bluuebunny/crossref_metadata_2025_split huggingface dataset:
The comprehensive regulatory network in seed oil biosynthesis
Authors: Wei Wei , Wang Long‐Fei , Tao Jian‐Jun , Zhang Wan‐Ke , Chen Shou‐Yi , Song Qingxin , Zhang Jin‐Song 
Published: January 2025

ABSTRACTPlant oils play a crucial role in human nutrition, industrial applications and biofuel production. While the enzymes involved in fatty acid (FA) biosynthesis are well‐studied, the regulatory networks governing these processes remain largely unexplored. This review explores the intricate regulatory networks modulating seed oil biosynthesis, focusing on key pathways and factors. Seed oil content is determined by the efficiency of de novo FA synthesis as well as influenced by sugar transport, lipid metabolism, FA synthesis inhibitors and fine‐tuning mechanisms. At the center of this regulatory network is WRINKLED1 (WRI1), which plays a conserved role in promoting seed oil content across various plant species. WRI1 interacts with multiple proteins, and its expression level is regulated by upstream regulators, including members of the LAFL network. Beyond the LAFL network, we also discuss a potential nuclear factor‐Y (NF‐Y) regulatory network in soybean with an emphasis on NF‐YA and NF‐YB and their associated proteins. This NF‐Y network represents a promising avenue for future efforts aimed at enhancing oil accumulation and improving stress tolerance in soybean. Additionally, the application of omics‐based approaches is of great significance. Advances in omics technologies have greatly facilitated the identification of gene resources, opening new opportunities for genetic improvement. Importantly, several transcription factors involved in oil biosynthesis also participate in stress responses, highlighting a potential link between the two processes. This comprehensive review elucidates the complex mechanisms underlying the regulation of oil biosynthesis, offering insights into potential biotechnological strategies for improving oil production and stress tolerance in oil crops.
Oxidised Apolipoprotein Peptidome Characterises Metabolic Dysfunction‐Associated Steatotic Liver Disease
Authors: Mocciaro Gabriele , George Amy L. , Allison Michael , Frontini Mattia , Huang‐Doran Isabel , Reiman Frank , Gribble Fiona , Griffin Julian L. , Vidal‐Puig Antonio , Azzu Vian , Kay Richard , Vacca Michele 
Published: January 2025

ABSTRACTBackgroundMetabolic Dysfunction‐Associated Steatotic Liver Disease (MASLD) encompasses a spectrum of histological conditions ranging from simple steatosis to fibrosing steatohepatitis, and is a risk factor for cardiovascular diseases (CVD). While oxidised apolipoproteins A and B have been linked to obesity and CVD, the association between other oxidised apolipoproteins and MASLD is yet to be established. To fill this gap, we characterised the circulating serum peptidome of patients with MASLD.MethodsWe studied the serum of 87 biopsy‐confirmed MASLD patients and 20 age‐ and sex‐matched control (CTRL) subjects. We first employed an untargeted LC‐MS/MS peptidomics approach (9 CTRL, 32 MASLD) to identify key hits differentially modulated, and subsequently validated the most relevant findings through targeted peptidomics in an enlarged study population (87 MASLD and 20 CTRL).ResultsUntargeted serum peptidomics identified several oxidised apolipoprotein peptide fragments, including ApoE and ApoC‐III, significantly upregulated in MASLD compared to CTRL. Specifically focusing on the oxidative status of intact ApoC‐III, studied through its major glycoforms (ApoC‐III0, ApoC‐IIIi and ApoC‐IIIii), we observed a marked reduction in non‐oxidised forms of these circulating peptides alongside substantially increased levels of their oxidised proteoforms in MASLD versus controls (but not within the disease stages). Oxidised ApoE and ApoC‐III peptide fragments were also significantly correlated with obesity, insulin resistance, dyslipidaemia and transaminases, suggesting a potential link between circulating apolipoprotein oxidation and systemic/hepatic metabolic dysfunction.ConclusionOur data reveals a previously unreported oxidised apolipoprotein profile associated with MASLD. The functional and clinical implications of these findings warrant further mechanistic investigation.
Maralixibat Reduces Serum Bile Acids and Improves Cholestatic Pruritus in Adolescents With Alagille Syndrome
Authors: Hirschfield Gideon , Vandriel Shannon M. , Mogul Douglas B. , Baek Marshall , Vig Pamela , Kamath Binita M. 
Published: January 2025

ABSTRACTBackgroundAlagille syndrome (ALGS) is a multisystem cholestatic disorder. Maralixibat is approved for the treatment of cholestatic pruritus in ALGS with limited data in adults.MethodsParticipants were included if they received ≥ 2 doses of maralixibat at age ≥ 16 years in one of the three previously published maralixibat ALGS clinical trials.ResultsEleven initiated treatment < 16 years old (median age, 13.0) with a median follow‐up of 4.1 years. Three participants began maralixibat at ≥ 16 years old, with a median follow‐up of 3.8 years. Participants starting maralixibat at age < 16 had minimal‐to‐no itch (change from baseline [CFB]: −1.8; p = 0.002) persisting throughout the study. Serum bile acids (sBA) decreased (CFB: 29 μmol/L; p = 0.03), persisting throughout the study. Participants starting maralixibat ≥ 16 years old had pruritus improvements (CFB: −2.8, −0.6, −1.0). One had a large decrease in sBA (CFB: −112 μmol/L), and two had small increases (CFB: 8, 11 μmol/L). Maralixibat was well tolerated.ConclusionParticipants receiving maralixibat in adolescence demonstrated improvements in pruritus and sBA, which persisted through young adulthood.
Viability Assessment During Normothermic Machine Liver Perfusion: A Literature Review
Authors: Jeddou Heithem , Tzedakis Stylianos , Chaouch Mohamed Ali , Sulpice Laurent , Samson Michel , Boudjema Karim 
Published: January 2025

ABSTRACTBackground and ObjectiveThe discrepancy between donor organ availability and demand leads to a significant waiting‐list dropout rate and mortality. Although quantitative tools such as the Donor Risk Index (DRI) help assess organ suitability, many potentially viable organs are still discarded due to the lack of universally accepted markers to predict post‐transplant outcomes. Normothermic machine perfusion (NMP) offers a platform to assess viability before transplantation. Thus, livers considered unsuitable for transplantation based on the DRI can be evaluated and potentially transplanted. During NMP, various viability criteria have been proposed. These criteria are neither homogeneous nor consensual. In this review, we aimed to describe the viability criteria during NMP and evaluate their ability to predict hepatic graft function following transplantation. We conducted a PubMed search using the terms ‘liver transplantation’, ‘normothermic machine perfusion’ and ‘assessment’, including only English publications up to February 2024. Viability assessment during NMP includes multiple hepatocellular and cholangiocellular criteria. Lactate clearance and bile production are commonly used indicators, but their ability to predict post‐transplant outcomes varies significantly. The predictive value of cholangiocellular criteria such as bile pH, bicarbonate and glucose levels remains under investigation. Novel markers, such as microRNAs and proteomic profiles, offer the potential to enhance graft evaluation accuracy and provide insights into the molecular mechanisms underlying liver viability. Combining perfusion parameters with biomarkers may improve the prediction of long‐term graft survival. Future research should focus on standardising viability assessment protocols and exploring real‐time biomarker evaluations, which could enhance transplantation outcomes and expand the donor pool.
Growth and Mortality of the Pink Shrimp Penaeus notialis (Pérez Farfante, 1967) (Decapoda: Dendrobranchiata: Penaeidae) in the Colombian Caribbean
Authors: Paramo Jorge , Pérez Daniel , Mildenberger Tobias 
Published: January 2025

ABSTRACTThe pink shrimp (Penaeus notialis) constitutes an important commercial fishery in the Colombian Caribbean. However, due to the lack of biological data and fisheries management information led to the overexploitation and collapse of the shrimp fishery. Despite the economic and commercial importance of this fishery in the Colombian Caribbean, no studies have been carried out on the growth and mortality of pink shrimp. The objective of the present study was to estimate for the first time robust von Bertalanffy growth parameters, mortality rates with empirical formulae and the length‐converted catch curve of the commercial pink shrimp (P. notialis) in the Colombian Caribbean. The samples were collected between June 2012 and May 2013, between Cartagena and the Gulf of Urabá. The parameters of the growth were estimated using the electronic Length frequency analysis. We calculated the natural mortality (M) with the K and L∞ parameters. A total of 5199 pink shrimp were collected. The estimates of growth parameters for P. notialis showed higher L∞ (females: 171.91 mm; males: 135.37 mm) and W∞ in females (44.74 g) than in males (19.44 g). The growth coefficient (K) was 0.74 in females and 1.19 in males. The ta estimated for females was −0.12 and for males −0.04. The maximum age (tmax) of this species was 3.91 year for female and 2.47 year for male. The natural mortality rate (M) for female was (0.61 year−1) and male (0.93 year−1).
Single‐Larva RNA Sequencing Reveals That Red Sea Urchin Larvae Are Vulnerable to Co‐Occurring Ocean Acidification and Hypoxia
Authors: Nguyen Tina , Pelletier Greg , Bednaršek Nina , Gracey Andrew 
Published: January 2025

ABSTRACTAnthropogenic carbon dioxide emissions have been increasing rapidly in recent years, driving pH and oxygen levels to record low concentrations in the oceans. Eastern boundary upwelling systems such as the California Current System (CCS) experience exacerbated ocean acidification and hypoxia (OAH) due to the physical and chemical properties of the transported deeper waters. Research efforts have significantly increased in recent years to investigate the deleterious effects of climate change on marine species, but have not focused on the impacts of simultaneous OAH stressor exposure. Additionally, few studies have explored the physiological impacts of these environmental stressors on the earliest life stages, which are more vulnerable and represent natural population bottlenecks in organismal life cycles. The physiological response of the ecologically and commercially important red sea urchin (Mesocentrotus franciscanus) was assessed by exposing larvae to a variety of OAH conditions, mimicking the range of ecologically relevant conditions encountered currently and in the near future along the CCS. Skeleton dissolution, larval development, and gene expression show a response with clearly delineated thresholds that were related to OAH severity. Skeletal dissolution and the induction of Acid‐sensing Ion Channel 1A at pH 7.94/5.70 DO mg/L provide particularly sensitive markers of OAH, with dramatic shifts in larval morphology and gene expression detected at the pH/DO transition of 7.71/3.71–7.27/2.72 mg/L. Experimental simulations that describe physiological thresholds and establish molecular markers of OAH exposure will provide fishery management with the tools to predict patterns of larval recruitment and forecast population dynamics.
The Unity of the Ideal Virtues
Authors: Siscoe Robert Weston 
Published: January 2025

ABSTRACTEven though the virtues may be interconnected, it seems obviously possible to have one of the virtues without having them all. Some have defended the unity thesis against this concern by arguing that the virtues are still unified in their ideal forms. The problem with this defense is that it simply admits that the unity thesis, as traditionally conceived, is mistaken, taking the unity of the virtues to be limited to the ideal case. In this paper, I outline a blueprint for how the ideal virtue response can be used to defend the original unity thesis.
Estimation of light utilisation and antioxidative protection in an alpine plant species (Soldanella alpina L.) during the leaf life cycle at high elevation
Authors: Streb Peter , Dubertrand Philippine , Cornic Gabriel , Soudani Kamel , Finazzi Giovanni 
Published: January 2025

AbstractPhotosynthesis, electron transport to carbon assimilation, photorespiration and alternative electron transport, light absorption of the two photosystems, antioxidative protection and pigment contents were investigated in S. alpina leaves. S. alpina is an alpine snow‐bed plant which can be found with green leaves after snowmelt. At least 24% of the leaves were formed at the beginning of the vegetation period in the previous year and survived two consecutive vegetation periods under contrasting environmental conditions. In leaves still covered by snow (SNOW), the parameters of antioxidative protection and carbon assimilation were lower than in leaves from the previous vegetation period (NEW) or several weeks after snowmelt (OLD). Directly after snowmelt, antioxidative protection was strongly but transitionally increased. The senescence of leaves did not depend on antioxidative scavenging capacity. Lower carbon assimilation was not related to increases in alternative electron flow (ETRalt) in SNOW leaves. In the second vegetation period, light absorption by PSII decreases in favour of PSI in OLD leaves. This allows OLD leaves to keep the electron transport chain more oxidised and to support photorespiration with increased ATP synthesis by cyclic electron transport around PSI. This study describes how the leaves of a unique plant can cope with contrasting environmental conditions.
A Novel Probe Based on Photoconductive Effect for Non-Destructive Testing
Authors: Xiang Jiawei , Li Qiang , Tian Qingze 
Published: January 2025

Abstract
This research is primarily motivated by the demand for a convenient and economical nondestructive testing solution in industrial scenarios. We present a novel nondestructive testing probe, which is ingeniously designed with a photoresistor sensor and an illuminated light board, possessing remarkable features such as outstanding portability, minimal power consumption, and low cost. The experimental evaluation of the probe involves a line-scanning process above the crack position of an aluminum plate. As a result, an output signal in the form of variable resistance values of the photoresistor sensor is obtained. Notably, distinct peaks emerge in the output signal precisely when the probe traverses defects. These peaks serve as a crucial indicator for detecting surface defects of aluminum plates. Moreover, the varying amplitudes of the peaks in the output signal offer a reliable means to discriminate between defects of different depths. This probe holds significant potential for application in the quality assurance of aluminum manufacturing, as well as in the routine inspection of metallic structures, facilitating enhanced safety and reliability in engineering applications.
Protamine protects against vancomycin-induced kidney injury
Authors: Shiau Justin , Engel Patti , Olsen Mark , Pais Gwendolyn , Chang Jack , Scheetz Marc H. 
Published: January 2025

ABSTRACT

Vancomycin causes kidney injury by accumulating in the proximal tubule, likely mediated by megalin uptake. Protamine is a putative megalin inhibitor that shares binding sites with heparin and is approved for the treatment of heparin overdose. We employed a well-characterized Sprague-Dawley rat model to assess kidney injury and function in animals that received vancomycin, protamine alone, or vancomycin plus protamine over 5 days. Urinary KIM-1 was used as the primary measure for kidney injury, while plasma iohexol clearance was calculated to assess kidney function. Animals had samples drawn pre-treatment in order to serve as their own controls. Additionally, since protamine is not a known nephrotoxin, the protamine group also served as a control. Cellular inhibition studies were performed to assess the ability of protamine to inhibit organic anion transporter (OAT1 and OAT3) and organic cation transporter-2 (OCT2). Rats that received vancomycin alone had significantly increased urinary KIM-1 on day 2 (24.9 ng/24 h, 95% CI 1.87–48.0) compared to the protamine alone group. By day 4, animals that received protamine with their vancomycin had KIM-1 amounts that were elevated compared to protamine alone as a base comparison (KIM-1 29.0 ng/24 h, 95% CI 5.0–53.0). No statistically observed differences were identified for iohexol clearance changes between drug groups or when comparing clearance change from baseline (
P
> 0.05). No substantial inhibition of OAT1, OAT3, or OCT2 was observed with protamine. IC
50
values for protamine were 0.1 mM for OAT1 and OAT3 and 0.043 mM for OCT2. Protamine, when added to vancomycin therapy, delays vancomycin-induced kidney injury as defined by urinary KIM-1 in the rat model by 1–3 days. Protamine putatively acts through the blockade of megalin and does not appear to have significant inhibition on OAT1, OAT3, or OCT2. Since protamine is an approved FDA medication, it has clinical potential as a therapeutic to reduce vancomycin-related kidney injury; however, greater utility may be found by pursuing compounds with fewer adverse event liabilities.
Emergence of antibiotic-specific
Mycobacterium tuberculosis
phenotypes during prolonged treatment of mice
Authors: Wynn Elizabeth A. , Dide-Agossou Christian , Al Mubarak Reem , Rossmassler Karen , Ektnitphong Victoria , Bauman Allison A. , Massoudi Lisa M. , Voskuil Martin I. , Robertson Gregory T. , Moore Camille M. , Walter Nicholas D. 
Published: January 2025

ABSTRACT

A major challenge in tuberculosis (TB) therapeutics is that antibiotic exposure leads to changes in the physiology of
M. tuberculosis
(
Mtb
), which may enable the pathogen to withstand treatment. While antibiotic-treated
Mtb
has been evaluated in
in vitro
experiments
,
it is unclear if and how long-term
in vivo
treatment with diverse antibiotics with varying treatment-shortening activity (sterilizing activity) affects
Mtb
physiologic processes differently. Here, we used SEARCH-TB, a pathogen-targeted RNA-sequencing platform, to characterize the
Mtb
transcriptome in the BALB/c high-dose aerosol infection mouse model following 4 weeks of treatment with three sterilizing and three non-sterilizing antibiotics. Certain transcriptional changes were shared among most antibiotics, including decreased expression of genes associated with protein synthesis and metabolism and the induction of certain genes associated with stress responses. However, the magnitude of this shared response differed between antibiotics. Sterilizing antibiotics rifampin, pyrazinamide, and bedaquiline generated a more quiescent
Mtb
state than did non-sterilizing antibiotics isoniazid, ethambutol, and streptomycin, as indicated by the decreased expression of genes associated with translation, transcription, secretion of immunogenic proteins, metabolism, and cell wall synthesis. Additionally, we identified distinguishing transcriptional effects specific to each antibiotic, indicating that different mechanisms of action induce distinct patterns in response to cellular injury. In addition to elucidating the
Mtb
physiologic changes associated with antibiotic stress, this study demonstrates the value of SEARCH-TB as a highly granular pharmacodynamic assay that reveals antibiotic effects that are not apparent based on culture alone.
Diversity of lake bacteria promotes human echovirus inactivation
Authors: Romanenko Andrii , Peter Hannes , Meibom Josephine , Borchardt Mark A. , Kohn Tamar 
Published: January 2025

ABSTRACT

Human enteric viruses can remain infective in surface waters for extended periods of time, posing a public health risk. Microbial activity contributes to the inactivation of waterborne enteric viruses, but while individual bacteria–virus interactions have been characterized, the importance of microbial diversity remains unknown. Here, we experimentally manipulated the diversity of bacterial communities from Lake Geneva across three seasons using a dilution-to-extinction approach and monitored the inactivation and genome decay of echovirus 11, a member of the
Enterovirus
genus. Long-read sequencing of the 16S rRNA gene revealed diversity gradients ranging between 373 and 2,722 bacterial species. Compared to sterile controls, echovirus 11 inactivation was enhanced by the presence of active bacteria and depended both on season and sample dilution. Throughout all seasons, the highest inactivation (between 3.0 and 7.9 log
10
fold reduction in infectivity over 96 h) was observed in the least diluted incubations (i.e., the highest bacterial richness). Genome decay exhibited a 24-h lag and was less pronounced than the corresponding infectivity loss (ranging between 2.3 and 3.8 log
10
fold over 96 h), indicating that microbial inactivation primarily targets the echovirus 11 capsid. We found a positive-saturating relationship between bacterial species richness and viral inactivation, suggesting functional redundancy and pointing toward the importance of rare species for viral inactivation. Biomarker analysis revealed several clades of bacteria, particularly members of
Chitinophagaceae
, to be significantly associated with echovirus 11 inactivation. Overall, these findings suggest that high microbial diversity enhances the capacity of surface waters to rid themselves of contamination by enteric viruses and hence protects public health.

IMPORTANCE
Human enteric viruses in natural waterbodies pose a public health risk. Microorganisms, particularly bacteria, contribute to the inactivation of enteroviruses, thereby mitigating this risk. We use experimental manipulations of lake water bacterial diversity to unravel the importance of diversity for the inactivation of echovirus 11, a model human pathogen. Our findings suggest that bacterial diversity is important for echovirus 11 inactivation and that specific, but numerically rare, bacteria present in the surface water of Lake Geneva across different seasons contribute to viral inactivation. These findings contribute to our understanding of the inactivation of human enteric viruses in natural waterbodies—a hitherto understudied ecosystem service.
Insights into pathologic mechanisms occurring during serious adverse events following live zoster vaccination
Authors: Kennedy Peter G. E. , Grose Charles 
Published: January 2025

ABSTRACT

An effective live zoster vaccine has been widely used around the world. Although no deaths occurred in the original large clinical trial, we analyzed 10 serious adverse events, including six deaths that have subsequently occurred in four countries. The goal is to define the viral pathogenesis of these unexpected adverse events secondary to a viremia with dissemination of the vaccine virus. We also propose a new hypothesis for acute retinal necrosis that occurs post-immunization.
Improving breast cancer treatments using pharmacomicrobiomics
Authors: Pai Aswin Anand , Bhatt Aadra Prashant 
Published: January 2025

ABSTRACT

Tamoxifen is the mainstay treatment for estrogen-positive breast cancer for over half a century. However, a significant proportion of patients experience disease recurrence due to treatment failure attributed to various factors, including disease pathology, genetics, and drug metabolism. Alam et al. introduce gut microbiota as a key factor influencing tamoxifen pharmacokinetics (Y. Alam, S. Hakopian, L. Ortiz de Ora, I. Tamburini, et al., mBio 16:e01679-24, 2024,
https://doi.org/10.1128/mbio.01679-24
). The authors present compelling evidence that functional differences in the gut microbiota, specifically the bacterial enzyme β-glucuronidase, leads to inter-individual variability in systemic exposure of tamoxifen, affecting drug efficacy. This study provides novel insights into the impact of the gut microbiota on tamoxifen pharmacokinetics, the latest example of how pharmacomicrobiomics, or the study of drug-microbe interactions, can enhance precision medicine for numerous diseases.