Levels of persistent organic pollutants (POPs) and the role of anthropic subsidies in the diet of avian scavengers tracked by stable isotopes

Persistent Organic Pollutants (POPs) have been identified as a significant factor driving declines in wildlife populations. These contaminants exhibit a dual tendency to biomagnify up the food chains and persist within tissues, rendering long-lived vertebrates, such as raptors, highly vulnerable to their adverse effects. We assessed the concentrations of polychlorinated biphenyls (PCBs) and organochlorine pesticides (OCPs) in fledglings of two vulture species, the Egyptian vulture (Neophron percnopterus) and the griffon vulture (Gyps fulvus), coexisting in northern Spain. Vultures, currently facing a severe threat with a population decline exceeding 90%, represent one of the most critically endangered avian groups in the Old World. Despite this critical situation, there remains a scarcity of research examining the intricate relationship between contaminant levels and individual foraging behaviors. In parallel, we analyzed stable isotope levels (δ15N and δ13C) in fledgling's feathers and prey hair to determine the association between individual dietary and contaminant burdens. Our findings revealed higher levels of PCBs in Egyptian vultures, while pesticide concentrations remained very similar between focal species. Furthermore, higher individual values of δ13C, indicating a diet based on intensive farming carcasses and landfills, were associated with higher levels of PCBs. While the levels of POPs found do not raise immediate alarm, the presence of individuals with unusually high values reveals the existence of accessible contamination sources in the environment for avian scavengers. The increasing reliance of these birds on intensive livestock farming and landfills, due to the decline of extensive livestock farming, necessitates long-term monitoring of potential contaminant effects on their populations.

Brief report: High incidence of peridiagnosis thromboembolic events in patients with BRAF-mutant lung cancer

INTRODUCTION

We aimed to determine if advanced BRAF-mutant NSCLC has a higher thromboembolic events (TEE) rate than the expected.

METHODS

Between 2008 and 2021, 182 patients with BRAF-mutant advanced NSCLC (BRAF V600E, n = 70; BRAF non-V600E, n = 112) were retrospectively identified from 18 centers in Spain. Patients received chemotherapy (n = 147), immunotherapy (n = 69), targeted therapy (n = 42), and immunotherapy + chemotherapy (n = 26).

RESULTS

Incidence rate of TEE was 26.4 % (95%CI: 19.9 %-32.9 %). A total of 72 TEE were documented among 48 patients, as 18 patients (37.5 %) developed more than one event. Median time to TEE onset was 2 months, 69 % of TEE occurred in the peridiagnostic period (+/- 90 days from cancer diagnosis), and in 16 pts. (33 %) TEE was the form of lung cancer presentation. Although most TEE were only venous (82 %; PE, n = 33; DVT, n = 16), arterial events were reported in 31 % and occurred earlier, or TEE presented in atypical locations (13.9 %). TEE were related to high hospitalization rate (59 %), recurrence (23 %), and mortality (10.4 %) despite appropriate anticoagulant/antiaggregant treatment. Median OS in patients without-TEE was 19.4 months (95%CI: 4.6-34.1), and significantly shorter in patients with arterial-TEE vs venous-TEE vs both of them: 9.9 months (95%CI: 0-23.5) vs 41.7 months (95%CI: 11.3-72.2 m) vs 2.7 months (95%CI: 2.1-3.3), p = 0.001. Neither clinical or molecular features (BRAF V600E/non-V600E), nor cancer treatment was associated to TEE occurrence. Khorana score underperformed to predict thrombosis at cancer diagnosis, as only 19.2 % of patients were classified as high-risk.

CONCLUSIONS

Thrombotic events represent a new clinical feature of BRAF-mutant lung cancer. Patients with almost a 30 % incidence of TEE should be offered systematic anticoagulation.

Optimization of Diffusion-Ordered NMR Spectroscopy Experiments for High-Throughput Automation in Human Metabolic Phenotyping

The diffusion-ordered nuclear magnetic resonance spectroscopy (DOSY) experiment allows the calculation of diffusion coefficient values of metabolites in complex mixtures. However, this experiment has not yet been broadly used for metabolic profiling due to lack of a standardized protocol. Here we propose a pipeline for the DOSY experimental setup and data processing in metabolic phenotyping studies. Due to the complexity of biological samples, three experiments (a standard DOSY, a relaxation-edited DOSY, and a diffusion-edited DOSY) have been optimized to provide DOSY metabolic profiles with peak-picked diffusion coefficients for over 90% of signals visible in the one-dimensional 1H general biofluid profile in as little as 3 min 36 s. The developed parameter sets and tools are straightforward to implement and can facilitate the use of DOSY for metabolic profiling of human blood plasma and urine samples.

Patient Stratification in Sepsis: Using Metabolomics to Detect Clinical Phenotypes, Sub-Phenotypes and Therapeutic Response

Infections are common and need minimal treatment; however, occasionally, due to inappropriate immune response, they can develop into a life-threatening condition known as sepsis. Sepsis is a global concern with high morbidity and mortality. There has been little advancement in the treatment of sepsis, outside of antibiotics and supportive measures. Some of the difficulty in identifying novel therapies is the heterogeneity of the condition. Metabolic phenotyping has great potential for gaining understanding of this heterogeneity and how the metabolic fingerprints of patients with sepsis differ based on survival, organ dysfunction, disease severity, type of infection, treatment or causative organism. Moreover, metabolomics offers potential for patient stratification as metabolic profiles obtained from analytical platforms can reflect human individuality and phenotypic variation. This article reviews the most relevant metabolomic studies in sepsis and aims to provide an overview of the metabolic derangements in sepsis and how metabolic phenotyping has been used to identify sub-groups of patients with this condition. Finally, we consider the new avenues that metabolomics could open, exploring novel phenotypes and untangling the heterogeneity of sepsis, by looking at advances made in the field with other -omics technologies.

Circulating Metabolome and White Matter Hyperintensities in Women and Men

BACKGROUND

White matter hyperintensities (WMH), identified on T2-weighted magnetic resonance images of the human brain as areas of enhanced brightness, are a major risk factor of stroke, dementia, and death. There are no large-scale studies testing associations between WMH and circulating metabolites.

METHODS

We studied up to 9290 individuals (50.7% female, average age 61 years) from 15 populations of 8 community-based cohorts. WMH volume was quantified from T2-weighted or fluid-attenuated inversion recovery images or as hypointensities on T1-weighted images. Circulating metabolomic measures were assessed with mass spectrometry and nuclear magnetic resonance spectroscopy. Associations between WMH and metabolomic measures were tested by fitting linear regression models in the pooled sample and in sex-stratified and statin treatment-stratified subsamples. Our basic models were adjusted for age, sex, age×sex, and technical covariates, and our fully adjusted models were also adjusted for statin treatment, hypertension, type 2 diabetes, smoking, body mass index, and estimated glomerular filtration rate. Population-specific results were meta-analyzed using the fixed-effect inverse variance-weighted method. Associations with false discovery rate (FDR)-adjusted P values (PFDR)<0.05 were considered significant.

RESULTS

In the meta-analysis of results from the basic models, we identified 30 metabolomic measures associated with WMH (PFDR<0.05), 7 of which remained significant in the fully adjusted models. The most significant association was with higher level of hydroxyphenylpyruvate in men (PFDR.full.adj=1.40×10-7) and in both the pooled sample (PFDR.full.adj=1.66×10-4) and statin-untreated (PFDR.full.adj=1.65×10-6) subsample. In men, hydroxyphenylpyruvate explained 3% to 14% of variance in WMH. In men and the pooled sample, WMH were also associated with lower levels of lysophosphatidylcholines and hydroxysphingomyelins and a larger diameter of low-density lipoprotein particles, likely arising from higher triglyceride to total lipids and lower cholesteryl ester to total lipids ratios within these particles. In women, the only significant association was with higher level of glucuronate (PFDR=0.047).

CONCLUSIONS

Circulating metabolomic measures, including multiple lipid measures (eg, lysophosphatidylcholines, hydroxysphingomyelins, low-density lipoprotein size and composition) and nonlipid metabolites (eg, hydroxyphenylpyruvate, glucuronate), associate with WMH in a general population of middle-aged and older adults. Some metabolomic measures show marked sex specificities and explain a sizable proportion of WMH variance.

Cell immortalization facilitates prelamin A clearance by increasing both cell proliferation and autophagic flux

Hutchinson-Gilford Progeria Syndrome is an ultrarare disease which is characterized by an accelerated senescence phenotype with deleterious consequences to people suffering this pathology. The production of an abnormal protein derived from lamin A, called progerin, presents a farnesylated domain, which is not eliminated by the causal mutation of the disease, and accumulates in the interior of the nucleus, provoking a disruption of nuclear membrane, chromatin organization and an altered gene expression. The mutation in these patients occurs in a single nucleotide change, which creates a de novo splicing site, producing a shorter version of the protein. Apart from this mutation, an alteration in the metalloproteinase Zmpste24, involved in the maturation of lamin A, causing a similar alteration than in progeria. However, in this case, patients accumulate a protein, called prelamin A, which generates similar alterations in the nucleus than progerin. The reduction of prelamin A protein levels facilitates the recovery of the phenotype in different mice models of the disease, reducing the aging process. Different strategies have been studied for eliminating this toxic protein. Here, we report that immortalization of primary cells derived from the Zmpste24 KO mice, facilitates prelamin A degradation by different mechanisms, being essential, the enhancing proliferative capacity that the immortalized cells present. Then, these data suggest that using different treatments for increasing proliferative capacity of these cells, potentially could have a beneficial effect, facilitating prelamin A toxicity.

Structure Elucidation and Mitigation of Endogenous Interferences in LC-MS-Based Metabolic Profiling of Urine

Liquid chromatography-mass spectrometry (LC-MS) is the main workhorse of metabolomics owing to its high degree of analytical sensitivity and specificity when measuring diverse chemistry in complex biological samples. LC-MS-based metabolic profiling of human urine, a biofluid of primary interest for clinical and biobank studies, is not widely considered to be compromised by the presence of endogenous interferences and is often accomplished using a simple "dilute-and-shoot" approach. Yet, it is our experience that broad obscuring signals are routinely observed in LC-MS metabolic profiles and represent interferences that lack consideration in the relevant metabolomics literature. In this work, we chromatographically isolated the interfering metabolites from human urine and unambiguously identified them via de novo structure elucidation as two separate proline-containing dipeptides: N,N,N-trimethyl-l-alanine-l-proline betaine (l,l-TMAP) and N,N-dimethyl-l-proline-l-proline betaine (l,l-DMPP), the latter reported here for the first time. Offline LC-MS/MS, magnetic resonance mass spectrometry (MRMS), and nuclear magnetic resonance (NMR) spectroscopy were essential components of this workflow for the full chemical and spectroscopic characterization of these metabolites and for establishing the coexistence of cis and trans isomers of both dipeptides in solution. Analysis of these definitive structures highlighted intramolecular ionic interactions as responsible for slow interconversion between these isomeric forms resulting in their unusually broad elution profiles. Proposed mitigation strategies, aimed at increasing the quality of LC-MS-based urine metabolomics data, include modification of column temperature and mobile-phase pH to reduce the chromatographic footprint of these dipeptides, thereby reducing their interfering effect on the underlying metabolic profiles. Alternatively, sample dilution and internal standardization methods may be employed to reduce or account for the observed effects of ionization suppression on the metabolic profile.

Seroprevalence and immunological memory against SARS-CoV-2 in lung cancer patients: the SOLID study

Background

At present, we did not find any articles that studied seroprevalence and its persistence several months later in lung cancer patients in the setting of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection. Most patients with coronavirus disease 2019 (COVID-19) go on to develop antibodies (Abs) against viral proteins. However, it is not known how long these Abs last nor whether cancer treatments could affect the duration of immune response.

Methods

This prospective, longitudinal, multicenter serological study in the setting of SARS-CoV-2 infection was carried out in 50 Spanish hospitals. Eligibility criterion was the diagnosis of any lung cancer. The determination of anti-SARS-CoV-2 IgG Abs was performed by qualitative immuno-enzymatic assay using enzyme-linked immunosorbent assay (ELISA) kit from NovaLisa whose Abs target the recombinant antigen N of the nucleocapsid of SARS-CoV-2. The first Ab determination was performed between April 21 and June 3, 2020. The second Ab determination was performed in all previously seropositive patients, between September 10 and November 20, 2020. Study objectives were to prospectively determine seroprevalence in unselected lung cancer patients during the first wave of the pandemic; the persistence of immunity; protection or lack thereof against reinfection; and the influence of treatments on maintenance or loss of immunity.

Results

Of 1,500 patients, 128 were seropositive, overall prevalence of 8.5% seropositivity [95% confidence interval (CI): 7.2–10.1%]. Seventy-five percent were in active cancer treatment. Forty-seven point seven percent of IgG positive participants had experienced a symptomatic illness suspected of being infected with SARS-CoV-2 (95% CI: 38.8–56.6%). A second determination was performed on average 4.5 months later [interquartile range (IQR), 4.0–5.0 months] and obtained for 104 of the initially seropositive patients (81%), it could not be obtained in 24 patients, the majority due to death caused by disease progression (73%). In the second determination, IgG was not detected in 30.8% of patients. The severity of the infection, the need for hospitalization (P=0.032) and the presence of symptoms at diagnosis (P=0.02) were associated with persistence of immunity in the second determination. No variables or treatments received were associated with Abs loss.

Conclusions

Immunity against SARS-CoV-2 does not appear to be compromised by treatment and persists beyond 4 months. Neither do mortality rates appear to be particularly high in this unselected population.

Trial Registration

ClinicalTrials.gov identifier: NCT04407143.

[An update on parathyroid carcinoma]

Parathyroid carcinoma is a rare malignant disease that presents as a sporadic or familial primary hyperparathyroidism (PHP). The latter is associated with some genetic syndromes. It occurs with equal frequency in both sexes, unlike PHP caused by parathyroid adenoma that is more common in women. It should be suspected in cases of severe hypercalcemia, with high parathyroid hormone levels and a palpable cervical mass. Given the difficulty in distinguishing between parathyroid carcinoma and adenoma prior to the surgery, the diagnosis is often made after parathyroidectomy. The only curative treatment is complete surgical resection with oncologic block resection of the primary tumor to ensure free margins. Adjuvant therapies with chemotherapy or radiation therapy do not modify overall or disease-free survival. Recurrences are common and re-operation of resectable recurrent disease is recommended. The palliative treatment of symptomatic hypercalcemia is crucial in persistent or recurrent disease after surgery since morbidity and mortality are more associated with hypercalcemia than with tumor burden.

Changes in the Nutrient Composition of Barley Grain (Hordeum vulgare L.) and of Morphological Fractions of Sprouts

The objectives of the current study were (1) to evaluate the effect of sprouting on protein, amino acids, fats, fatty acids, starch, total soluble carbohydrates, and ß-D-glucan content of barley grains and (2) to know the content of these nutrients in the morphological fractions of sprouts: green shoot, residual structure of sprouted grain (RSSG), residual structure of sprouted grain plus unsprouted grain (RSSG plus UG), and root fractions and to determine the proportion of each of these fractions (on fresh and dry basis) in the sprout biomass. Barley grain was sprouted in a commercial germination chamber for a period of 6 days. Raw grain was used as a control. Results showed that crude protein, ether extract, total soluble carbohydrates, and cellulose content increased, whereas starch and ß-D-glucan content decreased in sprouted when compared with the control grain. Amino acid and fatty acid profiles were also affected. Thus, aspartic acid, threonine, alanine, valine, isoleucine, lysine, and tryptophan content increased and only that of glutamic acid decreased after sprouting. Regarding fatty acids, an increase in the relative concentration of C18 : 0 and C18:3n-3 and a decrease in that of C18:1n-9 were detected. Partitioning of sprouted barley into three morphological component fractions showed that the residual structures of sprouted grains plus unsprouted grain fraction made up 82.9% and 93.6% of sprout biomass, on fresh and DM basis, respectively, and the remainder was provided by the root fraction, 10.3% and 3.2%, respectively, and by the green shoot fraction, 6.8% and 3.1%, respectively. The three morphological fractions differed in the content of the most analyzed nutrients.

Insulin Resistance and Diabetes Mellitus in Alzheimer's Disease

Type 2 diabetes mellitus is a progressive disease that is characterized by the appearance of insulin resistance. The term insulin resistance is very wide and could affect different proteins involved in insulin signaling, as well as other mechanisms. In this review, we have analyzed the main molecular mechanisms that could be involved in the connection between type 2 diabetes and neurodegeneration, in general, and more specifically with the appearance of Alzheimer's disease. We have studied, in more detail, the different processes involved, such as inflammation, endoplasmic reticulum stress, autophagy, and mitochondrial dysfunction.

Digital microscopic image application (DMIA), an automatic method for particle size distribution analysis in waste activated sludge

An important physical property in environmental samples is particle size distribution. Several processes exist to measure particle diameter, including change in electrical resistance, blocking of light, the fractionation of field flow and laser diffraction (these being the most commonly used). However, their use requires expensive and complex equipment. Therefore, a digital microscopic imaging application (DMIA) method was developed adapting the algorithms used in the helminth egg automatic detector software coupled with a neural network (NN) and Bayesian algorithms. This allowed the determination of particle size distribution in samples of waste activated sludge (WAS), recirculated sludge (RCS), and pre-treated sludge (PTS). The recirculation and electro-oxidation pre-treatment processes showed an effect in increasing the degree of solubilization, decreasing particle size and breakage factor with ranges between 44.29%, and 31.89%. Together with a final NN calibration process, it was possible to compare results. For example, the 90th percentile of equivalent diameter value obtained by the DMIA with the corresponding result for the laser diffraction method. DMIA values: 228.76 μm (WAS), 111.18 μm (RCS), and 84.45 μm (PTS). DMIA processing has advantages in terms of reducing complexity, cost and time, and offers an alternative to the laser diffraction method.

A Computationally Lightweight Algorithm for Deriving Reliable Metabolite Panel Measurements from 1D 1H NMR

Small Molecule Enhancement SpectroscopY (SMolESY) was employed to develop a unique and fully automated computational solution for the assignment and integration of 1H nuclear magnetic resonance (NMR) signals from metabolites in challenging matrices containing macromolecules (herein blood products). Sensitive and reliable quantitation is provided by instant signal deconvolution and straightforward integration bolstered by spectral resolution enhancement and macromolecular signal suppression. The approach is highly efficient, requiring only standard one-dimensional 1H NMR spectra and avoiding the need for sample preprocessing, complex deconvolution, and spectral baseline fitting. The performance of the algorithm, developed using >4000 NMR serum and plasma spectra, was evaluated using an additional >8800 spectra, yielding an assignment accuracy greater than 99.5% for all 22 metabolites targeted. Further validation of its quantitation capabilities illustrated a reliable performance among challenging phenotypes. The simplicity and complete automation of the approach support the application of NMR-based metabolite panel measurements in clinical and population screening applications.

Human amylin aggregates release within exosomes as a protective mechanism in pancreatic β cells: Pancreatic β-hippocampal cell communication

Pancreatic β cells are essential in the maintenance of glucose homeostasis during the progression to type 2 Diabetes Mellitus (T2DM), generating compensatory hyperinsulinemia to counteract insulin resistance. It is well known, that throughout the process there is an increased mTORC1 signaling pathway, with an impairment in different quality control systems including ubiquitin-proteasome system and autophagy. In addition, under this situation, pancreatic β cells start to accumulate amylin protein (IAPP) in aggregates, and this accumulation contributes to the failure of autophagy, damaging different organelles such as plasma membrane, endoplasmic reticulum, mitochondria, and others. Here, we report that IAPP can be incorporated to multivesicular bodies (MVB) and secreted into exosomes, a mechanism responsible for the exportation of these toxic aggregates as vehicles of cell to cell communication. On this regard, we have demonstrated that the exosomes bearing toxic hIAPP released from pancreatic β cells are capable to induce hyperactivation of mTORC1 signaling, a failure in the autophagic cellular quality control, and favor pro-fission status of the mitochondrial dynamics in hippocampal cells. In summary, our results show that harmful accumulation of hIAPP in pancreatic β cells may be detoxified by the release of exosomes, which may be captured by endocytosis mechanism damaging neuronal hippocampal cells, which suggest an underlying molecular mechanism to the link between type 2 diabetes and neurodegenerative diseases.

Metabolic phenotyping reveals a reduction in the bioavailability of serotonin and kynurenine pathway metabolites in both the urine and serum of individuals living with Alzheimer's disease

BACKGROUND

Both serotonergic signalling disruption and systemic inflammation have been associated with the pathogenesis of Alzheimer's disease (AD). The common denominator linking the two is the catabolism of the essential amino acid, tryptophan. Metabolism via tryptophan hydroxylase results in serotonin synthesis, whilst metabolism via indoleamine 2,3-dioxygenase (IDO) results in kynurenine and its downstream derivatives. IDO is reported to be activated in times of host systemic inflammation and therefore is thought to influence both pathways. To investigate metabolic alterations in AD, a large-scale metabolic phenotyping study was conducted on both urine and serum samples collected from a multi-centre clinical cohort, consisting of individuals clinically diagnosed with AD, mild cognitive impairment (MCI) and age-matched controls.

METHODS

Metabolic phenotyping was applied to both urine (n = 560) and serum (n = 354) from the European-wide AddNeuroMed/Dementia Case Register (DCR) biobank repositories. Metabolite data were subsequently interrogated for inter-group differences; influence of gender and age; comparisons between two subgroups of MCI - versus those who remained cognitively stable at follow-up visits (sMCI); and those who underwent further cognitive decline (cMCI); and the impact of selective serotonin reuptake inhibitor (SSRI) medication on metabolite concentrations.

RESULTS

Results revealed significantly lower metabolite concentrations of tryptophan pathway metabolites in the AD group: serotonin (urine, serum), 5-hydroxyindoleacetic acid (urine), kynurenine (serum), kynurenic acid (urine), tryptophan (urine, serum), xanthurenic acid (urine, serum), and kynurenine/tryptophan ratio (urine). For each listed metabolite, a decreasing trend in concentrations was observed in-line with clinical diagnosis: control > MCI > AD. There were no significant differences in the two MCI subgroups whilst SSRI medication status influenced observations in serum, but not urine.

CONCLUSIONS

Urine and serum serotonin concentrations were found to be significantly lower in AD compared with controls, suggesting the bioavailability of the neurotransmitter may be altered in the disease. A significant increase in the kynurenine/tryptophan ratio suggests that this may be a result of a shift to the kynurenine metabolic route due to increased IDO activity, potentially as a result of systemic inflammation. Modulation of the pathways could help improve serotonin bioavailability and signalling in AD patients.

Relevance of current PCB concentrations in edible fish species from the Mediterranean Sea

Legal restrictions and bans have led to a steady decrease in PCB environmental concentrations. Yet, in recent years PCBs have been found at very high levels in the Mediterranean Sea, for instance, in some apex predators. This work aimed to investigate current PCB (eighteen congeners: #28,52,77,81,101,105,114,118,123,126,138,153,156,157,167,169,180,189) concentrations in the Mediterranean Sea and their relevance today, focusing on their occurrence in edible fish species typically consumed in the Mediterranean diet. In spring 2017, a total of 48 fish samples from the Northern Thyrrenian Sea were collected: 16 specimens of sardine (Sardina pilchardus), 16 of anchovy (Engraulis encrasicolus) and 16 of bogue (Boops boops). PCBs were quantified in the muscle of the animals by means of GC-QqQ-MS. They were found in all samples at the greatest concentrations (ng/g w.w.) in sardine (4.15-17.9, range), and very similar values between anchovy (1.01-7.08) and bogue (1.46-7.22). WHO-TEQ PCB values followed the same order, i.e. sardine (0.410-1.24, range in pg/g w.w.) > anchovy (0.0778-0.396) ~ bogue (0.0726-0.268). These concentrations lied below the European limits of 75 ng/g (w.w.) for the six indicator PCBs and 6.5 pg/g WHO-TEQ for dioxins and dioxin-like PCBs in muscle meat of fish. Additionally, estimated weekly intakes (EWI, in pg WHO-TEQ/Kg/week) for sardine (1.2), anchovy (0.29) and bogue (0.35) scored below the safe value proposed by EFSA of 2 pg WHO-TEQ/Kg/week. When comparing with data reported for the same species in previous Mediterranean studies, values found here were lower than those surveyed in the late 90s and early 2000s; however, they were often not notably different from concentrations reported in last years. This builds up on the concept of a current slow decrease of PCBs in the Mediterranean Sea, likely linked to new inputs and/or remobilization of burdens, and reinforces the need of continous monitoring of these legacy contaminants still ubiquitous today.

Helminth Egg Automatic Detector (HEAD): Improvements in development for digital identification and quantification of helminth eggs and their application online

Helminths are parasitic worms that constitute a major public health problem. Conventional analytical techniques to evaluate helminth eggs in environmental samples rely on different steps, namely sedimentation, filtration, centrifugation, and flotation, to separate the eggs from a variety of particles and concentrate them in a pellet for direct observation under an optical microscope. To improve this process, a new approach was implemented in which various image processing algorithms were developed and implemented by a Helminth Egg Automatic Detector (HEAD). This allowed identification and quantification of pathogenic helminth eggs of global medical importance and it was found to be useful for relatively clean wastewater samples. After the initial version, two improvements were developed: first, a texture verification process that reduced the number of false positive results; and second, the establishment of the optimal thresholds (morphology and texture) for each helminth egg species. This second implementation, which was found to improve on the results of the former, was developed with the objective of using free software as a platform for the system. This does not require the purchase of a license, unlike the previous version that required a Mathworks® license to run. After an internal statistical verification of the system was carried out, trials in internationally recognized microbiology laboratories were performed with the aim of reinforcing software training and developing a web-based system able to receive images and perform the analysis throughout a web service. Once completed, these improvements represented a useful and cheap tool that could be used by environmental monitoring facilities and laboratories throughout the world; this tool is capable of identifying and quantifying different species of helminth eggs in otherwise difficult environmental samples: wastewater, soil, biosolids, excreta, and sludge, with a sensitivity and specificity for the TensorFlow (TF) model in the web service values of 96.82% and 97.96% respectively. Additionally, in the case of Ascaris, it may even differentiate between fertile and non-fertile eggs.

The supplementations with 2-hydroxyoleic acid and n-3 polyunsaturated fatty acids revert oxidative stress in various organs of diet-induced obese mice

Obesity and its related diseases have been associated with oxidative stress. Thus, the search for nutritional strategies to ameliorate oxidative stress in obese individuals seems important. We hypothesized that the supplementation with monounsaturated (2-hydroxyoleic acid (2-OHOA)) and with combined n-3 polyunsaturated (eicosapentaenoic acid (EPA) and docosahexaenoic acid (DHA)) fatty acids would ameliorate oxidative stress in different organs, including brain, liver, lungs, and kidneys of adult diet-induced obese (DIO) mice. Adult female ICR-CD1 mice were fed a high-fat diet (HFD) for 14 weeks. During the last 6 weeks of HFD feeding, one group of DIO mice received the same HFD, supplemented with 1500 mg of 2-OHOA per kg of HFD and another group with 1500 mg of EPA and 1500 mg of DHA per kg of HFD. At the end of the experiment, several parameters of oxidative stress were assessed. The supplementation with 2-OHOA or with EPA and DHA in DIO mice was able to revert oxidative stress, enhancing the activities of catalase and glutathione reductase, as well as diminishing the activity of xanthine oxidase, the concentration of thiobarbituric acid reactive substances (TBARS) and the ratio between oxidized glutathione and reduced glutathione in several organs. These reached similar values to those of control mice, which were fed a standard diet. These data suggest that supplementation with 2-OHOA and with EPA and DHA could be an effective nutritional intervention to restore an appropriate redox state in DIO mice.

Normal tissue content impact on the GBM molecular classification

Molecular classification of glioblastoma has enabled a deeper understanding of the disease. The four-subtype model (including Proneural, Classical, Mesenchymal and Neural) has been replaced by a model that discards the Neural subtype, found to be associated with samples with a high content of normal tissue. These samples can be misclassified preventing biological and clinical insights into the different tumor subtypes from coming to light. In this work, we present a model that tackles both the molecular classification of samples and discrimination of those with a high content of normal cells. We performed a transcriptomic in silico analysis on glioblastoma (GBM) samples (n = 810) and tested different criteria to optimize the number of genes needed for molecular classification. We used gene expression of normal brain samples (n = 555) to design an additional gene signature to detect samples with a high normal tissue content. Microdissection samples of different structures within GBM (n = 122) have been used to validate the final model. Finally, the model was tested in a cohort of 43 patients and confirmed by histology. Based on the expression of 20 genes, our model is able to discriminate samples with a high content of normal tissue and to classify the remaining ones. We have shown that taking into consideration normal cells can prevent errors in the classification and the subsequent misinterpretation of the results. Moreover, considering only samples with a low content of normal cells, we found an association between the complexity of the samples and survival for the three molecular subtypes.

Inactivation of helminth eggs in an electro-Fenton reactor: Towards full electrochemical disinfection of human waste using activated carbon

The disinfection of helminth eggs and Escherichia coli contaminated aqueous solutions, was studied using an electro-Fenton reactor equipped with a polarized activated carbon (AC) packed bed and two chambers loaded with cation exchange resins. Experiments using different arrangements and operation conditions, revealed that effective elimination of Escherichia coli takes place in all electrochemical disinfection tests. For the more resistant helminth eggs however, adsorption, electro-oxidation and electro-Fenton experiments showed retention within the reactor and pathogen inactivation values of 0, 16, and 25%, respectively. Using helminth eggs concentration data in different sections of the reactor, optical microscopy analysis and an exploratory computer simulation, differences in the disinfection performance were explained and new recirculation and flow direction and polarization switching operation schemes were defined. The corresponding experiments revealed that the effective coupling between adsorption and electro-Fenton phenomena, all along the AC packed bed compartment, results in 100% inactivation of helminth eggs.

Bevacizumab dose adjustment to improve clinical outcomes of glioblastoma

BACKGROUND

Glioblastoma (GBM) is one of the most aggressive and vascularized brain tumors in adults, with a median survival of 20.9 months. In newly diagnosed and recurrent GBM, bevacizumab demonstrated an increase in progression-free survival, but not in overall survival.

METHODS

We conducted an in silico analysis of VEGF expression, in a cohort of 1082 glioma patients. Then, to determine whether appropriate bevacizumab dose adjustment could increase the anti-angiogenic response, we used in vitro and in vivo GBM models. Additionally, we analyzed VEGFA expression in tissue, serum, and plasma in a cohort of GBM patients before and during bevacizumab treatment.

RESULTS

We identified that 20% of primary GBM did not express VEGFA suggesting that these patients would probably not respond to bevacizumab therapy as we proved in vitro and in vivo. We found that a specific dose of bevacizumab calculated based on VEGFA expression levels increases the response to treatment in cell culture and serum samples from mice bearing GBM tumors. Additionally, in a cohort of GBM patients, we observed a correlation of VEGFA levels in serum, but not in plasma, with bevacizumab treatment performance.

CONCLUSIONS

Our data suggest that bevacizumab dose adjustment could improve clinical outcomes in Glioblastoma treatment.

pJRES Binning Algorithm (JBA): a new method to facilitate the recovery of metabolic information from pJRES 1H NMR spectra

Motivation

Data processing is a key bottleneck for ¹H NMR-based metabolic profiling of complex biological mixtures, such as biofluids. These spectra typically contain several thousands of signals, corresponding to possibly few hundreds of metabolites. A number of binning-based methods have been proposed to reduce the dimensionality of 1 D ¹H NMR datasets, including statistical recoupling of variables (SRV). Here, we introduce a new binning method, named JBA (“pJRES Binning Algorithm”), which aims to extend the applicability of SRV to pJRES spectra.

Results

The performance of JBA is comprehensively evaluated using 617 plasma ¹H NMR spectra from the FGENTCARD cohort. The results presented here show that JBA exhibits higher sensitivity than SRV to detect peaks from low-abundance metabolites. In addition, JBA allows a more efficient removal of spectral variables corresponding to pure electronic noise, and this has a positive impact on multivariate model building

Availability and implementation

The algorithm is implemented using the MWASTools R/Bioconductor package.

Supplementary information

Supplementary data are available at Bioinformatics online.

SMolESY: an efficient and quantitative alternative to on-instrument macromolecular 1H-NMR signal suppression

One-dimensional (1D) proton-nuclear magnetic resonance (1H-NMR) spectroscopy is an established technique for measuring small molecules in a wide variety of complex biological sample types. It is demonstrably reproducible, easily automatable and consequently ideal for routine and large-scale application. However, samples containing proteins, lipids, polysaccharides and other macromolecules produce broad signals which overlap and convolute those from small molecules. NMR experiment types designed to suppress macromolecular signals during acquisition may be additionally performed, however these approaches add to the overall sample analysis time and cost, especially for large cohort studies, and fail to produce reliably quantitative data. Here, we propose an alternative way of computationally eliminating macromolecular signals, employing the mathematical differentiation of standard 1H-NMR spectra, producing small molecule-enhanced spectra with preserved quantitative capability and increased resolution. Our approach, presented in its simplest form, was implemented in a cheminformatic toolbox and successfully applied to more than 3000 samples of various biological matrices rich or potentially rich with macromolecules, offering an efficient alternative to on-instrument experimentation, facilitating NMR use in routine and large-scale applications.

Performance of metabonomic serum analysis for diagnostics in paediatric tuberculosis

We applied a metabonomic strategy to identify host biomarkers in serum to diagnose paediatric tuberculosis (TB) disease. 112 symptomatic children with presumptive TB were recruited in The Gambia and classified as bacteriologically-confirmed TB, clinically diagnosed TB, or other diseases. Sera were analysed using ¹H nuclear magnetic resonance (NMR) spectroscopy and mass spectrometry (MS). Multivariate data analysis was used to distinguish patients with TB from other diseases. Diagnostic accuracy was evaluated using Receiver Operating Characteristic (ROC) curves. Model performance was tested in a validation cohort of 36 children from the UK. Data acquired using ¹H NMR demonstrated a sensitivity, specificity and Area Under the Curve (AUC) of 69% (95% confidence interval [CI], 56-73%), 83% (95% CI, 73-93%), and 0.78 respectively, and correctly classified 20% of the validation cohort from the UK. The most discriminatory MS data showed a sensitivity of 67% (95% CI, 60-71%), specificity of 86% (95% CI, 75-93%) and an AUC of 0.78, correctly classifying 83% of the validation cohort. Amongst children with presumptive TB, metabolic profiling of sera distinguished bacteriologically-confirmed and clinical TB from other diseases. This novel approach yielded a diagnostic performance for paediatric TB comparable to that of Xpert MTB/RIF and interferon gamma release assays.

Patient self-management of oral anticoagulation with vitamin K antagonists in everyday practice: clinical outcomes in a single centre cohort after long-term follow-up

Background

Patient self-management (PSM) of vitamin K antagonists (VKA) seems a very promising model of care for oral anticoagulation in terms of efficacy and safety. In comparison with other management models of VKA therapy, the number of scientific publications supporting the advantages of PSM is more limited. Currently, most of the scarce information comes from randomized clinical trials. Moreover, a small number of studies have assessed PSM of VKA therapy in real life conditions.

Methods

We analyzed clinical outcomes of 927 patients in a single center (6018.6 patient-years of follow-up). Recruitment took place between 2002 and 2017. All patients followed a structured training program, conducted by specialized nurses.

Results

Fifty percent of individuals had a mechanical heart valve (MHV), 23% suffered from recurrent venous thromboembolism (VTE) or high-risk thrombophilia, and 13% received VKA therapy because of atrial fibrillation (AF). Median follow-up was 6.5 years (range 0.1–15.97 years), median age was 58.1 years (IQR 48–65.9) and 46.5% were women. The incidence of major complications (either hemorrhagic or thromboembolic) was 1.87% patient-years (pt-ys) with a 95% CI of 1.54–2.27. The incidence of major thromboembolic events was 0.86% pt-ys (95% CI 0.64–1.13) and that of major hemorrhagic events was 1.01% pt-ys (95% CI 0.77–1.31). The incidence of intracranial bleeding was 0.22% pt-ys (95% CI 0.12–0.38). In terms of clinical indication for VKA therapy, the incidence of total major complications was 2.4% pt-ys, 2.0% pt-ys, 0.9% pt-ys and 1.34% pt-ys for MHV, AF, VTE and other (including valvulopathies and myocardiopathies), respectively. Clinical outcomes were worse in patients with multiple comorbidities, previous major complications during conventional VKA therapy, and in older individuals. The percentage of time in therapeutic range (TTR) was available in 861 (93%) patients. Overall, the mean (SD) of TTR was 63.6 ± 13.4%, being higher in men (66.2 ± 13.1%) than women (60.6 ± 13.2%), p < 0.05.

Conclusions

In terms of clinically relevant outcomes (incidence of major complications and mortality), PSM in real life setting seems to be a very good alternative in properly trained patients.

The nPYc-Toolbox, a Python module for the pre-processing, quality-control and analysis of metabolic profiling datasets

SUMMARY

As large-scale metabolic phenotyping studies become increasingly common, the need for systemic methods for pre-processing and quality control (QC) of analytical data prior to statistical analysis has become increasingly important, both within a study, and to allow meaningful inter-study comparisons. The nPYc-Toolbox provides software for the import, pre-processing, QC and visualization of metabolic phenotyping datasets, either interactively, or in automated pipelines.

AVAILABILITY AND IMPLEMENTATION

The nPYc-Toolbox is implemented in Python, and is freely available from the Python package index https://pypi.org/project/nPYc/, source is available at https://github.com/phenomecentre/nPYc-Toolbox. Full documentation can be found at http://npyc-toolbox.readthedocs.io/ and exemplar datasets and tutorials at https://github.com/phenomecentre/nPYc-toolbox-tutorials.

Quick incubation process to determine inactivation of Ascaris and Toxocara eggs

Helminth eggs are among the most important biological contaminants in environmental engineering. They pose a significant health risk associated with poor sanitation, the use of contaminated water for irrigation, and the disposal of excreta or sludge to land. Helminths are parasitic worms transmitted to humans via their eggs, which is the infective stage of their life cycle. They are therefore relevant to public health and environmental fields due to their low infectious dose, their persistence in the environment (up to several years), and their high resistance to conventional disinfection processes. The evaluation of the efficiency of any process of inactivation, through the determination of the viability of these parasites, is fundamental, but the traditional incubation technique requires 20 days to determine both the viability and the infectivity of nematode eggs. However, the present study found that, using an inactivation process at a temperature of 60 °C for 1 hour and incubation at 28 °C and 34 °C, the absence of division of the nucleus of eggs of species from two genera, Ascaris lumbricoides and Toxocara canis, showed them to be inactivated following only 48 hours of incubation. Similar inactivation results were observed using an automatic system as long as the eggs were inactivated. The minimum time required to evaluate the inactivation of nematode eggs through the incubation technique was 48 hours.

Essential role of glucokinase in the protection of pancreatic β cells to the glucose energetic status

Energy sensing is indispensable to balance anabolic and catabolic processes for the maintenance of cell viability. Pancreatic β cells are especially relevant because of their involvement in the coordination of insulin secretion when glucose concentration arises in the local milieu. In this work, we uncover the increased susceptibility of pancreatic β cells to cell death in response to different energy stressors. Upon glucose decline, from 25 to 5 mM, caused by stimulation with either 2-deoxyglucose or metformin, only pancreatic β cells showed an increase in cell death. Very interestingly, when we transfected either mouse insulinoma cell or human embryo kidney cells with a phospho-mutant form of B cell lymphoma 2 associated agonist of cell death at serine 155 (BAD S155D), an increase in the pro-survival factor B cell lymphoma 2 was detected in pancreatic β cells and not in human embryonic kidney cells in the presence of the energetic stressors. This data suggests that the protective capacity of this mutant form is only present in cells that present glucokinase. In contrast, upon hyperactivation of mechanistic target of rapamycin complex 1 signaling by knocking-down tuberous sclerosis complex protein, we observed increased susceptibility to cell death in response to energy stress in both pancreatic and non-pancreatic β cells. Therefore, mechanistic target of rapamycin complex 1 signaling presents a dual effect on cell viability. On the one hand, a chronic inhibition of mechanistic target of rapamycin complex 1 activity in response to the energy status is deleterious for pancreatic β cells, being attenuated by the overexpression of B cell lymphoma 2 associated agonist of cell death S155D. On the other hand, mechanistic target of rapamycin complex 1 hyperactivity provokes a susceptibility to energetic stress-induced cell death. Taken together, these results may open potential implications for the use of glucokinase activators or mechanistic target of rapamycin complex 1 modulators for the maintenance of pancreatic β cells for longer periods of time avoiding its loss in different pathologies such as type 2 diabetes mellitus.

Systematic Isolation and Structure Elucidation of Urinary Metabolites Optimized for the Analytical-Scale Molecular Profiling Laboratory

Annotation and identification of metabolite biomarkers is critical for their biological interpretation in metabolic phenotyping studies, presenting a significant bottleneck in the successful implementation of untargeted metabolomics. Here, a systematic multistep protocol was developed for the purification and de novo structural elucidation of urinary metabolites. The protocol is most suited for instances where structure elucidation and metabolite annotation are critical for the downstream biological interpretation of metabolic phenotyping studies. First, a bulk urine pool was desalted using ion-exchange resins enabling large-scale fractionation using precise iterations of analytical scale chromatography. Primary urine fractions were collected and assembled into a “fraction bank” suitable for long-term laboratory storage. Secondary and tertiary fractionations exploited differences in selectivity across a range of reversed-phase chemistries, achieving the purification of metabolites of interest yielding an amount of material suitable for chemical characterization. To exemplify the application of the systematic workflow in a diverse set of cases, four metabolites with a range of physicochemical properties were selected and purified from urine and subjected to chemical formula and structure elucidation by respective magnetic resonance mass spectrometry (MRMS) and NMR analyses. Their structures were fully assigned as tetrahydropentoxyline, indole-3-acetic-acid-O-glucuronide, p-cresol glucuronide, and pregnanediol-3-glucuronide. Unused effluent was collected, dried, and returned to the fraction bank, demonstrating the viability of the system for repeat use in metabolite annotation with a high degree of efficiency.

Reduced plasma levels of small HDL particles transporting fibrinolytic proteins in pulmonary arterial hypertension

BACKGROUND

Aberrant lipoprotein metabolism has been implicated in experimental pulmonary hypertension, but the relevance to patients with pulmonary arterial hypertension (PAH) is inconclusive.

OBJECTIVE

To investigate the relationship between circulating lipoprotein subclasses and survival in patients with PAH.

METHODS

Using nuclear magnetic resonance spectroscopy, 105 discrete lipoproteins were measured in plasma samples from two cohorts of patients with idiopathic or heritable PAH. Data from 1124 plasma proteins were used to identify proteins linked to lipoprotein subclasses. The physical presence of proteins was confirmed in plasma lipoprotein subfractions separated by ultracentrifugation.

RESULTS

Plasma levels of three lipoproteins from the small high-density lipoprotein (HDL) subclass, termed HDL-4, were inversely related to survival in both the discovery (n=127) and validation (n=77) cohorts, independent of exercise capacity, comorbidities, treatment, N-terminal probrain natriuretic peptide, C reactive protein and the principal lipoprotein classes. The small HDL subclass rich in apolipoprotein A-2 content (HDL-4-Apo A-2) exhibited the most significant association with survival. None of the other lipoprotein classes, including principal lipoprotein classes HDL and low-density lipoprotein cholesterol, were prognostic. Three out of nine proteins identified to associate with HDL-4-Apo A-2 are involved in the regulation of fibrinolysis, namely, the plasmin regulator, alpha-2-antiplasmin, and two major components of the kallikrein-kinin pathway (coagulation factor XI and prekallikrein), and their physical presence in the HDL-4 subfraction was confirmed.

CONCLUSION

Reduced plasma levels of small HDL particles transporting fibrinolytic proteins are associated with poor outcomes in patients with idiopathic and heritable PAH.

[Guidelines of the Chilean Endocrinology Society for the correct clinical use of bone densitometry]

Osteoporosis is a silent and frequent disease, which increases fracture risk. Approximately half of women and one of five men over 50 years old will suffer an osteoporotic fracture throughout their lives. Dual-energy x-ray absorptiometry (DXA) allows a real bone mineral density (BMD) measurement in different parts of the skeleton and is considered the "gold standard" for quantifying osteoporosis with high accuracy and precision. The Board of the Chilean Society of Endocrinology and Diabetes (SOCHED) required from the Bone Disease Study Group to develop a consensus about the "Correct use of bone densitometry in clinical practice in Chilean population". Therefore, we elaborated 25 questions which addressed key aspects about the indications for a DXA scan, and the details of how to perform and report this test. Since some of the evidence obtained was of low quality or inconclusive, we decided to create a multidisciplinary group of national experts in osteoporosis to develop a consensus in this subject. The group consisted of 22 physicians including endocrinologists, gynecologists, geriatricians, radiologists, rheumatologists and nuclear medicine specialists. Using the Delphi methodology to analyze previously agreed questions, we elaborated statements that were evaluated by the experts who expressed their degree of agreement. The final report of this consensus was approved by the SOCHED board.

Evaluation of PCDD/Fs, dioxin-like PCBs and PBDEs in sperm whales from the Mediterranean Sea

Numerous studies to date have reported concentrations of Persistent Organic Pollutants (POPs) in different marine mammal species worldwide. Yet data on sperm whales are scarce from rich and unique biodiverse areas such as the Mediterranean Sea. This work aimed to assess levels of dioxin-like polychlorinated biphenyls (dl-PCBs), polybrominated diphenyl ethers (PBDEs), and polychlorodibenzo-p-dioxins and furans (PCDD/Fs) in blubber of sperm whales stranded along the Italian coast between 2008 and 2016. POP mean concentrations (dl-PCBs: 6410 ng/g l.w.; PBDEs: 612 ng/g l.w.; PCDD/Fs: 57.8 pg/g l.w.) were mostly in line with what has been previously reported on the same species in the Mediterranean environment and tended to be higher than those reported from other geographical regions. The relative abundance followed the order dl-PCBs > PBDEs ≫ PCDD/Fs. Interestingly, the non-ortho dl-PCB pattern (126 > 169 > 77) was similar to that described in other studies worldwide and different from what is described in its main prey. This could be linked to particular metabolic activities in sperm whales against these highly toxic contaminants. Total TEQs ranged from 275 to 987 pg/g l.w. and showed the pattern Σnon-ortho-dl-PCBs > Σortho-dl-PCBs > PCDDs > PCDFs, with PCBs' contribution about 96%. These findings highlight the high abundance of PCBs still found in the Mediterranean environment despite having been banned for decades. All sperm whales analyzed in this study surpassed the threshold of 210 pg WHO-TEQ/g l.w. proposed as starting point of immunosuppression in harbour seals; a level of contamination that may have contributed to an impairment of their immune system.

First assessment of persistent organic pollutant contamination in blubber of Chilean blue whales from Isla de Chiloé, southern Chile

Persistent organic pollutants (POPs) were assessed for the first time in blue whales from the South Pacific Ocean. Concentrations of polychlorinated biphenyls (PCBs), polybrominated diphenyl ethers (PBDEs), hexachlorobenzene (HCB) and dichlorodiphenyltrichloroethane and its main metabolites (DDTs), were determined in 40 blubber samples from 36 free-ranging individuals and one stranded, dead animal along the coast of southern Chile between 2011 and 2013. PCBs were the most abundant pollutants (2.97-975 ng/g l.w.), followed by DDTs (3.50-537 ng/g l.w.), HCB (nd-77.5 ng/g l.w.) and PBDEs (nd-33.4 ng/g l.w). There was evidence of differences between sexes, with lower loads in females potentially due to pollutants passing to calves. POP concentrations were higher in specimens sampled in 2013; yet, between-year differences were only statistically significant for HCB and PBDEs. Lower chlorinated (penta > tetra > tri) and brominated (tetra > tri) congeners were the most prevalent among PCBs and PBDEs, respectively, mostly in agreement with findings previously reported in blue and other baleen whales. The present study provides evidence of lower levels of contamination by POPs in eastern South Pacific blue whales in comparison to those reported for the Northern Hemisphere.

Quantitative Lipoprotein Subclass and Low Molecular Weight Metabolite Analysis in Human Serum and Plasma by 1H NMR Spectroscopy in a Multilaboratory Trial

We report an extensive 600 MHz NMR trial of quantitative lipoprotein and small-molecule measurements in human blood serum and plasma. Five centers with eleven 600 MHz NMR spectrometers were used to analyze 98 samples including 20 quality controls (QCs), 37 commercially sourced, paired serum and plasma samples, and two National Institute of Science and Technology (NIST) reference material 1951c replicates. Samples were analyzed using rigorous protocols for sample preparation and experimental acquisition. A commercial lipoprotein subclass analysis was used to quantify 105 lipoprotein subclasses and 24 low molecular weight metabolites from the NMR spectra. For all spectrometers, the instrument specific variance in measuring internal QCs was lower than the percentage described by the National Cholesterol Education Program (NCEP) criteria for lipid testing [triglycerides <2.7%; cholesterol <2.8%; low-density lipoprotein (LDL) cholesterol <2.8%; high-density lipoprotein (HDL) cholesterol <2.3%], showing exceptional reproducibility for direct quantitation of lipoproteins in both matrixes. The average relative standard deviations (RSDs) for the 105 lipoprotein parameters in the 11 instruments were 4.6% and 3.9% for the two NIST samples, whereas they were 38% and 40% for the 37 commercially sourced plasmas and sera, respectively, showing negligible analytical compared to biological variation. The coefficient of variance (CV) obtained for the quantification of the small molecules across the 11 spectrometers was below 15% for 20 out of the 24 metabolites analyzed. This study provides further evidence of the suitability of NMR for high-throughput lipoprotein subcomponent analysis and small-molecule quantitation with the exceptional required reproducibility for clinical and other regulatory settings.

Urinary Metabolic Phenotyping of Women with Lower Urinary Tract Symptoms

Lower urinary tract symptoms (LUTS), including urinary incontinence, urgency and nocturia, affect approximately half of women worldwide. Current diagnostic methods for LUTS are invasive and costly, while available treatments are limited by side effects leading to poor patient compliance. In this study, we aimed to identify urine metabolic signatures associated with LUTS using proton nuclear magnetic resonance (¹H NMR) spectroscopy. A total of 214 urine samples were collected from women attending tertiary urogynecology clinics (cases; n = 176) and healthy control women attending general gynecology clinics (n = 36). Despite high variation in the urine metabolome across the cohort, associations between urine metabolic profiles and BMI, parity, overactive bladder syndrome, frequency, straining, and bladder storage were identified using KODAMA (knowledge discovery by accuracy maximization). Four distinct urinary metabotypes were identified, one of which was associated with increased urinary frequency and low BMI. Urine from these patients was characterized by increased levels of isoleucine and decreased levels of hippurate. Our study suggests that metabolic profiling of urine samples from LUTS patients offers the potential to identify differences in underlying etiology, which may permit stratification of patient populations and the design of more personalized treatment strategies.

Metabolic Profiling in Patients with Pneumonia on Intensive Care

Clinical features and investigations lack predictive value when diagnosing pneumonia, especially when patients are ventilated and when patients develop ventilator associated pneumonia (VAP). New tools to aid diagnosis are important to improve outcomes. This pilot study examines the potential for metabolic profiling to aid the diagnosis in critical care.

In this prospective observational study ventilated patients with brain injuries or pneumonia were recruited in the intensive care unit and serum samples were collected soon after the start of ventilation. Metabolic profiles were produced using 1D ¹H NMR spectra. Metabolic data were compared using multivariate statistical techniques including Principal Component Analysis (PCA) and Orthogonal Partial Least Squares Discriminant Analysis (OPLS-DA).

We recruited 15 patients with pneumonia and 26 with brain injuries, seven of whom went on to develop VAP. Comparison of metabolic profiles using OPLS-DA differentiated those with pneumonia from those with brain injuries (R²Y = 0.91, Q²Y = 0.28, p = 0.02) and those with VAP from those without (R²Y = 0.94, Q²Y = 0.27, p = 0.05). Metabolites that differentiated patients with pneumonia included lipid species, amino acids and glycoproteins.

Metabolic profiling shows promise to aid in the diagnosis of pneumonia in ventilated patients and may allow a more timely diagnosis and better use of antibiotics.

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Metabolic profiling of serum from ventilated patients shows potential to aid in the diagnosis of pneumonia and ventilator associated pneumonia.

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Lipid species were particularly important in the discrimination of pneumonia and ventilator associated pneumonia from those with brain injuries.

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Metabolites including glycoproteins, amino acids and phospholipids also aided in discrimination.

Pneumonia is a common problem in patients requiring breathing support in Intensive Care Units (ICU). When pneumonia develops patients take longer to get back to full health and in some cases may die. Current diagnostic tests are not always helpful.

We measured an array of molecules, metabolites, in the blood of patients in ICU to compare those with pneumonia to those with brain injuries. We found that substances including lipids, amino acids and glycoproteins showed some ability to differentiate patients with pneumonia from other critically unwell patients. This technique, used with clinical data, may help improve the diagnosis of pneumonia.

K-Ras(V14I) -induced Noonan syndrome predisposes to tumour development in mice

The Noonan syndrome (NS) is an autosomal dominant genetic disorder characterized by short stature, craniofacial dysmorphism, and congenital heart defects. A significant proportion of NS patients may also develop myeloproliferative disorders (MPDs), including juvenile myelomonocytic leukaemia (JMML). Surprisingly, scarce information is available in relation to other tumour types in these patients. We have previously developed and characterized a knock-in mouse model that carries one of the most frequent KRAS-NS-related mutations, the K-Ras(V14I) substitution, which recapitulates most of the alterations described in NS patients, including MPDs. The K-Ras(V14I) mutation is a mild activating K-Ras protein; thus, we have used this model to study tumour susceptibility in comparison with mice expressing the classical K-Ras(G12V) oncogene. Interestingly, our studies have shown that these mice display a generalized tumour predisposition and not just MPDs. In fact, we have observed that the K-Ras(V14I) mutation is capable of cooperating with the p16Ink4a/p19Arf and Trp53 tumour suppressors, as well as with other risk factors such as pancreatitis, thereby leading to a higher cancer incidence. In conclusion, our results illustrate that the K-Ras(V14I) activating protein is able to induce cancer, although at a much lower level than the classical K-Ras(G12V) oncogene, and that it can be significantly modulated by both genetic and non-genetic events. Copyright © 2016 Pathological Society of Great Britain and Ireland. Published by John Wiley & Sons, Ltd.

Identification and quantification of pathogenic helminth eggs using a digital image system

A system was developed to identify and quantify up to seven species of helminth eggs (Ascaris lumbricoides -fertile and unfertile eggs-, Trichuris trichiura, Toxocara canis, Taenia saginata, Hymenolepis nana, Hymenolepis diminuta, and Schistosoma mansoni) in wastewater using different image processing tools and pattern recognition algorithms. The system was developed in three stages. Version one was used to explore the viability of the concept of identifying helminth eggs through an image processing system, while versions 2 and 3 were used to improve its efficiency. The system development was based on the analysis of different properties of helminth eggs in order to discriminate them from other objects in samples processed using the conventional United States Environmental Protection Agency (US EPA) technique to quantify helminth eggs. The system was tested, in its three stages, considering two parameters: specificity (capacity to discriminate between species of helminth eggs and other objects) and sensitivity (capacity to correctly classify and identify the different species of helminth eggs). The final version showed a specificity of 99% while the sensitivity varied between 80 and 90%, depending on the total suspended solids content of the wastewater samples. To achieve such values in samples with total suspended solids (TSS) above 150 mg/L, it is recommended to dilute the concentrated sediment just before taking the images under the microscope. The system allows the helminth eggs most commonly found in wastewater to be reliably and uniformly detected and quantified. In addition, it provides the total number of eggs as well as the individual number by species, and for Ascaris lumbricoides it differentiates whether or not the egg is fertile. The system only requires basically trained technicians to prepare the samples, as for visual identification there is no need for highly trained personnel. The time required to analyze each image is less than a minute. This system could be used in central analytical laboratories providing a remote analysis service.

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The system identifies and quantifies seven species of helminth eggs.

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The system shows a specificity of 99% and a sensitivity between 80 and 90%.

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The time required to analyze each image is less than a minute.

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The system reduces the need for highly trained personnel for the identification of helminth eggs.

Mad2 and BubR1 modulates tumourigenesis and paclitaxel response in MKN45 gastric cancer cells

Aneuploidy and chromosomal instability (CIN) are common features of gastric cancer (GC), but their contribution to carcinogenesis and antitumour therapy response is still poorly understood. Failures in the mitotic checkpoint induced by changes in expression levels of the spindle assembly checkpoint (SAC) proteins cause the missegregation of chromosomes in mitosis as well as aneuploidy. To evaluate the possible contribution of SAC to GC, we analyzed the expression levels of proteins of the mitotic checkpoint complex in a cohort of GC cell lines. We found that the central SAC proteins, Mad2 and BubR1, were the more prominently expressed members in disseminated GC cell lines. Silencing of Mad2 and BubR1 in MKN45 and ST2957 cells decreased their cell proliferation, migration and invasion abilities, indicating that Mad2 and BubR1 could contribute to cellular transformation and tumor progression in GC. We next evaluated whether silencing of SAC proteins could affect the response to microtubule poisons. We discovered that paclitaxel treatment increased cell survival in MKN45 cells interfered for Mad2 or BubR1 expression. However, apoptosis (assessed by caspase-3 activation, PARP proteolysis and levels of antiapoptotic Bcl 2-family members), the DNA damage response (assessed by H2Ax phosphorylation) and exit from mitosis (assessed by Cyclin B degradation and Cdk1 regulation) were activated equally between cells, independently of Mad2 or BubR1-protein levels. In contrast, we observed that the silencing of Mad2 or BubR1 in MKN45 cells showed the induction of a senescence-like phenotype accompanied by cell enlargement, increased senescence-associated β-galactosidase activity and increased IL-6 and IL-8 expression. In addition, the senescent phenotype is highly increased after treatment with PTX, indicating that senescence could prevent tumorigenesis in GC. In conclusion, the results presented here suggest that Mad2 and BubR1 could be used as prognostic markers of tumor progression and new pharmacological targets in the treatment for GC.

Histological alterations in the structure of the testis in tench (Tinca tinca) after exposure to 17 alpha-ethynylestradiol

Environmental pollution with synthetic estrogens may pose a serious threat to reproduction of aquatic wildlife species. The current study describes the effects of 17α-ethynylestradiol (EE2 ) on the structure of the testis in tench (Tinca tinca). Adult male tench were exposed to sublethal doses of EE2 (50, 100, and 500 μg/Kg t.w.) under semistatic conditions for a period of 30 days. The condition factor (CF), testicular somatic index (TSI), and histology (including a morphometric analysis) of the testis were examined. No consistent differences were observed in the CF of EE2 -exposed tench when compared with nonexposed fish. A significant decrease in TSI could only be observed at a 50 μg/Kg t.w. EE2 dose (p < 0.05) when compared with the control group. The histopathology of the testis was associated with loss of normal tubular structure with increased doses of exposure, decrease of tubule number, degeneration in Sertoli and Leydig cells, increase in necrotic testicular cells including formation of syncytia structures and, finally, a high incidence of fish with early primary oocytes at 100 and 500 μg/Kg t.w. EE2 . These results indicate that long-term exposure to EE2 may produce clear negative effects on testicular structure in tench.

Seasonal and spatial variation of organic tracers for biomass burning in PM1 aerosols from highly insolated urban areas

PM1 aerosol characterization on organic tracers for biomass burning (levoglucosan and its isomers and dehydroabietic acid) was conducted within the AERTRANS project. PM1 filters (N = 90) were sampled from 2010 to 2012 in busy streets in the urban centre of Madrid and Barcelona (Spain) at ground-level and at roof sites. In both urban areas, biomass burning was not expected to be an important local emission source, but regional emissions from wildfires, residential heating or biomass removal may influence the air quality in the cities. Although both areas are under influence of high solar radiation, Madrid is situated in the centre of the Iberian Peninsula, while Barcelona is located at the Mediterranean Coast and under influence of marine atmospheres. Two extraction methods were applied, i.e. Soxhlet and ASE, which showed equivalent results after GC-MS analyses. The ambient air concentrations of the organic tracers for biomass burning increased by an order of magnitude at both sites during winter compared to summer. An exception was observed during a PM event in summer 2012, when the atmosphere in Barcelona was directly affected by regional wildfire smoke and levels were four times higher as those observed in winter. Overall, there was little variation between the street and roof sites in both cities, suggesting that regional biomass burning sources influence the urban areas after atmospheric transport. Despite the different atmospheric characteristics in terms of air relative humidity, Madrid and Barcelona exhibit very similar composition and concentrations of biomass burning organic tracers. Nevertheless, levoglucosan and its isomers seem to be more suitable for source apportionment purposes than dehydroabietic acid. In both urban areas, biomass burning contributions to PM were generally low (2 %) in summer, except on the day when wildfire smoke arrive to the urban area. In the colder periods the contribution increase to around 30 %, indicating that regional biomass burning has a substantial influence on the urban air quality.

Precision high-throughput proton NMR spectroscopy of human urine, serum, and plasma for large-scale metabolic phenotyping

Proton nuclear magnetic resonance (NMR)-based metabolic phenotyping of urine and blood plasma/serum samples provides important prognostic and diagnostic information and permits monitoring of disease progression in an objective manner. Much effort has been made in recent years to develop NMR instrumentation and technology to allow the acquisition of data in an effective, reproducible, and high-throughput approach that allows the study of general population samples from epidemiological collections for biomarkers of disease risk. The challenge remains to develop highly reproducible methods and standardized protocols that minimize technical or experimental bias, allowing realistic interlaboratory comparisons of subtle biomarker information. Here we present a detailed set of updated protocols that carefully consider major experimental conditions, including sample preparation, spectrometer parameters, NMR pulse sequences, throughput, reproducibility, quality control, and resolution. These results provide an experimental platform that facilitates NMR spectroscopy usage across different large cohorts of biofluid samples, enabling integration of global metabolic profiling that is a prerequisite for personalized healthcare.

Two biomarker-directed randomized trials in European and Chinese patients with nonsmall-cell lung cancer: the BRCA1-RAP80 Expression Customization (BREC) studies

BACKGROUND

In a Spanish Lung Cancer Group (SLCG) phase II trial, the combination of BRCA1 and receptor-associated protein 80 (RAP80) expression was significantly associated with outcome in Caucasian patients with nonsmall-cell lung cancer (NSCLC). The SLCG therefore undertook an industry-independent collaborative randomized phase III trial comparing nonselected cisplatin-based chemotherapy with therapy customized according to BRCA1/RAP80 expression. An analogous randomized phase II trial was carried out in China under the auspices of the SLCG to evaluate the effect of BRCA1/RAP80 expression in Asian patients.

PATIENTS AND METHODS

Eligibility criteria included stage IIIB-IV NSCLC and sufficient tumor specimen for molecular analysis. Randomization to the control or experimental arm was 1 : 1 in the SLCG trial and 1 : 3 in the Chinese trial. In both trials, patients in the control arm received docetaxel/cisplatin; in the experimental arm, patients with low RAP80 expression received gemcitabine/cisplatin, those with intermediate/high RAP80 expression and low/intermediate BRCA1 expression received docetaxel/cisplatin, and those with intermediate/high RAP80 expression and high BRCA1 expression received docetaxel alone. The primary end point was progression-free survival (PFS).

RESULTS

Two hundred and seventy-nine patients in the SLCG trial and 124 in the Chinese trial were assessable for PFS. PFS in the control and experimental arms in the SLCG trial was 5.49 and 4.38 months, respectively [log rank P = 0.07; hazard ratio (HR) 1.28; P = 0.03]. In the Chinese trial, PFS was 4.74 and 3.78 months, respectively (log rank P = 0.82; HR 0.95; P = 0.82).

CONCLUSION

Accrual was prematurely closed on the SLCG trial due to the absence of clinical benefit in the experimental over the control arm. However, the BREC studies provide proof of concept that an international, nonindustry, biomarker-directed trial is feasible. Thanks to the groundwork laid by these studies, we expect that ongoing further research on alternative biomarkers to elucidate DNA repair mechanisms will help define novel therapeutic approaches.

TRIAL REGISTRATION

NCT00617656/GECP-BREC and ChiCTR-TRC-12001860/BREC-CHINA.

Histological alterations on the structure of the excretory renal system in tench (Tinca tinca) after exposure to 17-alpha-ethynylestradiol

This study describes the effects of 17-alpha-ethynylestradiol (EE2) on the structure of the excretory system of the kidney in tench. Adult male tench were exposed to sub-lethal doses of EE2 (50, 100 and 500 μg/kg b.w.) under semistatic conditions for a period of 30 days. The nephrosomatic index and histology (including a morphometric analysis) of the kidney were examined. Histopathological lesions in the kidney of exposed tench were: dilation of glomerular capillaries and increase in the area of the renal corpuscle, hyaline degeneration in the epithelial cells of the proximal tubules leading to necrotic changes, hemorrhages in the interstitial tissue and deposits of eosinophilic material. These lesions were observed with a greater degree of severity as the exposure doses were increased. These results indicate that long-term exposure to EE2 could produce clear negative effects on the excretory system of the kidney in tench and consequently on their physiological functions.

[Intravitreal ranibizumab in the treatment of subretinal neovascularization in a case of punctate inner choroidopathy]

CASE REPORT

We report the case of a 28-year old woman suffering loss of visual acuity in her left eye, who presented an image suggestive of a subretinal neovascular membrane in her left eye, and bilateral retinal lesions compatible with punctate inner choroidopathy (PIC). She was treated with intravitreal ranibizumab obtaining excellent results.

DISCUSSION

The differential diagnosis must be made between PIC and the rest of "white dot syndromes" and the presumed ocular histoplasmosis syndrome (POHS). Antiangiogenic drugs may be a good alternative for the treatment of such diseases when they develop a subretinal neovascular membrane.

Development of a prediction formula of Parkinson disease severity by optical coherence tomography

The aims of this study were to assess the peripapillary retinal nerve fiber layer (RNFL) thickness in patients with Parkinson's disease (PD), to determine its correlation with disease severity, and to define a simple biomarker for predicting clinical severity. One hundred two eyes from 52 patients affected by PD were compared with 97 eyes from 50 age-comparable controls. In all patients, peripapillary RNFL thickness was measured by optical coherence tomography (OCT). We used the Unified Parkinson's Disease Rating Scale (UPDRS) total score and measured responses in the on medication state. Eyes from patients with PD had a statistically significant decrease in average peripapillary RNFL thickness compared with control eyes (P < 0.001). This reduction was observed in every quadrant (inferior, superior, nasal [P < 0.001], and temporal [P = 0.017]) in patients with PD. Furthermore, a strong inverse correlation was found between the PD severity measured according to the UPDRS score and the average peripapillary RNFL thickness (r = -0.615; P < 0.001) and PD duration (r = -0.303; P = 0.002). From these results, we defined a regression equation that predicts the UPDRS score from the above-mentioned variables: UPDRS = 81.6 + 29.6 * log PD duration (years) - 0.6 * RFNL thickness (μm). We observed that, as the evolution and severity of PD progress, the peripapillary RNFL layer thickness, as evaluated by OCT, gradually diminishes. These results suggest that the average peripapillary RNFL thickness measured by OCT might be useful as a biomarker to detect the early onset and progression of PD.