Development and validation of a novel nomogram model for predicting delayed graft function in deceased donor kidney transplantation based on pre-transplant biopsies.

BACKGROUND: Delayed graft function (DGF) is an important complication after kidney transplantation surgery. The present study aimed to develop and validate a nomogram for preoperative prediction of DGF on the basis of clinical and histological risk factors. METHODS: The prediction model was constructed in a development cohort comprising 492 kidney transplant recipients from May 2018 to December 2019. Data regarding donor and recipient characteristics, pre-transplantation biopsy results, and machine perfusion parameters were collected, and univariate analysis was performed. The least absolute shrinkage and selection operator regression model was used for variable selection. The prediction model was developed by multivariate logistic regression analysis and presented as a nomogram. An external validation cohort comprising 105 transplantation cases from January 2020 to April 2020 was included in the analysis. RESULTS: 266 donors were included in the development cohort, 458 kidneys (93.1%) were preserved by hypothermic machine perfusion (HMP), 96 (19.51%) of 492 recipients developed DGF. Twenty-eight variables measured before transplantation surgery were included in the LASSO regression model. The nomogram consisted of 12 variables from donor characteristics, pre-transplantation biopsy results and machine perfusion parameters. Internal and external validation showed good discrimination and calibration of the nomogram, with Area Under Curve (AUC) 0.83 (95%CI, 0.78-0.88) and 0.87 (95%CI, 0.80-0.94). Decision curve analysis demonstrated that the nomogram was clinically useful. CONCLUSION: A DGF predicting nomogram was developed that incorporated donor characteristics, pre-transplantation biopsy results, and machine perfusion parameters. This nomogram can be conveniently used for preoperative individualized prediction of DGF in kidney transplant recipients.

Advances in All-Solid-State Lithium-Sulfur Batteries for Commercialization.

Solid-state batteries are commonly acknowledged as the forthcoming evolution in energy storage technologies. Recent development progress for these rechargeable batteries has notably accelerated their trajectory toward achieving commercial feasibility. In particular, all-solid-state lithium-sulfur batteries (ASSLSBs) that rely on lithium-sulfur reversible redox processes exhibit immense potential as an energy storage system, surpassing conventional lithium-ion batteries. This can be attributed predominantly to their exceptional energy density, extended operational lifespan, and heightened safety attributes. Despite these advantages, the adoption of ASSLSBs in the commercial sector has been sluggish. To expedite research and development in this particular area, this article provides a thorough review of the current state of ASSLSBs. We delve into an in-depth analysis of the rationale behind transitioning to ASSLSBs, explore the fundamental scientific principles involved, and provide a comprehensive evaluation of the main challenges faced by ASSLSBs. We suggest that future research in this field should prioritize plummeting the presence of inactive substances, adopting electrodes with optimum performance, minimizing interfacial resistance, and designing a scalable fabrication approach to facilitate the commercialization of ASSLSBs.

Exploring tumor heterogeneity in colorectal liver metastases by imaging: Unsupervised machine learning of preoperative CT radiomics features for prognostic stratification.

OBJECTIVES: This study aimed to investigate tumor heterogeneity of colorectal liver metastases (CRLM) and stratify the patients into different risk groups of prognoses following liver resection by applying an unsupervised radiomics machine-learning approach to preoperative CT images. METHODS: This retrospective study retrieved clinical information and CT images of 197 patients with CRLM from The Cancer Imaging Archive (TCIA) database. Radiomics features were extracted from a segmented liver lesion identified at the portal venous phase. Those features which showed high stability, non-redundancy, and indicative information were selected. An unsupervised consensus clustering analysis on these features was adopted to identify subgroups of CRLM patients. Overall survival (OS), disease-free survival (DFS), and liver-specific DFS were compared between the identified subgroups. Cox regression analysis was applied to evaluate prognostic risk factors. RESULTS: A total of 851 radiomics features were extracted, and 56 robust features were finally selected for unsupervised clustering analysis which identified two distinct subgroups (96 and 101 patients respectively). There were significant differences in the OS, DFS, and liver-specific DFS between the subgroups (all log-rank p < 0.05). The subgroup with worse outcome using the proposed radiomics model was consistently associated with shorter OS, DFS, and liver-specific DFS, with hazard ratios of 1.78 (95 %CI: 1.12-2.83), 1.72 (95 %CI: 1.16-2.54), and 1.59 (95 %CI: 1.10-2.31), respectively. The general performance of this radiomics model outperformed the traditional Clinical Risk Score and Tumor Burden Score in the prognosis prediction after surgery for CRLM. CONCLUSION: Radiomics features derived from preoperative CT images can reveal the heterogeneity of CRLM and stratify the patients with CRLM into subgroups with significantly different clinical outcomes.

Histopathological analysis of the wall enhancement of the spinal dural arteriovenous fistulae's draining veins.

OBJECTIVE: The mechanism behind SDAVF is still unclear. We discovered that the vessel wall of the SDAVF-DV occasionally showed enhancement in MRI, and this study assessed the relationship between the enhancement of the draining vein's wall and its histology. METHODS: For histopathologic analysis, 16 draining vein samples from 16 patients with SDAVF were included, 3 normal arteries and 3 normal veins were chosen as comparison. We assessed the imaging and microscopic characteristics of the draining veins in SDAVF patients. The former included the presence of significant enhancement of the wall of the draining vein in MRI, and the latter included the adherence, aggregation, infiltration of pro-inflammatory factors and inflammatory cells. Immuno-histochemical staining was performed using IL-1ß, IL-8, TGF-ß as well as MPO and MMP-9, and positive results were counted. Multiple logistic regression analysis was used to determine whether the infiltration of inflammatory cells was connected to vessel wall enhancement in the SDAVF-DV. RESULTS: Infiltration of inflammatory cells was significantly higher in SDAVF-DV compared to normal vessels, 7 out of 16 patients significantly had enhancement of the vessel wall of SDAVF-DV, and logistic regression analysis showed that samples with more infiltration of inflammatory cells were more likely to show enhancement of the SDAVF-DV walls. CONCLUSION: There was considerable inflammatory cells infiltration in SDAVF-DV, and this may explain why their vessel wall had such a significant enhancement in MRI.

Correction: Haegeman et al. Looking beyond Virus Detection in RNA Sequencing Data: Lessons Learned from a Community-Based Effort to Detect Cellular Plant Pathogens and Pests. Plants 2023, 12, 2139.

In the original publication [...].

Ancient Mitogenomes Reveal the Maternal Genetic History of East Asian Dogs.

Recent studies have suggested that dogs were domesticated during the Last Glacial Maximum (LGM) in Siberia, which contrasts with previous proposed domestication centers (e.g. Europe, the Middle East, and East Asia). Ancient DNA provides a powerful resource for the study of mammalian evolution and has been widely used to understand the genetic history of domestic animals. To understand the maternal genetic history of East Asian dogs, we have made a complete mitogenome dataset of 120 East Asian canids from 38 archaeological sites, including 102 newly sequenced from 12.9 to 1 ka BP (1,000 years before present). The majority (112/119, 94.12%) belonged to haplogroup A, and half of these (55/112, 49.11%) belonged to sub-haplogroup A1b. Most existing mitochondrial haplogroups were present in ancient East Asian dogs. However, mitochondrial lineages in ancient northern dogs (northeastern Eurasia and northern East Asia) were deeper and older than those in southern East Asian dogs. Results suggests that East Asian dogs originated from northeastern Eurasian populations after the LGM, dispersing in two possible directions after domestication. Western Eurasian (Europe and the Middle East) dog maternal ancestries genetically influenced East Asian dogs from approximately 4 ka BP, dramatically increasing after 3 ka BP, and afterwards largely replaced most primary maternal lineages in northern East Asia. Additionally, at least three major mitogenome sub-haplogroups of haplogroup A (A1a, A1b, and A3) reveal at least two major dispersal waves onto the Qinghai-Tibet Plateau in ancient times, indicating eastern (A1b and A3) and western (A1a) Eurasian origins.

TRIM29 facilitates gemcitabine resistance via MEK/ERK pathway and is modulated by circRPS29/miR-770-5p axis in PDAC.

AIMS: Pancreatic ductal adenocarcinoma (PDAC) is a highly lethal disease. Chemotherapy based on gemcitabine (GEM) remains the first-line drug for patients with advanced PDAC. However, GEM resistance impairs its therapeutic effectiveness. Therefore, identifying effective therapeutic targets are urgently needed to overcome GEM resistance. METHODS: The clinical significance of Tripartite Motif Containing 29 (TRIM29) was identified by exploring GEO datasets and TCGA database and its potential biological functions were predicted by GSEA analysis. The regulatory axis was established by bioinformatics analysis and validated by mechanical experiments. Then, in vitro and in vivo assays were performed to validate the roles of TRIM29 in PDAC GEM resistance. RESULTS: High TRIM29 expression was associated with poor prognosis of PDAC and functional experiments demonstrated that TRIM29 promoted GEM resistance in PDAC GEM-resistant (GR) cells. Furthermore, we revealed that circRPS29 promoted TRIM29 expression via competitive interaction with miR-770-5p and then activated MEK/ERK signaling pathway. Additionally, both in vitro and in vivo functional experiments demonstrated that circRPS29/miR-770-5p/TRIM29 axis promoted PDAC GEM resistance via activating MEK/ERK signaling pathway. CONCLUSION: Our results identify the significance of the signaling axis, circRPS29/miR-770-5p/TRIM29-MEK/ERK, in PDAC GEM resistance, which will provide novel therapeutic targets for PDAC treatment.

Prevalence, clinical features and prognosis of familial hypercholesterolemia in Chinese Han patients with acute coronary syndrome after a coronary event: a retrospective observational study.

BACKGROUND: Familial hypercholesterolemia (FH) is an autosomal semi-dominant disease, characterized by markedly elevated levels of low-density lipoprotein cholesterol (LDL-c) from conception and accelerated atherosclerotic cardiovascular disease, often resulting in early death. The aim of this study was to evaluate the prevalence of clinically defined FH in Chinese Han patients with acute coronary syndrome (ACS) and compare the long-term prognosis of ACS patients with and without FH receiving lipid-lowering therapy containing statins after a coronary event. METHODS: All ACS patients were screened at the Second Affiliated Hospital of Xi'an Jiaotong University between Jan 2019 and Sep 2020, and 531 participants were enrolled. All were examined for FH under the Dutch Lipid Clinical Network (DLCN) criteria, and those patients were divided into definite/probable FH, possible FH and unlikely FH. The severity of coronary artery disease was evaluated by the Gensini scoring system. Plasma levels of total cholesterol (TC), triacylglycerol (TG), HDL-cholesterol (HDL-c), LDL-cholesterol (LDL-c), very low-density lipoproteins-cholesterol (VLDL-c), apolipoprotein A1 (apoA1), apolipoprotein B (apoB) and lipoprotein (a) (Lp(a)) were determined centrally at baseline and the last follow-up visit in the fasting state. The non-high-density lipoprotein cholesterol (non-HDL-c) concentration, the TC/HDL-c and apoB/apoA1 ratios were calculated. After FH patients received lipid-lowering treatment containing statin, the target LDL-c levels recommended by the guidelines (LDL-c < 1.8 mmol/L or < 1.4 mmol/L and a reduction > 50% from baseline) were evaluated, and the occurrence of major adverse cardiovascular and cerebrovascular events (MACCE) during the 12-month follow-up was recorded. RESULTS: The prevalence of clinically definite or probable FH was 4.3%, and the prevalence of possible FH was 10.6%. Compared with the unlikely FH patients with ACS, the FH patients had higher levels of TC, LDL-c, apoB, Lp(a), non-HDL-c, TC/HDL-c and apoB/apoA1 ratio, more severe coronary artery diseases and greater prevalence of left main and triple or multiple vessel lesions. After lipid-lowering therapy containing statins, a minority of FH patients reached the target LDL-c levels defined by the guidelines (χ2 = 33.527, P < 0.001). During the 12-month follow-up, a total of 72 patients experienced MACCE. The survival curve in patients in the FH group was significantly lower than that in the unlikely FH group (HR = 1.530, log-rank test: P < 0.05). Furthermore, the survival curve in patients with high LDL-c (≥ 1.8 mmol/L) was significantly lower than that in patients with low LDL-c (< 1.8 mmol/L) at the 12-month follow-up visit (HR = 1.394, log-rank test: P < 0.05). No significant difference was observed between patients with LDL-c levels ≥ 1.4 mmol/L and with < 1.4 mmol/L at the 12-month follow-up visit by using Kaplan-Meier survival analysis (HR = 1.282, log-rank test: P > 0.05). CONCLUSIONS: FH was an independent risk factor for MACCE in adult patients after a coronary event during long-term follow-up. However, there was inadequate high-intensity statins prescriptions for high-risk patients in this current study. It is important for FH patients to optimize lipid-lowering treatment strategies to reach the target LDL-c level to improve the long-term prognosis of clinical outcomes.

Optimizing soil tetrabromobisphenol A remediation through iron-based activation of persulfate: A comparative analysis of homogeneous and heterogeneous systems.

Tetrabromobisphenol A (TBBPA) that widely exists in soil and poses a potential threat to ecological environment urgently needs economically efficient remediation techniques. This study utilized both homogeneous Fe2⁺ solution and heterogeneous iron-based nanomaterials (chemically synthesized nano zero-valence iron (nZVI) and green-synthesized iron nanoparticles (G-Fe NPs)) to activate persulfate (PS) and assess their efficacy in degrading TBBPA in soil. The results demonstrate the superior performance of heterogeneous catalytic systems (WG-Fe NPs/PS (82.07%) and WnZVI/PS (78.32%)) over homogeneous catalytic system (WFe2+/PS (71.69%)), In addition, G-Fe NPs and nZVI effectively controlled the slow release of Fe2+. The optimization analysis using response surface methodology (RSM) reveal the remarkable significance of the experimental model based on the box-behnken design. RSM show that G-Fe NPs/PS exhibited optimal process parameters and predicted the maximum soil TBBPA degradation efficiency reaching 98.77%. The results of density functional theory calculations suggest that C-Br are the primary targets for electrophilic substitution reactions. Based on the f0 value and △G, the degradation pathway of TBBPA is inferred to involve a sequential debromination process, followed by the cleavage of intermediate carbon-carbon bonds and subsequent oxidation reactions. Hence, G-Fe NPs/PS not only facilitate waste resource utilization but also hold significant application potential.

Mechanical activation induced treatment for the synergistic recovery of valuable elements from spent NdFeB magnets.

The efficient and sustainable recovery of rare earth resources from spent NdFeB magnets has received considerable and increasing attention. However, the currently prevalent NdFeB magnets recovery techniques focus only on the recovery for rare earth elements (REEs), some of which also recover cobalt (Co) or boron (B). Herein, a simple mechanochemical strategy was proposed to recover REE, Co, and B from spent NdFeB magnets by mixing the NdFeB magnets powder and FeCl3 6H2O through the grinding-roasting-water leaching technological route. The results indicated high leaching efficiencies of 98.94 % for REEs, 99.99 % for Co, and 93.36 % for B from the NdFeB magnets. Additionally, iron remains in the leaching residue as iron oxide (96.73 wt %), achieving the complete separation of REEs, Co, B, and Fe. This mechanochemical based technology offers a green and efficient recovery process, facilitating more effective synergistic recovery of valuable elements from spent NdFeB magnets.

Eliminating the Scattering of Thin Film Structures.

Rendering invisibility in the wide application scenarios has seen a surge in interest in recent years. Though various approaches have been proposed to realize concealments under different conditions, achieving polarization-independent invisibility for large objects remains a big challenge. Here, we propose to attain invisibility of a large dielectric slab with polarization constraints being totally lifted. This is accomplished by employing an antiscattering coating made of anisotropic metamaterials. We show that by tailoring the electric resonance of a triangular mushroom structure, antiphase electric dipole moment can be induced, resulting in an antipolarization response of the whole metamaterial coatings. By putting the proposed coatings on both sides of a large dielectric slab, a neutralization effect of the total polarization is observed, leading to the peculiar phenomenon of full-polarization invisibility. Our results are validated through full-wave simulations and experimental measurements. Remarkably, the intrinsic null-polarization property of the coating-slab-coating structure guarantees the invisibility feature of a large-scale bulk made by simply stacking the sandwiched composites, which facilitates the application of invisibility in practical scenarios such as the invisibility cloaks and the reflectionless antenna radomes.

Catalytic Enantioselective [4+2] Cycloadditions of Salicylaldehyde Acetals with Enol Ethers.

A readily accessible conjugate-base-stabilized carboxylic acid (CBSCA) catalyst facilitates highly enantioselective [4+2] cycloaddition reactions of salicylaldehyde-derived acetals and cyclic enol ethers, resulting in the formation of polycyclic chromanes with oxygenation in the 2- and 4-positions. Stereochemically more complex products can be obtained from racemic enol ethers. Spirocyclic products are also accessible.

Nearly Ideal Transparency with Artificially Designed Meta-Atoms.

The ideal electromagnetic transparency refers to the ability of an object to remain scatteringless to any incoming waves, resulting in vacuum invisibility. However, natural solid substances can hardly be transparent in free space as they are responsive to external polarizations. Completely eliminating the polarization effect of an obstacle under arbitrary field illumination is a long-standing scientific challenge. Here, it is shown that a subwavelength meta-atom can be nearly ideally transparent in the vacuum. The overall vacuum-like property of the meta-atom is achieved through judiciously designing its internal polarization and magnetization. Remarkably, any large-scale objects made by stacking the meta-atoms inherit the vacuum-like property and are scatteringless in free space. By both the simulations and experiments, the meta-atom's peculiar property is reasonably verified. The proposed meta-atoms are excellent candidates for a wide range of applications, such as perfect radar radomes, scatteringless walls, filtering devices, and self-stealth materials.

Comparison of endovenous microwave ablation versus radiofrequency ablation for lower limb varicose veins.

OBJECTIVE: Endovenous microwave ablation (EMA) is a recently developed thermal ablation technique used in the treatment of lower limb varicose veins. However, its efficacy and safety have been largely understudied. In the present study, we sought to explore the clinical results of EMA and radiofrequency ablation (RFA) in treating lower limb varicose veins. METHODS: Patients who underwent EMA (n = 65) or RFA (n = 46) at our institute from September 2018 to September 2020 were included in this retrospective investigation. The clinical results and complications were evaluated at 1, 3, 6, and 12 months after the procedure. The effects on disease severity and quality of life were evaluated using the venous clinical severity score and chronic venous insufficiency questionnaire (CIVIQ). RESULTS: The technical success rate was 100% for both experimental groups. Although the operative time between the two groups was comparable, the EMA technique was associated with lower direct costs (P < .001), although also with prolonged hospitalization (P < .001). We found that the use of EMA correlated with more pain at 48 hours postoperatively. Except for the visual analog scale scores, no statistically significant variations were observed in the occurrence of postoperative complications within the first 48 hours postoperatively between the EMA and RFA groups, including paresthesia, ecchymosis, induration, and phlebitis (P > .05). At 4 weeks postoperatively, significantly less pigmentation was observed in the RFA group than in the EMA group (13.04% vs 32.31%; P = .020). However, the pigmentation had resolved in all patients by 12 months postoperatively. The two groups had a reduction in the venous clinical severity scores and an increase in the CIVIQ scores after the procedure. However, the CIVIQ scores within the RFA group had increased more than had those within the EMA group (P < .05). No significant differences were found in recurrence between the two groups (EMA group, 1.54%; RFA group, 2.17%; P = .804). CONCLUSIONS: Both ablation techniques are safe and effective. RFA is associated with relatively higher treatment costs but shorter hospitalization and better quality of life improvement.

Immobilization of laccase on magnetic mesoporous silica as a recoverable biocatalyst for the efficient degradation of benzo[a]pyrene.

Laccase is an efficient green biocatalyst, widely used for the degradation of various organic pollutants. However, free laccase is unstable and difficult to recover, which limits its practical application. In this study, a multilayer core-shell magnetic mesoporous silica (Fe3O4@d-SiO2@p-SiO2) microsphere with high specific surface area (275 m2 g-1) was fabricated for immobilization of laccase. The unique structure of Fe3O4@d-SiO2@p-SiO2 enabled the successful immobilization of laccase. Under the optimal immobilization conditions of laccase concentration of 1.5 mg mL-1, immobilization time of 6 h, immobilization pH of 6, the loading capacity of laccase was up to 567 mg g-1. Compared with free laccase, immobilized laccase exhibited remarkable pH stability, thermal stability and storage stability. Moreover, the immobilized laccase was easy to achieve magnetic recovery and possessed excellent reusability, with its activity remaining 58.2% after 10 consecutive reuses. More importantly, immobilized laccase had good degradation performance for benzo[a]pyrene (BaP), which can achieve rapid and efficient degradation of low concentration BaP over a wide range of pH and temperature. The removal efficiency of BaP was up to 99.0% within 1 h, and still exceeded 35.0% after 5 cycles. The removal of BaP by immobilized laccase was achieved through both adsorption and degradation. The degradation products and possible degradation pathways were determined by GC-MS analysis. This study indicated that Fe3O4@d-SiO2@p-SiO2 could effectively enhance the stability and biocatalytic activity of laccase, which is expected to provide a new clean biotechnology for the remediation of BaP contaminated sites.

A novel dual-mode aptasensor based colorimetry and electrochemical detection of norovirus in fecal sample.

Norovirus is a leading cause of acute gastroenteritis in humans. This paper presents the development of a novel dual-mode aptasensor for detecting norovirus using colorimetry and electrochemical methods. The initial colorimetric method utilizes gold nanoparticles (AuNPs) and sodium chloride to establish a positive correlation between the concentration of norovirus in a solution and the absorbance ratio A650/A520. The naked eye can detect concentrations as low as 0.1 µg/mL, corresponding to a Ct value of 33 (2.2 copies/µL, CT = 34.102-3.2185·lgX), allowing for qualitative and semi-quantitative analysis. For more accurate trace analysis, a gold electrode is modified with a thiol-modified aptamer and closed with 6-Mercapto-1-hexanol. After incubation with norovirus, the virus specifically binds to the aptamer, causing changes in its spatial structure and distance from the electrode surface. These changes can then be detected using electrochemical square wave voltammetry (SWV). Under optimal reaction conditions, the peak current from SWV exhibits a strong linear relationship with the logarithm of norovirus concentrations between 10-9 µg/mL and 10-2 µg/mL. The regression equation Y = 14.76789 + 1.03983·lgX, with an R2 value of 0.987, accurately represents this relationship. The limit of detection was determined to be 1.365 × 10-10 µg/mL. Furthermore, the aptasensor demonstrated high specificity for norovirus in fecal samples, making it a promising tool for detecting norovirus in various sample types.

Colourimetric and SERS dual-mode aptasensor using Au@Ag and magnetic nanoparticles for the detection of Campylobacter jejuni.

A dual-mode aptasensor has been developed for the effective detection of Campylobacter jejuni (C. jejuni), a major cause of gastrointestinal disease worldwide. The aptasensor utilizes nanoparticles, specifically a core-shell structure consisting of gold and silver (Au@Ag NPs), along with magnetic nanoparticles (MNPs). When Campylobacter jejuni is introduced, "Au@Ag NPs-Aptamer-Campylobacter jejuni-Aptamer-MNPs" sandwich complexes are formed due to the high affinity of the aptamer for the bacterial surface membrane proteins. The dual-mode aptasensor can magnetically enrich the sample in just 15 min, and the presence of Campylobacter jejuni is determined by observing a color change. Additionally, the concentration of Campylobacter jejuni can be quantified using surface-enhanced Raman spectroscopy (SERS) and standard curves. This results in a wider linear range (1.8 × 101-108 CFU/mL) under optimal conditions, a lower limit of detection (6 CFU/mL), and a higher selectivity for the detection of bacteria compared to previously reported sensors. Compared with traditional microbial culture counting methods, the dual-mode aptasensor does not require Raman reporters. The physical action of magnetic enrichment, along with the application of Au@Ag NPs, improves the accuracy of the dual-mode aptasensor, offering the advantages of convenience and high sensitivity. Moreover, by utilizing different types of aptamers, this aptasensor can be modified to detect a wider range of harmful pathogens in various environments.

PhytoPipe: a phytosanitary pipeline for plant pathogen detection and diagnosis using RNA-seq data.

BACKGROUND: Detection of exotic plant pathogens and preventing their entry and establishment are critical for the protection of agricultural systems while securing the global trading of agricultural commodities. High-throughput sequencing (HTS) has been applied successfully for plant pathogen discovery, leading to its current application in routine pathogen detection. However, the analysis of massive amounts of HTS data has become one of the major challenges for the use of HTS more broadly as a rapid diagnostics tool. Several bioinformatics pipelines have been developed to handle HTS data with a focus on plant virus and viroid detection. However, there is a need for an integrative tool that can simultaneously detect a wider range of other plant pathogens in HTS data, such as bacteria (including phytoplasmas), fungi, and oomycetes, and this tool should also be capable of generating a comprehensive report on the phytosanitary status of the diagnosed specimen. RESULTS: We have developed an open-source bioinformatics pipeline called PhytoPipe (Phytosanitary Pipeline) to provide the plant pathology diagnostician community with a user-friendly tool that integrates analysis and visualization of HTS RNA-seq data. PhytoPipe includes quality control of reads, read classification, assembly-based annotation, and reference-based mapping. The final product of the analysis is a comprehensive report for easy interpretation of not only viruses and viroids but also bacteria (including phytoplasma), fungi, and oomycetes. PhytoPipe is implemented in Snakemake workflow with Python 3 and bash scripts in a Linux environment. The source code for PhytoPipe is freely available and distributed under a BSD-3 license. CONCLUSIONS: PhytoPipe provides an integrative bioinformatics pipeline that can be used for the analysis of HTS RNA-seq data. PhytoPipe is easily installed on a Linux or Mac system and can be conveniently used with a Docker image, which includes all dependent packages and software related to analyses. It is publicly available on GitHub at https://github.com/healthyPlant/PhytoPipe and on Docker Hub at https://hub.docker.com/r/healthyplant/phytopipe .

First report of three bunya-like viruses, apple luteovirus 1, and apple hammerhead viroid in apples from Hakkari, Türkiye.

Türkiye is a major apple fruit producer in the crossroads of Europe and the Middle East. Several reports have described the presence of multiple viruses affecting apple production in Türkiye, including apple stem grooving virus (ASGV), apple stem pitting virus (ASPV), apple chlorotic leafspot virus (ACLSV), and apple mosaic virus (ApMV) (Kurçman 1977; Fidan 1994; Çaglayan et al. 2003). However, there are no reports of the presence of the recently discovered bunya-like viruses citrus concave gum-associated virus (CCGaV), and apple rubbery wood viruses 1 and 2 (ARWV1 and 2), as well as apple luteovirus 1 (ALV-1), and apple hammerhead viroid (AHVd) in Türkiye, all of which have been previously reported in other apple-producing countries (Wright et al. 2018; Liu et al. 2018; Zhang et al. 2014). Leaves from one Gala, two Granny Smith, and one Golden Delicious apple trees showing mild symptoms of curling, chlorosis, and yellowing were collected from four different orchards in the province of Hakkari, southeast Türkiye during June 2022 and sent to USDA APHIS Plant Germplasm Quarantine Program (under permit) for virus and viroid HTS-based diagnostics. Total RNA was isolated using the RNeasy Plant Mini Kit (Qiagen) following the manufacturer's guidelines to prepare RNAseq libraries using the TruSeq Stranded Total RNA Library Plant Kit (Illumina, Inc) as described in Malapi-Wight et al. (2021). Libraries were sequenced on the NextSeq500 sequencer (PE 2x75), and approximately 45 million reads were obtained per each sample on average. Bioinformatic analysis was performed as described in Costa et al. (2022) using Phytopipe, where unclassified pathogen-derived reads were de novo assembled and contigs were compared to the NCBI viral nucleotide and protein databases by BlastN and BlastX respectively using a 10-4 e-value cutoff. Nearly complete genome contigs were obtained for ACLSV (OR640150) and ASPV (OR640151) in all four samples and for ASGV (OR640152) in 3 of the 4 samples. The average BlastN identity to sequences in GenBank was 92.3% for ACLSV, ranging from 89-94 %. BlastN identity for ASPV was 86%, ranging from 81-92 % while the ASGV average BlastN identity was 98.2%. Nearly complete genomes with average genome coverage of 92.4% and 95.6% for RNA1 and RNA2 of CCGaV (OR640153 and OR640154), were found in two of the four samples with BlastN identity of 94.7% and 94.8% to GenBank sequences. Additionally, nearly complete genome of the large (L), medium (M), and small (S) segments for ARWV1 were found in two samples with average genome coverage of 99.9%, 99.4%, and 100% respectively and BlastN identity of 98.8%, 95.2%, and 98.4% (OR640155, OR640156, OR640157). ARWV2 contigs were also found in 1 sample where M and S segments had a coverage of 99.8% and BlastN identity of 95.4% (OR640158 and OR640159). The nearly complete genome of ALV-1 was also found in two of four samples with genome coverage of 94.1% and an average BlastN identity of 93.4% (OR640160). AHVd was found in one of the Granny Smith trees with 19,260 mapped reads to the reference GenBank MH049335.1 and identity of 98.3% (OR640149). The HTS findings of CCGaV, ARWV1, ARWV2, and ALV-1, from Türkiye were later confirmed by Sanger sequencing using custom-designed primers targeting the coat protein, the RNA-dependent RNA polymerase, or ~390bp for the AHVd genome (Supplementary Table 1). To further learn about the incidence of these agents, we tested 12 other apple samples from six different neighboring orchards and found them at 18.8% rate for CCGaV, 12.5% for both ARWV1 and ARWV2, 25% for ALV-1, and 37.5% for AHVd respectively. To our knowledge, this is the first report of the apple viruses CCGaV, ARWV1, ARWV2, and ALV-1, and the AHVd viroid in Türkiye. Further studies of the impact of these agents on orchard's health are necessary, including their prevalence in high apple production regions of Türkiye.