Anti-bias training for (sc)RNA-seq: experimental and computational approaches to improve precision.

RNA-seq, including single cell RNA-seq (scRNA-seq), is plagued by insufficient sensitivity and lack of precision. As a result, the full potential of (sc)RNA-seq is limited. Major factors in this respect are the presence of global bias in most datasets, which affects detection and quantitation of RNA in a length-dependent fashion. In particular, scRNA-seq is affected by technical noise and a high rate of dropouts, where the vast majority of original transcripts is not converted into sequencing reads. We discuss these biases origins and implications, bioinformatics approaches to correct for them, and how biases can be exploited to infer characteristics of the sample preparation process, which in turn can be used to improve library preparation.

Desalination, Water Re-use, and Halophyte Cultivation in Salinized Regions: A Highly Productive Groundwater Treatment System.

Groundwater salinization is a problem affecting access to water in many world regions. Though desalination by conventional reverse osmosis (RO) can upgrade groundwater quality for drinking, its disadvantages include unmanaged brine discharge and accelerated groundwater depletion. Here, we propose a new approach combining RO, forward osmosis (FO), and halophyte cultivation, in which FO optimally adjusts the concentration of the RO reject brine for irrigation of Salicornia or Sarcocornia. The FO also re-uses wastewater, thus, reducing groundwater extraction and the wastewater effluent volume. To suit different groundwater salinities in the range 1-8 g/L, three practical designs are proposed and analyzed. Results include specific groundwater consumption (SGC), specific energy consumption (SEC), wastewater volume reduction, peak RO pressure, permeate water quality, efficiency of water resource utilization, and halophyte yield. Compared to conventional brackish water RO, the results show superior performance in almost all aspects. For example, SGC is reduced from 1.25 to 0.9 m3 per m3 of drinking water output and SEC is reduced from 0.79 to 0.70 kW h/m3 by a FO-RO-FO system treating groundwater of salinity 8 g/L. This system can produce 1.1 m3 of high-quality drinking water and up to 4.9 kg of edible halophyte per m3 of groundwater withdrawn.

The effect of dissolved chlorides on the photocatalytic degradation properties of titania in wastewater treatment.

We investigate the effect of chlorides on the photocatalytic degradation of phenol by titania polymorphs (anatase and rutile). We demonstrate how solubilised chlorides can affect the hydroxyl radical formation on both polymorphs with an overall effect on their photodegradative activity. Initially, the photocatalytic activity of anatase and rutile for phenol degradation is investigated in both standard water and brines. With anatase, a significant reduction of the phenol conversion rate is observed (from a pseudo-first-order rate constant k = 5.3 × 10-3 min-1 to k = 3.5 × 10-3 min-1). In contrast, the presence of solubilised chlorides results in enhancement of rutile activity under the same reaction conditions (from 2.3 × 10-3 min-1 to 4.8 × 10-3 min-1). Periodic DFT methods are extensively employed and we show that after the generation of charge separation in the modelled titania systems, adsorbed chlorides are the preferential site for partial hole localisation, although small energy differences are computed between partially localised hole densities over adsorbed chloride or hydroxyl. Moreover, chlorides can reduce or inhibit the ability of r-TiO2 (110) and a-TiO2 (101) systems to localise polarons in the slab structure. These results indicate that both mechanisms - hole scavenging and the inhibition of hole localisation - can be the origin of the effect of chlorides on photocatalytic activity of both titania polymorphs. These results provide fundamental insight into the photocatalytic properties of titania polymorphs and elucidate the effect of adsorbed anions over radical formation and oxidative decomposition of organic pollutants.

Siwa Oasis groundwater quality: factors controlling spatial and temporal changes.

Siwa Oasis is of great historical, environmental, and scientific importance, as it contains unique archeological and geological features. Groundwater is the main source of freshwater in that oasis. The carbonate aquifer groundwater, used for irrigation, was sampled to evaluate factors controlling quality changes spatially and temporally by applying hydrochemical and statistical analyses. The salinity of the aquifer varied spatially from 1367 to 8645 mg/l based on one hydrogeological condition, with the highest TDS (> 5432.5 mg/l, 25% of samples) at the central part of the study area. Temporally, the salinity changed slightly from 3754.3 mg/l (in 2014) to 4222.4 mg/l (in 2020). The cession of illegal wells, pumping control, and excavation of formed salts have a noticeable impact on salinity (mediate the increase in salinity) and ions. However, about 61% of the studied samples can be considered unsuitable for irrigation owing to salinity and can harm plant yield. The heavy metals studied (Fe, Mn, Cu, Pb), except Cd, were within the permissible limit for irrigation water. Finally, it is proposed to construct desalination stations to enhance water quality for irrigation in the study area and set up many companies for salt extraction.

Adaptations to the current ECCO/ESPGHAN guidelines on the management of paediatric acute severe colitis in the context of the COVID-19 pandemic: a RAND appropriateness panel.

OBJECTIVE: Paediatric acute severe colitis (ASC) management during the novel SARS-CoV-2/COVID-19 pandemic is challenging due to reliance on immunosuppression and the potential for surgery. We aimed to provide COVID-19-specific guidance using the European Crohn's and Colitis Organisation/European Society for Paediatric Gastroenterology, Hepatology and Nutrition guidelines for comparison. DESIGN: We convened a RAND appropriateness panel comprising 14 paediatric gastroenterologists and paediatric experts in surgery, rheumatology, respiratory and infectious diseases. Panellists rated the appropriateness of interventions for ASC in the context of the COVID-19 pandemic. Results were discussed at a moderated meeting prior to a second survey. RESULTS: Panellists recommended patients with ASC have a SARS-CoV-2 swab and expedited biological screening on admission and should be isolated. A positive swab should trigger discussion with a COVID-19 specialist. Sigmoidoscopy was recommended prior to escalation to second-line therapy or colectomy. Methylprednisolone was considered appropriate first-line management in all, including those with symptomatic COVID-19. Thromboprophylaxis was also recommended in all. In patients requiring second-line therapy, infliximab was considered appropriate irrespective of SARS-CoV-2 status. Delaying colectomy due to SARS-CoV-2 infection was considered inappropriate. Corticosteroid tapering over 8-10 weeks was deemed appropriate for all. After successful corticosteroid rescue, thiopurine maintenance was rated appropriate in patients with negative SARS-CoV-2 swab and asymptomatic patients with positive swab but uncertain in symptomatic COVID-19. CONCLUSION: Our COVID-19-specific adaptations to paediatric ASC guidelines using a RAND panel generally support existing recommendations, particularly the use of corticosteroids and escalation to infliximab, irrespective of SARS-CoV-2 status. Consideration of routine prophylactic anticoagulation was recommended.

The interaction of CO with a copper(ii) chloride oxy-chlorination catalyst.

The interaction of CO with an attapulgite-supported, KCl modified CuCl2 catalyst has previously been examined using a combination of XANES, EXAFS and DFT calculations. Exposing the catalyst to CO at elevated temperatures leads to the formation of CO2 as the only identifiable product. However, phosgene production can be induced by a catalyst pre-treatment stage, where the supported CuCl2 sample is exposed to a diluted stream of dichlorine; subsequent CO exposure at ∼643 K then leads to phosgene production. This communication describes a series of FTIR based micro-reactor measurements, coupled with characterisation measurements utilising TEM, XRD and XPS to define the nature of the catalyst at different stages of the reaction coordinate. The CuCl2 catalyst is able to support Deacon activity , establishing this work with the possibility of utilising the oxy-chlorination of CO to produce phosgene. Continuous dosing of CO at elevated temperatures over the chlorine pre-dosed CuCl2 catalyst shows diminishing phosgene production as a function of time-on-stream, indicating surface chlorine supply to be rate-limiting under the reaction conditions studied. A pictorial reaction scheme is proposed to account for the surface chemistry observed.

Structural behaviour of copper chloride catalysts during the chlorination of CO to phosgene.

The interaction of CO with an attapulgite-supported Cu(ii)Cl2 catalyst has been examined in a micro-reactor arrangement. CO exposure to the dried, as-received catalyst at elevated temperatures leads to the formation of CO2 as the only identifiable product. However, phosgene production can be induced by using a catalyst pre-treatment where the supported Cu(ii)Cl2 sample is exposed to a diluted stream of chlorine. Subsequent CO exposure at ∼370 °C then leads to phosgene production. In order to investigate the origins of this atypical set of reaction characteristics, a series of X-ray absorption experiments were performed that were supplemented by DFT calculations. XANES measurements establish that at the elevated temperatures connected with phosgene formation, the catalyst is comprised of Cu+ and a small amount of Cu2+. Moreover, the data show that unique to the chlorine pre-treated sample, CO exposure at elevated temperature results in a short-lived oxidation of the copper. On the basis of calculated CO adsorption energies, DFT calculations indicate that a mixed Cu+/Cu2+ catalyst is required to support CO chemisorption.

Modifying the Interface Edge to Control the Electrical Transport Properties of Nanocontacts to Nanowires.

Selecting the electrical properties of nanomaterials is essential if their potential as manufacturable devices is to be reached. Here, we show that the addition or removal of native semiconductor material at the edge of a nanocontact can be used to determine the electrical transport properties of metal-nanowire interfaces. While the transport properties of as-grown Au nanocatalyst contacts to semiconductor nanowires are well-studied, there are few techniques that have been explored to modify the electrical behavior. In this work, we use an iterative analytical process that directly correlates multiprobe transport measurements with subsequent aberration-corrected scanning transmission electron microscopy to study the effects of chemical processes that create structural changes at the contact interface edge. A strong metal-support interaction that encapsulates the Au nanocontacts over time, adding ZnO material to the edge region, gives rise to ohmic transport behavior due to the enhanced quantum-mechanical tunneling path. Removal of the extraneous material at the Au-nanowire interface eliminates the edge-tunneling path, producing a range of transport behavior that is dependent on the final interface quality. These results demonstrate chemically driven processes that can be factored into nanowire-device design to select the final properties.

Effect of slurry composition on the chemical mechanical polishing of thin diamond films.

Nanocrystalline diamond (NCD) thin films grown by chemical vapour deposition have an intrinsic surface roughness, which hinders the development and performance of the films' various applications. Traditional methods of diamond polishing are not effective on NCD thin films. Films either shatter due to the combination of wafer bow and high mechanical pressures or produce uneven surfaces, which has led to the adaptation of the chemical mechanical polishing (CMP) technique for NCD films. This process is poorly understood and in need of optimisation. To compare the effect of slurry composition and pH upon polishing rates, a series of NCD thin films have been polished for three hours using a Logitech Ltd. Tribo CMP System in conjunction with a polyester/polyurethane polishing cloth and six different slurries. The reduction in surface roughness was measured hourly using an atomic force microscope. The final surface chemistry was examined using X-ray photoelectron spectroscopy and a scanning electron microscope. It was found that of all the various properties of the slurries, including pH and composition, the particle size was the determining factor for the polishing rate. The smaller particles polishing at a greater rate than the larger ones.

Characterization of the effects of n-butanol on the cell envelope of E. coli.

Biofuel alcohols have severe consequences on the microbial hosts used in their biosynthesis, which limits the productivity of the bioconversion. The cell envelope is one of the most strongly affected structures, in particular, as the external concentration of biofuels rises during biosynthesis. Damage to the cell envelope can have severe consequences, such as impairment of transport into and out of the cell; however, the nature of butanol-induced envelope damage has not been well characterized. In the present study, the effects of n-butanol on the cell envelope of Escherichia coli were investigated. Using enzyme and fluorescence-based assays, we observed that 1 % v/v n-butanol resulted in the release of lipopolysaccharides from the outer membrane of E. coli and caused 'leakiness' in both outer and inner membranes. Higher concentrations of n-butanol, within the range of 2-10 % (v/v), resulted in inner membrane protrusion through the peptidoglycan observed by characteristic blebs. The findings suggest that strategies for rational engineering of butanol-tolerant bacterial strains should take into account all components of the cell envelope.

Development and Characterization of Amorphous Nanofiber Drug Dispersions Prepared Using Pressurized Gyration.

Nanofibrous systems are attracting increasing interest as a means of drug delivery, although a significant limitation to this approach has been manufacture on a scale commensurate with dosage form production. However, recent work has suggested that nanofibers may be successfully manufactured on a suitable scale using the novel process of pressurized gyration (PG). In this study, we explore the potential of PG as a novel means of generating amorphous solid dispersions of poorly water-soluble drugs with enhanced dissolution performance. We examine the effect of increasing drug loading on fiber properties including size, surface characteristics, and the physical state of both components. Dispersions of ibuprofen in poly(vinylpyrrolidone) (PVP) were prepared (up to 50% w/w loading) and characterized using a range of imaging, thermal, diffraction, and spectroscopic techniques, while the release profiles were studied using sink and non-sink (pH 1.0) conditions. The drug was found to be dispersed on a molecular basis within the fibers; attenuated total reflection FTIR indicated evidence for a direct interaction between the drug and polymer at lower drug loading by the identification of a strong single band in the carbonyl region and amide region of ibuprofen and PVP respectively. Dissolution studies under sink conditions indicated a substantial increase in release rate, while non-sink studies showed evidence for supersaturation. It is concluded that PG presents a viable method for the production of drug-loaded nanofibers for oral administration with enhanced in vitro dissolution rate enhancement.

Functional heterogeneity of pulmonary surfactant protein-D in cystic fibrosis.

Pulmonary surfactant protein-D (SP-D) is a soluble collagenous C-type lectin with important anti-microbial and anti-inflammatory properties. Although it is subject to functionally relevant modification by common polymorphisms and unregulated inflammation, the functional status of SP-D in cystic fibrosis (CF) remains unclear. Given the importance of infection and inflammation in CF lung pathology we have undertaken the first systematic analysis of SP-D lectin activity in this population. By ELISA, we found that airway lavage fluid SP-D expression was greater in CF compared to control patients but was reduced in CF patients with infection and correlated negatively with markers of neutrophilic inflammation. In a functional assay, the percentage of SP-D capable of binding zymosan rarely exceeded 60% in CF or control patients and similarly restricted binding activity was observed towards maltose-agarose. SP-D lectin activity also correlated negatively with infection and neutrophilic inflammation but there was little evidence of major proteolytic degradation amongst the non-bound material. SP-D which failed to bind zymosan exhibited features of lower oligomeric form compared to bound material when tested by native gel electrophoresis. Furthermore, when separated by gel chromatography, high and low oligomeric populations of SP-D were observed in CF lavage fluid but only high oligomeric forms exhibited substantial lectin activity towards yeast derived mannan. Our data demonstrate that oligomeric heterogeneity underlies functional diversity amongst SP-D in health and disease and that dynamic regulation of oligomerisation is an important feature of SP-D biology.

Paediatric sleep diagnostics in the 21st century: the era of "sleep-omics"?

Paediatric sleep diagnostics is performed using complex multichannel tests in specialised centres, limiting access and availability and resulting in delayed diagnosis and management. Such investigations are often challenging due to patient size (prematurity), tolerability, and compliance with "gold standard" equipment. Children with sensory/behavioural issues, at increased risk of sleep disordered breathing (SDB), often find standard diagnostic equipment difficult.SDB can have implications for a child both in terms of physical health and neurocognitive development. Potential sequelae of untreated SDB includes failure to thrive, cardiopulmonary disease, impaired learning and behavioural issues. Prompt and accurate diagnosis of SDB is important to facilitate early intervention and improve outcomes.The current gold-standard diagnostic test for SDB is polysomnography (PSG), which is expensive, requiring the interpretation of a highly specialised physiologist. PSG is not feasible in low-income countries or outwith specialist sleep centres. During the coronavirus disease 2019 pandemic, efforts were made to improve remote monitoring and diagnostics in paediatric sleep medicine, resulting in a paradigm shift in SDB technology with a focus on automated diagnosis harnessing artificial intelligence (AI). AI enables interrogation of large datasets, setting the scene for an era of "sleep-omics", characterising the endotypic and phenotypic bedrock of SDB by drawing on genetic, lifestyle and demographic information. The National Institute for Health and Care Excellence recently announced a programme for the development of automated home-testing devices for SDB. Scorer-independent scalable diagnostic approaches for paediatric SDB have potential to improve diagnostic accuracy, accessibility and patient tolerability; reduce health inequalities; and yield downstream economic and environmental benefits.

Amphiphilic Janus Particles for Aerobic Alcohol Oxidation in Oil Foams.

Amphiphilic Janus silica particles, tunable with oleophobic-oleophilic properties and low fluorine content (8 wt % F), exhibited prominent foamability for a variety of aromatic alcohols at low particle concentrations (<1 wt %) compared to randomly functionalized silica particles. When selectively loaded with Pd nanoparticles on the oleophilic hemisphere, the particles displayed more than a 2-fold increase in catalytic activity for the aerobic oxidation of benzyl alcohol compared to nonfoam bulk catalysis under ambient O2 pressure. The particles were conveniently recycled with high foamability and catalytic activity maintained for at least five consecutive runs.

Increased prevalence of low oligomeric state surfactant protein D with restricted lectin activity in bronchoalveolar lavage fluid from preterm infants.

BACKGROUND: Surfactant protein D (SP-D) is a soluble oligomeric C-type lectin known to protect against lipopolysaccharide and ventilator-induced lung injury in preterm lambs. Here we assess the expression and functional status of SP-D in bronchoalveolar lavage fluid (BALF) from preterm infants at risk of chronic lung disease (CLD) of prematurity and term controls. This is the first systematic evaluation of SP-D function in any clinical cohort. METHODS: SP-D was quantified in BALF from 28 ventilated preterm infants and five ventilated term infants. SP-D lectin activity was tested in a zymosan binding assay followed by sodium dodecyl sulfate polyacrylamide gel electrophoresis (SDS-PAGE) and western blot in BALF from the same infants. SP-D lectin activity was also tested towards maltose-agarose and mannan for selected BALF samples. RESULTS: SP-D expression was lower on day 1 in those preterm infants who subsequently developed CLD but increased over the first 5 days of life in term and preterm neonates. The percentage of neonatal SP-D capable of binding zymosan rarely exceeded 50% in any BALF sample and was 3.5 times lower in preterm infants than term infants on day 1 of life. Similar binding defects were observed towards maltose-agarose and mannan. SDS-PAGE analysis revealed that zymosan-bound SP-D was more highly oligomerised (≥12-mers) than unbound SP-D, which was composed primarily of trimers and lower oligomeric forms. CONCLUSIONS: Substantial and functionally relevant variation in the expression and oligomeric distribution of SP-D exists between preterm and term neonatal lung secretions. This has implications for proposed SP-D replacement therapy in this population.