Prognostic Effect of Tertiary Lymphoid Structures in Epstein-Barr Virus-Associated Gastric Carcinomas Measured by Digital Image Analysis.

Epstein-Barr virus-associated gastric carcinoma (EBVaGC) is characterized by prominent tumor-infiltrating lymphocytes (TILs) and has a favorable prognosis. Tertiary lymphoid structures (TLS), characterized by ectopic aggregated lymphocytes with high-endothelial venules (HEV), are associated with favorable outcomes in various solid tumors. We hypothesized that EBVaGC, characterized by intense TILs, may be closely associated with TLS or HEV. To test this hypothesis, we digitally analyzed the TLS, HEV, and TILs in 73 surgically resected advanced EBVaGCs. For HEV, dual MECA-79 and CD31 dual immunohistochemistry were performed, and the ectopic expression of MECA-79 in tumor cells was measured. In 73 patients with EBVaGC, a high-TLS ratio was found in 29 (39.7%) cases, high-tumor-associated HEV density in 44 (60.3%) cases, and high-CD8+ TIL density in 38 (52.1%) cases. Ectopic tumor expression of MECA-79 was observed in 36 patients (49.3%) cases. A low-TLS ratio and tumor-associated HEV density were significantly associated with lymph node metastasis (P = .005 and .042, respectively). Ectopic MECA-79 expression was significantly associated with lymph node metastasis (P = .003). Patients with a low-TLS ratio (P = .038), low-HEV density (P = .042), and ectopic tumor MECA-79 expression (P = .032) had significantly worse prognoses. In conclusion, TLS ratio and HEV density affect the survival of patients with EBVaGC and may be related to the immune response that interrupts lymph node metastasis.

Antiviral effects of umbelliferone against viral hemorrhagic septicemia virus in olive flounder (Paralichthys olivaceus).

Viral hemorrhagic septicemia virus (VHSV) poses a significant threat to global aquaculture, prompting ongoing efforts to identify potential drug candidates for disease prevention. Coumarin derivatives have recently emerged as a promising class of compounds effective against rhabdoviruses, which severely impact the aquaculture industry. In this study, we assessed the anti-VHSV activity of umbelliferone (7-hydroxycoumarin) in fathead minnow (FHM) cells and olive flounder Paralichthys olivaceus. Umbelliferone exhibited an EC50 of 100 µg/mL by reducing cytopathic effect, with a maximum cytotoxicity of 30.9 % at 750 µg/mL. Mechanistic analyses via a time-course plaque reduction assay revealed that direct incubation with the virus for 1 h resulted in 97.0 ± 1.8 % plaque reduction, showing excellent direct virucidal activity. Pretreatment for 4 h resulted in a 33.5 ± 7.8 % plaque reduction, which increased with longer incubation times. Cotreatment led to a 33.5 ± 2.9 % plaque reduction, suggesting interference with viral binding, whereas postinfection treatment proved less effective. Umbelliferone was prophylactically administered to the olive flounder through short-term (3 days) and long-term (14 days) medicated feeding, followed by a 4-day postinfection period. Short-term administration at 100 mg/kg body weight (bw)/day resulted in the highest relative percent survival (RPS) of 56 %, whereas long-term administration achieved a maximum RPS of 44 % at 30 mg/kg bw/day. Umbelliferone administration delayed mortality at these doses. Additionally, umbelliferone significantly inhibited the expression of the VHSV N gene during viral challenge, with no observed toxic effects in fish up to an administration dose of 30 mg/kg bw/day for 28 days. Our findings suggest that the protective mechanism of short-term administration of 100 mg umbelliferone against VHSV infection may involve the overexpression of TLR2, MDA5, STAT1, and NF-κB at 24 h postinfection (hpi). IL-8 and IFN II expression was upregulated, whereas TNF-α, IL-1ß, and IFN I expression was suppressed at 24 hpi. The upregulation of ISG15 at 48 hpi may contribute to the inhibition of VHSV replication, whereas the downregulation of Caspase 3 expression at 96 hpi suggests a possible inhibition of virus-induced apoptosis at later infection stages. Overall, umbelliferone exhibited anti-VHSV activity through multiple mechanisms, with the added advantage of convenient administration via medicated feed.

PIK3CA mutation subtype delineates distinct immune profiles in gastric carcinoma.

PIK3CA mutations in cancer regulate tumour immunogenicity. Given that PIK3CA mutation subtypes influence therapeutic responses to AKT inhibitor and that H1047R mutation confers selective growth advantages after immunotherapy, we hypothesised that immune phenotypes may depend on PIK3CA mutation subtypes. We investigated 133 gastric cancers (GCs) harbouring PIK3CA mutation [21 E542K (15.8%), 36 E545X (27.1%), 26 H1047X (19.5%), and 46 others (34.6%)]. Four patients (3.0%) had a combination of mutations (E542K + E545K in 3 patients and E545K + H1047R in 1 patient). Epstein-Barr virus (EBV) and microsatellite instability (MSI) status, PD-L1 (programmed death-ligand 1) combined positive score (CPS), and stromal tumour-infiltrating lymphocytes (TILs) were assessed. Concurrent genomic alterations, GeoMx digital spatial profiling (DSP), and OPAL multiplex immunohistochemistry (mIHC) were analysed, and correlation between the two assays was investigated. Of the 133 PIK3CA-mutant (PIK3CAm ) GCs, MSI-high GC was significantly frequent in the H1047X mutation subtype (p = 0.005), while EBV positivity did not affect the mutation subtypes. There was no significant survival difference between the E542K, E545X, and H1047X subgroups. However, in the subgroup analysis for EBV-positive GC, H1047Xm GC showed a trend towards shorter survival than E542K and E545Xm GC (p = 0.090 and 0.062). With DSP analysis, H1047Xm GC showed elevated VISTA (p = 0.0003), granzyme B (p < 0.0001), CD4 (p = 0.0001), and CD45 (p < 0.0001) expression compared with the E542Km or E545Xm GC subgroups, and only VISTA expression remained significant (p < 0.0001) using OPAL mIHC. DSP and OPAL analyses showed a moderate correlation of CD4 (ρ = 0.42, p = 0.004) and CD8 (ρ = 0.62, p < 0.001) expression levels in a comparison of six antibodies. Immune-related protein expression levels were evident when classified by the three PIK3CA hotspot mutations, and H1047Xm GC showed the highest immune-related protein expression compared with E542Km or E545Xm GC. Our results demonstrated distinct immune profiles in GC with PIK3CA hotspot mutations using GeoMx DSP and OPAL mIHC, and there was a correlation between the two multiplex platforms. © 2023 The Authors. The Journal of Pathology published by John Wiley & Sons Ltd on behalf of The Pathological Society of Great Britain and Ireland.

First Case of Septic Shock Caused by Cetobacterium Somerae.

BACKGROUND: Cetobacterium somerae rarely causes infection in humans. Most studies on C. somerae have analyzed its role in the intestinal system of freshwater fish. METHODS: Herein, we report a case of septic shock caused by C. somerae in an elderly patient. RESULTS: Blood culture revealed growth of a gram-negative, rod-shaped anaerobic bacterium, which was identified as C. somerae through MALDI-TOF analyses. Although C. somerae is a resident species in the gut, it can cause systemic infection, which can be fatal. CONCLUSIONS: When C. somerae is identified, consideration should be given to the possibility of the infection originating from the intestinal tract.

Evaluation of humoral immune response after ChAdOx1 nCoV-19 vaccination among health care workers.

We assessed the immunogenicity of ChAdOx1 nCoV-19 vaccination by evaluating the levels of SARS-CoV-2 IgG after vaccination and investigated the effect of diverse factors such as gender, age, and adverse reactions after vaccination. The study included a total of 1028 serum samples from 452 healthcare workers. SARS-CoV-2 IgG levels were assessed using the SARS-CoV-2 IgG II Quant assay. Participants completed a questionnaire regarding the intensity and duration of adverse reactions after vaccination. The seropositive rates after the first and second doses were 95.5% and 100%, respectively. The median antibody levels after the second dose showed a 4.2-fold increase compared with the first. Five months after the second dose, the median antibody levels decreased by 3.5-fold. The antibody levels in men were lower than those in women after the first dose and were higher after the second dose. There was no difference according to age groups after the first dose, but after the second dose, in subjects aged 50 and above, the rise in antibody levels was less than that in other age groups. The antibody levels among participants with moderate or severe symptoms were significantly higher than those among participants with mild symptoms after the first dose. There were no statistically significant differences according to the duration of symptoms. We could assume that different age groups and genders might have different immunogenicity following vaccination. The intensity of adverse symptoms was positively correlated with the antibody levels, implying that higher immunogenicity is related to the intensity of adverse symptoms after vaccination.

An antiviral optimized extract from Sanguisorba officinalis L. roots using response surface methodology, and its efficacy in controlling viral hemorrhagic septicemia of olive flounder (Paralichthys olivaceus).

Viral hemorrhagic septicemia causes considerable economic losses for Korea's olive flounder (Paralichthys olivaceus) aquaculture farms; therefore, effective antiviral agents for controlling viral hemorrhagic septicemia virus (VHSV) infection are imperative. The present study implemented a Box-Behnken design and cytopathic reduction assay to derive an optimized extract of Sanguisorba officinalis L. roots (OE-SOR) with maximum antiviral activity against VHSV. OE-SOR prepared under optimized extraction conditions (55% ethanol concentration at 50 °C for 5 h) exhibited potent antiviral activity against VHSV, with a 50% effective 0.21 µg/mL concentration and a 340 selective index. OE-SOR also showed direct virucidal activity in the plaque reduction assay. Administering OE-SOR to olive flounder exhibited substantial efficacies against VHSV infection. Fish receiving 100 mg/kg body weight/day of OE-SOR as a preventive (40.0%; p < 0.05) or therapeutic (44.4%; p < 0.05) exhibited a higher relative survival than the untreated VHSV-infected control group (mortalities of 100% and 90%, respectively). In addition, fish fed with OE-SOR (100 mg/kg body weight/day) for two weeks conveyed a significantly higher inflammatory cytokine expression (nuclear factor kappa-light-chain-enhancer of activated B cells [NF-κB], interleukin-1 beta [IL-1ß], and tumor necrosis factor-alpha [TNF-α]) than the control group one to two days post-administration. Moreover, no hematological or histological changes were observed in olive flounder treated with OE-SOR over four weeks. Liquid chromatography-quadrupole-time of flight tandem mass spectrometry and -triple quadrupole tandem mass spectrometry analyses identified ziyuglycoside I as a prominent OE-SOR constituent and marker compound (content: 14.5%). This study verifies that OE-SOR is an effective alternative for controlling viral hemorrhagic septicemia in olive flounder farms as it exhibits efficient in vivo anti-VHSV activity and increases innate immune responses.

In-vitro immunomodulatory responses and antiviral activities of antimicrobial peptide octominin against fish pathogenic viruses.

Antimicrobial peptides (AMPs) are considered a novel approach to stimulate fish antiviral mechanisms for defense against a broad range of viral infections by enhancing immunomodulatory activities. Octominin is an AMP derived from the defense proteins of Octopus minor. In this study, preliminary screening of octominin against viral hemorrhagic septicemia virus (VHSV), infectious hematopoietic necrosis virus (IHNV), and infectious pancreatic necrosis virus (IPNV) was carried out. Moreover, immune responses upon octominin treatment and IHNV challenge were investigated using fathead minnow (FHM) cells. The CC50s of octominin for FHM and Chinook salmon embryo-214 (CHSE-214) cells were 2146.2 and 1865.2 µg/mL, respectively. With octominin treatment, EC50 resulted in 732.8, 435.1, and 925.9 µg/mL for VHSV, IHNV, and IPNV, respectively. The selectivity indices were 2.9, 4.9, and 2.0, respectively. The transcriptional analysis results demonstrated the induced transcription factors (Irf3; 143-fold, Irf7; 105-fold, and NF-κB; 8-fold), stress response gene (HspB8; 2-fold), and apoptosis functional gene (p53; 3-fold) in octominin treated (500 µg/mL) FHM cells for 48 h. Moreover, IHNV viral copy number was slightly decreased with the octominin treatment (500 µg/mL) in FHM cells. Overall results suggest that octominin could be a potential antiviral agent, although further studies are necessary to understand its mode of action and the mechanism of its antiviral activity.

Verification and Establishment of Reference Intervals for Prothrombin Time and Activated Partial Thromboplastin Time for Children in a Clinical Laboratory.

BACKGROUND: Prothrombin time (PT) and activated partial thromboplastin time (aPTT) are routine coagulation tests. The absence of age-dependent reference interval (RI) may lead to abnormal results in children. In this study, we aimed to verify adult-based RIs in children and establish pediatric RIs for PT and aPTT. METHODS: We analyzed PT and aPTT results. Samples from inpatients and outpatients aged 1 - 18 years, considered healthy subjects, were divided into six groups by age. Verification and establishment of RIs were conducted. RESULTS: Applying adult-based RIs to pediatrics was statistically invalid for individuals aged 10 - 18 years for PT and invalid throughout childhood for aPTT. The new RI of PT for individuals aged 10 - 18 years was 11.1 - 14.1 seconds and that of aPTT for individuals aged 1 - 9 years was 28.2 - 46.0 seconds. CONCLUSIONS: Pediatric RIs were higher than adult-based RIs. Using pediatric RI can save time, labor, and costs to make clinical decision.

Anti-LW Confused with Anti-D: a Case Transfused RhD-positive RBCs and Literature Review.

BACKGROUND: Anti-LW is rarely identified, and it is known to have little clinical importance. However, it is often difficult to differentiate anti-LW from anti-D. METHODS: Here, we report a case where anti-LW was identified for pretransfusion testing in a patient suspected of having lymphoma. RESULTS: His blood group was O RhD-positive. Anti-D specificity, weak panreactivity and 2+ reactivity in auto control were shown as a result of antibody identification. The reactions became weaker with DTT-treated RBCs, which confirmed the specificity of an anti-LW. The patient received 8 units of O RhD-positive pRBC before discharge without any transfusion reaction. CONCLUSIONS: In conclusion, anti-LWs may show mimicking specificity of anti-D for antibody identification testing, but their clinical significance is completely different. Therefore, their prompt identification is important.

Successful Treatment of Thrombotic Thrombocytopenic Purpura in a Patient with Mixed Connective Tissue Disease.

BACKGROUND: Although the survival rate of thrombocytopenic purpura (TTP) has increased significantly due to the introduction of therapeutic plasma exchange (TPE). TTP in patients with mixed connective tissue disease (MCTD) has a very high mortality rate and a very small number of reported cases. In TTP, daily TPE is administered until a treatment response is achieved; however, in practice, TPE is often not performed for such long durations. METHODS: We report a case of TTP with MCTD in a female patient. She had developed thrombocytopenia and hemolytic anemia 9 months after delivery. She had status epilepticus and lapsed into a coma. RESULTS: The patient was successfully treated with extended sessions of TPE with corticosteroids and rituximab. CONCLUSIONS: Although the TTP regimen has not yet been established and remains controversial, this report demonstrates the importance of continuing daily TPE until achieving a treatment response.

Performance evaluation of biodegradable polymer sirolimus and ascorbic acid eluting stent systems.

The purpose of this study was to evaluate the performance of biodegradable polymer sirolimus and ascorbic acid eluting stent systems with four commercially available drug-eluting stents (DES). We investigated the characterization of mechanical properties by dimension, foreshortening, recoil, radial force, crossing profile, folding shape, trackability, and dislodgement force. Additionally, we identify the safety and efficacy evaluation through registry experiments. Each foreshortening and recoil of D + Storm® DES is 1.3 and 3.70%, which has better performance than other products. A post-marketing clinical study to evaluate the performance and safety of D + Storm® DES is ongoing in real-world clinical settings. Two hundred one patients were enrolled in this study and have now completed follow-up for up to 1 month. No major adverse cardiovascular event (MACE) occurred in any subjects, confirming the safety of D + Storm® DES in the clinical setting. An additional approximately 100 subjects will be enrolled in the study and the final safety profile will be assessed in 300 patients. In conclusion, this study reported the objective evaluation of DES performance and compared the mechanical responses of four types of DES available in the market. There is little difference between the four cardiovascular stents in terms of mechanical features, and it can help choose the most suitable stent in a specific clinical situation if those features are understood. Graphical abstract.

Septic shock caused by Slackia exigua in a patient with diabetes.

We report a case of septic shock caused by Slackia exigua, an obligatory anaerobic gram-positive rod, in an 82-year-old woman with diabetes. Dental assessment revealed a palatal lesion and untreated periodontitis. Although a resident species in the oral cavity and associated with localized disorders, S. exigua can cause extra-oral diseases, which can be fatal in individuals with risk factors, such as diabetes. Thus, control of oral lesions caused by S. exigua is important to prevent systemic infection.

BAT26 Only Microsatellite Instability with High Tumor Mutation Burden-A Rare Entity Associated with PTEN Protein Loss and High PD-L1 Expression.

Detecting microsatellite instability (MSI) in advanced cancers is crucial for clinical decision-making, as it helps in identifying patients with differential treatment responses and prognoses. BAT26 is a highly sensitive MSI marker that defines the mismatch repair (MMR) status with high sensitivity and specificity. However, isolated BAT26-only instability is rare and has not been previously reported. Of the 6476 cases tested using pentaplex MSI polymerase chain reaction, we identified two BAT26-only instability cases (0.03%) in this study. The case #1 patient was diagnosed with endometrial adenocarcinoma without MMR germline mutations. The endometrial tumor showed BAT26-only instability, partial loss of MLH1/PMS2 protein expression, and a high programmed cell death ligand 1 (PD-L1) combined positive score (CPS = 8). The tumor exhibited a somatic phosphatase and tensin homolog (PTEN) R303P missense mutation and loss of the PTEN protein. On a comprehensive cancer panel sequencing with ≥500 genes, the tumor showed an MSI score of 11.38% and high tumor mutation burden (TMB) (19.5 mt/mb). The case #2 patient was diagnosed with colorectal carcinoma with proficient MMR and PTEN protein loss without PTEN alteration, as well as a high PD-L1 CPS (CPS = 10). A pathogenic KRAS A146T mutation was detected with an MSI score of 3.36% and high TMB (13 mt/mb). In conclusion, BAT26-only instability is very rare and associated with PTEN protein loss, high TMB, and a high PD-L1 score. Our results suggest that patients with BAT26-only instability may show good responses to immunotherapy.

Bacteremia Caused by Moraxella Osloensis: a Fatal Case of an Immunocompromised Patient and Literature Review.

BACKGROUND: Moraxella osloensis rarely causes infection in humans, and most of the reported cases are not fatal. It is often difficult to identify M. osloensis using conventional biochemical methods. METHODS: Here, we report a bacteremia case caused by M. osloensis in a patient with advanced lung cancer who initially presented symptoms of fever. RESULTS: Blood culture revealed growth of a gram-negative bacterium, which was identified as M. osloensis through 16S rRNA gene sequencing and MALDI-TOF analyses. The patient could not recover from sepsis with empirical treatment. CONCLUSIONS: As M. osloensis can cause serious infections in immunocompromised patients, its prompt identification is important.

Antibacterial Activities of Prenylated Isoflavones from Maclura tricuspidata against Fish Pathogenic Streptococcus: Their Structure-Activity Relationships and Extraction Optimization.

Streptococcus zoonotic bacteria cause serious problems in aquaculture with clinical effects on humans. A structure-antibacterial activity relationships analysis of 22 isoflavones isolated from M. tricuspidata (leaves, ripe fruits, and unripe fruits) against S. iniae revealed that prenylation of the isoflavone skeleton was an important key for their antibacterial activities (minimum inhibitory concentrations: 1.95-500 µg/mL). Through principal component analysis, characteristic prenylated isoflavones such as 6,8-diprenlygenistein (4) were identified as pivotal compounds that largely determine each part's antibacterial activities. M. tiricuspidata ripe fruits (MTF), which showed the highest antibacterial activity among the parts tested, were optimized for high antibacterial activity and low cytotoxicity on fathead minnow cells using Box-Behnken design. Optimized extraction conditions were deduced to be 50%/80 °C/7.5 h for ethanol concentration/extraction temperature/time, and OE-MTF showed contents of 6,8-diprenlygenistein (4), 2.09% with a MIC of 40 µg/mL. These results suggest that OE-MTF and its active isoflavones have promising potential as eco-friendly antibacterial agents against streptococcosis in aquaculture.

Introduction of a Borderline Range for the Interpretation of QuantiFERON-TB Gold In-Tube Results in Korean Healthcare Workers.

BACKGROUND: South Korea is the only Organisation for Economic Co-operation and Development (OECD) country with a high incidence of tuberculosis (TB). Healthcare workers (HCWs) have an increased risk of TB infection. QuantiFERON-TB Gold In-Tube (QFT-GIT) testing is performed for occupational health screening to detect latent TB infection (LTBI). METHODS: We evaluated the introduction of new criteria for borderline ranges for interferon-gamma release assay (IGRA) results in HCWs. The results of QFT-GIT tests in HCWs in 2017 and 2018 were collected, with high-risk HCWs having two serial test results. Existing dichotomous criteria and new criteria with borderline ranges (bor-derline negative [BN], 0.20 - 0.34 IU/mL; borderline positive [BP], 0.35 - 0.99 IU/mL) were applied to each test re-sult. RESULTS: After applying the borderline range, 26.4% of the positive results were classified as BP (4% of total results), while 4.2% of the negative results were classified as BN (3.6% of total results). Among seven HCWs with initial results in the borderline range, two had repeated borderline results while 71.4% had low negative results. CONCLUSIONS: We recommend the introduction of borderline ranges in the interpretation of QFT-GIT results to reduce unnecessary TB therapy in HCWs.

Etest Methods for Screening Heterogeneous Vancomycin-Intermediate Staphylococcus aureus (hVISA) strains.

The importance of heterogeneous vancomycin-intermediate Staphylococcus aureus (hVISA) as a preceding stage for the development of vancomycin-resistant S. aureus is growing. We analyzed the prevalence of hVISA among bacteremia with methicillin-resistant S. aureus (MRSA) using two Etests and evaluated the clinical characteristics and outcomes. Ninety-eight MRSA isolates from blood were collected at two University hospitals in Korea. Macrodilution Etest and glycopeptide resistance detection Etests were used for detection of hVISA. Staphylococcal cassette chromosome mec (SCCmec) typing was performed by multiplex PCR. Clinical data were collected retrospectively from patient medical records. About 30% of MRSA strains were identified as hVISA. Diabetes mellitus was associated (P = 0.047) with hVISA infections. The hVISA isolates were associated with high teicoplanin MIC and multidrug resistance (P = 0.001). SCCmec type II accounted for the majority (79.3%) of hVISA strains. The prevalence of hVISA strains was increased and can lead to the development of multidrug-resistant strains. Patients with diabetes were found to have a greater risk for infection with hVISA strains. As the impact of hVISA on clinical outcome is not yet clear, large-scale studies about clinical outcomes and optimal detection methods of hVISA are needed. In conclusion, hVISA strains have a high prevalence in bloodstream MRSA infections. Awareness of the increase in hVISA strains should motivate laboratories to establish a system to detect and monitor hVISA.

Antiaging Potential of Fucoxanthin Concentrate Derived from Phaeodactylum tricornutum.

The aim of the study was to investigate the potential of a fucoxanthin concentrate prepared from Phaeodactylum tricornutum as a wrinkle care cosmetic agent. The concentrate (up to 25 µg/ml) did not affect the proliferation of human fibroblasts. In addition, the concentrate significantly increased procollagen synthesis in the fibroblasts at 12.5 and 25 µg/ml; however, it significantly decreased the expression of matrix metalloproteinase (MMP)-1, MMP-2, and MMP-9 at 25 µg/ml. In a follow-up study, a wrinkle care cream containing 0.03% of fucoxanthin concentrate was prepared and tested in women (aged 35-50 years, n = 21) for 8 weeks. The cream was applied twice daily. Safety assessment of the cream was carried out visually. In addition, interviews were conducted to investigate if adverse events such as erythema, edema, scaling, itching, stinging, burning, tightness, or prickling had occurred. No symptoms that threaten skin safety were reported. Evaluation of wrinkles around the eyes using the replica method showed a statistically significant decrease in wrinkles at week 8. Moreover, skin moisture and elasticity increased significantly from week 4. These results suggest that the fucoxanthin concentrate has no adverse effects on the skin and can be used as an active ingredient in wrinkle care cosmetics.

Novel approaches for bioinformatic analysis of salivary RNA sequencing data for development.

Motivation: Analysis of RNA sequencing (RNA-Seq) data in human saliva is challenging. Lack of standardization and unification of the bioinformatic procedures undermines saliva's diagnostic potential. Thus, it motivated us to perform this study. Results: We applied principal pipelines for bioinformatic analysis of small RNA-Seq data of saliva of 98 healthy Korean volunteers including either direct or indirect mapping of the reads to the human genome using Bowtie1. Analysis of alignments to exogenous genomes by another pipeline revealed that almost all of the reads map to bacterial genomes. Thus, salivary exRNA has fundamental properties that warrant the design of unique additional steps while performing the bioinformatic analysis. Our pipelines can serve as potential guidelines for processing of RNA-Seq data of human saliva. Availability and implementation: Processing and analysis results of the experimental data generated by the exceRpt (v4.6.3) small RNA-seq pipeline (github.gersteinlab.org/exceRpt) are available from exRNA atlas (exrna-atlas.org). Alignment to exogenous genomes and their quantification results were used in this paper for the analyses of small RNAs of exogenous origin. Contact: dtww@ucla.edu.

Clinical use of anti-DFS70 autoantibodies.

The dense fine speckled (DFS) nuclear pattern is one of the most common indirect immunofluorescence (IIF) patterns detected during routine anti-nuclear antibody (ANA) screening. There is a negative association between anti-DFS70 status and systemic autoimmune rheumatic disease (SARD), especially in the absence of concomitant SARD-specific autoantibodies. The purpose of this study was to determine the need for confirming anti-DFS70 status when a DFS pattern is observed in IIF-ANA. The frequency of anti-DFS70 detection on Western blot and the positive rate of connective tissue disease (CTD)-related autoantibody screening with a fluorescence-based enzyme immunoassay was evaluated in DFS (n = 182) and non-DFS (n = 359) groups. Specific autoantibodies against 15 autoantigens were identified by line immunoassay. We evaluated the frequency of cases of DFS mistaken for non-DFS and non-DFS cases mistaken for DFS, as well as the clinical impacts of these misinterpretations. Among cases of IIF-ANA with an observable DFS pattern, 68.1% had only anti-DFS70 without CTD-related autoantibodies, 20.3% were false positive for IIF-ANA, and the remaining 11.5% had CTD-related autoantibodies independent of anti-DFS70 status. These results indicated that CTD-related autoantibodies may be present with or without anti-DFS70 even if a DFS pattern is observed in IIF-ANA. Among patients who are ANA negative or have a low probability of SARD, an anti-DFS70 confirmation test has no clinical benefit and cannot replace specific tests for detecting CTD-related autoantibodies. Specific tests to detect CTD-related autoantibodies should be performed instead of anti-DFS70 confirmation tests when a DFS pattern is observed in IIF-ANA.