bluuebunny/crossref_metadata_2025 huggingface dataset:
Minimally invasive thoracoscopic resection of a micronodular thymoma with lymphoid stroma via a subxiphoid single-incision approach: A case report
Authors: Wu Qiang , Qiao Kun , Zhang Xiaoming , Zhou Zizi
Published: November 2024

Rationale:

This study aims to present a novel surgical approach for the resection of anterior mediastinal tumors, specifically focusing on micronodular thymoma with lymphoid stroma (MNT), a rare and distinct variant of thymoma. The single subxiphoid incision technique, although reported in limited cases, offers a minimally invasive option with potential benefits. We report the case of a 76-year-old male who underwent this innovative procedure and was diagnosed with MNT, providing insight into the management and outcomes of this rare pathology.

Patient concerns:

The patient presented for the excision of an anterior mediastinal tumor, with the surgery facilitated by sternal hooks to improve visualization. The rarity of MNT and its unclear prognosis underscore the need for enhanced diagnostic accuracy and tailored treatment strategies.

Diagnoses:

Initially diagnosed preoperatively with a thymic cyst, the patient’s final diagnosis was revised to MNT following surgery, highlighting the diagnostic challenges associated with this rare tumor.

Interventions:

The tumor was successfully removed using minimally invasive thoracoscopic surgery through a subxiphoid single-incision, demonstrating the feasibility and potential advantages of this approach.

Outcomes:

The patient had a favorable postoperative course, with a swift recovery and no complications, and remained in good health without signs of relapse at the 9-month follow-up.

Lessons:

This case underscores the importance of recognizing the unique pathological features of MNT and the need for a cautious diagnostic approach to differentiate it from other cystic lesions. Additionally, the successful use of single-port thoracoscopy under the xiphoid process for the removal of thymic tumors suggests its potential as an effective surgical method for these challenging cases.
Awareness and preparedness of health systems and emergency medicine systems to the climate change challenges and threats: an international survey
Authors: Petrino Roberta , Garcia-Castrillo Luis , Uccheddu Graziano , Meucci Letizia , Codecà Roberta
Published: November 2024

Background and importance

Climate change is widely recognised as a critical public health challenge.

Objective

The objective of this study was to assess the awareness, preparedness and mitigation plans for climate change threats.

Design, settings and participants

A cross-sectional observational study targeting emergency medical societies in different countries was conducted between 15 February and 15 March 2024.

Intervention or exposure

The survey featured 16 closed questions on climate change awareness, preparedness and risks. Focus groups of 4–6 members were organised by country. Results were correlated to income levels, United Nations (UN) regional classification and the World Risk Index.

Outcome measure and analysis

The questions were ranked using a Likert-like scale from 0 to 9 (9 being the highest). Descriptive statistics used central tendency estimators, and inferential analysis used chi-square and Kruskal–Wallis tests, with the significance level set at P < 0.05.

Results

Forty-two focus groups responded, representing 36 countries: 21 (50%) high-income, seven (16.7%) low-income, five (11.9%) lower middle-income and nine (21.4%) upper middle-income countries, representing 31 of the 22 UN regions. According to the World Risk Index, the respondent countries belonged to the different categories as follows: very low risk, 6 (14%); low risk, 8 (19%); medium risk, 5 (12%); high risk, 8 (19%) and very high risk, 14 (34%). The estimated impact of climate change on national health systems had a mean score of 6.75 (SD = 2.16), while on Emergency Medical Systems was 6.96 (SD = 2.05). Overall, assessment and preparedness measures were reported by just 21.4 and 37.6% of respondents, respectively. Analysis by income did not show significant differences, with the exception of food supply. The main differences in the analysis by region were the risks of extreme weather events, vector-borne diseases and wildfires, whereas the World Risk Index was food and chain of supplies. Education and integration of health services were indicated by all as the main mitigation actions.

Conclusion

Geographical position and country risk index influence risk perception among focus groups more than income economy, with vector-borne diseases, extreme weather events and food shortages being the threats with the most variability. The most important actions identified to mitigate Climate Change effects are educational and strategic plans.
Surgical resection of a rare scalp arteriovenous malformation: a case report
Authors: Haq Khitamul , Waqas Muhammad A. , Akhter Saleem , Cardona Juan J. , Scalia Gianluca , Umana Giuseppe E. , Chaurasia Bipin
Published: November 2024

Introduction and importance:

Scalp arteriovenous malformations (AVMs) are intricate vascular anomalies with abnormal connections between arteries and veins in the scalp, leading to serious complications and cosmetic concerns. Managing scalp AVMs is particularly complex in young female patients, where both functional and aesthetic outcomes are crucial. This case report highlights the successful treatment of a young woman with a scalp AVM, emphasizing the importance of early diagnosis and a multidisciplinary approach.

Case presentation:

A 30-year-old female presented with a pulsatile scalp mass and significant cosmetic concerns. Diagnostic imaging, including ultrasonography, brain CT scan, MRI, and carotid CT angiogram, confirmed a scalp AVM. The patient underwent a comprehensive treatment plan beginning with endovascular embolization to reduce blood flow to the AVM, followed by surgical resection to remove the lesion. Postoperative follow-up showed a marked reduction in symptoms and lesion volume, with no complications observed.

Clinical discussion:

Scalp AVMs, though rare, require prompt diagnosis due to the risk of severe complications such as hemorrhage and cosmetic impact. In this case, a combination of ultrasonography, CT, and MRI provided a detailed assessment of the AVM. A multidisciplinary approach, involving interventional radiology and surgical expertise, was crucial for success. Endovascular embolization minimized intraoperative bleeding and simplified surgical resection, leading to significant symptom and cosmetic improvements. Continuous monitoring is essential for long-term success and early detection of recurrences.

Conclusion:

This case underscores the effectiveness of a multidisciplinary approach in managing scalp AVMs in young female patients. Early diagnosis through advanced imaging techniques enables timely and targeted intervention. The combined use of endovascular embolization and surgical resection led to significant symptom resolution and aesthetic enhancement. Collaboration among specialists is vital for optimizing outcomes, and ongoing research will further refine treatment strategies, improving the quality of life for patients with scalp AVMs.
The effect of therapeutic education program on hypertensive Tunisian patients’ knowledge: a randomized controlled trial
Authors: Turki Fatma , Turki Imen , Jedidi Jihen , Said Houyem
Published: November 2024

Background:

Hypertension is a prevalent non-communicable disease and unequivocally one of the most serious health threats of the twenty-first century. The prevention of both immediate and long-term consequences depends on ongoing therapeutic education.

Aims:

To assess Tunisian hypertensive patients’ knowledge of hypertension and then evaluate the impact of an educational program on knowledge among this population.

Methods:

A randomized controlled trial was carried out among 639 hypertensive patients in Tunisia. The control group received only basic medical care, while the experimental group acquired additionally an educational program. The data collection tool was a questionnaire that included an information sheet and the Hypertension Knowledge Level Scale (HK-LS).

Results:

Before to the implementation of the program, only 12.1% of the participants had a good level of knowledge about hypertension (12.8% for the experimental group, vs. 10.5% for the control group, P=0.57). Following the program’s deployment, the rate of good level of knowledge became 63.6% for the experimental group vs. 11.4% for the control group, P<0.001). The results revealed that the experimental group showed a significant amelioration in the total score of the HK-LS: from 58.49 to 76.94%, P<0.0001. In contrast, no significant amelioration was noted in the control group. Concerning the six dimensions of the scale, the amelioration in the experimental group was observed in all dimensions, except the treatment dimension.

Conclusion:

Overall, the findings indicated low levels of knowledge about hypertension. This kind of approach proved an effective improvement in disease-related knowledge and may be essential for hypertension management.
The Importance of 18F-FDG PET/CT in a Rare Case of Multiple Myeloma Presenting With Nasal Plasmacytoma
Authors: Erol Fenercioğlu Özge , Çermik Tevfik Fikret
Published: November 2024

Nasopharyngeal plasmacytoma is a rare presentation of multiple myeloma. We emphasize the importance of imaging by presenting the 18F-FDG PET/CT findings of a patient with nasopharyngeal plasmacytoma and lytic hypermetabolic bone lesions.
Using Artificial Intelligence to Diagnose Lacrimal Passage Obstructions Based on Dacryocystography Images
Authors: Kim Suyoung , Lee Hyungwoo , Roh Hong Gee , Shin Hyun Jin
Published: November 2024

Dacryocystography (DCG) has been used to illustrate the morphological and functional aspects of the lacrimal drainage system in the evaluation of patients with maxillofacial trauma and epiphora. This study developed deep-learning models for the automatic classification of the status of the lacrimal passage based on DCG. The authors collected 719 DCG images from 430 patients with nasolacrimal duct obstruction. The obstruction images were further manually categorized into 2 binary categories based on the location of the obstruction: (1) upper obstruction and (2) lower obstruction. An upper obstruction was defined as one occurring within the canaliculus or common canaliculus, whereas a lower obstruction was defined as one within the lacrimal sac, duct–sac junction, or nasolacrimal duct. The authors then established a deep-learning model to automatically determine whether a passage was patent or obstruction. The accuracy, precision, sensitivity, F1 score, and area under the receiver operating characteristic curve for the evaluation set of each deep-learning model were 99.3%, 98.8%, 99.5%, 99.2%, and 0.9998, respectively, for obstruction detection, and 95.5%, 93.0%, 93.0%, 93.0%, and 0.9778 for classifying the obstruction location. Both receiver operating characteristic curves were skewed toward the left-upper region, indicating the high reliability of these models. The high accuracies of the obstruction detection model (99.3%) and the obstruction classification model (95.5%) demonstrate that deep-learning models can be reliable diagnostic tools for DCG images. This deep-learning model could enhance diagnostic consistency, enable non-specialists to interpret results accurately and facilitate the efficient allocation of medical resources.
Extrusion of High-density Porous Polyethylene Implants in the Nose
Authors: Machado Vanessa Fonseca , Chagas Rachel Santos das , dos Reis Philippi Machado , Grillo Ricardo
Published: November 2024

Few alloplastic implant materials have been successfully used in nasal reconstruction. The high-density porous polyethylene (HDPE) implant is the most widely accepted alloplastic material for reconstructing the nasal structure. Some authors suggest that the problems associated with using grafts and biocompatible materials are often due to errors on the part of the surgeon or the technique used. This study aims to report several cases of complications related to using HDPEs in the nose. A total of 23 patients who reacted negatively to alloplastic implants were treated. The removal of HDPE is complex due to the formation of connective tissue within it. These complications can cause permanent atrophic changes to the skin of the nose. Most of the patients presented with extrusion of their HDPE implants in the nasal columella region. All patients underwent implant removal, cleaning, disinfection, and secondary rhinoplasty. Surgeons must be able to recognize these possible complications and manage them successfully. Even today, many professionals use alloplastic grafts for reconstruction and esthetics of the nasal region. The potential for permanent damage to the skin and soft tissues, as well as complications such as infection and extrusion of the implant, makes the use of autogenous tissue preferable over alloplastic implants. Early detection and immediate treatment of complications are essential to minimize the severity of the deformity.
Cooperative control of environmental extremes by artificial intelligent agents
Authors: Sánchez-Fibla Martí , Moulin-Frier Clément , Solé Ricard
Published: November 2024

Humans have been able to tackle biosphere complexities by acting as ecosystem engineers, profoundly changing the flows of matter, energy and information. This includes major innovations that allowed to reduce and control the impact of extreme events. Modelling the evolution of such adaptive dynamics can be challenging, given the potentially large number of individual and environmental variables involved. This article shows how to address this problem by using fire as the source of extreme events. We implement a simulated environment where fire propagates on a spatial landscape, and a group of artificial agents learn how to harvest and exploit trees while avoiding the damaging effects of fire spreading. The agents need to solve a conflict to reach a group-level optimal state: while tree harvesting reduces the propagation of fires, it also reduces the availability of resources provided by trees. It is shown that the system displays two major evolutionary innovations that end up in an ecological engineering strategy that favours high biomass along with the suppression of large fires. The implications for potential artificial intelligence management of complex ecosystems are discussed.
A first vocal repertoire characterization of long-finned pilot whales (
Globicephala melas
) in the Mediterranean Sea: a machine learning approach
Authors: Poupard M. , Best P. , Morgan J. P. , Pavan G. , Glotin H.
Published: November 2024

The acoustic repertoires of long-finned pilot whales (
Globicephala melas
) in the Mediterranean Sea are poorly understood. This study aims to create a catalogue of calls, analyse acoustic parameters, and propose a classification tree for future research. An acoustic database was compiled using recordings from the Alboran Sea, Gulf of Lion and Ligurian Sea (Western Mediterranean Basin) between 2008 and 2022, totalling 640 calls. Using a deep neural network, the calls were clustered based on frequency contour similarities, leading to the identification of 40 distinct call types defining the local population’s vocal repertoire. These categories encompass pulsed calls with varied complexities, from simplistic to highly intricate structures comprising multiple elements and segments. This study marks the initial documentation of the vocal catalogue of long-finned pilot whales in the Mediterranean Sea. Subsequent research should delve deeper into this multifaceted communication system and explore its potential linkages with social structures.
Information consumption and firm size
Authors: Lee Edward D. , Kwan Alan P. , Hanel Rudolf , Bhatt Anjali , Neffke Frank
Published: November 2024

Social and biological collectives exchange information through internal networks to function. Less studied is the quantity and variety of information transmitted. We characterize the information flow into organizations, primarily business firms. We measure online reading using a large dataset of articles accessed by employees across millions of firms. We measure and relate quantitatively three aspects: reading volume, variety and firm size. We compare volume with size, showing that firm sizes grow sublinearly with reading volume. This is like an economy of scale in information consumption that exaggerates the classic Zipf’s law inequality for firm economics. We connect variety and volume to show that reading variety is limited. Firms above a threshold size read repetitively, consistent with the onset of a coordination problem between teams of employees in a simple model. Finally, we relate reading variety to size. The relationship is consistent with large firms that accumulate interests as they grow. We argue that this reflects structural constraints. Taking the scaling relations as a baseline, we show that excess reading is strongly correlated with returns and valuations. The results indicate how information consumption reflects internal structure, beyond individual employees, as is likewise important for collective information processing in other systems.
Beyond bigrams: call sequencing in the common marmoset (
Callithrix jacchus
) vocal system
Authors: Bosshard Alexandra B. , Burkart Judith M. , Merlo Paola , Cathcart Chundra , Townsend Simon W. , Bickel Balthasar
Published: November 2024

Over the last two decades, an emerging body of research has demonstrated that non-human animals exhibit the ability to combine context-specific calls into larger sequences. These structures have frequently been compared with language’s syntax, whereby linguistic units are combined to form larger structures, and leveraged to argue that syntax might not be unique to language. Currently, however, the overwhelming majority of examples of call combinations are limited to simple sequences comprising just two calls which differ dramatically from the open-ended hierarchical structuring of the syntax found in language. We revisit this issue by taking a whole-repertoire approach to investigate combinatoriality in common marmosets (
Callithrix jacchus
). We use Markov chain models to quantify the vocal sequences produced by marmosets providing evidence for structures beyond the bigram, including three-call and even combinations of up to eight or nine calls. Our analyses of these longer vocal sequences are suggestive of potential further internal organization, including some amount of recombination, nestedness and non-adjacent dependencies. We argue that data-driven, whole-repertoire analyses are fundamental to uncovering the combinatorial complexity of non-human animals and will further facilitate meaningful comparisons with language’s combinatoriality.
Appreciation of singing and speaking voices is highly idiosyncratic
Authors: Bruder Camila , Frieler Klaus , Larrouy-Maestri Pauline
Published: November 2024

Voice preferences are an integral part of interpersonal interactions and shape how people connect with each other. While a large number of studies have investigated the mechanisms behind (speaking) voice attractiveness, very little research was dedicated to other types of vocalizations. In this Registered Report, we proposed to investigate voice preferences with an integrative approach. To this end, we used a newly recorded and validated stimulus set of contrasting vocalizations by 22 highly trained female singers speaking and singing the same material (in Brazilian Portuguese) in contrasting styles (sung as a lullaby, as a pop song or as an opera aria; and spoken aloud as if directed to an adult audience and as if directed to an infant). We asked 62 participants to rate these vocalizations in terms of how much they liked them; and we compared the amount of shared taste (that is, how much participants agreed in their preferences) across styles. We found highly idiosyncratic preferences across all styles. Our predictions concerning shared taste were not confirmed: although shared taste was higher for lullaby than for pop singing, it was unexpectedly higher for operatic than pop singing, and higher for infant-directed than adult-directed speech. Conversely, our prediction of limited consistency in average preferences for some singers across styles was confirmed, contradicting sexual selection-based ideas of singing and speaking as ‘backup’ signals of individual fitness. Our findings draw attention to the role of individual differences in voice preferences and highlight the need for a broader approach to understanding the underlying mechanisms of voice preferences. Stage 1 recommendation and review history:
https://rr.peercommunityin.org/articles/rec?id=357
. Stage 2 recommendation and review history:
https://rr.peercommunityin.org/articles/rec?id=802
.
A Bayesian inverse approach to proton therapy dose delivery verification
Authors: Cox Alexander M. G. , Hattam Laura , Kyprianou Andreas E. , Pryer Tristan
Published: November 2024

This study presents a proof-of-concept for a novel Bayesian inverse method in a one-dimensional setting, aimed at proton beam therapy treatment verification. Our methodology is predicated on a hypothetical scenario wherein strategically positioned sensors detect prompt-

γ

s emitted from a proton beam when it interacts with defined layers of tissue. Using these data, we employ a Bayesian framework to estimate the proton beam’s energy deposition profile. We validate our Bayesian inverse estimations against a closed-form approximation of the Bragg Peak in a uniform medium and a layered lung tumour.
Impact of temperature-reliant thermal conductivity and viscosity variations on the convection of Jeffrey fluid in a rotating cellular porous layer
Authors: Yadav Dhananjay , Awasthi Mukesh Kumar , Ragoju Ravi , Bhattacharyya Krishnendu , Kodi Raghunath , Hassan Mohammad , Wang Junye
Published: November 2024

In this analysis, the collective impact of temperature-dependent thermal conductivity and viscosity variations on the convective instability of a Jeffrey fluid in a rotating layer of cellular porous material is examined using an improved Jeffrey–Darcy model. This study has significant implications for cellular foams made from plastics, ceramics and metals, in which radiative heat transmission can be taken as a diffusion practice. Utilizing the linear stability concept and Galerkin method, approximate analytical and numerical solutions accurate to one decimal place are offered. The analysis reveals that the effect of the thermal conductivity variation factor and the rotation factor is to postpone the convective wave, whereas the viscosity variation factor and the Jeffrey factor have a dual effect in the form of rotation. The range of the convective cell is reduced with cumulating thermal conductivity variation factor, viscosity variation factor, Jeffrey factor and rotation factor. In the absence of rotation, the range of the convective cell is not dependent on the Jeffrey factor or the viscosity variation factor. Furthermore, the outcomes are matched with the existing literature for the specific case of this investigation.
Manifestations of inertia on light dragging revealed in plasmas
Authors: Langlois Julien , Gueroult Renaud
Published: November 2024

Light dragging phenomena in accelerated media have classically been modelled neglecting the effect of inertia on the dielectric response of the media. Here, we show that the inertial corrections due to a rotating motion can have a profound impact on light-dragging manifestations, leading notably to birefringence in media that are isotropic at rest. By applying these findings to a rotating unmagnetized plasma, we further reveal how inertia plays, in this case, a dominant role, offering unique opportunities to expose these new effects. Inertia is notably demonstrated to be the source of non-zero drag and enhanced polarization drag, pointing to fundamental differences between linear and angular momentum coupling. In taking advantage of the singular properties of plasmas, this work more generally underlines how rest-frame properties are affected by an accelerated motion, and how these modifications can carry over to wave dynamics.
A solvable two-dimensional swarmalator model
Authors: O’Keeffe Kevin , Sar Gourab Kumar , Anwar Md Sayeed , Lizárraga Joao U. F. , de Aguiar Marcus A. M. , Ghosh Dibakar
Published: November 2024

Swarmalators are oscillators that swarm through space as they synchronize in time. Introduced a few years ago to model many systems that mix synchrony with self-assembly, they remain poorly understood theoretically. Here, we obtain the first analytic results on swarmalators moving in two spatial dimensions by introducing a simplified model where the swarmalators have no hard-shell interaction terms and move on a periodic plane. These simplifications allow expressions for order parameters, stabilities and bifurcations to be derived exactly.
An updated quantum complementarity principle
Authors: Starke Diego S. , Basso Marcos L. W. , Maziero Jonas
Published: November 2024

Bohr’s complementarity principle has long been a fundamental concept in quantum mechanics, positing that, within a given experimental set-up, a quantum system (or quanton) can exhibit either its wave-like character, denoted as

W

, or its particle-like character, denoted as

P

, but not both simultaneously. Modern interpretations of Bohr’s complementarity principle acknowledge the coexistence of these aspects in the same experiment while introducing the constraint

W
+
P
≤
α

. Notably, estimations of

W

or

P

frequently rely on indirect retrodiction methods, a practice that has led to the claim of the violation of Bohr’s complementarity principle. By taking a different route, recent advancements demonstrate that quantum complementarity relations can be rigorously derived from the axioms of quantum mechanics. To reconcile these observations and eliminate potential paradoxes or violations, we propose an updated formulation for the quantum complementarity principle, which is stated as follows: For a given quantum state preparation

ρ
t

at a specific instant of time

t

, the wave and particle behaviours of a quanton are constrained by a complementarity relation

𝔚
(

ρ
t

)
+
𝔓
(

ρ
t

)
≤
α
(
d
)

, which is derived directly from the axioms of quantum mechanics.
Quantifying and reducing the cost of tagging: combining computational fluid dynamics and diving experiments to reduce impact from animal-borne tags
Authors: McKnight J. Chris , Pass Chris , Thompson Dave , Balfour Steve , Brasseur Sophie M. J. M. , Embling Clare , Hastie Gordon , Milne Ryan , Kyte Adam , Moss Simon E. W. , Pemberton Richard , Russell Debbie J. F.
Published: November 2024

Animal-borne instruments are essential research tools for ecologists and physiologists. An increasing number of studies have shown impacts of carrying a tag on behaviour and energetics, which can have implications for animal welfare and data validity. Such impacts are a result of the additional mass and/or drag loads, with the latter requiring empirical measurements or computational fluid dynamics (CFD) to estimate. To quantify and effectively minimize tag impacts from drag, a novel combined empirical and CFD approach is required. Here, we demonstrate such an approach using captive phocid seals and the widely used Sea Mammal Research Unit (SMRU) Instrumentation Group GPS/GSM tag. We (i) show a significant change in the behaviour of grey seals when carrying a tag (gen 1; associated with 16.4% additional drag); (ii) redesigned the tag (gen 2) resulting in a lower additional drag of 8.6%; (iii) show significant differences in behaviour when carrying a gen 2 compared to gen 1 tag, demonstrating that the redesign successfully reduced impact; and (iv) observed changes in the swim speed of seals that were consistent with predictions from CFD estimates of drag. The gen 2 instrument is now commercially available. This non-trivial case study should pave the way for similar studies in other taxa and species.
Kelp forests versus urchin barrens: a comparison of ecosystem functions and services provided by two alternative stable marine habitats
Authors: Eger Aaron M. , Blain Caitlin O. , Brown Amelia L. , Chan Sharon S. W. , Miller Kelsey I. , Vergés Adriana
Published: November 2024

Kelp forests and urchin barrens are two stable states in rocky reef ecosystems, each providing unique ecosystem functions like habitat for marine species and primary production. While studies frequently show that kelp forests support higher levels of some ecosystem functions than urchin barren habitats, no research has yet compared average differences. To address this gap, we first conducted a meta-analysis of studies that directly compared the ecosystem functions, services and general attributes provided by each habitat. We also compiled individual studies on ecosystem properties from both habitats and qualitatively assessed the benefits provided. The meta-analysis included 388 observations from 55 studies across 14 countries. We found that kelp forests consistently delivered higher levels of ecosystem properties such as biodiversity, species richness, abalone abundance and sea urchin roe quality. Urchin barrens supported higher urchin density and crustose coralline algae cover. The qualitative review further supported these findings, showing that kelp forests ranked higher in 11 out of 15 ecosystem properties. These findings can help guide decisions on managing rocky reef habitats and demonstrate the benefits of preserving or expanding kelp forests.
Global analysis of acoustic frequency characteristics in birds
Authors: Sagar H. S. Sathya Chandra , Anand Akash , Persche Maia E. , Pidgeon Anna M. , Zuckerberg Benjamin , Şekercioğlu Çağan H. , Buřivalová Zuzana
Published: November 2024

Animal communication plays a crucial role in biology, yet the wide variability in vocalizations is not fully understood. Previous studies in birds have been limited in taxonomic and analytical breadth. Here, we analyse an extensive dataset of >140 000 recordings of vocalizations from 8450 bird species, representing nearly every avian order and family, under a structural causal model framework, to explore the influence of eco-evolutionary traits on acoustic frequency characteristics. We find that body mass, beak size, habitat associations and geography influence acoustic frequency characteristics, with varying degrees of interaction with song acquisition type. We find no evidence for the influence of vegetation density, sexual dimorphism, range size and competition on our measures of acoustic frequency characteristics. Our results, built on decades of researchers’ empirical observations collected across the globe, provide a new breadth of evidence about how eco-evolutionary processes shape bird communication.
Molecular Typing of Campylobacter jejuni diarrheal isolates in a Hospital in Makokou, Gabon by Enterobacterial Repetitive Intergenic Consensus Polymerase Chain Reaction (ERIC-PCR).
Authors: ZONG MINKO Ornella , YALA Jean Fabrice , MABIKA MABIKA Rolande , MOUNIOKO Franck , ONDJIANGUI Léonce Fauster , ARMESTO PAULA Jose-Miguel , ONDO-NANG Junior Eymard , MOYEN Rachel
Published: November 2024

2. Abstract

Context

Campylobacter jejuni is responsible for 80% of the cases of human foodborne bacterial enteric infections worldwide. However, limited data on its genetic diversity exist, especially using the Enterobacterial Repetitive Intergenic Consensus Polymerase Chain Reaction (ERIC-PCR). The aim of this study was to determine the genetic diversity of Campylobacter jejuni strains isolated from infant diarrheal feces at the Omar Bongo Ondimba Regional Health Center of Makokou (CHROBOM), Gabon.

Material and methods

58 strains of Campylobacter jejuni from patients with gastroenteritis were used for this work. The ERIC-PCR method was used to characterize genetic diversity. The binomial manual method via the online analysis system (http://insilico.ehu.es/dice_upgma/) was used to establish the dendrogram and calculate the discriminatory power of the Simpson diversity index (D).

Results

The genotyping of Campylobacter jejuni isolates by the ERIC-PCR method revealed a discriminatory index D=0.8451, dividing the 58 isolates into 10 clusters, with 33 genotypic profiles, including 22 non-repeated profiles and 11 repeated profiles. These results indicate a rather polymorphic diversity of Campylobacter jejuni in the Makokou region of Gabon.

Conclusion

The high discriminatory diversity index obtained in this study demonstrates the polymorphic richness within Campylobacter jejuni strains as revealed by the ERIC-PCR method.
PRECISE EXOME ANALYSIS OF BLASTOCYST BIOPSY SCALE SAMPLES USING PRIMARY TEMPLATE-DIRECTED AMPLIFICATION
Authors: Samitova Alina , Belova Vera , Vasiliadis Iuliia , Repinskaia Zhanna , Gorodnicheva Tatiana , Romanov Evgeny , Pogosyan Mariam , Gaysin Emil , Nazarenko Tatyana , Rebrikov Denis , Korostin Dmitriy
Published: November 2024

This study evaluates primary template-directed amplification (PTA) for whole exome sequencing (WES) on small fibroblast cell groups, mimicking the limited cell quantities typical of trophectoderm embryo biopsies. PTA’s consistent amplification reduces allelic dropout (ADO) and impoves uniform coverage, overcoming challenges associated with conventional methods such as multiple displacement amplification (MDA). Using fibroblast samples alongside well-characterised genomic references (E701, NA12878), we benchmarked PTA-WES, achieving 97.5% target region coverage at 10x, meeting American College of Medical Genetics and Genomics (ACMG) standards. Preliminary results from embryo biopsies sequenced with PTA-WES showed a median coverage of 102x, significantly improving upon the variability and coverage gaps observed in MDA-WES. The findings support PTA’s potential to enhance the clinical applicability of WES for preimplantation genetic testing for monogenic disorders (PGT-M), expanding capabilities to detect inherited and de novo mutations in embryos. Further optimisation and variant detection analyses are planned to evaluate PTA’s robustness for routine clinical use.
Single-nucleus transcriptome-wide association study of human brain disorders
Authors: Venkatesh Sanan , Wu Zhenyi , Anyfantakis Marios , Dillard Christian , Prashant N.M. , Burstein David , Mathur Deepika , Kosoy Roman , Chatzinakos Chris , Ajanaku Bukola , Tsetsos Fotis , Zeng Biao , Hong Aram , Casey Clara , Alvia Marcela , Shao Zhiping , Argyriou Stathis , Therrien Karen ,   VA Million Veteran Program,   PsychAD Consortium, Bigdeli Tim , Auluck Pavan , Bennett David A. , Marenco Stefano , Haroutunian Vahram , Girdhar Kiran , Bendl Jaroslav , Lee Donghoon , Fullard John F. , Hoffman Gabriel E. , Voloudakis Georgios , Roussos Panos
Published: November 2024

Neuropsychiatric and neurodegenerative disorders exhibit cell-type-specific characteristics1–8, yet most transcriptome-wide association studies have been constrained by the use of homogenate brain tissue9–11, limiting their resolution and power. Here, we present a single-nucleus transcriptome-wide association study (snTWAS) leveraging single-nucleus RNA sequencing of over 6 million nuclei from the dorsolateral prefrontal cortex of 1,494 donors across three ancestries—European, African, and Admixed American. We constructed ancestry-specific single-nucleus-derived transcriptomic imputation models (snTIMs) including up to 27 non-overlapping cellular populations, enhancing the resolution of genetically regulated gene expression (GReX) in the brain and uncovering novel gene-trait associations across 12 neuropsychiatric and neurodegenerative traits. Our snTWAS framework revealed cell-type-specific dysregulation of GReX, identifying over 4,000 novel gene-trait associations not detected by bulk tissue approaches. By applying these snTIMs to the Million Veteran Program, we validated major findings and explored the pleiotropy of cell-type-specific GReX, revealing cross-ancestry concordance and fine-mapping causal genes. This approach enhances the discovery of biologically relevant pathways and gene targets, highlighting the importance of cell-type resolution and ancestry-specific models in understanding the genetic architecture of complex brain disorders.
Substrate utilization and cross-feeding synergistically determine microbiome resistance to pathogen invasion
Authors: Yang Xinrun , Yang Tianjie , Zhang Ziru , Zhang Yaozhong , Mei Xinlan , Gao Yang , Wang Ningqi , Jiang Gaofei , Xu Yangchun , Shen Qirong , Medema Marnix H. , Wei Zhong , Jousset Alexandre
Published: November 2024

Understanding how microbiomes resist pathogen invasion remains a key challenge in natural ecosystems. Here, we combined genome-scale metabolic models with synthetic community experiments to unravel the mechanisms driving pathogen suppression. We developed curated genome-scale models for each strain, incorporating 48 common resource utilization profiles to fully capture their metabolic capacities. Trophic interactions inferred from models accurately predicted pathogen invasion outcomes, achieving an F1 score of 96% across 620 invasion tests involving diverse microbial communities and nutrient environments. Importantly, considering both substrate and metabolite features provided a more holistic understanding of pathogen suppression. In particular, cross-feeding metabolites within the native community emerged as crucial yet often overlooked predictors of community resistance, disproportionally favoring native species over invaders. This study lays the foundation for designing disease-resistant microbiomes, with broad implications for mitigating pathogen exposure in diverse environments.
Evolutionarily recent transcription factors partake in human cell cycle regulation
Authors: Pulver Cyril , Forey Romain , Lederer Alex R. , Begnis Martina , Rosspopoff Olga , Carlevaro-Fita Joana , Martins Filipe , Planet Evarist , Duc Julien , Raclot Charlène , Offner Sandra , Coudray Alexandre , Dorschel Arianna , Trono Didier
Published: November 2024

The cell cycle is a fundamental process in eukaryotic biology and is accordingly controlled by a highly conserved core signaling cascade. However, whether recently evolved proteins also influence this process is unclear. Here, we systematically map the influence of evolutionarily recent transcription factors (TFs) on human cell cycle progression. We find that the genomic targets of select young TFs, many of which belong to the rapidly evolving Krüppel-associated box (KRAB) zinc-finger proteins (KZFP) family, exhibit synchronized cell cycle expression. Systematic perturbation studies reveal that silencing recent TFs disrupts normal cell cycle progression, which we experimentally confirm for ZNF519, a simian-restricted KZFP. Further, we show that the therian-specific KZFP ZNF274 sets the cell cycle expression and replication timing of hundreds of clustered genes. These findings highlight an underappreciated level of lineage specificity in cell cycle regulation.
Gene expression divergence between locally adapted inland annual and coastal perennial ecotypes ofMimulus guttatusacross developmental stages
Authors: Olsen Jason D. , Gould Billie A , Chen Yani , Lowry David B.
Published: November 2024

The action of natural selection across heterogeneous natural landscapes drives local adaptation and the formation of plant ecotypes, the precursors to new species. Plant ecotypes typically differ greatly in morphology, physiology, and development, yet we have a poor understanding of the underlying genetic basis of this divergence. Despite their importance, studies of the molecular underpinnings of ecotypic divergence through developmental stages are rare. In this study, we compared gene expression at different developmental time points between two locally adapted populations derived from the coastal perennial and inland annual ecotypes of the yellow monkeyflower,Mimulus guttatus. We conducted gene co-expression network analyses to identify putative genetic and molecular mechanisms driving ecotypic divergence and evaluated gene ontology enrichment. Overall, we found significant global expression differences between the ecotypes and among developmental stages. We also found evidence to support the hypothesis that interacting hormone pathways, especially the gibberellin and jasmonic acid pathways, may play a key role in annual versus perennial ecotype divergence. Further, genes within known chromosomal inversions were more likely to be differentially expressed than genes in colinear regions, but only in leaves and not for floral buds. Collectively, our results reinforce our existing hypotheses about how ecotype formation has occurred in this system through shifts in hormone biosynthesis/signaling and help advance our understanding of the evolution of annuality versus perenniality in plants.
Geometrically balanced model of cell growth
Authors: Vazquez Alexei , Gedeon Tomáš
Published: November 2024

The proteome balance constraint in metabolic flux balance analysis asserts that the proteome is constructed by ribosomes, which themselves contain many proteins. This leads to a fundamental question of optimal allocation of limited proteome among different pools of enzymes, which include ribosomes themselves. However, recent work points to additional constraints imposed by the cell geometry. In this paper we deduce theproteogeometric constraint, whereπA,πPandπLare the proteomic fractions allocated to the cell surface area, protein synthesis and cell membrane phospholipids synthesis andandθare constants imposed by geometry of the cell. We illustrate the relevance of this constraint using a reduced model of cell metabolism, illuminating the interplay between cell metabolism and cell geometry.
Diverse ancestral representation improves genetic intolerance metrics
Authors: Han Alexander L. , Sands Chloe F. , Matelska Dorota , Butts Jessica C. , Ravanmehr Vida , Hu Fengyuan , Gonzalez Esmeralda Villavicencio , Katsanis Nicholas , Bustamante Carlos D. , Wang Quanli , Petrovski Slavé , Vitsios Dimitrios , Dhindsa Ryan S.
Published: November 2024

Rapidly expanding genomic databases have enabled the identification of regions in the human genome intolerant to variation and thus likely relevant to human disease. However, despite their unprecedented scale, these datasets remain constrained by limited ancestral diversity. Here, we systematically evaluate how genetic diversity impacts gene- and sub-genic intolerance metrics by analyzing whole-exome sequencing data from 460,551 UK Biobank participants and 125,748 gnomAD participants across diverse ancestral backgrounds. Through comprehensive analysis of randomly sampled datasets with varying ancestral compositions, we demonstrate that genetic diversity, rather than sample size alone, drives the performance of intolerance metrics in identifying functionally critical genes and genic sub-regions. Notably, scores trained on variation observed in African and Admixed American ancestral groups showed superior resolution in detecting neurodevelopmental disease risk genes and haploinsufficient genes compared to scores trained on variation observed in European ancestry cohorts. Most strikingly, the Missense Tolerance Ratio (MTR) trained on 43,000 multi-ancestry exomes demonstrated greater predictive power than when trained on a nearly 10-fold larger dataset of 440,000 non-Finnish European exomes, indicating that European ancestry-based scores are approaching saturation. These findings establish ancestral diversity as the fundamental determinant for advancing intolerance metrics and underscore the urgent scientific and ethical imperative for enhanced population representation in genomic resources to fully realize the potential of precision medicine and drug discovery.
PPD-H1Improves Stress Resistance and Energy Metabolism to Boost Spike Fertility under High Ambient Temperatures
Authors: Lan Tianyu , Walla Agatha , Çolpan Karışan Kumsal Ecem , Buchmann Gabriele , Wewer Vera , Metzger Sabine , Vardanega Isaia , Haraldsson Einar Baldvin , Helmsorig Gesa , Thirulogachandar Venkatasubbu , Simon Rüdiger , von Korff Maria
Published: November 2024

High ambient temperature (HT) impairs reproductive development and grain yield in temperate crops. To ensure reproductive success under HT, plants must maintain developmental stability. However, the mechanisms integrating plant development and temperature resilience are largely unknown. Here, we demonstrate thatPHOTOPERIOD 1(PPD-H1), homologous toPSEUDO RESPONSE REGULATORgenes of the Arabidopsis circadian clock, controls developmental stability in response to HT in barley. We analyzed HT responses in independent introgression lines with either the ancestral wild-typePpd-H1allele or the naturalppd-h1variant, selected in spring varieties to delay flowering and enhance yield under favourable conditions. HT delayed inflorescence development and reduced grain number inppd-h1mutant lines, while the wild-typePpd-H1genotypes accelerated reproductive development and showed a stable grain set under HT. Using a CRISPR/Cas9-inducedppd-h1mutant, we confirmed that the CCT domain ofPpd-H1controls developmental stability, but not clock gene expression. Transcriptome and phytohormone analyses in developing leaves and inflorescences revealed increased stress gene expression and abscisic acid levels in the leaf and inflorescence of the natural and induced mutantppd-h1lines. Furthermore, the mutantppd-h1lines downregulated photosynthesis-and energy metabolism-related genes, and reduced auxin and cytokinin levels in the inflorescence, which impaired anther and pollen development. By contrast, in the wild-typePpd-H1plants, the transcriptome and phytohormone levels and anther and pollen development remained stable under HT. Our findings suggest thatPpd-H1enhances stress resistance and energy metabolism, thereby stabilizing reproductive development, floret fertility and grain set under HT.
Sulfide-responsive transcription control inEscherichia coli
Authors: Hori Koichi , Balasubramanian Rajalakshmi , Masuda Shinji
Published: November 2024

To elucidate the mechanism of large-scale transcriptional changes dependent on sulfide inEscherichia coli, a large scale RNA-sequencing analysis was performed on wild-type and sulfide-responsive transcription factor YgaV deletion mutants grown under three conditions: aerobic, semi-aerobic, and semi-aerobic with sulfide. The resulting dataset from these six conditions was subjected to principal component analysis, which categorized the data into five principal components. Estimation of the typical gene expression regulatory mechanisms in each category suggested the presence of mechanisms that are dependent on sulfide but independent of YgaV, as well as those that depend on YgaV but not on sulfide. In YgaV-dependent transcriptional regulation, YgaV was found to function as both a repressor and an activator. These results support the previous hypothesis that YgaV acts as a global regulator responsible for redox homeostasis.
Structure of Blm10:13S proteasome intermediate reveals parallel assembly pathways for the proteasome core particle
Authors: Kaur Mandeep , Chen Xiang , Lee Stella Y. , Weaver Tyler M. , Freudenthal Bret D. , Walters Kylie J. , Roelofs Jeroen
Published: November 2024

Proteasomes are formed by chaperone-assisted assembly of core particles (CPs) and regulatory particles (RPs). The CP chaperone dimer Pba1/Pba2 binds early to proteasome subunits, and is thought to be replaced by Blm10 to form Blm10:CP, which promotes ATP-independent degradation of disordered proteins. Here, we present evidence of distinct parallel assembly pathways for CP by solving five cryo-EM structures including a Blm10:13S pre-assembly intermediate. Our data conflict with the current model of Blm10 and Pba1/Pba2 sequential activity in a single assembly pathway, as we find their CP binding is mutually exclusive and both are present on early and late assembly intermediates. CP affinity for Pba1/Pba2 is reduced during maturation, promoting Pba1/Pba2 release. We find Blm10 undergoes no such affinity switch, suggesting this pathway predominantly yields mature Blm10-bound CP. Altogether, our findings conflict with the current paradigm of sequential CP binding to instead indicate parallel assembly pathways by Pba1/Pba2 and Blm10.