Comparing RT-PCR of individual samples with high throughput sequencing of pooled plant samples for field-level surveillance of viruses in blackberry and wild Rubus.

Blackberry production is increasing in the southeastern U.S. with the availability of new cultivars. In addition to high production costs, growers are challenged by virus diseases. Blackberry yellow vein disease (BVYD) significantly limits blackberry production. BYVD is associated with the crinivirus blackberry yellow vein-associated virus (BYVaV) in mixed infections with other viruses. The specific disease etiology and ecological factors underlying BYVD are not well understood and rely on the effective diagnosis of several viruses involved in the complex. In 2021, we collected samples from blackberry plants showing BYVD symptoms, asymptomatic blackberry plants, and wild Rosaceae spp. from nine farms across South Carolina, for a total of 372 individual plant samples. RNA from individual samples was isolated and pooled into sample groups (i.e., symptomatic, asymptomatic, and wild) from each farm for a total of 24 pooled samples. We sequenced the pooled RNA using Illumina and analyzed sequence profiles using the Virtool bioinformatics application. We also tested each plant for six viruses by RT-PCR or RT-qPCR and compared plant (PCR)-level and field (high throughput sequencing (HTS))-level data. Virtool detected 17 known viruses in the pooled samples, including 11 blackberry viruses. PCR testing was mostly consistent with HTS, with some notable disagreements for specific viruses. Our study demonstrates that HTS could be used as an efficient tool to detect viruses in bulked samples in blackberry fields, though limitations to using HTS for field-level surveillance are also discussed here.

First report of soybean root rot caused by Fusarium falciforme in the Republic of Korea.

Phytopathogenic Fusarium species causing root and stem rot diseases in susceptible soybean (Glycine max (L.) Merrill) are a major threat to soybean production worldwide. Several Fusarium species have been reported to infect soybean plants in the Republic of Korea, including F. solani, F. oxysporum, F. fujikuroi, and F. graminearum (Cho et al., 2004; Choi et al., 2019; Kang et al., 2020). During the nationwide survey of soybean diseases in 2015, soybean plants showing symptoms of leaf chlorosis, wilting, and shoot death were found in soybean fields in Seosan, Chungnam. Fusarium isolates were obtained from the margins of sterilized necrotic symptomatic and asymptomatic regions of the stem tissues of diseased samples by culturing on potato dextrose agar (PDA). To examine the morphological characteristics, isolates were cultured on PDA at 25°C in the darkness for 10 days. Colonies produced white aerial mycelia with apricot pigments in the medium. Macroconidia were hyaline, slightly curved in shape with 3 or 4 septa, and their average length and width were 34.6± 0.56 µm (31.4 to 37.8 µm) and 4.7±0.16 µm (4.1 to 5.8 µm), respectively (n = 20). Microconidia were elongated, oval with 0 or 1 septum, and their average length and width were 11.4±0.87 and 5.2±0.32 µm, respectively (n = 20). The colonies and conidia exhibited morphological similarities to those of F. falciforme (Xu et al., 2022). Using the primers described by O'Donnell et al. (2008), identity of a representative strain '15-110' was further confirmed by sequencing portions of two genes, the translation elongation factor 1-alpha (EF-1α) and the second largest subunit of RNA polymerase II (RPB2). The two sequences (GenBank accession No. OQ992718 and OR060664) of 15-110 were 99% similar to those of two F. falciforme strains, 21BeanYC6-14 (GenBank accession nos. ON375419 and ON331931), and 21BeanYC6-16 (GenBank accession nos. ON697187 and ON331933). To test the pathogenicity, a single-spore isolate was cultured on carnation leaf agar (CLA) at 25℃ for 10 days. Pathogenicity test was performed by root-cutting assays using 14-day-old soybean seedlings of 'Daewon' and 'Taekwang'. Ten-day-old mycelia of 15-110 were collected from the CLA plates by scraping with distilled water, and the spore suspension was filtered and diluted to 1 × 106 conidia/mL. The roots of the soybean seedlings were partially cut and inoculated by soaking in the diluted spore suspension for two hours. The seedlings were then transplanted into 12 cm plastic pots (11 cm in height) and grown in a growth chamber at 25°C, 14h light/10h dark for 2 weeks. The infected plants exhibited wilting, observed brown discoloration on the root, and eventually died within 2 weeks, whereas the control plants inoculated with sterile water remained healthy. F. falciforme 15-110 was reisolated from infected plants, but not from the uninoculated controls. The morphology of the re-isolated fungus on PDA and its target gene sequences were identical to those of the original colony. To the best of our knowledge, this is the first report of root rot in soybean caused by F. falciforme in the Republic of Korea. Fusarium spp. induce a range of diseases in soybean plants, including root rot, damping-off, and wilt. Given the variable aggressiveness and susceptibility to fungicides among different Fusarium species, it is imperative to identify the Fusarium species posing a threat to soybean production. This understanding is crucial for developing a targeted and tailored disease management strategy to control Fusarium diseases.

A rotary transformer cross-subject model for continuous estimation of finger joints kinematics and a transfer learning approach for new subjects.

Introduction: Surface Electromyographic (sEMG) signals are widely utilized for estimating finger kinematics continuously in human-machine interfaces (HMI), and deep learning approaches are crucial in constructing the models. At present, most models are extracted on specific subjects and do not have cross-subject generalizability. Considering the erratic nature of sEMG signals, a model trained on a specific subject cannot be directly applied to other subjects. Therefore, in this study, we proposed a cross-subject model based on the Rotary Transformer (RoFormer) to extract features of multiple subjects for continuous estimation kinematics and extend it to new subjects by adversarial transfer learning (ATL) approach. Methods: We utilized the new subject's training data and an ATL approach to calibrate the cross-subject model. To improve the performance of the classic transformer network, we compare the impact of different position embeddings on model performance, including learnable absolute position embedding, Sinusoidal absolute position embedding, and Rotary Position Embedding (RoPE), and eventually selected RoPE. We conducted experiments on 10 randomly selected subjects from the NinaproDB2 dataset, using Pearson correlation coefficient (CC), normalized root mean square error (NRMSE), and coefficient of determination (R2) as performance metrics. Results: The proposed model was compared with four other models including LSTM, TCN, Transformer, and CNN-Attention. The results demonstrated that both in cross-subject and subject-specific cases the performance of RoFormer was significantly better than the other four models. Additionally, the ATL approach improves the generalization performance of the cross-subject model better than the fine-tuning (FT) transfer learning approach. Discussion: The findings indicate that the proposed RoFormer-based method with an ATL approach has the potential for practical applications in robot hand control and other HMI settings. The model's superior performance suggests its suitability for continuous estimation of finger kinematics across different subjects, addressing the limitations of subject-specific models.

Toward Patient Centricity: Why Do Patients With Inflammatory Bowel Disease Participate in Pharmaceutical Clinical Trials? A Mixed-Methods Exploration of Study Participants.

Background: A better understanding of motivations to participate as well as recommendations to reduce barriers to enrollment may assist in design of future clinical trials. Methods: We developed a 32-item electronic questionnaire to explore motivations, experiences, and recommendations of inflammatory bowel disease patients, who had participated in pharmaceutical clinical trials in a tertiary center in Canada over the last decade. We employed a mixed-methods approach that integrates both quantitative and qualitative research methods. Results: We distributed a total of 69 e-mails with surveys and received 46 responses (66.6% response rate). Study participants were mostly male (27/46, 58.7%), non-Hispanic White (43/46, 93.5%), with a mean age of 45.5 years (SD 10.9). Most decided to participate in a clinical trial to benefit future patients (29/46, 63.0%). Half of the participants (23/46, 50.0%) reported they were worried about the possibility of receiving placebo, although the majority (29/46, 63.0%) understood they could improve on placebo. The most challenging aspect reported was the number and length of questionnaires (15/46, 32.6%), as well as the number of colonoscopies (14/46, 30.4%). Strategies recommended to increase enrollment were reduction of the chance of receiving placebo (20/46, 43.5%), facilitating inclusion of patients who have failed multiple therapies (20/46, 43.5%), allowing virtual visits (18/46, 39.1%), including subtypes of disease traditionally excluded from trials (16/46, 34.8%) and improving outreach to underrepresented populations (13/46, 28.3%). The vast majority (37/46, 80.4%) reported their experience of participation to be better than expected. Conclusions: These results should help inform the design of future clinical trials with a focus on patient-centricity.

Molecular-Phylogenetic Characterization of Xanthomonas hortorum pv. pelargonii Strains Causing Leaf Spot of Geraniums in Iran.

Bacterial blight and leaf spot of geraniums is a destructive disease of cultivated Pelargonium species around the world. During 2020-2021, surveys were conducted in seven geranium-growing provinces of Iran to monitor the status of bacterial blight and leaf spot disease. The disease was observed in six surveyed provinces varying in the extent of occurrence and severity. Twenty-two Gram-negative pale-yellow bacterial strains resembling members of Xanthomonas were isolated from symptomatic leaves and stems. Pathogenicity and host range assays showed that the bacterial strains were pathogenic on Pelargonium grandiflorum, P. graveolens, P. peltatum, and P. zonale. All strains were positive for PCR test using the primer pair XcpM1/XcpM2 which is specific for Xanthomonas hortorum pv. pelargonii. Phylogenetic analysis using the sequences of gyrB and lepA genes showed that the 22 strains clustered in a clade among the sequences of X. hortorum pv. pelargonii strains retrieved from the GenBank, while distinct from the other pathovars of X. hortorum. BOX-PCR-based fingerprinting using BOX-A1R primer revealed that the strains isolated in this study were grouped into two clusters while no distinct correlation was observed between the host/area of isolation and BOX-PCR fingerprinting. None of the strains obtained in this study nor reference strain of the pathogen did produce bacteriocin against each other. Results obtained in this study shed light on the geographic distribution, taxonomic status and host range of the bacterial blight and leaf spot pathogen of geraniums in Iran, paving the path of further research on disease management.

Detection of Beet curly top virus in Solanum jamesii, Artemisia tridentata, Helianthus annuus, and Cannabis sativa in Utah.

Historically, beet curly top virus (BCTV; Geminiviridae, Curtovirus) is known for destroying the sugar beet industry in Utah and has been a persistent problem in the state since then (Ball, 1917). Starting in June of 2022, we began identifying plants in San Juan County, Utah with chlorosis and leaf curling. Of note, Solanum jamesii, the Four Corners potato, Artemisia tridentata, big sagebrush, and Helianthus annuus, common sunflower, were found with general chlorosis, severe leaf curling and in the case of the sage brush, completely lacking in smell whereas nearby sage plants without the yellowing were intensely fragrant. In August 2023, Cannabis sativa plants for hemp production were found with severe leaf curling in Juab County, Utah. Samples were collected and stored at -80°C for future work. DNA was extracted using the IBI Genomic Plant DNA kit (IBI Scientific, Dubuque, IA) and subjected to rolling circle amplification using Phi29 polymerase (NEB, Ipswich, MA). The primer set BCTV2 (Strausbaugh et al. 2008) for BCTV detection was then used on a subset of the RCA-positive samples for either one (A. tridentata, H. annus, and S. jamesii) or two (C. sativa) plants displaying classic BCTV symptoms, to amplify a 518 bp region. This amplicon was then sequenced by the Sanger method to a 4x coverage. The resulting sequences (accession nos. OR698900 to OR698904) share 98.94 to 99.80% nucleotide identity to the Worland strain (accession no. KU892789.1) for all samples. To confirm the detection, a triple antibody sandwich ELISA kit from Nano Diagnostics (San Jose, CA) was used on these, and other plants of similar species and symptoms from across the state. Samples that tested positive include 3/3 symptomatic H. annuus plants, 1/1 symptomatic S. jamesii, 3/3 symptomatic A. tridentata. The A. tridentata samples were collected from Juab, San Juan, and Utah Counties. None of three asymptomatic A. tridentata plants tested were ELISA positive. Of the C. sativa plants tested by ELISA, 9/9 of the plants displaying classic BCTV symptoms in that host were positive and 6/6 of the plants without classic BCTV symptoms were ELISA positive. The findings of these novel hosts indicate the need for increased testing and analysis of economically relevant crops and native flora across the state. These findings represent a concern for conservation in the case of S. jamesii and a potential threat to the growing hemp industry in the state due to the severity of BCTV symptoms on these plants. Additionally, the finding of A. tridentata as a host may represent a significant finding for the epidemiology of BCTV in the Mountain West region as A. tridentata is distributed from Mexico to Canada along the Rocky Mountain range and is found in much of the Western US in arid regions. This is the first report, to our knowledge, of S. jamesii and A. tridentata as hosts for BCTV and the first peer reviewed reports for H. annuus and C. sativa as hosts for BCTV in Utah.

First Report of Powdery Mildew Caused by Podosphaera xanthii on Acalypha indica in China.

Acalypha indica L. is an annual erect herb of the Euphorbiaceae family. This plant is found widely in the tropics and parts of Africa and Asia (Chakraborty et al. 2023). In China, A. indica is a vegetable and also used as a folk medicine due to its antipyretic and hemostatic, antibacterial and anti-inflammatory properties. In February 2022 and 2023, powdery mildew symptoms were observed on 70% of A. indica plants on the Hainan Medical University campus (19° 58' 53″ N; 110° 19' 47″ E) in Haikou, Hainan Province, China. Powdery mildew colonies covered the leaf surfaces and stems of affected plants, causing discoloration and defoliation. Mycelia were superficial and hyphal appressoria were nipple-shaped. Conidiophores (n =30) were unbranched, cylindrical, 66 to 150 × 10 to 15 µm, and produced three to five immature conidia in chains with a crenate outline. Foot cells (n =30) were cylindrical, straight or sometimes curved at the base, and 31 to 59 µm long. Conidia (n =100) were ellipsoid-ovoid to doliiform, 20 to 33 ×12 to 20 µm (length/width ratio = 1.3 to 2.4), with well-developed fibrosin bodies, and produced germ tubes from the lateral position. Based on these morphological characteristics, the pathogen was provisionally identified as Podosphaera xanthii (Braun and Cook 2012). The teleomorph was not observed. A specimen was deposited in the Hainan Medical University Plant Pathology Herbarium as HMAI-23. To confirm the genus identification and ascertain a putative species, genomic DNA was extracted from mycelium, conidiophores, and conidia using a fungal DNA kit (Omega Bio-Tek, USA). The rDNA internal transcribed spacer (ITS) region was amplified with primers ITS1/ITS4 (White et al. 1990) and sequenced directly. The resulting 575-bp sequence was deposited in GenBank (accession no. OR775733). A BLASTn search in GenBank of this sequence showed 99% similarity with the ITS sequences of P. xanthii on plants of Fabaceae, Malvaceae and Cucurbitaceae family from China (MH143485, MT242593, MK439611 and MH143483), Thailand (LC270779 and LC270778), Korea (MG754404), Vietnam (KM260704), and Puerto Rico (OP882310). Additionally, the 28S rDNA region was amplified using the primer pairs NL1 and NL4 (O´Donnell 1993; accession no. OR784547). This region shared 99% similarity with P. xanthii isolates (LC371333, LC270780, AB936277, and OP765401) as well. To confirm pathogenicity, five healthy potted plants of A. indica were inoculated by gently pressing a powdery mildew-infected leaf onto 15 young leaves. Five non-inoculated plants served as controls. All plants were maintained in a greenhouse at 24 to 30°C, 70% relative humidity, with a 16-h photoperiod. After 7 days, inoculated leaves showed powdery mildew symptoms whereas no symptoms were observed on control plants. The fungal colonies observed on inoculated plants were morphologically identical to those found on the originally infected leaves collected from Hainan Province. Based on the morphological characteristics and molecular identification, the fungus was identified as P. xanthii. In different countries and regions, P. xanthii has been previously reported on A. indica from Sudan and India (Amano 1986). To our knowledge, this is the first record of P. xanthii infecting A. indica in China. We are concerned that the pathogen could become a threat to the widespread planting of A. indica in the future.

First report of leaf blight caused by Stemphylium lycopersici on Salvia splendens in China.

Salvia splendens is a popular ornamental plant in China with extensive potentials, including value in traditional Chinese medicine and in environmental restoration function (Li et al. 2008). In September 2019, leaf blight disease was observed on road side plants of S. splendens in Bayi park, Nanchang city, Jiangxi province, China. The typical symptoms appeared as irregular necrotic spots or leaf blight, accompanied by extensive scorch necrosis or ultimately defoliation. Small segments cut from diseased leaves were surface sterilized in a 2% sodium hypochlorite solution for 2 min and rinsed three times with sterile distilled water. Then, the samples were placed on potato dextrose agar (PDA) plates incubated at 25°C in darkness. Pure cultures were obtained by the hyphal tip method. Morphologically, all 11 colonies were identical to each other on PDA. Two strains, YZU 191468 and YZU 191481, were selected for further study and deposited in the Fungal Herbarium of Yangtze University (YZU), Jingzhou, Hubei, China. The 7-day-old colonies were circular, 53 to 56 mm in diameter, and consisted of white mycelium with a buff margin, and were cinnamon colored in the center of the reverse side. To examine conidial morphology, the mycelium was transferred onto potato carrot agar (PCA) and incubated at 23°C with a period of 8 h light/16 h dark for 7 days. Conidia were normally solitary or two in a chain, ellipsoid or long ellipsoid, beakless, 10 to 23×30 to 60 µm in size (n=50). Based on morphology, the isolates were consistent with Stemphylium lycopersici (Yamamoto 1960). To confirm the identification, genomic DNA was extracted from both isolates and used to amplify the internal transcribed spacer rDNA region (ITS), glyceraldehydes-3-phosphate dehydrogenase (GAPDH) and calmodulin (CAL) genes with primer pairs ITS5/ITS4, gpd1/gpd2, and CALDF1/CALDR2, respectively (Woudenberg et al. 2017). Sequences were deposited in GenBank with accession numbers OP564983 and OP564984 (ITS), OP892529 and OP892530 (GAPDH), OP584970 and OP584971 (CAL). A neighbor-joining tree was constructed with Mega 7.0 based on the combined dataset with 1,000 bootstrap replicates. The resulting phylogenetic tree showed that the strains from S. splendens clustered with S. lycopersici (CBS 122639 and CBS 124980) supported with 100% bootstrap values. The molecular analyses confirmed that the species causing leaf blight symptoms was S. lycopersici. To test pathogenicity, healthy leaves of S. splendens were surface sterilized and inoculated by mycelium blocks (6 mm in diameter) and spore suspension (1×106 spore/mL) of representative strains YZU 191468 and YZU 191481, respectively. Controls were inoculated with blocks of PDA and sterile water. Each strain was inoculated on three leaves of a plant. One clean plant was used as control. The test was replicated three times. After inoculation, the plants were covered with plastic bags and incubated in a greenhouse (25℃, 80 % relative humidity, 8 h light/16 h dark). After 5 days, the inoculated leaves exhibited dark brown spots with white mycelium, followed by withering of necrotic tissues. There were no symptoms observed on the controls. The fungal isolates inoculated leaves had the same morphological characteristics as the strains used for inoculation. S. lycopersici has been found on eggplant and Zinnia elegans in China (He et al. 2019; Yang et al. 2017). To the best of our knowledge, this is the first report of S. lycopersici causing leaf blight on S. splendens in China. This finding offers a new reference for the management and control of S. splendens leaf diseases in China.

First Report of Anthracnose on Euonymus japonicus Thunb. Caused by a Provisionally Novel Species of Colletotrichum in the Magnum Complex in South Korea.

Euonymus japonicus Thunb., also known as the evergreen spindle tree, is an evergreen tree, which is widely planted as a hedge plant along streets in South Korea. In April 2022, severe anthracnose symptoms were observed on the leaves of this tree in Jangsu in the Jeonbuk Province of the country (35°43'49.44″N, 127°34'53.7″E). About 80% of the leaves of each affected tree within a 0.03-ha area showed incidence of the disease on approximately 30 trees were planted along the roadside (~30 m). These symptoms typically included circular or irregularly shaped whitish-gray lesions with a diameter of 2.0 to 3.0 cm. In cases where some leaves were severely affected, larger blotches formed. To isolate the pathogen, about ten leaves showing anthracnose symptoms on each tree were randomly selected and brought to the laboratory. Fungal isolations were made from acervuli filled with conidial masses on infected evergreen tissues, followed by plating onto 2% potato dextrose agar (PDA) as well as incubated at 25℃. On the PDA, colonies were circular, raised, green-grey or dark grey, and had a distinct white margin. The conidia were single-celled, transparent, cylindrical with rounded ends, had smooth walls, with a length ranging from 12 µm to 16.7 µm and a width raging from 4 µm to 6.5 µm (av. = 14.1 X 5.0 µm, n=40). Of those that were successfully recovered with approximately 90% frequency, two monoconidial isolates were deposited to the culture collection at Chungnam National University in South Korea (Accession number: CDH059-060). To ensure the identity of the fungus, genomic DNAs were extracted from the selected isolates, CDH059-060, and were sequenced. This was achieved based on partial sequences of the internal transcribed spacer (ITS), actin and beta-tubulin (TUB2) gene regions which were amplified using ITS1F / ITS4 (Gardes and Bruns 1993; White et al. 1990), ACT-512F / ACT-783R (Carbone and Kohn 1999), and T1 / Bt2b (O'Donnell and Cigelnik 1997; Glass and Donaldson 1995) primer pairs, respectively. The resulting sequences were deposited to GenBank (OR984424-425) for ITS, (OR996289-290) for actin, and (OR996291-292) for TUB2. For a phylogenetic analysis, sequences from different gene regions (ITS, actin and TUB2) retrieved from GenBank were aligned, concatenated, and analyzed as a single dataset based on a maximum likelihood analysis. The phylogenetic result revealed that the fungus isolated in this study was positioned in a clearly distinct lineage, provisionally representing an undetermined species of Colletotrichum, which is most closely related to Colletotrichum liaoningense (Y.Z. Diao, C. Zhang, L. Cai & X.L. Liu, CGMCC3.17616 (KP890104 for ITS, KP890097 for actin, and KP890111 for TUB, Diao et al. 2017). Sequence comparisons revealed that this pathogen differed from C. liaoningense at 20 of 494 characters (∼4.0%) in the ITS and 2 of 251 (∼1.0%) in the actin sequences. For pathogenicity tests, three seedlings of E. japonicus were used. The leaves for each tree were treated with 10 ml of a conidial suspension by spraying (1x106 conidia ml-1 of the isolate, CDH059), while the three seedlings were treated with distilled water as control. After sprayed, the treated areas were sealed with plastic bags for a day to maintain humidity. Anthracnose symptoms identical to those observed in the field appeared seven days after inoculations, while no symptoms were observed in the control. Re-isolations were successfully achieved from the treatments, fulfilling Koch's postulates. Anthracnose associated with the provisionally novel species of Colletotrichum sp. on E. japonicus has not been recorded elsewhere, and in this regard, this is the first report of anthracnose caused by Colletotrichum sp. on E. japonicus in Korea. To effectively control the disease, more attention should be paid to the host range of the pathogen and other regions where the disease caused by the pathogen might occur in the country.

First Report of Tomato Yellow Mottle-Associated Virus Infecting Tobacco in China.

Tomato yellow mottle-associated virus (TYMaV) belongs to the genus Cytorhabdovirus in the family Rhabdoviridae and has been reported to infect a variety of Solanaceae crops, such as Solanum lycopersicum, S. nigrum, Capsicum annuum and Nicotiana benthamiana (Li et al. 2022, Li et al. 2023, Xu et al. 2017, Zhou et al. 2019). In August 2022, about 500 out of 2000 tobacco (N. tabacum) plants showing leaf distortion, crinkling and mosaic symptoms were found in one tobacco growing field in Xingren City, Guizhou Province, China. To identify the causal pathogen(s), leaves from 20 symptomatic tobacco plants were collected and pooled to perform small RNA deep sequencing (sRNA-Seq) and assembly. Briefly, total RNA was extracted with TRIzol Reagent (Takara, Kusatsu, Japan). A small RNA cDNA library was constructed by the small RNA Sample Pre Kit. sRNA-Seq was performed with an Illumina NovaSeq 6000 platform. About 29 million reads were obtained and 334 contigs generated after removal of host-derived sequences. Among them, 31 unique contigs mapped to the TYMaV genome (NC_034240.1), covering 28.43% of the genome with the mean read coverage of 0.92%. Meanwhile, 226 contigs mapped to the genome of a potyvirus, chilli veinal mottle virus (ChiVMV, NC_005778.1), covering 88.79% of the genome with the mean read coverage of 0.83%. To verify the sRNA-Seq result for TYMaV identification, reverse transcription (RT)- PCR was performed with specific primers TYMaV-F (5'-CTGACGTAGTGTTGGCAGAT-3') and TYMaV-R (5'-AACCTCCATGCAGAACCATGG-3'). The expected-size 936-bp fragment was amplified from total RNA of all 20 samples. Dot enzyme-linked immunosorbent assays (Dot-ELISA) with antibody for TYMaV (kindly provided by Dr. Zhenggang Li from Guangdong Academy of Agricultural Sciences) were performed and further verified TYMaV infection. In addition, five asymptomatic tobacco plants from the same field as controls were used to detect TYMaV by RT-PCR and Dot-ELISA, and all samples showed negative test results. Subsequently, 17 primer pairs (Supplementary Table 1) were used to obtain the full-length sequence of TYMaV from a single positive tobacco sample by RT-PCR, followed by Sanger sequencing at Sangon Biotech (Shanghai, China). The resulting amplicon sequences were assembled into a nearly full-length genome sequence of a TYMaV isolate from tobacco in Guizhou (TYMaV-GZ). BLASTn analysis of the 13, 393 nt-long sequence (GeneBank accession number, PP444718) revealed 84.7% and 87.2% nt sequence identity with the TYMaV tomato isolate (KY075646.1) and the TYMaV S. nigrum isolate (MW527091.1), respectively. Moreover, five S. nigrum plants showing leaf crinkling and mosaic symptoms from tobacco fields tested positive for TYMaV by RT-PCR assay, suggesting a potential spread of TYMaV between tobacco and S. nigrum, which may serve as a reservoir for the virus in the tobacco fields. However, the transmission route of TYMaV remains unknown, and further verification is needed. To our knowledge, this is the first report of TYMaV infecting tobacco crop in China. It will be important to assess the potential economic importance of TYMaV to tobacco production in China and elsewhere, and to elucidate the respective roles of this virus and ChiVMV in the leaf distorting and yellowing symptoms.

First Report of Globisporangium (Pythium) mastophorum causing Damping-off / Root Rot on Parsley in Slovenia.

Pythium-like species cause damping-off symptoms of various hosts, including umbelliferous crops. In April 2023, parsley plantlets (Petroselinum crispum), showing stunted growth, yellowing, decayed roots and damping-off, were obtained from a nursery in central Slovenia, where parsley was grown in polystyrene trays in a greenhouse. Nearly 30% of plants were symptomatic. Sampled roots of ten plants contained ornamented oogonia (avg. 33.3 ± 1.4 µm in diam) with conical projections (5.2 ± 0.5 µm long) (Figure S1 A, B) in microscopically analyzed squash mounts. The pathogen was isolated from root pieces treated for surface disinfection with 0.5% sodium hypochlorite for 30 s, and washed with sterile water. Four 1-2 mm root pieces were taken from each of 10 plants, plated on the selective medium P5ARP, and incubated at 21 °C. Mycelia emerging from root pieces were transferred to carrot piece agar (CPA). Twenty-two equally looking oomycetous colonies were obtained; all sampled plants were infested. Oogonia formed by all colonies were similar to those observed on decayed roots and suggested that Globisporangium (Pythium) mastophorum is the causal disease agent. Analyses of partial ß-tubulin (Kroon et al. 2004) and mitochondrial cytochrome c oxidase I (COI) gene sequences (Robideau et al. 2011) confirmed the identification. Obtained COI (Genbank accession number OR725417) sequence was 100% identical to that from G. mastophorum strain CBS 375.72 (EU350523), whereas the ß-tubulin sequence (OR725416) corresponded to 99.6 % pairwise identity (KJ595502). Further, pathogenicity of an obtained isolate was tested on 4 wk-old curly leaf (cv. Petra F1) parsley. Half of a 7 d-old CPA culture, consisting of mycelium and oogonia, was finely cut and mixed with ca 50 ml of nonsterile commercial substrate (Potgrond H, AGRO-FertiCrop) in each of six 400 ml pots. Pots were filled with ca 300 ml additional substrate, into which 5 parsley seedlings were planted. Control plants were treated equally but with sterile CPA. Plantlets were watered with sterile tap water and held at ambient light conditions and temperature (night 18 °C - day 23 °C). After 14 d, inoculated plants started wilting and yellowing and showed stunted growth. After 21 d, roots were severely decayed and the seedlings damped-off (Figure S1 C). Four pieces each from 10 decayed roots were plated. Thirty-one pieces revealed pythium-like colonies. Obtained isolates were morphologically identical to the strain used for inoculation and identified as G. mastophorum. Control plants developed no foliar or root symptoms and no pythium-like species was obtained. Agricultural advisors observed occurrence of parsley damping-off also in other nurseries in Slovenia what may lead to spreading the pathogen to parsley in production fields and private gardens. The case emphasizes the need for implementing phytosanitary measures in order to eliminate primary inoculum. Reports from field-infected plants showed that G. mastophorum is a pathogen of parsley in Australia (Petkowski et al. 2013) and the USA (Tsuchida et al. 2018), and celery in the Czech Republic (Safránková and Holková 2017). Others isolated G. mastophorum from parsley in The Netherlands (online database of the Westerdijk Fungal Biodiversity Institute, strain CBS 243.86). However, the here described case is, to the best of our knowledge, one of the rare documentations of damping-off due to G. mastophorum in Europe (Safránková and Holková 2017) and the first in Slovenia. Funding: The work was funded by the Ministry of Agriculture, Forestry and Food of Slovenia, and Slovenian Research and Innovation Agency (ARIS Programs P4-0431 and P4-0072).

First Report of Alternaria alternata Causing Leaf Spot on Catalpa bungei in China.

Catalpa bungei originates from China. It is fast-growing and possesses a vertically aligned trunk, rendering it a commendable construction material and a significant economic species. In July 2022, a serious leaf spot occurred in the LanLake farm (surveyed area of about 700 acres) in Nanyang (33°3'23" N, 112°28'50" E), Henan Province, China. The incidence rate of leaf disease reached 54% (n=100). The disease initially manifested as irregular round spots with a yellowish-brown hue, subsequently extending in all directions. Later, the lesion periphery exhibited a darkening effect, leading to yellowing. Twenty diseased leaves were randomly collected and cut into small pieces at the interfaces between infected and healthy tissues. The tissues were sterilized in a solution of 75% ethanol and 1% NaClO for 30 seconds and 1 minute, respectively. After rinsing in sterile water, the pieces were placed on potato dextrose agar (PDA) plates and incubated at 25°C for 5 days. A total of 29 purified fungal strains were acquired, exhibiting comparable phenotypes in terms of morphological characteristics. Three strains (QS1-1, QS1-2, and QS1-3) were isolated for subsequent investigations. The colony exhibited abundant aerial mycelium with shades ranging from dark green to grey-brown on the reverse side. To analyze the morphological characteristics of conidia, potato carrot agar (PCA) was used as the culture medium and incubated at 25°C with a 12-hour light/dark cycle. Conidia were obclavate or spheroidal, dark brown, with 3 to 5 transverse septa, and 1 to 4 longitudinal septa, measuring 12.4 to 36.7 × 4.4 to 9.0 µm (n=100), with conical beak lengths ranging from 0 to 4.3 µm. These morphological traits suggested that the pathogen shares similarities with the Alternaria species. The rDNA internal transcribed spacer (ITS), translation elongation factor 1-alpha gene (tef1), glyceraldehyde 3-phosphate dehydrogenase gene (gapdh), and RNA polymerase II second largest subunit (rpb2) were amplified for further molecular identification. The resultant sequences were submitted to GenBank with the following accession numbers: OR733559, OR742124, OR761873 (ITS), OR939796, OR939797, OR939798 (tef1), OR939801, OR939802, OR939803 (gapdh), and PP054846, PP054847, PP054848 (rpb2). A Phylogenetic tree was constructed of combined genes (ITS, tef1, gapdh, and rpb2) of sequences, alongside the sequences of the type strains by the neighbor-joining method. The three strains formed a clade with the strains CBS 121456 of Alternaria alternata in phylogenetic trees, being separated from other Alternaria spp. The morphological features and molecular analyses supported the strains as members of Alternaria alternata (Woudenberg et al. 2015). To validate pathogenicity, a conidial suspension (106 conidia ml-1) of all three strains was inoculated onto three healthy leaves of five seedlings, with 50 µl of inoculum absorbed with cotton balls. Another group of five plants received sterile water as a control. All plants were incubated in a climate chamber at 28°C and 90% relative humidity. Four days post-inoculation, lesions resembling natural phenomena were observed, whereas control plants showed no symptoms. Subsequent reisolation produced cultures that were morphologically and molecularly identical to the original strains, fulfilling Koch's postulates. Stem canker of C. bungei caused by Phytophthora nicotianae has been reported in China (Chang et al. 2022). This is the first report of A. alternata causing leaf spots on C. bungei in China. Further research is required on management options to control this disease and the host range still needs to be clarified for accurate disease management.

First Report of White Mold Caused by Sclerotinia sclerotiorum on Echeveria gigantea in Mexico.

Echeveria gigantea, native of Mexico (Reyes et al. 2011), holds economic importance as it is marketed as a potted plant and cut flower due to its drought-tolerant capabilities and aesthetic appeal. In September 2023, a field sampling was conducted at the Research Center in Horticulture and Native Plants (18°55'56.6" N, 98°24'01.5" W) of UPAEP University. Echeveria gigantea cv. Quilpalli plants with white mold symptoms were found in an area of 0.5 ha, with an incidence of 40% and severity of 50% on severely affected stems. The symptoms included chlorosis of older foliage, necrosis at the base of the stem, and soft rot with abundant white to gray mycelium and abundant production of irregular sclerotia resulting in wilted plants. The fungus was isolated from 30 symptomatic plants. Sclerotia were collected, sterilized in 3% NaOCl, rinsed with sterile distilled water (SDW), and plated on Potato Dextrose Agar (PDA) with sterile forceps. Subsequently, a dissecting needle was used to place fragments of mycelium directly on PDA. Plates were incubated at 23 °C in darkness. A total of 30 isolates were obtained using the hyphal-tip method, one from each diseased plant (15 isolates from sclerotia and 15 from mycelium). After 6 days, colonies had fast-growing, dense, cottony-white aerial mycelium forming irregular sclerotia of 3.67 ± 1.13 mm (n=100). Each Petri dish produced 32.47 ± 7.5 sclerotia (n=30), after 12 days. The sclerotia were initially white and gradually turned black. The isolates were tentatively identified as Sclerotinia sclerotiorum based on morphological characteristics (Saharan and Mehta 2008). Two isolates were selected for molecular identification. Genomic DNA was extracted using the CTAB protocol. The ITS region and the glyceraldehyde 3-phosphate dehydrogenase (G3PDH) gene were sequenced for two randomly selected isolates (White et al. 1990; Staats et al. 2005). The ITS and G3PDH sequences of the SsEg9 isolate were deposited in GenBank (ITS-OR816006; G3PDH-OR879212). BLAST analysis of the partial ITS (510 bp) and G3PDH (915 bp) sequences showed 100% and 99.78% similarity to S. sclerotiorum isolates (GenBank: MT101751 and MW082601). Pathogenicity was confirmed by inoculating 30 120-day-old E. gigantea cv. Quilpalli plants grown in pots with sterile soil. Ten sclerotia were deposited at the base of the stem, 10 mm below the soil surface. As control treatment, SDW was applied to 10 plants. The plants were placed in a greenhouse at 23 °C and 90% relative humidity. After 16 days, all inoculated plants displayed symptoms similar to those observed in the field. Control plants did not display any symptoms. The fungus was reisolated from the inoculated stems, fulfilling Koch's postulates. The pathogenicity tests were repeated three times. Recently S. sclerotiorum has been reported causing white mold on cabbage in the state of Puebla, Mexico (Terrones-Salgado et al. 2023). To the best of our knowledge, this is the first report of S. sclerotiorum causing white mold on E. gigantea in Mexico. Information about diseases affecting this plant is very limited, so this research is crucial for designing integrated management strategies and preventing spread to other production areas.

First report of citrus leaf blotch virus infecting Forsythia viridissima in China.

Green-stem forsythia (Forsythia viridissima), also known as golden bell, is cultivated widely in China as an early spring flowering shrub. In July 2020, yellow or white vein clearing symptoms on leaves were observed in approximate 15% golden bell plants along a landscape river in Ningbo city, Zhejiang province, China. Symptomatic leaves from six different plants were collected and pooled. Total RNA was extracted from about 200 mg pooled sample using TRIzol Reagent (Invitrogen, Carlsbad, USA) and used for high-throughput sequencing (HTS). The cDNA library was constructed using a TruSeq RNA Sample Preparation Kit (Illumina) and an Illumina NovaSeq 6000 platform was utilized to yield 150 nt paired-end reads. CLC Genomic Workbench 11 (QIAGEN) with default parameters were used for data analysis. A total of 41,604,174 paired-end reads were obtained, and 156,853 contigs (16 - 26,665 nt) were generated de novo and compared with sequences in the NCBI nt and nr database using BLASTn and BLASTx, respectively. A total of 197,277 reads were mapped to the citrus leaf blotch virus (CLBV; genus Citrivirus, family Betaflexiviridae) genome with an average coverage of 3191×. A contig of 8783 nt (excluding the poly(A) tail) was aligned to CLBV isolate Vib (accession No. OP751940) by BLASTn with the highest nt sequence identity of 99.7% and 99% query coverage, suggesting that the samples were infected with CLBV (Myung-Hwi Kim et al. 2023). No other virus was detected by this analysis. Subsequently, leaves of the six plants collected above, three plants with mild chlorotic symptoms and three plants without obvious symptoms were tested separately by RT-PCR and all were positive for CLBV. Sap from multiple symptomatic F. viridissima leaves was mechanically inoculated to Nicotiana benthamiana, N. tabacum and Datura stramonium in sextuplicate, but after two months, none of the inoculated plants had obvious symptoms and all of them tested negative for CLBV using RT-PCR. To determine the genome sequence of CLBV present in F. viridissima, a single sample from one plant was selected for genome validtion. The contig sequence was confirmed by Sanger sequencing of RT-PCR products amplified using CLBV-specific primers, and the 5' terminal sequence of the virus was determined using a commercial SUPERSWITCH RACE cDNA Synthesis Kit (Tiosbio, Beijing, China). The complete genomic sequence of CLBV isolated from F. viridissima was 8787 nts long, excluding the poly(A) tail, has the expected three predicted ORFs and was deposited in the GenBank database (accession no. OR766026). Phylogenetic analysis of different CLBV genome sequences from fruit trees and other hosts in GenBank using MEGA11 showed that the golden bell isolate was most closely related to isolate Vib (OP751940) from Viburnum lentago in South Korea, with which it was almost identical (99.7% complete nt sequence identity and >99% aa sequence identity in each of the three ORFs). Ten viruses have been previously reported from Forsythia spp. (Kaminska, M. 1985; Lee et al. 1997), but this is the first report of CLBV in this host. CLBV mainly infects citrus, kiwifruit and apple causing mosaic, chlorosis or yellow vein clearing symptoms, however, bud union disorder was observed in 'Nagami' kumquat infected by CLBV, which caused serious production losses (Cao et al. 2017; Li et al. 2018; Liu et al. 2019; Galipienso et al. 2001). Therefore, further investigation is needed to assess if F. viridissima can be an intermediate host to transfer CLBV to other crops.

First Report of Stem and Foliage Blight of Chrysanthemum morifolium cv. Fubaiju Caused by Stagonosporopsis chrysanthemi in China.

Chrysanthemum (Chrysanthemum morifolium cv. Fubaiju) is used as medicinal herb (Chen et al. 2020). In October 2021, a leaf spot disease was observed on leaves of C. morifolium in Huanggang, Hubei province. Disease incidence was approximately 40%. Leaf lesions manifested as necrotic spots, coalesced, and expanded to form brown-black spots, leading to wilting of the leaves. On stems, the lesions manifested as dark brown necrotic spots. To identify the pathogen, 29 pieces (5 × 5 mm) from lesion margins were surface sterilized in 1% NaOCl and rinsed three times with sterile water. The pieces were transferred onto potato dextrose agar (PDA) for incubation at 25℃ for 3 d in the dark. Fifteen fungal colonies were successfully isolated. The colony morphology with flat wavy edge, sparse aerial mycelia, and surface olivaceous black were observed at 7 days post incubation. Subglobular pycnidia were brown with a short beak, and pycnidia diameters were thick (212 to 265 × 189 to 363 µm, n = 20). Ovoid conidia were aseptate and hyaline, conidia diameters were thick (4.0 to 9.8 × 1.8 to 4.7 µm, n = 100). The morphological characters of these isolates were consistent with those of Stagonosporopsis chrysanthemi (Zhao et al. 2021). Pure culture of representative HGNU2021-18 isolated from the diseased leaves subjected to molecular identification. Sequences of the rDNA internal transcribed spacer (ITS) region, 28S large subunit ribosomal RNA (LSU), ß-tubulin (TUB2), actin (ACT), and partial RNA polymerase II largest subunit (RPB2) genes were amplified from genomic DNA of isolate HGNU2021-18 using the following primer pairs: ITS1/ITS4 (White et al. 1990), LR0R/LR5 (Rehner et al. 1994), Btub2Fd/Btub4Rd (Woudenberg et al. 2009), ACT512F/ACT783R (Carbone et al.1999), and RPB2-5F2 (Sung et al. 2007)/fRPB2-7cR (Liu et al. 1999), respectively. The PCR products were purified and then sequenced by Sangon Biotech (China). Nucleotide sequences of ITS (544 bp, OM346748), LSU (905 bp, OM758418), TUB2 (563 bp, OM945724), ACT (294 bp, OM793715), and RPB2 (957 bp, OM793716) amplified from the isolate HGNU2021-18 were subjected to BLASTn analysis. The results showed that ITS, LSU, TUB2, ACT, and RPB2 shared 100.00%, 99.45%, 99.20%, 100.00%, and 100.00% sequence identity to the five published sequences (MW810272.1, MH869953.1, MW815129.1, JN251973.1, and MT018012.1, respectively) of the S. chrysanthemi isolate CBS 500.63. Phylogenetic analysis of the multilocus sequences of ITS, LSU, RPB2, ACT, and TUB2 belonging to different Stagonosporopsis species was performed in MEGA 7.0 (Chen et al. 2015). Isolate HGNU2021-18 was placed in a clade with S. chrysanthemi with 99% bootstrap support. Thus, the results of morphological and molecular analyses indicated that the disease symptoms on chrysanthemum plants were caused by S. chrysanthemi. Under conditions of 25°C and 85% relative humidity, pathogenicity test was performed on 2-month-old healthy plants using isolate HGNU2021-18. The leaves were inoculated with 5 mm diameter mycelial plugs or with sterile agar plugs (control). Six plants were used in each treatment. Disease symptoms were observed on treated plants at 2 weeks post inoculation which were those previously observed in the field, while the control plants remained symptomless. The pathogen was re-isolated from the diseased plants, and S. chrysanthemi was confirmed as the causal pathogen. This is the first report of S. chrysanthemi causing stem and foliage blight of chrysanthemum in China.

First report of Candidatus Phytoplasma australasia (16SrII- subgroup D) associated with virescence of Chia (Salvia hispanica L.) from India.

Chia (Salvia hispanica L., Lamiaceae) is an important commercial and medicinal crop recently popularized in India and widely cultivated in Karnataka (Joy et al., 2022). During the field survey of chia crop diseases, characteristic virescence like symptoms were observed at Main Agricultural Research Station, UAS, Raichur as well as at Mysuru and HD Kote region. The incidence was ranged from 2 - 4 per cent in an area of 30 hectares. Typical symptoms associated with chia are malformed shoot and/or inflorescence axis with reduced floral parts with greenish florets. The stem axis become thick, flattened, leaves are reduced towards terminal region. A total of five phytoplasma suspected samples and five suspected healthy samples were used for identification purpose. The Plant Genomic DNA Miniprep Kit (Sigma Aldrich, USA) was used to extract the DNA from five symptomatic and five asymptomatic samples and the DNA was used as template to amplify the phytoplasma-specific 16S rDNA gene using P1/P7 primers (Deng and Hiruki, 1991; Schneider et al., 1995) followed by nested PCR using R16F2n/R16R2 primers (Gundersen and Lee 1996). The expected 1.25-kb amplicon was detected from the suspected symptomatic samples. Nested PCR products were purified and sequenced from both the directions using ABIX370 Genetic Analyzer (Applied Biosystems, Waltham, MA). The analysis revealed that all five sequences shared 100 per cent identity with Candidatus Phytoplasma aurantifolia (OM649850, ON975012) and Tomato big bud phytoplasma (EF193359). The in-silico RFLP pattern of F2n/R2 primed region of 16S rDNA gene analyzed by using iPhyClassifier (Zhao et al. 2009) revealed that the sequence shared 98.72 per cent nucleotide sequence similarity with coefficient value of 1.00 to the reference strain RFLP pattern of 16Sr group II, subgroup D (witches'-broom disease of lime; U15442). Based on 16SrDNA sequences and in-silico RFLP analysis, the phytoplasma associated with the chia virescence was identified as a member of 16SrII-D group. Further, SecA gene was also amplified from the samples using SecAfor1/SecArev3 primer pair (Hodgetts et al., 2008). All samples produced ~400 bp products and sequenced as detailed above. Sequence analysis by nBLAST revealed 100 per cent similarity to Ca. P. australasia (MW020545) and Ca. P. aurantifolia isolate Idukki Kerala 1 (MK726369) both representing 16SrII-D group phytoplasma. The representative sequence (16Sr: PP359693, PP359694; secA:PP386558, PP386559) were deposited in GenBank. Chia virescence phytoplasma belonging to Ca. phytoplasma australasia has not been reported anywhere. The phytopathological studies associated with chia crop are very limited. Joy et al. (2022) reported the occurrence of foot rot disease caused by Athelia rolfsii. Several hosts are recorded to be associated with 16SrII D phytoplasma which includes china aster, eggplant and crotalaria (Mahadevakumar et al., 2017, Yadav et al., 2016a, b). Now the wide occurrence of the phytoplasma in the area might have transmitted by vectors. The occurrence of virescence is of great importance as it affects the overall yield which reduces the market value. To our knowledge, this is the first report of a group 16SrII-D phytoplasma associated with chia virescence in India.

Bidirectional brain-body interactions during natural story listening.

Narratives can synchronize neural and physiological signals between individuals, but the relationship between these signals, and the underlying mechanism, is unclear. We hypothesized a top-down effect of cognition on arousal and predicted that auditory narratives will drive not only brain signals but also peripheral physiological signals. We find that auditory narratives entrained gaze variation, saccade initiation, pupil size, and heart rate. This is consistent with a top-down effect of cognition on autonomic function. We also hypothesized a bottom-up effect, whereby autonomic physiology affects arousal. Controlled breathing affected pupil size, and heart rate was entrained by controlled saccades. Additionally, fluctuations in heart rate preceded fluctuations of pupil size and brain signals. Gaze variation, pupil size, and heart rate were all associated with anterior-central brain signals. Together, these results suggest bidirectional causal effects between peripheral autonomic function and central brain circuits involved in the control of arousal.

Comparing the Performance of Popular Large Language Models on the National Board of Medical Examiners Sample Questions.

INTRODUCTION: Large language models (LLMs) have transformed various domains in medicine, aiding in complex tasks and clinical decision-making, with OpenAI's GPT-4, GPT-3.5, Google's Bard, and Anthropic's Claude among the most widely used. While GPT-4 has demonstrated superior performance in some studies, comprehensive comparisons among these models remain limited. Recognizing the significance of the National Board of Medical Examiners (NBME) exams in assessing the clinical knowledge of medical students, this study aims to compare the accuracy of popular LLMs on NBME clinical subject exam sample questions. METHODS: The questions used in this study were multiple-choice questions obtained from the official NBME website and are publicly available. Questions from the NBME subject exams in medicine, pediatrics, obstetrics and gynecology, clinical neurology, ambulatory care, family medicine, psychiatry, and surgery were used to query each LLM. The responses from GPT-4, GPT-3.5, Claude, and Bard were collected in October 2023. The response by each LLM was compared to the answer provided by the NBME and checked for accuracy. Statistical analysis was performed using one-way analysis of variance (ANOVA). RESULTS: A total of 163 questions were queried by each LLM. GPT-4 scored 163/163 (100%), GPT-3.5 scored 134/163 (82.2%), Bard scored 123/163 (75.5%), and Claude scored 138/163 (84.7%). The total performance of GPT-4 was statistically superior to that of GPT-3.5, Claude, and Bard by 17.8%, 15.3%, and 24.5%, respectively. The total performance of GPT-3.5, Claude, and Bard was not significantly different. GPT-4 significantly outperformed Bard in specific subjects, including medicine, pediatrics, family medicine, and ambulatory care, and GPT-3.5 in ambulatory care and family medicine. Across all LLMs, the surgery exam had the highest average score (18.25/20), while the family medicine exam had the lowest average score (3.75/5).  Conclusion: GPT-4's superior performance on NBME clinical subject exam sample questions underscores its potential in medical education and practice. While LLMs exhibit promise, discernment in their application is crucial, considering occasional inaccuracies. As technological advancements continue, regular reassessments and refinements are imperative to maintain their reliability and relevance in medicine.

Parallel Multilink Group Joint ICA: Fusion of 3D Structural and 4D Functional Data Across Multiple Resting fMRI Networks.

Multimodal neuroimaging research plays a pivotal role in understanding the complexities of the human brain and its disorders. Independent component analysis (ICA) has emerged as a widely used and powerful tool for disentangling mixed independent sources, particularly in the analysis of functional magnetic resonance imaging (fMRI) data. This paper extends the use of ICA as a unifying framework for multimodal fusion, introducing a novel approach termed parallel multilink group joint ICA (pmg-jICA). The method allows for the fusion of gray matter maps from structural MRI (sMRI) data to multiple fMRI intrinsic networks, addressing the limitations of previous models. The effectiveness of pmg-jICA is demonstrated through its application to an Alzheimer's dataset, yielding linked structure-function outputs for 53 brain networks. Our approach leverages the complementary information from various imaging modalities, providing a unique perspective on brain alterations in Alzheimer's disease. The pmg-jICA identifies several components with significant differences between HC and AD groups including thalamus, caudate, putamen with in the subcortical (SC) domain, insula, parahippocampal gyrus within the cognitive control (CC) domain, and the lingual gyrus within the visual (VS) domain, providing localized insights into the links between AD and specific brain regions. In addition, because we link across multiple brain networks, we can also compute functional network connectivity (FNC) from spatial maps and subject loadings, providing a detailed exploration of the relationships between different brain regions and allowing us to visualize spatial patterns and loading parameters in sMRI along with intrinsic networks and FNC from the fMRI data. In essence, developed approach combines concepts from joint ICA and group ICA to provide a rich set of output characterizing data-driven links between covarying gray matter networks, and a (potentially large number of) resting fMRI networks allowing further study in the context of structure/function links. We demonstrate the utility of the approach by highlighting key structure/function disruptions in Alzheimer's individuals.

No Common Candidate Genes for Resistance to Fusarium graminearum, F. proliferatum, F. sporotrichioides, and F. subglutanins in Soybean (Glycine max L.) Accessions from Maturity Groups 0 and I: Findings from Genome-Wide Association Mapping.

Seedling diseases and root rot, caused by species of Fusarium, can limit soybean (Glycine max L.) production in the United States. Currently, there are few commercially available cultivars resistant to Fusarium. This study was conducted to assess the resistance of soybean maturity group (MG) accessions from 0 and I to Fusarium proliferatum, F. sporotrichioides, and F. subglutinans, as well as to identify common quantitative trait loci (QTL) for resistance to these pathogens, in addition to F. graminearum, using a genome-wide association study (GWAS). A total of 155, 91, and 48 accessions from the USDA soybean germplasm collection from maturity groups 0 and I were screened with a single isolate each of F. proliferatum, F. sporotrichioides, and F. subglutinans, respectively, using the inoculum layer inoculation method in the greenhouse. The disease severity was assessed 21 days post-inoculation and analyzed using non-parametric statistics to determine the relative treatment effects (RTE). Eleven and seven accessions showed significantly lower RTEs when inoculated with F. proliferatum and F. subglutinans, respectively, compared to the susceptible cultivar 'Williams 82'. One accession was significantly less susceptible to both F. proliferatum and F. subglutinans. The GWAS conducted with 41,985 single-nucleotide markers identified one QTL associated with resistance to both F. proliferatum and F. sporotrichioides, as well as another QTL for resistance to both F. subglutinans and F. graminearum. However, no common QTLs were identified for the four pathogens. The USDA accessions and QTLs identified in this study can be utilized to selectively breed resistance to multiple species of Fusarium.