Post hoc support vector machine learning for impedimetric biosensors based on weak protein-ligand interactions.

Impedimetric biosensors for measuring small molecules based on weak/transient interactions between bioreceptors and target analytes are a challenge for detection electronics, particularly in field studies or in the analysis of complex matrices. Protein-ligand binding sensors have enormous potential for biosensing, but achieving accuracy in complex solutions is a major challenge. There is a need for simple post hoc analytical tools that are not computationally expensive, yet provide near real time feedback on data derived from impedance spectra. Here, we show the use of a simple, open source support vector machine learning algorithm for analyzing impedimetric data in lieu of using equivalent circuit analysis. We demonstrate two different protein-based biosensors to show that the tool can be used for various applications. We conclude with a mobile phone-based demonstration focused on the measurement of acetone, an important biomarker related to the onset of diabetic ketoacidosis. In all conditions tested, the open source classifier was capable of performing as well as, or better, than the equivalent circuit analysis for characterizing weak/transient interactions between a model ligand (acetone) and a small chemosensory protein derived from the tsetse fly. In addition, the tool has a low computational requirement, facilitating use for mobile acquisition systems such as mobile phones. The protocol is deployed through Jupyter notebook (an open source computing environment available for mobile phone, tablet or computer use) and the code was written in Python. For each of the applications, we provide step-by-step instructions in English, Spanish, Mandarin and Portuguese to facilitate widespread use. All codes were based on scikit-learn, an open source software machine learning library in the Python language, and were processed in Jupyter notebook, an open-source web application for Python. The tool can easily be integrated with the mobile biosensor equipment for rapid detection, facilitating use by a broad range of impedimetric biosensor users. This post hoc analysis tool can serve as a launchpad for the convergence of nanobiosensors in planetary health monitoring applications based on mobile phone hardware.

Safe limit of arsenic in soil in relation to dietary exposure of arsenicosis patients from Malda district, West Bengal- A case study.

Safe limit of arsenic in soil in relation to dietary exposure of arsenicosis patients was established in Malda district of West Bengal. Out of 182 participants examined, 80 (43.9%) participants showed clinical features of arsenicosis, characterized by arsenical skin lesion (pigmentation and keratosis), while 102 participants did not have any such lesion (control). Experimental results of the twenty eight soils (own field) of the participants showed the mean Olsen extractable and total arsenic concentration of 0.206 and 6.70mgkg-1, respectively. Arsenic concentration in rice grain ranged from 2.00 to 1260µgkg-1 with the mean value of 146µgkg-1. The hazard quotient (HQ) for intake of As by human through consumption of rice varied from 0.03 to 3.52. HQ exceeds 1.0 for drinking water and rice grain grown in the study area in many cases. As high as 77.6% variation in As content in rice grain could be explained by the solubility-free ion activity model. Toxic limit of extractable As in soil for rice in relation to soil properties and human health hazard, associated with consumption of rice grain by human, was established. For example, the permissible limit of Olsen extractable As in soil would be 0.43mgkg-1 for rice cultivation, if soil pH and organic carbon content were 7.5% and 0.50%, respectively. However, the critical limit of Olsen extractable As in soil would be 0.54mgkg-1, if soil pH and organic carbon were 8.5% and 0.75%, respectively. The conceptual framework of fixing the toxic limit of arsenic in soils with respect to soil properties and human health under modeling-framework was established.

Release of zinc and cadmium from sludge amended soil as influenced by varying levels of moisture and temperature.

Limited information is available related to the effect of moisture and temperature on release of metals from sludge treated soils. In an incubation experiment, effect of ten levels of sludge (0, 1.12, 2.24, 4.48, 8.96, 17.9, 35.8, 71.6, 142, 285 g kg(-1)), two levels of moisture (field capacity and 2.5 cm standing water) and two levels of temperature (20 and 35 degrees C) on the release of zinc and cadmium was evaluated in acid and alkaline soils. The results indicated that application of sludge was more effective in enhancing EDTA extractable Zn and Cd in acid soil than in alkaline soil. On an average, maximum increase in release of EDTA extractable Zn and Cd were 32.0 and 5.2 fold in sludge treated soil over control. There was decrease in EDTA extractable Zn and Cd by 37.7% and 25.4%, respectively under submergence as compared to that under field capacity. On an average, the amount of EDTA extractable Zn and Cd increased by 22.6% and 43.6%, respectively at 35 degrees C than that at 20 degrees C.

Predicting bioavailability of metals from sludge-amended soils.

We attempted to develop a protocol for fixing the maximum permissible limit of sludge in agricultural lands based on transfer of metals from sludge-amended soils to human food chain. For this purpose, spinach was grown as a test crop on acid and alkaline soils with graded doses of sludge (0, 1.12, 2.24, 4.48, 8.96, 17.9, 35.8, 71.6, 142 and 285 g kg(-1) of soil) in a pot experiment. Biomass yield of spinach was increased due to sludge application in both acid and alkaline soils. Among the chemical extractants, EDTA extracted the highest amount of metals from sludge-amended soil followed by diethylenetriaminepentaacetic acid (DTPA) and CaCl2. Elevated levels of Zn, Cu, Fe, Mn, Ni, Cd and Pb in spinach were observed due to sludge application over control. Application of sludge was more effective in increasing metal content in spinach grown on acid soil than alkaline soil. Solubility-free ion activity model as a function of pH, organic carbon and extractable metal was far more effective in predicting metal uptake by spinach grown on sludge-amended soils as compared to that of chemical extractants. Risk in terms of hazard quotient (HQ) for intake of metals through consumption of spinach by humans grown on sludge-treated soils was computed for different metals separately. In a 90-day pot experiment, safe rates of sludge application were worked out as 4.48 and 71.6 g kg(-1) for acid and alkaline soils, respectively.

Identification of the solid phase in relation to the solubility of nickel in alluvial soils.

The chemical equillibria between nickel (Ni) ion present in soil solution and solid phases govern the solubility vis-a-vis availability of Ni in soil. Therefore, stability of various Ni containing minerals in relation to pH was studied to identify the probable solid phases, which govern the solubility of Ni in some alluvial soils under intensive cultivation in and around Delhi. Free Ni2+ activity (pNi2+) as estimated by Baker soil test, ranged from 13.1 to 16.2. Highest free Ni2+ activity (pNi2+ = 13.1) was recorded in industrial effluent irrigated soil collected from Sonepat, Haryana. Free Ni2+ activity was 13.6 in soil collected from agricultural lands of Keshopur, receiving irrigation through sewage effluents. Soils receiving irrigation through tube well water showed relatively lower free Ni2+ activity (pNi2+ = 14.6 to 16.2). Ni-ferrite in equilibrium with Fe(OH)3 (amorphous) is likely to control the activity of Ni in two intensively Ni contaminated soil having pH around 8. Free Ni2+ activity is likely to be buffered by exchangeable Ni in soils having neutral pH.

Prediction of the solubility of zinc, copper, nickel, cadmium, and lead in metal-contaminated soils.

Risk assessment of metal-contaminated soil depends on how precisely one can predict the solubility of metals in soils. Responses of plants and soil organisms to metal toxicity are explained by the variation in free metal ion activity in soil pore water. This study was undertaken to predict the free ion activity of Zn, Cu, Ni, Cd, and Pb in metal-contaminated soil as a function of pH, soil organic carbon, and extractable metal content. For this purpose, 21 surface soil samples (0-15 cm) were collected from agricultural lands of various locations receiving sewage sludge and industrial effluents for a long period. One soil sample was also collected from agricultural land which has been under intensive cropping and receiving irrigation through tube well water. Soil samples were varied widely in respect of physicochemical properties including metal content. Total Zn, Cu, Ni, Cd, and Pb in experimental soils were 2,015 ± 3,373, 236 ± 286, 103 ± 192, 29.8 ± 6.04, and 141 ± 270 mg kg(-1), respectively. Free metal ion activity, viz., pZn(2+), pCu(2+), pNi(2+), pCd(2+), and pPb(2+), as estimated by the Baker soil test was 9.37 ± 1.89, 13.1 ± 1.96, 12.8 ± 1.89, 11.9 ± 2.00, and 11.6 ± 1.52, respectively. Free metal ion activity was predicted by pH-dependent Freundlich equation (solubility model) as a function of pH, organic carbon, and extractable metal. Results indicate that solubility model as a function of pH, Walkley-Black carbon (WBC), and ethylenediaminetetraacetic acid (EDTA)-extractable metals could explain the variation in pZn(2+), pCu(2+), pNi(2+), pCd(2+), and pPb(2+) to the extent of 59, 56, 46, 52, and 51%, respectively. Predictability of the solubility model based on pH, KMnO4-oxidizable carbon, and diethylenetriaminepentaacetic acid-extractable or CaCl2-extractable metal was inferior compared to that based on EDTA-extractable metals and WBC.

Labile and stabilised fractions of soil organic carbon in some intensively cultivated alluvial soils.

The present investigation was undertaken in view of the limited information on the relative proportion of labile and stabilized fractions of soil organic carbon (SOC) in intensively cultivated lands, particularly under tropics. The specific objectives were i) to study the comparative recovery of SOC by different methods of labile carbon estimation under intensively cultivated lands and ii) to evaluate the impact of agricultural practices on carbon management index. For this purpose, in all, 105 surface soil samples were collected from intensively cultivated tube well and sewage irrigated agricultural lands. These samples were analysed for total as well as labile pools of SOC. Results indicated that Walkley and Black, KMnO4-oxidizable and microbial biomass carbon constituted the total SOC to the extent of 10.2 to 47.4, 1.66 to 23.2 and 0.30 to 5.49%, respectively with the corresponding mean values of 26.2, 9.16 and 2.15%. Lability of SOC was considerably higher in sewage irrigated soils than tube well irrigated soils under intensive cropping. Under soybean-wheat, the higher values of carbon management index (CMI) (279 and 286) were associated with the treatments where entire amount of nitrogen was supplied through FYM. Similar results were obtained under rice-wheat, whereas in case of maize-wheat the highest value of CMI was recorded under treatment receiving NPK through chemical fertilizer along with green manure. There was also a significant improvement in CMI under integrated (chemical fertilizer + organics) and chemical fertilizer-treated plots. The values of CMI ranged from 220 to 272 under cultivated lands receiving irrigation through sewage and industrial effluents.

A new approach to establish safe levels of available metals in soil with respect to potential health hazard of human.

Safe levels of extractable pollutant elements in soil have not been universally established. Prediction of metal solubility in polluted soils and the subsequent transfer of these metals from soil pore water to the human food supply via crops are required for effective risk assessment from polluted soils. Thus an attempt has been made to develop a novel approach to protect human health from exposure to toxic metals through assessing risk from metal polluted soils utilised for agriculture. In this study, we assess the relative efficacy of various forms of 'free ion activity model' (FIAM) for predicting the concentration of cadmium (Cd), lead (Pb), nickel (Ni), zinc (Zn) and copper (Cu) in spinach and wheat as example crops, thereby providing an assessment of risk to human health from consumption of these crops. Free metal ion activity in soil solution was estimated using the Windermere Humic Aqueous Model VII (WHAM-VII) and the Baker soil test. Approximately 91, 81, 75, 94 and 70% of the variability in Cd, Pb, Ni, Zn and Cu content, respectively, of spinach could be described by a FIAM using an estimate of the free ion activity of the metals provided by WHAM-VII. Owing to the different concentration of ethylenediamine tetraacetic acid (EDTA) and diethylenetriamine pentaacetic acid (DTPA) used in the present experiment, higher prediction coefficients were obtained using EDTA (0.05 M), rather than DTPA (0.005 M), as the metal extractant in an integrated solubility-FIAM model. Out of three formulations, the FIAM, based on free ion activity of metals in soil pore water, determined from solution extracted with Rhizon samplers, was distinctly superior to the other formulations in predicting metal uptake by spinach and wheat. A safe level of extractable metal in soil was prescribed using a hazard quotient derived from predicted plant metal content and estimated dietary intake of wheat and spinach by a human population. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1007/s12665-021-09988-7.

Prediction of free metal ion activity in contaminated soils using WHAM VII, baker soil test and solubility model.

Bioavailability and ecotoxicity of metals in contaminated soils depend largely on their solubility. The present investigation was carried out to predict the free ion activity of Zn2+, Cu2+, Ni2+, Pb2+ and Cd2+ in contaminated soils as a function of pH, organic carbon content and extractable metal concentration. Twenty-five composite soil samples were collected from various locations which had a history of receiving sewage sludge (Keshopur and IARI, Delhi), municipal solid waste (Kolkata, West Bengal), polluted river water (Madanpur, Delhi) and industrial effluents (Debari, Rajasthan and Sonepat, Haryana). Four composite soil samples were also collected from adjacent fields which had not received contaminated amendments. Free ion activities (-log10 values), viz. pZn2+, pCu2+, pNi2+, pPb2+ and pCd2+ as measured by the Baker soil test, were 10.1 ± 1.12, 13.4 ± 1.23, 12.9 ± 0.85, 11.6 ± 0.74 and 12.6 ± 2.26, respectively. Free metal ion activities were also determined using the geochemical speciation model WHAM-VII following extraction of soil solution with porous Rhizon samplers from the rhizosphere of growing plants. pH dependent Freundlich model based on soil properties could explain the variation in pZn2+, pCu2+, pNi2+, pPb2+ and pCd2+ to the extent of 84, 52, 73, 60 and 70%, respectively, in the case of data from Rhizon samplers coupled with speciation modelling. Whereas, C-Q model could explain 84, 57, 82, 72 and 74% variability in pZn2+, pCu2+, pNi2+, pPb2+ and pCd2+, respectively, based on soil properties and free metal ion activity as determined with integrated use of Rhizon-WHAM-VII. Modelling approach was superior compared to that based on the Baker soil test solution.

Pre-monsoon spatial distribution of available micronutrients and sulphur in surface soils and their management zones in Indian Indo-Gangetic Plain.

The efficient (site-specific) management of soil nutrients is possible by understanding the spatial variability in distribution of phyto-available nutrients (here after called available nutrients) and identifying the soil management zones (MZs) of agricultural landscapes. There is need for delineating soil MZs of agricultural landscapes of the world for efficient management of soil nutrients in order to obtain sustainability in crop yield. The present study was, therefore, undertaken to understand the spatial distribution pattern of available micronutrients (zinc (Zn), boron (B), iron (Fe), manganese (Mn) and copper (Cu)), available sulphur (S), and soil properties (soil acidity (pH), electrical conductivity (EC) and organic carbon (SOC) content) in soils of intensively cultivated Indo-Gangetic Plain (IGP) of India and to delineate soil MZs for efficient management of soil nutrients. Totally, 55101 soil samples from 0-15 cm depth were obtained from 167 districts of IGP during 2014 to 2017 and were analysed for different soil parameters. Soil pH, EC and SOC content varied from 4.44 to 9.80, 0.02 to 2.13 dS m-1 and 0.10 to 1.99%, respectively. The concentration of available Zn, B, Fe, Mn, Cu and S varied from 0.01 to 3.27, 0.01 to 3.51, 0.19 to 55.7, 0.05 to 49.0, 0.01 to 5.29 and 1.01 to 108 mg kg-1, respectively. Geostatistical analysis resulted in varied distribution pattern of studied soil parameters with moderate to strong spatial dependence. The extent (% area) of nutrient deficiencies in IGP followed the order: S > Zn > B > Mn > Cu > Fe. Principal component analysis and fuzzy c-means clustering produced six distinctly different soil MZs of IGP for implementation of zone-specific soil nutrient management strategies for attaining sustainability in crop yield. The developed MZ maps could also be utilized for prioritization and rationalization of nutrients supply in IGP of India.

Serum zinc, copper and iron status of children with coeliac disease on three months of gluten-free diet with or without four weeks of zinc supplements: a randomised controlled trial.

Data about the effect of zinc supplementation with gluten-free diet on normalisation of plasma zinc, copper and iron in patients with coeliac disease are scanty. We evaluated the effect of zinc supplementation on serum zinc, copper and iron levels in patients with coeliac disease, by randomising 71 children newly diagnosed with coeliac disease into two groups: Group A = gluten-free diet (GFD); and Group B = gluten-free diet with zinc supplements (GFD +Zn). The rise in iron and zinc was significantly higher in the latter, but the mean rise of copper levels was slightly higher in the former, but the difference was not significant.

A direct comparison of biological response modulation and clinical side effects by interferon-beta ser, interferon-gamma, or the combination of interferons beta ser and gamma in humans.

To directly compare clinical side effects and biological response modification, IFN-beta ser, IFN-gamma, or the combination of IFN-beta ser plus IFN-gamma was administered to 21 cancer patients. Each IFN or the combination was given intravenously on days 1, 8, and 15 in varied order. Each IFN and the combination resulted in significant (P less than 0.05) modulation of IFN-induced proteins. IFN-beta ser was more effective than IFN-gamma in enhancing 2-5A synthetase activity (P = 0.001). IFN-gamma was more effective than IFN-beta ser in enhancing serum beta 2 microglobulin expression (P = 0.05) and indoleamine dioxygenase activity, as assessed by decreased serum tryptophan (P = 0.03). The combination enhanced tryptophan catabolism more effectively than IFN-beta ser in a dose-dependent manner (P less than 0.03). IFN-beta ser/IFN-gamma did not potentiate natural killer cells or antibody-dependent cellular toxicity (ADCC). IFN-beta ser/IFN-gamma enhanced monocyte guanylate cyclase activity, as assessed by serum neopterin, more effectively than IFN-gamma alone (P = 0.005). Both IFNs and the combination resulted in increases in HLA class II expression on monocytes. However, no significant difference in the level of induction of HLA DQ and HLA DR expression between IFN-beta ser/IFN-gamma and either IFN-beta ser or IFN-gamma was noted. Although frequency and servity of side effects of IFN-beta ser, IFN-gamma, or the combination were dose related, induction of induced proteins (with exception of influences on tryptophan catabolism) were not a function of dose administered over the 10-fold range. Continued treatment with the combination intravenously three times a week for 4 wk sustained but did not further potentiate, most of the changes in interferon-induced proteins. Thus, IFN-beta ser and IFN-gamma each resulted in effective and essentially equivalent patterns of induction of induced proteins. When combined, however, these IFNs did not result in potentiation of biological response modification in vivo.

Human biologic response modification by interferon in the absence of measurable serum concentrations: a comparative trial of subcutaneous and intravenous interferon-beta serine.

The effect on a range of biologic responses of interferon-beta serine (IFN-beta ser), administered by either the sc or the iv route, was examined in 16 patients. Despite the absence of IFN in the serum of 13 of 16 patients after sc administration, biologic changes associated with IFN administration occurred. Significant increases in peripheral mononuclear cell surface proteins were evident. Monocyte human leukocyte antigen-DR (HLA-DR) showed a 23% increase in mean fluorescent intensity (P = .04) and a 9% increase in percentage of positive cells (P = .02); lymphocyte OKT10 had an 11% increase in percentage of positive cells (P less than .0001) and a 26% increase in mean fluorescent intensity (P = .002). Natural killer cell activity against the Change target increased by 125% (P = .004). Intracellular activity of 2',5'-oligoadenylate synthetase increased 297% at 24 hours and 226% at 48 hours (P less than .0001). Significant increases in serum concentrations of beta 2 microglobulin (24% at 24 hr and 27% at 48 hr, P less than .0001) and neopterin (85%, P = .0001 and 165%, P = .00001) were observed. These alterations after sc administration were similar quantitatively to those resulting from the same dose of IFN-beta ser given iv. Thus, serum IFN concentrations did not have to be measurable for IFN-beta ser to exert biologic activity. The different effects of two dose levels, 45 X 10(6) IU and 180 X 10(6) IU, also were compared independent of route. The higher dose resulted in greater increases over baseline of 2',5'-oligoadenylate synthetase activity (344% vs. 145% at 24 hr; 231% vs. 83% at 48 hr) and serum neopterin concentrations (185% vs. 99% at 24 hr; 271% vs. 153% at 48 hr). For all the other parameters, there was no significant difference between the two doses.

Long-term impact of sewage irrigation on soil properties and assessing risk in relation to transfer of metals to human food chain.

A case study was undertaken to assess the risk of sewage-irrigated soils in relation to the transfer of trace elements to rice and wheat grain. For this purpose, peri-urban agricultural lands under the Keshopur Effluent Irrigation Scheme (KEIS) of Delhi were selected. These agricultural lands have been receiving irrigation through sewage effluents since 1979. Sewage effluent, groundwater, soil, and plant (rice and wheat grain) samples were collected with GPS coordinates from this peri-urban area. Under wheat crop, sewage irrigation for four decades resulted into a significant buildup of zinc (141 %), copper (219 %), iron (514 %), nickel (75.0 %), and lead (28.1 %) in sewage-irrigated soils over adjacent tube well water-irrigated ones. Under rice crop, there was also a significant buildup of phosphorus (339 %), sulfur (130 %), zinc (287 %), copper (352 %), iron (457 %), nickel (258 %), lead (136 %), and cadmium (147 %) in sewage-irrigated soils as compared to that of tube well water-irrigated soils. The values of hazard quotient (HQ) for intake of trace toxic elements by humans through consumption of rice and wheat grain grown on these sewage-irrigated soils were well within the safe permissible limit. The variation in Zn, Ni, and Cd content in wheat grain could be explained by solubility-free ion activity model (FIAM) to the extent of 50.1, 56.8, and 37.2 %, respectively. Corresponding values for rice grain were 49.9, 41.2, and 42.7 %, respectively. As high as 36.4 % variation in As content in rice grain could be explained by solubility-FIAM model. Toxic limit of extractable Cd and As in soil for rice in relation to soil properties and human health hazard associated with consumption of rice grain by humans was established. A similar exercise was also done in respect of Cd for wheat. The conceptual framework of fixing the toxic limit of extractable metals and metalloid in soils with respect to soil properties and human health hazard under the modeling framework was established.

Implications of interferon-induced tryptophan catabolism in cancer, auto-immune diseases and AIDS.

Tryptophan (Trp) is an indispensable amino acid required for biosynthesis of proteins, serotonin and niacin. Indoleamine 2,3-dioxygenase (IDO) is induced by infections, viruses, lipopolysaccharides, or interferons (IFNs) and this results in significant catabolism of Trp along the kynurenine (Kyn) pathway. Intracellular growth of Toxoplasma gondii and Chlamydia psittaci in human fibroblasts in vitro is inhibited by IFN-gamma and this inhibition is negated by extra Trp in the medium. Similarly, growth of a number of human cell lines in vitro is inhibited by IFN-gamma and addition of extra Trp restores growth. Thus, in some in vitro systems, antiproliferative effects of IFN-gamma are mediated by induced depletion of Trp. We find that cancer patients given Type I or Type II IFNs can induce IDO which results in decreased serum Trp levels (20-50% of pretreatment) and increased urinary metabolites of the Kyn pathway (5 to 500 fold of pretreatment). We speculate that in vivo antineoplastic effects of IFNs and clinical side effects are mediated, at least in part, by a general or localized depletion of Trp. In view of reported increases of IFNs in autoimmune diseases and our earlier findings of elevated urinary Trp metabolites in autoimmune diseases, it seems likely that systemic or local depletion of Trp occurs in autoimmune diseases and may relate to degeneration, wasting and other symptoms in such diseases. We find high levels of IDO in cells isolated from synovia of arthritic joints. IFNs are also elevated in human immunodeficiency virus (HIV) patients and increasing IFN levels are associated with a worsening prognosis. We propose that IDO is induced chronically by HIV infection, is further increased by opportunistic infections, and that this chronic loss of Trp initiates mechanisms responsible for the cachexia, dementia, diarrhea and possibly immunosuppression of AIDS patients. In these symptoms, AIDS resembles classical pellagra due to dietary deficiency of Trp and niacin. In preliminary studies, others report low levels of Trp and serotonin, and elevated levels of Kyn and quinolinic acid in AIDS patients. The implications of these data in cancer, autoimmune diseases and AIDS are discussed.