Facilitating bioinformatics reproducibility with QIIME 2 Provenance Replay.

Study reproducibility is essential to corroborate, build on, and learn from the results of scientific research but is notoriously challenging in bioinformatics, which often involves large data sets and complex analytic workflows involving many different tools. Additionally, many biologists are not trained in how to effectively record their bioinformatics analysis steps to ensure reproducibility, so critical information is often missing. Software tools used in bioinformatics can automate provenance tracking of the results they generate, removing most barriers to bioinformatics reproducibility. Here we present an implementation of that idea, Provenance Replay, a tool for generating new executable code from results generated with the QIIME 2 bioinformatics platform, and discuss considerations for bioinformatics developers who wish to implement similar functionality in their software.

Colorectal cancer survivors' experiences and views of shared and telehealth models of survivorship care: A qualitative study.

OBJECTIVES: The number of colorectal cancer (CRC) survivors is increasing and current models of survivorship care are unsustainable. There is a drive to implement alternative models of care including shared care between general practitioners (GPs) and hospital-based providers. The primary objective of this study was to explore perspectives on facilitators and barriers to shared care. The secondary objective was to explore experiences of telehealth-delivered care. METHOD: Qualitative data were collected via semi-structured interviews with participants in the Shared Care for Colorectal Cancer Survivors (SCORE) randomised controlled trial. Interviews explored patient experiences of usual and shared survivorship care during the SCORE trial. In response to the COVID pandemic, participant experiences of telehealth appointments were also explored. Interviews were recorded and transcribed for thematic analysis. RESULTS: Twenty survivors of CRC were interviewed with an even number in the shared and usual care arms; 14 (70%) were male. Facilitators to shared care included: good relationships with GPs; convenience of GPs; good communication between providers; desire to reduce public health system pressures. Barriers included: poor communication between clinicians; inaccessibility of GPs; beliefs about GP capacity; and a preference for follow-up care with the hospital after positive treatment experiences. Participants also commonly expressed a preference for telehealth-based follow-up when there was no need for a clinical examination. CONCLUSIONS: This is one of few studies that have explored patient experiences with shared and telehealth-based survivorship care. Findings can guide the implementation of these models, particularly around care coordination, communication, preparation, and personalised pathways of care.

Pseudobudding: ruptured glands do not represent true tumor buds.

Tumor budding (TB) is a strong biomarker of poor prognosis in colorectal cancer and other solid cancers. TB is defined as isolated single cancer cells or clusters of up to four cancer cells at the invasive tumor front. In areas with a large inflammatory response at the invasive front, single cells and cell clusters surrounding fragmented glands are observed appearing like TB. Occurrence of these small groups is referred to as pseudobudding (PsB), which arises due to external influences such as inflammation and glandular disruption. Using a combination of orthogonal approaches, we show that there are clear biological differences between TB and PsB. TB is representative of active invasion by presenting features of epithelial-mesenchymal transition and exhibiting increased deposition of extracellular matrix within the surrounding tumor microenvironment (TME), whereas PsB represents a reactive response to heavy inflammation where increased levels of granulocytes within the surrounding TME are observed. Our study provides evidence that areas with a strong inflammatory reaction should be avoided in the routine diagnostic assessment of TB. © 2023 The Authors. The Journal of Pathology published by John Wiley & Sons Ltd on behalf of The Pathological Society of Great Britain and Ireland.

Transcriptomics and proteomics reveal distinct biology for lymph node metastases and tumour deposits in colorectal cancer.

Both lymph node metastases (LNMs) and tumour deposits (TDs) are included in colorectal cancer (CRC) staging, although knowledge regarding their biological background is lacking. This study aimed to compare the biology of these prognostic features, which is essential for a better understanding of their role in CRC spread. Spatially resolved transcriptomic analysis using digital spatial profiling was performed on TDs and LNMs from 10 CRC patients using 1,388 RNA targets, for the tumour cells and tumour microenvironment. Shotgun proteomics identified 5,578 proteins in 12 different patients. Differences in RNA and protein expression were analysed, and spatial deconvolution was performed. Image-based consensus molecular subtype (imCMS) analysis was performed on all TDs and LNMs included in the study. Transcriptome and proteome profiles identified distinct clusters for TDs and LNMs in both the tumour and tumour microenvironment segment, with upregulation of matrix remodelling, cell adhesion/motility, and epithelial-mesenchymal transition (EMT) in TDs (all p < 0.05). Spatial deconvolution showed a significantly increased abundance of fibroblasts, macrophages, and regulatory T-cells (p < 0.05) in TDs. Consistent with a higher fibroblast and EMT component, imCMS classified 62% of TDs as poor prognosis subtype CMS4 compared to 36% of LNMs (p < 0.05). Compared to LNMs, TDs have a more invasive state involving a distinct tumour microenvironment and upregulation of EMT, which are reflected in a more frequent histological classification of TDs as CMS4. These results emphasise the heterogeneity of locoregional spread and the fact that TDs should merit more attention both in future research and during staging. © 2023 The Authors. The Journal of Pathology published by John Wiley & Sons Ltd on behalf of The Pathological Society of Great Britain and Ireland.

A comparison of DNA sequencing and gene expression profiling to assist tissue of origin diagnosis in cancer of unknown primary.

Cancer of unknown primary (CUP) is a syndrome defined by clinical absence of a primary cancer after standardised investigations. Gene expression profiling (GEP) and DNA sequencing have been used to predict primary tissue of origin (TOO) in CUP and find molecularly guided treatments; however, a detailed comparison of the diagnostic yield from these two tests has not been described. Here, we compared the diagnostic utility of RNA and DNA tests in 215 CUP patients (82% received both tests) in a prospective Australian study. Based on retrospective assessment of clinicopathological data, 77% (166/215) of CUPs had insufficient evidence to support TOO diagnosis (clinicopathology unresolved). The remainder had either a latent primary diagnosis (10%) or clinicopathological evidence to support a likely TOO diagnosis (13%) (clinicopathology resolved). We applied a microarray (CUPGuide) or custom NanoString 18-class GEP test to 191 CUPs with an accuracy of 91.5% in known metastatic cancers for high-medium confidence predictions. Classification performance was similar in clinicopathology-resolved CUPs - 80% had high-medium predictions and 94% were concordant with pathology. Notably, only 56% of the clinicopathology-unresolved CUPs had high-medium confidence GEP predictions. Diagnostic DNA features were interrogated in 201 CUP tumours guided by the cancer type specificity of mutations observed across 22 cancer types from the AACR Project GENIE database (77,058 tumours) as well as mutational signatures (e.g. smoking). Among the clinicopathology-unresolved CUPs, mutations and mutational signatures provided additional diagnostic evidence in 31% of cases. GEP classification was useful in only 13% of cases and oncoviral detection in 4%. Among CUPs where genomics informed TOO, lung and biliary cancers were the most frequently identified types, while kidney tumours were another identifiable subset. In conclusion, DNA and RNA profiling supported an unconfirmed TOO diagnosis in one-third of CUPs otherwise unresolved by clinicopathology assessment alone. DNA mutation profiling was the more diagnostically informative assay. © 2022 The Authors. The Journal of Pathology published by John Wiley & Sons Ltd on behalf of The Pathological Society of Great Britain and Ireland.

A Quantitative Assessment of Staphylococcus aureus Community Carriage in Yuma, Arizona.

BACKGROUND: Disease control relies on pathogen identification and understanding reservoirs. Staphylococcus aureus infection prevention is based upon decades of research on colonization and infection, but diminishing returns from mitigation efforts suggest significant knowledge gaps. Existing knowledge and mitigation protocols are founded upon culture-based detection, with almost no information about pathogen quantities. METHODS: We used culture and a quantitative polymerase chain reaction assay on samples from 3 body sites to characterize colonization more comprehensively than previous studies by describing both prevalence and pathogen quantity. RESULTS: We show a much higher overall prevalence (65.9%) than previously documented, with higher quantities and prevalence associated with the nares, non-Hispanic males (86.9%), and correlating with colonization in other body sites. These results suggest that research and clinical practices likely misclassify over half of colonized persons, limiting mitigation measures and their impact. CONCLUSIONS: This work begins the process of rebuilding foundational knowledge of S aureus carriage with more accurate and wholistic approaches.

Open conversion in laparoscopic cholecystectomy and bile duct exploration: subspecialisation safely reduces the conversion rates.

BACKGROUND: Open conversion rates during laparoscopic cholecystectomy vary depending on many factors. Surgeon experience and operative difficulty influence the decision to convert on the grounds of patient safety but occasionally due to technical factors. We aim to evaluate the difficulties leading to conversion, the strategies used to minimise this event and how subspecialisation influenced conversion rates over time. METHODS: Prospectively collected data from 5738 laparoscopic cholecystectomies performed by a single surgeon over 28 years was analysed. Routine intraoperative cholangiography and common bile duct exploration when indicated are utilised. Patients undergoing conversion, fundus first dissection or subtotal cholecystectomy were identified and the causes and outcomes compared to those in the literature. RESULTS: 28 patients underwent conversion to open cholecystectomy (0.49%). Morbidity was relatively high (33%). 16 of the 28 patients (57%) had undergone bile duct exploration. The most common causes of conversion in our series were dense adhesions (9/28, 32%) and impacted bile duct stones (7/28, 25%). 173 patients underwent fundus first cholecystectomy (FFC) (3%) and 6 subtotal cholecystectomy (0.1%). Morbidity was 17.3% for the FFC and no complications were encountered in the subtotal cholecystectomy patients. These salvage techniques have reduced our conversion rate from a potential 3.5% to 0.49%. CONCLUSION: Although open conversion should not be seen as a failure, it carries a high morbidity and should only be performed when other strategies have failed. Subspecialisation and a high emergency case volume together with FFC and subtotal cholecystectomy as salvage strategies can reduce conversion and its morbidity in difficult cholecystectomies.

SaQuant: a real-time PCR assay for quantitative assessment of Staphylococcus aureus.

BACKGROUND: Molecular assays are important tools for pathogen detection but need to be periodically re-evaluated with the discovery of additional genetic diversity that may cause assays to exclude target taxa or include non-target taxa. A single well-developed assay can find broad application across research, clinical, and industrial settings. Pathogen prevalence within a population is estimated using such assays and accurate results are critical for formulating effective public health policies and guiding future research. A variety of assays for the detection of Staphylococcus aureus are currently available. The utility of commercial assays for research is limited, given proprietary signatures and lack of transparent validation. RESULTS: In silico testing of existing peer-reviewed assays show that most suffer from a lack of sensitivity and specificity. We found no assays that were specifically designed and validated for quantitative use. Here we present a qPCR assay, SaQuant, for the detection and quantification of S. aureus as might be collected on sampling swabs. Sensitivity and specificity of the assay was 95.6 and 99.9 %, respectively, with a limit of detection of between 3 and 5 genome equivalents and a limit of quantification of 8.27 genome equivalents. The presence of DNA from non-target species likely to be found in a swab sample, did not impact qualitative or quantitative abilities of the assay. CONCLUSIONS: This assay has the potential to serve as a valuable tool for the accurate detection and quantification of S. aureus collected from human body sites in order to better understand the dynamics of prevalence and transmission in community settings.

Optimising the outcomes of index admission laparoscopic cholecystectomy and bile duct exploration for biliary emergencies: a service model.

AIMS: The rate of acute laparoscopic cholecystectomy remains low due to operational constraints. The purpose of this study is to evaluate a service model of index admission cholecystectomy with referral protocols, refined logistics and targeted job planning. METHODS: A prospectively maintained dataset was evaluated to determine the processes of care and outcomes of patients undergoing emergency biliary surgery. The lead author has maintained a 28 years prospective database capturing standard demographic data, intraoperative details including the difficulty of cholecystectomy as well as postoperative outcome parameters and follow up data. RESULTS: Over five thousand (5555) consecutive laparoscopic cholecystectomies were performed. Only patients undergoing emergency procedures (2399,43.2% of entire group) were analysed for this study. The median age was 52 years with 70% being female. The majority were admitted with biliary pain (34%), obstructive jaundice (26%) and acute cholecystitis (16%). 63% were referred by other surgeons. 80% underwent surgery within 5 days (40% within 24 h). Cholecystectomies were performed on scheduled lists (44%) or dedicated emergency lists (29%). Two thirds had suspected bile duct stones and 38.1% underwent bile duct exploration. The median operating time was 75 min, median hospital stay 7 days, conversion rate 0.8%, morbidity 8.9% and mortality rate 0.2%. CONCLUSION: Index admission cholecystectomy for biliary emergencies can have low rates of morbidity and mortality. Timely referral and flexible theatre lists facilitate the service, optimising clinical results, number of biliary episodes, hospital stay and presentation to resolution intervals. Cost benefits and reduced interval readmissions need to be weighed against the length of hospital stay per episode.

Autologous stem cell transplantation in elderly multiple myeloma patients aged ≥65 years: a two-centre Australian experience.

There are currently limited Australian data on the outcomes of autologous stem cell transplantation (ASCT) in elderly multiple myeloma (MM) patients. We present the largest cohort of elderly MM patients aged ≥65 years undergoing ASCT in Australia and report their outcomes based on our two-centre experience. Our study affirms that ASCT is well tolerated, safe and effective in elderly MM patients aged ≥65 years and should be considered an important component of treatment in patients who are fit enough for the procedure.

Mercury-bearing wastes: Sources, policies and treatment technologies for mercury recovery and safe disposal.

Due to the lenient environmental policies in developing economies, mercury-containing wastes are partly produced as a result of the employment of mercury in manufacturing and consumer products. Worldwide, the presence of mercury as an impurity in several industrial processes leads to significant amounts of contaminated waste. The Minamata Convention on Mercury dictates that mercury-containing wastes should be handled in an environmentally sound way according to the Basel Convention Technical Guidelines. Nevertheless, the management policies differ a great deal from one country to another because only a few deploy or can afford to deploy the required technology and facilities. In general, elemental mercury and mercury-bearing wastes should be stabilized and solidified before they are disposed of or permanently stored in specially engineered landfills and facilities, respectively. Prior to physicochemical treatment and depending on mercury's concentration, the contaminated waste may be thermally or chemically processed to reduce mercury's content to an acceptable level. The suitability of the treated waste for final disposal is then assessed by the application of standard leaching tests whose capacity to evaluate its long-term behavior is rather questionable. This review critically discusses the main methods employed for the recovery of mercury and the treatment of contaminated waste by analyzing representative examples from the industry. Furthermore, it gives a complete overview of all relevant issues by presenting the sources of mercury-bearing wastes, explaining the problems associated with the operation of conventional discharging facilities and providing an insight of the disposal policies adopted in selected geographical regions.

A Highly Tunable Approach to Enhance CO2 Capture with Liquid Alkali/amines.

A diverse range of alkali/amine infused hydrogels (AIHs) were generated by incorporating the liquids into a hydrogel particle for carbon capture application. As a consequence, the CO2 uptake was significantly enhanced owing to the increased contact area. This AIHs technique was highly tunable as it could be applicable to varying species of alkali chemicals and it was found that their molecular structure and architectures could impact the CO2 uptake. Compared to stirred bulk alkali/amine solutions, the CO2 absorption capacity of AIHs was increased by 400% within 30 min with a low hydrogel loading (10 w/w%). In addition, the recyclability of various AIHs was assessed and was found to be extremely encouraging. The effect of salinity on the performance of AIHs was also investigated and high salinity was found to have a minimal effect on CO2 absorption. Most importantly, the preparation of AIHs is fast and straightforward with few wastes and byproducts formed in the preparation process. In all, extensive investigations were presented and the AIHs were found to be a highly tunable and effective approach to enhance CO2 capture with liquid alkali/amines.

Soluble Hyperbranched Porous Organic Polymers.

Soluble porous organic polymers (SPOPs) are currently the subject of extensive investigation due to the enhanced processability compared to insoluble counterparts. Here, a new concept for the construction of SPOPs is presented, which combines the unique topological structure of hyperbranched polymers with rigid building blocks. By using this facile, one-step strategy, a class of novel SPOPs which possess surface areas up to 646 m2 g-1 have been synthesized. The extended π-conjugated backbone affords the polymers bright fluorescence under UV irradiation. Interestingly, after dissolution in a suitable solvent that was slowly evaporated, the polymers retain a large extent of porosity. The SPOPs are potential candidates for gas storage and separation, photovoltaic, and biological applications. In particular, due to the presence of an internal porous structure and open conformations, they show high drug loading efficiency (1.91 g of ibuprofen per gram), which is considerably higher than conventional porous organic polymers.

Lack of durable disease control with chemotherapy for mycosis fungoides and Sézary syndrome: a comparative study of systemic therapy.

Numerous systemic treatment options exist for patients with mycosis fungoides (MF) and Sézary syndrome (SS), but no large comparative studies are published. To study the efficacy of treatments, a retrospective analysis of our cutaneous lymphoma database was undertaken, with 198 MF/SS patients undergoing systemic therapies. The primary end point was time to next treatment (TTNT). Patients with advanced-stage disease made up 53%. The median follow-up time from diagnosis for all alive patients was 4.9 years (range 0.3-39.6), with a median survival of 11.4 years. Patients received a median of 3 lines of therapy (range 1-13), resulting in 709 treatment episodes. Twenty-eight treatment modalities were analyzed. The median TTNT for single- or multiagent chemotherapy was only 3.9 months (95% confidence interval [CI] 3.2-5.1), with few durable remissions. α-interferon gave a median TTNT of 8.7 months (95% CI 6.0-18.0), and histone deacetylase inhibitors (HDACi) gave a median TTNT of 4.5 months (95% CI 4.0-6.1). When compared directly with chemotherapy, interferon and HDACi both had greater TTNT (P < .00001 and P = .01, respectively). This study confirms that all chemotherapy regimens assessed have very modest efficacy; we recommend their use be restricted until other options are exhausted.

Hypercrosslinked Additives for Ageless Gas-Separation Membranes.

The loss of internal pores, a process known as physical aging, inhibits the long-term use of the most promising gas-separation polymers. Previously we reported that a porous aromatic framework (PAF-1) could form a remarkable nanocomposite with gas-separation polymers to stop aging. However, PAF-1 synthesis is very onerous both from a reagent and reaction-condition perspective, making it difficult to scale-up. We now reveal a highly dispersible and scalable additive based on α,α'-dichloro-p-xylene (p-DCX), that inhibits aging more effectively, and crucially almost doubles gas-transport selectivity. These synergistic effects are related to the intimately mixed nanocomposite that is formed though the high dispersibility of p-DCX in the gas-separation polymer. This reduces particle-size effects and the internal free volume is almost unchanged over time. This study shows this inexpensive and scalable polymer additive delivers exceptional gas-transport performance and selectivity.

Hierarchical Porous Polystyrene Monoliths from PolyHIPE.

Hierarchical porous polystyrene monoliths (HCP-PolyHIPE) are obtained by hypercrosslinking poly(styrene-divinylbenzene) monoliths prepared by polymerization of high internal phase emulsions (PolyHIPEs). The hypercrosslinking is achieved using an approach known as knitting which employs formaldehyde dimethyl acetal (FDA) as an external crosslinker. Scanning electron microscopy (SEM) confirms that the macroporous structure in the original monolith is retained during the knitting process. By increasing the amount of divinylbenzene (DVB) in PolyHIPE, the BET surface area and pore volume of the HCP-PolyHIPE decrease, while the micropore size increases. BET surface areas of 196-595 m(2) g(-1) are obtained. The presence of micropores, mesopores, and macropores is confirmed from the pore size distribution. With a hierarchical porous structure, the monoliths reveal comparable gas sorption properties and potential applications in oil spill clean-up.

Synthesizing Hypercrosslinked Polymers with Deep Eutectic Solvents to Enhance CO2/N2 Selectivity.

Hypercrosslinked polymers (HCPs) are widely used in ion exchange, water purification, and gas separation. However, HCP synthesis typically requires hazardous halogenated solvents e. g., dichloroethane, dichloromethane and chloroform which are toxic to human health and environment. Herein we hypothesize that the use of halogenated solvents in HCP synthesis can be overcome with deep eutectic solvents (DES) comprising metal halides-FeCl3, ZnCl2 that can act as both the solvent hydrogen bond donor and catalyst for polymer crosslinking via Friedel Crafts alkylation. We validated our hypothesis by synthesizing HCPs in DESs via internal and external crosslinking strategies. [ChCl][ZnCl2]2 and [ChCl][FeCl3]2 was more suitable for internal and external hypercrosslinking, respectively. The specific surface areas of HCPs synthesized in DES were 20-60 % lower than those from halogenated solvents, but their CO2/N2 selectivities were up to 453 % higher (CO2/N2 selectivity of poly-α,α'-dichloro-p-xylene synthesized in [ChCl][ZnCl2]2 via internal crosslinking reached a value of 105). This was attributed to the narrower pore size distributions of HCPs synthesized in DESs.

Facile Synthesis of Self-Supported Solid Amine Sorbents for Direct Air Capture.

Conventional usage of tetraethylenepentamine (TEPA) via being supported on porous solid materials for carbon capture is susceptible to oxidative degradation during regeneration cycles. This study reports a novel method to synthesize a TEPA based solid polymer for efficient CO2 removal via direct air capture (DAC). The polymer was obtained through epoxy-amine crosslinking reaction, leading to the transformation of liquid TEPA to a self-supported solid polymer. The synthesis was conducted under ambient conditions via a one-pot process with no waste products, which is aligned with green synthesis. The performance of the solid amine was evaluated in DAC under realistic conditions and compared with TEPA supported on SiO2 and zeolite 13X prepared through the conventional method. The solid TEPA amine exhibited a high CO2 uptake of 6.2 wt.% comparable to the conventional counterparts. More importantly, the solid TEPA amine demonstrated high resistance to oxidation during the accelerated ageing process at 80 °C in air for 24 h, whereas the two supported TEPA samples experienced severe degradation, with zeolite 13X supported TEPA incurring a reduction of 86.5 % in CO2 capturing capacity after the ageing. This work sheds light on the novel usage of TEPA as an efficient solid amine for practical DAC operation.