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Urban farming is a sustainable and adaptable farming alternative. Especially during the COVID-19 pandemic, urban farming is an efficient alternative since it does not require high mobility. This study examined the efficacy of implementing urban farming with the Community’s Economic Impact Analysis (EIA). This type of research is qualitative research with deep interview techniques by the 7 participants. The participants are the people of Kauman Village, Malang City, East Java, Indonesia. The results showed that the impact of urban farming in Kauman significantly increased the community’s Economic Impact Analysis (EIA). The public’s perception of the application of urban farming is quite good. Most people perceive the benefits of implementing urban farming, including using green land around their houses. According to Economic Impact Analysis, implementing urban farming can increase well-being in terms of food security. Community participation in implementing urban farming looks quite effective and enthusiastic so that people, individually and in groups, perceive the benefits of implementing this farming system.

This study focuses on the production of silica sand in the Kingdom of Saudi Arabia in the light of the Kingdom's industrialization strategies and policies, which are aimed at the diversification of income sources and widening of production fields in the context of the consecutive development plans during the period 1390 - 1430 AH. Silica sand procession/production is considered as an indicator for evaluating the range of success and applying a series of government strategies, on the top of, is the strategy of utilization of the local resources, adopted by a number of development plans, through encouraging local and foreign private sector investment, and exploring and developing unexploited mineral resources. Silica sand production, among 33 unexploited industrial minerals on the soil of the Kingdom, needs to be carefully studied. The intended study highlights the importance of the product, its production stages, and the geographical distribution of location in the Kingdom of Saudi Arabia. The economic value of silica sand will also be tackled through concentrating on its study as one of the industrial factors of development with the purpose of becoming less dependant on importation and even planning for its exportation in the future. Figures prove that the Kingdom's production of silica sand the year 1427 has amounted to 600000 tons. [ABSTRACT FROM AUTHOR]

Background: Lung cancer is a heterogeneous disease and the primary cause of cancer-related mortality worldwide. Somatic mutations, including large structural variants, are important biomarkers in lung cancer for selecting targeted therapy. Genomic studies in lung cancer have been conducted using short-read sequencing. Emerging long-read sequencing technologies are a promising alternative to study somatic structural variants, however there is no current consensus on how to process data and call somatic events. In this study, we preformed whole genome sequencing of lung cancer and matched non-tumour samples using long and short read sequencing to comprehensively benchmark three sequence aligners and seven structural variant callers comprised of generic callers (SVIM, Sniffles2, DELLY in generic mode and cuteSV) and somatic callers (Severus, SAVANA, nanomonsv and DELLY in somatic modes)., Results: Different combinations of aligners and variant callers influenced somatic structural variant detection. The choice of caller had a significant influence on somatic structural variant detection in terms of variant type, size, sensitivity, and accuracy. The performance of each variant caller was assessed by comparing to somatic structural variants identified by short-read sequencing. When compared to somatic structural variants detected with short-read sequencing, more events were detected with long-read sequencing. The mean recall of somatic variant events identified by long-read sequencing was higher for the somatic callers (72%) than generic callers (53%). Among the somatic callers when using the minimap2 aligner, SAVANA and Severus achieved the highest recall at 79.5% and 79.25% respectively, followed by nanomonsv with a recall of 72.5%., Conclusion: Long-read sequencing can identify somatic structural variants in clincal samples. The longer reads have the potential to improve our understanding of cancer development and inform personalized cancer treatment., (© 2024. The Author(s).)

Endobronchial ultrasound-guided transbronchial needle aspiration (EBUS-TBNA) is often the only source of tumor tissue from patients with advanced, inoperable lung cancer. EBUS-TBNA aspirates are used for the diagnosis, staging, and genomic testing to inform therapy options. Here we extracted DNA and RNA from 220 EBUS-TBNA aspirates to evaluate their suitability for whole genome (WGS), whole exome (WES), and comprehensive panel sequencing. For a subset of 40 cases, the same nucleic acid extraction was sequenced using WGS, WES, and the TruSight Oncology 500 assay. Genomic features were compared between sequencing platforms and compared with those reported by clinical testing. A total of 204 aspirates (92.7%) had sufficient DNA (100 ng) for comprehensive panel sequencing, and 109 aspirates (49.5%) had sufficient material for WGS. Comprehensive sequencing platforms detected all seven clinically reported tier 1 actionable mutations, an additional three (7%) tier 1 mutations, six (15%) tier 2-3 mutations, and biomarkers of potential immunotherapy benefit (tumor mutation burden and microsatellite instability). As expected, WGS was more suited for the detection and discovery of emerging novel biomarkers of treatment response. WGS could be performed in half of all EBUS-TBNA aspirates, which points to the enormous potential of EBUS-TBNA as source material for large, well-curated discovery-based studies for novel and more effective predictors of treatment response. Comprehensive panel sequencing is possible in the vast majority of fresh EBUS-TBNA aspirates and enhances the detection of actionable mutations over current clinical testing.

Introduction: Tumour Mutation Burden (TMB) is a potential biomarker for immune cancer therapies. Here we investigated parameters that might affect TMB using duplicate cytology smears obtained from endobronchial ultrasound transbronchial needle aspiration (EBUS TBNA)-sampled malignant lymph nodes., Methods: Individual Diff-Quik cytology smears were prepared for each needle pass. DNA extracted from each smear underwent sequencing using large gene panel (TruSight Oncology 500 (TSO500 - Illumina)). TMB was estimated using the TSO500 Local App v. 2.0 (Illumina)., Results: Twenty patients had two or more Diff-Quik smears (total 45 smears) which passed sequencing quality control. Average smear TMB was 8.7 ± 5.0 mutations per megabase (Mb). Sixteen of the 20 patients had paired samples with minimal differences in TMB score (average difference 1.3 ± 0.85). Paired samples from 13 patients had concordant TMB (scores below or above a threshold of 10 mutations/Mb). Markedly discrepant TMB was observed in four cases, with an average difference of 11.3 ± 2.7 mutations/Mb. Factors affecting TMB calling included sample tumour content, the amount of DNA used in sequencing, and bone fide heterogeneity of node tumour between paired samples., Conclusion: TMB assessment is feasible from EBUS-TBNA smears from a single needle pass. Repeated samples of a lymph node station have minimal variation in TMB in most cases. However, this novel data shows how tumour content and minor change in site of node sampling can impact TMB. Further study is needed on whether all node aspirates should be combined in 1 sample, or whether testing independent nodes using smears is needed., Competing Interests: The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest., (Copyright © 2023 Fielding, Dalley, Singh, Nandakumar, Lakis, Chittoory, Fairbairn, Patch, Kazakoff, Ferguson, Bashirzadeh, Bint, Pahoff, Son, Ryan, Hodgson, Sharma, Pearson, Waddell, Lakhani, Hartel, Simpson and Nones.)

Introduction: Maximising alternative sample types for genomics in advanced lung cancer is important because bronchoscopic samples may sometimes be insufficient for this purpose. Further, the clinical applications of comprehensive molecular analysis such as whole genome sequencing (WGS) are rapidly developing. Diff-Quik cytology smears from EBUS TBNA is an alternative source of DNA, but its feasibility for WGS has not been previously demonstrated., Methods: Diff-Quik smears were collected along with research cell pellets., Results: Tumour content of smears were compared to research cell pellets from 42 patients, which showed good correlation (Spearman correlation 0.85, P < 0.0001). A subset of eight smears underwent WGS, which presented similar mutation profiles to WGS of the matched cell pellet. DNA yield was predicted using a regression equation of the smears cytology features, which correctly predicted DNA yield > 1500 ng in 7 out of 8 smears., Conclusions: WGS of commonly collected Diff-Quik slides is feasible and their DNA yield can be predicted., (© 2023. Crown.)

Background: Cytology smears are commonly collected during endobronchial ultrasound-guided transbronchial needle aspiration (EBUS TBNA) procedures but are rarely used for molecular testing. Studies are needed to demonstrate their great potential, in particular for the prediction of malignant cell DNA content and for utility in molecular diagnostics using large gene panels., Methods: A prospective study was performed on samples from 66 patients with malignant lymph nodes who underwent EBUS TBNA. All patients had air-dried, Diff-Quik cytology smears and formalin-fixed, paraffin-embedded cell blocks collected for cytopathology and molecular testing. One hundred eighty-five smears were evaluated by microscopy to estimate malignant cell percentage and abundance and to calculate smear size and were subjected to DNA extraction. DNA from 56 smears from 27 patients was sequenced with the TruSight Oncology 500 assay (Illumina)., Results: Each microscopy parameter had a significant effect on the DNA yield. An algorithm was developed that predicted a >50-ng DNA yield of a smear with an area under the curve of 0.86. Fifty DNA samples (89%) with varying malignant yields were successfully sequenced. Low-malignant-cell content (<25%) and smear area (<15%) were the main reasons for failure. All standard-of-care mutations were detected in replicate smears from individual patients, regardless of malignant cell content. Tier 1/2 mutations were discovered in two cases where standard-of-care specimens were inadequate for sequencing. Smears were scored for tumor mutation burden., Conclusions: Microscopy of Diff-Quik smears can triage samples for comprehensive panel sequencing, which highlights smears as an excellent alternative to traditional testing with cell blocks., (© 2023 The Authors. Cancer Cytopathology published by Wiley Periodicals LLC on behalf of American Cancer Society.)

Introduction: Endobronchial ultrasound-guided transbronchial needle aspiration (EBUS TBNA) is an important means of obtaining a tissue for advanced lung cancer. Optimizing the EBUS TBNA needling technique is important to maintain procedural simplicity and maximize sample quality for emerging molecular diagnostics., Methods: We prospectively explored three versus 10 agitations of the needle in sequential passes into the lymph node using separate needles. Resulting Diff-Quik cytology smears were quantitatively assessed using microscopic (tumor cell cellularity, abundance scores, erythrocyte contamination) and DNA yields. Microscopy was reported by two cytopathologists, and an inter-rater assessment was made by four additional cytopathologists., Results: In 86 patients confirmed as having malignant disease by EBUS TBNA (45 males, 41 females), a mean of 5.3 smears were made per patient with a total of 459 smears scored by pathologists and 168 paired smears extracted for DNA. There was no significant difference between three versus 10 agitations for smear cellularity ( p  = 0.44), DNA yield ( p  = 0.84), or DNA integrity ( p  = 0.20), but there was significantly less contamination by erythrocytes from three agitations (chi-square p  = 0.008). There was significantly more DNA in the first pass into the node using three agitations than with other passes and with 10 agitations (pass × agitations interaction, p  = 0.031). Reviewing pathologists correctly classified smears as more than or equal to 25% cellularity 86.3% of the time (κ = 0.63 [95% confidence interval: 0.55-0.71])., Conclusions: Three agitations are noninferior to 10 agitations for overall abundance of malignant cells and DNA content on smears. A smear with adequate DNA for panel sequencing could almost always be made with the first needle pass using three agitations., (Crown Copyright © 2022 Published by Elsevier Inc. on behalf of the AGA Institute.)

Background: Respiratory Acute Discharge Service (RADS) is a novel early discharge service with nurse-led community based recovery in selected patients with acute exacerbations of chronic obstructive pulmonary disease., Aim: This pilot study aimed to determine the efficacy and safety of the programme in an Australian tertiary hospital., Methods: All patients who were recruited to RADS at Sunshine Coast University Hospital over a 6 months period from June to November 2018 were included. The co-primary outcomes were length of hospital days saved and rate of readmission within 30 days from discharge., Results: A total of 166 patients (median age 74 years (interquartile range 70-80 years)) was recruited to the programme over the study period. The mean forced expiratory volume in one second (FEV1%) of the patients was 42% (standard deviation 19). The median length-of-stay prior to discharge on the RADS programme was 1 day (range 0-5), compared to a previous average of 5.8 days in our health service. Patients were on the programme for a median of 4 days (range 1-6). A total of 613 hospital bed days was saved over the study period, with significant cost savings. Forty-one (24.7%) patients represented to hospital within 30 days, the majority (64%) were due to recurrent symptoms. The rate of 30-day all-cause mortality for the study population was 1 (0.6%)., Conclusion: Early supported discharge care model with nurse-led community based recovery after an acute exacerbation of chronic obstructive pulmonary disease in selected patients is safe, and has the potential to provide greater flow through the hospital systems with cost effective care., (© 2019 Royal Australasian College of Physicians.)

Background: An optimal sampling sequence in radial guide sheath endobronchial ultrasound lung biopsy (R-EBUS) is unclear. This prospective single-center pilot randomized controlled trial aimed to determine if the initial method and sequence of sampling affect the diagnostic accuracy of the procedure., Methods: Consecutive patients undergoing R-EBUS for lesions >15 mm with a bronchus sign were randomly assigned (1:1:1) to biopsy first (group A), brushings first (group B) or combination (group C). The primary outcome was a positive diagnosis from any sampling method., Results: Fifty-four patients were randomized. The overall diagnostic yield of the procedure was 77.8% (95% confidence interval: 66%-89%), with no difference between groups. A higher rate of positive cytology from brushings was seen if the biopsies were performed before brushings (77.8% in group A vs. 44.4% in group B, P=0.03). The rate of positive cytology from washings was higher if the washings were obtained just after the brushings (61.1% in group A vs. 11.1% in group B, P=0.02). There was no difference in the rate of positive biopsy histology in the groups (P=0.27). All 3 sampling modalities were more likely to be positive in group A (50.0% vs. 11.1% in group B and 22.2% in group C, P=0.04). Complications rate was low and not significantly different between groups., Conclusion: The overall rate of a positive R-EBUS procedure was not affected by the initial sampling method or sequence. However, all 3 sampling modalities were more likely to be positive if biopsies were performed first, followed by brushings and washings.

Granulomatous lymphocytic interstitial lung disease (GLILD) is characterized by lymphocytic and granulomatous pulmonary infiltration occurring in common variable immunodeficiency (CVID). It is associated with increased mortality compared with CVID patients without GLILD. There are no treatment guidelines due to the low prevalence and the heterogeneity of the condition. A case review of three patients diagnosed with GLILD was performed from a single Australian centre. Patients met the European Society of Immunodeficiency criteria for CVID and a diagnosis of GLILD was confirmed by a multidisciplinary team. Patients were managed with immunoglobulin (Ig) replacement and immunosuppressive agents if required: the decision for immunosuppression was made on the basis of symptoms and declining pulmonary function. All patients clinically improved. One patient had immunosuppressive treatment ceased. GLILD responds to varying immunosuppressive regimes when IgG monotherapy fails. Immunosuppressive therapy can be discontinued following improvement, but patients require close observation. This series helps inform future GLILD treatment guidelines., (© 2020 The Authors. Respirology Case Reports published by John Wiley & Sons Australia, Ltd on behalf of The Asian Pacific Society of Respirology.)

Rhodococcus equi is a gram positive bacterium most commonly presenting clinically as pneumonia, however can disseminate to cause disease in virtually any human tissue. Although it is predominantly an opportunistic pathogen, a number of case series have described infection occurring among individuals with a normal immune system. We describe two cases of Rhodococcus equi infection which highlight the diversity of disease presentations of this rare organism.

Introduction: Malignant pleural effusions (MPEs) can complicate most cancers, causing dyspnoea and impairing quality of life (QoL). Indwelling pleural catheters (IPCs) are a novel management approach allowing ambulatory fluid drainage and are increasingly used as an alternative to pleurodesis. IPC drainage approaches vary greatly between centres. Some advocate aggressive (usually daily) removal of fluid to provide best symptom control and chance of spontaneous pleurodesis. Daily drainages however demand considerably more resources and may increase risks of complications. Others believe that MPE care is palliative and drainage should be performed only when patients become symptomatic (often weekly to monthly). Identifying the best drainage approach will optimise patient care and healthcare resource utilisation., Methods and Analysis: A multicentre, open-label randomised trial. Patients with MPE will be randomised 1:1 to daily or symptom-guided drainage regimes after IPC insertion. Patient allocation to groups will be stratified for the cancer type (mesothelioma vs others), performance status (Eastern Cooperative Oncology Group status 0-1 vs ≥2), presence of trapped lung (vs not) and prior pleurodesis (vs not). The primary outcome is the mean daily dyspnoea score, measured by a 100 mm visual analogue scale (VAS) over the first 60 days. Secondary outcomes include benefits on physical activity levels, rate of spontaneous pleurodesis, complications, hospital admission days, healthcare costs and QoL measures. Enrolment of 86 participants will detect a mean difference of VAS score of 14 mm between the treatment arms (5% significance, 90% power) assuming a common between-group SD of 18.9 mm and a 10% lost to follow-up rate., Ethics and Dissemination: The Sir Charles Gairdner Group Human Research Ethics Committee has approved the study (number 2015-043). Results will be published in peer-reviewed journals and presented at scientific meetings., Trial Registration Number: ACTRN12615000963527; Pre-results., (Published by the BMJ Publishing Group Limited. For permission to use (where not already granted under a licence) please go to http://www.bmj.com/company/products-services/rights-and-licensing/)

Introduction: Malignant pleural effusion can complicate most cancers. It causes breathlessness and requires hospitalisation for invasive pleural drainages. Malignant effusions often herald advanced cancers and limited prognosis. Minimising time spent in hospital is of high priority to patients and their families. Various treatment strategies exist for the management of malignant effusions, though there is no consensus governing the best choice. Talc pleurodesis is the conventional management but requires hospitalisation (and substantial healthcare resources), can cause significant side effects, and has a suboptimal success rate. Indwelling pleural catheters (IPCs) allow ambulatory fluid drainage without hospitalisation, and are increasingly employed for management of malignant effusions. Previous studies have only investigated the length of hospital care immediately related to IPC insertion. Whether IPC management reduces time spent in hospital in the patients' remaining lifespan is unknown. A strategy of malignant effusion management that reduces hospital admission days will allow patients to spend more time outside hospital, reduce costs and save healthcare resources., Methods and Analysis: The Australasian Malignant Pleural Effusion (AMPLE) trial is a multicentred, randomised trial designed to compare IPC with talc pleurodesis for the management of malignant pleural effusion. This study will randomise 146 adults with malignant pleural effusions (1:1) to IPC management or talc slurry pleurodesis. The primary end point is the total number of days spent in hospital (for any admissions) from treatment procedure to death or end of study follow-up. Secondary end points include hospital days specific to pleural effusion management, adverse events, self-reported symptom and quality-of-life scores., Ethics and Dissemination: The Sir Charles Gairdner Group Human Research Ethics Committee has approved the study as have the ethics boards of all the participating hospitals. The trial results will be published in peer-reviewed journals and presented at scientific conferences., Trial Registration Numbers: Australia New Zealand Clinical Trials Registry-ACTRN12611000567921; National Institutes of Health-NCT02045121., (Published by the BMJ Publishing Group Limited. For permission to use (where not already granted under a licence) please go to http://group.bmj.com/group/rights-licensing/permissions.)

Endobronchial ultrasound-guided transbronchial needle aspiration (EBUS-TBNA) is a minimally invasive technique that allows lung cancer nodal staging and biopsy of parabronchial and paratracheal tissue. Its simplicity, high diagnostic yield, ability to diagnose both benign and malignant conditions, and exceedingly low complication rate has resulted in rapid widespread adoption by surgeons and physicians. EBUS-TBNA-related complications, however, do occur and need to be considered when assessing the risk-benefit profile of performing the procedure, and if the patient represents with unexpected symptoms after the procedure. We describe a 64-year-old woman who presented with a mediastinal abscess 5 days after EBUS-TBNA. This case demonstrates the importance of considering EBUS-TBNA-related complications to guide relevant imaging decisions and antibiotic choices. We review the published literature regarding infective complications of EBUS-TBNA and propose possible pathophysiologies. These complications are likely to increase in frequency as the technique is more widely adopted.

The usefulness of tumour ploidy as a prognostic determinant in lung cancer was evaluated in a group of 100 surgically treated patients. Archival paraffin sections of the tumours were analysed by flow cytometry. 45% of tumours were aneuploid and 55% were diploid. Overall, patients with aneuploid tumours had significantly shorter survival (p less than 0.0005) than those with diploid tumours. The subset of patients without nodal involvement at operation and with diploid tumours had a particularly long survival rate. Of these 45 patients 41 (91%) were alive at 2 years compared with only 16 (55%) of the 29 with aneuploid tumours (p less than 0.05). A group with such a favourable prognosis has not previously been recognised except when staging is based on total mediastinal nodal clearance. Ploidy was found to be independent of age, sex, type of operation, site of primary tumour, histology, or TNM category. On Cox multivariate analysis ploidy was the most important and independent prognostic determinant. Therefore, in patients with operable lung cancer, ploidy should be taken into account in planning of management, in estimation of prognosis, and in stratification for treatment trials.

A large total population study of childhood saltwater immersion accidents is reported. A total of 49 cases (16 fatalities, 33 survivors) occurred in the five year period from 1971 to 1975 in southeastern Queensland. As a group, more children survive a potentially fatal saltwater immersion (67%) than do those who lose consciousness in freshwater (50%). The serious saltwater accident rate (loss of consciousness or death) in childhood (from 0 to 15 years inclusive, is 3.37/100,000 children per year at risk (fatality rate 1.12). This is low; comparison with freshwater data shows that although the surf presents special hazards to children, it is very much safer than other types of water. Age-specific and site-specific accident and survival rates for saltwater immersions are presented for the first time. Toddlers are disproportionately represented (33% of all children) and their survival rates are lowest. Boating and the use of surfboards, in current practice, are negligible threats to children. The saltwater immersion rate is increasing (although the absolute risk is small) and reasons for this are discussed. Childhood saltwater immersions were unaffected by tidal state. All but one case of immersion occurred during daylight hours, and in younger children immersion occurred often on weekends.