Evaluating the risk of malignancies of the diagnostic categories proposed by the World Health Organization System for Reporting Lung Cytopathology: a two-year single institutional experience.

Introduction The WHO System of Reporting Lung Cytopathology proposed a 5-tiered system in 2023. We report the risk of malignancies (ROMs) of bronchial washing/lavage and percutaneous fine needle aspiration (FNA) specimens. We also evaluated the change of ROMs when image correlation is required. Methods Lung cytology cases in 2021 and 2022 with histologic follow-up were included. CT reports were reviewed to identify cases with a solid nodule/tumor but benign cytological findings. These were reassigned from the "Benign" to "Non-diagnostic" category, and the ROMs were re-estimated. Results A total of 1031 bronchial washing/lavage and 206 FNAs were identified. The ROMs of bronchial washing/lavage were "Non-diagnostic" 56.5% (13/23), "Benign" 41.9% (320/764), "Atypical" 71.7% (71/99), "Suspicious for malignancy" 94.7% (72/76), and "Malignant" 100% (70/70). The ROMs of FNAs were "Non-diagnostic" 66% (33/50), "Benign" 58.2% (39/67), "Atypical" 70% (28/40), "Suspicious for malignancy" 96.2% (25/26), and "Malignant" 100% (70/70). When image finding was considered, cases initially assigned as "Benign" were re-classified to "Non-diagnostic" with decreases in ROMs for the "Benign " category. Conclusions Malignancy risks associated with the WHO System of Reporting Lung Cytopathology diagnostic groups were reported. Image correlation for the "Benign" category led to a decrease in case number and ROM.

Next-Generation Sequencing in Lung Cancers-A Single-Center Experience in Taiwan.

Background and Objectives: Lung cancer is a leading cause of cancer mortality in Taiwan. With rapid advancement of targeted therapeutics in non-small cell lung cancers, next-generation sequencing (NGS) is becoming an important tool for biomarker testing. In this study, we describe institutional experience of NGS analysis in non-small cell carcinoma (NSCLC). Materials and Methods: A cohort of 73 cases was identified from the institutional pathology archive in the period between November 2020 and December 2022. Results: Adenocarcinoma was the most common histologic type (91.8%). Most patients presented with stage IIIB and beyond (87.7%). Twenty-nine patients (39.7%) were evaluated at the time of initial diagnosis, while the others had received prior chemotherapy or targeted therapy. The most frequently mutated gene was EGFR (63%), and this was followed by TP53 (50.7%), KRAS (13.7%), RB1 (13.7%), and CDKN2A (13.7%). Clinically actionable mutations associated with a guideline-suggested targeted therapy were identified in 55 cases (75.3%) overall, and in 47.1% of cases excluding EGFR TKI-sensitizing mutation. Biomarkers other than EGFR TKI-sensitizing mutations were compared. Cases without TKI-sensitizing EGFR mutation had more level 1 or 2 biomarkers (excluding EGFR TKI-sensitizing mutations) than cases with TKI-sensitizing EGFR mutations (47.1% versus 20.1%, p = 0.016). Progressive disease was associated with co-occurrence of clinically actionable mutations (20.5% versus 0%, p < 0.05). Eight of the nine cases with co-occurring actionable genetic alternations had an EGFR mutation. After an NGS test, 46.1% of actionable or potentially actionable genetic alternations led to patients receiving a matched therapy. Conclusions: Our study demonstrated that NGS analysis identifies therapeutic targets and may guide treatment strategies in NSCLC. NGS tests may be advantageous over multiple single-gene tests for optimization of treatment plans, especially for those with non-EGFR mutations or those with progressive disease.

Co-exposure of dimethomorph and imidacloprid: effects on soil bacterial communities in vineyard soil.

In Taiwan, the pesticides dimethomorph and imidacloprid are recommended for pest control in vineyards. Therefore, tank-mixing of these two pesticides is usually a routine practice before application. This study analyzed the influence of vineyard soil microbial flora under the recommended and high dosages (100 times the recommended dosage) of dimethomorph and imidacloprid. Individual and combined applications of pesticides were also tested through batches of soil incubation experiments. Four treatments-control (C), dimethomorph (DT), imidacloprid (IM), and mixed application of dimethomorph and imidacloprid (ID)-were used in the experimental design. From the soil metabolism, no significant reaction was observed after 2 months in the recommended dosage group, regardless of whether the pesticides were being applied individually or combined. For the high dosage, imidacloprid showed a higher effect than the co-exposure treatments, showing a possible prolonged effect after its repetitive application. From PCoA analysis, pesticide treatments altered the soil ecology after 2 months, and the effect of imidacloprid can be explicitly observed at high dosages. At the phylum level, Acidobacteria can indicate pesticide application around the recommended dosage. It was inhibited by ID on day 7 and was augmented by all pesticides on day 63. The effect of the recommended dosage of pesticide mixtures after 2 months of incubation was revealed in the minor families Gemmataceae and Pirellulaceae, while the high dosage treatments affected both the core and the minor families. Our findings verified the changes in the composition of microbial communities upon pesticide application, which would affect carbon, nitrogen, sulfur, phosphorous cycles, and contaminant removal ability within the vineyard.

Effect of seed biopriming with selected endophytes on the growth and chilling tolerance of rice plants.

The aim of this study was to develop an efficient bioinoculant for amelioration of adverse effects from chilling stress (10°C), which are frequently occurred during rice seedling stage. Seed germination bioassay under chilling condition with rice (Oryza sativa L.) cv. Tainan 11 was performed to screen for plant growth-promoting (PGP) bacteria among 41 chilling-tolerant rice endophytes. And several agronomic traits were used to evaluate the effects of bacterial inoculation on rice seedling, which were experienced for 7-d chilling stress in walk-in growth chamber. The field trials were further used to verify the performance of potential PGP endophytes on rice growth. A total of three endophytes with multiple PGP traits were obtained. It was demonstrated that Pseudomonas sp. CC-LS37 inoculation led to 18% increase of maximal efficiency of Photosystem II (PSII) after 7-d chilling stress and 7% increase of chlorophyll a content, and 64% decline of malondialdehyde content in shoot after 10-d recovery at normal temperature in walk-in growth chamber. In field trial, biopriming of seeds with strain CC-LS37 caused rice plants to increase shoot chlorophyll soil plant analysis development values (by 2.9% and 2.5%, respectively) and tiller number (both by 61%) under natural climate and chilling stress during the end of tillering stage, afterward 30% more grain yield was achieved. In conclusion, strain CC-LS37 exerted its function in increase of tiller number of chilling stress-treated rice seedlings via improvement of photosynthetic characteristics, which in turn increases the rice grain yield. This study also proposed multiple indices used in the screening of potential endophytes for conferring chilling tolerance of rice plants.

Endometriosis-associated epithelial ovarian cancer is a more complicated disease than we suspected before.

OBJECTIVE: Endometriosis-associated epithelial ovarian cancer (EOC) often includes clear cell carcinoma and endometrioid-type carcinoma. Due to the low incidence of primary mucinous EOC and absence of association between endometriosis and primary mucinous EOC, we present an unusual endometriosis-associated mixed mucinous and endometrioid adenocarcinoma arising from the same ovary. CASE REPORT: A 54-year-old woman had an abdominal palpable mass for months. Medical and surgical history, as well as preoperative surveys was unremarkable, except of presence of a pelvic mass. She underwent an exploration laparotomy, and a 22-cm right ovarian tumor was found. Grossly, right ovarian tumor containing brownish cloudy cystic fluid 2450 ml and an apparent 4 × 4 × 2 cm-sized papillary growth. Microscopically, a confluent glandular and infiltrative pattern presented endometrioid adenocarcinoma, and cells with intracytoplasmic mucin and stratified elongated epithelial cells presented mucinous adenocarcinoma. Surgico-pathological stage was FIGO IIIA due to tumor invading to the peritoneum above the pelvis. Postoperatively, the dose-dense chemotherapy was applied with uneventful outcome. CONCLUSION: This is a rare case, composed with mixed mucinous and endometrioid adenocarcinoma of the same ovary, suggesting that careful pathological diagnosis of endometriosis-associated EOC is needed.

Could prokinetic agents protect long-term nasogastric tube-dependent patients from being hospitalized for pneumonia? A nationwide population-based case-crossover study.

BACKGROUND: Some studies have indicated that the use of prokinetic agents may reduce pneumonia risk in some populations. Nasogastric tube insertion is known to increase the risk of pneumonia because it disrupts lower esophageal sphincter function. The aim of this study was to evaluate whether prokinetic agents could protect long-term nasogastric tube-dependent patients in Taiwan from being hospitalized for pneumonia. METHODS: A case-crossover study design was applied in this study. Long-term nasogastric tube-dependent patients who had a first-time admission to a hospital due to pneumonia from 1996 to 2013 that was recorded in the Taiwan National Health Insurance Research Database were included. The case period was set to be 30 days before admission, and two control periods were selected for analysis. Prokinetic agent use during those three periods was then assessed for the included patients. Conditional logistic regression was used to calculate the odds ratio (OR) for pneumonia admission with the use of prokinetic agents. RESULTS: A total of 639 first-time hospitalizations for pneumonia among patients with long-term nasogastric tube dependence were included. After adjusting the confounding factors for pneumonia, no negative association between prokinetic agent use and pneumonia hospitalization was found, and the adjusted OR was 1.342 (95% CI 0.967-1.86). In subgroup analysis, the adjusted ORs were 1.401 (0.982-1.997), 1.256 (0.87-1.814), 0.937 (0.607-1.447) and 2.222 (1.196-4.129) for elderly, stroke, diabetic and parkinsonism patients, respectively. CONCLUSION: Prokinetic agent use had no negative association with pneumonia admission among long-term nasogastric tube-dependent patients in Taiwan.

Effects of Hospice Care for Terminal Head and Neck Cancer Patients: A Nationwide Population-Based Matched Cohort Study.

Background: Head and neck cancer was the fourth-most common cause of cancer death among Taiwanese men in 2018. Hospice care has been proven to reduce the use of invasive medical interventions and expenditures in caring for cancer patients. Aim: This study examined the effects of hospice care for terminal head and neck cancer patients. Design: A matched cohort study was used to compare the use of invasive interventions and expenditures among hospice care and nonhospice care patients. Setting/Participants: The investigated patients consisted of patients who died of head and neck cancer in Taiwan from 2004 to 2013 and were included in the Registry for Catastrophic Illness Patients in Taiwan and the Taiwan National Health Research Insurance Database. Results: A total of 45,948 terminal head and neck cancer patients were identified, and 9883 patients remained in each group after matching for comorbidities. After that matching, the rates of intensive care unit admission (23.9% vs. 38.94%, p < 0.0001), endotracheal intubation (10.05% vs. 31.32%, p < 0.0001), cardiopulmonary resuscitation (2.93% vs. 20.18%, p < 0.0001), defibrillation (0.51% vs. 4.36%. p < 0.0001), ventilator use (21.92% vs. 46.47%, p < 0.0001), blood transfusion (71.25% vs. 73.45%, p = 0.006), and hemodialysis (1.06% vs. 3.26%. p < 0.0001) were significantly lower in the hospice group than the nonhospice group, although the rates of parenteral nutrition for the two groups were similar (7.74% vs. 7.97%, p = 0.5432). The mean medical expenditure per person in the six months before death was 460,531 New Taiwan Dollar (NTD) for the nonhospice group and 389,079 NTD for those provided hospice care for more than three months, which was the lowest amount among various hospice enrollment durations. Conclusions: Hospice care can effectively reduce the use of invasive medical interventions in caring for terminal head and neck cancer patients and may improve their quality of death. Moreover, hospice care enrollment for more than three months can save on unnecessary medical expenditures for terminal head and neck cancer patients.

Frequency, Recognition, and Potential Risk Factors of Incidental Findings on Trauma Computed Tomography Scans: A Cross-Sectional Study at an Urban Level One Trauma Center.

BACKGROUND: Computed tomography (CT) use in injured patients has continuously increased in the past decades. We designed and undertook this study to evaluate the frequency, and potential risks of incidental findings (IFs), and how they were processed in trauma patients receiving CT scans. METHODS: We retrospectively reviewed CT scans, official CT reports, and basic demographics in trauma patients who received CT scans at our emergency department in 2016. Scans with IFs prompted a detailed review of medical records to determine clinical significance and how they were processed. IFs were classified into three categories: category I (potentially severe condition, in-time management required), category II (not urgent, follow-up needed), and category III (of minor concern). Multivariable logistic regression models were fitted to determine patient characteristics associated with IFs. RESULTS: In the 4,092 scans enrolled, IFs were identified in 649 (15.9%). There were 13 (2.0%) category I, 306 (47.2%) category II, and 330 (50.8%) category III IFs. Patients with IFs were older than those without. No sex-based difference was found. Most (61.5%) of the scans were performed for the head; however, the abdomen had the highest IF prevalence (26.2%). Documentation about IFs was poor; 31% of category I, 91.9% of category II, and 97.0% of category III have no related record. Old age remains the risk predicting the presence of IFs, and every year of increasing age was independently associated with a higher prevalence of IFs (OR: 1.019; 95% CI: 1.015-1.024). CONCLUSIONS: IFs are common in trauma CT scans; however, recognition and management remain poor. Abdomen and chest scans, and CT in older patients should remind us of increasing risks of IFs.

Characterization of Driver Mutations in Anaplastic Thyroid Carcinoma Identifies RAS and PIK3CA Mutations as Negative Survival Predictors.

Anaplastic thyroid carcinoma (ATC) is rare but highly aggressive. We investigated the association of selected driver mutations, including BRAF, RAS, PIK3CA, TERT promoter, TP53, POLE, and mismatch repair deficiency (MMR-D) with the clinicopathological features of ATC to identify prognostic and predictive biomarkers. Thirty-nine retrospective cases from pathology archives were enrolled for clinicopathology analysis and immunohistochemistry, and 27 cases had sufficient specimens for further molecular testing using targeted next-generation sequencing and mass spectrometry. BRAFV600E and RAS mutations were identified in 25.9% and 40.7% of ATC, respectively. BRAFV600E mutation was significantly associated with coexisting papillary thyroid carcinoma (p = 0.009) and RAS mutations with female gender (p = 0.012). In univariant analysis, the non-BRAF/RAS tumors were significantly associated with the presence of a sarcomatoid pattern (p = 0.045). PIK3CA, TERT promoter, and TP53 mutations were identified in 14.8%, 81.5%, and 70.4% of cases, respectively. No MMR-D or POLE mutations were detected. In survival analyses, RAS and PIK3CA mutations were significantly associated with inferior outcomes (p = 0.03 and p = 0.006, respectively). In conclusion, driver mutations in ATC are associated with distinct clinicopathological features. RAS and PIK3CA mutations were negative predictors for patient survival. Emerging therapeutic agents targeting BRAF, RAS, and PI3 kinase may benefit a substantial proportion of ATC patients.

Endometriosis-associated epithelial ovarian cancer: Primary synchronous different cellular type on each ovary.

OBJECTIVE: Endometriosis-associated epithelial ovarian cancer (EOC) is a specific category of EOC, containing either endometrioid or clear cell carcinoma subtype. The characteristic of endometriosis-associated EOC includes an early stage at the diagnosis, presence of single histology type, and better prognosis. The synchronous two subtypes of endometriosis-associated EOC and presentation of far-advanced stage status at the initial diagnosis is rarely reported. CASE REPORT: We reported a 60-year-old postmenopausal woman with FIGO IA endometriosis-associated endometrioid carcinoma at right ovary and FIGO IVA endometriosis-associated clear cell carcinoma at left ovary, right tube, omentum, lymph node and cytology of pleural effusion and ascites treated with optimal debulking surgery and dose-intensity taxane/platinum based chemotherapy. CONCLUSION: This case report confirms the long-term concept that clear cell carcinoma has much more aggressive behavior than endometrioid cell carcinoma does, regardless of association of endometriosis or not.

Screening and Assessment of Potential Plant Growth-promoting Bacteria Associated with Allium cepa Linn.

Plant growth-promoting bacteria (PGPB) are beneficial microbes that increase plant growth and yield. However, limited information is currently available on PGPB in onion (Allium cepa Linn.). The aims of the present study were to isolate and identify PGPB in onion and examine the effects of isolated PGPB on germination and growth during the vegetative stage in onion, pak choy (Brassica chinensis), and sweet pepper (Capsicum annuum). Twenty-three strains of PGPB were isolated from the roots, bulbs, and rhizosphere soil of onion. All isolated bacterial strains showed one or more PGP traits, including indole acetic acid production, phosphate solubilization ability, and 1-aminocyclopropane-1-carboxylate deaminase and nitrogenase activities; most of these traits were derived from Bacillus sp., Microbacterium sp., and Pseudomonas sp. Eight bacteria that exhibited strong abilities to produce indole acetic acid were selected for a Petri dish trial, soil pot test, and vermiculate pot test. The Petri dish trial showed that strains ORE8 and ORTB2 simultaneously increased radicle and hypocotyl lengths in onion, but inhibited growth in sweet pepper after 7 d. The soil pot experiment on onion revealed that strains ORE5, ORE8, and ORTB2 strongly promoted growth during the vegetative stage with only a half dose of chemical fertilizer. The present results indicate that ORE8 (Bacillus megaterium) and ORTB2 (Pantoea sp.) are the most promising biofertilizers of onion and may simultaneously inhibit the seedling growth of other plants.

Differential visible spectral influence on carbon metabolism in heterotrophic marine flavobacteria.

The visible spectrum of solar radiation is known to stimulate photoheterotrophic bacterial carbon metabolism. However, its impact on 'strictly' heterotrophic bacteria remains less explored. Here, we show that heterotrophic flavobacteria exhibit enhanced uptake and mineralization of dissolved organic carbon with increasing wavelengths of visible light, without employing any 'known' light-harvesting mechanisms. RNA sequencing identified blue light as a major constraint in the extracellular enzymatic hydrolysis of polymeric carbohydrates and acquisition of sugars, despite acting as a stimulus for inorganic carbon sequestration. In contrast, green-red and continuous full-spectrum lights activated diverse hydrolytic enzymes and sugar transporters, but obstructed inorganic carbon fixation. This 'metabolic switching' was apparent through limited nutrient uptake, suppressed light-sensitivity, oxidative stress response and promotion of inorganic carbon sequestration pathways under blue light. The visible light impact on metabolism may be of significant ecological relevance as it appears to promote cell-mediated mineralization of organic carbon in 'green-colored' chlorophyll-rich copiotrophic coastal seawater and inorganic carbon sequestration in 'blue-colored' oligotrophic open ocean. Thus, a novel regulatory role played by light on heterotrophic metabolism and a hidden potential of flavobacteria to sense and respond differentially to monochromatic lights influencing marine carbon cycling were unraveled.

Description of Gemmobacter aestuarii sp. nov., isolated from estuarine surface water and reclassification of Cereibacter changlensis as Gemmobacter changlensis Chen et al. 2013.

A Gram-stain-negative, tyrosine-metabolizing, non-motile, strictly aerobic, non-spore-forming, rod-shaped marine bacterium, designated strain CC-PW-75T, was isolated from the estuarine water off Pintung, Taiwan. Strain CC-PW-75T formed a distinct phyletic lineage associated with Gemmobacter species, sharing the highest 16S rRNA gene sequence similarity with G. megaterium CF17T and G. straminiformis CAM-8T (96.0% each) followed by G. aquatilis IFAM 1031T and G. nectariphilus AST4T (95.8% each). Analysis of the draft genome (3.76 Mbp) revealed the presence of genes encoding light-harvesting complexes, photosynthetic reaction centers and proteins involved in the metabolism of CO, CO2, HCO3‒ and H2S. However, bacteriochlorophyll a was not detected. Average nucleotide identity values between the genome sequence of CC-PW-75T and the related Gemmobacter species (n = 6) were estimated to be 72.8-76.3%. Polar lipid analysis revealed the presence of phosphatidylglycerol, phosphatidylethanolamine and an unidentified lipid in major amounts, and phosphatidylmonomethylethanolamine, phosphatidylcholine, an unidentified aminolipid and an unidentified lipid in minor amounts. C18:1ω7c and/or C18:1ω6c, C18:0 and C18:1ω7c 11-methyl were identified to be major fatty acids. The DNA G + C content was 66.2 mol% (draft genome sequence). Ubiquinone-10 (Q-10) was the sole respiratory quinone. Based on the polyphasic taxonomic evidence, CC-PW-75T is most likely a novel species of the genus Gemmobacter, affiliated to the family Rhodobacteraceae, for which the name Gemmobacter aestuarii sp. nov. is proposed. The type strain is CC-PW-75T (= JCM 19754T = BCRC 80759T). Also, we propose the reclassification of Cereibacter changlensis as Gemmobacter changlensis Chen et al. 2013 using the polyphasic data presented in this study.

Draft genome sequence reveals co-occurrence of multiple antimicrobial resistance and plant probiotic traits in rice root endophytic strain Burkholderia sp. LS-044 affiliated to Burkholderia cepacia complex.

OBJECTIVES: Members of the Burkholderia cepacia complex (Bcc) have been isolated from various environmental and clinical samples and reportedly pose a threat to human health. Here we examine the draft genome sequence of Burkholderia sp. LS-044, an antibiotic-resistant endophytic strain affiliated to the Bcc (ST895) inhabiting rice (Oryza sativa ssp. japonica cv. Tainung 71) root. METHODS: Antimicrobial susceptibility of LS-044 was evaluated comparatively with other Burkholderia sp. (CC-Al74 and CC-3XP9) using commercial ATB PSE 5 test strips. The genome of LS-044 was sequenced using an Illumina MiSeq platform. Plant probiotic and antimicrobial resistance genes were screened by Rapid Annotation using Subsystem Technology (RAST), CARD 2017, NCBI and/or UniProt. RESULTS: Plant-associated members of Bcc (LS-044 and CC-Al74) exhibited greater resistance to the majority of antibiotics tested. The draft genome sequence of LS-044 contained 8.78 Mbp in 62 contigs having a G + C content of 66.5%, 8868 coding sequences and 75 RNAs. The genome harboured genes coding for LysR-type ß-lactamase transcription regulator, classes A, C and D ß-lactamases, several metal-dependent ß-lactamases, antibiotic efflux proteins, and proteins conferring resistance to colistin, streptothricin, colicin and fluoroquinolones. Similarly, it also possessed genes for copper homeostasis, copper-cobalt-zinc-cadmium-chromium resistance and reduction of mercury. Genes involved in flagellar motility, hydrolysis of murein and chitin, production of siderophore and auxin, and metabolism of aromatic compounds were also found. CONCLUSION: Genome sequence data revealed an interlinked occurrence of plant probiotic traits and antimicrobial resistance in the rice root endophyte LS-044.

PAX8 expression in anaplastic thyroid carcinoma is less than those reported in early studies: a multi-institutional study of 182 cases using the monoclonal antibody MRQ-50.

Anaplastic thyroid carcinoma (ATC) is an aggressive malignant tumor composed of undifferentiated thyroid follicular cells. Pathological diagnosis of ATC can be challenging as the tumor may show morphological overlap with other neoplasms with anaplastic morphology. Immunohistochemical demonstration of thyroid origin facilitates the diagnosis of ATC. Previous studies using the polyclonal anti-PAX8 antibody 10336-1-AP suggested that PAX8 was the most sensitive marker, expressed in up to 80% of ATC. According to a 2018 NordiQC report, the monoclonal anti-PAX8 antibody MRQ-50 has become the most commonly used anti-PAX8 antibody worldwide. However, validation of this antibody in ATC is lacking. In this study, we recruited 182 ATC cases from seven institutions. Pathology slides were subjected to histology review. PAX8 immunohistochemistry using the MRQ-50 antibody was performed in whole tissue slides (n = 147) or tissue microarray sections (n = 35). We found PAX8 expression in 54.4% of the cases, which was significantly lower than those reported in prior studies with the polyclonal antibody. PAX8 expression was positively correlated with the presence of an epithelial pattern (63.6% vs 37.5%, p = 0.0008) and a coexisting differentiated thyroid carcinoma component (71.6% vs 44.3%, p = 0.0004), but was not associated with age, gender, specimen type, or presence of giant cell and sarcomatoid patterns. In conclusion, we demonstrated PAX8 expression using the monoclonal antibody MRQ-50 in only half of the cases in a large ATC series. Pathologists should be aware that PAX8 expression in ATC is less than those reported in early studies to avoid misdiagnosis.