bluuebunny/crossref_metadata_2025 huggingface dataset:
Unchartered territory? Navigating voice, accountability, and prevention in suicide‐related domestic homicide reviews in England and Wales
Authors: MUNRO VANESSA E. , DANGAR SARAH , ANDRADE LOTTE YOUNG
Published: December 2024

Distinct from a criminal justice investigation, which focuses on the retrospective attribution of responsibility and the imposition of punishment on a perpetrator of abuse, domestic homicide reviews (DHRs) involve a contextual exploration of the circumstances in which the death occurred, with a view to learning lessons that can facilitate improved safeguarding, agency engagement, and support provision. In this article, we report on an analysis of reviews completed in England and Wales in cases of domestic abuse‐related suicide, and interviews with professionals and bereaved family members. We highlight challenges faced in relation to facilitating voice and participation, encouraging critical reflection and accountability, and ensuring implementation and prevention. With the DHR regime under review in England and Wales, and a focus on its applicability to deaths by suicide, we reflect on lessons that might be learned from other processes where efforts to cultivate a ‘just’ rather than a ‘blame’ culture have also been made.
Genetic and Genomic Approaches to the Study of Drug‐Induced Liver Injury
Authors: Daly Ann K.
Published: December 2024

Idiosyncratic hepatotoxicity induced by prescribed drugs has been known since the early 20th century. Identifying risk factors, including genetic factors, that trigger this drug‐induced liver injury (DILI) has been an important priority for many years, both to prevent drugs that cause liver injury being licensed and as a potential means of preventing at‐risk patients being prescribed causative drugs. Improved methods for genomic analysis, particularly the development of genome‐wide association studies, have facilitated the identification of genomic risk factors for DILI, but, to date, there are only two main examples, liver injury caused by amoxicillin‐clavulanate (AC) and by flucloxacillin, where genetic risk factors causing the injury have been identified and replicated with understanding of the underlying mechanism. There has also been progress on identifying genetic risk factors for liver injury caused by other anti‐infective agents, herbal remedies and nonsteroidal anti‐inflammatory drugs. The majority of genetic risk factors identified to date are specific human leucocyte antigen (HLA) alleles and evidence that these alleles preferentially present self‐peptides inappropriately to T cells in the liver has been obtained. Non‐HLA genes also contribute to genetic susceptibility, both as co‐factors in T‐cell responses and, in the case of isoniazid‐only, drug metabolism. Polygenic risk scores to predict DILI have been developed, both a simple score that predicts AC injury and complex scores that may be applied to DILI more generally and provide evidence that additional risk factors other than HLA genes exist.
International Benchmarks for the Practice Environment Scale of the Nursing Work Index: A Meta‐Analysis
Authors: Lake Eileen T. , Zhang Bingyu , Tong Jiayi , Mpundu Gloria , Gross Kelsey N. , Correa Malini H. , Wethman Lauren B. , Moronski Lynne , Villani Domenique , Chen Yong
Published: December 2024

The Practice Environment Scale of the Nursing Work Index has been used worldwide to measure nurse work environments. International benchmark values for this scale can assist managers in assessing their work environment. The objective was to conduct a meta‐analysis of this instrument's composite and subscale values across continents, nursing unit types, and time. Studies published up until September 30, 2023 were identified in CINAHL, MEDLINE, and Embase. One‐hundred and sixty publications representing 38 countries were included. Most studies were rated as high certainty and low to moderate risk of bias. The pooled point estimate (2.70) indicated that hospital work environments were modestly positive. The weakest work environment domain was Staffing and Resource Adequacy (2.47). Europe had significantly weaker work environments than Asia and North America. Africa and South America had few studies. Better work environments were reported in neonatal intensive care, as compared to medical surgical and critical care units. A small, positive slope over time, which was detected in the three continents, was significant in North America. To promote evidence‐based management globally, benchmark values are now available by setting and continent.
Assessing Changes in China's Pond Water Quality From 1989 to 2020: Implications for Green Development in Aquaculture
Authors: Duan Yuanshuai , Liu Lu , Tang Rong , Xie Shouqi , Yang Mingmei , Zhang Zhimin , Li Dapeng
Published: December 2024

Since 1989, China has become the world's largest aquaculture producer through pond culture, significantly contributing to global food security but potentially posing environmental threats. However, little is known about the changes in the pond water quality at broad spatial and temporal scales, thus creating challenges in the sustainability of pond aquaculture. Herein, we explore changes in water quality in China's aquaculture ponds from 1989 to 2020 and assess the waterbody's health status to optimize sustainable management strategies. This study highlights pond water quality changes closely associated with China's aquaculture practices, development, and related policies. Seasonal and regional farming variations significantly impact water quality, with peak aquaculture seasons and Central China and North China associated with the lowest water quality scores. Pond water quality initially declined with the rise of intensive aquaculture but improved after 2012 with the adoption of ecological engineering measures, eco‐farming practices, and policies supporting green development. Under a scenario combining these efforts, the water quality score in 2035 is projected to increase by 57% of the 2020 level. These findings reveal that national ecological initiatives and advancements in green aquaculture techniques and public policies can significantly enhance the water quality of China's aquaculture ponds, offering valuable insights into environmental governance in global agriculture.
Immunohistochemical Expression of Programmed Death‐Ligand 1 and Cytotoxic T‐Lymphocyte Antigen‐4 in Canine Cutaneous Mast Cell Tumours
Authors: Ribeiro Mariana Pinto , Canadas‐Sousa Ana , Aluai‐Cunha Catarina , de Fátima Carvalho Maria , Santos Andreia Ferreira
Published: December 2024

Mast cell tumours (MCTs) are the most frequent cutaneous neoplasia of the dog, and they have very variable biological behaviour and survival times. Surgery is still the best treatment, and despite the several adjuvant therapies described, many cases are very aggressive and resistant to these treatments making it urgent to find new therapeutic targets. Nowadays, immunotherapy targeting immune checkpoints has been described as a complementary treatment for several human cancers, but it is still very scarcely studied in veterinary medicine. Therefore, this study aimed to investigate the expression of the checkpoint proteins programmed death‐ligand 1 (PD‐L1) and cytotoxic T‐lymphocyte antigen‐4 (CTLA‐4) to evaluate their potential as therapeutic targets for MCT. Through immunohistochemical study, it was analysed the expression of PD‐L1 and CTLA‐4 in 74 MCT cases from the archive of the Veterinary Pathology Laboratory of the University of Porto (LabPatVet). Tumour size, histological grade, ki‐67 proliferation index, mitotic count and presence of metastatic disease were also assessed. Most of the cases expressed both immune checkpoints in neoplastic cells. There was a statistically significant inverse association between the expression of CTLA‐4 and MCT grade (p < 0,001) and mitotic count (p < 0.001). PD‐L1 was significantly and negatively related to HG (p = 0.004), and tumour size (р = 0.014). Tumour size, histological grade and mitotic count were positively associated with metastatic disease. Additionally, it was observed that the expression of PD‐L1 and CTLA‐4 was interrelated (p < 0.001). This study demonstrated that MCT cells express both PD‐L1 and CTLA‐4 and that their expression was associated with MCT prognostic factors.
A refined, minimally invasive, reproducible ovine ischaemia–reperfusion–infarction model using implantable defibrillators: Methodology and validation
Authors: Pius Charlene , Niort Barbara , Radcliffe Emma J. , Trafford Andrew W.
Published: December 2024

Ischaemic heart disease remains a leading cause of premature mortality and morbidity. Understanding the associated pathophysiological mechanisms of cardiac dysfunction arising from ischaemic heart disease and the identification of sites for new therapeutic interventions requires a preclinical model that reproduces the key clinical characteristics of myocardial ischaemia, reperfusion and infarction. Here, we describe and validate a refined and minimally invasive translationally relevant approach to induce ischaemia, reperfusion and infarction in the sheep. The novelty and refinement in the procedure stems from utilization of implantable cardiac defibrillators prior to coronary engagement, balloon angioplasty to induce infarction, and intra‐operative anti‐arrhythmic drug protocols to reduce adverse arrhythmic events. The protocol is readily adoptable by researchers with access to standard fluoroscopic instrumentation, and it requires minimally invasive surgery. These refinements lead to a substantial reduction of intra‐operative mortality to 6.7% from previously published values ranging between 13% and 43%. The model produces key characteristics associated with the fourth universal definition of myocardial infarction, including ECG changes, elevated cardiac biomarkers and cardiac wall motility defects. In conclusion, the model closely replicates the clinical paradigm of myocardial ischaemia, reperfusion and infarction in a translationally relevant large animal setting, and the applied refinements reduce the incidence of intra‐operative mortality typically associated with preclinical myocardial infarction models.
Role of forelimb morphology in muscle sensorimotor functions during locomotion in the cat
Authors: Rahmati Seyed Mohammadali , Klishko Alexander N. , Martin Ramaldo S. , Bunderson Nate E. , Meslie Jeswin A. , Nichols T. Richard , Rybak Ilya A. , Frigon Alain , Burkholder Thomas J. , Prilutsky Boris I.
Published: December 2024

Previous studies established strong links between morphological characteristics of mammalian hindlimb muscles and their sensorimotor functions during locomotion. Less is known about the role of forelimb morphology in motor outputs and generation of sensory signals. Here, we measured morphological characteristics of 46 forelimb muscles from six cats. These characteristics included muscle attachments, physiological cross‐sectional area (PCSA) and fascicle length. We also recorded full‐body mechanics and EMG activity of forelimb muscles during level overground and treadmill locomotion in seven and 16 adult cats of either sex, respectively. We computed forelimb muscle forces along with force‐ and length‐dependent sensory signals mapped onto corresponding cervical spinal segments. We found that patterns of computed muscle forces and afferent activities were strongly affected by the muscle's moment arm, PCSA and fascicle length. Morphology of the shoulder muscles suggests distinct roles of the forelimbs in lateral force production and movements. Patterns of length‐dependent sensory activity of muscles with long fibres (brachioradialis, extensor carpi radialis) closely matched patterns of overall forelimb length, whereas the activity pattern of biceps brachii length afferents matched forelimb orientation. We conclude that cat forelimb muscle morphology contributes substantially to locomotor function, particularly to control lateral stability and turning, rather than propulsion.

image

Key points

Little is known about the role of forelimb muscle morphology in producing motor outputs and generating somatosensory signals. This information is needed to understand the contributions of forelimbs in locomotor control.

We measured morphological characteristics of 46 muscles from cat forelimbs, recorded cat walking mechanics and electromyographic activity, and computed patterns of moment arms, length, velocity, activation, and force of forelimb muscles, as well as length‐ and force‐dependent afferent activity during walking.

We demonstrated that moment arms, physiological cross‐sectional area and fascicle length of forelimb muscles contribute substantially to muscle force production and proprioceptive activity, to the regulation of locomotor cycle phase transitions and to control of lateral stability.

The obtained information can guide the development of biologically accurate neuromechanical models of quadrupedal locomotion for exploring and testing novel methods of treatments of central nervous system pathologies by modulating activities in neural pathways controlling forelimbs/arms.
Gemology and Geochemistry of Staurolites from the Casa Nova Region, Brazil
Authors: Gomes de Oliveira Isaac , Pinto Bezerra Isabelle , Ravielly dos Santos Breno , De Sousa Silva Larissa , Leal Neto Antonio , Dos Santos Lucilene , Falcão de Oliveira Neri Tereza
Published: December 2024

The properties of minerals used as gemstones could help or even reveal new aspects about the geological evolution of the region where a mineral was found. The objective of this study was the gemological characterization and acquisition of chemical data on staurolites from the city of Casa Nova (Bahia, Brazil). The gemological data are within the normal range for the staurolite mineral, except for the absence of pleochroism, above-average densities in two specimens, and a rare color (intense red) in a sample. The intrinsic part of these gems is in possible correlations involving their properties, such as: color, refractive index, birefringence, relative density, and the amounts of FeO in the samples. The geochemistry of these samples is unusual; FeO and MgO appear in considerably above-average quantities, and Al2O3 is up to 8% below average; the presence of CaO is also rare. Therefore, staurolites from Casa Nova (Bahia) have the potential to be used as gemstones, and their geochemistry combined with the gemology of these samples is a great indication for further studies.
Social Representations of Nursing Care for Women Victims of Intimate Partner Violence: Perspectives from Medellín (Colombia)
Authors: Otálvaro Gallego Jennifer Alejandra
Published: December 2024

Introduction: Intimate partner violence (IPV) is a social and public health problem that profoundly impacts women's lives. Nursing professionals, as the first point of contact within the health system, play a key role in detecting and addressing this phenomenon. However, their social representations (SR) of IPV and the care provided can influence the quality of interventions. Objective: To understand the SR of nursing professionals regarding the care of women victims of IPV in the city of Medellín. Method: A qualitative study conducted between 2021 and 2022, based on the SR Theory with a procedural approach. Twelve semi-structured interviews were conducted with nursing professionals with over five years of experience, selected through convenience and snowball sampling. Data were analyzed using the constructivist approach of Charmaz's Grounded Theory. Results: The SR of nursing professionals reflect broad but stigmatizing perceptions of women victims, who are seen as fragile and dependent. The care provided is perceived as insufficient due to institutional barriers and a lack of specific training, although active listening and emotional support are recognized as central strategies. Conclusions: Transforming these SR through formative and reflective processes is essential to promote comprehensive and humanized care. Furthermore, it is necessary to strengthen policies and protocols that expand the role of nursing professionals in the integral care and long-term follow-up of women victims.
Experimental Study on Vibration Characteristics of Rotor-Rotor Inter-Shaft Labyrinth Seal Rubbing Faults in a Counter-Rotating Aero-Engine
Authors: Wang Zhiliang , Zhao Wei , Ma Yingqun , Ren Sanqun , Yang Xuesen , Zhao Qingjun
Published: December 2024

In order to solve the problem of rotor-rotor inter-shaft labyrinth seal rubbing fault during the test run of a counter-rotating dual-rotor aero-engine, based on the fast Fourier transform, the vibration time-domain signals of three groups of cross-sectional measuring points on the casing are analyzed in the frequency domain, and the three-dimensional waterfall diagrams of each cross-sectional measuring point and the spectrum diagrams of the step section of the time-domain signal are drawn. The analysis results show that when the high- and low-pressure speeds are both in steady-state, the rotor-rotor inter-shaft labyrinth seal rubbing causes a sudden increase in the amplitude of some measuring points on the casing; the spectrum diagrams at the measuring points of the intake casing and turbine casing sections show regular combined frequencies f1 + k2f2 and k1f1 + f2 characteristics, and the frequency 2f1 + f2 component is dominant; the double fundamental frequency components of the rotating frequency with different amplitudes appear at some of the cross-sectional measuring points. Finally, based on the vibration transfer path analysis method, the vibration characteristics of the rotor-rotor inter-shaft labyrinth seal rubbing fault are analyzed mechanistically, and combined with the results of engine disassembly inspection, it is comprehensively judged that the fault is due to the increase in rotor vibration caused by the rise in high- and low-pressure speeds. Furthermore, the labyrinth seal on the low-pressure rotor expands more due to the high temperature than the wear-resistant coating area, resulting in a reduction in the gap between the labyrinth seal and the wear-resistant coating on the inner side of the high-pressure rotor, which leads to the rotor-rotor inter-shaft labyrinth seal rubbing fault.
Assessment of honey bees health in relation to varroa (Acari: Varroidae) infestation and morphometric analysis of the mite in two phytogeographic zones of Burkina Faso, West Africa
Authors: Sawadogo Souhaïbou , Dingtoumda Oswald Gilbert , Bazié Hugues Roméo , Zella Sinali , Bationo Modeste Florentin , Aebi Alexandre , Ilboudo Zakaria
Published: December 2024

Varroa mite threatens honey bees worldwide by affecting larvae and adults and causing viral diseases associated with colony collapse. This study investigates its prevalence and infestation level, and morphometric traits in Southern Sudanese (SS) and Northern Sudanese (NS) phytogeographical zones of Burkina Faso. We visited 238 hives from 48 apiaries in 9 provinces. Phoretic varroa mites were detected through a 70% alcohol wash on approximately 300 worker bees. Once in the laboratory, 7 morphometric characters were measured on 1 to 10 varroa mites per hive. According to these measurements, the mites were identified as Varroa destructor, Anderson & Trueman, 2000. Data analysis reveals that 91.6% of colonies of the whole sample are infested with varroa. In NS zone, the provinces of Bazega and Zoundweogo show high infestation level (5.93% and 7.18% respectively), while in the SS zone, Nahouri and Ziro exhibit the highest level (8.19% and 9.00%) respectively. In terms of body length and body width (BL and BW), varroa mites from SS zone display averages of 1176.04 ± 40.1 µm and 1765.14 ± 49.2 µm, while those from the NS zone have average values of 1167.44 ± 40.8 µm and 1755.36 ± 53.42 µm. These morphological differences are statistically significant (P ≤ 0.05), highlighting variability that may result from local adaptations or genetic variations. The morphological diversity of this parasite has implications for its biology, dispersion, and virulence towards bees. Future studies should explore genetic factors influencing parasitic dynamics and bee resistance for effective management strategies.
A bacterial methyltransferase that initiates biotin synthesis, an attractive anti-ESKAPE druggable pathway
Authors: Su Zhi , Zhang Weizhen , Shi Yu , Cui Tao , Xu Yongchang , Yang Runshi , Huang Man , Zhou Chun , Zhang Huimin , Lu Ting , Qu Jiuxin , He Zheng-Guo , Gan Jianhua , Feng Youjun
Published: December 2024

The covalently attached cofactor biotin plays pivotal roles in central metabolism. The top-priority ESKAPE-type pathogens,
Acinetobacter baumannii
and
Klebsiella pneumoniae
, constitute a public health challenge of global concern. Despite the fact that the late step of biotin synthesis is a validated anti-ESKAPE drug target, the primary stage remains fragmentarily understood. We report the functional definition of two BioC isoenzymes (AbBioC for
A. baumannii
and KpBioC for
K. pneumoniae
) that act as malonyl-ACP methyltransferase and initiate biotin synthesis. The physiological requirement of biotin is diverse within ESKAPE pathogens. CRISPR-Cas9–based inactivation of
bioC
rendered
A. baumannii
and
K. pneumoniae
biotin auxotrophic. The availability of soluble AbBioC enabled the in vitro reconstitution of DTB/biotin synthesis. We solved two crystal structures of AbBioC bound to SAM cofactor (2.54 angstroms) and sinefungin (SIN) inhibitor (1.72 angstroms). Structural and functional study provided molecular basis for SIN inhibition of BioC. We demonstrated that BioC methyltransferase plays dual roles in
K. pneumoniae
infection and
A. baumannii
colistin resistance.
Domain adaptation in small-scale and heterogeneous biological datasets
Authors: Orouji Seyedmehdi , Liu Martin C. , Korem Tal , Peters Megan A. K.
Published: December 2024

Machine-learning models are key to modern biology, yet models trained on one dataset are often not generalizable to other datasets from different cohorts or laboratories due to both technical and biological differences. Domain adaptation, a type of transfer learning, alleviates this problem by aligning different datasets so that models can be applied across them. However, most state-of-the-art domain adaptation methods were designed for large-scale data such as images, whereas biological datasets are smaller and have more features, and these are also complex and heterogeneous. This Review discusses domain adaptation methods in the context of such biological data to inform biologists and guide future domain adaptation research. We describe the benefits and challenges of domain adaptation in biological research and critically explore some of its objectives, strengths, and weaknesses. We argue for the incorporation of domain adaptation techniques to the computational biologist’s toolkit, with further development of customized approaches.
Molecular basis for plasma membrane recruitment of PI4KA by EFR3
Authors: Suresh Sushant , Shaw Alexandria L. , Pemberton Joshua G. , Scott Mackenzie K. , Harris Noah J. , Parson Matthew A. H. , Jenkins Meredith L. , Rohilla Pooja , Alvarez-Prats Alejandro , Balla Tamas , Yip Calvin K. , Burke John E.
Published: December 2024

The lipid kinase phosphatidylinositol 4 kinase III α (PI4KIIIα/PI4KA) is a master regulator of the lipid composition and asymmetry of the plasma membrane. PI4KA exists primarily in a heterotrimeric complex with its regulatory proteins TTC7 and FAM126. Fundamental to PI4KA activity is its targeted recruitment to the plasma membrane by the lipidated proteins EFR3A and EFR3B. Here, we report a cryogenic electron microscopy structure of the C terminus of EFR3A bound to the PI4KA-TTC7B-FAM126A complex, with extensive validation using both hydrogen deuterium exchange mass spectrometry, and mutational analysis. The EFR3A C terminus undergoes a disorder-order transition upon binding to the PI4KA complex, with an unexpected direct interaction with both TTC7B and FAM126A. Complex disrupting mutations in TTC7B, FAM126A, and EFR3 decrease PI4KA recruitment to the plasma membrane. Multiple posttranslational modifications and disease linked mutations map to this site, providing insight into how PI4KA membrane recruitment can be regulated and disrupted in human disease.
Bacteriophage treatment is effective against carbapenem-resistant
Klebsiella pneumoniae
(KPC) in a neutropenic murine model of gastrointestinal translocation and renal infection
Authors: Zagaliotis Panagiotis , Michalik-Provasek Jordyn , Mavridou Eleftheria , Naing Ethan , Vizirianakis Ioannis S. , Chatzidimitriou Dimitrios , Gill Jason J. , Walsh Thomas J.
Published: December 2024

Carbapenemase-producing
Klebsiella pneumoniae
(KPC) are globally emerging pathogens that cause life-threatening infections. Novel treatment alternatives are urgently needed. We therefore investigated the effectiveness of three novel bacteriophages (Spivey, Pharr, and Soft) in a neutropenic murine model of KPC gastrointestinal colonization, translocation, and disseminated infection. Bacteriophage efficacy was determined by residual bacterial burden of KPC (CFU/g) in kidneys. Parallel studies were conducted of bacteriophage pharmacokinetics and resistance. Treatment of mice with 5 × 10
9
PFU of phage cocktail via intraperitoneal injection was effective in significantly reducing renal KPC CFU by 100-fold (
P
< 0.01) when administered every 24 h and 1000-fold (
P
< 0.01) every 12 h. Moreover, a combination of bacteriophage and ceftazidime-avibactam produced a synergistic effect, resulting in a 10
5
-fold reduction in bacterial burden in cecum and kidney (
P
< 0.001 in both tissues). Prophylactic administration of bacteriophages via oral gavage did not prevent KPC translocation to the kidneys. Bacteriophage decay determined by linear regression of the ln of mean concentrations demonstrated R
2
values in plasma of 0.941, kidney 0.976, and cecum 0.918, with half-lives of t
1/2
= 2.5 h. Furthermore, a phage-resistant mutant displayed increased sensitivity to serum killing
in vitro
, but did not show significant defects in renal infection
in vivo
. A combination of bacteriophages demonstrated significant efficacy alone and synergy with ceftazidime/avibactam in the treatment of experimental disseminated KPC infection in neutropenic mice.
Use of voriconazole to predict susceptibility and resistance to isavuconazole for
Aspergillus fumigatus
using CLSI methods and interpretive criteria
Authors: Winkler Marisa L. , Rhomberg Paul R. , Fedler Kelley A. , Huband Michael D. , Karr Maura , Kimbrough John H. , Castanheira Mariana
Published: December 2024

Aspergillus fumigatus
is a common cause of pulmonary and invasive mold infections among immunocompromised hosts. Mortality in immunocompromised hosts with invasive
Aspergillus
infections (IAI) has been reported to be as high as 80%. Therefore, appropriate therapy is essential in treating IAI. Both isavuconazole and voriconazole are first-line agents in treatment guidelines for IAI, but isavuconazole has favorable properties, often leading it to be preferred over voriconazole, given the lengthy duration of treatment. It is difficult to perform mold antifungal susceptibility testing, which often requires a reference lab and several weeks to determine results. Therefore, use of surrogate markers can be helpful to infer susceptibility when testing is not possible or delayed. We performed isavuconazole and voriconazole broth microdilution susceptibility testing by the Clinical and Laboratory Standards Institute (CLSI) method on a collection of 976 non-duplicate
A. fumigatus
isolates from a global surveillance program between 2017 and 2022. We found that voriconazole and isavuconazole have a very high essential agreement within two doubling dilutions at 99.9% and a categorical agreement of 92.7% with no very major errors, one major error (0.11%), and <10% minor errors. Many of the minor errors were in the setting of voriconazole testing at a MIC of 0.5 mg/L (susceptible) but isavuconazole at 2 mg/L (intermediate). Genetic analysis of
cyp51
genes confirmed that isavuconazole and voriconazole susceptibility testing identified isolates with
cyp51A
and
cyp51B
mutations. Voriconazole can be used to predict the isavuconazole susceptibility testing result when
A. fumigatus
is tested by CLSI broth microdilution methodology.
The palmitoyl-CoA ligase Fum16 is part of a
Fusarium verticillioides
fumonisin subcluster involved in self-protection
Authors: Gherlone Fabio , Jojić Katarina , Huang Ying , Hoefgen Sandra , Valiante Vito , Janevska Slavica
Published: December 2024

Fusarium verticillioides
produces the mycotoxin fumonisin B
1
(FB
1
), which disrupts sphingolipid biosynthesis by inhibiting ceramide synthase and affects the health of plants, animals, and humans. The means by which
F. verticillioides
protects itself from its own mycotoxin are not completely understood. Some fumonisin (
FUM
) cluster genes do not contribute to the biosynthesis of the compound, but their function has remained enigmatic. Recently, we showed that
FUM17
,
FUM18,
and
FUM19
encode two ceramide synthases and an ATP-binding cassette transporter, respectively, which play a role in antagonizing the toxicity mediated by FB
1
. In the present work, we uncovered functions of two adjacent genes,
FUM15
and
FUM16
. Using homologous and heterologous expression systems, in
F. verticillioides
and
Saccharomyces cerevisiae
, respectively, we provide evidence that both contribute to protection against FB
1
. Our data indicate a potential role for the P450 monooxygenase Fum15 in the modification and detoxification of FB
1
since the deletion and overexpression of the respective gene affected extracellular FB
1
levels in both hosts. Furthermore, relative quantification of ceramide intermediates and an
in vitro
enzyme assay revealed that Fum16 is a functional palmitoyl-CoA ligase. It co-localizes together with the ceramide synthase Fum18 to the endoplasmic reticulum, where they contribute to sphingolipid biosynthesis. Thereby,
FUM15-19
constitute a subcluster within the
FUM
biosynthetic gene cluster dedicated to the fungal self-protection against FB
1
.

IMPORTANCE

The study identifies a five-gene
FUM
subcluster (
FUM15-19
) in
Fusarium verticillioides
involved in self-protection against FB
1
.
FUM16
(palmitoyl-CoA ligase),
FUM17,
and
FUM18
(ceramide synthases) enzymatically supplement ceramide biosynthesis, while
FUM19
(ATP-binding cassette transporter) acts as a repressor of the
FUM
cluster. The evolutionary conservation of
FUM15
(P450 monooxygenase) in
Fusarium
and
Aspergillus FUM
clusters is discussed, and its effect on extracellular FB
1
levels in both native (
F. verticillioides
) and heterologous (
Saccharomyces cerevisiae
) hosts is highlighted. These findings enhance our understanding of mycotoxin self-protection mechanisms and could inform strategies for predicting biological activity of unknown secondary metabolites, managing mycotoxin contamination, and developing resistant crop cultivars.
Complete genome sequence of an enterotoxigenic
Bacteroides fragilis
strain 2-078382-3 from an infant with diarrhea
Authors: Lee Eunbi , Kang Heekyoung , Song Hyun Beom , Yeom Jinki
Published: December 2024

This study presents that
Bacteroides fragilis
strain 2-078382-3, isolated from an infant with diarrhea, has a 5.2 million base pair chromosome with a 43.2% GC content and a 5,600 base pairs plasmid pBFP53 with a 39.6% GC content. The strain contains 4,262 genes, including 4,105 coding sequences.
Virome assembly reveals draft genomes of native Pseudomonas phages isolated from a paediatric bronchoalveolar lavage sample
Authors: Agudelo-Romero Patricia , Caparros-Martin Jose A. , Sharma Abhinav , Saladié Montserrat , Sly Peter D. , Stick Stephen M. , O'Gara Fergal ,   COMBAT study group
Published: December 2024

We present lung virome data recovered through shotgun metagenomics in bronchoalveolar lavage fluid from an infant with cystic fibrosis, who tested positive for
Stenotrophomonas maltophilia
infection. Using a bioinformatic pipeline for virus characterization in shotgun metagenomic data, we identified five viral contigs representing Pseudomonas phages classified as Caudoviricetes.
Draft genome sequences of six high pH adapted
Marinobacter shengliensis
strains isolated from Mariana forearc serpentinite mud volcanoes
Authors: Elkassas Sabrina M. , Serres Margrethe H. , Navarro Michael , Patterson Amina , Zhivkova Teodora , Petersen Madelyn , Weeks Katelyn , Lang Susan , Seewald Jeffrey , Wheat Geoffrey , Trembath-Reichert Elizabeth , Huber Julie A.
Published: December 2024

Six marine bacterial isolates were obtained from fluid and sediments collected at alkaline serpentinite mud volcanoes of the Mariana forearc to examine life at high pH in a marine environment. Here, we present the draft genome sequences of these six isolates, classified as strains of the species
Marinobacter shengliensis
.
Complete genome sequence of a penicillin-resistant
Fusobacterium necrophorum
subsp.
funduliforme isolate
from a tonsillitis patient
Authors: G C Bibek , Jensen Anders , Wu Chenggang
Published: December 2024

We report the complete genome sequence of a penicillin-resistant
Fusobacterium necrophorum
subsp.
funduliforme
isolate, AJ79, from a tonsillitis patient. The AJ79 genome consists of a chromosome (2,440,359 bp) and plasmid (9,887 bp), providing insights into the genetic basis of penicillin resistance in
F. necrophorum
and its implications for treating tonsillitis.
Not all is lost: resilience of microbiome samples to freezer failures and long-term storage
Authors: Pulido Barriga M. Fabiola , Randolph James W. J. , Glassman Sydney I.
Published: December 2024

Advances in technology have facilitated extensive sample collection to explore microbiomes across diverse systems, leading to a growing reliance on ultracold freezers for storing both samples and extracted DNA. However, freezer malfunctions can jeopardize data integrity. To evaluate the impact of an unexpected −80°C freezer failure and the recoverability of thawed soil samples, we extracted DNA and compared it to long-term DNA stored at −20°C and original 16S and ITS2 sequencing data collected before the malfunction. Using Illumina MiSeq, we assessed how the freezer failure and long-term storage influenced the resilience of bacterial or fungal richness or community composition and our ability to accurately determine experimental treatment effects. Our results reveal substantial resilience in fungal richness and both bacterial and fungal beta-diversity to soil sample thawing and extended frozen DNA storage. This resilience facilitated biological inferences that closely mirrored those observed in the original study. Notably, fungi exhibited greater resilience to short-term thawing compared to bacteria, which showed sensitivity to both thawing and long-term freezing. Moreover, taxonomic composition analysis revealed the persistence of dominant microbial taxa under thawing and prolonged freezing, suggesting that dominant microbes remain viable for tracking across temporal studies. In conclusion, our study highlights that beta-diversity is more robust than alpha-diversity and fungi are more resilient to freezer failure than bacteria. Furthermore, our findings underscore the effectiveness of soil storage at −80°C compared to storage of extracted DNA at −20°C, despite potential freezer failures, as the most robust method for long-term storage in microbiome studies.

IMPORTANCE

Microbiome studies heavily rely on ultracold freezers for sample storage. Unfortunately, these freezers are prone to frequent malfunctions, resulting in the loss of invaluable samples at laboratories worldwide. Such losses can halt research progress due to potential issues with sample reliability. Our research demonstrates that not all is lost when an unforeseen freezer failure occurs. Samples can still be reliably used to assess treatment effects, which is particularly important for long-term temporal studies where samples cannot be readily obtained again.
Supplemental Material: Sequential phreatomagmatic eruptions during the lateral propagation of giant dyke swarms
Authors: Pryce Evan , Cartwright Joe , al. et
Published: December 2024

Background, methods, and data. 
Supplemental Material: On-land evidence for subduction of the proto–South China Sea beneath Northern Borneo and tectonic reconstruction of Southeast Asia during the early Permian–Oligocene
Authors: Zhang Xin-Chang , al. et
Published: December 2024

Table S1: Location and mineral composition of the andesite tuff analyzed by TESCAN Integrated Mineral Analyzer (TIMA). Table S2: Zircon U-Pb ages and in situ Lu-Hf isotopes of the Sabah tuffs. Table S3: Whole-rock major and trace elements of the Sabah tuffs. Table S4: Location, whole-rock major and trace elements, and Nd isotope values of the Eocene–Pliocene sedimentary rocks. Table S5: Detailed zircon geochemistry of the Sabah tuffs, including trace-element analysis.
Spatial and Temporal impacts of climate change to the Tarium Niryutait Marine Protected Area, Beaufort Sea, Canada
Authors: Lee Rebecca , Whalen Dustin , Scharffenberg Kevin Charles , MacPhee Shannon A. , Loseto Lisa L.
Published: December 2024

The Tarium Niryutait Marine Protected Area (TN MPA), composed of three distinct parcels (Niaqunnaq, Okeevik, Kittigaryuit), was established in the Western Canadian Arctic to protect the Eastern Beaufort Sea beluga (Delphinapterus leucas) population and their critical habitat in the Mackenzie Estuary. In this study, we compare the past and current state of environmental parameters – wave regimes, water conditions, storminess, erosion, and landfast ice break-up in the TN MPA. We found significant differences in the characteristics of these environmental parameters between each of the three MPA parcels, which may be impacted differently by climate change. The break-up of landfast ice is occurring earlier in all three parcels of the TN MPA, with the greatest rate of change at Kittigaryuit. Rates of coastal erosion are increasing at Kittigaryuit while slightly decreasing at Okeevik. We did not identify any significant changes in storm characteristics over the study period. Our results suggest that ecological monitoring should occur within each parcel of the TN MPA to ensure a comprehensive understanding of the area overall. A better understanding of spatial and temporal differences of these environmental parameters will help to inform local users and resource managers to more effectively monitor and manage the MPA.
Testing loop quantum gravity by quasi-periodic oscillations: rotating blackholes
Authors: Khodagholizadeh Jafar , Jafari Ghadir , Allahyari Alireza , Vahedi Ali
Published: December 2024

We investigate a compelling model of a rotating black hole that is deformed by the effects of loop quantum gravity (LQG). We present a simplified metric and explore two distinct geometries: one in which the masses of the black hole and white hole are equal, and another in which they differ. Our analysis yields the radius of the innermost stable circular orbits (ISCO), as well as the energy and angular momentum of a particle within this framework. Additionally, we find the frequency of the first-order resonance separately. We constrain the model by the quasi-periodic oscillations (QPO) of the X-ray binary GRO J1655-40. We show that

$$\lambda =0.15^{+0.23}_{-0.14}$$

λ
=
0
.

15

-
0.14

+
0.23

at

$$1\sigma $$

1
σ

confidence level for equal mass black hole and white hole geometry. For the other geometry we get

$$\lambda =0.11^{+0.07}_{-0.07}$$

λ
=
0
.

11

-
0.07

+
0.07

at

$$1\sigma $$

1
σ

confidence level. We encounter a degeneracy in the parameter space that hinders our ability to constrain

$$\lambda $$

λ

with greater precision.
Energy conditions in Gauss–Bonnet gravity
Authors: Bajardi Francesco
Published: December 2024

We study the Energy Conditions in modified

$$f(\mathcal {G})$$

f
(
G
)

gravity, with

$$\mathcal {G}$$

G

being the topological Gauss–Bonnet term. Then we use the cosmographic parameters to constrain the functional form of the gravitational action and investigate the possibility to have standard inflation in the early time. Specifically, we select models containing symmetries within the modified

$$f(\mathcal {G})$$

f
(
G
)

theory and obtain conditions for which (i) the energy conditions can be violated and (ii) the magnitude of the slow-roll parameters is small, thus suggesting that under given limits the analyzed theory can potentially trace the cosmic history both at early and at the late times.
Periapsis precession in general stationary and axisymmetric spacetimes
Authors: He Jinhong , Xu Shaofei , Jia Junji
Published: December 2024

This work studies the periapsis shift in the equatorial plane of arbitrary stationary and axisymmetric spacetimes. Two perturbative methods are systematically developed. The first works for small eccentricity but very general orbit size and the second, which is post-Newtonian and includes two variants, is more accurate for orbits of large size but allows general eccentricity. Results from these methods are shown to be equivalent under small eccentricity and large size limits. The periapsis shift of Kerr–Newman, Kerr–Sen and Kerr–Taub-NUT spacetimes is computed to high orders. The electric charge and NUT charge are shown to contribute to the leading order but with opposite signs. The frame-dragging term and high-order effect of spacetime spin are given. The electric and NUT charges of the Earth, Sun and Sgr A* are constrained using the Mercury, satellite and S2 precession data. Periapsis shifts of other spacetimes are obtained too.
Heavy $$K^*$$ mesons with open charm from $$KD^{(*)}D^*$$ interactions
Authors: Ren Xiu-Lei , Khemchandani K. P. , Torres A. Martínez
Published: December 2024

In view of the recent discovery of

$$T_{cc}$$

T

cc

, which can be described as a

$$DD^*$$

D

D
∗

molecular state, we perform a study of the

$$KDD^*$$

K
D

D
∗

system, and its extension to studying

$$KD^*D^*$$

K

D
∗

D
∗

, where

$$D^*D^*$$

D
∗

D
∗

is bound as a spin 1

$$T_{cc}$$

T

cc

-like state, to search for the possible existence of exotic mesons with the open flavors ccs being part of their quark configuration. Considering the additional attractive interactions present in the KD and

$$KD^*$$

K

D
∗

subsystems, where the states

$$D^*_{s0}(2317)$$

D

s
0

∗

(
2317
)

and

$$D_{s1}(2460)$$

D

s
1

(
2460
)

are generated, we solve the Faddeev equations considering the fixed-center approximation for the mentioned three-body systems and find the existence of two doubly charmed

$$K^*$$

K
∗

-like mesons,

$$K_{cc}^*(4309)$$

K

cc

∗

(
4309
)

and

$$K_{cc}^*(4449)$$

K

cc

∗

(
4449
)

, with quantum numbers

$$I(J^P)=1/2\,(1^-)$$

I

(

J
P

)

=
1
/
2

(

1
-

)

. Considering the respective three-body thresholds of the two systems, both

$$K_{cc}$$

K

cc

-states are bound by around 60 MeV. An experimental confirmation will bring evidence for the existence of a degree of exoticity beyond charm +2.
An efficient evacuation time prediction model for different types of subway stations
Authors: Yang Xiaoxia , Qu Lei , Shao Chuang , Li Yongxing
Published: December 2024

Passenger evacuation time prediction is a crucial basis for subway station management to better formulate safety control measures. It becomes possible to reasonably plan the flow of passengers within the station and configure safety devices such as signage and sprinkler systems with a known and explicit time framework, thereby reducing passenger congestion and panic. However, methods based on crowd dynamics simulation require a significant amount of time and effort to build models, and the rapidity of time prediction is challenging to ensure. Real human evacuation experiments involve ethical, safety and practical operational issues. To address this challenge, an evacuation time prediction model for subway passengers is established based on the CPA-SVR machine learning method, enhancing the speed and accuracy of prediction. The reliability of simulation results is validated by comparing observed values of passenger alighting and boarding time and traffic time at stairs with simulation values from MassMotion software. Fourteen factors related to the subway station structure, passengers and train status are selected as influence factors for evacuation time. A foundation data set for the evacuation time prediction model is obtained through 179 evacuation experiments under different influence factors using the MassMotion simulation system at 32 constructed stations. The SHAP interpretation method is applied to identify the importance of influence factors in the experimental results. A CPA-SVR passenger evacuation time prediction model is established, with accuracy concentrated between 85%–100%, based on training and validation sets. Further testing with 45 additional sets of fresh experimental data demonstrates the model’s strong predictive capability for new data, indicating good generalization ability. Finally, a focused analysis of passenger evacuation behaviors at bottlenecks such as stairs, gates and exits is conducted, accompanied by relevant optimization strategies.
Eco-friendly resistive plate chamber detectors for HEP applications
Authors: Pastore A. , Congedo L. , Abbrescia M. , Aly R. , Serio M. De , Galati G. , Pugliese G. , Ramos D. , Simone S. , Boscherini D. , Bruni A. , Massa L. , Polini A. , Romano M. , Guida R. , Mandelli B. , Rigoletti G. , Benussi L. , Bianco S. , Piccolo D. , Saviano G. , Samalan A. , Tytgat M. , Zaganidis N. , Eysermans J. , Buontempo S. , Arena M. C. , Salvini P. , Aielli G. , Camarri P. , Cardarelli R. , Ciaccio A. Di , Stante L. Di , Liberti B. , Pastori E. , Proto G. , Pizzimento L. , Rocchi A. , Santonico R. , Ferretti A. , Gagliardi M. , Quaglia L. , Terlizzi L. , Vercellin E. , Verzeroli M. , Barroso Ferreira Filho M. , Dupieux P. , Joly B. , Manen S. P.
Published: December 2024

Resistive Plate Chamber detectors are largely employed in current High Energy Physics experiments, thanks to their relatively low cost and good spatial/time resolution. They are typically operated in avalanche mode with large fractions of Tetrafluoroethane (C2H2F4), a gas recently banned by the European Union due to its high Global Warming Potential (GWP). An intense R&D activity is ongoing to improve RPC technology in view of present and future High Energy Particle Physics (HEP) applications. Since a few years, a joint effort among the ALICE, ATLAS, CMS, LHCb/SHiP and CERN Detector Technology (EP-DT) Communities is in place to search for potential eco-friendly gas mixtures and assess the performance of RPCs under different irradiation conditions. Tests are in progress at the CERN Gamma Irradiation Facility (GIF++). In this paper, a review on the promising results of these studies and future plans will be given.
Determinant of the OU matrix of a braid diagram
Authors: Shimizu Ayaka , Yaguchi Yoshiro
Published: December 2024

In this paper, we define the over–under matrix (OU matrix) of a braid diagram and discuss how the OU matrix reflects the warping degree or the layeredness of the braid diagram, and show that the determinant of the OU matrix of a layered braid diagram is the product of the determinants of the layers. We also introduce invariants of positive braids which are derived from the OU matrix.
The influence of hardcore concept in the improvement of the beta decay calculation
Authors: Sobhani Hadi , Luo Yan-An , Jalili Amir , Hassanabadi Hassan
Published: December 2024

This work investigates the impact of incorporating the hard-core concept in nuclear physics on theoretical beta decay calculations. The paper delves into the mathematical formalism employed to integrate this concept. Subsequently, it presents two sets of calculations for the beta decay chain within the [Formula: see text] nucleus using the shell model framework. A comparative analysis is conducted between the obtained results, along with a comparison to experimental data. This analysis aims to elucidate how the inclusion of the hard-core concept refines theoretical predictions for beta decay calculations.