bluuebunny/crossref_metadata_2025_split huggingface dataset:
scToppR: a coding-friendly R interface to ToppGene
Authors: Granger Bryan , Berto Stefano 
Published: September 2024

Abstract

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

Summary
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

Abstract
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

Abstract
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

Abstract
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

Abstract

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 (&lt;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

Abstract

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 &lt; 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

Abstract
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

Abstract
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

Abstract
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

Abstract
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

Abstract
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

Abstract
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

Abstract
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 &gt; 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 &lt; 0.05), a 7-fold increase for IL-8 from 1.5 to 2.5 h (P &lt; 0.05), and 8-fold induction for SOD2 from 2 to 6 h (P &lt; 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

Abstract
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.