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Dissolution mechanisms and kinetics have a key role in better understanding of processes. In this work, magnetite and hematite powder were dissolved in oxalic and nitric acid mixtures at different temperatures. Higher temperature and higher amounts of oxalic acid in the system accelerated the dissolution kinetics but did not result in higher solubility levels. Oxalic acid had also drawbacks in the process since higher amounts in the system promoted formation of a solid product, humboldtine (Fe(II)C2O4∙2H2O), which, in turn, inhibited the dissolution. This problem may be overcome by adding even a small amount of nitric acid to the system. Kinetic analysis showed, in the variable-rate-controlling step, that two linear fits of the Kabai model described the dissolution better in an oxalic acid and acid mixture of 70/30. Thermodynamic data and special cubic models showed that the nitric acid concentration had a significant role in the solubility, whereas the concentration of oxalic acid had only minor effects on solubility. The results also showed that measuring the oxalate and nitrate concentrations did not provide additional information about the dissolution mechanism itself. The pH, however, might be a tool for following the extent of dissolution, even though it is not a direct indicator of the dissolution mechanism.

The robustness and sensitivity of gene networks to environmental changes is critical for cell survival. How gene networks produce specific, chronologically ordered responses to genome-wide perturbations, while robustly maintaining homeostasis, remains an open question. We analysed if short- and mid-term genome-wide responses to shifts in RNA polymerase (RNAP) concentration are influenced by the known topology and logic of the transcription factor network (TFN) of Escherichia coli. We found that, at the gene cohort level, the magnitude of the single-gene, mid-term transcriptional responses to changes in RNAP concentration can be explained by the absolute difference between the gene’s numbers of activating and repressing input transcription factors (TFs). Interestingly, this difference is strongly positively correlated with the number of input TFs of the gene. Meanwhile, short-term responses showed only weak influence from the TFN. Our results suggest that the global topological traits of the TFN of E. coli shape which gene cohorts respond to genome-wide stresses.

This study focuses on characterisation of side streams including biomass fly ash, biomass bottom ash, coal fly ash, green liquor dregs, limestone mine tailings, and electric arc furnace steel slag from different industrial locations in Finland. It was found that the fly ash samples contained the highest Al2O3 and SiO2 concentrations, a large number of spherical particles of small sizes and high specific surface areas. Fly ashes and steel slag were observed to contain higher amounts of amorphous phases compared to the other side streams. The high loss on ignition value of the coal fly ash and green liquor dregs was found to exceed the limitations for their application in geopolymer composites. Despite their relatively high concentrations in ashes and steel slag, the leaching tests have shown that no hazardous metal leached out from the streams. Finally, test specimens of geopolymer composites (GP2) were prepared by the application of biomass fly ash, bottom ash, and limestone mine tailings without any pre-treatment process, in addition to the ordinary Portland cement-(R) and metakaolin-based geopolymer composites (GP1). The measured compressive (14.1 MPa) and flexural strength (3.5 MPa) of GP2 suggest that it could be used in concrete kerbs and paving flags. The data has also shown that over 500% of the compressive strength was developed between 7 and 28 days in GP2, whereas in the case of reference concrete (R) and the metakaolin-based geopolymer composite (GP1) it was developed in the first 7 days.

This research explores the influence of fly ash source, alkali concentration and temperature on the dissolution kinetics of Al and Si. The characteristics of the reaction products and the solid residue were evaluated with ICP-MS, SEM-EDS, and quantitative XRD. It was found that Al dissolution occurs faster with a higher yield compared to Si for both ash types. The temperature and the NaOH concentration had a similar effect on the dissolution of Al, while the dissolution of Si was influenced more by the NaOH concentration. The simultaneous dissolution of aluminosilicates was achieved by keeping the temperature at 30 °C, where the precipitation of Al was prevented, and the concentration of the dissolved Si was close to its maximum value. The Kabai Model was the most suitable to explain the dissolution of Al for both ash sources, while the Si dissolution was described with 1-dimensional diffusion, Jander and Ginstling-Brounsthein models. Post-print / Final draft

Aims: socio-economic conditions in early life are important contributors to cardiovascular disease – the leading cause of mortality globally – in later life. We studied coronary heart disease (CHD) and stroke in adulthood among people born out of wedlock in two historical periods: before and during World War II in Finland. Methods: we compared offspring born out of wedlock before (1934–1939) and during (1940–1944) World War II with the offspring of married mothers in the Helsinki Birth Cohort Study. The war affected the position of unmarried mothers in society. We followed the study subjects from 1971 to 2014 and identified deaths and hospital admissions from CHD and stroke. Data were analysed using a Cox regression, adjusting for other childhood and adulthood socio-economic circumstances. Results: the rate of out-of-wedlock births was 240/4052 (5.9%) before World War II and 397/9197 (4.3%) during World War II. Among those born before World War II, out-of-wedlock birth was associated with an increased risk of stroke (hazard ratio (HR)=1.44; 95% confidence interval (CI) 1.00–2.07) and CHD (HR=1.37; 95% CI 1.02–1.86). Among those born out of wedlock during World War II, the risks of stroke (HR=0.89; 95% CI 0.58–1.36) and CHD (HR=0.70; 95% CI 0.48=1.03) were similar to those observed for the offspring of married mothers. The p-values for interaction of unmarried×World War II were (p=0.015) for stroke and (p=0.003) for CHD. Conclusions: in a society in which marriage is normative, being born out of wedlock is an important predictor of lifelong health disadvantage. However, this may change rapidly when societal circumstances change, such as during a war.

Motivation Non-parametric dimensionality reduction techniques, such as t-distributed stochastic neighbor embedding (t-SNE), are the most frequently used methods in the exploratory analysis of single-cell datasets. Current implementations scale poorly to massive datasets and often require downsampling or interpolative approximations, which can leave less-frequent populations undiscovered and much information unexploited. Results We implemented a fast t-SNE package, qSNE, which uses a quasi-Newton optimizer, allowing quadratic convergence rate and automatic perplexity (level of detail) optimizer. Our results show that these improvements make qSNE significantly faster than regular t-SNE packages and enables full analysis of large datasets, such as mass cytometry data, without downsampling. Availability and implementation Source code and documentation are openly available at https://bitbucket.org/anthakki/qsne/. Supplementary information Supplementary data are available at Bioinformatics online.

In this study, batch electrocoagulation (EC) experiments were performed with synthetic mining water in various conditions in a laboratory-scale 1L reactor. The process was scaled up and the selected results were verified with both synthetic and real mining water in a 70 L reactor. The generated solids were characterized by XRD, SEM, and a laser diffraction particle size analyzer. After preconcentration by settling and decantation, the EC solids were separated by constant pressure filtration at 2–6 bar. In order to improve the separation, various filter aids were used in body-feed and precoat modes. The results show that the overall removal efficiency was the highest with consumable electrode pairs such as Fe/Fe, Al/Al and Fe/Al, and the highest treatment efficiency was achieved with Fe/Al electrodes where 100/100% of the nitrate and 96/87% of the sulfate were removed in small/large-scale experiments. Depending on the dissolved electrode material, different solid species were formed: crystalline primary particles with a minor degree of agglomeration were observed in Fe/Fe slurry, whereas aluminium-containing solids (Al/Al and Fe/Al) were mainly amorphous agglomerates. High values of average specific cake resistances (αav = 2·1012 - 4·1013), average porosities (>90%) and moisture contents (>68 wt%) of filter cakes were obtained for all filtered samples. The highest values of the above-mentioned cake characteristics were observed for aluminium-based solids, which might be explained by its highly amorphous structure. The application of filter aids improved the filterability of the sludges by reducing the average specific cake resistance by as much as 95–96% in the body-feed mode and by 84% in the precoat mode. Post-print / Final draft

A new designed sonicated, continuous modular crystallizer was investigated and developed. The concept and design criteria for the designed crystallizer were examined and studied in a cooling crysta...

The energy consumption of vacuum filtration operations in cake filtration depends on the properties of the cake, the filtration conditions applied, and the progress of the cake dewatering process. Operating a vacuum filter at a high pressure difference requires a high air flow rate and thus has high energy consumption. By taking the filtered solids content into consideration together with the power demand and energy consumed at a certain pressure difference level, it is possible to investigate the specific power demand and energy consumption relative to the filtered cake solids content. When the mother liquor in the void space of the filter cake is replaced by air, the flow rate of air through the cake increases, which has a dramatic influence on the specific energy consumption. In this study, dewatering of calcite mine tailings is investigated with respect to the specific power demand and energy consumption of vacuum generation calculated using the assumption of an ideal isentropic process. The results of this study demonstrate clearly that both the air flow rate and the specific energy consumption in dewatering increase sharply after a certain solid content of the cake is reached. The results suggest that pumping costs in vacuum filtration can be reduced substantially by allowing a slight increase in the residual moisture content of the filter cake.

A major challenge in analyzing cancer patient transcriptomes is that the tumors are inherently heterogeneous and evolving. We analyzed 214 bulk RNA samples of a longitudinal, prospective ovarian cancer cohort and found that the sample composition changes systematically due to chemotherapy and between the anatomical sites, preventing direct comparison of treatment-naive and treated samples. To overcome this, we developed PRISM, a latent statistical framework to simultaneously extract the sample composition and cell type specific whole-transcriptome profiles adapted to each individual sample. Our results indicate that the PRISM-derived composition-free transcriptomic profiles and signatures derived from them predict the patient response better than the composite raw bulk data. We validated our findings in independent ovarian cancer and melanoma cohorts, and verified that PRISM accurately estimates the composition and cell type specific expression through whole-genome sequencing and RNA in situ hybridization experiments. PRISM is freely available with full source code and documentation.

Human population growth and urbanization are aggravating water quality problems in many regions, and wastewater volumes and quantities of pollutants are increasing due to greater industrial and urban activity. Thus, it is necessary to find efficient, sustainable and simple methods to separate miscellaneous impurities from wastewaters. One potential separation methods is freeze crystallization, because of its non-selective nature. However, previous research investigating freeze separation using real wastewaters has been rather marginal. This study examines natural freeze crystallization in purification of urban origin wastewaters, that is, municipal wastewater and landfill leachate of various organic and inorganic matter concentration. The effect of different freezing conditions on ice growth and separation efficiency in terms of ice impurity relative to initial solution impurity was investigated with a laboratory scale winter simulator. The results showed air flow velocity to have an almost as significant an influence on ice mass growth as air temperature. Although separation efficiencies decreased linearly with increased ice growth rates, no clear correlation was found between the impurity concentration of the wastewater and the ice mass growth rate. This finding notwithstanding, the separation efficiency of freeze crystallization of concentrated wastewater (landfill leachate) was noted to decrease more clearly with increased ice growth rate. Purification efficiencies of 95% to nearly 100%, determined by indicators such as chemical oxygen demand (COD), were achieved in treatment of municipal wastewater when using low ice growth rates. These findings indicate that the approach can meet future legislative requirements for treatment plants and that further research of the utilization of freezing techniques for wastewater purification is warranted. Post-print / Final draft

Many genes are spaced closely, allowing coordination without explicit control through shared regulatory elements and molecular interactions. We study the dynamics of a stochastic model of a gene-pair in a head-to-head configuration, sharing promoter elements, which accounts for the rate-limiting steps in transcription initiation. We find that only in specific regions of the parameter space of the rate-limiting steps is orderly coexpression exhibited, suggesting that successful cooperation between closely spaced genes requires the coevolution of compatible rate-limiting step configuration. The model predictions are validated using in vivo single-cell, single-RNA measurements of the dynamics of pairs of genes sharing promoter elements. Our results suggest that, in E. coli , the kinetics of the rate-limiting steps in active transcription can play a central role in shaping the dynamics of gene-pairs sharing promoter elements.

Summary Anduril is an analysis and integration framework that facilitates the design, use, parallelization and reproducibility of bioinformatics workflows. Anduril has been upgraded to use Scala for pipeline construction, which simplifies software maintenance, and facilitates design of complex pipelines. Additionally, Anduril’s bioinformatics repository has been expanded with multiple components, and tutorial pipelines, for next-generation sequencing data analysis. Availabilityand implementation Freely available at http://anduril.org. Supplementary information Supplementary data are available at Bioinformatics online.

The moisture content of filter cakes is probably the most important characteristic that should be kept at a desired level in industrial cake filtration applications to maintain consistent product quality and minimize energy consumption. Most of the currently applied methods for contactless real-time monitoring of the moisture content are based for example on x-ray or microwave techniques, and therefore, the equipment for the purpose is highly specialized. This paper introduces a novel soft sensor for filter cake moisture estimation that uses machine learning algorithms and data collected with basic process instrumentation. The method is primarily based on the cooling effect observed in the cake and air, caused by evaporation of liquid from the cake during the dewatering period, and it can be supported by other process data. The specific energy consumption of vacuum filtration and the subsequent thermal drying to zero moisture is also analyzed. The results of pilot-scale experiments with calcite slurry and a horizontal belt vacuum filter show that in order to minimize the specific energy consumption of vacuum filtration, it is crucial to find the right combination of slurry concentration, vacuum level, and mass of filter cake per unit area. The proposed method for estimating the filter cake moisture content is especially suitable for real-time monitoring and control, enabling also considerable reduction in the energy consumption of the overall process. When applying the proposed soft sensor method in a pilot-scale process, the mean absolute error of the estimated moisture content of the filter cake is ∼0.4 percentage points when the temperature of air at the vacuum pump inlet and the vacuum pump air flow rate are included in the input variables. Post-print / Final draft

The mining industry is known to be a major producer of sulfate-rich waters that are harmful to aquatic systems, accelerate acid mine drainage formation and hinder the reuse and recycling of process water. In recent years, many treatment techniques have been studied and developed to treat sulfate-rich streams. One such technique, electrocoagulation (EC), was proposed as a possible alternative to conventional treatment technologies. Electrocoagulation has been used for the removal of nitrate, cyanide and toxic metals from mining waters, but the information about sulfate removal is scarce. In this paper, the results from a systematic study on sulfate removal by EC with iron electrodes applying a 33-full factorial design are discussed. The results show the leading role of applied current on sulfate removal. In addition, the study concludes that the utilisation of iron electrodes was more efficient in terms of sulfate removal comparing to aluminium electrodes. The removal of sulfate was as high as 54% and 10% using iron and aluminium electrodes respectively. Under the studied experimental conditions, sulfate was proposed to be removed because of particle charge neutralisation and enmeshment of the studied anion in iron oxides and hydroxides. Post-print / Final draft

This study analyses social heterogamy in western and southern Finland during the early stages of industrialisation, from 1700 to 1910. Marriage patterns are examined by comparing the social classes of spouses' parents, which can be understood as the social origin of the spouse. The rate of heterogamy within the freeholder class was only 19.8%, whereas it was 71.1% in the upper classes, 59.7% in the tenant class and 76.5% in the labour class. In addition, only roughly 20-30% of grooms whose fathers were landowners married brides from lower social classes. Certain individual- and family-level characteristics increased the odds of a heterogamous marriage: remarrying, age difference, being an illegitimate child or a single mother, and the first marriages of those in the labour class. Regarding macro-level variables, we found that higher rates of emigration and poor-relief recipients, along with having a larger Finnish-speaking population, led to higher levels of heterogamy. Other issues increasing the odds of heterogamy included living in the more urbanised or industrialised regions and moving to different regions. This study identified strict marriage patterns, which did not significantly change with respect to heterogamy. Nevertheless, indications exist that industrialisation and urbanisation began eroding the prevailing traditions.

The presence of hazardous trace elements (HTE) in the chemical recovery cycle of Kraft pulp mills is the main obstacle for the utilization of the inorganic residues of the process. Electrostatically precipitated (ESP) recovery boiler fly ash (RBFA), consisting mainly of sodium sulfate Na2SO4, is a solid side stream where HTE are concentrated. Unlike most other ashes, RBFA is to a great extent water-soluble. A novel reverse leaching method, based on the dissolution behavior of RBFA in water, is introduced in this paper. The method is founded on the use of an appropriate liquid/solid mass ratio and a favorable pH, which together contribute to the formation of a small and readily settling solid residue where almost all HTE are concentrated. This paper focuses on evaluating the influence of the treatment conditions on HTE removal, energy consumption and material losses. The results of this study show that the removal efficiency of the investigated HTE and other analyzed metals was excellent under alkaline conditions, the apparently suitable pH range for the removal of most of these metals being approximately 11.7–12.2. Lead was observed to be the most difficult HTE to remove: the highest obtained degree of removal of Pb was 89%. The removal rate of Cd and Zn was approx. 100% within the mentioned pH range. Post-print / Final draft

Solute analysis of bauxite residue filter cakes is an important but not very well understood operation carried out at refineries and in scientific research. As more and more refineries rely currently on dry cake disposal after filtration, washing and deliquoring of the cakes, the importance of correctly performed cake analysis will increase. Chemical analysis of bauxite residue filter cakes regarding their soluble compounds, such as the total caustic, soda and aluminate, is performed after forming a slurry from the cake and pure water by using a selected liquid/solid (L/S) ratio. This paper shows that there is currently no cake analysis procedure which could be used without unexpected variation in the results. This is because several factors affect the analysis result at the filtration and sample preparation stages. The factors discussed in this paper are divided into two groups, including the filtration and washing conditions and the sample preparation procedures. In the filtration stage, the filtration temperature and pressure were found to have a considerable effect on the solute recovery. On the other hand, the sample preparation procedure was observed to be affected by factors like the L/S ratio, the composition of the diluting liquid (with respect to its Na2CO3 concentration), the temperature, and the cake leaching time. In addition to the cake solute analysis, particle size measurements and calculation of alkali recovery for the solid-liquid separation stage are discussed as well. To summarize the main findings, it can be stated that significant differences in the results can be seen when any detail in the sample preparation procedure is changed. Post-print / Final draft

Solid-liquid separation of bauxite residue is a topical issue in the alumina industry, not least due to the great quantity and problematic properties of this highly alkaline residue. The objective of this contribution is to provide deeper knowledge about the solid-liquid separation of pH-adjusted (pH 11) bauxite residue by investigating the local filtration properties of filter cakes produced with a piston press. Two bauxite residue samples having different particle size distribution were investigated. Measured local data of the hydrostatic pressure and solidosity was used together with flow rate data to calculate local specific filtration resistance as well as compressibility data. For the investigated pressure range (0.2 to 2 MPa) it was found that the residue formed slightly/ moderately compressible filter cakes with a specific cake resistance between 5·1011 to 1.5·1012 m/kg. The sodium recovery and final cake solidosity were strongly dependent on the applied pressure, but only to a minor extent on the particle size reduction obtained by the applied mechanical treatment. The filter cakes formed from the mechanically treated samples did, however, display a somewhat higher pressure dependence for the local specific filtration resistance compared to the non-ground samples. Post-print / Final draft

The filtration properties of mineral slurries depend for instance on the properties of the solid particles and on the way how these particles arrange themselves when the filter cake is formed. In cake filtration applications, the focus is often on particle size instead of the shape of particle size distribution (PSD). The aim of this experimental study is to demonstrate the influence of the width of PSD on the properties of the filter cake in the pressure filtration of Ni-Cu mine tailings. Modification of PSD is performed by using a stirred media mill at various operational conditions. The results show that not only particle size should be considered when the filtration properties are evaluated: a significant reduction of the average specific cake resistance (>60%) and increase of the average porosity (almost 30%) can be achieved by stirred media grinding at optimal conditions, in spite of reducing the median particle size. On the other hand, the selection of unfavorable grinding conditions may cause substantial increase in cake resistance. Above all, the results imply that the size of particles in the coarse end of PSD should be reduced while avoiding grinding of the finest particles. This seems to be obtainable by paying special attention to the size of the grinding medium. The main outcomes of this study will help in reducing the energy consumption of dewatering of tailings to be disposed of, and recovering valuable elements from tailings deposited in ponds, requiring the use of optimized grinding circuits and solid-liquid separation operations. However, the benefits obtained in the filtration stage should overcome the increased costs caused by the installation and energy consumption of the grinding systems. This means that the demonstrated grinding method may be profitably utilized in industrial scale only when the material is easy to grind and the filtration properties can be significantly improved, or when the filtration plant is the main bottleneck of the process. Post-print / Final draft

Transcription kinetics is limited by its initiation steps, which differ between promoters and with intra- and extracellular conditions. Regulation of these steps allows tuning both the rate and stochasticity of RNA production. We used time-lapse, single-RNA microscopy measurements in live Escherichia coli to study how the rate-limiting steps in initiation of the Plac/ara-1 promoter change with temperature and induction scheme. For this, we compared detailed stochastic models fit to the empirical data in maximum likelihood sense using statistical methods. Using this analysis, we found that temperature affects the rate limiting steps unequally, as nonlinear changes in the closed complex formation suffice to explain the differences in transcription dynamics between conditions. Meanwhile, a similar analysis of the PtetA promoter revealed that it has a different rate limiting step configuration, with temperature regulating different steps. Finally, we used the derived models to explore a possible cause for why the identified steps are preferred as the main cause for behavior modifications with temperature: we find that transcription dynamics is either insensitive or responds reciprocally to changes in the other steps. Our results suggests that different promoters employ different rate limiting step patterns that control not only their rate and variability, but also their sensitivity to environmental changes., Author Summary Temperature affects the behavior of cells, such as their growth rate. However, it is not well understood how these changes result from the changes at the single molecule level. We observed the production of individual RNA molecules in live cells under a wide range of temperatures. This allowed us to determine not only how fast they are produced, but also how much variability there is in this process. Next, we fit a stochastic model to the data to identify which rate-limiting steps during RNA production are responsible for the observed differences between conditions. We found that genes differ in how their RNA production is limited by different steps and in how these are affected by the temperature, which explains why different genes respond differently to temperature fluctuations.

Bauxite residue, the main waste fraction of alumina production, is extremely hazardous to the environment, as well as to human health. After the recovery of the pregnant liquor, the washed and thickened bauxite residue is typically pumped as thick slurry to a residue disposal area. The use of filter presses for the final washing, in order to further enhance the recovery of alkali and aluminum, together with effective deliquoring, may be beneficial in many cases. In this study, a vertical filter press (A = 0.1 m2) was used for the filtration and washing of industrial bauxite residue. The effectiveness of various washing sequences, as well as variation in the local washing results in the filter cakes, was compared. The results show that Na recovery of 98% can be obtained at a wash ratio as low as 1.4. It was also observed that not only the wash ratio is important: temperature and pressure have a significant effect on the dissolution of Na. Post-print / Final draft

Chemical and process industries utilize stirred media mills for efficient fine grinding of solids. Stirred media mills, also referred to as stirred ball or stirred bead mills, generally have a good ability to produce fine particles with a relatively narrow particle size distribution. Wet grinding with vertical stirred ball mills is typically carried out for slurries containing particles smaller than 200 μm, such as industrial minerals and pigments. Filtration is an important unit operation, which is performed in order to reduce the water content of the slurry after grinding and concentration, and prior to drying and transportation. Pressure filters are used to obtain the maximum dryness of the product. A number of properties of solids affect the filtration performance. The particle size and shape, the width of particle size distribution, and the net surface charge of the particles are among the factors having a significant influence on the filtration characteristics. In this study, the dependency of the pressure filtration properties of wet ground calcium carbonate (GCC) slurries on the grinding result obtained by a stirred media mill is investigated. After grinding, subsequent filtration experiments were carried out with a laboratory-scale pressure filter. Average specific cake resistances, porosities of the filter cakes, and cake compressibility parameters were determined from the filtration data. The results showed clear correlations between the particle size data and the related filtration properties. Interesting observations were also made regarding the average porosity of the filter cakes and the uncertainty of the experiments. Post-print / Final draft

Dry cake disposal is the preferred technique for the disposal of bauxite residue, when considering environmental issues together with possible future utilisation of the solids. In order to perform dry cake disposal in an economical way, the deliquoring of the residue must be carried out efficiently, and it is also important to wash the obtained solids well to minimise the amount of soluble soda within the solids. The study presented in this article aims at detecting the most important variables influencing the deliquoring and washing of bauxite residue, performed with a horizontal membrane filter press and by determining the optimal washing conditions. The results obtained from pilot-scale experiments are evaluated by considering the properties of the solids, for instance, the residual alkali and aluminium content, as well as the consumption of wash liquid. Two different cake washing techniques, namely classic washing and channel washing, are also used and their performances compared. The results show that cake washing can be performed successfully in a horizontal membrane filter press, and significant improvements in the recovery of alkali and aluminium can be achieved compared with pressure filtration carried out without washing, or especially compared with the more traditionally used vacuum filtration. Post-print / Final draft

Separation processes in general present a significant challenge in the production of bioethanol from lignocellulosic materials. Solid-liquid separation,prior to the concentration of ethanol (for instance, by distillation),is often essential and upstream process conditions may determine how effectively this separation can be performed.In this experimental study, the properties of a lignocellulosic solid residue, generated through the enzymatic hydrolysis of biomass, and solid-liquid separations after the hydrolysis stagewere studied, focusing on the fiber and particle size distribution(FSD and PSD) of the solids.During the course of enzymatic hydrolysis, fiber and particle size distributions of the biomassduring and after enzymatic hydrolysis were measured using a fiber tester and a laser diffraction analyzer, respectively,in order to quantify the effect of enzymatic saccharification on the size distribution of the suspended solids.The main target, however, was to investigate the filtration properties of hydrolyzed and agitated suspensions using a pressure filter. The particle size distributions of the filtered samples were measured with the laser diffraction analyzer. Even though the filtration properties were strongly influenced by agitation, the effect on particle size distributions was found to be much smaller. During enzymatic hydrolysis, the most significant reduction in the size of the solidstook place rapidly after the cellulase addition. The width of the fibers was not observed to decrease during the hydrolysis stage. Post-print / Final draft

Steam dewatering of filter cakes is recognized as a competitive alternative to conventional air drying and thermally assisted mechanical dewatering (TAMD). The main benefit of cake dewatering with high-pressure steam is that mechanical and thermal dewatering can be efficiently performed in a single process step. The target of this study was to determine the potential of a steam-dewatering technique for two industrial mineral suspensions. The first mineral, kaolin, was very difficult to dewater using conventional mechanical dewatering techniques, whereas the second one, ground calcium carbonate (GCC), represented only moderate resistance to filtration. The secondary objective was to compare the filterability of the original kaolin slurry with the same slurry treated with a coagulant (aluminum sulphate, Al2(SO4)3 · 16H2O). Four different kinds of experiments were performed: tests without any kind of cake dewatering, tests with air drying, tests with steam drying, and tests with both coagulation and steam drying. The obtained results show that steam dewatering is an efficient technique for achieving lower cake-moisture contents. Also, the positive influence of coagulation on the filtration capacity was found to be considerable in the case of kaolin. An approximate energy balance was created for the steam-drying process and the determined energy efficiencies were compared with those obtainable with an ideal thermal drier. The main conclusion from these comparisons is that steam drying can be effectively used instead of traditional thermal drying if the large energy losses can be reduced by proper insulation and heat recovery systems. Post-print / Final draft

Background Evidence suggests that in prokaryotes sequence-dependent transcriptional pauses affect the dynamics of transcription and translation, as well as of small genetic circuits. So far, a few pause-prone sequences have been identified from in vitro measurements of transcription elongation kinetics. Results Using a stochastic model of gene expression at the nucleotide and codon levels with realistic parameter values, we investigate three different but related questions and present statistical methods for their analysis. First, we show that information from in vivo RNA and protein temporal numbers is sufficient to discriminate between models with and without a pause site in their coding sequence. Second, we demonstrate that it is possible to separate a large variety of models from each other with pauses of various durations and locations in the template by means of a hierarchical clustering and a random forest classifier. Third, we introduce an approximate likelihood function that allows to estimate the location of a pause site. Conclusions This method can aid in detecting unknown pause-prone sequences from temporal measurements of RNA and protein numbers at a genome-wide scale and thus elucidate possible roles that these sequences play in the dynamics of genetic networks and phenotype.

Cellulosic wastes, from sources such as low-quality cardboard and paper, are regarded as potential feedstocks for bioethanol production. One pathway from these cellulosic materials to ethanol is saccharification (hydrolysis) followed by fermentation. Saccharification is commonly performed using enzymes that are able to cleave the cellulosic structure to smaller units, preferably to glucose monomers. During the hydrolysis, mixing conditions have a considerable impact on the performance of the enzymes. Thus mixing conditions in the hydrolysis tank can also influence the downstream operations and, consequently, the overall economy of the bioethanol process. In this experimental study, four types of impeller, at different hydrolysis conditions were used. The effect of mixing on the glucose yield and on the filtration characteristics of the hydrolysate was evaluated. It was shown that not only the sugar yield depended on the mixing conditions: the effect on the solid–liquid separation step was even more significant. Post-print / Final draft

We present a delayed stochastic model of transcription at the single nucleotide level. The model accounts for the promoter open complex formation and includes alternative pathways to elongation, namely pausing, arrest, misincorporation and editing, pyrophosphorolysis, and premature termination. We confront the dynamics of this detailed model with a single-step multi-delayed stochastic model and with measurements of expression of a repressed gene at the single molecule level. At low expression rates both models match the experiments but, at higher rates the two models differ significantly, with consequences to cell-to-cell phenotypic variability. The alternative pathway reactions, due to, for example, causing polymerases to collide more often on the template, are the cause for the difference in dynamical behaviors. Next, we confront the model with measurements of the transcriptional dynamics at the single RNA level of an induced gene and show that RNA production, besides its bursting dynamics, also exhibits pulses (2 or more RNAs produced in intervals smaller than the smallest interval between initiations). The distribution of occurrences and amplitudes of pulses match the experimental measurements. This pulsing and the noise at the elongation stage are shown to play a role in the dynamics of a genetic switch.

The effect of meteorological factors, the total sulphur content of the needles, and SO concentration in the ambient air on total peroxidase activity of Scots pine ( L.) needles was investigated in material obtained from Southern Finland. The correlation between temperature and total peroxidase activity was highest during the most active growing period. Linear correlation between relative humidity and total peroxidase activity appears to be low. The correlation between atmospheric SO concentration and total peroxidase activity was also low and varied inconsistently. The detected low association between the sulphur dioxide pollutant and the total peroxidase activity was assumed to be related to the sensitivity of peroxidase activity, many eco-physiological factors and to the genetic variation in conifers. It is difficult to separate a response due to this pollutant from environmental and genetic factors in a complex coniferous forest. Using total peroxidase activity as a routine indicator of air pollution seems to be unsuitable because of the large sample size required in order to obtain a reliable measurement of the pollutantâs effect under low pollution levels.2Pinus sylvestris2

RNA in situ hybridization (RNA-ISH) is a powerful spatial transcriptomics technology to characterize target RNA abundance and localization in individual cells. This allows analysis of tumor heterogeneity and expression localization, which are not readily obtainable through transcriptomic data analysis. RNA-ISH experiments produce large amounts of data and there is a need for automated analysis methods. Here we present QuantISH, a comprehensive open-source RNA-ISH image analysis pipeline that quantifies marker expressions in individual carcinoma, immune, and stromal cells on chromogenic or fluorescent in situ hybridization images. QuantISH is designed to be modular and can be adapted to various image and sample types and staining protocols. We show that in chromogenic RNA in situ hybridization images of high-grade serous carcinoma (HGSC) QuantISH cancer cell classification has high precision, and signal expression quantification is in line with visual assessment. We further demonstrate the power of QuantISH by showing that CCNE1 average expression and DDIT3 expression variability, as captured by the variability factor developed herein, act as candidate biomarkers in HGSC. Altogether, our results demonstrate that QuantISH can quantify RNA expression levels and their variability in carcinoma cells, and thus paves the way to utilize RNA-ISH technology.

Background In Escherichia coli the mean and cell-to-cell diversity in RNA numbers of different genes vary widely. This is likely due to different kinetics of transcription initiation, a complex process with multiple rate-limiting steps that affect RNA production. Results We measured the in vivo kinetics of production of individual RNA molecules under the control of the lar promoter in E. coli. From the analysis of the distributions of intervals between transcription events in the regimes of weak and medium induction, we find that the process of transcription initiation of this promoter involves a sequential mechanism with two main rate-limiting steps, each lasting hundreds of seconds. Both steps become faster with increasing induction by IPTG and Arabinose. Conclusions The two rate-limiting steps in initiation are found to be important regulators of the dynamics of RNA production under the control of the lar promoter in the regimes of weak and medium induction. Variability in the intervals between consecutive RNA productions is much lower than if there was only one rate-limiting step with a duration following an exponential distribution. The methodology proposed here to analyze the in vivo dynamics of transcription may be applicable at a genome-wide scale and provide valuable insight into the dynamics of prokaryotic genetic networks.