Feature-specific quantile normalization and feature-specific mean-variance normalization deliver robust bi-directional classification and feature selection performance between microarray and RNAseq data.

BACKGROUND: Cross-platform normalization seeks to minimize technological bias between microarray and RNAseq whole-transcriptome data. Incorporating multiple gene expression platforms permits external validation of experimental findings, and augments training sets for machine learning models. Here, we compare the performance of Feature Specific Quantile Normalization (FSQN) to a previously used but unvalidated and uncharacterized method we label as Feature Specific Mean Variance Normalization (FSMVN). We evaluate the performance of these methods for bidirectional normalization in the context of nested feature selection. RESULTS: FSQN and FSMVN provided clinically equivalent bidirectional model performance with and without feature selection for colon CMS and breast PAM50 classification. Using principal component analysis, we determine that these methods eliminate batch effects related to technological platforms. Without feature selection, no statistical difference was identified between the performance of FSQN and FSMVN of cross-platform data compared to within-platform distributions. Under optimal feature selection conditions, balanced accuracy was FSQN and FSMVN were statistically equivalent to the within-platform distribution performance in multivariable linear regression analysis. FSQN and FSMVN also provided similar performance to within-platform distributions as the number of selected genes used to create models decreases. CONCLUSIONS: In the context of generating supervised machine learning classifiers for molecular subtypes, FSQN and FSMVN are equally effective. Under optimal modeling conditions, FSQN and FSMVN provide equivalent model accuracy performance on cross-platform normalization data compared to within-platform data. Using cross-platform data should still be approached with caution as subtle performance differences may exist depending on the classification problem, training, and testing distributions.

Multiple stressors alter greenhouse gas concentrations in streams through local and distal processes.

Streams are significant contributors of greenhouse gases (GHG) to the atmosphere, and the increasing number of stressors degrading freshwaters may exacerbate this process, posing a threat to climatic stability. However, it is unclear whether the influence of multiple stressors on GHG concentrations in streams results from increases of in-situ metabolism (i.e., local processes) or from changes in upstream and terrestrial GHG production (i.e., distal processes). Here, we hypothesize that the mechanisms controlling multiple stressor effects vary between carbon dioxide (CO2) and methane (CH4), with the latter being more influenced by changes in local stream metabolism, and the former mainly responding to distal processes. To test this hypothesis, we measured stream metabolism and the concentrations of CO2 (pCO2) and CH4 (pCH4) in 50 stream sites that encompass gradients of nutrient enrichment, oxygen depletion, thermal stress, riparian degradation and discharge. Our results indicate that these stressors had additive effects on stream metabolism and GHG concentrations, with stressor interactions explaining limited variance. Nutrient enrichment was associated with higher stream heterotrophy and pCO2, whereas pCH4 increased with oxygen depletion and water temperature. Discharge was positively linked to primary production, respiration and heterotrophy but correlated negatively with pCO2. Our models indicate that CO2-equivalent concentrations can more than double in streams that experience high nutrient enrichment and oxygen depletion, compared to those with oligotrophic and oxic conditions. Structural equation models revealed that the effects of nutrient enrichment and discharge on pCO2 were related to distal processes rather than local metabolism. In contrast, pCH4 responses to nutrient enrichment, discharge and temperature were related to both local metabolism and distal processes. Collectively, our study illustrates potential climatic feedbacks resulting from freshwater degradation and provides insight into the processes mediating stressor impacts on the production of GHG in streams.

Os rios são grandes emissores de gases com efeito de estufa (GEE) para a atmosfera, e o crescente número de agentes de stress que degradam os rios pode exacerbar este processo, e constituir uma ameaça à estabilidade climática. No entanto, não é claro se o efeito dos impactos humanos nas concentrações de GEE na água está associado ao aumento do metabolismo local do rio (processos locais) ou ao aumento da produção de GEE nas zonas a montante dos rios ou nas zonas terrestres adjacentes (processos distais). A nossa hipótese é que os mecanismos que controlam os efeitos dos impactos humanos na emissão de GEE variam entre o dióxido de carbono (CO2) e o metano (CH4). A nossa previsão é que o CO2 responde principalmente a processos distais, enquanto o CH4 é mais influenciado por alterações no metabolismo local dos cursos de água. Para avaliar esta hipótese, medimos o metabolismo aquático e as concentrações de CO2 (pCO2) e CH4 (pCH4) em 50 rios que abrangem gradientes de enriquecimento em nutrientes, depleção de oxigénio, stress térmico, degradação da zona ribeirinha e caudal. Os nossos resultados indicam que estes agentes de stress tiveram efeitos aditivos no metabolismo e nas concentrações de GEE nos rios, e que as interações entre os agentes de stress tiveram pouca capacidade preditiva. O enriquecimento em nutrientes foi associado a um aumento da heterotrofia e pCO2, enquanto o pCH4 aumentou com a depleção de oxigénio e com a temperatura da água. O caudal estava positivamente correlacionado com a produção primária, a respiração e a heterotrofia, mas negativamente correlacionado com o pCO2. Os nossos modelos indicam que as concentrações equivalentes de CO2 podem duplicar em rios eutrofizados e com baixa concentração de oxigénio, em comparação com os rios oligotróficos e com águas bem oxigenadas. A aplicação de modelos de equações estruturais mostrou que os efeitos do enriquecimento em nutrientes e do caudal no pCO2 estavam relacionados com processos distais e não com o metabolismo local. Em contrapartida, as respostas do pCH4 ao enriquecimento de nutrientes, ao caudal e à temperatura estavam relacionadas tanto com o metabolismo local como com processos distais. O nosso estudo demonstra que a degradação dos rios e dos ecossistemas ribeirinhos pode ter efeitos negativos na estabilidade climática e fornece informação relevante sobre os processos biogeoquímicos que medeiam os impactos humanos na produção de GEE nos rios.

Treated and highly diluted, but wastewater still impacts diversity and energy fluxes of freshwater food webs.

Wastewater treatment plants (WWTPs) have greatly improved water quality globally. However, treated effluents still contain a complex cocktail of pollutants whose environmental effects might go unnoticed, masked by additional stressors in the receiving waters or by spatiotemporal variability. We conducted a BACI (Before-After/Control-Impact) ecosystem manipulation experiment, where we diverted part of the effluent of a large tertiary WWTP into a small, unpolluted stream to assess the effects of a well-treated and highly diluted effluent on riverine diversity and food web dynamics. We sampled basal food resources, benthic invertebrates and fish to search for changes on the structure and energy transfer of the food web with the effluent. Although effluent toxicity was low, it reduced diversity, increased primary production and herbivory, and reduced energy fluxes associated to terrestrial inputs. Altogether, the effluent decreased total energy fluxes in stream food webs, showing that treated wastewater can lead to important ecosystem-level changes, affecting the structure and functioning of stream communities even at high dilution rates. The present study shows that current procedures to treat wastewater can still affect freshwater ecosystems and highlights the need for further efforts to treat polluted waters to conserve aquatic food webs.

A global synthesis of human impacts on the multifunctionality of streams and rivers.

Human impacts, particularly nutrient pollution and land-use change, have caused significant declines in the quality and quantity of freshwater resources. Most global assessments have concentrated on species diversity and composition, but effects on the multifunctionality of streams and rivers remain unclear. Here, we analyse the most comprehensive compilation of stream ecosystem functions to date to provide an overview of the responses of nutrient uptake, leaf litter decomposition, ecosystem productivity, and food web complexity to six globally pervasive human stressors. We show that human stressors inhibited ecosystem functioning for most stressor-function pairs. Nitrate uptake efficiency was most affected and was inhibited by 347% due to agriculture. However, concomitant negative and positive effects were common even within a given stressor-function pair. Some part of this variability in effect direction could be explained by the structural heterogeneity of the landscape and latitudinal position of the streams. Ranking human stressors by their absolute effects on ecosystem multifunctionality revealed significant effects for all studied stressors, with wastewater effluents (194%), agriculture (148%), and urban land use (137%) having the strongest effects. Our results demonstrate that we are at risk of losing the functional backbone of streams and rivers if human stressors persist in contemporary intensity, and that freshwaters are losing critical ecosystem services that humans rely on. We advocate for more studies on the effects of multiple stressors on ecosystem multifunctionality to improve the functional understanding of human impacts. Finally, freshwater management must shift its focus toward an ecological function-based approach and needs to develop strategies for maintaining or restoring ecosystem functioning of streams and rivers.

Water diversion and pollution interactively shape freshwater food webs through bottom-up mechanisms.

Water diversion and pollution are two pervasive stressors in river ecosystems that often co-occur. Individual effects of both stressors on basal resources available to stream communities have been described, with diversion reducing detritus standing stocks and pollution increasing biomass of primary producers. However, interactive effects of both stressors on the structure and trophic basis of food webs remain unknown. We hypothesized that the interaction between both stressors increases the contribution of the green pathway in stream food webs. Given the key role of the high-quality, but less abundant, primary producers, we also hypothesized an increase in food web complexity with larger trophic diversity in the presence of water diversion and pollution. To test these hypotheses, we selected four rivers in a range of pollution subject to similar water diversion schemes, and we compared food webs upstream and downstream of the diversion. We characterized food webs by means of stable isotope analysis. Both stressors directly changed the availability of basal resources, with water diversion affecting the brown food web by decreasing detritus stocks, and pollution enhancing the green food web by promoting biofilm production. The propagation of the effects at the base of the food web to higher trophic levels differed between stressors. Water diversion had little effect on the structure of food webs, but pollution increased food chain length and trophic diversity, and reduced trophic redundancy. The effects at higher trophic levels were exacerbated when combining both stressors, as the relative contribution of biofilm to the stock of basal resources increased even further. Overall, we conclude that moderate pollution increases food web complexity and that the interaction with water abstraction seems to amplify this effect. Our study shows the importance of assessing the interaction between stressors to create predictive tools for a proper management of ecosystems.

Yield of routine staging laparoscopy in patients with gastric cancer in Alberta, Canada.

BACKGROUND: Despite guidelines recommending diagnostic laparoscopy in patients with gastric cancer, implementation is low. We aimed to explore trends in the use of laparoscopy for staging of gastric cancer in Alberta, Canada, determine the rate of positive findings and identify factors predictive of positive staging laparoscopy (SL) findings in this patient population. METHODS: In August 2018, we sent a survey to all general surgeons in Alberta who were members of the Alberta Association of General Surgeons to identify those treating gastric cancer. The survey inquired about type of practice (academic or community), gastric cancer case volume, routine versus selective use of SL and, if selective use of SL, criteria used to select cases. Participants were also asked to provide data from their SL cases from July 2007 to February 2019. We double-checked surgeon records with chart review. The primary outcome was evidence of metastatic disease on SL or cytologic examination or both. We performed logistic regression analysis to identify factors predictive of positive laparoscopy findings. RESULTS: The survey was completed by 41 of 127 surgeons (response rate 32.3%). We reviewed 116 cases from 5 surgeons at 4 centres. Gross metastatic disease or positive findings on cytologic examination or both were identified in 37 patients (31.9%). On univariate analysis, the following were associated with an increased risk of identification of metastatic disease at laparoscopy: visualization of the primary tumour on computed tomography (CT) (odds ratio [OR] 9.8, 95% confidence interval [CI] 1.2-76.5), presence of abdominal lymphadenopathy greater than 1 cm (OR 2.4, 95% CI 1.1-5.4) and presence of ascites (OR 19.1, 95% CI 2.2-161.8). Visualization of the primary tumour on CT (OR 8.4, 95% CI 1.0-68.3) and the presence of ascites (OR 15.9, 95% CI 1.8-137.0) remained statistically significant predictors on multivariate analysis. CONCLUSION: Metastatic disease was identified at SL in almost one-third of cases, which suggests that SL should still be used routinely in gastric cancer staging in Canadian centres. Our study identified several preoperative imaging findings associated with evidence of metastatic disease on laparoscopy; however, further studies are needed to establish robust predictors of positive findings before advocating for a selective SL approach.

Evaluating the utility of computed tomography of the chest for gastric cancer staging

Background: International guidelines recommend routine computed tomography (CT) of the chest for gastric cancer staging. In Asian countries, where the incidence of pulmonary metastases is less than 1%, some guidelines recommend chest CT only for gastroesophageal junction cancers. If the incidence of pulmonary metastases is also low in Canada, routine chest CT may not be beneficial. Methods: We performed a retrospective review of patients in northern Alberta with newly diagnosed gastric cancer from January 2010 to July 2016. The primary aim of the study was to determine the incidence of pulmonary metastases at the time of diagnosis in this population. A secondary aim was to identify potential predictors of pulmonary metastases. We reviewed CT reports for pulmonary metastases. Imaging data also included liver metastases, abdominal lymphadenopathy (> 1 cm), ascites and omental or peritoneal nodules. Other data recorded were age, sex, primary tumour location, histologic type and tumour grade. Results: Four hundred and sixty-two patients (311 men, 151 women) were included in the analysis. Pulmonary metastases were identified in 25 patients (5.4%) overall and in 11 of 299 patients (3.7%) whose primary cancer was not in the cardia. On univariate analysis the presence of liver metastases (odds ratio [OR] 7.72, 95% confidence interval [CI] 3.24­18.37, p < 0.001) and abdominal lymphadenopathy (OR 3.30, 95% CI 1.29­8.48, p = 0.01) was associated with an increased risk of pulmonary metastases. Liver metastases retained statistical significance on multivariate analysis (OR 6.17, 95% CI 2.53­15.03, p < 0.001). Conclusion: The incidence of pulmonary metastases at the time of gastric cancer diagnosis is higher in northern Alberta than previously reported in Asian studies. Abdominal lymphadenopathy and liver metastases confer an elevated risk of pulmonary metastases.

Contexte: Les lignes directrices internationales recommandent une tomodensitométrie (TDM) thoracique de routine pour la stadification du cancer de l'estomac. Dans les pays asiatiques, où l'incidence des métastases pulmonaires est inférieure à 1 %, certaines lignes directrices recommandent la TMD thoracique seulement dans les cancers de la jonction gastro-oesophagienne. Si l'incidence des métastases pulmonaires est également faible au Canada, la TDM thoracique de routine pourrait ne pas être bénéfique. Méthodes: Nous avons procédé à une analyse rétrospective des patients du Nord de l'Alberta ayant reçu un diagnostic de cancer de l'estomac entre janvier 2010 et juillet 2016. L'objectif principal de l'étude était de déterminer l'incidence des métastases pulmonaires au moment du diagnostic chez cette population. Un objectif secondaire consistait à identifier les prédicteurs potentiels des métastases pulmonaires. Les rapports de TDM ont été passés en revue pour ce qui est des métastases pulmonaires. Les données provenant des épreuves d'imagerie incluaient aussi les métastases hépatiques, la lymphadénopathie abdominale (> 1 cm), l'ascite et les nodules épiploïques ou péritonéaux. Parmi les autres données consignées, mentionnons l'âge, le sexe, de même que la localisation, le type histologique et le grade de la tumeur principale. Résultats: Quatre cent soixante-deux patients (311 hommes, 151 femmes) ont été inclus dans l'analyse. Globalement, des métastases pulmonaires ont été observées chez 25 patients (5,4 %), et chez 11 patients sur 299 (3,7 %) dont le cancer principal ne se situait pas dans le cardia. À l'analyse univariée, la présence de métastases hépatiques (rapport des cotes [RC] 7,72, intervalle de confiance [IC] de 95 % de 3,24 à 18,37, p < 0,001) et de lymphadénopathie abdominale (RC 3,30, IC de 95 %, de 1,29 à 8,48, p = 0,01) a été associée à un risque accru de métastases pulmonaires. Les métastases hépatiques ont conservé leur portée statistique lors de l'analyse multivariée (RC 6,17, IC de 95 % de 2,53 à 15,03, p < 0,001). Conclusion: L'incidence des métastases pulmonaires au moment où un diagnostic de cancer de l'estomac est posé s'est révélée plus élevée dans le Nord de l'Alberta que dans les rapports d'études asiatiques précédentes. La lymphadénopathie abdominale et les métastases hépatiques confèrent un risque élevé de métastases pulmonaires.

Simulating rewetting events in intermittent rivers and ephemeral streams: A global analysis of leached nutrients and organic matter.

Climate change and human pressures are changing the global distribution and the extent of intermittent rivers and ephemeral streams (IRES), which comprise half of the global river network area. IRES are characterized by periods of flow cessation, during which channel substrates accumulate and undergo physico-chemical changes (preconditioning), and periods of flow resumption, when these substrates are rewetted and release pulses of dissolved nutrients and organic matter (OM). However, there are no estimates of the amounts and quality of leached substances, nor is there information on the underlying environmental constraints operating at the global scale. We experimentally simulated, under standard laboratory conditions, rewetting of leaves, riverbed sediments, and epilithic biofilms collected during the dry phase across 205 IRES from five major climate zones. We determined the amounts and qualitative characteristics of the leached nutrients and OM, and estimated their areal fluxes from riverbeds. In addition, we evaluated the variance in leachate characteristics in relation to selected environmental variables and substrate characteristics. We found that sediments, due to their large quantities within riverbeds, contribute most to the overall flux of dissolved substances during rewetting events (56%-98%), and that flux rates distinctly differ among climate zones. Dissolved organic carbon, phenolics, and nitrate contributed most to the areal fluxes. The largest amounts of leached substances were found in the continental climate zone, coinciding with the lowest potential bioavailability of the leached OM. The opposite pattern was found in the arid zone. Environmental variables expected to be modified under climate change (i.e. potential evapotranspiration, aridity, dry period duration, land use) were correlated with the amount of leached substances, with the strongest relationship found for sediments. These results show that the role of IRES should be accounted for in global biogeochemical cycles, especially because prevalence of IRES will increase due to increasing severity of drying events.

Immediate and legacy effects of urban pollution on river ecosystem functioning: A mesocosm experiment.

Effluents from urban wastewater treatment plants (WWTP) consist of complex mixtures of substances that can affect processes in the receiving ecosystems. Some of these substances (toxic contaminants) stress biological activity at all concentrations, while others (e.g., nutrients) subsidize it at low concentrations and stress it above a threshold, causing subsidy-stress responses. Thus, the overall effects of WWTP effluents depend mostly on their composition and the dilution capacity of the receiving water bodies. We assessed the immediate and legacy effects of WWTP effluents in artificial streams, where we measured the uptake of soluble reactive phosphorus (SRP) by the biofilm, biomass accrual, benthic metabolism and organic matter decomposition (OMD). In a first phase (32 d), the channels were subjected to a gradient of effluent contribution, from pure stream water to pure effluent. WWTP effluent affected the ecosystem processes we measured, although we found no clear subsidy-stress patterns except for biofilm biomass accrual. Instead, most of the processes were subsidized, although they showed complex and process-specific patterns. Benthic metabolism and OMD were subsidized without saturation, as they peaked at medium and high levels of pollution, respectively, but they never fell below control levels. SRP uptake was the only process that decreased with increasing effluent concentration. In a second phase of the experiment (23 d), all channels were kept on pure stream water to analyse the legacy effects of the effluent. For most of the processes, there were clear legacy effects, which followed either subsidy, stress, or subsidy-stress patterns. SRP uptake capacity was stressed with increasing pollution legacy, whereas algal accrual and benthic metabolism continued being subsidized. Conversely, biofilm biomass accrual and OMD showed no legacy effects. Overall, the WWTP effluent caused complex and process-specific responses in our experiment, mainly driven by the mixed contribution of subsidizers and stressors. These results help improving our understanding of the effects of urban pollution on stream ecosystem functioning.

Drivers of nitrogen transfer in stream food webs across continents.

Studies of trophic-level material and energy transfers are central to ecology. The use of isotopic tracers has now made it possible to measure trophic transfer efficiencies of important nutrients and to better understand how these materials move through food webs. We analyzed data from thirteen 15 N-ammonium tracer addition experiments to quantify N transfer from basal resources to animals in headwater streams with varying physical, chemical, and biological features. N transfer efficiencies from primary uptake compartments (PUCs; heterotrophic microorganisms and primary producers) to primary consumers was lower (mean 11.5%, range <1% to 43%) than N transfer efficiencies from primary consumers to predators (mean 80%, range 5% to >100%). Total N transferred (as a rate) was greater in streams with open compared to closed canopies and overall N transfer efficiency generally followed a similar pattern, although was not statistically significant. We used principal component analysis to condense a suite of site characteristics into two environmental components. Total N uptake rates among trophic levels were best predicted by the component that was correlated with latitude, DIN:SRP, GPP:ER, and percent canopy cover. N transfer efficiency did not respond consistently to environmental variables. Our results suggest that canopy cover influences N movement through stream food webs because light availability and primary production facilitate N transfer to higher trophic levels.

A population-based study of outcomes in patients with gastrointestinal neuroendocrine tumours.

BACKGROUND: Neuroendocrine tumours (NETs) are heterogeneous, with varying presentations and treatment options. To our knowledge, there are no randomized and few long-term studies of patient outcomes. The role of surgical and medical therapy for local, regional and metastatic disease continues to be evaluated in the literature. METHODS: We conducted a population-based search of the provincial cancer registry to identify patients with gastrointestinal NETs from the stomach, small intestine, colon and rectum diagnosed between 1990 and 2005 and assessed their outcomes. RESULTS: We examined clinicopathological information on the outcomes of 530 patients with gastrointestinal NETs. The overall incidence of NETs increased from 11 per million to 19 per million during the study period. Advancing stage and patient age were associated with poor overall or disease-specific outcomes. Surgery, both curative and palliative, was associated with decreased risk of overall (hazard ratio [HR] 0.5, p < 0.001) and disease-specific (HR 0.5, p < 0.001) death. The biggest benefit was observed in patients with distant disease, in whom 5-year disease-specific survival for R0 resections was nearly double that for patients with macroscopic residual disease (92% v. 48%, p = 0.009). Older age was associated with poor 5-year overall and disease-specific survival (p < 0.001). CONCLUSION: There has been a significant increase in incidence of gastrointestinal NETs, and advancing patient age, but not sex, is linked to poor outcomes in terms of overall and disease-specific survival. Surgery, both curative and palliative, was associated with decreased risk of overall and disease-specific death. Compared with patients with residual macroscopic disease, patients with distant disease were nearly twice as likely to survive 5 years if they had R0 resections. The use of radioisotope therapy and long-acting octreotide therapy was also associated with improved outcomes overall.

CONTEXTE: Les tumeurs neuroendocrines (TNE) sont hétérogènes, et les tableaux et options thérapeutiques sont variables. À notre connaissance, il n'existe pas d'études randomisées et il y a peu d'études à long terme sur les résultats chez les patients. Le rôle du traitement chirurgical et médicamenteux de la maladie locale, régionale et métastatique continue d'être évalué dans la littérature. MÉTHODES: Nous avons procédé à une interrogation démographique du Registre provincial du cancer pour recenser les patients atteints de TNE gastro-intestinales provenant de l'estomac, de l'intestin grêle, du côlon et du rectum, diagnostiqués entre 1990 et 2005 et nous avons évalué les résultats. RÉSULTATS: Nous avons examiné les données clinico-pathologiques des résultats enregistrés chez 530 patients atteints de TNE gastro-intestinales. L'incidence globale des TNE a augmenté de 11 par million à 19 par million pendant la période de l'étude. Le stade de la maladie et l'âge avancés ont été associés à des résultats globaux ou spécifiques à la maladie moins favorables. La chirurgie, curative et palliative, a été associée à un risque moindre de décès global (risque relatif [RR] 0.5, p < 0,001) et spécifique à la maladie (RR 0,5, p < 0,001). L'avantage le plus marqué a été observé chez les patients présentant une maladie distale, chez qui la survie à 5 ans spécifique à la maladie pour les résections R0 était près de 2 fois celle des patients présentant une maladie macroscopique résiduelle (92 % c. 48 %, p = 0,009). L'âge avancé a été associé à une survie à 5 ans globale et spécifique à la maladie défavorable (p < 0,001). CONCLUSION: L'incidence des TNE gastro-intestinales a significativement augmenté, et l'âge avancé des patients, mais non le sexe, est lié à des résultats défavorables aux plans de la survie globale et spécifique à la maladie. La chirurgie, curative et palliative, a été associée à un risque moindre de décès global et spécifique à la maladie. Comparativement aux patients ayant une maladie macroscopique résiduelle, ceux qui avaient une maladie distale étaient près de 2 fois plus susceptibles de survivre 5 ans s'ils avaient des résections R0. Les traitements par radio-isotopes et octréotide à longue durée d'action ont aussi été associés à une amélioration globale des résultats.

(1)H-NMR urinary metabolomic profiling for diagnosis of gastric cancer.

BACKGROUND: Metabolomics has shown promise in gastric cancer (GC) detection. This research sought to identify whether GC has a unique urinary metabolomic profile compared with benign gastric disease (BN) and healthy (HE) patients. METHODS: Urine from 43 GC, 40 BN, and 40 matched HE patients was analysed using (1)H nuclear magnetic resonance ((1)H-NMR) spectroscopy, generating 77 reproducible metabolites (QC-RSD <25%). Univariate and multivariate (MVA) statistics were employed. A parsimonious biomarker profile of GC vs HE was investigated using LASSO regularised logistic regression (LASSO-LR). Model performance was assessed using Receiver Operating Characteristic (ROC) curves. RESULTS: GC displayed a clear discriminatory biomarker profile; the BN profile overlapped with GC and HE. LASSO-LR identified three discriminatory metabolites: 2-hydroxyisobutyrate, 3-indoxylsulfate, and alanine, which produced a discriminatory model with an area under the ROC of 0.95. CONCLUSIONS: GC patients have a distinct urinary metabolite profile. This study shows clinical potential for metabolic profiling for early GC diagnosis.

Stream drying drives microbial ammonia oxidation and first-flush nitrate export.

Stream microbial communities and associated processes are influenced by environmental fluctuations that may ultimately dictate nutrient export. Discharge fluctuations caused by intermittent stream flow are increasing worldwide in response to global change. We examined the impact of flow cessation and drying on in-stream nitrogen cycling. We determined archaeal (AOA) and bacterial ammonia oxidizer (AOB) abundance and ammonia oxidation activity in surface and deep sediments from different sites along the Fuirosos stream (Spain) subjected to contrasting hydrological conditions (i.e., running water, isolated pools, and dry streambeds). AOA were more abundant than AOB, with no major changes across hydrological conditions or sediment layers. However, ammonia oxidation activity and sediment nitrate content increased with the degree of stream drying, especially in surface sediments. Upscaling of our results shows that ammonia oxidation in dry streambeds can contribute considerably (~50%) to the high nitrate export typically observed in intermittent streams during first-flush events following flow reconnection. Our study illustrates how the dry channels of intermittent streams can be potential hotspots of ammonia oxidation. Consequently, shifts in the duration, spatial extent and severity of intermittent flow can play a decisive role in shaping nitrogen cycling and export along fluvial networks in response to global change.

Individual Survival Distributions Generated by Multi-Task Logistic Regression Yield a New Perspective on Molecular and Clinical Prognostic Factors in Gastric Adenocarcinoma.

Recent advances in our understanding of gastric cancer biology have prompted a shift towards more personalized therapy. However, results are based on population-based survival analyses, which evaluate the average survival effects of entire treatment groups or single prognostic variables. This study uses a personalized survival modelling approach called individual survival distributions (ISDs) with the multi-task logistic regression (MTLR) model to provide novel insight into personalized survival in gastric adenocarcinoma. We performed a pooled analysis using 1043 patients from a previously characterized database annotated with molecular subtypes from the Cancer Genome Atlas, Asian Cancer Research Group, and tumour microenvironment (TME) score. The MTLR model achieved a 5-fold cross-validated concordance index of 72.1 ± 3.3%. This model found that the TME score and chemotherapy had similar survival effects over the entire study time. The TME score provided the greatest survival benefit beyond a 5-year follow-up. Stage III and Stage IV disease contributed the greatest negative effect on survival. The MTLR model weights were significantly correlated with the Cox model coefficients (Pearson coefficient = 0.86, p < 0.0001). We illustrate how ISDs can accurately predict the survival time for each patient, which is especially relevant in cases of molecular subtype heterogeneity. This study provides evidence that the TME score is principally associated with long-term survival in gastric adenocarcinoma. Additional external validation and investigation into the clinical utility of this ISD model in gastric cancer is an area of future research.

The Tumour Immune Microenvironment Drives Survival Outcomes and Therapeutic Response in an Integrated Molecular Analysis of Gastric Adenocarcinoma.

PURPOSE: We performed an integrated analysis of molecular classification systems proposed by The Cancer Genome Atlas (TCGA), the Asian Cancer Research Group (ACRG) and the Tumour Microenvironment Score (TME) to identify which classification scheme(s) are most promising to pursue in subsequent translational investigations. EXPERIMENTAL DESIGN: Supervised machine learning classifiers were created using 10-fold nested cross-validation for TCGA, ACRG and TME subtypes and applied to 2,202 gastric cancer patients from 11 separate publicly available datasets. Overall survival was assessed with a multivariable Cox proportional hazards model. A propensity score matched analysis was performed to evaluate the subgroup effect of adjuvant chemotherapy on molecular subtypes. A public external cohort comprised of metastatic gastric cancer treated with immunotherapy was used to externally validate the molecular subtypes. RESULTS: Classification models for TCGA, ACRG and TME achieved an accuracy ± standard deviation of 89.5% ± 0.04, 84.7% ± 0.04 and 89.3% ± 0.02, respectively. We identified the TME score as the only significantly prognostic classification system (HR 0.54 [95% CI 0.39, 0.74], global Wald test p<0.001). In our subgroup analysis, patients who received adjuvant chemotherapy achieved greater survival with increasing TME score (HR 0.47 [95% CI 0.29, 0.74], interaction p<0.05). The combination of TME High and microsatellite instability (MSI) scores significantly outperformed MSI as a univariable predictor of immunotherapy response. CONCLUSIONS: We conclude that the Tumour Microenvironment Score is a predominate driver of prognosis as well as chemotherapy and immunotherapy-related outcomes in gastric cancer. This paper provides a foundation for additional analyses and translational work.

Unravelling large-scale patterns and drivers of biodiversity in dry rivers.

More than half of the world's rivers dry up periodically, but our understanding of the biological communities in dry riverbeds remains limited. Specifically, the roles of dispersal, environmental filtering and biotic interactions in driving biodiversity in dry rivers are poorly understood. Here, we conduct a large-scale coordinated survey of patterns and drivers of biodiversity in dry riverbeds. We focus on eight major taxa, including microorganisms, invertebrates and plants: Algae, Archaea, Bacteria, Fungi, Protozoa, Arthropods, Nematodes and Streptophyta. We use environmental DNA metabarcoding to assess biodiversity in dry sediments collected over a 1-year period from 84 non-perennial rivers across 19 countries on four continents. Both direct factors, such as nutrient and carbon availability, and indirect factors such as climate influence the local biodiversity of most taxa. Limited resource availability and prolonged dry phases favor oligotrophic microbial taxa. Co-variation among taxa, particularly Bacteria, Fungi, Algae and Protozoa, explain more spatial variation in community composition than dispersal or environmental gradients. This finding suggests that biotic interactions or unmeasured ecological and evolutionary factors may strongly influence communities during dry phases, altering biodiversity responses to global changes.

Pancreatic ductal adenocarcinoma is associated with a distinct urinary metabolomic signature.

BACKGROUND: Pancreatic ductal adenocarcinoma (PDAC) is an aggressive malignancy with poor prognosis in part due to the lack of early detection and screening methods. Metabolomics provides a means for noninvasive screening of tumor-associated perturbations in cellular metabolism. METHODS: Urine samples of PDAC patients (n = 32), healthy age and gender-matched controls (n = 32), and patients with benign pancreatic conditions (n = 25) were examined using (1)H-NMR spectroscopy. Targeted profiling of spectra permitted quantification of 66 metabolites. Unsupervised (principal component analysis, PCA) and supervised (orthogonal partial-least squares discriminant analysis, OPLS-DA) multivariate pattern recognition techniques were applied to discriminate between sample spectra using SIMCA-P(+) (version 12, Umetrics, Sweden). RESULTS: Clear distinction between PDAC and controls was noted when using OPLS-DA. Significant differences in metabolite concentrations between cancers and controls (p < 0.001) were noted. Model parameters for both goodness of fit, and predictive capability were high (R (2) = 0.85; Q (2) = 0.59, respectively). Internal validation methods were used to confirm model validity. Sensitivity and specificity of the multivariate OPLS-DA model were summarized using a receiver operating characteristics (ROC) curve, with an area under the curve (AUROC) = 0.988, indicating strong predictive power. Preliminary analysis revealed an AUROC = 0.958 for the model of benign pancreatic disease compared with PDAC, and suggest that the cancer-associated metabolomic signature dissipates following RO resection. CONCLUSIONS: Urinary metabolomics detected distinct differences in the metabolic profiles of pancreatic cancer compared with healthy controls and benign pancreatic disease. These preliminary results suggest that metabolomic approaches may facilitate discovery of novel pancreatic cancer biomarkers.

Increased CD4/CD8 Lymphocyte ratio predicts favourable neoadjuvant treatment response in gastric cancer: A prospective pilot study.

BACKGROUND: Despite optimal neoadjuvant chemotherapy only 40% of gastric cancer tumours achieve complete or partial treatment response. In the absence of treatment response, neoadjuvant chemotherapy in gastric cancer contributes to adverse events without additional survival benefit compared to adjuvant treatment or surgery alone. Additional strategies and methods are required to optimize the allocation of existing treatment regimens such as FLOT chemotherapy (5-Fluorouracil, Leucovorin, Oxaliplatin and Docetaxel). Predictive biomarkers detected using immunohistochemistry (IHC) methods may provide useful data regarding treatment response. AIM: To investigate the utility of CD4, CD8, Galectin-3 and E-cadherin in predicting neoadjuvant FLOT chemotherapy tumour response in gastric adenocarcinoma. METHODS: Forty-three adult patients with gastric adenocarcinoma, of which 18 underwent neoadjuvant chemotherapy, were included in a prospective clinical cohort. Endoscopic biopsies were obtained from gastric cancer and normal adjacent gastric mucosa. Differences in expression of Galectin-3, E-cadherin, CD4+ and CD8+ molecules between tumours with and without treatment response to neoadjuvant chemotherapy were assessed with IHC. Treatment response was graded by clinical pathologists using the Tumour Regression Score according to the College of American Pathologists criteria. Treatment response was defined as complete or near complete tumour response, whereas partial or poor/no response was defined as incomplete. Digital IHC images were annotated and quantitatively assessed using QuPath 0.3.1. Biomarker expression between responsive and incomplete response tumours was assessed using a two-sided Wilcoxon test. Biomarker expression was also compared between normal and cancer tissue and between 15 paired tumour samples before and after chemotherapy. We performed a preliminary multivariate analysis and power analysis to guide future study. Statistical analyses were completed using R 4.1.2. RESULTS: The ratio between CD4+ and CD8+ lymphocytes was significantly greater in treatment responsive tumours (Wilcoxon, P = 0.03). In univariate models, CD4+/CD8+ ratio was the only biomarker that significantly predicted favourable treatment response (Accuracy 86%, P < 0.001). Using a glmnet multivariate model, high CD4+/CD8+ ratio and low Galectin-3 expression were the most influential variables in predicting a favourable treatment response. Analyses of paired samples found that FLOT chemotherapy also results in increased expression of CD4+ and CD8+ tumour infiltrating lymphocytes (Paired Wilcoxon, P = 0.002 and P = 0.008, respectively). Our power analysis suggests future study requires at least 35 patients in each treatment response group for CD8 and Galectin-3 molecules, whereas 80 patients in each treatment response group are required to assess CD4 and E-cadherin biomarkers. CONCLUSION: We demonstrate that an elevated CD4+/CD8+ Ratio is a promising IHC-based biomarker to predict favourable treatment response to FLOT neoadjuvant chemotherapy in locally advanced gastric cancer.

Pulse, Shunt and Storage: Hydrological Contraction Shapes Processing and Export of Particulate Organic Matter in River Networks.

Streams and rivers act as landscape-scale bioreactors processing large quantities of terrestrial particulate organic matter (POM). This function is linked to their flow regime, which governs residence times, shapes organic matter reactivity and controls the amount of carbon (C) exported to the atmosphere and coastal oceans. Climate change impacts flow regimes by increasing both flash floods and droughts. Here, we used a modelling approach to explore the consequences of lateral hydrological contraction, that is, the reduction of the wet portion of the streambed, for POM decomposition and transport at the river network scale. Our model integrates seasonal leaf litter input as generator of POM, transient storage of POM on wet and dry streambed portions with associated decomposition and ensuing changes in reactivity, and transport dynamics through a dendritic river network. Simulations showed that the amount of POM exported from the river network and its average reactivity increased with lateral hydrological contraction, due to the combination of (1) low processing of POM while stored on dry streambeds, and (2) large shunting during flashy events. The sensitivity analysis further supported that high lateral hydrological contraction leads to higher export of higher reactivity POM, regardless of transport coefficient values, average reactivity of fresh leaf litter and differences between POM reactivity under wet and dry conditions. Our study incorporates storage in dry streambed areas into the pulse-shunt concept (Raymond and others in Ecology 97(1):5-16, 2016. 10.1890/14-1684.1), providing a mechanistic framework and testable predictions about leaf litter storage, transport and decomposition in fluvial networks. Supplementary Information: The online version contains supplementary material available at 10.1007/s10021-022-00802-4.

Urinary metabolomic signature of esophageal cancer and Barrett's esophagus.

BACKGROUND: Esophageal adenocarcinoma (EAC) often presents at a late, incurable stage, and mortality has increased substantially, due to an increase in incidence of EAC arising out of Barrett's esophagus. When diagnosed early, however, the combination of surgery and adjuvant therapies is associated with high cure rates. Metabolomics provides a means for non- invasive screening of early tumor-associated perturbations in cellular metabolism. METHODS: Urine samples from patients with esophageal carcinoma (n = 44), Barrett's esophagus (n = 31), and healthy controls (n = 75) were examined using (1)H-NMR spectroscopy. Targeted profiling of spectra using Chenomx software permitted quantification of 66 distinct metabolites. Unsupervised (principal component analysis) and supervised (orthogonal partial least-squares discriminant analysis OPLS-DA) multivariate pattern recognition techniques were applied to discriminate between samples using SIMCA-P(+) software. Model specificity was also confirmed through comparison with a pancreatic cancer cohort (n = 32). RESULTS: Clear distinctions between esophageal cancer, Barrett's esophagus and healthy controls were noted when OPLS-DA was applied. Model validity was confirmed using two established methods of internal validation, cross-validation and response permutation. Sensitivity and specificity of the multivariate OPLS-DA models were summarized using a receiver operating characteristic curve analysis and revealed excellent predictive power (area under the curve = 0.9810 and 0.9627 for esophageal cancer and Barrett's esophagus, respectively). The metabolite expression profiles of esophageal cancer and pancreatic cancer were also clearly distinguishable with an area under the receiver operating characteristics curve (AUROC) = 0.8954. CONCLUSIONS: Urinary metabolomics identified discrete metabolic signatures that clearly distinguished both Barrett's esophagus and esophageal cancer from controls. The metabolite expression profile of esophageal cancer was also discrete from its precursor lesion, Barrett's esophagus. The cancer-specific nature of this profile was confirmed through comparison with pancreatic cancer. These preliminary results suggest that urinary metabolomics may have a future potential role in non-invasive screening in these conditions.