Response to Ustekinumab Therapy Is Associated with an Improvement of Nutritional Status in Patients with Crohn's Disease.

The presence of sarcopenia has been associated with the worst outcome of Crohn's disease (CD). At present, no studies have evaluated the impact of ustekinumab (UST) in terms of its effects on body composition. The aim of this prospective study was to evaluate whether UST treatment could modify the parameters of body composition as assessed by bioelectrical impedance assay (BIA) in patients with CD. We prospectively enrolled consecutive patients with CD treated with UST, evaluating the therapeutic outcome at week 48 in terms of clinical remission and mucosal healing. BIA was performed at baseline and at week 48, assessing body cellular mass, total body water, phase angle, and body mass index. Out of 44 patients enrolled, 26 (59%) were in clinical remission and 22 (50%) achieved mucosal healing at the end of follow up. No significant differences were observed at baseline in all the BIA parameters between responders and non-responders. Phase angle increased over time in responders, while this was not observed in non-responders (test for the interaction between time and outcome, p-value = 0.009 and 0.007 for clinical remission and mucosal healing, respectively). The same differential increase was observed for body cellular mass (test for the interaction between time and outcome, p-value = 0.03 and 0.05 for clinical remission and mucosal healing, respectively). Total body water and BMI increased homogenously over time regardless of the outcomes (tests for the association with time, p-values of 0.01). To conclude, responsiveness to UST therapy seems to be associated with body composition modifications in patients with CD. In particular, the increase in phase angle in responders suggests that a significant improvement of nutritional status occurred in these patients.

Density declines, richness increases, and composition shifts in stream macroinvertebrates.

Documenting trends of stream macroinvertebrate biodiversity is challenging because biomonitoring often has limited spatial, temporal, and taxonomic scopes. We analyzed biodiversity and composition of assemblages of >500 genera, spanning 27 years, and 6131 stream sites across forested, grassland, urban, and agricultural land uses throughout the United States. In this dataset, macroinvertebrate density declined by 11% and richness increased by 12.2%, and insect density and richness declined by 23.3 and 6.8%, respectively, over 27 years. In addition, differences in richness and composition between urban and agricultural versus forested and grassland streams have increased over time. Urban and agricultural streams lost the few disturbance-sensitive taxa they once had and gained disturbance-tolerant taxa. These results suggest that current efforts to protect and restore streams are not sufficient to mitigate anthropogenic effects.

Novel Field-Based Protein Detection Method Using Light Transmission Spectroscopy and Antibody Functionalized Gold Nanoparticles.

Protein detection is a universal tool critical to many applications in medicine, agriculture, and biotechnology. We developed a novel protein detection method combining light transmission spectroscopy and particle-size analysis of gold nanospheres monovalently functionalized with polyclonal antibodies and applied it to an emerging challenge for such technologies─the monitoring of environmental proteins (eProteins) present in natural aquatic systems. These are an underreported source of pollution and include the pseudopersistent Cry toxins that enter aquatic ecosystems from surrounding genetically engineered crops. The assay is capable of detecting proteins in complex matrices, such as water samples collected in the field, making it a competitive assay for eProtein detection. It is sensitive, reaching 1.25 ng mL-1, and we demonstrate its application to the detection of Cry1Ab from subsurface tile-drain and streamwater samples from agricultural waterways. The assay can also be quickly adapted for other protein detection applications in the future.

Urban net primary production: Concepts, field methods, and Baltimore, Maryland, USA case study.

Given the large and increasing amount of urban, suburban, and exurban land use on Earth, there is a need to accurately assess net primary productivity (NPP) of urban ecosystems. However, the heterogeneous and dynamic urban mosaic presents challenges to the measurement of NPP, creating landscapes that may appear more similar to a savanna than to the native landscape replaced. Studies of urban biomass have tended to focus on one type of vegetation (e.g., lawns or trees). Yet a focus on the ecology of the city should include the entire urban ecosystem rather than the separate investigation of its parts. Furthermore, few studies have attempted to measure urban aboveground NPP (ANPP) using field-based methods. Most studies project growth rates from measurements of tree diameter to estimate annual ANPP or use remote sensing approaches. In addition, field-based methods for measuring NPP do not address any special considerations for adapting such field methods to urban landscapes. Frequent planting and partial or complete removal of herbaceous and woody plants can make it difficult to accurately quantify increments and losses of plant biomass throughout an urban landscape. In this study, we review how ANPP of urban landscapes can be estimated based on field measurements, highlighting the challenges specific to urban areas. We then estimated ANPP of woody and herbaceous vegetation over a 15-year period for Baltimore, MD, USA using a combination of plot-based field data and published values from the literature. Baltimore's citywide ANPP was estimated to be 355.8 g m-2 , a result that we then put into context through comparison with other North American Long-Term Ecological Research (LTER) sites and mean annual precipitation. We found our estimate of Baltimore citywide ANPP to be only approximately half as much (or less) than ANPP at forested LTER sites of the eastern United States, and more comparable to grassland, oldfield, desert, or boreal forest ANPP. We also found that Baltimore had low productivity for its level of precipitation. We conclude with a discussion of the significance of accurate assessment of primary productivity of urban ecosystems and critical future research needs.

Artificial Intelligence in the Diagnosis of Upper Gastrointestinal Diseases.

Artificial intelligence (AI) has enormous potential to support clinical routine workflows and therefore is gaining increasing popularity among medical professionals. In the field of gastroenterology, investigations on AI and computer-aided diagnosis (CAD) systems have mainly focused on the lower gastrointestinal (GI) tract. However, numerous CAD tools have been tested also in upper GI disorders showing encouraging results. The main application of AI in the upper GI tract is endoscopy; however, the need to analyze increasing loads of numerical and categorical data in short times has pushed researchers to investigate applications of AI systems in other upper GI settings, including gastroesophageal reflux disease, eosinophilic esophagitis, and motility disorders. AI and CAD systems will be increasingly incorporated into daily clinical practice in the coming years, thus at least basic notions will be soon required among physicians. For noninsiders, the working principles and potential of AI may be as fascinating as obscure. Accordingly, we reviewed systematic reviews, meta-analyses, randomized controlled trials, and original research articles regarding the performance of AI in the diagnosis of both malignant and benign esophageal and gastric diseases, also discussing essential characteristics of AI.

The meta-gut: community coalescence of animal gut and environmental microbiomes.

All animals carry specialized microbiomes, and their gut microbiota are continuously released into the environment through excretion of waste. Here we propose the meta-gut as a novel conceptual framework that addresses the ability of the gut microbiome released from an animal to function outside the host and alter biogeochemical processes mediated by microbes. We demonstrate this dynamic in the hippopotamus (hippo) and the pools they inhabit. We used natural field gradients and experimental approaches to examine fecal and pool water microbial communities and aquatic biogeochemistry across a range of hippo inputs. Sequencing using 16S RNA methods revealed community coalescence between hippo gut microbiomes and the active microbial communities in hippo pools that received high inputs of hippo feces. The shared microbiome between the hippo gut and the waters into which they excrete constitutes a meta-gut system that could influence the biogeochemistry of recipient ecosystems and provide a reservoir of gut microbiomes that could influence other hosts. We propose that meta-gut dynamics may also occur where other animal species congregate in high densities, particularly in aquatic environments.

Dosing the Coast: Leaking Sewage Infrastructure Delivers Large Annual Doses and Dynamic Mixtures of Pharmaceuticals to Urban Rivers.

Pharmaceuticals are commonly detected at low concentrations in surface waters, where they disrupt biological and ecological processes. Despite their ubiquity, the annual mass of pharmaceuticals exported from watersheds is rarely quantified. We used liquid chromatography-mass spectroscopy to screen for 92 pharmaceuticals in weekly samples from an urban stream network in Baltimore, MD, USA, that lacks wastewater treatment effluents. Across the network, we detected 37 unique compounds, with higher concentrations and more compounds in streams with higher population densities. We also used concentrations and stream discharge to calculate annual pharmaceutical loads at the watershed outlet, which range from less than 1 kg to ∼15 kg and are equivalent to tens of thousands of human doses. By calculating annual watershed mass balances for eight compounds, we show that ∼0.05 to ∼42% of the pharmaceuticals consumed by humans in this watershed are released to surface waters, with the importance of different pathways (leaking sewage vs treated wastewater effluent) differing among compounds. These results demonstrate the importance of developing, maintaining, and improving sewage infrastructure to protect water resources from pharmaceutical contamination.

Dietary Management of Eosinophilic Esophagitis: Tailoring the Approach.

Eosinophilic esophagitis (EoE) is a unique form of non-immunoglobulin E-mediated food allergy, restricted to the esophagus, characterized by esophageal eosinophil-predominant inflammation and dysfunction. The diagnosis requires an esophago-gastroduodenoscopy with esophageal biopsies demonstrating active eosinophilic inflammation with 15 or more eosinophils/high-power field, following the exclusion of alternative causes of eosinophilia. Food allergens trigger the disease, withdairy/milk, wheat/gluten, egg, soy/legumes, and seafood the most common. Therapeutic strategies comprise dietary restrictions, proton pump inhibitors, topical corticosteroids, biologic agents, and esophageal dilation when strictures are present. However, avoidance of trigger foods remains the only option targeting the cause, and not the effect, of the disease. Because EoE relapses when treatment is withdrawn, dietary therapy offers a long-term, drug-free alternative to patients who wish to remain off drugs and still be in remission. There are currently multiple dietary management strategies to choose from, each having its specific efficacy, advantages, and disadvantages that both clinicians and patients should acknowledge. In addition, dietary regimens should be tailored around each individual patient to increase the chance of tolerability and long-term adherence. In general, liquid elemental diets devoid of antigens and elimination diets restricting causative foods are valuable options. Designing diets on the basis of food allergy skin tests results is not reliable and should be avoided. This review summarizes the most recent knowledge regarding the clinical use of dietary measures in EoE. We discussed endpoints, rationale, advantages and disadvantages, and tailoring of diets, as well as currently available dietary regimens for EoE.

Fate of Environmental Proteins (eProteins) from Genetically Engineered Crops in Streams is Controlled by Water pH and Ecosystem Metabolism.

Environmental proteins (eProteins), such as Cry proteins associated with genetically engineered (GE) organisms, are present in ecosystems worldwide, but only rarely reach concentrations with detectable ecosystem-level impacts. Despite their ubiquity, the degradation and fate of Cry and other eProteins are mostly unknown. Here, we report the results of an experiment where we added Cry proteins leached from GE Bt maize to a suite of 19 recirculating experimental streams. We found that Cry exhibited a biphasic degradation with an initial phase of rapid and variable degradation within 1 h, followed by a slow and steady phase of degradation with traces of protein persisting after 48 h. The initial degradation was correlated with heterotrophic respiration and water column dissolved oxygen, confirming a previously documented association with stream metabolism. However, protein degradation persisted even with no biofilm and was faster at a more acidic pH, suggesting that water chemistry is also a critical factor in both degradation and subsequent detection. We suggest that Cry, as well as other eProteins, will have a rapid degradation caused by denaturation of proteins and pH changes, which confirms that the detection of Cry proteins in natural streams must be the result of steady and consistent leaching into the environment.

Nutrients and Pharmaceuticals Structure Bacterial Core Communities in Urban and Montane Stream Biofilms.

Bacteria in stream biofilms contribute to stream biogeochemical processes and are potentially sensitive to the substantial levels of pollution entering urban streams. To examine the effects of contaminants on stream biofilm bacteria in situ, we exposed growing biofilms to experimental additions of nutrients [nitrogen (N), phosphorus (P), and iron (Fe)], pharmaceuticals (caffeine and diphenhydramine), nutrients plus pharmaceuticals, or no contaminants using contaminant exposure substrates (CES) in three catchments in northern Utah. We performed our study at montane and urban sites to examine the influence of existing pollution on biofilm response. We identified bacterial core communities (core) for each contaminant treatment at each land-use type (e.g., nutrient addition montane bacterial core, nutrient addition urban bacterial core, pharmaceutical addition montane bacterial core) by selecting all taxa found in at least 75% of the samples belonging to each specific grouping. Montane and urban land-use distinguished bacterial cores, while nutrients and pharmaceuticals had subtle, but nonetheless distinct effects. Nutrients enhanced the dominance of already abundant copiotrophs [i.e., Pseudomonadaceae (Gammaproteobacteria) and Comamonadaceae (Betaproteobacteria)] within bacterial cores at montane and urban sites. In contrast, pharmaceuticals fostered species-rich bacterial cores containing unique contaminant-degrading taxa within Pseudomonadaceae and Anaerolineaceae (Chloroflexi). Surprisingly, even at urban sites containing ambient pharmaceutical pollution, pharmaceutical additions increased bacterial core richness, specifically within DR-16 (Betaproteobacteria), WCHB1-32 (Bacteroidetes), and Leptotrichiaceae (Fusobacteria). Nutrients exerted greater selective force than pharmaceuticals in nutrient plus pharmaceutical addition treatments, creating bacterial cores more closely resembling those under nutrient rather than pharmaceutical addition, and promoting unique Oscillatoriales (Cyanobacteria) taxa in urban streams. Our results show that additions of N, P, and Fe intensified the dominance of already abundant copiotrophs, while additions of caffeine and diphenhydramine enabled unique taxa associated with contaminant degradation to participate in bacterial cores. Further, biofilm bacteria at urban sites remained sensitive to pharmaceuticals commonly present in waters, suggesting a dynamic interplay among pharmaceutical pollution, bacterial diversity, and contaminant degradation.

Theoretical Perspectives of the Baltimore Ecosystem Study: Conceptual Evolution in a Social-Ecological Research Project.

The Earth's population will become more than 80% urban during this century. This threshold is often regarded as sufficient justification for pursuing urban ecology. However, pursuit has primarily focused on building empirical richness, and urban ecology theory is rarely discussed. The Baltimore Ecosystem Study (BES) has been grounded in theory since its inception and its two decades of data collection have stimulated progress toward comprehensive urban theory. Emerging urban ecology theory integrates biology, physical sciences, social sciences, and urban design, probes interdisciplinary frontiers while being founded on textbook disciplinary theories, and accommodates surprising empirical results. Theoretical growth in urban ecology has relied on refined frameworks, increased disciplinary scope, and longevity of interdisciplinary interactions. We describe the theories used by BES initially, and trace ongoing theoretical development that increasingly reflects the hybrid biological-physical-social nature of the Baltimore ecosystem. The specific mix of theories used in Baltimore likely will require modification when applied to other urban areas, but the developmental process, and the key results, will continue to benefit other urban social-ecological research projects.

Limnological effects of a large Amazonian run-of-river dam on the main river and drowned tributary valleys.

Run-of-river dams are often considered to have lower environmental impacts than storage dams due to their smaller reservoirs and low potential for flow alteration. However, this has been questioned for projects recently built on large rivers around the world. Two of the world's largest run-of-river dams-Santo Antônio and Jirau-were recently constructed on the Madeira River, a major tributary to the Amazon River in Brazil. Here we evaluate the effects of the creation of the Santo Antônio dam on the water chemistry and thermal structure of the Madeira River mainstem and back-flooded valleys of tributaries within the reservoir inundated area. In contrast to the mainstem river, some back-flooded tributaries periodically developed thermal stratification, which is associated with higher water residence times. Additionally, biochemical oxygen demand, partial pressure of CO2, and organic carbon all increased in the tributary valleys inundated by the reservoir, possibly due to increased input of allochthonous organic matter and its subsequent mineralization upon back-flooding-a common feature of newly flooded impoundments. The mainstem did not show detectable dam-related changes in water chemistry and thermal structure. Although the majority of the reservoir area maintained riverine conditions, the lateral valleys formed upon back-flooding-corresponding to ~30% of the Santo Antônio reservoir area-developed lake-like conditions akin to a typical reservoir of a storage dam.

Robotic correction of iatrogenic ureteral stricture: preliminary experience from a tertiary referral centre.

Objective: Iatrogenic stenosis is a relatively common complication and it could happen after urological procedures in the entire course of the ureter. The aim of this study is to report the surgical outcomes of 36 consecutive patients (period April 2013-November 2018) submitted to robot-assisted correction of benign stricture with previous urological surgery in a tertiary referral center.Methods: Elective criteria were to have had a benign ureteral stricture development after at least one urological procedure. Patients were classified as failures in the event of post-operative ultrasound demonstrating persistent hydronephrosis with or without symptoms or persistent symptoms with renal scan evidence of obstruction or redo procedures.Results: Eighteen patients (50%) were treated for calculosis, seven (19.4%) patients were submitted to double J ureteral stenting and previous pyeloplasty was performed in 11 (30.5%) patients. Overall median operative time was 160 min (IQR = 120-180). Five (13.8%) complications with three (8.3%) surgical post-operative complications occurred. Length of stay was 6 (IQR = 5-7) days. At last follow-up, ranging between 7-60 months, the overall success rate was 86.1% (31/36): three of them (8.3%) were submitted to retrograde holmium laser endopyelotomy, while two (5.5%) underwent a redo robot-assisted correction.Conclusions: Robot-assisted correction procedures can be done safely with good perioperative outcomes and a high post-operative success rate in a tertiary referral center. Further randomized clinical trials are mandatory to confirm the safety of this procedure.

Stoichiometry and daily rhythms: experimental evidence shows nutrient limitation decouples N uptake from photosynthesis.

Diel variability in nutrient concentrations is common but not universal in aquatic ecosystems. Theoretical models of photoautotrophic systems attribute the absence of diel uptake variation to nutrient scarcity, such that diel variability in nutrient uptake disappears as nutrients become limiting. We tested this prediction in a mesocosm experiment, by exposing benthic algal communities to a range of nitrogen (N) and phosphorus concentrations and recording the rates of uptake during both day and night. We found that higher concentrations of N produced diel variability in uptake and that the difference between the day and night total mass uptakes approximately equaled N demand for observed primary production as seen in other studies. At lower concentrations of N, uptake rates during the day and night were indistinguishable. These results are the first empirical evidence to imply that diel nitrate patterns in streams and rivers indicate a release from N limitation and offer a new way to assess nutrient limitation.

Seeing the light: urban stream restoration affects stream metabolism and nitrate uptake via changes in canopy cover.

The continually increasing global population residing in urban landscapes impacts numerous ecosystem functions and services provided by urban streams. Urban stream restoration is often employed to offset these impacts and conserve or enhance the various functions and services these streams provide. Despite the assumption that "if you build it, [the function] will come," current understanding of the effects of urban stream restoration on stream ecosystem functions are based on short term studies that may not capture variation in restoration effectiveness over time. We quantified the impact of stream restoration on nutrient and energy dynamics of urban streams by studying 10 urban stream reaches (five restored, five unrestored) in the Baltimore, Maryland, USA, region over a two-year period. We measured gross primary production (GPP) and ecosystem respiration (ER) at the whole-stream scale continuously throughout the study and nitrate (NO3- -N) spiraling rates seasonally (spring, summer, autumn) across all reaches. There was no significant restoration effect on NO3- -N spiraling across reaches. However, there was a significant canopy cover effect on NO3- -N spiraling, and directly comparing paired sets of unrestored-restored reaches showed that restoration does affect NO3- -N spiraling after accounting for other environmental variation. Furthermore, there was a change in GPP : ER seasonality, with restored and open-canopied reaches exhibiting higher GPP : ER during summer. The restoration effect, though, appears contingent upon altered canopy cover, which is likely to be a temporary effect of restoration and is a driver of multiple ecosystem services, e.g., habitat, riparian nutrient processing. Our results suggest that decision-making about stream restoration, including evaluations of nutrient benefits, clearly needs to consider spatial and temporal dynamics of canopy cover and trade-offs among multiple ecosystem services.

Transport and instream removal of the Cry1Ab protein from genetically engineered maize is mediated by biofilms in experimental streams.

The majority of maize planted in the US is genetically-engineered to express insecticidal properties, including Cry1Ab protein, which is designed to resist the European maize borer (Ostrinia nubilalis). After crop harvest, these proteins can be leached into adjacent streams from crop detritus left on fields. The environmental fate of Cry1Ab proteins in aquatic habitats is not well known. From June-November, we performed monthly short-term additions of leached Cry1Ab into four experimental streams with varying benthic substrate to estimate Cry1Ab transport and removal. At the start of the experiments, when rocks were bare, we found no evidence of Cry1Ab removal from the water column, but uptake steadily increased as biofilm colonized the stream substrate. Overall, Cry1Ab uptake was strongly predicted by measures of biofilm accumulation, including algal chlorophyll a and percent cover of filamentous algae. Average Cry1Ab uptake velocity (vf = 0.059 ± 0.009 mm s-1) was comparable to previously reported uptake of labile dissolved organic carbon (DOC; mean vf = 0.04 ± 0.008 mm s-1). Although Cry1Ab has been shown to rapidly degrade in stream water, benthic biofilms may decrease the distance proteins are transported in lotic systems. These results emphasize that once the Cry1Ab protein is leached, subsequent detection and transport through agricultural waterways is dependent on the structure and biology of receiving stream ecosystems.

Hippos (Hippopotamus amphibius): The animal silicon pump.

While the importance of grasslands in terrestrial silicon (Si) cycling and fluxes to rivers is established, the influence of large grazers has not been considered. Here, we show that hippopotamuses are key actors in the savannah biogeochemical Si cycle. Through a detailed analysis of Si concentrations and stable isotope compositions in multiple ecosystem compartments of a savannah-river continuum, we constrain the processes influencing the Si flux. Hippos transport 0.4 metric tons of Si day-1 by foraging grass on land and directly egesting in the water. As such, they bypass complex retention processes in secondary soil Si pools. By balancing internal processes of dissolution and precipitation in the river sediment, we calculate that hippos affect up to 76% of the total Si flux. This can have a large impact on downstream lake ecosystems, where Si availability directly affects primary production in the diatom-dominated phytoplankton communities.

A 2000-year sediment record reveals rapidly changing sedimentation and land use since the 1960s in the Upper Mara-Serengeti Ecosystem.

The Mara River basin is a trans-boundary basin of international importance. It forms the headwaters of the Nile River and serves as the primary dry season water source for an estimated 1.1 million rural people and the largest remaining overland migration of 1.4 million wildebeest in the Serengeti-Mara Ecosystem. Changes throughout the basin are impacting the quantity and quality of the Mara River, yet the historical context of environmental conditions in the basin is not well known. We collected sediment cores throughout the wetland at the mouth of the Mara River, and we used isotopic dating methods and a suite of analyses to examine historical patterns of sediment quantity and source, mercury contamination, and carbon and nutrient loading. Our results show that ecological conditions in the Mara River basin were fairly stable over paleoecological time scales (2000-1000 years before present), but there has been a period of rapid change in the basin over the last 250 years, particularly since the 1960s. A shift in the source and quantity of sediments in the river began in the late 1700s and became much more pronounced in the 1950s and 1960s, coincident with increasing mercury concentrations. The quantity of sediment from the Upper Mara increased, particularly since 1960, but the proportion of total sediment from this region decreased as the Talek and Middle Mara portions of the basin began producing more sediment. The decadal oscillation in sediment accumulation was congruent with known periods of extreme precipitation events. Carbon and nitrogen loading also increased since the 1960s, and the shift in the isotopic ratio of nitrogen provides evidence for increased anthropogenic loading. Altogether, these data likely reflect patterns of change also experienced in other basins throughout East Africa.

A diverse suite of pharmaceuticals contaminates stream and riparian food webs.

A multitude of biologically active pharmaceuticals contaminate surface waters globally, yet their presence in aquatic food webs remain largely unknown. Here, we show that over 60 pharmaceutical compounds can be detected in aquatic invertebrates and riparian spiders in six streams near Melbourne, Australia. Similar concentrations in aquatic invertebrate larvae and riparian predators suggest direct trophic transfer via emerging adult insects to riparian predators that consume them. As representative vertebrate predators feeding on aquatic invertebrates, platypus and brown trout could consume some drug classes such as antidepressants at as much as one-half of a recommended therapeutic dose for humans based on their estimated prey consumption rates, yet the consequences for fish and wildlife of this chronic exposure are unknown. Overall, this work highlights the potential exposure of aquatic and riparian biota to a diverse array of pharmaceuticals, resulting in exposures to some drugs that are comparable to human dosages.