scholarly journals Review on biological process of soil improvement in the mitigation of liquefaction in sandy soil

2018 ◽  
Vol 250 ◽  
pp. 01017 ◽  
Author(s):  
Abubakar Sadiq Muhammed ◽  
Khairul Anuar Kassim ◽  
Muttaqa Uba Zango
Keyword(s):  
Biological Process ◽  
Soil Improvement ◽  
Emerging Technology ◽  
Biological Processes ◽  
Reagent Concentration ◽  
Calcite Precipitation ◽  
Cyclic Resistance ◽  
Environmental Friendly ◽  
Long Time ◽  
Cyclic Resistance Ratio

Recently, the concept of using biological process in soil improvement otherwise called bio-mediated soil improvement technique has shown greater prospects in the mitigation of liquefiable soils. It is an environmental friendly technique that has generated great interest to geotechnical engineers. This paper presents a review on the microorganism responsible for the biological processes in soil improvement system, factors that affect biological process, identifying the mechanism of liquefaction and commonly adopted method to mitigate liquefaction. Next, the effect of microbial induced calcite precipitation (MICP) on the strength and cyclic response were also analyzed, where it was identified that higher cementation level leads to formation of larger sized calcite crystals which in turn leads to the improved shear strength, stiffness and cyclic resistance ratio of the soil. However, the effects of various bacteria, cementation reagent concentrations amongst other factors were not fully explored in most of the studies. Finally, some of the challenges that lay ahead for the emerging technology are optimizing treatment factors (bacteria and cementation reagent concentration), upscaling process, training of researchers/technologist and long – time durability of the improved soils.

scholarly journals Integrative, multi-omics, analysis of blood samples improves model predictions: applications to cancer

2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Erica Ponzi ◽  
Magne Thoresen ◽  
Therese Haugdahl Nøst ◽  
Kajsa Møllersen
Keyword(s):  
Lung Cancer ◽  
Biological Process ◽  
Case Control ◽  
Integrative Analysis ◽  
Data Sources ◽  
Omics Data ◽  
Biological Processes ◽  
Blood Samples ◽  
Model Predictions

Abstract Background Cancer genomic studies often include data collected from several omics platforms. Each omics data source contributes to the understanding of the underlying biological process via source specific (“individual”) patterns of variability. At the same time, statistical associations and potential interactions among the different data sources can reveal signals from common biological processes that might not be identified by single source analyses. These common patterns of variability are referred to as “shared” or “joint”. In this work, we show how the use of joint and individual components can lead to better predictive models, and to a deeper understanding of the biological process at hand. We identify joint and individual contributions of DNA methylation, miRNA and mRNA expression collected from blood samples in a lung cancer case–control study nested within the Norwegian Women and Cancer (NOWAC) cohort study, and we use such components to build prediction models for case–control and metastatic status. To assess the quality of predictions, we compare models based on simultaneous, integrative analysis of multi-source omics data to a standard non-integrative analysis of each single omics dataset, and to penalized regression models. Additionally, we apply the proposed approach to a breast cancer dataset from The Cancer Genome Atlas. Results Our results show how an integrative analysis that preserves both components of variation is more appropriate than standard multi-omics analyses that are not based on such a distinction. Both joint and individual components are shown to contribute to a better quality of model predictions, and facilitate the interpretation of the underlying biological processes in lung cancer development. Conclusions In the presence of multiple omics data sources, we recommend the use of data integration techniques that preserve the joint and individual components across the omics sources. We show how the inclusion of such components increases the quality of model predictions of clinical outcomes.

scholarly journals Biochemical Enhancement of Geotechnical Properties of Marginal Soils

2018 ◽  
Vol 203 ◽  
pp. 03010
Author(s):  
Murtala Hassan Mohammed ◽  
Ado Yusuf Abdulfatah
Keyword(s):  
Hydraulic Conductivity ◽  
Treatment Duration ◽  
Soil Improvement ◽  
Engineering Properties ◽  
Treatment Technique ◽  
Reagent Concentration ◽  
Soil Variables ◽  
Treatment Conditions ◽  
Metabolic Activities ◽  
Marginal Soil

Microbially-induced calcite precipitation (MICP) is a relatively new and sustainable soil improvement technique. This technique utilizes bio-activity of microorganism to precipitate calcite through metabolic activities of the organisms which decompose urea in to ammonium and carbon dioxide. The carbonate so produced combined with the supplied calcium to precipitate calcite. This calcite improves engineering properties of soil through the formation of coating and bonds between soil particles. Preliminary results have proved the feasibility of the isolated bacteria in MICP treatment technique to improve the engineering properties of marginal soil. The main objective of this study is to determine the preference conditions for effective MICP treatment in improving the soil engineering properties (Unconfined Compressive Strength, California Bearing Ratio and Hydraulic Conductivity) of a typical marginal soil. Variables such as; treatment duration (24, 48, and 72hours), reagent concentration (0.1, 0.25, 0.5, and 0.75M), and concentration of the isolates (1×105, 1×106, and 1×107cfu/ml) were considered in the MICP treatment. The results suggested that the preference treatment conditions were 72hours treatment duration, 0.75M reagent concentration, and 1×107cfu/ml concentration of the isolates. The corresponding alterations recorded were 94.86KN/m2 (295%) and 30.8% (92.5%) increment for CBR and UCS while 0.93X10-6m/s (78.95%) reduction was recorded for hydraulic conductivity. The calcite content showed a reasonably good comparison with the improvements in the soil engineering properties. The pH of effluents increased during MICP treatment indicating the presence of urease bio-activity.

scholarly journals Annotating proteins with generalized functional linkages

2008 ◽  
Vol 105 (46) ◽  
pp. 17700-17705 ◽  
Author(s):  
Richard Llewellyn ◽  
David S. Eisenberg
Keyword(s):  
Protein Function ◽  
Biological Process ◽  
Computational Method ◽  
Majority Voting ◽  
Target Protein ◽  
Biological Processes ◽  
Gene Products ◽  
Protein Protein Interaction ◽  
Protein Protein Interaction Networks

As genome sequencing outstrips the rate of high-quality, low-throughput biochemical and genetic experimentation, accurate annotation of protein function becomes a bottleneck in the progress of the biomolecular sciences. Most gene products are now annotated by homology, in which an experimentally determined function is applied to a similar sequence. This procedure becomes error-prone between more divergent sequences and can contaminate biomolecular databases. Here, we propose a computational method of assignment of function, termed Generalized Functional Linkages (GFL), that combines nonhomology-based methods with other types of data. Functional linkages describe pairwise relationships between proteins that work together to perform a biological task. GFL provides a Bayesian framework that improves annotation by arbitrating a competition among biological process annotations to best describe the target protein. GFL addresses the unequal strengths of functional linkages among proteins, the quality of existing annotations, and the similarity among them while incorporating available knowledge about the cellular location or individual molecular function of the target protein. We demonstrate GFL with functional linkages defined by an algorithm known as zorch that quantifies connectivity in protein–protein interaction networks. Even when using proteins linked only by indirect or high-throughput interactions, GFL predicts the biological processes of many proteins in Saccharomyces cerevisiae, improving the accuracy of annotation by 20% over majority voting.

scholarly journals Geotechnical engineering behaviors of gellan gum biopolymer treated sand

2016 ◽  
Vol 53 (10) ◽  
pp. 1658-1670 ◽  
Author(s):  
Ilhan Chang ◽  
Jooyoung Im ◽  
Gye-Chun Cho
Keyword(s):  
Geotechnical Engineering ◽  
Friction Angle ◽  
Soil Improvement ◽  
Gellan Gum ◽  
Strengthening Effect ◽  
Calcite Precipitation ◽  
Unconfined Compression Test ◽  
Sand Particles ◽  
Engineering Practices ◽  
Moisture Conditions

Biological approaches have recently been explored as environmentally friendly alternatives to engineered soil methods in geotechnical engineering practices. The use of microbial induced calcite precipitation, reactive enzymes, and microbial polymers, such as biopolymers, in soil improvement has been studied by researchers around the world. In the present study, gellan gum, a microbial polysaccharide generally used in the food industry due to its hydrogel rheology, was used to strengthen sand. The effects of gellan gum on the geotechnical behaviors of cohesionless sand were evaluated through a series of experimental programs including an unconfined compression test, direct shear test, falling head permeability test, and scanning electron microscopy. The geotechnical properties (friction angle, cohesion, and unconfined compressive strength) of gellan gum–treated sands were determined based on varying moisture conditions: initial, dried, and re-submerged. Gellan gum has a distinct strengthening effect on cohesionless sands through artificial cohesion that varies with the moisture conditions. The strengthening effect of gellan gum on sand appears to be a result of the combination of enhanced bonding between unreactive sand particles and the agglomeration of sand particles through hydrogel condensation, in which the agglomerated sand particles behave as enlarged aggregates in soil.

scholarly journals Hidden in plain sight: What remains to be discovered in the eukaryotic proteome?

2018 ◽  
Author(s):  
Valerie Wood ◽  
Antonia Lock ◽  
Midori A. Harris ◽  
Kim Rutherford ◽  
Jürg Bähler ◽  
...  
Keyword(s):  
Gene Ontology ◽  
Fission Yeast ◽  
Genome Sequencing ◽  
Large Scale ◽  
Biological Process ◽  
Blind Spot ◽  
Model Organisms ◽  
Biological Processes ◽  
Health And Disease

AbstractThe first decade of genome sequencing stimulated an explosion in the characterization of unknown proteins. More recently, the pace of functional discovery has slowed, leaving around 20% of the proteins even in well-studied model organisms without informative descriptions of their biological roles. Remarkably, many uncharacterized proteins are conserved from yeasts to human, suggesting that they contribute to fundamental biological processes. To fully understand biological systems in health and disease, we need to account for every part of the system. Unstudied proteins thus represent a collective blind spot that limits the progress of both basic and applied biosciences.We use a simple yet powerful metric based on Gene Ontology (GO) biological process terms to define characterized and uncharacterized proteins for human, budding yeast, and fission yeast. We then identify a set of conserved but unstudied proteins in S. pombe, and classify them based on a combination of orthogonal attributes determined by large-scale experimental and comparative methods. Finally, we explore possible reasons why these proteins remain neglected, and propose courses of action to raise their profile and thereby reap the benefits of completing the catalog of proteins’ biological roles.

scholarly journals PERANCANGAN FONDASI TIANG PANCANG PADA TANAH BERPOTENSI LIKUIFAKSI DI SULAWESI

2020 ◽  
Vol 3 (3) ◽  
pp. 865
Author(s):  
Markus Jusuf ◽  
Aksan Kawanda
Keyword(s):  
Soil Layer ◽  
Cyclic Stress ◽  
Lateral Spreading ◽  
Soil Pressure ◽  
Spreading Effect ◽  
Cyclic Resistance ◽  
Cyclic Resistance Ratio ◽  
Liquefied Soils ◽  
Moment Effect ◽  
The Moment

ABSTRACTIndonesia is a country located in the most active earthquake paths in the world. This makes Indonesia prone to earthquakes and has the potential to experience liquefaction. Liquefaction can cause pile failure, so several things need to be considered in designing piles on potentially liquefied soils. One project in Sulawesi has a profile of uniform grained saturated soil that is susceptible to liquefaction. Two things that need to be considered in the design of piles on potentially liquefied soils is to ignore the capacity of pile friction and calculate the moment due to lateral spreading effects. Calculation of liquefaction potential is done by comparing the ratio of the cyclic stress and the cyclic resistance ratio and is compared by four other methods namely: the Seed et al. (2003), Tsuchida (1970), Seed et al. (2003), and Bray & Sancio (2004). The lateral spreading effect is calculated by referring to the JRA Code where the liquefied soil layer gives pressure to the pile at 30% of the overburden stress and the soil layer above the liquefied soil gives passive soil pressure to the pole. The moment effect caused by lateral spreading results in the addition of dimensions or number of poles.Keywords: liquefaction; lateral spreading; bearing capacity; JRA Code; pile foundationABSTRAKIndonesia adalah negara yang terletak di jalur gempa teraktif di dunia. Hal ini menyebabkan Indonesia rawan gempa dan memiliki potensi untuk mengalami likuifaksi. Likuifaksi dapat menyebabkan kerusakan/kegagalan struktur yang sangat merugikan, sehingga perlu diperhatikan beberapa hal dalam merancang tiang pada tanah berpotensi likuifaksi. Salah satu proyek di Sulawesi memiliki profil tanah pasir berbutir seragam dan jenuh air yang memiliki potensi likuifaksi. Dua hal yang perlu diperhitungkan dalam perancangan tiang pada tanah berpotensi likuifaksi adalah mengabaikan daya dukung friksi tiang dan memperhitungkan momen akibat efek lateral spreading. Perhitungan potensi likuifaksi dilakukan dengan membandingkan rasio tegangan siklik (CSR) dan rasio hambatan siklik (CRR) serta dibandingkan dengan empat metode lainnya yaitu: metode Seed et al. (2003), Tsuchida (1970), Seed et al. (2003), dan Bray & Sancio (2004). Daya dukung aksial pada tiang pancang mengalami pengurangan 32% akibat lapisan tanah yang terlikuifaksi. Efek lateral spreading dihitung dengan acuan JRA Code dimana lapisan tanah terlikuifaksi memberikan tekanan ke tiang sebesar 30% dari tegangan overburden dan lapisan tanah di atas tanah terlikuifaksi memberikan tekanan tanah pasif ke tiang. Efek momen yang diakibatkan oleh lateral spreading mengakibatkan penambahan dimensi ataupun jumlah tiang.Kata kunci: likuifaksi; lateral spreading; daya dukung; JRA Code; fondasi tiang    

scholarly journals The Contribution of the 20S Proteasome to Proteostasis

Biomolecules ◽  
2019 ◽  
Vol 9 (5) ◽  
pp. 190 ◽  
Author(s):  
Fanindra Kumar Deshmukh ◽  
Dana Yaffe ◽  
Maya Olshina ◽  
Gili Ben-Nissan ◽  
Michal Sharon
Keyword(s):  
Biological Process ◽  
Intrinsically Disordered Protein ◽  
26S Proteasome ◽  
20S Proteasome ◽  
Biological Processes ◽  
Neuronal Communication ◽  
Intrinsically Disordered ◽  
Disordered Protein ◽  
The Core ◽  
Functional Aspects

The last decade has seen accumulating evidence of various proteins being degraded by the core 20S proteasome, without its regulatory particle(s). Here, we will describe recent advances in our knowledge of the functional aspects of the 20S proteasome, exploring several different systems and processes. These include neuronal communication, post-translational processing, oxidative stress, intrinsically disordered protein regulation, and extracellular proteasomes. Taken together, these findings suggest that the 20S proteasome, like the well-studied 26S proteasome, is involved in multiple biological processes. Clarifying our understanding of its workings calls for a transformation in our perception of 20S proteasome-mediated degradation—no longer as a passive and marginal path, but rather as an independent, coordinated biological process. Nevertheless, in spite of impressive progress made thus far, the field still lags far behind the front lines of 26S proteasome research. Therefore, we also touch on the gaps in our knowledge of the 20S proteasome that remain to be bridged in the future.

scholarly journals Disentangling the behavioural variability of confined cell migration

2020 ◽  
Vol 17 (163) ◽  
pp. 20190689 ◽  
Author(s):  
David B. Brückner ◽  
Alexandra Fink ◽  
Joachim O. Rädler ◽  
Chase P. Broedersz
Keyword(s):  
Cell Migration ◽  
Dynamical Systems ◽  
Stochastic Dynamics ◽  
Systems Approach ◽  
Time Windows ◽  
Population Heterogeneity ◽  
Biological Processes ◽  
Long Time ◽  
Cell To Cell Variability ◽  
Additional Variance

Cell-to-cell variability is inherent to numerous biological processes, including cell migration. Quantifying and characterizing the variability of migrating cells is challenging, as it requires monitoring many cells for long time windows under identical conditions. Here, we observe the migration of single human breast cancer cells (MDA-MB-231) in confining two-state micropatterns. To describe the stochastic dynamics of this confined migration, we employ a dynamical systems approach. We identify statistics to measure the behavioural variance of the migration, which significantly exceeds that predicted by a population-averaged stochastic model. This additional variance can be explained by the combination of an ‘ageing’ process and population heterogeneity. To quantify population heterogeneity, we decompose the cells into subpopulations of slow and fast cells, revealing the presence of distinct classes of dynamical systems describing the migration, ranging from bistable to limit cycle behaviour. Our findings highlight the breadth of migration behaviours present in cell populations.

scholarly journals Decomposition of food waste using bulking agent and bio-drying technology

2018 ◽  
Vol 73 ◽  
pp. 05013
Author(s):  
Oktiawan Wiharyanto ◽  
Hadiwidodo Mochtar ◽  
Bagus Priyambada Ika ◽  
Purwono Purwono
Keyword(s):  
Food Waste ◽  
Bulking Agent ◽  
Biological Processes ◽  
Compost Maturity ◽  
Short Period ◽  
Long Time ◽  
Mature Compost ◽  
Biological Decomposition ◽  
Drying Technology ◽  
Maturity Parameters

Technology to process food waste should be easy maintenance, fast, economical, affordable, environmentally friendly, and socially acceptable. Processing food waste according to the principle is biological decomposition. Biological processes usually take quite a long time (30 days). This study aims to accelerate the process of decomposition of food waste and produce a quality fertilizer products. Bulking agent (biofilm), bio activator (microorganism from cassava), and bio-drying technology are used to accelerate the decomposition process. The ratio of food waste and bulking agent is 7:3 (v/v). Mature product serves as a bulking agent and additive microorganisms. Additive microorganisms are also done by adding microorganism derived from cassava with a ratio of 10ml/500 g (Ml); 20 ml/500 g (M2); and 10ml/500 g of food waste (M3). The results showed the temperature of the food waste reached 50 ? at first. The addition of bulking agent and Additive microorganisms causes the thermophilic phase to occur early. This shows the thermophilic phase being achieved in a short period. Based on testing of compost maturity parameters, food waste has matured within 3 days. The C-Organic Concentration was 27.57%, N-total 1.98%, C/N ratio of 13.92, P-Total 0.23% and K-total 0.83%. In conclusion of this study, mature compost can be used as bulking agent with mature compost ratio and 7: 3 (v/v) bulking agent. Processing food waste is quite effective using a combination of bulking agent (mature compost), additive microorganisms and bio-drying technology.

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