bluuebunny/crossref_metadata_2025 huggingface dataset:
Suspending life, controlling change: cryotechnology, genetic identity, and ecological separation
Authors: Wolff Leon
Published: September 2024

The collection and freezing of plant seeds in gene banks has been an integral part of global biodiversity policy since the early twentieth century. In recent years, the use of cryopreservation technologies (the storage of biological material at temperatures as low as −196 °C) has been advocated as a complement to these strategies. This technology promises that it will be possible to freeze significantly more plant varieties for longer periods of time. The article draws on scientific publications to analyze the current discourse on cryopreservation technology in the field of agricultural plant conservation. It underpins and intensifies biopolitical trajectories that have been inherent in ex situ conservation from the outset. First, cryotechnology submits to a pure line ontology which frames living beings as having an intrinsic genetic identity, and aims to secure this genetic identity against unplanned changes. Second, cryopreservation is linked to an imaginary of ecological separation that implies the idea that biodiversity can ultimately be preserved without a habitat. The article concludes by pointing to the material limitations and unsolved problems cryotechnologies inevitably face.
Role of green finance and higher education in fostering the sustainability and energy transition practices
Authors: Meng Bingfeng , Hao Zhihao
Published: September 2024

This paper offers a qualitative analysis of how higher education and green finance impact the promotion of sustainable energy within the Regional Comprehensive Economic Partnership (RCEP) region from 2000 to 2020. The analysis reveals that higher education has a positive effect on sustainable energy development, with a 1% increase in the higher education population associated with a 0.19% rise in short-term and a 0.29% rise in long-term sustainable energy progress. Green finance also plays a crucial role, significantly accelerating green energy development in the RCEP region—each 1% increase in green finance results in a 0.43% boost in short-term and a 0.38% boost in long-term sustainable energy advancement. In contrast, increased fossil fuel production hampers sustainable energy development. Enhanced internet access further supports green energy progress, contributing to a 0.43% increase in the short-term and a 0.53% increase in the long-term. Policy recommendations include expanding the green finance market, advancing sustainable education initiatives, reducing reliance on fossil fuels, and improving internet access to further sustainable energy development in the RCEP region.
Effect of thermal annealing on the average and local structure of superconducting polycrystalline NbRe films
Authors: Makhdoumi Kakhaki Z , Martinelli A , Avitabile F , Di Bernardo A , Attanasio C , Cirillo C
Published: September 2024

Nb
x

Re

1
−
x

is a non-centrosymmetric superconductor recently realized in thin film form. The access to the basic physics that governs this material is hindered by the polycrystalline structure of the films which consist of grains of small dimensions. In these conditions, films are not decisive in revealing the nature of the superconducting order parameter, and, in particular, the possible presence of a spin-triplet component. In this work, post-deposition annealing procedures were performed to improve the crystalline quality of the as-grown films. As determined by x-ray diffraction measurements, by tuning the annealing process, it was possible to increase the crystalline size from 1–2 nm up to several nanometers, beyond the values of the superconducting coherence length. Pair distribution function analyses revealed the non-centrosymmetric crystal structure of the treated NbRe films. Finally, electrical transport measurements, performed to study the relationship between structural and transport properties of the samples, showed an improved metallicity and a reduction of the superconducting critical temperature after the thermal treatment. This last result can be reasonably ascribed, for instance, to oxygen contamination, modification of the electronic density of states at the Fermi level, or change in the electron–phonon coupling. The results of this work are useful to realize films for future experiments meant to access nature of the superconducting order parameter.
Decoding Judicial Cross-Citations: How Do European Judges Engage with Foreign Case Law?
Authors: De Witte Folker , Krisztián Anna , Kukavica Jaka , Potocka-Sionek Nastazja , Siems Mathias , Yiatrou Vasiliki
Published: September 2024

How do judges engage with foreign case law? While prior research has identified some instances of courts willing to cite foreign judgments, details about the mode of engagement and the motivation of such cross-citations have often been left unexplored. This Article fills these gaps. It presents the results of the coding of a sample of 456 judgments with cross-citations between the private law supreme courts of twenty-eight European countries. Twenty-five variables were coded for each citation: for example, the length of the discussion of foreign case law, whether the court was interested in the result or the reasoning of foreign judgments, and whether the citations occurred within the context of EU law, international law and/or specific areas of the law. This Article presents and contextualizes (i.e., “decodes”) this quantitative information. Amongst others, we find that courts from common law countries more often cite older foreign case law and provide a greater depth of engagement with it than courts from civil law countries, that many of the courts are mainly interested in the result and not the reasoning of foreign judgments, that most cross-citations are driven by reasons of comparative law (and not, for example, EU law or international law), and that cross-citations due to EU law are particularly prevalent in IP law and conflict of laws. More generally, we observe a form of bifurcation of citations across many of the topics analyzed, suggesting a divide, not between common and civil law countries, but between courts from smaller and larger jurisdictions (e.g., with smaller jurisdictions using citations in more traditional areas of law, citing mainly one other court, citing older cases, and more often being interested in the reasoning of foreign judgments).
Expanding the spectrum of progressive familial intrahepatic cholestasis: A report of 3 cases
Authors: Jiao Jingjing , Morotti Raffaella , Shafizadeh Nafis , Jain Dhanpat
Published: September 2024

Objectives

Progressive familial intrahepatic cholestasis (PFIC) is a group of autosomal recessive disorders caused by defects in bile secretion or transport usually presenting as cholestasis in pediatric age. Herewith, we describe 3 PFIC cases with diagnostic challenges and highlight the role of genetic analysis.

Methods

The clinical history, laboratory data, liver biopsy, and molecular analysis for each case were reviewed.

Results

Case 1, a Hispanic male from Puerto Rico with hepatomegaly since age 2 months, was eventually diagnosed with PFIC3 following identification of a homozygous splice site variant in ATP binding cassette subfamily B member 4 (ABCB4) (c.2784-12T>C) at age 17 years by whole-exome sequencing (WES). Case 2 was a 37-year-old man with a history of alcoholism, abnormal liver function tests, and ductopenia on biopsy. Molecular testing revealed a pathogenic heterozygous ABCB4 mutation (c.1633C>T) variant leading to a diagnosis of PFIC3. Case 3 was a 2-year-old female initially presenting as a drug-induced liver injury but was diagnosed with PFIC10 following identification of a heterozygous frameshift mutation (p.Asp300Trpfs*19) and a heterozygous missense mutation (c.1357T>C) in myosin VB (MYO5B) by WES.

Conclusions

These PFIC cases highlight the heterogenous presentation and diagnostic challenges, and they emphasize the role of next-generation sequencing, particularly the utility of WES.
Feasibility and Clinical Effectiveness of Computer-Based Cognitive Rehabilitation in Illiterate and Low-Educated Individuals with Mild Cognitive Impairment: Preliminary Data
Authors: Petri Maria Christina , Messinis Lambros , Patrikelis Panayiotis , Nasios Grigorios , Dimitriou Nefeli , Nousia Anastasia , Kosmidis Mary H
Published: September 2024

Objective

We investigated the feasibility of the RehaCom cognitive rehabilitation software in illiterate and low-educated individuals with mild cognitive impairment (MCI) and its clinical effectiveness in improving cognitive functions.

Methods

Twenty illiterate or low-educated individuals with MCI were randomly assigned to an intervention (IG; n = 10) and control group (CG; n = 10). The IG participated in the cognitive enhancement program for 6 weeks, twice a week and a duration of 50–60 min for each session, while the CG did not receive any kind of intervention.

Results

The two groups were demographically matched. The IG successfully completed all sessions of the cognitive enhancement program. A within-subject comparison between baseline and post-intervention assessment of cognitive functions indicated that the IG improved significantly on all administered neuropsychological tests, in contrast to the CG, whose performance remained stable between baseline and final assessment. A between-group comparison found statistically significant differences between the IG and CG groups on the Hindi Mental State Examination, Mini-Mental State Examination, and on delayed memory and recognition tasks, in favor of the IG.

Conclusions

The findings of the present study support the feasibility of applying computerized cognitive enhancement programs to illiterate and low-educated individuals. Moreover, these programs appear to contribute positively to improving the cognitive functions of this population group. In order to generalize and confirm similar findings in a broader population of illiterate and low-educated individuals, future studies should include larger samples, possibly with longer duration of treatment and control groups that will receive non-targeted interventions as placebo interventions.
Synergistic effect of cerium chloride and calcium chloride alters calcium signaling in keratinocytes to promote epidermal differentiation
Authors: Tsukui Kei , Suzuki Masamitsu , Amma Miyu , Tokudome Yoshihiro
Published: September 2024

Epidermal keratinocytes undergo morphological and functional changes during differentiation, eventually being enucleated to become corneocytes. Calcium has been shown to be involved in various cellular functions of epidermal cells, including proliferation, differentiation, and apoptosis. Cerium is a lanthanide-series element and rare earth metal. For skin, cerium oxide has been investigated for use in absorbing UV and promoting wound healing. However, the functions and physiological effects of inorganic cerium on the skin have rarely been investigated. Here, we focused on cerium's function in epidermal keratinocytes and its interaction with calcium by investigating their effects on cell differentiation and intracellular calcium concentration. This study showed that applying cerium chloride to epidermal keratinocytes altered calcium signaling. It also suggested that cerium and calcium induced an increase in intracellular calcium concentration and promoted keratinocyte differentiation.
FAVOR-GPT: a generative natural language interface to whole genome variant functional annotations
Authors: Li Thomas Cheng , Zhou Hufeng , Verma Vineet , Tang Xiangru , Shao Yanjun , Van Buren Eric , Weng Zhiping , Gerstein Mark , Neale Benjamin , Sunyaev Shamil R , Lin Xihong
Published: September 2024

Motivation

Functional Annotation of genomic Variants Online Resources (FAVOR) offers multi-faceted, whole genome variant functional annotations, which is essential for Whole Genome and Exome Sequencing (WGS/WES) analysis and the functional prioritization of disease-associated variants. A versatile chatbot designed to facilitate informative interpretation and interactive, user-centric summary of the whole genome variant functional annotation data in the FAVOR database is needed.

Results

We have developed FAVOR-GPT, a generative natural language interface powered by integrating large language models (LLMs) and FAVOR. It is developed based on the Retrieval Augmented Generation (RAG) approach, and complements the original FAVOR portal, enhancing usability for users, especially those without specialized expertise. FAVOR-GPT simplifies raw annotations by providing interpretable explanations and result summaries in response to the user’s prompt. It shows high accuracy when cross-referencing with the FAVOR database, underscoring the robustness of the retrieval framework.

Availability and implementation

Researchers can access FAVOR-GPT at FAVOR’s main website (https://favor.genohub.org).
Second-order group knockoffs with applications to genome-wide association studies
Authors: Chu Benjamin B , Gu Jiaqi , Chen Zhaomeng , Morrison Tim , Candès Emmanuel , He Zihuai , Sabatti Chiara
Published: September 2024

Motivation

Conditional testing via the knockoff framework allows one to identify—among a large number of possible explanatory variables—those that carry unique information about an outcome of interest and also provides a false discovery rate guarantee on the selection. This approach is particularly well suited to the analysis of genome-wide association studies (GWAS), which have the goal of identifying genetic variants that influence traits of medical relevance.

Results

While conditional testing can be both more powerful and precise than traditional GWAS analysis methods, its vanilla implementation encounters a difficulty common to all multivariate analysis methods: it is challenging to distinguish among multiple, highly correlated regressors. This impasse can be overcome by shifting the object of inference from single variables to groups of correlated variables. To achieve this, it is necessary to construct “group knockoffs.” While successful examples are already documented in the literature, this paper substantially expands the set of algorithms and software for group knockoffs. We focus in particular on second-order knockoffs, for which we describe correlation matrix approximations that are appropriate for GWAS data and that result in considerable computational savings. We illustrate the effectiveness of the proposed methods with simulations and with the analysis of albuminuria data from the UK Biobank.

Availability and implementation

The described algorithms are implemented in an open-source Julia package Knockoffs.jl. R and Python wrappers are available as knockoffsr and knockoffspy packages.
scToppR: a coding-friendly R interface to ToppGene
Authors: Granger Bryan , Berto Stefano
Published: September 2024

Motivation

The scToppR package provides a ToppGene interface from R programs/scripts to fully access/control the database for functional enrichment without the need for active interaction on its Web site (https://toppgene.cchmc.org/).

Results

The library facilitates the functional enrichment analysis and visualization by interacting with ToppGene, downloading the functional enrichment dataframes, and using R environment to visualize the final results.

Availability and implementation

Code and documentation are currently available at https://github.com/BioinformaticsMUSC/scToppR
Boosting the power of kernel two-sample tests
Authors: Chatterjee A , Bhattacharya B B
Published: September 2024

The kernel two-sample test based on the maximum mean discrepancy is one of the most popular methods for detecting differences between two distributions over general metric spaces. In this paper we propose a method to boost the power of the kernel test by combining maximum mean discrepancy estimates over multiple kernels using their Mahalanobis distance. We derive the asymptotic null distribution of the proposed test statistic and use a multiplier bootstrap approach to efficiently compute the rejection region. The resulting test is universally consistent and, since it is obtained by aggregating over a collection of kernels/bandwidths, is more powerful in detecting a wide range of alternatives in finite samples. We also derive the distribution of the test statistic for both fixed and local contiguous alternatives. The latter, in particular, implies that the proposed test is statistically efficient, that is, it has nontrivial asymptotic (Pitman) efficiency. The consistency properties of the Mahalanobis and other natural aggregation methods are also explored when the number of kernels is allowed to grow with the sample size. Extensive numerical experiments are performed on both synthetic and real-world datasets to illustrate the efficacy of the proposed method over single-kernel tests. The computational complexity of the proposed method is also studied, both theoretically and in simulations. Our asymptotic results rely on deriving the joint distribution of the maximum mean discrepancy estimates using the framework of multiple stochastic integrals, which is more broadly useful, specifically, in understanding the efficiency properties of recently proposed adaptive maximum mean discrepancy tests based on kernel aggregation and also in developing more computationally efficient, linear-time tests that combine multiple kernels. We conclude with an application of the Mahalanobis aggregation method for kernels with diverging scaling parameters.
Ecological risk assessment when species-specific data are scarce: how trait-based approaches and modeling can help
Authors: Galic Nika , Forbes Valery , Grimm Volker , Schmolke Amelie , Vaugeois Maxime , Brain Richard
Published: September 2024

Ecological risk assessments are legally required to ensure that there are no unacceptable risks to living organisms from exposure to chemicals and other anthropogenic stressors. Significant data gaps, however, make it difficult to conduct such assessments for all species that we wish to protect. Consequently, there is growing interest in trait-based approaches because they provide a more functional and context-independent basis for characterizing biodiversity that is useful for biomonitoring, conservation, and management. In the present article, we discuss how trait-based approaches can support risk assessment, identify vulnerable and representative species to be used in ecological modeling, and inform decision-making more generally. We use examples to demonstrate the utility of trait-based approaches but also highlight some of the challenges and open questions that remain to be addressed.
A Fresh Start or a False Dawn? Assessing the Crime-Preventive Effect of Debt Settlements for People With a History of Conviction
Authors: Gålnander Robin , Bäckman Olof , Rojas Yerko
Published: September 2024

People with convictions often face financial challenges, which hinder desistance from crime as they have few legal opportunities to address their financial burdens. In some countries, those severely insolvent can apply for ‘debt settlement’ through Enforcement Authorities. This study explores whether such settlements are crime-preventative for people with conviction histories. Analyzing Swedish administrative data and a sample of 1,621 previously convicted applicants in 2016–17, we match and compare reconviction rates between approved and declined cases. Approved cases show much lower reconviction rates, but this effect diminishes rapidly, virtually disappearing within six months. These findings prompt a discussion of the helpfulness of debt settlements for people wanting to desist from crime. Implications for future research, policy, and practice are discussed.
Hydroxychloroquine may be beneficial as an adjuvant therapy for folliculitis decalvans: a 5-year retrospective study with 49 patients
Authors: Doche Isabella , Sotto Mirian N , Hordinsky Maria K , Melhado Isabela P , Gerlero Paula , Rivitti-Machado Maria Cecília
Published: September 2024

Folliculitis decalvans (FD) is a chronic and recurrent neutrophilic scarring alopecia that mostly affects the vertex scalp of young male patients. It manifests as painful alopecic lesions surrounded by pustules, tuftings and intense scalp fibrosis. However, the occurrence of less active or ‘lichen planopilaris-like’ forms of FD questions the exact role of Staphylococcus aureus in the pathogenic mechanism of this disease. The management of FD is very challenging, as relapses are frequent and prolonged use of combined antibiotics is often required. Recent evidence showed the presence of S. aureus and lymphocytic inflammation also in nonlesional FD scalp. This suggested the potential use of immunomodulating drugs such as hydroxychloroquine to better control the chronic inflammatory status of this ­disease.
Managing heart failure with reduced ejection fraction merged with myocardial infarction with non-obstructive coronary arteries: a case report
Authors: Ikebe So , Yamamoto Masahiro , Ishii Masanobu , Yamamoto Eiichiro , Tsujita Kenichi
Published: September 2024

Background

The concepts of myocardial infarction with non-obstructive coronary arteries (MINOCA) are now widely accepted. Calcium channel blockers (CCBs) are the first-line medication for coronary spastic angina (coronary spastic angina: CSA/vasospastic angina: VSA), while β-blockers sometimes do not improve CSA/VSA. However, β-blockers are essential for managing symptoms of coronary microvascular dysfunction and considered vital for treating heart failure with reduced ejection fraction (HFrEF).

Case summary

We present the case of an 83-year-old female admitted with shortness of breath persisting for over 1 year and worsening ejection fraction (EF) from 65% to 32%. On admission, she experienced chest pain at rest despite finding no significant stenosis on coronary angiography. Several days later, we performed functional coronary angiography (FCA), revealing diffuse epicardial coronary spasm upon injecting acetylcholine. The coronary flow reserve was 4.4 (≧2.0), and the microvascular resistance index was 20 (<25). We diagnosed the patient with a myocardial injury event induced by CSA/VSA and initiated dihydropyridine CCBs. A few months later, her chest pain resolved; the HF symptoms improved (NYHA: from Ⅲ to Ⅱ), accompanied by a reduction in B-type natriuretic peptide levels (from 4561.2 to 75.4 pg/mL) and EF improvement (from 32.0% to 62.6%).

Discussion

We managed a patient with HFrEF and MINOCA. Although CCBs are not routinely recommended for HFrEF, we added dihydropyridine CCBs to treat CSA/VSA based on comprehensive diagnostic procedures. This approach sedated chest pain and may have contributed to her EF improvement. Detailed examinations and tailored treatment strategies might be helpful for HF treatment.
Redo surgical aortic valve replacement for bioprosthetic structural valve deterioration
Authors: Raschpichler Matthias , Kiefer Philip , Otto Wolfgang , Noack Thilo , Gerber Maria , De Waha Suzanne , Dashkevich Alexey , Leontyev Sergey , Misfeld Martin , Borger Michael A
Published: September 2024

OBJECTIVES

To compare isolated primary bioprosthetic surgical aortic valve replacement (SAVR) with isolated redo surgical aortic valve replacement (rSAVR) due to structural valve deterioration (SVD).

METHODS

Clinical data of consecutive patients who underwent primary isolated SAVR and isolated rSAVR due to SVD between 1 January 2011 and 31 December 2022, at Leipzig Heart Center were retrospectively compared with regard to the primary outcome of all-cause mortality or stroke during hospitalization. Secondary outcomes of interest included myocardial infarction, re-exploration for bleeding, and permanent pacemaker implantation.

RESULTS

A total of 2620 patients, 39.5% females, with a median EuroSCORE II of 1.7 [interquartile range (IQR) 1.1–2.7] were identified, of which rSAVR was performed in 174 patients (6.6%). Patients undergoing primary SAVR were older (69 vs 67 years of age, P = 0.001) and were less likely to have a history of prior stroke (0.9% vs 4.0%, P = 0.003). Although both all-cause death and death or stroke occurred less often following primary SAVR (0.5% vs 5.8%, and 2.2% vs 6.9%, respectively; P < 0.001), prior surgery was not associated with adverse clinical outcome in multivariable analysis. In a matched comparison of 322 patients, rates of death or stroke did not differ between groups (4.8% for both rSAVR and SAVR, P = 1.0).

CONCLUSIONS

Although redo surgery for SVD is associated with increased rates of early mortality and stroke by univariate analysis, much of this increased risk can be accounted for by comorbidities. Patients undergoing rSAVR on an elective basis can expect an outcome similar to that of primary SAVR.
How market integration impacts human disease ecology
Authors: Kolinski Lev , Barrett Tyler M , Kramer Randall A , Nunn Charles L
Published: September 2024

Market integration (MI), or the shift from subsistence to market-based livelihoods, profoundly influences health, yet its impacts on infectious diseases remain underexplored. Here, we synthesize the current understanding of MI and infectious disease to stimulate more research, specifically aiming to leverage concepts and tools from disease ecology and related fields to generate testable hypotheses. Embracing a One Health perspective, we examine both human-to-human and zoonotic transmission pathways in their environmental contexts to assess how MI alters infectious disease exposure and susceptibility in beneficial, detrimental and mixed ways. For human-to-human transmission, we consider how markets expand contact networks in ways that facilitate infectious disease transmission while also increasing access to hygiene products and housing materials that likely reduce infections. For zoonotic transmission, MI influences exposures to pathogens through agricultural intensification and other market-driven processes that may increase or decrease human encounters with disease reservoirs or vectors in their shared environments. We also consider how MI-driven changes in noncommunicable diseases affect immunocompetence and susceptibility to infectious disease. Throughout, we identify statistical, survey and laboratory methods from ecology and the social sciences that will advance interdisciplinary research on MI and infectious disease.
The physiological role of Acinetobacter baumannii DacC is exerted through influencing cell shape, biofilm formation, the fitness of survival, and manifesting DD-carboxypeptidase and beta-lactamase dual-enzyme activities
Authors: Pal Shilpa , Jain Diamond , Biswal Sarmistha , Rastogi Sumit Kumar , Kumar Gaurav , Ghosh Anindya S
Published: September 2024

With the growing threat of drug-resistant Acinetobacter baumannii, there is an urgent need to comprehensively understand the physiology of this nosocomial pathogen. As penicillin-binding proteins are attractive targets for antibacterial therapy, we have tried to explore the physiological roles of two putative DD-carboxypeptidases, viz., DacC and DacD, in A. baumannii. Surprisingly, the deletion of dacC resulted in a reduced growth rate, loss of rod-shaped morphology, reduction in biofilm-forming ability, and enhanced susceptibility towards beta-lactams. In contrast, the deletion of dacD had no such effect. Interestingly, ectopic expression of dacC restored the lost phenotypes. The ∆dacCD mutant showed properties similar to the ∆dacC mutant. Conversely, in vitro enzyme kinetics assessments reveal that DacD is a stronger DD-CPase than DacC. Finally, we conclude that DacC might have DD-CPase and beta-lactamase activities, whereas DacD is a strong DD-CPase.
RNA 5-Methylcytosine Modification: Regulatory Molecules, Biological Functions, and Human Diseases
Authors: Lu Yanfang , Yang Liu , Feng Qi , Liu Yong , Sun Xiaohui , Liu Dongwei , Qiao Long , Liu Zhangsuo
Published: September 2024

RNA methylation modifications influence gene expression, and disruptions of these processes are often associated with various human diseases. The common RNA methylation modification 5-methylcytosine (m5C), which is dynamically regulated by writers, erasers, and readers, widely occurs in transfer RNAs (tRNAs), messenger RNAs (mRNAs), ribosomal RNAs (rRNAs), enhancer RNAs (eRNAs), and other non-coding RNAs (ncRNAs). RNA m5C modification regulates metabolism, stability, nuclear export, and translation of RNA molecules. An increasing number of studies have revealed the critical roles of the m5C RNA modification and its regulators in the development, diagnosis, prognosis, and treatment of various human diseases. In this review, we summarized the recent studies on RNA m5C modification and discussed the advances in its detection methodologies, distribution, and regulators. Furthermore, we addressed the significance of RNAs modified with m5C marks in essential biological processes as well as in the development of various human disorders, from neurological diseases to cancers. This review provides a new perspective on the diagnosis, treatment, and monitoring of human diseases by elucidating the complex regulatory network of the epigenetic m5C modification.
Enhancing aphid resistance in horticultural crops: a breeding prospective
Authors: Zhang Lili , Chen Chaoyan , Li Yao , Suo Chunyu , Zhou Wei , Liu Xiaowei , Deng Yizhuo , Sohail Hamza , Li Ziyi , Liu Fang , Chen Xuehao , Yang Xiaodong
Published: September 2024

Increasing agricultural losses caused by insect infestations are a significant problem, so it is important to generate pest-resistant crop varieties to address this issue. Several reviews have examined aphid–plant interactions from an entomological perspective. However, few have specifically focused on plant resistance mechanisms to aphids and their applications in breeding for aphid resistance. In this review, we first outline the types of resistance to aphids in plants, namely antixenosis, tolerance (cell wall lignification, resistance proteins), and antibiosis, and we discuss strategies based on each of these resistance mechanisms to generate plant varieties with improved resistance. We then outline research on the complex interactions amongst plants, viruses, and aphids, and discuss how aspects of these interactions can be exploited to improve aphid resistance. A deeper understanding of the epigenetic mechanisms related to induced resistance, i.e. the phenomenon where plants become more resistant to a stress they have encountered previously, may allow for its exploitation in breeding for aphid resistance. Wild relatives of crop plants serve as important sources of resistance traits. Genes related to these traits can be introduced into cultivated crop varieties by breeding or genetic modification, and de novo domestication of wild varieties can be used to exploit multiple excellent characteristics, including aphid resistance. Finally, we discuss the use of molecular design breeding, genomic data, and gene editing to generate new aphid-resistant, high-quality crop varieties.
Grapevine cell response to carbon deficiency requires transcriptome and methylome reprogramming
Authors: Berger Margot M J , Garcia Virginie , Lacrampe Nathalie , Rubio Bernadette , Decros Guillaume , Pétriacq Pierre , Flandin Amélie , Cassan Cédric , Hilbert-Masson Ghislaine , Colombié Sophie , Atanassova Rossitza , Gallusci Philippe
Published: September 2024

Sugar limitation has dramatic consequences on plant cells, which include cell metabolism and transcriptional reprogramming, and the recycling of cellular components to maintain fundamental cell functions. There is however no description of the contribution of epigenetic regulations to the adaptation of plant cells to limited carbon availability. We investigated this question using nonphotosynthetic grapevine cells (Vitis vinifera, cv Cabernet Sauvignon) cultured in vitro with contrasted glucose concentrations. Sugar depletion in the culture medium led to a rapid cell growth arrest and a major metabolic shift that include the depletion in soluble sugar and total amino acids and modulation of the cell redox status. Consistently, flux modeling showed a dramatic slowdown of many pathways required for biomass accumulation such as cell wall and protein synthesis. Sugar depletion also resulted in a major transcriptional reprogramming, characterized by the induction of genes involved in photosynthesis, and the repression of those related to sucrose mobilization or cell cycle control. Similarly, the epigenetic landscape was deeply modified. Glucose-depleted cells showed a higher global DNA methylation level than those grown with glucose. Changes in DNA methylation mainly occurred at transposable elements, and at genes including some of those differentially expressed, consistent with an important role for methylation to the adaptation of cells to limited sugar availability. In addition, genes encoding histone modifiers were differentially expressed suggesting that additional epigenetic mechanisms may be at work in plant cells under carbon shortage.
A cost-effective oligo-based barcode system for chromosome identification in longan and lychee
Authors: Yu Zehuai , Qi Yiying , Wei Yuxuan , Zhuang Gui , Li Yihan , Wang Baiyu , Akbar Sehrish , Xu Yi , Hua Xiuting , Xu Qiutao , Deng Zuhu , Zhang Jisen , Huang Yongji , Yu Fan , Zhou Jiannan
Published: September 2024

Oligonucleotide (Oligo)-based fluorescence in situ hybridization (FISH) represents a highly effective methodology for identifying plant chromosomes. Longan is a commercially significant fruit species, yet lacking basic chromosomal markers has hindered its cytogenetic research. In this study, we developed a cost-effective oligo-based system for distinguishing chromosomes of longan (Dimocarpus longan Lour., 2n = 2x = 30). For this system, each synthesized oligo contained two chromosome-specific sequences that spanned a distance of over 200 kb, and a PCR-based flexible amplification method coupled with nested primers was used for probe labeling. The use of these oligo-based barcodes enabled the marking of 36 chromosomal regions, which allowed for the unambiguous distinction of all 15 chromosomes in both longan and lychee (Litchi chinensis Sonn., 2n = 2x = 30) species. Based on the identification of individual chromosomes, we constructed karyotypes and detected genome assembly errors involving the 35S ribosomal RNA gene (35S rDNA) in longan and lychee. Developing oligo-based barcodes offers considerable promise for advancing cytogenetic research in longan, lychee, and their related species. Furthermore, this cost-effective synthesis system can be referred to the development of new oligo libraries among other species.
The effect of repeated lipopolysaccharide endotoxin challenge on immune response of breeding ewes and subsequent lamb performance
Authors: Austin Molly M , Castro Briza , Ochoa Luis , Dominguez Arellanes Jeffrey F , Luna Karime L , Salas Yulianna A , Gurule Sara C , Soto-Navarro Sergio , Gifford Craig A , Hernandez Gifford Jennifer A
Published: September 2024

Infectious disease caused by exposure to Gram-negative bacterial endotoxin lipopolysaccharide (LPS) is recognized to suppress female fertility. However, the effect of varying low-dose endotoxin exposure during distinct stages of follicle development on immune response, reproductive performance, and lamb performance has yet to be elucidated. Therefore, the objective of this study was to evaluate acute phase response, mRNA abundance of inflammatory markers, reproductive performance and lamb growth characteristics of ewes challenged with subclinical doses of LPS. Rambouillet ewes (n = 36; 68.2 ± 1.1 kg; age 3 to 7 yr) stratified by body weight (BW) and age were assigned to treatment groups. Ewes received subcutaneous injections of saline (CON, n = 12), 1.5 µg/kg BW LPS (LOW, n = 12), or 3.0 µg/kg BW LPS (HIGH, n = 12) on days 5, 10, and 15 of a synchronized follicular wave. Ewes were subsequently placed with a raddle-painted ram on day 16 for a 35-d breeding season. On treatment days 5 and 15, blood samples, peripheral blood leukocytes, and rectal temperature were collected before and at regular intervals for 12 h after LPS challenge. Immune response to LPS was confirmed by increased temperature and serum cortisol concentrations on days 5 and 15. Endotoxin increased circulating plasma concentration of the acute phase protein, haptoglobin by greater than 15%, in both LPS-treated groups on days 5 and 15 at 12 h compared with control (P≤ 0.05). Pro- and anti-inflammatory mRNA gene expression demonstrated no differences in expression for tumor necrosis factor-α or peroxisome proliferator-activated receptor gamma among treatment groups (P > 0.10). Likewise, Toll-like receptor 4 (TLR4), interleukin-8 (IL-8), and superoxide dismutase 2 (SOD2) expression was similar among treatment groups on day 5. However, ewes challenged with LPS on day 15 displayed greater mRNA expression for TLR4 from 2 to 6 h (P < 0.05), a 7-fold increase for IL-8 from 1.5 to 2.5 h (P < 0.05), and 8-fold induction for SOD2 from 2 to 6 h (P < 0.05) as compared with controls. First service conception rates were 90% for control ewes and 75% for both treated groups (P  = 0.84). Treated ewes demonstrated a reduction in lamb birth weight compared with controls (P ≤ 0.05) and a tendency for reduction of 60-d adjusted weaning weight (P = 0.09). Data suggest that subacute endotoxin exposure aligning with key follicle and oocyte maturation events results in detrimental growth performance of the subsequent lamb.
Intracellular biliverdin dynamics during ferroptosis
Authors: Nakajima Kazuma , Nishizawa Hironari , Chen Guan , Tsuge Shunichi , Yamanaka Mie , Kiyohara Machi , Irikura Riko , Matsumoto Mitsuyo , Tanaka Kozo , Narikawa Rei , Igarashi Kazuhiko
Published: September 2024

Ferroptosis is a cell death mechanism mediated by iron-dependent lipid peroxidation. Although ferroptosis has garnered attention as a cancer-suppressing mechanism, there are still limited markers available for identifying ferroptotic cells or assessing their sensitivity to ferroptosis. The study focused on biliverdin, an endogenous reducing substance in cells, and examined the dynamics of intracellular biliverdin during ferroptosis using a biliverdin-binding cyanobacteriochrome. It was found that intracellular biliverdin decreases during ferroptosis and that this decrease is specific to ferroptosis amongst different forms of cell death. Furthermore, the feasibility of predicting sensitivity to ferroptosis by measuring intracellular biliverdin was demonstrated using a ferroptosis model induced by the re-expression of the transcription factor BACH1. These findings provide further insight into ferroptosis research and are expected to contribute to the development of cancer therapies that exploit ferroptosis.
Clinical features, management, and complications of paediatric button battery ingestions in Canada: an active surveillance study using surveys of Canadian paediatricians and paediatric subspecialists
Authors: Hudson Alexandra S , Carroll Matthew W
Published: September 2024

Background

Button battery ingestions pose a serious threat to paediatric health and are on the rise worldwide. Little is known about Canadian data. This study described the type of button battery ingestions Canadian paediatric physicians have observed, including treatment and complications.

Methods

A Canadian Paediatric Surveillance Program (CPSP) survey was sent to paediatricians and paediatric subspecialists. The questions were developed through a literature review and consultation with 19 CPSP members, before piloting with 5 paediatric physicians. Descriptive analyses were conducted.

Results

The response rate was 39% (n = 1067/2716). Few were aware of treatment options with honey (n = 189/1067, 18%) and sucralfate (n = 118/1067, 11%). Two hundred and ninety-nine physicians (28%) had been involved in a case in the past 1 year (n = 132 case details). Children < 3 years were most affected (n = 67/132, 51%). In unwitnessed ingestions (n = 41/132, 31%), the most common symptoms were dysphagia (n = 14/41, 34%) and coughing (n = 10/41, 24%). When it was known where the child found the battery, it was most commonly loose in the environment (n = 34/132, 26%). Seventy per cent of patients (n = 92/132) presented within 6 h following the ingestion. Six per cent (n = 8/132) reported the battery eroding into important adjacent structures (eg, aorta and trachea).

Interpretation

A high degree of suspicion for button battery ingestion is needed in young children presenting with dysphagia and coughing. Prevention efforts should be aimed at battery disposal and security. There is a need for dissemination of guidelines to physicians caring for paediatric patients, since modifiable patient factors, such as honey and/or sucralfate administration while awaiting definitive treatment, can improve outcomes.
Do diet and Fumagillin treatment impact Vairimorpha (Nosema) spp. (Microspora: Nosematidae) infections in honey bees (Hymenoptera: Apidae) and improve survival and growth of colonies overwintered in cold storage?
Authors: DeGrandi-Hoffman Gloria , Corby-Harris Vanessa , Graham Henry , Chambers Mona , Watkins deJong Emily , Snyder Lucy
Published: September 2024

Vairimorpha (Microsporidia: Nosematidae) is a microsporidian that infects honey bees especially in winter. Fumagillin can reduce infections, but whether overwintering survival is improved is unclear. The diet also may influence the severity of Nosema infections. We examined the relationship between Nosema and colony size and survival in hives overwintered in cold storage facilities. In year 1, no Fumagillin treatments were applied. Colony size and survival after cold storage and almond bloom were comparable between groups with high and low pre-cold storage infections. In year 2, size and survival were compared among colonies with and without Fumagillin treatment that were fed either pollen or protein supplement prior to overwintering. Colonies treated with Fumagillin had lower spore numbers than untreated, but colony sizes and survival were similar among the treatments. However, more colonies with zero spores per bee could be rented for almond pollination and were alive after bloom than those averaging >1 million spores per bee. Fat body metrics can affect overwintering success. In both years, fat body weights and protein concentrations increased, and lipid concentrations decreased while bees were in cold storage. Fat body metrics did not differ with Nosema infection levels. However, Fumagillin negatively affected pre-cold storage fat body protein concentrations and colony sizes after cold storage and almond bloom. Treating with Fumagillin before overwintering in cold storage might result in greater colony survival if spore numbers are high, but undetectable or even negative effects when spore numbers are low.
Immunometabolic chaos in septic shock
Authors: Shrestha Deepmala , Pant Bishnu D , Roychowdhury Sanjoy , Gandhirajan Anugraha , Cross Emily , Chhabria Mamta , Bauer Seth R , Jeng Margaret , Mitchell Megan , Mehkri Omar , Zaidi Fatima , Ahuja Akash , Wang Xiaofeng , Wang Yuxin , McDonald Christine , Longworth Michelle S , Stappenbeck Thaddeus S , Stark George R , Scheraga Rachel G , Vachharajani Vidula
Published: September 2024

Septic shock is associated with over 40% mortality. The immune response in septic shock is tightly regulated by cellular metabolism and transitions from early hyper-inflammation to later hypo-inflammation. Patients are susceptible to secondary infections during hypo-inflammation. The magnitude of the metabolic dysregulation and the effect of plasma metabolites on the circulating immune cells in septic shock are not reported. We hypothesized that the accumulated plasma metabolites affect the immune response in septic shock during hypo-inflammation. Our study took a unique approach. Using peripheral blood from adult septic shock patients and healthy controls, we studied: (i) Whole blood stimulation ± E. Coli lipopolysaccharide (LPS: endotoxin) to analyze plasma TNF protein, and (ii). Plasma metabolomic profile by Metabolon. Inc. (iii) We exposed peripheral blood mononuclear cells (PBMCs) from healthy controls to commercially available carbohydrate, amino acid, and fatty acid metabolites and studied the response to LPS. We report that: (i) The whole blood stimulation of the healthy control group showed a significantly upregulated TNF protein, while the septic shock group remained endotoxin tolerant, a biomarker for hypo-inflammation. (ii) A significant accumulation of carbohydrate, amino acid, fatty acid, ceramide, sphingomyelin, and TCA cycle pathway metabolites in septic shock plasma. (iii) In vitro exposure to 5 metabolites repressed while 2 metabolites upregulated the inflammatory response of PBMCs to LPS. We conclude that the endotoxin-tolerant phenotype of septic shock is associated with a simultaneous accumulation of plasma metabolites from multiple metabolic pathways, and these metabolites fundamentally influence the immune response profile of circulating cells.
Unlocking the potential of large-scale 3D imaging with tissue clearing techniques
Authors: Susaki Etsuo A
Published: September 2024

The three-dimensional (3D) anatomical structure of living organisms is intrinsically linked to their functions, yet modern life sciences have not fully explored this aspect. Recently, the combination of efficient tissue clearing techniques and light-sheet fluorescence microscopy for rapid 3D imaging has improved access to 3D spatial information in biological systems. This technology has found applications in various fields, including neuroscience, cancer research and clinical histopathology, leading to significant insights. It allows imaging of entire organs or even whole bodies of animals and humans at multiple scales. Moreover, it enables a form of spatial omics by capturing and analyzing cellome information, which represents the complete spatial organization of cells. While current 3D imaging of cleared tissues has limitations in obtaining sufficient molecular information, emerging technologies such as multi-round tissue staining and super-multicolor imaging are expected to address these constraints. 3D imaging using tissue clearing and light-sheet microscopy thus offers a valuable research tool in the current and future life sciences for acquiring and analyzing large-scale biological spatial information.
Clinicopathological differences between classical schwannomas and cellular schwannomas in the retroperitoneum
Authors: Zhang Xiaoying , Zheng Haining , Li Guilan , Li Ting
Published: September 2024

This study aimed to compare clinical and pathological features of retroperitoneal classical schwannomas and cellular schwannomas. A total of 64 cases of retroperitoneal classical schwannoma and 48 cases of cellular schwannoma were studied. Histopathological analysis was performed using hematoxylin and eosin staining and immunohistochemistry. Retroperitoneal cellular schwannomas exhibited 100% (48/48) and 75% (36/48) positive expression for glial fibrillary acidic protein (GFAP) and cytokeratins (CK), respectively. Classical schwannomas showed rates of 6.25% (4/64) and 15.63% (10/64), respectively (P < .05). In classic schwannomas, 85.9% (55/64) showed a reticular pattern of positive anti-CD34 staining around tumor margins and subcapsular areas vs 52.1% (25/48) in cellular schwannomas (P < .05). Cellular schwannomas exhibited more mitotic figures than classical schwannoma (P < .05). The recurrence rate of cellular schwannomas was 10.42% (5/48), while that of classical schwannomas was 1.56% (1/64) (P < .05). Retroperitoneal cellular schwannomas commonly express GFAP and CK compared to classical schwannomas, suggesting that cellular schwannoma may originate from unmyelinated Schwann cells, while classical schwannoma may originate from myelinated Schwann cells. Anti-CD34 staining patterns may be used to distinguish between the 2 types. Retroperitoneal cellular schwannomas also show higher mitotic activity and are more prone to recurrence.