nasendoscopy, fluoroscopy, magnetic resonance imaging, and nasometry. Surgical treatments including palatal lengthening with buccal myomucosal flaps, conversion Furlow palatoplasty, sphincter pharyngoplasty, and pharyngeal flap are discussed. Selection of an optimal surgical treatment is addressed.
Does surgical sequencing influence the accuracy of maxillary positioning in bimaxillary cleft orthognathic surgery?
Authors: Badiee Ryan K. , Ettinger Russell E. , Kapadia Hitesh , Sheller Barbara , Susarla Srinivas M.
Published: July 2024

PURPOSE:

To evaluate whether the sequence of osteotomies influences the accuracy of maxillary positioning in patients with cleft palate ± cleft lip undergoing bimaxillary orthognathic surgery (OGS).

METHODS:

This was a prospective study of patients with Veau 2-4 clefts who underwent bimaxillary OGS at tertiary-care children’s hospital over a 3-year period. The primary predictor variable was the sequence of osteotomies (maxilla-first versus mandible-first). The primary outcome of interest was the concordance between the planned and achieved maxillary position, as assessed using linear and angular measurements. Secondary study predictors were demographic and surgical variables. Differences between groups were compared using non-parametric independent samples tests for continuous measures (data reported as median and interquartile range, IQR) and chi-squared tests for categorical measures. For all analyses, p≤ 0.05 was considered significant.

RESULTS:

Subjects who underwent maxilla-first (n=15) and mandible-first (n=16) operations were comparable with regard to age, gender, cleft type, skeletal classification, segmental maxillary osteotomy, and magnitude of maxillary movement (p ≥ 0.09). The planned sagittal and vertical positions of the maxilla were similarly accurate between the two groups (p ≥ 0.68). Angular accuracy was also comparable (p ≥ 0.56) between the study groups.

CONCLUSION:

In patients with CP ± CL undergoing bimaxillary orthognathic surgery, use of mandible-first sequencing, when compared to maxilla-first sequencing, does not impact accuracy of maxillary positioning in the immediate post-operative period in well-selected patients.
Diagnostic Challenges in Invasive Mole With 18F-FDG PET/CT
Authors: Minami Akihiko , Nakamoto Ryusuke , Shimamura Takuto , Kitano Yurika , Nakamoto Yuji
Published: July 2024

A 34-year-old woman underwent 18F-FDG PET/CT scan following a diagnosis of an invasive mole. Although CT indicated multiple lung metastases, FDG uptakes were not evident. In contrast, FDG uptakes were observed in the pelvic lesion including the left ovary, suggestive of ovarian metastasis. MRI disclosed a ring-shaped enhancement typical of a corpus luteum. This corpus luteum was supposed to be maintained by the elevated human chorionic gonadotropin excreted from the invasive mole. This case underlines the importance of careful interpretation of 18F-FDG PET/CT in the evaluation of invasive moles, highlighting potential false positive in corpus luteum.
Host behaviour driven by awareness of infection risk amplifies the chance of superspreading events
Authors: Parag Kris V. , Thompson Robin N.
Published: July 2024

We demonstrate that heterogeneity in the perceived risks associated with infection within host populations amplifies chances of superspreading during the crucial early stages of epidemics. Under this behavioural model, individuals less concerned about dangers from infection are more likely to be infected and attend larger sized (riskier) events, where we assume event sizes remain unchanged. For directly transmitted diseases such as COVID-19, this leads to infections being introduced at rates above the population prevalence to those events most conducive to superspreading. We develop an interpretable, computational framework for evaluating within-event risks and derive a small-scale reproduction number measuring how the infections generated at an event depend on transmission heterogeneities and numbers of introductions. This generalizes previous frameworks and quantifies how event-scale patterns and population-level characteristics relate. As event duration and size grow, our reproduction number converges to the basic reproduction number. We illustrate that even moderate levels of heterogeneity in the perceived risks of infection substantially increase the likelihood of disproportionately large clusters of infections occurring at larger events, despite fixed overall disease prevalence. We show why collecting data linking host behaviour and event attendance is essential for accurately assessing the risks posed by invading pathogens in emerging stages of outbreaks.
The affinity–efficacy problem: an essential part of pharmacology education
Authors: Higham James P. , Colquhoun David
Published: July 2024

A fundamental mistake in receptor theory has led to an enduring misunderstanding of how to estimate the affinity and efficacy of an agonist. These properties are inextricably linked and cannot be easily separated in any case where the binding of a ligand induces a conformation change in its receptor. Consequently, binding curves and concentration–response relationships for receptor agonists have no straightforward interpretation. This problem—the affinity–efficacy problem—remains overlooked and misunderstood despite it being recognized in 1987. To avoid the further propagation of this misunderstanding, we propose in this review that the affinity–efficacy problem should be included in the core curricula for pharmacology undergraduates proposed by the British Pharmacological Society and the International Union of Basic and Clinical Pharmacology (IUPHAR).
Taxonomy for physics beyond quantum mechanics
Authors: Adlam Emily , Hance Jonte R. , Hossenfelder Sabine , Palmer Tim N.
Published: July 2024

We propose terminology to classify interpretations of quantum mechanics and models that modify or complete quantum mechanics. Our focus is on models which have previously been referred to as superdeterministic (strong or weak), retrocausal (with or without signalling, dynamical or non-dynamical), future-input-dependent, atemporal and all-at-once, not always with the same meaning or context. Sometimes, these models are assumed to be deterministic, sometimes not, the word deterministic has been given different meanings, and different notions of causality have been used when classifying them. This has created much confusion in the literature, and we hope that the terms proposed here will help to clarify the nomenclature. The general model framework that we will propose may also be useful to classify other interpretations and modifications of quantum mechanics. This document grew out of the discussions at the 2022 Bonn Workshop on Superdeterminism and Retrocausality.
The geometry of induced currents in two-dimensional media
Authors: Lopez-Monsalvo Cesar S. , Vargas-Serdio Servando , Alzate-Cardenas Julian A. , Flores-Alfonso Daniel
Published: July 2024

We present a framework that allows us to clearly identify the geometric features underlying the phenomenon of superconductivity in two-dimensional materials. In particular, we show that any such medium whose response to an externally applied electromagnetic field is a geodesically flowing induced current, must be a superconductor. In this manner, we conclude that the underlying geometry of this type of media is that of a Lorentzian contact manifold. Moreover, we show that the macroscopic hallmark of their superconducting state is a purely topological condition equivalent to the geodesic nature of the induced current: the non-vanishing of its helicity.
Universal deformations and inhomogeneities in isotropic Cauchy elasticity
Authors: Yavari Arash
Published: July 2024

For a given class of materials, universal deformations are those deformations that can be maintained in the absence of body forces and by applying solely boundary tractions. For inhomogeneous bodies, in addition to the universality constraints that determine the universal deformations, there are extra constraints on the form of the material inhomogeneities—universal inhomogeneity constraints. Those inhomogeneities compatible with the universal inhomogeneity constraints are called universal inhomogeneities. In a Cauchy elastic solid, stress at a given point and at an instance of time is a function of strain at that point and that exact moment in time, without any dependence on prior history. A Cauchy elastic solid does not necessarily have an energy function, i.e. Cauchy elastic solids are, in general, non-hyperelastic (or non-Green elastic). In this paper, we characterize universal deformations in both compressible and incompressible inhomogeneous isotropic Cauchy elasticity. As Cauchy elasticity includes hyperelasticity, one expects the universal deformations of Cauchy elasticity to be a subset of those of hyperelasticity both in compressible and incompressible cases. It is also expected that the universal inhomogeneity constraints to be more stringent than those of hyperelasticity, and hence, the set of universal inhomogeneities to be smaller than that of hyperelasticity. We prove the somewhat unexpected result that the sets of universal deformations of isotropic Cauchy elasticity and isotropic hyperelasticity are identical, in both the compressible and incompressible cases. We also prove that their corresponding universal inhomogeneities are identical as well.
Visual continuum in non-human animals: serial dependence revealed in dogs
Authors: Lõoke Miina , Guérineau Cécile , Broseghini Anna , Mongillo Paolo , Marinelli Lieta
Published: July 2024

Serial dependence is a recently described phenomenon by which the perceptual evaluation of a stimulus is biased by a previously attended one. By integrating stimuli over time, serial dependence is believed to ensure a stable conscious experience. Despite increasing studies in humans, it is unknown if the process occurs also in other species. Here, we assessed whether serial dependence occurs in dogs. To this aim, dogs were trained on a quantity discrimination task before being presented with a discrimination where one of the discriminanda was preceded by a task-irrelevant stimulus. If dogs are susceptible to serial dependence, the task-irrelevant stimulus was hypothesized to influence the perception of the subsequently presented quantity. Our results revealed that dogs perceived the currently presented quantity to be closer to the one presented briefly before, in accordance with serial dependence. The direction and strength of the effect were comparable to those observed in humans. Data regarding dogs’ attention during the task suggest that dogs used two different quantity estimation mechanisms, an indication of a higher cognitive mechanism involved in the process. The present results are the first empirical evidence that serial dependence extends beyond humans, suggesting that the mechanism is shared by phylogenetically distant mammals.
The genetic basis of incipient sexual isolation in
Drosophila melanogaster
Authors: Yamamoto Akihiko , Huang Wen , Carbone Mary Anna , Anholt Robert R. H. , Mackay Trudy F. C.
Published: July 2024

Speciation is a fundamental evolutionary process but the genetic changes accompanying speciation are difficult to determine since true species do not produce viable and fertile offspring. Partially reproductively isolated incipient species are useful for assessing genetic changes that occur prior to speciation.
Drosophila melanogaster
from Zimbabwe, Africa are partially sexually isolated from other
D. melanogaster
populations whose males have poor mating success with Zimbabwe females. We used the North American
D. melanogaster
Genetic Reference Panel (DGRP) to show that there is significant genetic variation in mating success of DGRP males with Zimbabwe females, to map genetic variants and genes associated with variation in mating success and to determine whether mating success to Zimbabwe females is associated with other quantitative traits previously measured in the DGRP. Incipient sexual isolation is highly polygenic and associated with the common African inversion
In(3R)K
and the amount of the sex pheromone 5,9-heptacosadiene in DGRP females. We functionally validated the effect of eight candidate genes using RNA interference to provide testable hypotheses for future studies investigating the molecular genetic basis of incipient sexual isolation in
D. melanogaster
.
Differential pathogenicity and lethality of bubonic plague (1720–1945) by sex, age and place
Authors: Mongillo J. , Zedda N. , Rinaldo N. , Bellini T. , Manfrinato M. C. , Du Z. , Yang R. , Stenseth N. C. , Bramanti B.
Published: July 2024

COVID-19 brought back to the attention of the scientific community that males are more susceptible to infectious diseases. What is clear for other infections—that sex and gender differences influence both risk of infection and mortality—is not yet fully elucidated for plague, particularly bubonic plague, although this knowledge can help find specific defences against a disease for which a vaccine is not yet available. To address this question, we analysed data on plague from hospitals in different parts of the world since the early eighteenth century, which provide demographic information on individual patients, diagnosis and course of the disease in the pre-antibiotic era. Assuming that the two sexes were equally represented, we observe a worldwide prevalence of male cases hospitalized at any age, a result which seems better explained by gender-biased (thus cultural) behaviours than biological sex-related factors. Conversely, case fatality rates differ among countries and geographic macro-areas, while globally, lethality appears slightly prevalent in young females and older adults (regardless of sex). Logistic regression models confirm that the main risk factor for bubonic plague death was the geographical location of the cases and being older than 50 years, whereas sex only showcased a slight trend.
Visual evoked potential in myelin oligodendrocyte glycoprotein antibody-associated disease
Authors: Chikashi Yano , Eiji Matsuura , Tomonori Nakamura , Ayako Sonoda , Ayano Shigehisa , Masahiro Ando , Satoshi Nozuma , Yujiro Higuchi , Yusuke Sakiyama , Akihiro Hashiguchi , Kumiko Michizono , Hiroshi Takashima
Published: July 2024

The visual evoked potential (VEP) patterns of optic neuritis are known to often differ between multiple sclerosis (MS) and neuromyelitis optica spectrum disorder (NMOSD) but have been less reported in myelin oligodendrocyte glycoprotein antibody-associated disease (MOGAD). This study aimed to characterize the VEP pattern in MOGAD and evaluate its utility in distinguishing MOGAD from MS and NMOSD. We retrospectively reviewed the clinical manifestations and VEP findings in patients with MS (n = 29), NMOSD (n = 14), and MOGAD (n = 10). In eyes with acute visual impairment, VEP responses were detectable in all eyes with MOGAD but were undetectable in a significant percentage of eyes with MS (27.3%) and NMOSD (42.9%). In addition, VEP abnormalities in eyes without acute visual impairment were rare in MOGAD (23.1%) compared to MS (55.3%) and NMOSD (42.9%). Our results indicated that subclinical VEP abnormalities or undetectable VEP responses were less common in patients with MOGAD compared to patients with MS and NMOSD. VEP testing demonstrates potential diagnostic utility in distinguishing among these conditions.
Epigenetic Dynamics in Meniscus Cell Migration and its Zonal Dependency in Response to Inflammatory Conditions: Implications for Regeneration Strategies
Authors: Zhang Yize , Zhang Yujia , Wang Catherine , Heo Yuna , Tumenbayar Bat-Ider , Lee Se-Hwan , Bae Yongho , Heo Su Chin
Published: July 2024

Meniscus injuries pose significant challenges in clinical settings, primarily due to the intrinsic heterogeneity of the tissue and the limited efficacy of current treatments. Endogenous cell migration is crucial for the healing process, yet the regulatory mechanisms of meniscus cell migration and its zonal dependency within the meniscus are not fully understood. Thus, this study investigates the role of epigenetic mechanisms in governing meniscus cell migration under inflammatory conditions, with a focus on their implications for injury healing and regeneration. Here, we discovered that a proinflammatory cytokine, TNF-α treatment significantly impedes the migration speed of inner meniscus cells, while outer meniscus cells are unaffected, underscoring a zonal-dependent response within the meniscus. Our analysis identified distinct histone modification patterns and chromatin dynamics between inner and outer meniscus cells during migration, highlighting the necessity to consider these zonal-dependent properties in devising repair strategies. Specifically, we found that TNF-α differentially influences histone modifications, particularly H3K27me3, between the two cell types. Transcriptome analysis further revealed that TNF-α treatment induces substantial gene expression changes, with inner meniscus cells exhibiting more pronounced alterations than outer cells. Gene cluster analysis pointed to distinct responses in chromatin remodeling, extracellular matrix assembly, and wound healing processes between the zonal cell populations. Moreover, we identified potential therapeutic targets by employing existing epigenetic drugs, GSKJ4 (a histone demethylase inhibitor) and C646 (a histone acetyltransferase inhibitor), to successfully restore the migration speed of inner meniscus cells under inflammatory conditions. This highlights their potential utility in treating meniscus tear injuries. Overall, our findings elucidate the intricate interplay between epigenetic mechanisms and meniscus cell migration, along with its meniscus zonal dependency. This study provides insights into potential targets for enhancing meniscus repair and regeneration, which may lead to improved clinical outcomes for patients with meniscus injuries and osteoarthritis.
Demultiplexing and barcode-specific adaptive sampling for nanopore direct RNA sequencing
Authors: van der Toorn Wiep , Bohn Patrick , Liu-Wei Wang , Olguin-Nava Marco , Smyth Redmond P , von Kleist Max
Published: July 2024

Nanopore direct RNA sequencing (dRNA-seq) enables unique insights into (epi-)transcriptomics. However, applications are currently limited by the lack of accurate and cost-effective sample multiplexing. We introduce WarpDemuX, an ultra-fast and highly accurate adapter-barcoding and demultiplexing approach. WarpDemuX enhances speed and accuracy by fast processing of the raw nanopore signal, use of a light-weight machine-learning algorithm and design of optimized barcode sets. We demonstrate its utility by performing a rapid phenotypic profiling of different SARS-CoV-2 viruses, crucial for pandemic prevention and response, through multiplexed sequencing of longitudinal samples on a single flowcell. This identifies systematic differences in transcript abundance and poly(A) tail lengths during infection. Additionally, integrating WarpDemuX into sequencing control software enables real-time enrichment of target molecules through barcode-specific adaptive sampling, which we demonstrate by enriching low abundance viral RNA. In summary, WarpDemuX is a broadly applicable, high-performance, and economical multiplexing solution for nanopore dRNA-seq, facilitating advanced (epi-)transcriptomic research.
Molecular and structural innovations of the stator motor complex at the dawn of flagellar motility
Authors: Puente-Lelievre Caroline , Ridone Pietro , Douglas Jordan , Amritkar Kaustubh , Kaçar Betül , Baker Matthew , Matzke Nicholas
Published: July 2024

The rotation of the bacterial flagellum is powered by the MotAB stator complex, which converts ion flux into torque. The origin and evolution of this remarkable complex is understudied. Here, we perform the first phylogenetic and structural characterisation and classification of MotAB and nonflagellar relatives. Using 193 genomes sampled across 27 bacterial phyla, we estimated phylogenies and ancestral sequences, and generated AlphaFold predictions for all extant and reconstructed proteins. We then mapped them onto the phylogeny to determine patterns of diversity and distribution of structural innovations. We identify two discrete groups: the Flagellar Ion Transporters (FIT) and the Generic Ion Transporters (GIT). The FIT proteins are structurally conserved and have a square fold domain and a torque-generating interface (TGI). FIT proteins are divided into two clades, termed TGI4 and TGI5, referring to whether there have 4 or 5 short helices in the TGI. TGI5 motors are predominantly found in Proteobacteria and include the well-studiedE. coliK12 system, while TGI4 motors are found in diverse phyla and include the Na+-powered polar motors ofVibrio(PomAB). The GIT proteins, on the other hand, are structurally diverse and lack these attributes. The interaction between the A and B subunits is conserved across the FIT and GIT proteins. The two subunits are jointly necessary for function, with the genes typically adjacent within an operon. Motility assays inE. colishow that the structural elements unique to FIT play an important role in flagellar motility. Our results indicate that the stator motor complex has a single origin and shares unique motility-related structural traits.

Significance Statement

Flagellar motility is a key feature in bacterial pathogenicity and survival. It allows bacteria to propel themselves and direct movement according to environmental conditions. We investigated the molecular and structural diversity of the stator motor proteins that provide the ion motive force to power flagellar rotation. This study integrates phylogenetics, 3D protein structure modeling, motility assays and ancestral state reconstruction (ASR) to provide insights into the structural mechanisms that first powered the flagellar motor. We provide the first phylogenetic and structural characterisation and classification of MotAB and relatives.
DFAST_QC: Quality Assessment and Taxonomic Identification Tool for Prokaryotic Genomes
Authors: Elmanzalawi Mohamed , Fujisawa Takatomo , Mori Hiroshi , Nakamura Yasukazu , Tanizawa Yasuhiro
Published: July 2024

Motivation

Accurate taxonomic assignments of genomic data are crucial across various biological databases. With a rapid increase in submitted genomes in recent years, ensuring precise classification is important to maintain database integrity. Mislabeled genomes can confuse researchers, hinder analyses, and produce false results. Therefore, there is a critical need for computationally efficient tools that ensure accurate taxonomic classification for data to be deposited into genomic databases.

Results

Here we introduce DFAST_QC, a quality control and taxonomic classification tool of prokaryotic genomes based on NCBI and GTDB taxonomies. We benchmarked DFAST_QC’s performance against NCBI taxonomy assignments, showing high consistency with them. Our results demonstrate that DFAST_QC achieves high consistency to NCBI taxonomy classification.

Availability and implementation

DFAST_QC is implemented in Python and is available both as a web service (https://dfast.ddbj.nig.ac.jp/dqc) and as a stand-alone command line tool. The source code is available under the GPLv3 license at:https://github.com/nigyta/dfast_qc, and the conda package is also available from Bioconda. The data and scripts used for the benchmarking process are publicly available on GitHub (https://github.com/Mohamed-Elmanzalawi/DFAST_QC_Benchmark).

Contact

yt@nig.ac.jp

Supplementary information

Supplementary data are available at Bioinformatics online.
Long-distance gene flow and recombination shape the evolutionary history of a maize pathogen
Authors: Rogério Flávia , Oosterhout Cock Van , De Mita Stéphane , Cuevas-Fernández Francisco Borja , García-Rodríguez Pablo , Becerra Sioly , Gutiérrez-Sánchez Silvia , Jacquat Andrés G. , Bettiol Wagner , Hosaka Guilherme Kenichi , Ulla Sofia B. , Hiltbrunner Jürg , Santiago Rogelio , Revilla Pedro , Dambolena José S. , Vicente-Villardón José L. , Buhiniček Ivica , Sukno Serenella A. , Thon Michael R.
Published: July 2024

The evolutionary history of crop pathogens is shaped by a complex interaction of natural and anthropogenic factors. The ascomycete fungusColletotrichum graminicolacauses maize anthracnose. The disease can result in significant yield losses and is also an important model for genetic studies. We conducted a comprehensive investigation into the evolutionary genomics ofC. graminicolausing a collection of 212 isolates from 17 countries. Genomic analyses supported the existence of three geographically isolated genetic lineages, with a significant pattern of isolation by distance. We identified two distinct gene flow patterns, driven by short and long-distance dispersion, likely resulting from the natural spread of the pathogen and the exchange of contaminated seeds. We present evidence of genetic introgression between lineages, suggesting a long history of recombination. We identified significant recombination events coalescing at distinct points in time, with the North American lineage displaying evidence of most ancient recombination. Demographic modeling indicated that North America is an intermediate between Brazil, Europe and an ancestral, unsampled source population, hypothesized to be Mesoamerican. Our analyses revealed that the global genomic structure ofC. graminicolais shaped by geographic differentiation driven by long-distance migration and a long history of recombination and introgression. We show historical relationships among these lineages, identifying a potential route for fungal spread, with the North American population emerging ancestrally, followed sequentially by the Brazilian and European populations. Our research indicates that the European lineage is more virulent, which has implications for the potential emergence of new outbreaks of maize anthracnose in Europe.
Arabidopsis NIM1-INTERACTING1 (NIMIN1) is a multi-domain protein controlling transition from systemic acquired resistance (SAR) to cell death
Authors: Saur Mathias , Steilner Kristin , Masroor Ashir , Hubel Philipp , Pfitzner Artur J.P. , Pfitzner Ursula M.
Published: July 2024

NIM1-INTERACTING (NIMIN) proteins were identified by interaction with the systemic acquired resistance (SAR) key regulator NPR1. The Arabidopsis family comprises four related, yet distinct members. Ample evidence predicts that NIMIN1 is a multi-domain protein which comes into action after the onset of salicylic acid (SA) signaling prior to induction of the PR-1 defense gene. Bioinformatics, protein-protein interaction assays and expression studies in tobacco were applied to explore functions of NIMIN1. The N-terminal sequence encompassing amino acids 1 to 15 conveyed accumulation of NIMIN1 protein in planta. This newly identified segment and the known conserved NIMIN1 domains, i.e., two distinct NPR1 binding sites and an EAR motif, are neatly separated from each other by disordered regions. Co-expression of NIMIN1 and NPR1 reinforced accumulation of NPR1 protein while ectopic overexpression of NIMIN1 promoted emergence of cell death driven by the EAR motif and disturbed development of tobacco plants. We suggest that NIMIN1 acts as a dynamic signaling agent controlling transition of pathogen-infected leaves from survival to tissue collapse. Initially, NIMIN1 binding renders the NPR1 transcription complex sensitive to the SAR signal SA enabling PR-1 transcription. At high levels of SA, NIMIN1 is outcompeted by SA from the NPR1 C-terminus, and accumulating NIMIN1 engages via its EAR motif with TOPLESS-RELATED3, thereby affecting global hormone signaling and inducing cell death in severely endangered tissue.
Drivers of temporal bias in biodiversity recording by citizen scientists
Authors: Rosário Inês.T. , Tiago Patrícia. , Chozas Sergio , Capinha César
Published: July 2024

Citizen science data is increasingly important for ecological research, biodiversity conservation and monitoring. However, these data often suffer from biases due to uneven recording efforts by citizen scientists. Biases caused by intra-annual differences in recording activity can be particularly severe, hindering the use of citizen science data in research areas such as population dynamics and phenology. Therefore, understanding the factors driving recording activity is essential.

In this study, we provide a detailed assessment of how weather and calendar-related factors influence biodiversity recording activity by citizen scientists at a daily resolution. To perform this, we analyse the recording patterns for six tree species in the Iberian Peninsula, which maintain a fairly consistent appearance throughout the year. Observation data were collected from iNaturalist, a leading platform for citizen-science data. We used boosted regression trees (BRT) to compare observed recording activity patterns with those expected by chance. Our analysis included a comprehensive set of explanatory variables, such as day of the week, month, holidays, temperature, accumulated precipitation, wind intensity, and snow depth.

The BRT models effectively identified the drivers of recording activity, with the correlation between predicted and observed temporal patterns (left out of model training) ranging from 0.47 to 0.96, depending on the species. The day of the week, daily temperature, and month of the year consistently emerged as the main drivers. Recording activity was higher on weekends, to some extent on Fridays, and during the spring months. Extreme low and high temperatures generally correlated with lower recording activity, although there were exceptions. Wind speed and precipitation had a moderate influence, with higher wind intensity and accumulated precipitation leading to decreased activity. Holidays and accumulated snow had very minor relevance across species.

Our findings show that citizen scientists record more frequently on weekends, during mild weather, and in spring. By addressing these biases, we can maximize the utility of citizen-collected data for research and applied purposes, ensuring robust and reliable conclusions that enhance ecological understanding and conservation efforts.