bluuebunny/crossref_metadata_2025_split huggingface dataset:
Occurrence and molecular characterization of Diaporthe eres causing stem canker on sweet cherry trees (Prunus avium) in northern China
Authors: Dai Qidong , Zhang Qijing , He Mingli , Ai Jiayin , Cai Feng 
Published: May 2024

AbstractSweet cherry (Prunus avium) is a commercially important species in China, experiencing a rapid increase in production. In June 2022, a severe infection, affecting more than 8% of sweet cherry trees, was observed on the Tetian cultivar in a 2–3‐year‐old orchard in Dalian City, northern China. Initially, spindle‐shaped brown disease spots formed on the surfaces of the branches. These spots continued to spread and merge, and the middle portion of the cankers sunk inward and gradually dried. Small black particles were found on the surface of the stems. The disease spread was more prevalent during the rainy season, leading to the withering of numerous branches and the death of the whole plant. Seven isolates, named lncy1‐1, lncy4‐1, lncy5‐1, lncy6‐1, lncy7‐1, lncy8‐1 and lncy9‐1, were obtained from 24 disease samples. Phylogenetic analysis based on three loci (rDNA ITS, TEF1 and TUB2) coupled with morphological identification confirmed that these seven isolates belong to Diaporthe eres. A representative isolate, lncy1‐1, was inoculated onto sweet cherry branches in a controlled environment, and showed that the isolate lncy1‐1 was pathogenic. The fungus isolated from diseased tissues was identified as D. eres based on morphological and molecular criteria. To the best of our knowledge, this is the first report of stem canker in sweet cherry caused by D. eres in China, which will promote disease management and expand the known host range of D. eres.
Protein Detection and Localization in Plant Cells Using Spot‐Tagging
Authors: Mentzelopoulou Andriani , Liu Chen , Moschou Panagiotis Nikolaou 
Published: May 2024

AbstractFluorescent labelling of proteins enables the determination of their spatiotemporal localization but, sometimes, it can perturb their activity, native localization, and functionality. Spot‐tag is a12‐amino acid peptide recognized by a single–domain nanobody and could potentially resolve the issues associated with large fluorescence tags due to its small size. Here, using as an example the microtubule motor CENTROMERIC PROTEIN E–RELATED KINESIN 7.3 (KIN7.3), we introduce the spot–tag for protein labelling in fixed and living plant cells. Spot–tagging and detection by an anti‐spot nanobody of ectopically expressed KIN7.3 did not interfere with its native localization. Most importantly, our spot‐tagging pipeline facilitated the localization of KIN7.3 much more rapidly and likely accurately than labelling with large fluorescent proteins or even immunolocalization approaches. We should, though, note some limitations we have not resolved yet. Spot–tagging is functional only in fixed cells; it is available only as two fluorophores and may create a noisy background during imaging. However, we foresee that, besides the limitations of this method, spot‐tagging will apply to many proteins, offsetting activity perturbations and low photon quantum yields of other protein‐tagging approaches.
Understanding Human Cognition Through Computational Modeling
Authors: Hsiao Janet Hui‐wen 
Published: May 2024

AbstractOne important goal of cognitive science is to understand the mind in terms of its representational and computational capacities, where computational modeling plays an essential role in providing theoretical explanations and predictions of human behavior and mental phenomena. In my research, I have been using computational modeling, together with behavioral experiments and cognitive neuroscience methods, to investigate the information processing mechanisms underlying learning and visual cognition in terms of perceptual representation and attention strategy. In perceptual representation, I have used neural network models to understand how the split architecture in the human visual system influences visual cognition, and to examine perceptual representation development as the results of expertise. In attention strategy, I have developed the Eye Movement analysis with Hidden Markov Models method for quantifying eye movement pattern and consistency using both spatial and temporal information, which has led to novel findings across disciplines not discoverable using traditional methods. By integrating it with deep neural networks (DNN), I have developed DNN+HMM to account for eye movement strategy learning in human visual cognition. The understanding of the human mind through computational modeling also facilitates research on artificial intelligence's (AI) comparability with human cognition, which can in turn help explainable AI systems infer humans’ belief on AI's operations and provide human‐centered explanations to enhance human−AI interaction and mutual understanding. Together, these demonstrate the essential role of computational modeling methods in providing theoretical accounts of the human mind as well as its interaction with its environment and AI systems.
Milnor–Wood inequality for klt varieties of general type and uniformization
Authors: Costantini Matteo , Greb Daniel 
Published: May 2024

AbstractWe generalize the definition of the Toledo invariant for representations of fundamental groups of smooth varieties of general type due to Koziarz and Maubon to the context of singular klt varieties, where the natural fundamental groups to consider are those of smooth loci. Assuming that the rank of the target Lie group is not greater than two, we show that the Toledo invariant satisfies a Milnor–Wood‐type inequality and we characterize the corresponding maximal representations.
Iwahori‐metaplectic duality
Authors: Brubaker Ben , Buciumas Valentin , Bump Daniel , Gustafsson Henrik P. A. 
Published: May 2024

AbstractWe construct a family of solvable lattice models whose partition functions include ‐adic Whittaker functions for general linear groups from two very different sources: from Iwahori‐fixed vectors and from metaplectic covers. Interpolating between them by Drinfeld twisting, we uncover unexpected relationships between Iwahori and metaplectic Whittaker functions. This leads to new Demazure operator recurrence relations for spherical metaplectic Whittaker functions. In prior work of the authors it was shown that the row transfer matrices of certain lattice models for spherical metaplectic Whittaker functions could be represented as ‘half‐vertex operators’ operating on the ‐Fock space of Kashiwara, Miwa and Stern. In this paper the same is shown for all the members of this more general family of lattice models including the one representing Iwahori Whittaker functions.
Selective depletion of HBV-infected hepatocytes by class A capsid assembly modulators requires high levels of intrahepatic HBV core protein
Authors: Kornyeyev Dmytro , Song Zhijuan , Eng Stacey , Soulette Cameron , Ramirez Ricardo , Tang Jennifer , Yue Qin , Subramanian Raju , Zaboli Shiva , Moon Christina , Tam Jane , Brodbeck Jens , Aggarwal Abhishek , Diehl Lauri , Fletcher Simon P. , Hyrina Anastasia , Holdorf Meghan M. , Burdette Dara 
Published: May 2024

ABSTRACT

Capsid assembly mediated by hepatitis B virus (HBV) core protein (HBc) is an essential part of the HBV replication cycle, which is the target for different classes of capsid assembly modulators (CAMs). While both CAM-A (“aberrant”) and CAM-E (“empty”) disrupt nucleocapsid assembly and reduce extracellular HBV DNA, CAM-As can also reduce extracellular HBV surface antigen (HBsAg) by triggering apoptosis of HBV-infected cells in preclinical mouse models. However, there have not been substantial HBsAg declines in chronic hepatitis B (CHB) patients treated with CAM-As to date. To investigate this disconnect, we characterized the antiviral activity of tool CAM compounds in HBV-infected primary human hepatocytes (PHHs), as well as in HBV-infected human liver chimeric mice and mice transduced with adeno-associated virus-HBV. Mechanistic studies in HBV-infected PHH revealed that CAM-A, but not CAM-E, induced a dose-dependent aggregation of HBc in the nucleus which is negatively regulated by the ubiquitin-binding protein p62. We confirmed that CAM-A, but not CAM-E, induced HBc-positive cell death in both mouse models via induction of apoptotic and inflammatory pathways and demonstrated that the degree of HBV-positive cell loss was positively correlated with intrahepatic HBc levels. Importantly, we determined that there is a significantly lower level of HBc per hepatocyte in CHB patient liver biopsies than in either of the HBV mouse models. Taken together, these data confirm that CAM-As have a unique secondary mechanism with the potential to kill HBc-positive hepatocytes. However, this secondary mechanism appears to require higher intrahepatic HBc levels than is typically observed in CHB patients, thereby limiting the therapeutic potential.
In defense of children’s brain: reshuffling the laboratory toolbox for the diagnosis of congenital toxoplasmosis
Authors: Montoya Jose G. 
Published: May 2024

ABSTRACT

For decades, an immunosorbent agglutination assay (ISAGA) has been considered the gold standard method for the detection of
Toxoplasma gondii
-specific IgM in infants for the diagnosis of congenital toxoplasmosis (CT). The Toxoplasma IgM ISAGA was consistently reported as having superior sensitivity. Unfortunately, the commercial kit for the detection of Toxoplasma IgM ISAGA will no longer be available in 2024 and alternatives will only be available at a handful of reference laboratories as in-house or laboratory-developed tests. In a recent study, S. Arkhis, C. Rouges, N. Dahane, H. Guegan, et al. (J Clin Microbiol 62:e01222-23, 2024,
https://doi.org/10.1128/jcm.01222-23
), reported that the performance of the PLATELIA Toxo IgM was comparable to that of the ISAGA method for the diagnosis of CT. A second study revealing similar results supports the PLATELIA Toxo IgM as the new gold standard for the detection of
T. gondii
-specific IgM in infants. Although the laboratory toolbox for CT diagnosis has been reshuffled successfully, it is by universally implementing all available serological and molecular tools at the earliest possible time during gestation that we can best defend children’s brain from the potential harm caused by trans-placentally transmitted
T. gondii
.
Phages enhance both phytopathogen density control and rhizosphere microbiome suppressiveness
Authors: Wang Xiaofang , Wang Shuo , Huang Mingcong , He Yilin , Guo Saisai , Yang Keming , Wang Ningqi , Sun Tianyu , Yang Hongwu , Yang Tianjie , Xu Yangchun , Shen Qirong , Friman Ville-Petri , Wei Zhong 
Published: May 2024

ABSTRACT

Bacteriophages, viruses that specifically target plant pathogenic bacteria, have emerged as a promising alternative to traditional agrochemicals. However, it remains unclear how phages should be applied to achieve efficient pathogen biocontrol and to what extent their efficacy is shaped by indirect interactions with the resident microbiota. Here, we tested if the phage biocontrol efficacy of
Ralstonia solanacearum
phytopathogenic bacterium can be improved by increasing the phage cocktail application frequency and if the phage efficacy is affected by pathogen-suppressing bacteria already present in the rhizosphere. We find that increasing phage application frequency improves
R. solanacearum
density control, leading to a clear reduction in bacterial wilt disease in both greenhouse and field experiments with tomato. The high phage application frequency also increased the diversity of resident rhizosphere microbiota and enriched several bacterial taxa that were associated with the reduction in pathogen densities. Interestingly, these taxa often belonged to
Actinobacteria
known for antibiotics production and soil suppressiveness. To test if they could have had secondary effects on
R. solanacearum
biocontrol, we isolated Actinobacteria from
Nocardia
and
Streptomyces
genera and tested their suppressiveness to the pathogen
in vitro
and
in planta
. We found that these taxa could clearly inhibit
R. solanacearum
growth and constrain bacterial wilt disease, especially when combined with the phage cocktail. Together, our findings unravel an undiscovered benefit of phage therapy, where phages trigger a second line of defense by the pathogen-suppressing bacteria that already exist in resident microbial communities.

IMPORTANCE

Ralstonia solanacearum
is a highly destructive plant-pathogenic bacterium with the ability to cause bacterial wilt in several crucial crop plants. Given the limitations of conventional chemical control methods, the use of bacterial viruses (phages) has been explored as an alternative biological control strategy. In this study, we show that increasing the phage application frequency can improve the density control of
R. solanacearum
, leading to a significant reduction in bacterial wilt disease. Furthermore, we found that repeated phage application increased the diversity of rhizosphere microbiota and specifically enriched Actinobacterial taxa that showed synergistic pathogen suppression when combined with phages due to resource and interference competition. Together, our study unravels an undiscovered benefit of phages, where phages trigger a second line of defense by the pathogen-suppressing bacteria present in resident microbial communities. Phage therapies could, hence, potentially be tailored according to host microbiota composition to unlock the pre-existing benefits provided by resident microbiota.
Complete genome sequence of
Imperialibacter roseus
strain P4
T
Authors: Tizabi Daniela , Bachvaroff Tsvetan , Hill Russell T. 
Published: May 2024

ABSTRACT

Imperialibacter roseus
strain P4
T
is a bacterial strain isolated from Permian groundwater. The complete genome of
Imperialibacter roseus
strain P4
T
was sequenced to reveal a single circular chromosome of 6,747,663 bp with a GC content of 46.5%.
Lactobacillus-
derived protoporphyrin IX and SCFAs regulate the fiber size via glucose metabolism in the skeletal muscle of chickens
Authors: Cai Liyuan , Wang Xinkai , Zhu Xiaoyan , Xu Yunzheng , Qin Wenxia , Ren Jing , Jiang Qin , Yan Xianghua 
Published: May 2024

ABSTRACT

The gut microbiota contributes to skeletal muscle energy metabolism and is an indirect factor affecting meat quality. However, the role of specific gut microbes in energy metabolism and fiber size of skeletal muscle in chickens remains largely unknown. In this study, we first performed cecal microbiota transplantation from Chinese indigenous Jingyuan chickens (JY) to Arbor Acres chickens (AA), to determine the effects of microbiota on skeletal muscle fiber and energy metabolism. Then, we used metagenomics, gas chromatography, and metabolomics analysis to identify functional microbes. Finally, we validated the role of these functional microbes in regulating the fiber size via glucose metabolism in the skeletal muscle of chickens through feeding experiments. The results showed that the skeletal muscle characteristics of AA after microbiota transplantation tended to be consistent with that of JY, as the fiber diameter was significantly increased, and glucose metabolism level was significantly enhanced in the pectoralis muscle.
L. plantarum
,
L. ingluviei
,
L. salivarius,
and their mixture could increase the production of the microbial metabolites protoporphyrin IX and short-chain fatty acids, therefore increasing the expression levels of genes related to the oxidative fiber type (
MyHC SM
and
MyHC FRM
), mitochondrial function (
Tfam
and
CoxVa
), and glucose metabolism (
PFK
,
PK
,
PDH
,
IDH
, and
SDH
), thereby increasing the fiber diameter and density. These three
Lactobacillus
species could be promising probiotics to improve the meat quality of chicken.

IMPORTANCE

This study revealed that the
L. plantarum, L. ingluviei
, and
L. salivarius
could enhance the production of protoporphyrin IX and short-chain fatty acids in the cecum of chickens, improving glucose metabolism, and finally cause the increase in fiber diameter and density of skeletal muscle. These three microbes could be potential probiotic candidates to regulate glucose metabolism in skeletal muscle to improve the meat quality of chicken in broiler production.
Strigolactones shape the assembly of root-associated microbiota in response to phosphorus availability
Authors: Chen Pubo , Huang Pingliang , Yu Haiyang , Yu Huang , Xie Weicheng , Wang Yuehua , Zhou Yu , Chen Li , Zhang Meng , Yao Ruifeng 
Published: May 2024

ABSTRACT

Plants rely on strigolactones (SLs) to regulate their development and form symbiotic relationships with microbes as part of the adaptive phosphorus (P) efficiency strategies. However, the impact of SLs on root-associated microbial communities in response to P availability remains unknown. Here, root microbiota of SL biosynthesis (
max3-11
) and perception (
d14-1
) were compared to wild-type Col-0 plants under different P concentrations. Using high-throughput sequencing, the relationship between SLs, P concentrations, and the root-associated microbiota was investigated to reveal the variation in microbial diversity, composition, and interaction. Plant genotypes and P availability played important but different roles in shaping the root-associated microbial community. Importantly, SLs were found to attract
Acinetobacter
in low P conditions, which included an isolated CP-2 (
Acinetobacter soli
) that could promote plant growth in cocultivation experiments. Moreover, SLs could change the topologic structure within co-occurrence networks and increase the number of keystone taxa (e.g., Rhizobiaceae and Acidobacteriaceae) to enhance microbial community stability. This study reveals the key role of SLs in mediating root-associated microbiota interactions.

IMPORTANCE
Strigolactones (SLs) play a crucial role in plant development and their symbiotic relationships with microbes, particularly in adapting to phosphorus levels. Using high-throughput sequencing, we compared the root microbiota of plants with SL biosynthesis and perception mutants to wild-type plants under different phosphorus concentrations. These results found that SLs can attract beneficial microbes in low phosphorus conditions to enhance plant growth. Additionally, SLs affect microbial network structures, increasing the stability of microbial communities. This study highlights the key role of SLs in shaping root-associated microbial interactions, especially in response to phosphorus availability.
Popliteal venous access for renal replacement therapy in a critically ill patient with central access failure
Authors: Hamed Muhanad Omer , Abdelmagid Mohanad , Ahmed Mohannad 
Published: May 2024

A woman in her 80s was admitted to the emergency department with an acute infective exacerbation of chronic obstructive pulmonary disease and type 2 respiratory failure, culminating in cardiac arrest for 2 min. She was successfully resuscitated, connected to a mechanical ventilator and subsequently transferred to the intensive care unit. Later in her hospital stay, the patient underwent a tracheostomy following prolonged intubation.During this period, she developed septic shock with complications, including acute kidney injury, metabolic acidosis and volume overload. As a result, the nephrologist recommended emergency haemodialysis. Initially, a left femoral haemodialysis catheter was established but had to be withdrawn a few days later due to the development of deep vein thrombosis (DVT). A left internal jugular catheter was then inserted but was removed after 5 days due to another DVT. It was subsequently replaced with a central line for vasopressor support.A Doppler scan revealed a large thrombus in the right internal jugular vein, extending to the area just above the superior vena cava. A similar thrombus was detected in the left internal jugular vein, with weak blood flow observed in both the right and left subclavian veins. Although the subclavian vein flows were deemed adequate, there was unsatisfactory blood flow through the catheter after insertion, rendering it unsuitable for haemodialysis.Due to an earlier central line-related infection, the right femoral site exhibited signs of infection and the presence of a pus pocket, making it unsuitable for haemodialysis access. To address this, the right popliteal vein was chosen for catheterisation using a 20-cm, 12 French catheter, the longest available catheter in the country at the time. The patient was placed in a prone position, and the catheter was smoothly inserted with ultrasound guidance, resulting in good flow. Subsequent haemodialysis sessions were carried out regularly.
Epidural analgesia during labour and severe maternal morbidity: population based study
Authors: Kearns Rachel J , Kyzayeva Aizhan , Halliday Lucy O E , Lawlor Deborah A , Shaw Martin , Nelson Scott M 
Published: May 2024

Abstract

Objectives
To determine the effect of labour epidural on severe maternal morbidity (SMM) and to explore whether this effect might be greater in women with a medical indication for epidural analgesia during labour, or with preterm labour.

Design
Population based study.

Setting
All NHS hospitals in Scotland.

Participants
567 216 women in labour at 24+0 to 42+6 weeks’ gestation between 1 January 2007 and 31 December 2019, delivering vaginally or through unplanned caesarean section.

Main outcome measures
The primary outcome was SMM, defined as the presence of ≥1 of 21 conditions used by the US Centers for Disease Control and Prevention (CDC) as criteria for SMM, or a critical care admission, with either occurring at any point from date of delivery to 42 days post partum (described as SMM). Secondary outcomes included a composite of ≥1 of the 21 CDC conditions and critical care admission (SMM plus critical care admission), and respiratory morbidity.

Results
Of the 567 216 women, 125 024 (22.0%) had epidural analgesia during labour. SMM occurred in 2412 women (4.3 per 1000 births, 95% confidence interval (CI) 4.1 to 4.4). Epidural analgesia was associated with a reduction in SMM (adjusted relative risk 0.65, 95% CI 0.50 to 0.85), SMM plus critical care admission (0.46, 0.29 to 0.73), and respiratory morbidity (0.42, 0.16 to 1.15), although the last of these was underpowered and had wide confidence intervals. Greater risk reductions in SMM were detected among women with a medical indication for epidural analgesia (0.50, 0.34 to 0.72) compared with those with no such indication (0.67, 0.43 to 1.03; P<0.001 for difference). More marked reductions in SMM were seen in women delivering preterm (0.53, 0.37 to 0.76) compared with those delivering at term or post term (1.09, 0.98 to 1.21; P<0.001 for difference). The observed reduced risk of SMM with epidural analgesia was increasingly noticeable as gestational age at birth decreased in the whole cohort, and in women with a medical indication for epidural analgesia.

Conclusion
Epidural analgesia during labour was associated with a 35% reduction in SMM, and showed a more pronounced effect in women with medical indications for epidural analgesia and with preterm births. Expanding access to epidural analgesia for all women during labour, and particularly for those at greatest risk, could improve maternal health.