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SWaveform, a newly created open genome-wide resource for read depth signal in the vicinity of structural variant (SV) breakpoints, aims to boost development of computational tools and algorithms for discovery of genomic rearrangement events from sequencing data. SVs are a dominant force shaping genomes and substantially contributing to genetic diversity. Still, there are challenges in reliable and efficient genotyping of SVs from whole genome sequencing data, thus delaying translation into clinical applications and wasting valuable resources. SWaveform includes a database containing ~7 M of read depth profiles at SV breakpoints extracted from 911 sequencing samples generated by the Human Genome Diversity Project, generalised patterns of the signal at breakpoints, an interface for navigation and download, as well as a toolbox for local deployment with user’s data. The dataset can be of immense value to bioinformatics and engineering communities as it empowers smooth application of intelligent signal processing and machine learning techniques for discovery of genomic rearrangement events and thus opens the floodgates for development of innovative algorithms and software.

This study demonstrates the possibility of \"contactless\" mass transfer between two aqueous slugs (droplets) separated by an oil slug in Taylor flow inside milli-channels. Separation of the alternating aqueous slugs at the outlet was performed by switching a couple of solenoid valves at branched outlets according to signals obtained by an optical sensor at the branch. Transfer of bromothymol blue (BTB) from acidic to basic aqueous slugs was performed for demonstration. In some cases, aqueous slugs separated by oil, merged catching on each other due to the velocity difference. Interfacial tension which was affected by the solute concentration was responsible for the velocity difference. Position-specific mass transfer activity at the rear end of the aqueous slugs was found on the course of the experiment. A meandering channel decreased the velocity difference and enhanced mass transfer. Almost complete (93%) transfer of BTB was achieved within a short residence time of several minutes under optimized conditions. The presented system opens a way for advanced separation using minimum amounts of the oil phase and allows concentrating the solute by altering relative lengths of the sender and receiver slugs.

The paper compares conceptual designs of a microstructured reactor/heat-exchanger for the small-scale production of C8+ range hydrocarbons from methanol over H-ZSM-5 catalytic coatings. In these designs, air was used as a cooling fluid in the adjacent cooling channels. The heat transfer characteristics of a single-zone reactor (with channels 500 μm in diameter) and a two-zone reactor (with an additional coolant inlet) have been compared. A single reaction zone was not able to reduce the temperature gradient below 15 K, while a two-zone configuration, with a counter-current fluid flow in the upstream section and co-current flow in the downstream section, demonstrated a near-isothermal behaviour, with a mean temperature of 653 K.

A comparative analysis of whole genome sequencing (WGS) and genotype calling was initiated for ten human genome samples sequenced by St. Petersburg State University Peterhof Sequencing Center and by three commercial sequencing centers outside of Russia. The sequence quality, efficiency of DNA variant and genotype calling were compared with each other and with DNA microarrays for each of ten study subjects. We assessed calling of SNPs, indels, copy number variation, and the speed of WGS throughput promised. Twenty separate QC analyses showed high similarities among the sequence quality and called genotypes. The ten genomes tested by the centers included eight American patients afflicted with autoimmune hepatitis (AIH), plus one case's unaffected parents, in a prelude to discovering genetic influences in this rare disease of unknown etiology. The detailed internal replication and parallel analyses allowed the observation of two of eight AIH cases carrying a rare allele genotype for a previously described AIH-associated gene (FTCD), plus multiple occurrences of known HLA-DRB1 alleles associated with AIH (HLA-DRB1-03:01:01, 13:01:01 and 7:01:01). We also list putative SNVs in other genes as suggestive in AIH influence.

At least 50% of factors predisposing to alcohol dependence (AD) are genetic and women affected with this disorder present with more psychiatric comorbidities, probably indicating different genetic factors involved. We aimed to run a genome-wide association study (GWAS) followed by a bioinformatic functional annotation of associated genomic regions in patients with AD and eight related clinical measures. A genome-wide significant association of rs220677 with AD (p-value = 1.33 × 10−8 calculated with the Yates-corrected χ2 test under the assumption of dominant inheritance) was discovered in female patients. Associations of AD and related clinical measures with seven other single nucleotide polymorphisms listed in previous GWASs of psychiatric and addiction traits were differently replicated in male and female patients. The bioinformatic analysis showed that regulatory elements in the eight associated linkage disequilibrium blocks define the expression of 80 protein-coding genes. Nearly 68% of these and of 120 previously published coding genes associated with alcohol phenotypes directly interact in a single network, where BDNF is the most significant hub gene. This study indicates that several genes behind the pathogenesis of AD are different in male and female patients, but implicated molecular mechanisms are functionally connected. The study also reveals a central role of BDNF in the pathogenesis of AD.

Semihydrogenation of 2-methyl-3-butyn-2-ol (MBY) was studied in a 5 m tube reactor wall-coated with a 5 wt% Pd/ZnO catalyst. The system allowed for the excellent selectivity towards the intermediate alkene of 97.8 ± 0.2% at an ambient H2 pressure and a MBY conversion below 90%. The maximum alkene yield reached 94.6% under solvent-free conditions and 96.0% in a 30 vol % MBY aqueous solution. The reactor stability was studied for 80 h on stream with a deactivation rate of only 0.07% per hour. Such a low deactivation rate provides a continuous operation of one month with only a two-fold decrease in catalyst activity and a metal leaching below 1 parts per billion (ppb). The excellent turn-over numbers (TON) of above 105 illustrates a very efficient utilisation of the noble metal inside catalyst-coated tube reactors. When compared to batch operation at 70 °C, the reaction rate in flow reactor can be increased by eight times at a higher reaction temperature, keeping the same product decomposition of about 1% in both cases.

A novel continuous flow process for selective hydrogenation of α, β-unsaturated aldehyde (cinnamaldehyde, CAL) to the unsaturated alcohol (cinnamyl alcohol, COL) has been reported in a tube reactor coated with a Pt/SiO2 catalyst. A 90% selectivity towards the unsaturated alcohol was obtained at the aldehyde conversion of 98.8%. This is a six-fold improvement in the selectivity compared to a batch process where acetals were the main reaction products. The increased selectivity in the tube reactor was caused by the suppression of acid sites responsible for the acetal formation after a short period on stream in the continuous process. In a fixed bed reactor, it had a similar acetal suppression phenomenon but showed lower product selectivity of about 47–72% due to mass transfer limitations. A minor change in selectivity and conversion caused by product inhibition was observed during the 110 h on stream with a turnover number (TON) reaching 3000 and an alcohol production throughput of 0.36 kg gPt−1 day−1 in the single tube reactor. The catalysts performance after eight reaction cycles was fully restored by calcination in air at 400 °C. The tube reactors provide an opportunity for process intensification by increasing the reaction rates by a factor of 2.5 at the reaction temperature of 150 °C compared to 90 °C with no detrimental effects on catalyst stability or product selectivity.

Although there have been many studies of gene variant association with different stages of HIV/AIDS progression in United States and European cohorts, few gene-association studies have assessed genic determinants in sub-Saharan African populations, which have the highest density of HIV infections worldwide. We carried out genome-wide association studies on 766 study participants at risk for HIV-1 subtype C (HIV-1C) infection in Botswana. Three gene associations (AP3B1, PTPRA, and NEO1) were shown to have significant association with HIV-1C acquisition. Each gene association was replicated within Botswana or in the United States–African American or United States–European American AIDS cohorts or in both. Each associated gene has a prior reported influence on HIV/AIDS pathogenesis. Thirteen previously discovered AIDS restriction genes were further replicated in the Botswana cohorts, extending our confidence in these prior AIDS restriction gene reports. This work presents an early step toward the identification of genetic variants associated with and affecting HIV acquisition or AIDS progression in the understudied HIV-1C afflicted Botswana population.

The desorption of methanol and dimethyl ether has been studied over fresh and hydrocarbon-occluded ZSM-5 catalysts with Si/Al ratios of 25, 36 and 135 using a temporal analysis of products reactor. The catalysts were characterized by XRD, SEM, N 2 physisorption and pyridine FT-IR. The crystal size increases with Si/Al ratio from 0.10 to 0.78 µm. The kinetic parameters were obtained using the Redhead method and a plug flow reactor model with coupled convection, adsorption and desorption steps. ZSM-5 catalysts with Si/Al ratios of 25 and 36 exhibit three adsorption sites (low, medium, and high temperature sites), while there is no difference between medium and high temperature sites at a Si/Al ratio of 135. Molecular adsorption on the low temperature site and dissociative adsorption on the medium and high temperature sites give a good match between experiment and the plug flow reactor model. The DME desorption activation energy was systematically higher than that of methanol. Adsorption stoichiometry shows that methanol and DME form clusters onto the binding sites. When non-activated re-adsorption is accounted for, a local equilibrium is reached only on the low and medium temperature binding sites. No differences were observed, other than in site densities, when extracting the kinetic parameters for fresh and activated ZSM-5 catalysts at full coverage. Graphical Abstract

The metal–organic framework MIL-101(Cr) is known as a solid–acid catalyst for the solution conversion of biomass-derived glucose to 5-hydroxymethyl furfural (5-HMF). We study the substitution of Cr3+ by Fe3+ and Sc3+ in the MIL-101 structure in order to prepare more environmentally benign catalysts. MIL-101(Fe) can be prepared, and the inclusion of Sc is possible at low levels (10% of Fe replaced). On extended synthesis times the polymorphic MIL-88B structure instead forms.Increasing the amount of Sc also only yields MIL-88B, even at short crystallisation times. The MIL-88B structure is unstable under hydrothermal conditions, but in dimethylsulfoxide solvent, it provides 5-HMF from glucose as the major product. The optimum material is a bimetallic (Fe,Sc) form of MIL-88B, which provides ~70% conversion of glucose with 35% selectivity towards 5-HMF after 3 hours at 140 °C: this offers high conversion compared to other heterogeneous catalysts reported in the same solvent.