Efficient Pre-Processing of Single-Cell Assay for Transposase Accessible Chromatin with High-Throughput Sequencing Data

The primary tool currently used to pre-process 10X chromium single-cell ATAC-seq data is Cell Ranger, which can take very long to run on standard datasets. To facilitate rapid pre-processing that enables reproducible workflows, we present a suite of tools called scATAK for pre-processing single-cell ATAC-seq data that is 15 to 18 times faster than Cell Ranger on mouse and human samples. Our tool can also calculate chromatin interaction potential matrices and generate open chromatin signal and interaction traces for cell groups. We use scATAK tool to explore the chromatin regulatory landscape of a healthy adult human brain and unveil cell-type specific features, and show that it provides a convenient and computational efficient approach for pre-processing single-cell ATAC-seq data.

Modeling of Cobalt-Chromium-Molybdenum Alloy Implant for Fractured Distal Femur

Distal femur fractures are the cause of abnormal gloomy. Several types of surgical treatments have been adopted by the practitioners to restore the fractured region of distal femur. Still within this domain of study, unstable fixation remains a challenge for orthopedists. In the present study, a fixation implant is designed and analyzed under physiological loading conditions for cobalt-chromium-molybdenum alloy (Co-Cr-Mo). It has been found that the stresses and deformation developed are quite low. It means that customized fixation plates will provide stable fixation resulting in improved fracture union.

Chemical Leaching of Metals from Landfill’s Fine Fraction

Leaching of heavy metals (chromium, zinc, copper) from the fine fraction of the Torma landfill (Estonia) was investigated. The leaching kinetics studies have determined the dependence of some metal’s concentration on the leaching time. Metals were leached with Aqua Regia, distilled water and EDTA (Ethylenediaminetetraacetic acid); process was most intensive 2 hours after the start of the experiment, except for copper with EDTA (0.5 h) and lead with EDTA (4 h). During leaching, steady concentrations of Fe, Mn, Cd and Pb were fully stabilized after 8 h; however concentrations of Cu and Ni were not stabilized after 10 h.

Surface Water Pollution by Open Refuse Dumpsite in North Central of Nigeria

Water is a vital resource that is important in ensuring the growth and development of any country. To sustain the basic human needs and the demands for agriculture, industry, conservational and ecosystem, enough quality and quantity water is needed. Contamination of water resources is now a global and public health concern. Hence, this study assessed the water quality of Ndawuse River by measuring the physicochemical parameters and heavy metals concentrations of the river using standard methods. In total, 16 surface water samples were obtained from five locations along the river, from upstream to downstream as well as samples from the dumpsite. The results obtained were compared with the standard limits set by both the World Health Organization and the Federal Environmental Protection Agency for domestic purposes. The results of the measured parameters indicated that biological oxygen demand (85.88 mg/L), turbidity (44.51 NTU), Iron (0.014 - 3.511 mg /L) and chromium (0.078 - 0.14 mg /L) were all above the standard limits. The results further showed that the quality of surface water is being significantly affected by human activities around the Ndawuse River which could pose an adverse health risk to several communities that rely on this river as their primary source of water. Therefore, there is a need for strict enforcement of environmental laws to protect the aquatic ecosystem and to avoid long term cumulative exposure risk that heavy metals may pose on human health.

Formation of Protective Aluminum-Oxide Layer on the Surface of Fe-Cr-Al Sintered-Metal-Fibers via Multi-Stage Thermal Oxidation

The objective of this paper is to investigate the formation and adhesion of a protective aluminum-oxide (Al2O3, alumina) layer on the surface of Iron-Chromium-Aluminum Alloy (Fe-Cr-Al) sintered-metal-fibers. The oxide-scale layer was developed via multi-stage thermal oxidation at 930 oC for 1 hour, followed by 1 hour at 960 oC, and finally at 990 oC for 2 hours. Scanning Electron Microscope (SEM) images show that the multi-stage thermal oxidation resulted in the formation of predominantly Al2O3 platelets-like and whiskers. SEM images also reveal non-uniform oxide-scale growth on the surface of the fibers. Furthermore, peeling/spalling of the alumina protective layer occurred after minimum handling, which indicates weak adhesion forces between the protective layer and the base metal alloy.  Energy Dispersive Spectroscopy (EDS) analysis of the heat-treated Fe-Cr-Al sintered-metal-fibers confirmed the high aluminum content on the surface of the protective layer, and the low aluminum content on the exposed base metal alloy surface. In conclusion, the failure of the oxide-scale protective layer exposes the base metal alloy to further oxidation, and the fragile non-uniform oxide-scale is not suitable as a support for catalysts.

Geostatistical Analysis of Contamination of Soils in an Urban Area in Ghana

Urbanization remains one of the unique predominant factors which is linked to the destruction of urban environment and its associated cases of soil contamination by heavy metals through the natural and anthropogenic activities. These activities are important sources of toxic heavy metals such as arsenic (As), cadmium (Cd), chromium (Cr), copper (Cu), iron (Fe), manganese (Mn), and lead (Pb), nickel (Ni) and zinc (Zn). Often, these heavy metals lead to increased levels in some areas due to the impact of atmospheric deposition caused by their proximity to industrial plants or the indiscriminately burning of substances. Information gathered on potentially hazardous levels of these heavy metals in soils leads to establish serious health and urban agriculture implications. However, characterization of spatial variations of soil contamination by heavy metals in Ghana is limited. Kumasi is a Metropolitan city in Ghana, West Africa and is challenged with the recent spate of deteriorating soil quality due to rapid economic development and other human activities such as “Galamsey”, illegal mining operations within the metropolis. The paper seeks to use both univariate and multivariate geostatistical techniques to assess the spatial distribution of heavy metals in soils and the potential risk associated with ingestion of sources of soil contamination in the Metropolis. Geostatistical tools have the ability to detect changes in correlation structure and how a good knowledge of the study area can help to explain the different scales of variation detected. To achieve this task, point referenced data on heavy metals measured from topsoil samples in a previous study, were collected at various locations. Linear models of regionalisation and coregionalisation were fitted to all experimental semivariograms to describe the spatial dependence between the topsoil heavy metals at different spatial scales, which led to ordinary kriging and cokriging at unsampled locations and production of risk maps of soil contamination by these heavy metals. Results obtained from both the univariate and multivariate semivariogram models showed strong spatial dependence with range of autocorrelations ranging from 100 to 300 meters. The risk maps produced show strong spatial heterogeneity for almost all the soil heavy metals with extremely risk of contamination found close to areas with commercial and industrial activities. Hence, ongoing pollution interventions should be geared towards these highly risk areas for efficient management of soil contamination to avert further pollution in the metropolis.

Erosion in Abrasive Jet Nozzles: A Comprehensive Study

Abrasive jet machining is one of the promising non-traditional machining processes which uses mechanical energy (pressure and velocity) for machining various materials. The process parameters that influence the metal removal rate are kerfs, surface finish, depth of cut, air pressure, and distance between nozzle and work piece, nozzle diameter, abrasive type, abrasive shape, and mass flow rate of abrasive particles. The abrasive particles coming out with high pressure not only hits work surface but also passes through the nozzle resulting in erosion. This paper focuses mainly on the effect of different parameters on the erosion of nozzle in Abrasive jet machining. Three different types of nozzles made of sapphire, tungsten carbide, and high carbon high chromium steel (HCHCS) are used for machining glass and the erosion of these nozzles are calculated. The results are shown in tabular form and graphical representation.

Examination of Internally and Externally Coated Cr3C2 Exhaust Pipe of a Diesel Engine via Plasma Spray Method

In this experimental study; internal and external parts of an exhaust pipe were coated with a chromium carbide (Cr3C2) material having a thickness of 100 micron by using the plasma spray method. A diesel engine was used as the test engine. Thus, the results of continuing chemical reaction in coated and uncoated exhaust pipes were investigated. Internally and externally coated exhaust pipe was compared with the standard exhaust system. External heat transfer occurring as a result of coating the internal and external parts of the exhaust pipe was reduced and its effects on harmful exhaust emissions were investigated. As a result of the experiments; a remarkable improvement was determined in emission values as a result of delay in cooling of exhaust gases due to the coating.

Human Health Risk Assessment from Metals Present in a Soil Contaminated by Crude Oil

The main sources of soil pollution due to petroleum contaminants are industrial processes involve crude oil. Soil polluted with crude oil is toxic for plants, animals, and humans. Human exposure to the contaminated soil occurs through different exposure pathways: Soil ingestion, diet, inhalation, and dermal contact. The present study research is focused on soil contamination with heavy metals as a consequence of soil pollution with petroleum products. Human exposure pathways considered are: Accidentally ingestion of contaminated soil and dermal contact. The purpose of the paper is to identify the human health risk (carcinogenic risk) from soil contaminated with heavy metals. The human exposure and risk were evaluated for five contaminants of concern of the eleven which were identified in soil. Two soil samples were collected from a bioremediation platform from Muntenia Region of Romania. The soil deposited on the bioremediation platform was contaminated through extraction and oil processing. For the research work, two average soil samples from two different plots were analyzed: The first one was slightly contaminated with petroleum products (Total Petroleum Hydrocarbons (TPH) in soil was 1420 mg/kgd.w.), while the second one was highly contaminated (TPH in soil was 24306 mg/kgd.w.). In order to evaluate risks posed by heavy metals due soil pollution with petroleum products, five metals known as carcinogenic were investigated: Arsenic (As), Cadmium (Cd), ChromiumVI (CrVI), Nickel (Ni), and Lead (Pb). Results of the chemical analysis performed on samples collected from the contaminated soil evidence soil contamination with heavy metals as following: As in Site 1 = 6.96 mg/kgd.w; As in Site 2 = 11.62 mg/kgd.w, Cd in Site 1 = 0.9 mg/kgd.w; Cd in Site 2 = 1 mg/kgd.w; CrVI was 0.1 mg/kgd.w for both sites; Ni in Site 1 = 37.00 mg/kgd.w; Ni in Site 2 = 42.46 mg/kgd.w; Pb in Site 1 = 34.67 mg/kgd.w; Pb in Site 2 = 120.44 mg/kgd.w. The concentrations for these metals exceed the normal values established in the Romanian regulation, but are smaller than the alert level for a less sensitive use of soil (industrial). Although, the concentrations do not exceed the thresholds, the next step was to assess the human health risk posed by soil contamination with these heavy metals. Results for risk were compared with the acceptable one (10-6, according to World Human Organization). As, expected, the highest risk was identified for the soil with a higher degree of contamination: Individual Risk (IR) was 1.11×10-5 compared with 8.61×10-6. 

Thermo-Mechanical Treatment of Chromium Alloyed Low Carbon Steel

Thermo-mechanical processing with various processing parameters was applied to 0.2%C-0.6%Mn-2S%i-0.8%Cr low alloyed high strength steel. The aim of the processing was to achieve the microstructures typical for transformation induced plasticity (TRIP) steels. Thermo-mechanical processing used in this work incorporated two or three deformation steps. The deformations were in all the cases carried out during the cooling from soaking temperatures to various bainite hold temperatures. In this way, 4-10% of retained austenite were retained in the final microstructures, consisting further of ferrite, bainite, martensite and pearlite. The complex character of TRIP steel microstructure is responsible for its good strength and ductility. The strengths achieved in this work were in the range of 740 MPa – 836 MPa with ductility A5mm of 31-41%.

Studies on Bioaccumulation of 51Cr by Ulva sp. and Ruppia maritima

This study aims at contributing to the characterization of the process of biological incorporation of chromium by two benthonic species, the macroalgae Ulva sp. and the aquatic macrophyte Ruppia maritima, to subsidize future activities of monitoring the contamination of aquatic biota. This study is based on laboratory experiments to characterize the incorporation kinetics of the radiotracer 51Cr in two oxidation states (III and VI), under different salinities (7, 15, and 21 ‰). Samples of two benthonic species were collected on the margins of Rodrigo de Freitas Lagoon (Rio de Janeiro, Brazil), acclimated in the laboratory and subsequently subjected to experiments. In tests with 51Cr (III and IV), it was observed that accumulation of the metal in Ulva sp. has inverse relationship with salinity, while for R. maritima, the maximum accumulation occurs in salinity 21‰. In experiments with Cr(III), increases in the uptake of ion by both species were verified. The activity of Cr(III) was up to 19 times greater than the Cr(VI). As regards the potential for accumulation of metals, a better sensitivity of Ulva sp. for any chromium tri or hexavalent forms was verified, while for the Cr(VI) it will require low salinities and longer exposure (>24h). For R. maritima, the results showed the uptake of Cr(VI) increase along with time (>20h), because this species is more resistant for the hexavalent form and useful for any salinity as well.

High Temperature Oxidation of Cr-Steel Interconnects in Solid Oxide Fuel Cells

Solid Oxide Fuel Cell (SOFC) is a promising solution for the energy resources leakage. Ferritic stainless steel becomes a suitable candidate for the SOFCs interconnects due to the recent advancements. Different steel alloys were designed to satisfy the needed characteristics in SOFCs interconnect as conductivity, thermal expansion and corrosion resistance. Refractory elements were used as alloying elements to satisfy the needed properties. The oxidation behaviour of the developed alloys was studied where the samples were heated for long time period at the maximum operating temperature to simulate the real working conditions. The formed scale and oxidized surface were investigated by SEM. Microstructure examination was carried out for some selected steel grades. The effect of alloying elements on the behaviour of the proposed interconnects material and the performance during the working conditions of the cells are explored and discussed. Refractory metals alloying of chromium steel seems to satisfy the needed characteristics in metallic interconnects.

Phytoremediation Potential of Tomato for Cd and Cr Removal from Polluted Soils

Cadmium and chromium are toxic to most organisms and different mechanisms have been developed for overcoming with the toxic effects of these heavy metals. We studied the uptake and distribution of cadmium and chromium in different organs of tomato (Lycopersicon esculentum L.) plants in nine heavy metal polluted soils in western Hormozgan province, Iran. The accumulation of chromium was in increasing pattern of fruit peel

Decontamination of Chromium Containing Ground Water by Adsorption Using Chemically Modified Activated Carbon Fabric

Chromium in the environment is considered as one of the most toxic elements probably next only to mercury and arsenic. It is acutely toxic, mutagenic and carcinogenic in the environment. Chromium contamination of soil and underground water due to industrial activities is a very serious problem in several parts of India covering Karnataka, Tamil Nadu, Andhra Pradesh etc. Functionally modified Activated Carbon Fabrics (ACF) offer targeted chromium removal from drinking water and industrial effluents. Activated carbon fabric is a light weight adsorbing material with high surface area and low resistance to fluid flow. We have investigated surface modification of ACF using various acids in the laboratory through batch as well as through continuous flow column experiments with a view to develop the optimum conditions for chromium removal. Among the various acids investigated, phosphoric acid modified ACF gave best results with a removal efficiency of 95% under optimum conditions. Optimum pH was around 2 – 4 with 2 hours contact time. Continuous column experiments with an effective bed contact time (EBCT) of 5 minutes indicated that breakthrough occurred after 300 bed volumes. Adsorption data followed a Freundlich isotherm pattern. Nickel adsorbs preferentially and sulphate reduces chromium adsorption by 50%. The ACF could be regenerated up to 52.3% using 3 M NaOH under optimal conditions. The process is simple, economical, energy efficient and applicable to industrial effluents and drinking water.

Effects of Cellular Insulin Receptor Stimulators with Alkaline Water on Performance, Plasma Cholesterol, Glucose, Triglyceride Levels and Hatchability in Breeding Japanese Quail

Aim of this study is to determine the effects of cellular insulin receptor stimulators on performance, plasma glucose, high density lipoprotein (HDL), low density lipoprotein (LDL), total cholesterol, triglyceride, triiodothyronine (T3) and thyroxine (T4) hormone levels, and incubation features in the breeding Japanese quails (Coturnix japonica). In the study, a total of 84 breeding quails was used, 6 weeks’ age, 24 are male and 60, female. Rations used in experiment are 2900 kcal/kg metabolic energy and 20% crude protein. Water pH is calibrated to 7.45. Ration and water were administered ad-libitum to the animals. As metformin source, metformin-HCl was used and as chrome resource, chromium picolinate was used. Trial groups were formed as control group (basal ration), metformin group (basal ration, added metformin at the level of feed of 20 mg/kg), and chromium picolinate (basal ration, added feed of 1500 ppb Cr) group. When regarded to the results of performance at the end of experiment, it is seen that live weight gain, feed consumption, egg weight, feed conversion ratio (Feed consumption/ egg weight), and egg production were affected at the significant level (p < 0.05). When the results are evaluated in terms of incubation features, hatchability and hatchability of fertile egg ratio were not affected from the treatments. Fertility ratio was significantly affected by metformin and chromium picolinate treatments and fertility rose at the significant level compared to control group (p < 0.05). According to results of experiment, plasma glucose level was not affected by metformin and chromium picolinate treatments. Plasma, total cholesterol, HDL, LDL, and triglyceride levels were significantly affected from insulin receptor stimulators added to ration (p < 0.05). Hormone level of Plasma T3 and T4 were also affected at the significant level from insulin receptor stimulators added to ration (p < 0.05).

Beneficiation of Low Grade Chromite Ore and Its Characterization for the Formation of Magnesia-Chromite Refractory by Economically Viable Process

Chromite ores are primarily used for extraction of chromium, which is an expensive metal. For low grade chromite ores (containing less than 40% Cr2O3), the chromium extraction is not usually economically viable. India possesses huge quantities of low grade chromite reserves. This deposit can be utilized after proper physical beneficiation. Magnetic separation techniques may be useful after reduction for the beneficiation of low grade chromite ore. The sample collected from the sukinda mines is characterized by XRD which shows predominant phases like maghemite, chromite, silica, magnesia and alumina. The raw ore is crushed and ground to below 75 micrometer size. The microstructure of the ore shows that the chromite grains surrounded by a silicate matrix and porosity observed the exposed side of the chromite ore. However, this ore may be utilized in refractory applications. Chromite ores contain Cr2O3, FeO, Al2O3 and other oxides like Fe-Cr, Mg-Cr have a high tendency to form spinel compounds, which usually show high refractoriness. Initially, the low grade chromite ore (containing 34.8% Cr2O3) was reduced at 1200 0C for 80 minutes with 30% coke fines by weight, before being subjected to magnetic separation. The reduction by coke leads to conversion of higher state of iron oxides converted to lower state of iron oxides. The pre-reduced samples are then characterized by XRD. The magnetically inert mass was then reacted with 20% MgO by weight at 1450 0C for 2 hours. The resultant product was then tested for various refractoriness parameters like apparent porosity, slag resistance etc. The results were satisfactory, indicating that the resultant spinel compounds are suitable for refractory applications for elevated temperature processes.

Assessment of Heavy Metal Concentrations in Tunas Caught from Lakshweep Islands, India

The toxic metal contamination and their biomagnification in marine fishes is a serious public health concern specially, in the coastal areas and the small islands. In the present study, concentration of toxic heavy metals like zinc (Zn), cadmium (Cd), lead (Pb), nickel (Ni), cobalt (Co), chromium (Cr) and mercury (Hg) were determined in the tissues of tunas (T. albacores) caught from the area near to Lakshdweep Islands. The heavy metals are one of the indicators for the marine water pollution. Geochemical weathering, industrialization, agriculture run off, fishing, shipping and oil spills are the major pollutants. The presence of heavy toxic metals in the near coastal water fishes at both western coast and eastern coast of India has been well established. The present study was conducted assuming that the distant island will not have the metals presence in a way it is at the near main land coast. However, our study shows that there is a significant amount of the toxic metals present in the tissues of tuna samples. The gill, lever and flash samples were collected in waters around Lakshdweep Islands. They were analyzed using ICP–AES for the toxic metals after microwave digestion. The concentrations of the toxic metals were found in all fish samples and the general trend of presence was in decreasing order as Zn > Al > Cd > Pb > Cr > Ni > Hg. The amount of metals was found to higher in fish having more weight.

Chromium-Leaching Study of Cements in Various Environments

Cement is a basic material used for building construction. Chromium as an indelible non-volatile trace element of raw materials occurs in cement clinker in the trivalent or hexavalent form. Hexavalent form of chromium is harmful and allergenic having very high water solubility and thus can easily come into contact with the human skin. The paper is aimed at analyzing the content of total chromium in Portland cements and leaching rate of hexavalent chromium in various leachants: Deionized water, Britton-Robinson buffer, used to simulate the natural environment, and hydrochloric acid (HCl). The concentration of total chromium in Portland cement samples was in a range from 173.2 to 218.5 mg/kg. The content of dissolved hexavalent chromium ranged 0.23-3.19, 2.0-5.78 and 8.88-16.25 mg/kg in deionized water, Britton-Robinson solution and hydrochloric acid, respectively. The calculated leachable fraction of Cr(VI) from cement samples was observed in the range 0.1--7.58 %.

Study on Metabolic and Mineral Balance, Oxidative Stress and Cardiovascular Risk Factors in Type 2 Diabetic Patients on Different Therapy

Intense oxidative stress, increased glycated hemoglobin and mineral imbalance represent risk factors for complications in diabetic patients. Cardiovascular complications are most common in these patients, including nephropathy. This study was conducted in 2015 at the Procardia Laboratory in Tîrgu Mureș, Romania on 40 type 2 diabetic adults. Routine biochemical tests were performed on the Konleab 20XTi analyzer (serum glucose, total cholesterol, LDL and HDL cholesterol, triglyceride, creatinine, urea). We also measured serum uric acid, magnesium and calcium concentration by photometric procedures, potassium, sodium and chloride by ion selective electrode, and chromium by atomic absorption spectrometry in a group of patients. Glycated hemoglobin (HbA1c) dosage was made by reflectometry. Urine analysis was performed using the HandUReader equipment. The level of oxidative stress was measured by serum malondialdehyde dosage using the thiobarbituric acid reactive substances method. MDRD (Modification of Diet in Renal Disease) formula was applied for calculation of creatinine-derived glomerular filtration rate. GraphPad InStat software was used for statistical analysis of the data. The diabetic subject included in the study presented high MDA concentrations, showing intense oxidative stress. Calcium was deficient in 5% of the patients, chromium deficiency was present in 28%. The atherogenic cholesterol fraction was elevated in 13% of the patients. Positive correlation was found between creatinine and MDRD-creatinine values (p

Risk Assessment of Trace Element Pollution in Gymea Bay, NSW, Australia

The main purpose of this study is to assess the sediment quality and potential ecological risk in marine sediments in Gymea Bay located in south Sydney, Australia. A total of 32 surface sediment samples were collected from the bay. Current track trajectories and velocities have also been measured in the bay. The resultant trace elements were compared with the adverse biological effect values Effect Range Low (ERL) and Effect Range Median (ERM) classifications. The results indicate that the average values of chromium, arsenic, copper, zinc, and lead in surface sediments all reveal low pollution levels and are below ERL and ERM values. The highest concentrations of trace elements were found close to discharge points and in the inner bay, and were linked with high percentages of clay minerals, pyrite and organic matter, which can play a significant role in trapping and accumulating these elements. The lowest concentrations of trace elements were found to be on the shoreline of the bay, which contained high percentages of sand fractions. It is postulated that the fine particles and trace elements are disturbed by currents and tides, then transported and deposited in deeper areas. The current track velocities recorded in Gymea Bay had the capability to transport fine particles and trace element pollution within the bay. As a result, hydrodynamic measurements were able to provide useful information and to help explain the distribution of sedimentary particles and geochemical properties. This may lead to knowledge transfer to other bay systems, including those in remote areas. These activities can be conducted at a low cost, and are therefore also transferrable to developing countries. The advent of portable instruments to measure trace elements in the field has also contributed to the development of these lower cost and easily applied methodologies available for use in remote locations and low-cost economies.