Mathematical Modeling of Perfect Decoupled Control System and Its Application: A Reverse Osmosis Desalination Industrial-Scale Unit

This short paper outlines the computer simulation using real data of a decoupled control system for a desalination unit. The control strategy incorporated a perfect decoupled controller for the control of the fresh water flow and conductivity. The model was estimated using real data and empirical tools instead of mass balances. The success is demonstrated in the reduction of wide fluctuations in the variables of the process and decreasing of the sensibility to the changes of pressure and/or pH and allows predicting problems of quality of water and waste of energy in the future

Multi-band high resolution spectroscopy rules out the hot Jupiter BD+20 1790b - First data from the GIARPS Commissioning

Context. Stellar activity is currently challenging the detection of young planets via the radial velocity (RV) technique. Aims. We attempt to definitively discriminate the nature of the RV variations for the young active K5 star BD+20 1790, for which visible (VIS) RV measurements show divergent results on the existence of a substellar companion. Methods. We compare VIS data with high precision RVs in the near infrared (NIR) range by using the GIANO - B and IGRINS spectrographs. In addition, we present for the first time simultaneous VIS-NIR observations obtained with GIARPS (GIANO - B and HARPS - N) at Telescopio Nazionale Galileo (TNG). Orbital RVs are achromatic, so the RV amplitude does not change at different wavelengths, while stellar activity induces wavelength-dependent RV variations, which are significantly reduced in the NIR range with respect to the VIS. Results. The NIR radial velocity measurements from GIANO - B and IGRINS show an average amplitude of about one quarter with respect to previously published VIS data, as expected when the RV jitter is due to stellar activity. Coeval multi-band photometry surprisingly shows larger amplitudes in the NIR range, explainable with a mixture of cool and hot spots in the same active region. Conclusions. In this work, the claimed massive planet around BD+20 1790 is ruled out by our data. We exploited the crucial role of multi- wavelength spectroscopy when observing young active stars: thanks to facilities like GIARPS that provide simultaneous observations, this method can reach its maximum potential.Comment: 12 pages, 7 figure

Three years of HARPS-N high-resolution spectroscopy and precise radial velocity data for the Sun

Context. The solar telescope connected to HARPS-N has been observing the Sun since the summer of 2015. Such a high-cadence, long-baseline data set is crucial for understanding spurious radial-velocity signals induced by our Sun and by the instrument. On the instrumental side, this data set allowed us to detect sub- m s−1 systematics that needed to be corrected for. Aims. The goals of this manuscript are to (i) present a new data reduction software for HARPS-N, (ii) demonstrate the improvement brought by this new software during the first three years of the HARPS-N solar data set, and (iii) release all the obtained solar products, from extracted spectra to precise radial velocities. Methods. To correct for the instrumental systematics observed in the data reduced with the current version of the HARPS-N data reduction software (DRS version 3.7), we adapted the newly available ESPRESSO DRS (version 2.2.3) to HARPS-N and developed new optimised recipes for the spectrograph. We then compared the first three years of HARPS-N solar data reduced with the current and new DRS. Results. The most significant improvement brought by the new DRS is a strong decrease in the day-to-day radial-velocity scatter, from 1.27 to 1.07 m s−1; this is thanks to a more robust method to derive wavelength solutions, but also to the use of calibrations closer in time. The newly derived solar radial-velocities are also better correlated with the chromospheric activity level of the Sun in the long term, with a Pearson correlation coefficient of 0.93 compared to 0.77 before, which is expected from our understanding of stellar signals. Finally, we also discuss how HARPS-N spectral ghosts contaminate the measurement of the calcium activity index, and we present an efficient technique to derive an index free of instrumental systematics. Conclusions. This paper presents a new data reduction software for HARPS-N and demonstrates its improvements, mainly in terms of radial-velocity precision, when applied to the first three years of the HARPS-N solar data set. Those newly reduced solar data, representing an unprecedented time series of 34 550 high-resolution spectra and precise radial velocities, are released alongside this paper. Those data are crucial to understand stellar activity signals in solar-type stars further and develop the mitigating techniques that will allow us to detect other Earths.</jats:p

Common folate gene variant, MTHFR C677T, is associated with brain structure in two independent cohorts of people with mild cognitive impairment☆

A commonly carried C677T polymorphism in a folate-related gene, MTHFR, is associated with higher plasma homocysteine, a well-known mediator of neuronal damage and brain atrophy. As homocysteine promotes brain atrophy, we set out to discover whether people carrying the C677T MTHFR polymorphism which increases homocysteine, might also show systematic differences in brain structure. Using tensor-based morphometry, we tested this association in 359 elderly Caucasian subjects with mild cognitive impairment (MCI) (mean age: 75 ± 7.1 years) scanned with brain MRI and genotyped as part of Alzheimer's Disease Neuroimaging Initiative. We carried out a replication study in an independent, non-overlapping sample of 51 elderly Caucasian subjects with MCI (mean age: 76 ± 5.5 years), scanned with brain MRI and genotyped for MTHFR, as part of the Cardiovascular Health Study. At each voxel in the brain, we tested to see where regional volume differences were associated with carrying one or more MTHFR ‘T’ alleles. In ADNI subjects, carriers of the MTHFR risk allele had detectable brain volume deficits, in the white matter, of up to 2–8% per risk T allele locally at baseline and showed accelerated brain atrophy of 0.5–1.5% per T allele at 1 year follow-up, after adjusting for age and sex. We replicated these brain volume deficits of up to 5–12% per MTHFR T allele in the independent cohort of CHS subjects. As expected, the associations weakened after controlling for homocysteine levels, which the risk gene affects. The MTHFR risk variant may thus promote brain atrophy by elevating homocysteine levels. This study aims to investigate the spatially detailed effects of this MTHFR polymorphism on brain structure in 3D, pointing to a causal pathway that may promote homocysteine-mediated brain atrophy in elderly people with MCI

MaxDIA enables library-based and library-free data-independent acquisition proteomics

MaxDIA is a software platform for analyzing data-independent acquisition (DIA) proteomics data within the MaxQuant software environment. Using spectral libraries, MaxDIA achieves deep proteome coverage with substantially better coefficients of variation in protein quantification than other software. MaxDIA is equipped with accurate false discovery rate (FDR) estimates on both library-to-DIA match and protein levels, including when using whole-proteome predicted spectral libraries. This is the foundation of discovery DIA-hypothesis-free analysis of DIA samples without library and with reliable FDR control. MaxDIA performs three- or four-dimensional feature detection of fragment data, and scoring of matches is augmented by machine learning on the features of an identification. MaxDIA's bootstrap DIA workflow performs multiple rounds of matching with increasing quality of recalibration and stringency of matching to the library. Combining MaxDIA with two new technologies-BoxCar acquisition and trapped ion mobility spectrometry-both lead to deep and accurate proteome quantification. The software platform MaxDIA streamlines analysis of data-independent acquisition proteomics

Common folate gene variant, MTHFR C677T, is associated with brain structure in two independent cohorts of people with mild cognitive impairment

AbstractA commonly carried C677T polymorphism in a folate-related gene, MTHFR, is associated with higher plasma homocysteine, a well-known mediator of neuronal damage and brain atrophy.As homocysteine promotes brain atrophy, we set out to discover whether people carrying the C677T MTHFR polymorphism which increases homocysteine, might also show systematic differences in brain structure.Using tensor-based morphometry, we tested this association in 359 elderly Caucasian subjects with mild cognitive impairment (MCI) (mean age: 75±7.1years) scanned with brain MRI and genotyped as part of Alzheimer's Disease Neuroimaging Initiative. We carried out a replication study in an independent, non-overlapping sample of 51 elderly Caucasian subjects with MCI (mean age: 76±5.5years), scanned with brain MRI and genotyped for MTHFR, as part of the Cardiovascular Health Study. At each voxel in the brain, we tested to see where regional volume differences were associated with carrying one or more MTHFR ‘T’ alleles.In ADNI subjects, carriers of the MTHFR risk allele had detectable brain volume deficits, in the white matter, of up to 2–8% per risk T allele locally at baseline and showed accelerated brain atrophy of 0.5–1.5% per T allele at 1year follow-up, after adjusting for age and sex. We replicated these brain volume deficits of up to 5–12% per MTHFR T allele in the independent cohort of CHS subjects.As expected, the associations weakened after controlling for homocysteine levels, which the risk gene affects. The MTHFR risk variant may thus promote brain atrophy by elevating homocysteine levels.This study aims to investigate the spatially detailed effects of this MTHFR polymorphism on brain structure in 3D, pointing to a causal pathway that may promote homocysteine-mediated brain atrophy in elderly people with MCI

BioContainers: An open-source and community-driven framework for software standardization

Motivation BioContainers (biocontainers.pro) is an open-source and community-driven framework which provides platform independent executable environments for bioinformatics software. BioContainers allows labs of all sizes to easily install bioinformatics software, maintain multiple versions of the same software and combine tools into powerful analysis pipelines. BioContainers is based on popular open-source projects Docker and rkt frameworks, that allow software to be installed and executed under an isolated and controlled environment. Also, it provides infrastructure and basic guidelines to create, manage and distribute bioinformatics containers with a special focus on omics technologies. These containers can be integrated into more comprehensive bioinformatics pipelines and different architectures (local desktop, cloud environments or HPC clusters). Availability and Implementation The software is freely available at github.com/BioContainers/.publishedVersio