Accounting for data heterogeneity in integrative analysis and prediction methods: An application to Chronic Obstructive Pulmonary Disease

Epidemiologic and genetic studies in chronic obstructive pulmonary disease (COPD) and many complex diseases suggest subgroup disparities (e.g., by sex). We consider this problem from the standpoint of integrative analysis where we combine information from different views (e.g., genomics, proteomics, clinical data). Existing integrative analysis methods ignore the heterogeneity in subgroups, and stacking the views and accounting for subgroup heterogeneity does not model the association among the views. To address analytical challenges in the problem of our interest, we propose a statistical approach for joint association and prediction that leverages the strengths in each view to identify molecular signatures that are shared by and specific to males and females and that contribute to the variation in COPD, measured by airway wall thickness. HIP (Heterogeneity in Integration and Prediction) accounts for subgroup heterogeneity, allows for sparsity in variable selection, is applicable to multi-class and to univariate or multivariate continuous outcomes, and incorporates covariate adjustment. We develop efficient algorithms in PyTorch. Our COPD findings have identified several proteins, genes, and pathways that are common and specific to males and females, some of which have been implicated in COPD, while others could lead to new insights into sex differences in COPD mechanisms

2014-2021, 8 years without bottom-reaching deep water formation in the Western Mediterranean. Probably, the longest known period

Deep Water Formation (DWF) appeared almost regularly every year, during central winter months, in an area located offshore the Gulf of Lions in the NW Mediterranean Sea. Since the early 1960s, the processes involved in the DWF have been monitored, more or less intensively by regular hydrographic surveys or by moored instruments. It is worth noting the international efforts carried out in late 60s-early 70s by the so-called MEDOC Group to obtain a quite precise description of the whole process. Although the intensity of the DWF, as well as the amount of the newly formed Western Mediterranean Deep Water (WMDW), have shown high interanual variability, those years when the DWF was absent were exceptional, e.g. 1990, and those not reaching the bottom were scarce, e.g. 1997. Typically, they were years with almost no cold northerly winds during winter. By contrast, in some years the amount of newly formed WMDW was exceptional, e.g. 1987, and in some cases, an extra amount of this water came from dense shelf cascading, e.g. 1999. Moreover, in some years, the so-called variable Bottom Water, a slightly warm and salty layer, appeared near the bottom. It was a layer not thicker than 300 m, attributed to a large area affected by DWF which caused an extra amount of Levantine Intermediate Water (LIW) involved in the process, e.g. 1973. Other concomitant conditions that contributed to the DWF variability across the years was the presence of a blocking anticyclone in the Balearic Sea, that would play a role in intensifying the exposure of surface water to the northerlies, e.g. 1999. In winter 2005, all the factors contributing to an intense DWF process acted simultaneously, resulting in a new structure within the WMDW. The amount of newly formed WMDW, with higher density, T and S, was so extraordinary that affected the entire western Mediterranean basin, and it was identified as the Western Mediterranean Transition (WMT). The remnants of the WMDW previous to the WMT have been uplifted as to being available for a relevant contribution to the Mediterranean Outlfow Water (MOW) through the Gibraltar sill. After the WMT, the MOW showed both lower T and S than previously recorded up to around 2015, indicating that the old WMDW has been almost completely lost by leakage and diffusion. After the 2005 episode, the WMDW has evolved, changing its TS shape and increasing both T and S at the bottom, but still maintaining a deep layer with higher stratification than before 2005. In a previous work, we attributed the long period (2014-2018) without DWF to a combination of mild winters, the absence of the old WMDW, and the deep stratification. Such a process would be similar to the recovery of the Eastern Mediterranean Transient. In the present communication we incorporate 3 new years of data to the series, discuss the current situation and try to identify the requirements for a successful bottom-reaching DWF

Quantitative isotope-dilution high-resolution-mass-apectrometry analysis of multiple intracellular metabolites in Clostridium autoethanogenum with uniformly 13C-labeled standards derived from Spirulina

We have investigated the applicability of commercially available lyophilized spirulina (Arthrospira platensis), a microorganism uniformly labeled with 13C, as a readily accessible source of multiple 13C-labeled metabolites suitable as internal standards for the quantitative determination of intracellular bacterial metabolites. Metabolites of interest were analyzed by hydrophilic-interaction liquid chromatography coupled with high-resolution mass spectrometry. Multiple internal standards obtained from uniformly (U)-13C-labeled extracts from spirulina were used to enable isotope-dilution mass spectrometry (IDMS) in the identification and quantification of intracellular metabolites. Extraction of the intracellular metabolites of Clostridium autoethanogenum using 2:1:1 chloroform/methanol/water was found to be the optimal method in comparison with freeze–thaw, homogenization, and sonication methods. The limits of quantification were ≤1 μM with excellent linearity for all of the calibration curves (R2 ≥ 0.99) for 74 metabolites. The precision and accuracy were found to be within relative standard deviations (RSDs) of 15% for 49 of the metabolites and within RSDs of 20% for all of the metabolites. The method was applied to study the effects of feeding different levels of carbon monoxide (as a carbon source) on the central metabolism and Wood–Ljungdahl pathway of C. autoethanogenum grown in continuous culture over 35 days. Using LC-IDMS with U-13C spirulina allowed the successful quantification of 52 metabolites in the samples, including amino acids, carboxylic acids, sugar phosphates, purines, and pyrimidines. The method provided absolute quantitative data on intracellular metabolites that was suitable for computational modeling to understand and optimize the C. autoethanogenum metabolic pathways active in gas fermentation

ANTIOXIDANT AND ANTI-PROLIFERATIVE EFFECTS OF AN ETHYL ACETATE FRACTION OF THE HYDRO-ETHANOLIC EXTRACT OF SYNEDRELLA NODIFLORA (L) GAERTN

Objective: Synedrella nodiflora is traditionally used in the treatment of several ailments. Pharmacologically, this plant has anticonvulsant, sedative, anti-nociceptive and anti-proliferative effects. This study further investigated S. nodiflora for its antioxidant and in vitro inhibition of cancerous cell lines. Methods: Phytochemical assays, and the DPPH radical scavenging method were employed in preliminary screening for antioxidant activities of the crude hydro-ethanolic extract (SNE) and resulting fractions. The potent ethyl acetate fraction (EAF), was further investigated for total phenol and flavonoid contents, reducing power, lipid peroxidation potential, and cytotoxic effects on human breast cancer (MCF-7), leukemic (Jurkat), and normal liver (Chang’s liver) cell lines. Results: The extract contained phenols, flavonoids, tannins, glycosides, sterols, terpenoids, and alkaloids. It scavenged for DPPH with an IC50 of 114 µg/ml, whereas that of EAF was 8.9 µg/ml. EAF prevented peroxidation of egg lecithin at an IC50 of 24.01±0.08 µg/ml. These IC50s are four and three times lower than the reference standards. EAF produced anti-proliferative effects against MCF-7, and Jurkat cell lines with IC50s of 205.2 and 170.9 µg/ml, respectively. EAF had a high IC50 of 252.2 µg/ml against Chang’s liver cells. At 0.1 mg/ml EAF had similar total flavonoid content to SNE, but a significantly higher total phenol content. Conclusion: The ethyl acetate fraction of S. nodiflora, exhibited the most potent antioxidant activity. It inhibited the proliferation of breast and leukemic cancer cell lines, whiles having weak cytotoxic effect on normal liver cells. These can be explored for further drug development

Ocean Circulation over Formigas and Ormonde Seamounts

Seamounts constitute an obstacle to the free ocean flow, modifying the patter of circulation. As a result of these alterations, a variety of hydrodynamical processes and phenomena may take place in seamounts, among others, Taylor columns/caps. These oceanographic effects may turn seamounts into very productive ecosystems with high biodiversity. Under these conditions seamounts provide a particularly good environment for the settle of some organisms, acting as stepping stones and contributing to its dispersal. In this study, we verify if these oceanographic effects explain the presence of cold-water corals of Mediterranean origin in the Atlantic. To achieve this, three seamounts in the path of the Mediterranean Outflow Water (MOW) through the Eastern North Atlantic were selected: the Gazul mud volcano, and the Ormonde and Formigas seamounts. In order to determine the hydrographic and dynamical conditions in each one of the three locations, CTD, LADPC and biochemical observations were carried out. Taylor columns were not observed in any of the three sampled areas. Although we found suggestions of upwelling/downwelling systems, their effect was barely noticed in the circulation pattern. The oceanographic processes in those areas are more influenced by the vertical distribution of water masses, which determine the stability of the water column. Moreover, the high values of the Brunt-Väisälä frequency around the MOW halocline can lead to the formation of internal waves. These perturbations in the water column can enhance the vertical mixing, producing suspension, which, in turn, could affect the vertical distribution of cold-water corals

Engineering improved ethylene production: Leveraging systems Biology and adaptive laboratory evolution

Ethylene is a small hydrocarbon gas widely used in the chemical industry. Annual worldwide production currently exceeds 150 million tons, producing considerable amounts of CO2 contributing to climate change. The need for a sustainable alternative is therefore imperative. Ethylene is natively produced by several different microorganisms, including Pseudomonas syringae pv. phaseolicola via a process catalyzed by the ethylene forming enzyme (EFE), subsequent heterologous expression of EFE has led to ethylene production in non-native bacterial hosts including E. coli and cyanobacteria. However, solubility of EFE and substrate availability remain rate limiting steps in biological ethylene production. We employed a combination of genome scale metabolic modelling, continuous fermentation, and protein evolution to enable the accelerated development of a high efficiency ethylene producing E. coli strain, yielding a 49-fold increase in production, the most significant improvement reported to date. Furthermore, we have clearly demonstrated that this increased yield resulted from metabolic adaptations that were uniquely linked to the EFE enzyme (WT vs mutant). Our findings provide a novel solution to deregulate metabolic bottlenecks in key pathways, which can be readily applied to address other engineering challenges

Ocean Circulation over North Atlantic underwater features in the path of the Mediterranean Outflow Water: Ormonde and Formigas seamounts, and the Gazul mud volcano

Seamounts constitute an obstacle to the ocean circulation, modifying it. As a result, a variety of hydrodynamical processes and phenomena may take place over seamounts, among others, flow intensification, current deflection, upwelling, Taylor caps, and internal waves. These oceanographic effects may turn seamounts into very productive ecosystems with high species diversity, and in some cases, are densely populated by benthic organisms, such corals, gorgonians, and sponges. In this study, we describe the oceanographic conditions over seamounts and other underwater features in the path of the Mediterranean Outflow Water (MOW), where populations of benthic suspensions feeders have been observed. Using CTD, LADPC and biochemical measurements carried out in the Ormonde and Formigas seamounts and the Gazul mud volcano (Northeast Atlantic), we show that Taylor caps were not observed in any of the sampled features. However, we point out that the relatively high values of the Brunt–Väisälä frequency in the MOW halocline, in conjunction with the slope of the seamount flanks, set up conditions for the breakout of internal waves and amplification of the currents. This may enhance the vertical mixing, resuspending the organic material deposited on the seafloor and, therefore, increasing the food availability for the communities dominated by benthic suspension feeders. Thus, we hypothesize that internal waves could be improving the conditions for benthic suspension feeders to grow on the slope of seamounts.En prens

Quantitative Bioreactor Monitoring of Intracellular Bacterial Metabolites in Clostridium autoethanogenum Using Liquid Chromatography–Isotope Dilution Mass Spectrometry

We report a liquid chromatography–isotope dilution mass spectrometry method for the simultaneous quantification of 131 intracellular bacterial metabolites of Clostridium autoethanogenum. A comprehensive mixture of uniformly 13C-labeled internal standards (U-13C IS) was biosynthesized from the closely related bacterium Clostridium pasteurianum using 4% 13C–glucose as a carbon source. The U-13C IS mixture combined with 12C authentic standards was used to validate the linearity, precision, accuracy, repeatability, limits of detection, and quantification for each metabolite. A robust-fitting algorithm was employed to reduce the weight of the outliers on the quantification data. The metabolite calibration curves were linear with R2 ≥ 0.99, limits of detection were ≤1.0 μM, limits of quantification were ≤10 μM, and precision/accuracy was within RSDs of 15% for all metabolites. The method was subsequently applied for the daily monitoring of the intracellular metabolites of C. autoethanogenum during a CO gas fermentation over 40 days as part of a study to optimize biofuel production. The concentrations of the metabolites were estimated at steady states of different pH levels using the robust-fitting mathematical approach, and we demonstrate improved accuracy of results compared to conventional regression. Metabolic pathway analysis showed that reactions of the incomplete (branched) tricarboxylic acid “cycle” were the most affected pathways associated with the pH shift in the bioreactor fermentation of C. autoethanogenum and the concomitant changes in ethanol production

Dendritic Spike Saturation of Endogenous Calcium Buffer and Induction of Postsynaptic Cerebellar LTP

The architecture of parallel fiber axons contacting cerebellar Purkinje neurons retains spatial information over long distances. Parallel fiber synapses can trigger local dendritic calcium spikes, but whether and how this calcium signal leads to plastic changes that decode the parallel fiber input organization is unknown. By combining voltage and calcium imaging, we show that calcium signals, elicited by parallel fiber stimulation and mediated by voltage-gated calcium channels, increase non-linearly during high-frequency bursts of electrically constant calcium spikes, because they locally and transiently saturate the endogenous buffer. We demonstrate that these non-linear calcium signals, independently of NMDA or metabotropic glutamate receptor activation, can induce parallel fiber long-term potentiation. Two-photon imaging in coronal slices revealed that calcium signals inducing long-term potentiation can be observed by stimulating either the parallel fiber or the ascending fiber pathway. We propose that local dendritic calcium spikes, evoked by synaptic potentials, provide a unique mechanism to spatially decode parallel fiber signals into cerebellar circuitry changes

Efaproxiral red blood cell concentration predicts efficacy in patients with brain metastases

Efaproxiral (Efaproxyn™, RSR13), a synthetic allosteric modifier of haemoglobin (Hb), decreases Hb-oxygen (O2) binding affinity and enhances oxygenation of hypoxic tumours during radiation therapy. This analysis evaluated the Phase 3, Radiation Enhancing Allosteric Compound for Hypoxic Brain Metastases; RT-009 (REACH) study efficacy results in relation to efaproxiral exposure (efaproxiral red blood cell concentration (E-RBC) and number of doses). Recursive partitioning analysis Class I or II patients with brain metastases from solid tumours received standard whole-brain radiation therapy (3 Gy/fraction × 10 days), plus supplemental O2 (4 l/min), either with efaproxiral (75 or 100 mg/kg daily) or without (control). Efaproxiral red blood cell concentrations were linearly extrapolated to all efaproxiral doses received. Three patient populations were analysed: (1) all eligible, (2) non-small-cell lung cancer (NSCLC) as primary cancer, and (3) breast cancer primary. Efficacy endpoints were survival and response rate. Brain metastases patients achieving sufficient E-RBC (⩾483 μg/ml) and receiving at least seven of 10 efaproxiral doses were most likely to experience survival and response benefits. Patients with breast cancer primary tumours generally achieved the target efaproxiral exposure and therefore gained greater benefit from efaproxiral treatment than NSCLC patients. This analysis defined the efaproxiral concentration-dependence in survival and response rate improvement, and provided a clearer understanding of efaproxiral dosing requirements