ResearchPad - physical-properties https://www.researchpad.co Default RSS Feed en-us © 2020 Newgen KnowledgeWorks <![CDATA[iterb-PPse: Identification of transcriptional terminators in bacterial by incorporating nucleotide properties into PseKNC]]> https://www.researchpad.co/article/elastic_article_14750 Terminator is a DNA sequence that gives the RNA polymerase the transcriptional termination signal. Identifying terminators correctly can optimize the genome annotation, more importantly, it has considerable application value in disease diagnosis and therapies. However, accurate prediction methods are deficient and in urgent need. Therefore, we proposed a prediction method “iterb-PPse” for terminators by incorporating 47 nucleotide properties into PseKNC-Ⅰ and PseKNC-Ⅱ and utilizing Extreme Gradient Boosting to predict terminators based on Escherichia coli and Bacillus subtilis. Combing with the preceding methods, we employed three new feature extraction methods K-pwm, Base-content, Nucleotidepro to formulate raw samples. The two-step method was applied to select features. When identifying terminators based on optimized features, we compared five single models as well as 16 ensemble models. As a result, the accuracy of our method on benchmark dataset achieved 99.88%, higher than the existing state-of-the-art predictor iTerm-PseKNC in 100 times five-fold cross-validation test. Its prediction accuracy for two independent datasets reached 94.24% and 99.45% respectively. For the convenience of users, we developed a software on the basis of “iterb-PPse” with the same name. The open software and source code of “iterb-PPse” are available at https://github.com/Sarahyouzi/iterb-PPse.

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<![CDATA[Software-aided workflow for predicting protease-specific cleavage sites using physicochemical properties of the natural and unnatural amino acids in peptide-based drug discovery]]> https://www.researchpad.co/article/5c3e50a9d5eed0c484d840db

Peptide drugs have been used in the treatment of multiple pathologies. During peptide discovery, it is crucially important to be able to map the potential sites of cleavages of the proteases. This knowledge is used to later chemically modify the peptide drug to adapt it for the therapeutic use, making peptide stable against individual proteases or in complex medias. In some other cases it needed to make it specifically unstable for some proteases, as peptides could be used as a system to target delivery drugs on specific tissues or cells. The information about proteases, their sites of cleavages and substrates are widely spread across publications and collected in databases such as MEROPS. Therefore, it is possible to develop models to improve the understanding of the potential peptide drug proteolysis. We propose a new workflow to derive protease specificity rules and predict the potential scissile bonds in peptides for individual proteases. WebMetabase stores the information from experimental or external sources in a chemically aware database where each peptide and site of cleavage is represented as a sequence of structural blocks connected by amide bonds and characterized by its physicochemical properties described by Volsurf descriptors. Thus, this methodology could be applied in the case of non-standard amino acid. A frequency analysis can be performed in WebMetabase to discover the most frequent cleavage sites. These results were used to train several models using logistic regression, support vector machine and ensemble tree classifiers to map cleavage sites for several human proteases from four different families (serine, cysteine, aspartic and matrix metalloproteases). Finally, we compared the predictive performance of the developed models with other available public tools PROSPERous and SitePrediction.

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<![CDATA[Construction of an integrated database for hERG blocking small molecules]]> https://www.researchpad.co/article/5b4a289e463d7e4513b8980e

The inhibition of the hERG potassium channel is closely related to the prolonged QT interval, and thus assessing this risk could greatly facilitate the development of therapeutic compounds and the withdrawal of hazardous marketed drugs. The recent increase in SAR information about hERG inhibitors in public databases has led to many successful applications of machine learning techniques to predict hERG inhibition. However, most of these reports constructed their prediction models based on only one SAR database because the differences in the data format and ontology hindered the integration of the databases. In this study, we curated the hERG-related data in ChEMBL, PubChem, GOSTAR, and hERGCentral, and integrated them into the largest database about hERG inhibition by small molecules. Assessment of structural diversity using Murcko frameworks revealed that the integrated database contains more than twice as many chemical scaffolds for hERG inhibitors than any of the individual databases, and covers 18.2% of the Murcko framework-based chemical space occupied by the compounds in ChEMBL. The database provides the most comprehensive information about hERG inhibitors and will be useful to design safer compounds for drug discovery. The database is freely available at http://drugdesign.riken.jp/hERGdb/.

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<![CDATA[Large Scale Chromosome Folding Is Stable against Local Changes in Chromatin Structure]]> https://www.researchpad.co/article/5989da3cab0ee8fa60b8827a

Characterizing the link between small-scale chromatin structure and large-scale chromosome folding during interphase is a prerequisite for understanding transcription. Yet, this link remains poorly investigated. Here, we introduce a simple biophysical model where interphase chromosomes are described in terms of the folding of chromatin sequences composed of alternating blocks of fibers with different thicknesses and flexibilities, and we use it to study the influence of sequence disorder on chromosome behaviors in space and time. By employing extensive computer simulations, we thus demonstrate that chromosomes undergo noticeable conformational changes only on length-scales smaller than 105 basepairs and time-scales shorter than a few seconds, and we suggest there might exist effective upper bounds to the detection of chromosome reorganization in eukaryotes. We prove the relevance of our framework by modeling recent experimental FISH data on murine chromosomes.

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<![CDATA[Common contextual influences in ambiguous and rivalrous figures]]> https://www.researchpad.co/article/5989db59ab0ee8fa60bdf18d

Images that resist binocular fusion undergo alternating periods of dominance and suppression, similarly to ambiguous figures whose percepts alternate between two interpretations. It has been well documented that the perceptual interpretations of both rivalrous and ambiguous figures are influenced by their spatio-temporal context. Here we consider whether an identical spatial context similarly influences the interpretation of a similar rivalrous and ambiguous figure. We developed a binocularly rivalrous stimulus whose perceptual experience mirrors that of a Necker cube. We employed a paradigm similar to that of Ouhnana and Kingdom (2016) to correlate the magnitude of influence of context between the rivalrous and ambiguous target. Our results showed that the magnitude of contextual influence is significantly correlated within observers between both binocularly rivalrous and ambiguous target figures. This points to a similar contextual-influence mechanism operating on a common mechanism underlying the perceptual instability in both ambiguous and rivalrous figures.

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<![CDATA[Implied Spatial Meaning and Visuospatial Bias: Conceptual Processing Influences Processing of Visual Targets and Distractors]]> https://www.researchpad.co/article/5989db14ab0ee8fa60bcce0e

Concepts with implicit spatial meaning (e.g., "hat", "boots") can bias visual attention in space. This result is typically found in experiments with a single visual target per trial, which can appear at one of two locations (e.g., above vs. below). Furthermore, the interaction is typically found in the form of speeded responses to targets appearing at the compatible location (e.g., faster responses to a target above fixation, after reading "hat"). It has been argued that these concept-space interactions could also result from experimentally-induced associations between the binary set of locations and the conceptual categories with upward and downward meaning. Thus, rather than reflecting a conceptually driven spatial bias, the effect could reflect a benefit for compatible cue-target sequences that occurs only after target onset. We addressed these concerns by going beyond a binary set of locations and employing a search display consisting of four items (above, below, left, and right). Within each search trial, before performing a visual search task, participants performed a conceptual task involving concepts with implicit upward or downward meaning. The search display, in addition to including a target, could also include a salient distractor. Assuming a conceptually driven visual bias, we expected to observe, first, a benefit for target processing at the compatible location and, second, an increase in the cost of the salient distractor. The findings confirmed both predictions, suggesting that concepts do indeed generate a spatial bias. Finally, results from a control experiment, without the conceptual task, suggest the presence of an axis-specific effect, in addition to the location-specific effect, suggesting that concepts might cause both location-specific and axis-specific spatial bias. Taken together, our findings provide additional support for the involvement of spatial processing in conceptual understanding.

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<![CDATA[Identification of 14-3-3 Proteins Phosphopeptide-Binding Specificity Using an Affinity-Based Computational Approach]]> https://www.researchpad.co/article/5989da9cab0ee8fa60ba3f2e

The 14-3-3 proteins are a highly conserved family of homodimeric and heterodimeric molecules, expressed in all eukaryotic cells. In human cells, this family consists of seven distinct but highly homologous 14-3-3 isoforms. 14-3-3σ is the only isoform directly linked to cancer in epithelial cells, which is regulated by major tumor suppressor genes. For each 14-3-3 isoform, we have 1,000 peptide motifs with experimental binding affinity values. In this paper, we present a novel method for identifying peptide motifs binding to 14-3-3σ isoform. First, we propose a sampling criteria to build a predictor for each new peptide sequence. Then, we select nine physicochemical properties of amino acids to describe each peptide motif. We also use auto-cross covariance to extract correlative properties of amino acids in any two positions. Finally, we consider elastic net to predict affinity values of peptide motifs, based on ridge regression and least absolute shrinkage and selection operator (LASSO). Our method tests on the 1,000 known peptide motifs binding to seven 14-3-3 isoforms. On the 14-3-3σ isoform, our method has overall pearson-product-moment correlation coefficient (PCC) and root mean squared error (RMSE) values of 0.84 and 252.31 for N–terminal sublibrary, and 0.77 and 269.13 for C–terminal sublibrary. We predict affinity values of 16,000 peptide sequences and relative binding ability across six permutated positions similar with experimental values. We identify phosphopeptides that preferentially bind to 14-3-3σ over other isoforms. Several positions on peptide motifs are in the same amino acid category with experimental substrate specificity of phosphopeptides binding to 14-3-3σ. Our method is fast and reliable and is a general computational method that can be used in peptide-protein binding identification in proteomics research.

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<![CDATA[Responses of absolute and specific enzyme activity to consecutive application of composted sewage sludge in a Fluventic Ustochrept]]> https://www.researchpad.co/article/5989db5cab0ee8fa60bdfe0d

Composted sewage sludge (CS) is considered a rich source of soil nutrients and significantly affects the physical, chemical, and biological characteristics of soil, but its effect on specific enzyme activity in soil is disregarded. The present experiment examined the absolute and specific enzyme activity of the enzymes involved in carbon, nitrogen, and phosphorus cycles, the diversity of soil microbial functions, and soil community composition in a Fluventic Ustochrept under a maize—wheat rotation system in North China during 2012–2015. Application of CS led to increase in MBC and in its ratio to both total organic carbon (TOC) and microbial biomass nitrogen (MBN). Absolute enzyme activity, except that of phosphatase, increased in CS-treated soils, whereas specific activity of all the enzymes declined, especially at the highest dose of CS (45 t ha−1). The diversity of soil microbial community also increased in CS-treated soils, whereas its functional diversity declined at higher doses of CS owing to the lowered specific enzyme activity. These changes indicate that CS application induced the domination of microorganisms that are not metabolically active and those that use resources more efficiently, namely fungi. Redundancy analysis showed that fundamental alterations in soil enzyme activity depend on soil pH. Soil specific enzyme activity is affected more than absolute enzyme activity by changes in soil properties, especially soil microbial activity and composition of soil microflora (as judged by the following ratios: MBC/TOC, MBC/MBN, and TOC/LOC, that is labile organic carbon) through the Pearson Correlation Coefficient. Specific enzyme activity is thus a more accurate parameter than absolute enzyme activity for monitoring the effect of adding CS on the activities and structure of soil microbial community.

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<![CDATA[Effect of Carboxymethylation on the Rheological Properties of Hyaluronan]]> https://www.researchpad.co/article/5989dab0ab0ee8fa60bab333

Chemical modifications made to hyaluronan to enable covalent crosslinking to form a hydrogel or to attach other molecules may alter the physical properties as well, which have physiological importance. Here we created carboxymethyl hyaluronan (CMHA) with varied degree of modification and investigated the effect on the viscosity of CMHA solutions. Viscosity decreased initially as modification increased, with a minimum viscosity for about 30–40% modification. This was followed by an increase in viscosity around 45–50% modification. The pH of the solution had a variable effect on viscosity, depending on the degree of carboxymethyl modification and buffer. The presence of phosphates in the buffer led to decreased viscosity. We also compared large-scale production lots of CMHA to lab-scale and found that large-scale required extended reaction times to achieve the same degree of modification. Finally, thiolated CMHA was disulfide crosslinked to create hydrogels with increased viscosity and shear-thinning aspects compared to CMHA solutions.

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<![CDATA[Effects of Ionizing Radiation on Physical Properties of Peripherally Inserted Central Catheter]]> https://www.researchpad.co/article/5989db42ab0ee8fa60bd746e

Peripherally inserted central catheter (PICC) has been widely used to treat cancer patients. It is unknown whether or not it can be applied safely during radiotherapy. The study aimed to investigate the direct effects of gamma radiation on physical properties of PICC. A total of 60 catheters were included in this study. Thirty PICCs were exposed to a radiation field, and another 30 PICCs received radiation in a 3-cm homogeneity water equivalent phantom and then were irradiated. Each group was divided into three subgroups: 10 PICCs were given conventional fractionation, 2 Gy per fraction, 5 fractions per week; 10 PICCs were continuously given hypofractionation, 10 Gy per fraction, for 6 weeks; and 10 PICCs were given mock radiation as controls. The physical properties of these catheters were analyzed after radiation. None of the PICCs leaked under 300-kPa airflow pressure lasting 15 seconds. Fracture force values and liquid velocity values of all PICCs were within the normal range. The liquid velocity values of the control groups were higher than the two groups that received radiation (P < 0.05), and there was no difference between the two irradiation groups (P > 0.05). There were no statistical differences among the conventional fractionation group, hypofractionation group, and control group when compared to the fracture force values in two parts (P > 0.05). The physical property of PICC is quite stable with a clinically relevant dose of gamma radiation. It is likely that PICC can be used safely in patients receiving radiotherapy, although further in vivo and clinical studies are required.

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<![CDATA[A Patient-Specific Polylactic Acid Bolus Made by a 3D Printer for Breast Cancer Radiation Therapy]]> https://www.researchpad.co/article/5989da8fab0ee8fa60b9f788

Purpose

The aim of this study was to assess the feasibility and advantages of a patient-specific breast bolus made using a 3D printer technique.

Methods

We used the anthropomorphic female phantom with breast attachments, which volumes are 200, 300, 400, 500 and 650 cc. We simulated the treatment for a right breast patient using parallel opposed tangential fields. Treatment plans were used to investigate the effect of unwanted air gaps under bolus on the dose distribution of the whole breast. The commercial Super-Flex bolus and 3D-printed polylactic acid (PLA) bolus were applied to investigate the skin dose of the breast with the MOSFET measurement. Two boluses of 3 and 5 mm thicknesses were selected.

Results

There was a good agreement between the dose distribution for a virtual bolus generated by the TPS and PLA bolus. The difference in dose distribution between the virtual bolus and Super-Flex bolus was significant within the bolus and breast due to unwanted air gaps. The average differences between calculated and measured doses in a 200 and 300 cc with PLA bolus were not significant, which were -0.7% and -0.6% for 3mm, and -1.1% and -1.1% for 5 mm, respectively. With the Super-Flex bolus, however, significant dose differences were observed (-5.1% and -3.2% for 3mm, and -6.3% and -4.2% for 5 mm).

Conclusion

The 3D-printed solid bolus can reduce the uncertainty of the daily setup and help to overcome the dose discrepancy by unwanted air gaps in the breast cancer radiation therapy.

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<![CDATA[Multi-walled carbon nanotube-physicochemical properties predict the systemic acute phase response following pulmonary exposure in mice]]> https://www.researchpad.co/article/5989db51ab0ee8fa60bdc3a9

Pulmonary exposure to multi-walled carbon nanotubes (MWCNTs) has been linked to an increased risk of developing cardiovascular disease in addition to the well-documented physicochemical-dependent adverse lung effects. A proposed mechanism is through a strong and sustained pulmonary secretion of acute phase proteins to the blood. We identified physicochemical determinants of MWCNT-induced systemic acute phase response by analyzing effects of pulmonary exposure to 14 commercial, well-characterized MWCNTs in female C57BL/6J mice pulmonary exposed to 0, 6, 18 or 54 μg MWCNT/mouse. Plasma levels of acute phase response proteins serum amyloid A1/2 (SAA1/2) and SAA3 were determined on day 1, 28 or 92. Expression levels of hepatic Saa1 and pulmonary Saa3 mRNA levels were assessed to determine the origin of the acute phase response proteins. Pulmonary Saa3 mRNA expression levels were greater and lasted longer than hepatic Saa1 mRNA expression. Plasma SAA1/2 and SAA3 protein levels were related to time and physicochemical properties using adjusted, multiple regression analyses. SAA3 and SAA1/2 plasma protein levels were increased after exposure to almost all of the MWCNTs on day 1, whereas limited changes were observed on day 28 and 92. SAA1/2 and SAA3 protein levels did not correlate and only SAA3 protein levels correlated with neutrophil influx. The multiple regression analyses revealed a protective effect of MWCNT length on SAA1/2 protein level on day 1, such that a longer length resulted in lowered SAA1/2 plasma levels. Increased SAA3 protein levels were positively related to dose and content of Mn, Mg and Co on day 1, whereas oxidation and diameter of the MWCNTs were protective on day 28 and 92, respectively. The results of this study reveal very differently controlled pulmonary and hepatic acute phase responses after MWCNT exposure. As the responses were influenced by the physicochemical properties of the MWCNTs, this study provides the first step towards designing MWCNT that induce less SAA.

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<![CDATA[Green material selection for sustainability: A hybrid MCDM approach]]> https://www.researchpad.co/article/5989db5aab0ee8fa60bdf7a8

Green material selection is a crucial step for the material industry to comprehensively improve material properties and promote sustainable development. However, because of the subjectivity and conflicting evaluation criteria in its process, green material selection, as a multi-criteria decision making (MCDM) problem, has been a widespread concern to the relevant experts. Thus, this study proposes a hybrid MCDM approach that combines decision making and evaluation laboratory (DEMATEL), analytical network process (ANP), grey relational analysis (GRA) and technique for order performance by similarity to ideal solution (TOPSIS) to select the optimal green material for sustainability based on the product's needs. A nonlinear programming model with constraints was proposed to obtain the integrated closeness index. Subsequently, an empirical application of rubbish bins was used to illustrate the proposed method. In addition, a sensitivity analysis and a comparison with existing methods were employed to validate the accuracy and stability of the obtained final results. We found that this method provides a more accurate and effective decision support tool for alternative evaluation or strategy selection.

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<![CDATA[Bamboo-inspired optimal design for functionally graded hollow cylinders]]> https://www.researchpad.co/article/5989db5aab0ee8fa60bdf4af

The optimal distribution of the reinforcing fibers for stiffening hollow cylindrical composites is explored using the linear elasticity theory. The spatial distribution of the vascular bundles in wild bamboo, a nature-designed functionally graded material, is the basis for the design. Our results suggest that wild bamboos maximize their flexural rigidity by optimally regulating the radial gradation of their vascular bundle distribution. This fact provides us with a plant-mimetic design principle that enables the realization of high-stiffness and lightweight cylindrical composites.

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<![CDATA[Effects of Salivary Oxidative Markers on Edentulous Patients’ Satisfaction with Prosthetic Denture Treatments: A Pilot Study]]> https://www.researchpad.co/article/5989d9f9ab0ee8fa60b713c6

Objectives

The purpose of this study was to assess relationships among periodontal conditions, salivary antioxidant levels, and patients’ satisfaction with their prostheses.

Methods

This study was conducted at the Division of Prosthodontics, Department of Dentistry, Taipei Medical University Hospital. The periodontal condition of patients was based on an assessment of the plaque index (PI) and gingival index (GI). The pH value, flow rate, and buffer capacity of the saliva were estimated. The salivary total antioxidant status (TAS) and superoxide dismutase (SOD) level were also determined. Patients’ satisfaction with prosthetic treatments was evaluated using the Chinese version of the short-form Oral Health Impact Profile (OHIP-14C). A multivariate regression model was used to determine whether patients’ satisfaction with prosthetic treatment was affected by their oral health status.

Results

In total, 35 edentulous patients were recruited. In the Spearman correlation analysis, salivary pH (r = -0.36, p = 0.03) and the buffer ability (r = -0.48, p<0.01) were associated with OHIP-14C scores. In the multivariate analysis, patients who had a higher GI also had a higher score of physical disabilities (β = 1.38, p = 0.04). Levels of SOD increased with the scores of psychological discomfort (β = 0.33 U/g protein, p = 0.04).

Conclusions

This study suggested that both the GI and SOD levels were associated with patients’ satisfaction with prosthetic treatments. To the best of our knowledge, this is the first study to elucidate the relationship between OHIP scores and salivary oxidative markers in edentulous patients.

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<![CDATA[A Numerical Investigation of the Electric and Thermal Cell Kill Distributions in Electroporation-Based Therapies in Tissue]]> https://www.researchpad.co/article/5989da94ab0ee8fa60ba1532

Electroporation-based therapies are powerful biotechnological tools for enhancing the delivery of exogeneous agents or killing tissue with pulsed electric fields (PEFs). Electrochemotherapy (ECT) and gene therapy based on gene electrotransfer (EGT) both use reversible electroporation to deliver chemotherapeutics or plasmid DNA into cells, respectively. In both ECT and EGT, the goal is to permeabilize the cell membrane while maintaining high cell viability in order to facilitate drug or gene transport into the cell cytoplasm and induce a therapeutic response. Irreversible electroporation (IRE) results in cell kill due to exposure to PEFs without drugs and is under clinical evaluation for treating otherwise unresectable tumors. These PEF therapies rely mainly on the electric field distributions and do not require changes in tissue temperature for their effectiveness. However, in immediate vicinity of the electrodes the treatment may results in cell kill due to thermal damage because of the inhomogeneous electric field distribution and high current density during the electroporation-based therapies. Therefore, the main objective of this numerical study is to evaluate the influence of pulse number and electrical conductivity in the predicted cell kill zone due to irreversible electroporation and thermal damage. Specifically, we simulated a typical IRE protocol that employs ninety 100-µs PEFs. Our results confirm that it is possible to achieve predominant cell kill due to electroporation if the PEF parameters are chosen carefully. However, if either the pulse number and/or the tissue conductivity are too high, there is also potential to achieve cell kill due to thermal damage in the immediate vicinity of the electrodes. Therefore, it is critical for physicians to be mindful of placement of electrodes with respect to critical tissue structures and treatment parameters in order to maintain the non-thermal benefits of electroporation and prevent unnecessary damage to surrounding healthy tissue, critical vascular structures, and/or adjacent organs.

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<![CDATA[Use of an Enactive Insole for Reducing the Risk of Falling on Different Types of Soil Using Vibrotactile Cueing for the Elderly]]> https://www.researchpad.co/article/5989db28ab0ee8fa60bd0b41

Background

Our daily activities imply displacements on various types of soil. For persons with gait disorder or losing functional autonomy, walking on some types of soil could be challenging because of the risk of falling it represents.

Methods

In this paper, we present, in a first part, the use of an enactive shoe for an automatic differentiation of several types of soil. In a second part, using a second improved prototype (an enactive insole), twelve participants with Parkinson’s disease (PD) and nine age-matched controls have performed the Timed Up and Go (TUG) test on six types of soil with and without cueing. The frequency of the cueing was set at 10% above the cadence computed at the lower risk of falling (walking over the concrete). Depending on the cadence computed at the lower risk, the enactive insole activates a vibrotactile cueing aiming to improve gait and balance control. Finally, a risk index is computed using gait parameters in relation to given type of soil.

Results

The frequency analysis of the heel strike vibration allows the differentiation of various types of soil. The risk computed is associated to an appropriate rhythmic cueing in order to improve balance and gait impairment. The results show that a vibrotactile cueing could help to reduce the risk of falling.

Conclusions

Firstly, this paper demonstrates the feasibility of reducing the risk of falling while walking on different types of soil using vibrotactile cueing. We found a significant difference and a significant decrease in the computed risks of falling for most of types of soil especially for deformable soils which can lead to fall. Secondly, heel strike provides an approximation of the impulse response of the soil that can be analyzed with time and frequency-domain modeling. From these analyses, an index is computed enabling differentiation the types of soil.

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<![CDATA[Yield Response of Spring Maize to Inter-Row Subsoiling and Soil Water Deficit in Northern China]]> https://www.researchpad.co/article/5989da7eab0ee8fa60b99a02

Background

Long-term tillage has been shown to induce water stress episode during crop growth period due to low water retention capacity. It is unclear whether integrated water conservation tillage systems, such asspringdeepinter-row subsoiling with annual or biennial repetitions, can be developed to alleviate this issue while improve crop productivity.

Methods

Experimentswere carried out in a spring maize cropping system on Calcaric-fluvicCambisolsatJiaozuoexperimentstation, northern China, in 2009 to 2014. Effects of threesubsoiling depths (i.e., 30 cm, 40 cm, and 50 cm) in combination with annual and biennial repetitionswasdetermined in two single-years (i.e., 2012 and 2014)againstthe conventional tillage. The objectives were to investigateyield response to subsoiling depths and soil water deficit(SWD), and to identify the most effective subsoiling treatment using a systematic assessment.

Results

Annualsubsoiling to 50 cm (AS-50) increased soil water storage (SWS, mm) by an average of8% in 0–20 cm soil depth, 19% in 20–80 cm depth, and 10% in 80–120 cm depth, followed by AS-40 and BS-50, whereas AS-30 and BS-30 showed much less effects in increasing SWS across the 0–120 cm soil profile, compared to the CK. AS-50 significantly reduced soil water deficit (SWD, mm) by an average of123% during sowing to jointing, 318% during jointing to filling, and 221% during filling to maturity, compared to the CK, followed by AS-40 and BS-50. An integrated effect on increasing SWS and reducing SWD helped AS-50 boost grain yield by an average of 31% and biomass yield by 30%, compared to the CK. A power function for subsoiling depth and a negative linear function for SWD were used to fit the measured yields, showing the deepest subsoiling depth (50 cm) with the lowest SWD contributed to the highest yield. Systematic assessment showed that AS-50 received the highest evaluation index (0.69 out of 1.0) among all treatments.

Conclusion

Deepinter-row subsoilingwith annual repetition significantly boosts yield by alleviating SWD in critical growth period and increasing SWS in 20–80 cm soil depth. The results allow us to conclude that AS-50 can be adopted as an effective approach to increase crop productivity, alleviate water stress, and improve soil water availability for spring maize in northern China.

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<![CDATA[Insights on the mechanism of action of immunostimulants in relation to their pharmacological potency. The effects of imidazoquinolines on TLR8]]> https://www.researchpad.co/article/5989db5cab0ee8fa60be02f8

Imidazoquinolines are powerful immunostimulants (IMMS) that function through Toll-like receptors, particularly TLR7 and TLR8. In addition to enhancing the immune response, IMMS also function as antineoplastic drugs and vaccine adjuvants. These small compounds display almost the same molecular structure, except in some cases in which atom in position 1 varies and changes the imidazole characteristics. A variable acyclic side chain is also always attached at atom in position 2, while another chain may be attached at atom in position 1. These structural differences alter immune responses, such as the production of interferon regulatory factor and nuclear factor-κB (IRF-NFκB). In this work, quantum mechanics theory and computational chemistry methods were applied to study the physicochemical properties of the crystal binding site of TLR8 complexed with the following six IMMS molecules: Hybrid-2, XG1-236, DS802, CL075, CL097 and R848 (resiquimod). The PDB IDs of the crystals were: 4R6A, 4QC0, 4QBZ, 3W3K, 3W3J, and 3W3N respectively. Thus, were calculated, the total energy, solvation energy, interaction energy (instead of free energy) of the system and interaction energy of the polar region of the IMMS. Additionally, the dipole moment, electrostatic potential, polar surface, atomic charges, hydrogen bonds, and polar and hydrophobic interactions, among others, were assessed. Together, these properties revealed important differences among the six TLR8-immunostimulant complexes, reflected as different interaction energies and therefore different electrostatic environments and binding energies. Remarkably, the interaction energy of a defined polar region composed of the highly polarized N3, N5 atoms and the N11 amino group, acted as a polar pharmacophore that correlates directly with the reported immunopharmacological potency of the six complexed molecules. Based on these results, it was concluded that accurate physicochemical analysis of the crystal binding site could reveal the binding energy (measured as interaction energy) and associated molecular mechanism of action between IMMS and TLR8. These findings may facilitate the development and design of improved small molecules with IMMS properties that are targeted to the TLR system and have enhanced pharmacological effectiveness and reduced toxicity.

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<![CDATA[DNABP: Identification of DNA-Binding Proteins Based on Feature Selection Using a Random Forest and Predicting Binding Residues]]> https://www.researchpad.co/article/5989da2dab0ee8fa60b830f3

DNA-binding proteins are fundamentally important in cellular processes. Several computational-based methods have been developed to improve the prediction of DNA-binding proteins in previous years. However, insufficient work has been done on the prediction of DNA-binding proteins from protein sequence information. In this paper, a novel predictor, DNABP (DNA-binding proteins), was designed to predict DNA-binding proteins using the random forest (RF) classifier with a hybrid feature. The hybrid feature contains two types of novel sequence features, which reflect information about the conservation of physicochemical properties of the amino acids, and the binding propensity of DNA-binding residues and non-binding propensities of non-binding residues. The comparisons with each feature demonstrated that these two novel features contributed most to the improvement in predictive ability. Furthermore, to improve the prediction performance of the DNABP model, feature selection using the minimum redundancy maximum relevance (mRMR) method combined with incremental feature selection (IFS) was carried out during the model construction. The results showed that the DNABP model could achieve 86.90% accuracy, 83.76% sensitivity, 90.03% specificity and a Matthews correlation coefficient of 0.727. High prediction accuracy and performance comparisons with previous research suggested that DNABP could be a useful approach to identify DNA-binding proteins from sequence information. The DNABP web server system is freely available at http://www.cbi.seu.edu.cn/DNABP/.

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