Setup errors analysis in iterative kV CBCT: A clinical study of cervical cancer treated with Volumetric Modulated Arc Therapy.

OBJECTIVE: This study aims to analyze setup errors in pelvic Volumetric Modulated Arc Therapy (VMAT) for patients with non-surgical primary cervical cancer, utilizing the onboard iterative kV cone beam CT (iCBCT) imaging system on the Varian Halcyon 2.0 ring gantry structure accelerator to enhance radiotherapy precision. METHOD: We selected 132 cervical cancer patients who underwent VMAT with daily iCBCT imaging guidance. Before each treatment session, a registration method based on the bony structure was employed to acquire iCBCT images with the corresponding planning CT images. Following verification and adjustment of image registration results along the three axes (but not rotational), setup errors in the lateral (X-axis), longitudinal (Y-axis), and vertical (Z-axis) directions were recorded for each patient. Subsequently, we analyzed 3642 iCBCT image setup errors. RESULTS: The mean setup errors for the X, Y, and Z axes were 4.50 ± 3.79 mm, 6.08 ± 6.30 mm, and 1.48 ± 2.23 mm, respectively. Before correction with iCBCT, setup margins based on the Van Herk formula for the X, Y, and Z axes were 6.28, 12.52, and 3.26 mm, respectively. In individuals aged 60 years and older, setup errors in the X and Y axes were significantly larger than those in the younger group (p < 0.05). Additionally, there is no significant linear correlation between setup errors and treatment fraction numbers. CONCLUSION: Data analysis underscores the importance of precise Y-axis setup for cervical cancer patients undergoing VMAT. Radiotherapy centers without daily iCBCT should appropriately extend the planning target volume (PTV) along the Y-axis for cervical cancer patients receiving pelvic VMAT. Elderly patients exhibit significantly larger setup errors compared to younger counterparts. In conclusion, iCBCT-guided radiotherapy is recommended for cervical cancer patients undergoing VMAT to improve setup precision.

RAGE mediates hippocampal pericyte responses and neurovascular unit lesions after TBI.

Traumatic brain injury impairs brain function through various mechanisms. Recent studies have shown that alterations in pericytes in various diseases affect neurovascular function, but the effects of TBI on hippocampal pericytes remain unclear. Here, we investigated the effects of RAGE activation on pericytes after TBI using male C57BL/6 J mice. Hippocampal samples were collected at different time points within 7 days after TBI, the expression of PDGFR-ß, NG2 and the HMGB1-S100B/RAGE signaling pathway was assessed by Western blotting, and the integrity of the hippocampal BBB at different time points was measured by immunofluorescence. RAGE-associated BBB damage in hippocampal pericytes occurred early after cortical impact. By culturing primary mouse brain microvascular pericytes, we determined the different effects of HMGB1-S100B on pericyte RAGE. To investigate whether RAGE blockade could protect neurological function after TBI, we reproduced the process of CCI by administering FPS-ZM1 to RAGE-/- mice. TEM images and BBB damage-related assays showed that inhibition of RAGE resulted in a significant improvement in the number of hippocampal vascular basement membranes and tight junctions and a reduction in perivascular oedema compared with those in the untreated group. In contrast, mouse behavioural testing and doublecortin staining indicated that targeting the HMGB1-S100B/RAGE axis after CCI could protect neurological function by reducing pericyte-associated BBB damage. In conclusion, the present study provides experimental evidence for the strong correlation between the pericyte HMGB1-S100B/RAGE axis and NVU damage in the hippocampus at the early stage of TBI and further demonstrates that pericyte RAGE serves as an important target for the protection of neurological function after TBI.

Tandem Protocol for Diversified Deuteration of Secondary Aliphatic Amines under Mild Conditions.

Deuteration of amine compounds has been widely of concern because of its practical role in organic reaction mechanisms and drug research; however, only limited deuteration label methods are accessible with D2O as a deuterium source. Herein, we propose a convenient deuteration protocol, including preparing D2 by the AlGa activation method, using PtRu nanowires as catalysts, and utilizing the elementary step in the couple reaction involving an imine unit, to realize the rapid preparation of a secondary amine with a diversified deuteration label. The self-coupling between nitriles not only provides a symmetric secondary amine with four α-D atoms but also produces high-valued ND3 in an atomic-economic way.

Zwitterionic Thiolate-Protected Ag22(0/I) and Ag20(I) Clusters: Assembly, Structural Characterization, and Antibacterial Activity.

Zwitterionic thiolate ligands have the potential to introduce novel assembly modes and functions for noble metal clusters. However, their utilization in the synthesis of silver clusters remains understudied, particularly for the clusters containing reductive Ag(0) species. In this article, we report the first synthesis of a mixed-valence silver(0/I) cluster protected by zwitterionic Tab as thiolate ligands (Tab = 4-(trimethylammonio)benzenethiolate), denoted as [Ag22(Tab)24](PF6)20·16CH3OH·6Et2O (Ag22·16CH3OH·6Et2O), alongside an Ag(I) cluster [Ag20(Tab)12(PhCOO)10(MeCN)2(H2O)](PF6)10·11MeCN (Ag20·11MeCN). Ag22 has a distinct hierarchical supratetrahedral structure with a central {Ag6} kernel surrounded by four [Ag4(Tab)6]4+ units. High-resolution electrospray ionization mass spectra demonstrate that Ag22 has two free electrons, indicating a superatomic core. Ag20 has a drum-like [Ag12(Tab)6(PhCOO)6(H2O)]6+ inner core capped by two tetrahedral-like [Ag4(Tab)3(PhCOO)2(MeCN)]2+ units. Ag20 can be transformed into Ag22 after its reaction with NaBH4 in solution. Antibacterial measurements reveal that Ag22 has a significantly lower minimum inhibitory concentration than that of the Ag20 cluster. This work not only extends the stabilization of silver(0/I) clusters to neutral thiol ligands but also offers new materials for the development of novel antibacterial materials.

Unraveling the dynamic transcriptomic changes during the dimorphic transition of Talaromyces marneffei through time-course analysis.

Introduction: Systemic dimorphic fungi pose a significant public health challenge, causing over one million new infections annually. The dimorphic transition between saprophytic mycelia and pathogenic yeasts is strongly associated with the pathogenesis of dimorphic fungi. However, despite the dynamic nature of dimorphic transition, the current omics studies focused on dimorphic transition primarily employ static strategies, partly due to the lack of suitable dynamic analytical methods. Methods: We conducted time-course transcriptional profiling during the dimorphic transition of Talaromyces marneffei, a model organism for thermally dimorphic fungi. To capture non-uniform and nonlinear transcriptional changes, we developed DyGAM-NS (dynamic optimized generalized additive model with natural cubic smoothing). The performance of DyGAM-NS was evaluated by comparison with seven other commonly used time-course analysis methods. Based on dimorphic transition induced genes (DTIGs) identified by DyGAM-NS, cluster analysis was utilized to discern distinct gene expression patterns throughout dimorphic transitions of T. marneffei. Simultaneously, a gene expression regulatory network was constructed to probe pivotal regulatory elements governing the dimorphic transitions. Results: By using DyGAM-NS, model, we identified 5,223 DTIGs of T. marneffei. Notably, the DyGAM-NS model showcases performance on par with or superior to other commonly used models, achieving the highest F1 score in our assessment. Moreover, the DyGAM-NS model also demonstrates potential in predicting gene expression levels throughout temporal processes. The cluster analysis of DTIGs suggests divergent gene expression patterns between mycelium-to-yeast and yeast-to-mycelium transitions, indicating the asymmetrical nature of two transition directions. Additionally, leveraging the identified DTIGs, we constructed a regulatory network for the dimorphic transition and identified two zinc finger-containing transcription factors that potentially regulate dimorphic transition in T. marneffei. Discussion: Our study elucidates the dynamic transcriptional profile changes during the dimorphic transition of T. marneffei. Furthermore, it offers a novel perspective for unraveling the underlying mechanisms of fungal dimorphism, emphasizing the importance of dynamic analytical methods in understanding complex biological processes.

Polyhedral {Ag12} and {Ag16} Clusters: Synthesis, Structural Characterization and Third-Order Nonlinear Optical Properties.

Two polyhedral silver-thiolate clusters, [S@Ag16(Tab)10(MeCN)8](PF6)14 (Ag16) and [Ag12(Tab)6(DMF)12](PF6)12 (Ag12), were synthesized by using electroneutral Tab species as protective ligands (Tab=4-(trimethylammonio)benzenethiolate, DMF=N,N-dimethylformamide, MeCN=acetonitrile). Ag16 has a decahedral shape composed of eight pentagon {Ag5} units and two square {Ag4} units. The structure of Ag12 is a cuboctahedron, a classical Archimedean structure composed of six triangular faces and eight square faces. The former configuration is discovered in silver-thiolate cluster for the first time, possibly benefited from the more flexible coordination between the Tab ligand and Ag+ facilitated by the electropositive -N(CH3)3 + substituent group. Third-order nonlinear optical studies show that both clusters in DMF exhibit reverse saturate absorption response under the irradiation of 532 nm laser.

Engineering Single-Atom Sites with the Irving-Williams Series for the Simultaneous Co-photocatalytic CO2 Reduction and CH3CHO Oxidation.

The bonding effects between 3d transition-metal single sites and supports originate from crystal field stabilization energy (CFSE). The 3d transition-metal atoms of the spontaneous geometrical distortions, that is the Jahn-Teller effect, can alter CFSE, thereby leading to the Irving-Williams series. However, engineering single-atom sites (SASs) using the Irving-Williams series as an ideal guideline has not been reported to date. Herein, alkynyl-linked covalent phenanthroline frameworks (CPFs) with phenanthroline units are developed to anchor the desired 3d single metal ions from d5 to d10 (Mn2+, Fe3+, Co2+, Ni2+, Cu2+, and Zn2+). The Irving-Williams series was employed to accurately predict the bonding effects between 3d transition-metal atoms and phenanthroline units. To verify this, theoretical calculations and experimental results reveal that Cu-SASs/CPFs exhibits higher stability and faster charge-transfer efficiency, far surpassing other metal-SASs/CPFs. As expected, Cu-SASs/CPFs demonstrates a high photoreduction of CO2-to-CO activity (~30.3 µmol ⋅ g-1 ⋅ h-1) and an exceptional photooxidation of CH3CHO-to-CH3COOH activity (~24.7 µmol ⋅ g-1 ⋅ h-1). Interestingly, the generated *O2 - is derived from the process of CO2 reduction, thereby triggering a CH3CHO oxidation reaction. This work provides a novel design concept for designing SASs by the Irving-Williams to regulate the catalytic performances.

Self-Assembly of Cluster-Mediated 3D Catenanes with Size-Specific Recognition Behavior.

Although interlocked three-dimensional molecules display unique properties associated with their spatial structures, their synthesis and study of their host-guest properties remain challenging. We report the formation of a novel [2]catenane, [Et4N]@[(Tp*WS3Cu3Cl)2(cis-bpype)3]2(OTf)5 ([Et4N][1](OTf)5), by self-assembly of the cluster node [Tp*WS3Cu3Cl]+ and the organic linker (Z)-1,2-diphenyl-1,2-bis(4-(pyridin-4-yl)phenyl)ethene (cis-bpype). Single-crystal X-ray and NMR analyses established that [1]4+ is formed by the interpenetration of two cluster-organic cages. Unique cation-in-cation host-guest complexes were observed with this catenane. The crystalline, empty catenane was formed by taking advantage of the electrostatic repulsion-induced weak binding of the host. Encapsulation experiments also reveal that the empty catenane can adaptively encapsulate cations such as [Et4N]+ and [Pr4N]+ in the cross cavity but is unable to encapsulate [Bu4N]+ and [Me4N]+, although the size of the latter is compatible with that of the cavity. Theoretical calculations and volume analysis allow to unravel the ingenious role of catenane structures and the interplay between electrostatic repulsion and attractive noncovalent interactions for size-specific recognition behavior in host-guest systems involving species with similar electric charges.

From Helices to Crystals: Multiscale Representation of Chirality in Double-Helix Structures.

Single crystals with chiral shapes aroused the interest of chemists due to their fascinating polarization rotation properties. Although the formation of large-scale spiral structures is considered to be a potential factor in chiral crystals, the precise mechanism behind their formation remains elusive. Herein, we present a rare phenomenon involving the multitransfer and expression of chirality at micro-, meso-, and macroscopic levels, starting from chiral carbon atoms and extending to the double-helical secondary structure, ultimately resulting in the chiral geometry of crystals. The assembly of the chiral double helices is facilitated by the dual characteristics of amide groups derived from amino acids, which serve as both hydrogen bond donors and receptors, similar to the assembly pattern observed in DNA. Crystal face analysis and theoretical morphology reveal two critical factors for the mechanism of the chiral crystal: inherent intrinsically symmetrical distribution of crystal faces and their acquired growth. Importantly, the magnetic circular dichroism (MCD) study reveals the strong magneto-optical response of the hypersensitive f-f transition in the UV-vis-NIR region, which is much stronger than previously observed signals. Remarkably, an external magnetic field can reverse the CD signal. This research highlights the potential of lanthanide-based chiral helical structures as promising magneto-optical materials.

Exploration and Insights on Topology Adjustment of Giant Heterometallic Cages Featuring Inorganic Skeletons Assisted by Machine Learning.

Inorganic molecular cages are emerging multifunctional molecular-based platforms with the unique merits of rigid skeletons and inherited properties from constituent metal ions. However, the sensitive coordination bonds and vast synthetic space have limited their systematic exploration. Herein, two giant cage-like clusters featuring the organic ligand-directed inorganic skeletons of Ni4[La74Ni104(IDA)96(OH)184(C2O4)12(H2O)76]·(NO3)38·(H2O)120 (La74Ni104, 5 × 5 × 3 - C2O4) and [La84Ni132(IDA)108(OH)168(C2O4)24(NO3)12(H2O)116]·(NO3)72·(H2O)296 (La84Ni132, 5 × 5 × 5 - C2O4) were discovered by a high-throughput synthetic search. With the assistance of machine learning analysis of the experimental data, phase diagrams of the two clusters in a four-parameter synthetic space were depicted. The effect of alkali, oxalate, and other parameters on the formation of clusters and the mechanism regulating the size of two n × m × l clusters were elucidated. This work uses high-throughput synthesis and machine learning methods to improve the efficiency of 3d-4f cluster discovery and finds the highest-nuclearity 3d-4f cluster to date by regulating the size of the n × m × l inorganic cages through oxalate ions, which pushes the synthetic methodology study on elusive inorganic giant cages in a significantly systematic way.

A Cut-to-Link Strategy for Cubane-Based Heterometallic Sulfide Clusters with Giant Third-Order Nonlinear Optical Response.

Although the synthesis of low-dimensional metal sulfides by assembling cluster-based units is expected to promote the development of optical materials and models of enzyme active centers such as dinitrogenase, it is faced with limited assembly methodology. Herein we present a cut-to-link strategy to generate high-nuclearity assemblies, inspired by the formation of a Z-type dimer of the W-S-Cu analogues of PN cluster through in situ release of active linkers. Four new compounds with structures based on the same {Tp*WS3Cu3} incomplete cubane-like units were obtained using varied combinations of mild reagents. Open-aperture Z-scan measurements demonstrated the highest-nuclearity complex has the largest nonlinear optical absorption coefficient among discrete cluster-based materials reported to date. This approach enables building high-nuclearity metal sulfide clusters through cluster-based building blocks and opens a way to the design and exploration of materials based on well-identified building blocks.

Low Prealbumin Levels Were Associated with Increased Frequency of Hepatic Encephalopathy in Hepatitis B Virus (HBV)-Related Decompensated Cirrhosis.

BACKGROUND The role of nutritional parameter prealbumin in predicting the incidence of hepatic encephalopathy (HE) remains unclear. This study was designed to assess the diagnostic performance of prealbumin in predicting the incidence of HE in hepatitis B virus (HBV)-related decompensated liver cirrhosis patients. MATERIAL AND METHODS A retrospective cohort of 262 patients with HBV-related decompensated liver cirrhosis was involved in this study. Prealbumin, albumin, and other indicators were collected at admission, and independent factors were identified by logistic regression analysis. The Mann-Whitney U test and receiver operating characteristic (ROC) curves were used to compare the groups and indicators. RESULTS A total of 262 patients were enrolled in the study, including 197 men and 65 women. In patients with HBV-related decompensated liver cirrhosis accompanied by HE, the model for end-stage liver disease (MELD) scores, and prothrombin time (PT) and international normalized ratio (INR) values were significantly increased, while prealbumin and albumin levels were significantly decreased. Multivariate analysis showed that only serum prealbumin level (P=0.014) was independently related to the incidence of HE. Moreover, prealbumin level was negatively correlated with MELD (r=-0.63, P<0.001) and Child-Turcotte-Pugh (r=-0.35, P<0.001) scores. ROC curves were performed, and prealbumin showed the highest area under the ROC curve (0.781) compared with MELD and Child-Turcotte-Pugh scores. CONCLUSIONS Low prealbumin levels were associated with increased frequency of hepatic encephalopathy in HBV-related decompensated cirrhosis, which showed better performance than traditional models.

Circularly polarized luminescence and performance modulation of chiral europium-titanium (Eu2Ti4)-oxo clusters.

The designed synthesis of chiral luminescent molecules with excellent circularly polarized luminescence (CPL) performance and high quantum yield (QY) levels has attracted great interest but remains very challenging. Herein, we report three pairs of chiral europium-titanium-oxo clusters featuring both modest CPL characteristics and high QY levels (up to 79%), which can be regulated by switching between different ligand substituents.

Depression recognition using a proposed speech chain model fusing speech production and perception features.

BACKGROUND: Increasing depression patients puts great pressure on clinical diagnosis. Audio-based diagnosis is a helpful auxiliary tool for early mass screening. However, current methods consider only speech perception features, ignoring patients' vocal tract changes, which may partly result in the poor recognition. METHODS: This work proposes a novel machine speech chain model for depression recognition (MSCDR) that can capture text-independent depressive speech representation from the speaker's mouth to the listener's ear to improve recognition performance. In the proposed MSCDR, linear predictive coding (LPC) and Mel-frequency cepstral coefficients (MFCC) features are extracted to describe the processes of speech generation and of speech perception, respectively. Then, a one-dimensional convolutional neural network and a long short-term memory network sequentially capture intra- and inter-segment dynamic depressive features for classification. RESULTS: We tested the MSCDR on two public datasets with different languages and paradigms, namely, the Distress Analysis Interview Corpus-Wizard of Oz and the Multi-modal Open Dataset for Mental-disorder Analysis. The accuracy of the MSCDR on the two datasets was 0.77 and 0.86, and the average F1 score was 0.75 and 0.86, which were better than the other existing methods. This improvement reveals the complementarity of speech production and perception features in carrying depressive information. LIMITATIONS: The sample size was relatively small, which may limit the application in clinical translation to some extent. CONCLUSION: This experiment proves the good generalization ability and superiority of the proposed MSCDR and suggests that the vocal tract changes in patients with depression deserve attention for audio-based depression diagnosis.

The landscape of hervRNAs transcribed from human endogenous retroviruses across human body sites.

BACKGROUND: Human endogenous retroviruses (HERVs), the remnants of ancient retroviruses, account for 8% of the human genome, but most have lost their transcriptional abilities under physiological conditions. However, mounting evidence shows that several expressed HERVs do exert biological functions. Here, we systematically characterize physiologically expressed HERVs and examine whether they may give insight into the molecular fundamentals of human development and disease. RESULTS: We systematically identify 13,889 expressed HERVs across normal body sites and demonstrate that they are expressed in body site-specific patterns and also by sex, ethnicity, and age. Analyzing cis-ERV-related quantitative trait loci, we find that 5435 hervRNAs are regulated by genetic variants. Combining this with a genome-wide association study, we elucidate that the dysregulation of expressed HERVs might be associated with various complex diseases, particularly neurodegenerative and psychiatric diseases. We further find that physiologically activated hervRNAs are associated with histone modifications rather than DNA demethylation. CONCLUSIONS: Our results present a locus-specific landscape of physiologically expressed hervRNAs, which represent a hidden layer of genetic architecture in development and disease.

Interplay between anisotropy and magnetic exchange to modulate the magnetic relaxation behaviours of phenoxo bridged Dy2 dimers with axial ß-diketonate co-ligands.

A series of Schiff base LH ((E)-2-((pyridin-2-ylmethylene)amino)phenol) supported phenoxo bridged symmetric [Dy2(L)2(hfac)4] (1), [Dy2(L)2(tfac)4] (2) and asymmetric [Dy2(L)2(thd)3(NO3)]·1.5H2O (3) binuclear complexes were isolated using differently substituted ß-diketonate co-ligands (Hhfac = hexafluoroacetylacetonate, Htfac = trifluoroacetylacetonate, and Hthd = 2,2,6,6-tetramethyl-3,5-heptanedione). In all the three complexes 1-3, the two LH ligands provide phenoxo bridging and N-donor atoms. The {Dy2(µ2-O)2} magnetic core structures with LH ligands are found to be the same in 1-3 while the dissimilar functionalities of the axially coordinated different ß-diketonate co-ligands play a crucial role in modulating the magnetic anisotropy of individual DyIII sites and magnetic exchange between them. The experimental static magnetic behaviour suggests the presence of intramolecular antiferromagnetic interactions in all the three complexes 1-3. The strength of the magnetic exchange coupling decreases with increasing magnetic anisotropy of individual DyIII ions from complex 1 to complex 3 and simultaneously their zero-field slow magnetic relaxation behaviors were found to increase with effective energy barriers (ΔE/kB) of 9.04 K, 24.06 K and 25.65 K, respectively. Furthermore, the DFT and ab initio theoretical calculations performed on the X-ray structures of complexes 1-3 support our experimental findings.

Facile Synthesis of Ag/Carbon Quantum Dots/Graphene Composites for Highly Conductive Water-Based Inks.

The development of graphene conductive inks with a high conductivity and dispersion stability in water poses considerable challenges. Herein, a highly conductive Ag/carbon quantum dots (CQDs)/graphene (G) composite with good dispersity and stability in water was prepared for the first time through the in situ photoreduction of AgNO3 and deposition of Ag onto graphene nanosheets obtained via CQD-assisted liquid-phase exfoliation. Ag nanoparticles with an average size of ∼1.88 nm were uniformly dispersed on graphene nanosheets. The Ag/CQDs/G composite exhibited good dispersity and stability in water for 30 days. The formation mechanism of the Ag/CQDs/G composites was also discussed. CQDs played a vital role in coordinating with Ag+ and reducing it under visible light conditions. The addition of only 1.58 wt % of Ag NPs to the CQDs/G film resulted in a significant decrease in the electrical resistivity by approximately 89.5%, reaching a value of 0.054 Ω cm for a 40 µm thick Ag/CQDs/G film. A low resistivity of 2.15 × 10-3 Ω cm for the Ag/CQDs/G film was achieved after rolling compression with a compression ratio of 78%. The Ag/CQDs/G film exhibited good conductivity and durability when bent, rolled, or twisted. Moreover, the resistivity of the film displayed a slight deviation after 5000 bending cycles, indicating its outstanding stability. This study provides an efficient strategy for preparing graphene-based conductive composites with good dispersibility and stability in water as well as novel high-performance conductive inks for application in flexible printed electronics.

Photoluminescence of Lanthanide-Titanium-Oxo Clusters Eu9Ti2 and Tb9Ti2 Based on a ß-Diketone Ligand.

A series of acetylacetone-protected lanthanide-titanium-oxo clusters (LTOCs), formulated as [La6Ti(µ3-OH)8(acac)12(CH3O)2(CH3OH)6] (La6Ti; Hacac = acetylacetone) and [Ln9Ti2(µ4-O)(µ3-OH)14(acac)17(CH3O)2(CH3OH)3] [Ln = Eu (Eu9Ti2) and Tb (Tb9Ti2)], were synthesized through the reactions of LnCl3·6H2O (Ln = La, Eu, and Tb), Hacac, Ti(OiPr)4, and triethylamine in methanol. Crystal structural analysis shows that La6Ti exhibits an hourglass-like structure consisting of two La3Ti cubane subunits by sharing one Ti4+ ion, while Eu9Ti2 can be viewed as a combination of four Eu3Ti cubane subunits by sharing three corners and one side. The photoluminescence (PL) measurements show that Tb9Ti2 exhibits excellent PL properties with a high quantum yield (QY) of 34.8%, while Eu9Ti2 only has a QY of 1.4% because of the different photosensitizations of ligands to Eu3+ and Tb3+ ions in the photophysical process.

Efficient and specific DNA oligonucleotide rRNA probe-based rRNA removal in Talaromyces marneffei.

Emerging evidence showed that lncRNAs play important roles in a wide range of biological processes of fungi such as Saccharomyces cerevisiae. However, systemic identification of lncRNAs in non-model fungi is a challenging task as the efficiency of rRNA removal has been proved to be affected by mismatches of universal rRNA-targeting probes of commercial kits, which forces deeper sequencing depth and increases costs. Here, we developed a low-cost and simple rRNA depletion method (rProbe) that could efficiently remove more than 99% rRNA in both yeast and mycelium samples of Talaromyces marneffei. The efficiency and robustness of rProbe were demonstrated to outperform the Illumina Ribo-Zero kit. Using rProbe RNA-seq, we identified 115 differentially expressed lncRNAs and constructed lncRNA-mRNA co-expression network related to dimorphic switch of T. marneffei. Our rRNA removal method has the potential to be a useful tool to explore non-coding transcriptomes of non-model fungi by adjusting rRNA probe sequences species specifically.

Immunocompromised rabbit model of chronic HEV reveals liver fibrosis and distinct efficacy of different vaccination strategies.

BACKGROUND AND AIMS: HEV infection can lead to chronicity and rapid progression to liver fibrosis and cirrhosis in immunocompromised organ transplant recipients. Robust animal models are urgently needed to study the pathogenesis and test the efficacy of vaccines and antiviral drugs in immunosuppressed settings. APPROACH AND RESULTS: Cyclosporin A was used to induce immunosuppression. Rabbits were challenged with genotype 3 or 4 HEV (i.e., the rabbit-derived HEV3 and human-derived HEV3 or HEV4). We assessed HEV markers within 13 weeks post inoculation (wpi) and pathological changes by hematoxylin and eosin and Masson staining at 4, 8, or 13 wpi. Chronic HEV infection was successfully established in immunocompromised rabbits. HEV RNA and/or antigens were detected in the liver, kidney, intestine, urine, and cerebrospinal fluid samples. Chronically infected animals exhibited typical characteristics of liver fibrosis development. Intrahepatic transcriptomic analysis indicated activation of both innate and adaptive immunity. Establishment of HEV chronicity likely contributed to the inhibited T-cell immune response. Ribavirin is effective in clearing HEV infection in immunocompromised rabbits. Most interestingly, vaccination completed before immunosuppression conferred full protection against both HEV3 and HEV4 infections, but vaccination during immunosuppression was only partially protective, and the efficacy did not improve with increased or additional vaccine doses. CONCLUSIONS: The immunocompromised rabbit model of both chronic HEV3 and HEV4 infection that was established captured the key features of chronic HEV infection in transplant patients, including liver fibrogenesis, and revealed the distinct effectiveness of vaccination administered before or under immunosuppression. This rabbit model is valuable for understanding the pathogenesis of chronic hepatitis E, as well as for evaluating antiviral agents and vaccines.