bluuebunny/crossref_metadata_2025 huggingface dataset:
Leishmania and the Model of Predominant Clonal Evolution
Authors: Tibayrenc Michel , Ayala Francisco J.
Published: November 2021

As it is the case for other pathogenic microorganisms, the respective impact of clonality and genetic exchange on Leishmania natural populations has been the object of lively debates since the early 1980s. The predominant clonal evolution (PCE) model states that genetic exchange in these parasites’ natural populations may have a high relevance on an evolutionary scale, but is not sufficient to erase a persistent phylogenetic signal and the existence of bifurcating trees. Recent data based on high-resolution markers and genomic polymorphisms fully confirm the PCE model down to a microevolutionary level.
Role of Bifidobacteria on Infant Health
Authors: Saturio Silvia , Nogacka Alicja M. , Alvarado-Jasso Guadalupe M. , Salazar Nuria , de los Reyes-Gavilán Clara G. , Gueimonde Miguel , Arboleya Silvia
Published: November 2021

Bifidobacteria are among the predominant microorganisms during infancy, being a dominant microbial group in the healthy breastfed infant and playing a crucial role in newborns and infant development. Not only the levels of the Bifidobacterium genus but also the profile and quantity of the different bifidobacterial species have been demonstrated to be of relevance to infant health. Although no definitive proof is available on the causal association, reduced levels of bifidobacteria are perhaps the most frequently observed alteration of the intestinal microbiota in infant diseases. Moreover, Bifidobacterium strains have been extensively studied by their probiotic attributes. This review compiles the available information about bifidobacterial composition and function since the beginning of life, describing different perinatal factors affecting them, and their implications on different health alterations in infancy. In addition, this review gathers exhaustive information about pre-clinical and clinical studies with Bifidobacterium strains as probiotics in neonates.
Potential of Acidithiobacillus ferrooxidans to Grow on and Bioleach Metals from Mars and Lunar Regolith Simulants under Simulated Microgravity Conditions
Authors: Kaksonen Anna H. , Deng Xiao , Morris Christina , Khaleque Himel Nahreen , Zea Luis , Gumulya Yosephine
Published: November 2021

The biomining microbes which extract metals from ores that have been applied in mining processes worldwide hold potential for harnessing space resources. Their cell growth and ability to extract metals from extraterrestrial minerals under microgravity environments, however, remains largely unknown. The present study used the model biomining bacterium Acidithiobacillus ferrooxidans to extract metals from lunar and Martian regolith simulants cultivated in a rotating clinostat with matched controls grown under the influence of terrestrial gravity. Analyses included assessments of final cell count, size, morphology, and soluble metal concentrations. Under Earth gravity, with the addition of Fe3+ and H2/CO2, A. ferrooxidans grew in the presence of regolith simulants to a final cell density comparable to controls without regoliths. The simulated microgravity appeared to enable cells to grow to a higher cell density in the presence of lunar regolith simulants. Clinostat cultures of A. ferrooxidans solubilised higher amounts of Si, Mn and Mg from lunar and Martian regolith simulants than abiotic controls. Electron microscopy observations revealed that microgravity stimulated the biosynthesis of intracellular nanoparticles (most likely magnetite) in anaerobically grown A. ferrooxidans cells. These results suggested that A. ferrooxidans has the potential for metal bioleaching and the production of useful nanoparticles in space.
Genomic Insights into Denitrifying Methane-Oxidizing Bacteria Gemmobacter fulva sp. Nov., Isolated from an Anabaena Culture
Authors: Jin Long , Jin Chun-Zhi , Lee Hyung-Gwan , Lee Chang Soo
Published: November 2021

The genus Gemmobacter grows phototrophically, aerobically, or anaerobically, and utilizes methylated amine. Here, we present two high-quality complete genomes of the strains con4 and con5T isolated from a culture of Anabaena. The strains possess sMMO (soluble methane monooxygenase)-oxidizing alkanes to carbon dioxide. Functional genes for methane-oxidation (prmAC, mimBD, adh, gfa, fdh) were identified. The genome of strain con5T contains nirB, nirK, nirQ, norB, norC, and norG genes involved in dissimilatory nitrate reduction. The presence of nitrite reductase gene (nirK) and the nitric-oxide reductase gene (norB) indicates that it could potentially use nitrite as an electron acceptor in anoxic environments. Taxonomic investigations were also performed on two strains through polyphasic methods, proposing two isolates as a novel species of the genus Gemmobacter. The findings obtained through the whole genome analyses provide genome-based evidence of complete oxidation of methane to carbon dioxide. This study provides a genetic blueprint of Gemmobacter fulva con5T and its biochemical characteristics, which help us to understand the evolutionary biology of the genus Gemmobacter.
Microbial Community Dynamics during Biodegradation of Crude Oil and Its Response to Biostimulation in Svalbard Seawater at Low Temperature
Authors: Nõlvak Hiie , Dang Nga Phuong , Truu Marika , Peeb Angela , Tiirik Kertu , O’Sadnick Megan , Truu Jaak
Published: November 2021

The development of oil exploration activities and an increase in shipping in Arctic areas have increased the risk of oil spills in this cold marine environment. The objective of this experimental study was to assess the effect of biostimulation on microbial community abundance, structure, dynamics, and metabolic potential for oil hydrocarbon degradation in oil-contaminated Arctic seawater. The combination of amplicon-based and shotgun sequencing, together with the integration of genome-resolved metagenomics and omics data, was applied to assess microbial community structure and metabolic properties in naphthenic crude oil-amended microcosms. The comparison of estimates for oil-degrading microbial taxa obtained with different sequencing and taxonomic assignment methods showed substantial discrepancies between applied methods. Consequently, the data acquired with different methods was integrated for the analysis of microbial community structure, and amended with quantitative PCR, producing a more objective description of microbial community dynamics and evaluation of the effect of biostimulation on particular microbial taxa. Implementing biostimulation of the seawater microbial community with the addition of nutrients resulted in substantially elevated prokaryotic community abundance (103-fold), a distinctly different bacterial community structure from that in the initial seawater, 1.3-fold elevation in the normalized abundance of hydrocarbon degradation genes, and 12% enhancement of crude oil biodegradation. The bacterial communities in biostimulated microcosms after four months of incubation were dominated by Gammaproteobacterial genera Pseudomonas, Marinomonas, and Oleispira, which were succeeded by Cycloclasticus and Paraperlucidibaca after eight months of incubation. The majority of 195 compiled good-quality metagenome-assembled genomes (MAGs) exhibited diverse hydrocarbon degradation gene profiles. The results reveal that biostimulation with nutrients promotes naphthenic oil degradation in Arctic seawater, but this strategy alone might not be sufficient to effectively achieve bioremediation goals within a reasonable timeframe.
PHA Production from Cheese Whey and “Scotta”: Comparison between a Consortium and a Pure Culture of Leuconostoc mesenteroides
Authors: Bosco Francesca , Cirrincione Simona , Carletto Riccardo , Marmo Luca , Chiesa Francesco , Mazzoli Roberto , Pessione Enrica
Published: November 2021

It is urgent to expand the market of biodegradable alternatives to oil-derived plastics owing to (i) increasingly limited oil availability/accessibility, and (ii) the dramatic impact of traditional plastics on aquatic life, the food chain, all Earth ecosystems, and ultimately, human health. Polyhydroxyalkanoates (PHAs) are promising biodegradable polymers that can be obtained through microbial fermentation of agro-industrial byproducts, e.g., milk and cheese whey. Here, the PHA-accumulating efficiency of a mixed microbial culture (MMC, derived from activated sludges) grown on dairy byproducts (cheese and scotta whey) was measured. Bioreactor tests featuring temperature and pH control showed that both scotta and pre-treated Toma cheese whey could be used for PHA production by MMC, although scotta cheese whey supported higher PHA yield and productivity. The advantages of open MMCs include their plasticity and versatility to fast changing conditions; furthermore, no growth-medium sterilization is needed prior to fermentation. However, the use of pure cultures of efficient PHA producers may support better metabolic performances. Therefore, PHA-producing strains were isolated from a MMC, leading to the satisfactory identification of two bacterial strains, Citrobacter freundii and Leuconostoc spp., whose ability to accumulate PHAs in synthetic media was confirmed. A more detailed investigation by mass spectrometry revealed that the strain was L. mesenteroides. Although the validation of L. mesenteroides potential to produce PHA through fermentation of agro-industrial byproducts requires further investigations, this is the first study reporting PHA production with the Leuconostoc genus.
Comparative Genomics across Three Ensifer Species Using a New Complete Genome Sequence of the Medicago Symbiont Sinorhizobium (Ensifer) meliloti WSM1022
Authors: Baxter Laura , Roy Proyash , Picot Emma , Watts Jess , Jones Alex , Wilkinson Helen , Schäfer Patrick , Gifford Miriam , Lagunas Beatriz
Published: November 2021

Here, we report an improved and complete genome sequence of Sinorhizobium (Ensifer) meliloti strain WSM1022, a microsymbiont of Medicago species, revealing its tripartite structure. This improved genome sequence was generated combining Illumina and Oxford nanopore sequencing technologies to better understand the symbiotic properties of the bacterium. The 6.75 Mb WSM1022 genome consists of three scaffolds, corresponding to a chromosome (3.70 Mb) and the pSymA (1.38 Mb) and pSymB (1.66 Mb) megaplasmids. The assembly has an average GC content of 62.2% and a mean coverage of 77X. Genome annotation of WSM1022 predicted 6058 protein coding sequences (CDSs), 202 pseudogenes, 9 rRNAs (3 each of 5S, 16S, and 23S), 55 tRNAs, and 4 ncRNAs. We compared the genome of WSM1022 to two other rhizobial strains, closely related Sinorhizobium (Ensifer) meliloti Sm1021 and Sinorhizobium (Ensifer) medicae WSM419. Both WSM1022 and WSM419 species are high-efficiency rhizobial strains when in symbiosis with Medicago truncatula, whereas Sm1021 is ineffective. Our findings report significant genomic differences across the three strains with some similarities between the meliloti strains and some others between the high efficiency strains WSM1022 and WSM419. The addition of this high-quality rhizobial genome sequence in conjunction with comparative analyses will help to unravel the features that make a rhizobial symbiont highly efficient for nitrogen fixation.
Effect of Nutrition on Age-Related Metabolic Markers and the Gut Microbiota in Cats
Authors: Ephraim Eden , Jewell Dennis E.
Published: November 2021

Age-related changes in the gut microbiota and metabolites are associated with the increased risk of detrimental conditions also seen with age. This study evaluated whether a test food with potential anti-aging benefits results in favorable changes in plasma and fecal metabolites and the fecal microbiota in senior cats. Forty healthy domestic cats aged 8.3–13.5 years were fed a washout food for 30 days, then control or test food for 30 days. After another 30-day washout, cats were switched to the other study food for 30 days. Assessment of plasma and fecal metabolites showed lower levels of metabolites associated with detrimental processes (e.g., uremic toxins) and higher levels of metabolites associated with beneficial processes (e.g., tocopherols) after cats consumed the test food compared with the control food. A shift toward proteolysis with the control food is supported by higher levels of amino acid metabolites and lower levels of carbohydrate metabolites. Operational taxonomic units of greater abundance with the test food positively correlated with carbohydrate and nicotinic acid metabolites, and negatively correlated with uremic toxins, amino acid metabolism, secondary bile salts, and branched-chain fatty acids. Taken together, the test food appears to result in greater levels of metabolites and microbiota associated with a healthier state.
Selection and Amplification of Fungicide Resistance in Aspergillus fumigatus in Relation to DMI Fungicide Use in Agronomic Settings: Hotspots versus Coldspots
Authors: Doughty Kevin J. , Sierotzki Helge , Semar Martin , Goertz Andreas
Published: November 2021

Aspergillus fumigatus is a ubiquitous saprophytic fungus. Inhalation of A. fumigatus spores can lead to Invasive Aspergillosis (IA) in people with weakened immune systems. The use of triazole antifungals with the demethylation inhibitor (DMI) mode of action to treat IA is being hampered by the spread of DMI-resistant “ARAf” (azole-resistant Aspergillus fumigatus) genotypes. DMIs are also used in the environment, for example, as fungicides to protect yield and quality in agronomic settings, which may lead to exposure of A. fumigatus to DMI residues. An agronomic setting can be a “hotspot” for ARAf if it provides a suitable substrate and favourable conditions for the growth of A. fumigatus in the presence of DMI fungicides at concentrations capable of selecting ARAf genotypes at the expense of the susceptible wild-type, followed by the release of predominantly resistant spores. Agronomic settings that do not provide these conditions are considered “coldspots". Identifying and mitigating hotspots will be key to securing the agronomic use of DMIs without compromising their use in medicine. We provide a review of studies of the prevalence of ARAf in various agronomic settings and discuss the mitigation options for confirmed hotspots, particularly those relating to the management of crop waste.
ABO Blood Groups Do Not Predict Schistosoma mansoni Infection Profiles in Highly Endemic Villages of Uganda
Authors: Francoeur Rachel , Atuhaire Alon , Arinaitwe Moses , Adriko Moses , Ajambo Diana , Nankasi Andrina , Babayan Simon , Lamberton Poppy
Published: November 2021

Schistosoma mansoni is a parasite which causes significant public-health issues, with over 240 million people infected globally. In Uganda alone, approximately 11.6 million people are affected. Despite over a decade of mass drug administration in this country, hyper-endemic hotspots persist, and individuals who are repeatedly heavily and rapidly reinfected are observed. Human blood-type antigens are known to play a role in the risk of infection for a variety of diseases, due to cross-reactivity between host antibodies and pathogenic antigens. There have been conflicting results on the effect of blood type on schistosomiasis infection and pathology. Moreover, the effect of blood type as a potential intrinsic host factor on S. mansoni prevalence, intensity, clearance, and reinfection dynamics and on co-infection risk remains unknown. Therefore, the epidemiological link between host blood type and S. mansoni infection dynamics was assessed in three hyper-endemic communities in Uganda. Longitudinal data incorporating repeated pretreatment S. mansoni infection intensities and clearance rates were used to analyse associations between blood groups in school-aged children. Soil-transmitted helminth coinfection status and biometric parameters were incorporated in a generalised linear mixed regression model including age, gender, and body mass index (BMI), which have previously been established as significant factors influencing the prevalence and intensity of schistosomiasis. The analysis revealed no associations between blood type and S. mansoni prevalence, infection intensity, clearance, reinfection, or coinfection. Variations in infection profiles were significantly different between the villages, and egg burden significantly decreased with age. While blood type has proven to be a predictor of several diseases, the data collected in this study indicate that it does not play a significant role in S. mansoni infection burdens in these high-endemicity communities.
A New ICEclc Subfamily Integrative and Conjugative Element Responsible for Horizontal Transfer of Biphenyl and Salicylic Acid Catabolic Pathway in the PCB-Degrading Strain Pseudomonas stutzeri KF716
Authors: Hirose Jun , Watanabe Takahito , Futagami Taiki , Fujihara Hidehiko , Kimura Nobutada , Suenaga Hikaru , Goto Masatoshi , Suyama Akiko , Furukawa Kensuke
Published: November 2021

Integrative and conjugative elements (ICEs) are chromosomally integrated self-transmissible mobile genetic elements. Although some ICEs are known to carry genes for the degradation of aromatic compounds, information on their genetic features is limited. We identified a new member of the ICEclc family carrying biphenyl catabolic bph genes and salicylic acid catabolic sal genes from the PCB-degrading strain Pseudomonas stutzeri KF716. The 117-kb ICEbph-salKF716 contains common core regions exhibiting homology with those of degradative ICEclc from P. knackmussii B13 and ICEXTD from Azoarcus sp. CIB. A comparison of the gene loci collected from the public database revealed that several putative ICEs from P. putida B6-2, P, alcaliphila JAB1, P. stutzeri AN10, and P. stutzeri 2A20 had highly conserved core regions with those of ICEbph-salKF716, along with the variable region that encodes the catabolic genes for biphenyl, naphthalene, toluene, or phenol. These data indicate that this type of ICE subfamily is ubiquitously distributed within aromatic compound-degrading bacteria. ICEbph-salKF716 was transferred from P. stutzeri KF716 to P. aeruginosa PAO1 via a circular extrachromosomal intermediate form. In this study, we describe the structure and genetic features of ICEbph-salKF716 compared to other catabolic ICEs.
Establishment Genes Present on pLS20 Family of Conjugative Plasmids Are Regulated in Two Different Ways
Authors: Val-Calvo Jorge , Miguel-Arribas Andrés , Freire Fernando , Abia David , Wu Ling Juan , Meijer Wilfried J.J.
Published: November 2021

During conjugation, a conjugative DNA element is transferred from a donor to a recipient cell via a connecting channel. Conjugation has clinical relevance because it is the major route for spreading antibiotic resistance and virulence genes. The conjugation process can be divided into different steps. The initial steps carried out in the donor cell culminate in the transfer of a single DNA strand (ssDNA) of the conjugative element into the recipient cell. However, stable settlement of the conjugative element in the new host requires at least two additional events: conversion of the transferred ssDNA into double-stranded DNA and inhibition of the hosts’ defence mechanisms to prevent degradation of the transferred DNA. The genes involved in this late step are historically referred to as establishment genes. The defence mechanisms of the host must be inactivated rapidly and—importantly—transiently, because prolonged inactivation would make the cell vulnerable to the attack of other foreign DNA, such as those of phages. Therefore, expression of the establishment genes in the recipient cell has to be rapid but transient. Here, we studied regulation of the establishment genes present on the four clades of the pLS20 family of conjugative plasmids harboured by different Bacillus species. Evidence is presented that two fundamentally different mechanisms regulate the establishment genes present on these plasmids. Identification of the regulatory sequences were critical in revealing the establishment regulons. Remarkably, whereas the conjugation genes involved in the early steps of the conjugation process are conserved and are located in a single large operon, the establishment genes are highly variable and organised in multiple operons. We propose that the mosaical distribution of establishment genes in multiple operons is directly related to the variability of defence genes encoded by the host bacterial chromosomes.
Geochemical Insights from Clinopyroxene Phenocrysts into the Magma Evolution of an Alkaline Magmatic System from the Sanshui Basin, South China
Authors: Chen Peijia , Fang Nianqiao , Yuan Xiaobo
Published: November 2021

The Sanshui Basin is located at the northern continental margin of the South China Sea and characterized by a continental rift basin. The bimodal volcanic rocks in Sanshui Basin record the early Cenozoic magmatic activity in the South China Block, but the magmatic evolution that produced the bimodal volcanic rocks is poorly understood. Clinopyroxenes in bimodal volcanic rocks in the Sanshui Basin provide an opportunity to investigate magma during magma ascent. In this work, we classified nine types of clinopyroxene phenocrysts according to composition and texture in cogenetic basalt-trachyandesite-comenditic trachyte, while the composition of unzoned clinopyroxene have an evolution sequence of diopside-hedenbergite-aegirine along with an increase in trace element contents with a decrease of Mg#, indicating that the genesis of clinopyroxene was dominated by fractional crystallization in a closed magma system. However, the clinopyroxenes with reversed zoning and multiple zoning record the process of magma mixing and recharge indicating an open magma system. While fractional crystallization is the dominant process, magma mixing, recharge, and crystal settling were also found to influence magma evolution. Thermobarometric calculations showed that clinopyroxene crystallized a several structural levels in the crust during magma ascent. In this study, we established a magma plumbing system that provides new constraints for the magma evolution in the Sanshui Basin.
Improvement in pH and Total Iron Concentration of Acid Mine Drainage after Backfilling: A Case Study of an Underground Abandoned Mine in Japan
Authors: Yamaguchi Kohei , Tomiyama Shingo , Igarashi Toshifumi , Yamagata Saburo , Ebato Masanori , Sakoda Masatoshi
Published: November 2021

If the excavated underground veins are not backfilled, they may be a factor in the continued outflow of acid mine drainage (AMD). The flow rate of AMD can be reduced by backfilling underground drifts from abandoned mines. In addition, the quality of AMD may be improved as the flow rate of AMD reduces. In this paper, the quality of the AMD after backfilling was evaluated by a three-dimensional geochemical analysis model when the groundwater level was recovered after backfilling. The measured dissolved iron (Fe) and sulfate ion (SO42−) concentrations and pH before backfilling the drift were reproduced by the calibration of the simulation. Using the calibrated model, the pH at the outlet of the drift was changed from about pH 3 before backfilling to about pH 4 to 5 after backfilling. When calcite was contained in the filling materials of the drift, the pH approached neutral. However, when gypsum was formed, the neutralization was inhibited. The Fe concentration discharged from the drift was calculated at approximately 0.002 mol/L before backfilling. The total Fe concentration was calculated at 0.0004 mol/L or less after backfilling, and the dissolved Fe concentration decreased by several orders of magnitude after backfilling. A geochemical model quantitatively evaluated the improvement in water quality after backfilling the drifts. This method can be applied to the other abandoned mines with similar hydrogeological conditions.
Investigation of Magneto-/Radio-Metric Behavior in Order to Identify an Estimator Model Using K-Means Clustering and Artificial Neural Network (ANN) (Iron Ore Deposit, Yazd, IRAN)
Authors: Shirazy Adel , Hezarkhani Ardeshir , Timkin Timofey , Shirazi Aref
Published: November 2021

The study area is located near Toot village in the Yazd province of Iran, which is considered in terms of its iron mineralization potential. In this area, due to radioactivity, radiometric surveys were performed in a part of the area where magnetometric studies have also been performed. According to geological studies, the presence of magnetic anomalies can have a complex relationship with the intensity of radioactivity of radioactive elements. Using the K-means clustering method, the centers of the clusters were calculated with and without considering the coordinates of radiometric points. Finally, the behavior of the two variables of magnetic field strength and radioactivity of radioactive elements relative to each other was studied, and a mathematical relationship was presented to analyze the behavior of these two variables relative to each other. On the other hand, the increasing and then decreasing behavior of the intensity of the Earth’s magnetic field relative to the intensity of radioactivity of radioactive elements shows that it is possible to generalize the results of magnetometric surveys to radiometry without radiometric re-sampling in this region and neighboring areas. For this purpose, using the general regression neural network and backpropagation neural network (BPNN) methods, radiometric data were estimated with very good accuracy. The general regression neural network (GRNN) method, with more precision in estimation, was used as a model for estimating the radiation intensity of radioactive elements in other neighboring areas.
A Messinian Gypsum Deposit in the Ionian Forearc Basin (Benestare, Calabria, Southern Italy): Origin and Paleoenvironmental Indications
Authors: Cipriani Mara , Dominici Rocco , Costanzo Alessandra , D'Antonio Massimo , Guido Adriano
Published: November 2021

This study reports the first accurate record of the Messinian Resedimented Gypsum in the forearc and back-arc basins connected to the Calabrian-Peloritan orogen. A multidisciplinary approach has been used to investigate a gypsum deposit located in the Benestare’s area (Calabria, Southern Italy). Such deposit is made of bedded gypsrudites displaying clastic selenite with chaotical textures. On the top, the gypsrudites are interspersed with gypsum lenses belonging to the branching-like facies. Despite these two facies seem different macroscopically, they show petrographic features, fluid inclusions, organic matter and Strontium isotopic values very similar to each other. On the other hand, both facies show fractured and folded crystals. Crystals are only locally corroded and preserve primary structure relict as well as allochthonous (organic debris) and autochthonous putative microbial remains. All crystals are rich in fluid inclusions but these are visibly affected by stretching and leaking (re-equilibration processes) suggesting a moderate plastic deformation during re-sedimentation and subsequent burial. Minimal transport of the deposit is testified by subangular shapes of the gypsum crystals. The gypsrudite and branching-like facies reveal an 87Sr/86Sr average value of 0.709045 and 0.709082, respectively. These values suggest a strong connection with the global Ocean and reduced freshwater input. The Benestare’s deposit originated from the partial to complete dismantling of selenite crystals related to the first stage (5.97–5.60 Ma) of the Messinian Salinity Crisis through gravitational collapse due to local controlling factors.
Characterization of Natural Consolidated Halloysite Nanotube Structures
Authors: Jin Jiaqi , Assemi Shoeleh , Asgar Hassnain , Gadikota Greeshma , Tran Thang , Nguyen William , McLennan John D. , Miller Jan D.
Published: November 2021

Halloysite is a unique 1:1 clay mineral frequently appearing with nanotubular morphology, and having surfaces of different polarity with interesting and important technological applications. HNTs can be consolidated naturally in the earth by pressure and thermal flows. In this study of natural consolidated HNTs, the strength and hardness of these materials were found to be dependent on the presence of impurities (gibbsite, alunite, quartz, and other silica minerals), which accounted for the increased stability of such samples. In the absence of impurities, the strength of consolidated HNTs was significantly lower. The first 3D mapping of the pore structure of natural consolidated HNT is provided. The contributions of the porosity within the nanotubes and between the nanotubes were delineated using a combination of non-invasive ultra-small and small-angle X-ray scattering (USAXS/SAXS) analyses, BET/BJH pore size analyses, and computed tomography studies. A total porosity of 40%, as determined by X-ray attenuation and He porosimetry, was found for the natural consolidated HNTs, of which about one-third was due to the inter-HNT porosity. Nano-X-ray computed tomography (nano-XCT) analyses also indicated that 76% of the inter-HNT pores were smaller than 150 nm in diameter. The intra-HNT pore size determined by combined USAXS/SAXS and BET/BJH was about 10 nm. This pore network information is essential for the utilization of natural consolidated HNTs as a model geomaterial to investigate the effects of surface characteristics on confined fluid flow.
A Study of Thermal Stability of Hydroxyapatite
Authors: Bulina Natalia V. , Makarova Svetlana V. , Baev Sergey G. , Matvienko Alexander A. , Gerasimov Konstantin B. , Logutenko Olga A. , Bystrov Vladimir S.
Published: November 2021

High-temperature powder sintering is an integral part of the dense ceramic manufacturing process. In order to find the optimal conditions for producing a ceramic product, the information about its behavior at high temperatures is required. However, the data available in the literature are very contradictory. In this work, the thermal stability of hydroxyapatite prepared by a solid-state mechanochemical method and structural changes occurring during sintering were studied. Stoichiometric hydroxyapatite was found to remain as a single-phase apatite structure with the space group P63/m up to 1300 °C inclusively. A further increase in the sintering temperature leads to its partial decomposition, a decrease in the crystallite size of the apatite phase, and the appearance of significant structural strains. It was shown that small deviations from stoichiometry in the Ca/P ratio upward or downward during the hydroxyapatite synthesis lead to a significant decrease in the thermal stability of hydroxyapatite. An apatite containing almost no hydroxyl groups, which is close to the composition of oxyapatite, was prepared. It was shown that the congruent melting of stoichiometric hydroxyapatite upon slow heating in a high-temperature furnace does not occur. At the same time, the fast heating of hydroxyapatite by laser radiation allows, under certain conditions, its congruent melting with the formation of a recrystallized monolayer of oxyhydroxyapatite. The data obtained in this study can be used when choosing sintering conditions to produce hydroxyapatite-based ceramics.
Detoxification of Arsenic-Containing Copper Smelting Dust by Electrochemical Advanced Oxidation Technology
Authors: Li Meng , Yuan Junfan , Liu Bingbing , Du Hao , Dreisinger David , Cao Yijun , Han Guihong
Published: November 2021

A large amount of arsenic-containing solid waste is produced in the metallurgical process of heavy nonferrous metals (copper, lead, and zinc). The landfill disposal of these arsenic-containing solid waste will cause serious environmental problems and endanger people’s health. An electrochemical advanced oxidation experiment was carried out with the cathode modified by adding carbon black and polytetrafluoroethylene (PTFE) emulsion. The removal rate of arsenic using advanced electrochemical oxidation with the modified cathode in 75 g/L NaOH at 25 °C for 90 min reached 98.4%, which was significantly higher than 80.69% of the alkaline leaching arsenic removal process. The use of electrochemical advanced oxidation technology can efficiently deal with the problem of arsenic-containing toxic solid waste, considered as a cleaner and efficient method.
Interzeolitic Transformation of Clinoptilolite into GIS and LTA Zeolite
Authors: de Lima Renata C. F. , Oliveira Daniele da Silva , Pergher Sibele B. C.
Published: November 2021

A natural clinoptilolite zeolite was transformed into other zeolites of greater industrial interest, such as zeolites with GIS and LTA structures. The synthesis conditions were studied, and the interzeolitic transformation was characterized by X-ray diffraction (XRD), X-ray fluorescence (FRX), Fourier transform infrared spectroscopy (FTIR), and scanning electron microscopy (SEM). From the results, it was possible to observe that the GIS and LTA zeolites were successfully synthesized. Furthermore, the results revealed that a synthesis time of 4 days was enough to obtain the GIS structure, and 4 h was sufficient to obtain LTA. The interzeolitic transformation can be explained by the RBU (Ring Building Unit) approach using C4 units from the HEU topology. The use of clinoptilolite in the synthesis of other zeolites is an innovative, economically viable, and environmentally sustainable process that exploits a material that exists in large quantities and is still little explored by industry.
An Autochthonous Acidithiobacillus ferrooxidans Metapopulation Exploited for Two-Step Pyrite Biooxidation Improves Au/Ag Particle Release from Mining Waste
Authors: Jiménez-Paredes Andrea E. , Alfaro-Saldaña Elvia F. , Hernández-Sánchez Araceli , García-Meza J. Viridiana
Published: November 2021

Pyrite bio-oxidation by chemolithotrophic acidophile bacteria has been applied in the mining industry to bioleach metals or to remove pyritic sulfur from coal. In this process, it is desirable to use autochthonous and already adapted bacteria isolated directly from the mining sites where biomining will be applied. Bacteria present in the remnant solution from a mining company were identified through cloning techniques. For that purpose, we extracted total RNA and performed reverse transcription using a novel pair of primers designed from a small region of the 16S gene (V1–V3) that contains the greatest intraspecies diversity. After cloning, a high proportion of individuals of the strains ATCC-23270 (NR_074193.1 and NR_041888.1) and DQ321746.1 of the well-known species Acidithiobacillus ferrooxidans were found, as well as two new wild strains of A. ferrooxidans. This result showed that the acidic remnant solution comprises a metapopulation. We assayed these strains to produce bioferric flocculant to enhance the subsequent pyrite bio-oxidation, applying two-stage chemical–bacterial oxidation. It was shown that the strains were already adapted to a high concentration of endogenous Fe2+ (up to 20 g·L−1), increasing the volumetric productivity of the bioferric flocculant. Thus, no preadaptation of the community was required. We detected Au and Ag particles originally occluded in the old pyritic flotation tailings assayed, but the extraction of Au and Ag by cyanidation resulted in ca. 30.5% Au and 57.9% Ag.
Anthropogenic рollution of the coastal zone and hydrochemical analysis of the waters of Lake Baikal within the borders of the Republic of Buryatia
Authors: Kotomina Gulnara Akhmetovna , Pishchenko Elena Vital’evna , Shatalin Vladislav Andreevich
Published: November 2021

Anthropogenic impact on Lake Baikal is currently a big problem for the world community as a whole. Its solution depends on a number of factors, the main of which is the assessment of the level of impact and its maximum reduction. According to various researchers, a gradual accumulation of a number of chemical elements occurs in the waters of Lake Baikal, which leads to a change in the ecosystem as a whole. The purpose of this work was to assess the state of the coastal zone and to assess the hydrochemical regime of the coastal zone of the northeastern coast of Lake Baikal. According to the results of the observations, the coastal zone of Maximikha and Oymur villages is the most polluted, where a large amount of rotting algae was observed, as well as anthropogenic pollution. The least polluted is the coastline about c. Ust-Barguzin. According to the results of the study of physical indicators of Lake Baikal water, the achievement of the upper limit of the MPC in terms of color in the water samples of the Dulan ulus in the summer of 2020 and in the spring of 2021, as well as in the spring in the water samples of the village of Sukhaya was found. In addition, the turbidity index of the water near the Dulan ulus in the spring period was 2 EMF, which is also on the border of the norm. According to the results of the study of chemical parameters of water, the pH at most points is slightly alkaline, the water hardness at all stations did not exceed 3°. The total alkalinity of water at all stations ranged from 92.8 to 23.2 mg-eq/dm³. The ion content of various substances does not exceed the values established by other authors for oz. Baikal is: dissolved oxygen (O₂) — from 6 to 12 mg/dm³, chlorine ions (CL⁻) — from 0.1 to 0.5 mg/dm³. The value of permanganate oxidizability is 2 mg/dm³.
Digitalization of the tax system in Russia
Authors: Bezdolnaya T. Y. , Nesterenko A. V. , Khoruzhy V. I.
Published: November 2021

The article deals with international problems in the field of tax digitalization, ways and measures to solve them within the framework of the tax system of the Russian Federation. The main directions and current development programs adopted at the legislative level for the previous and planned reporting periods and the consequences of measures to digitalize this system in Russia are also outlined.
Association of Urine Findings with Metabolic Syndrome Traits in a Population of Patients with Nephrolithiasis
Authors: Hood Virginia L. , Sternberg Kevan M. , de Waal Desiree , Asplin John R. , Mulligan Carley , Callas Peter W.
Published: November 2021

Key Points

Stone-forming patients with metabolic syndrome have metabolic and diet factors contributing to stone risk, including high acid excretion and low urine pH.

Greater acid excretion is largely the result of higher protein intake, although this does not fully explain the urine pH trends.

Low urine pH with high supersaturation of uric acid and low supersaturation of calcium phosphate contributed to the distribution of stone composition in those with more metabolic syndrome traits.

Background

The odds of nephrolithiasis increase with more metabolic syndrome (MetS) traits. We evaluated associations of metabolic and dietary factors from urine studies and stone composition with MetS traits in a large cohort of stone-forming patients.

Methods

Patients >18 years old who were evaluated for stones with 24-hour urine collections between July 2009 and December 2018 had their records reviewed retrospectively. Patient factors, laboratory values, and diagnoses were identified within 6 months of urine collection and stone composition within 1 year. Four groups with none, one, two, and three or four MetS traits (hypertension, obesity, dyslipidemia, and diabetes) were evaluated. Trends across groups were tested using linear contrasts in analysis of variance and analysis of covariance.

Results

A total of 1473 patients met the inclusion criteria (835 with stone composition). MetS groups were 684 with no traits, 425 with one trait, 211 with two traits, and 153 with three or four traits. There were no differences among groups for urine volume, calcium, or ammonium excretion. There was a significant trend (P<0.001) for more MetS traits being associated with decreasing urine pH, increasing age, calculated dietary protein, urine uric acid (UA), oxalate, citrate, titratable acid phosphate, net acid excretion, and UA supersaturation. The ratio of ammonium to net acid excretion did not differ among the groups. After adjustment for protein intake, the fall in urine pH remained strong, while the upward trend in acid excretion was lost. Calcium oxalate stones were most common, but there was a trend for more UA (P<0.001) and fewer calcium phosphate (P=0.09) and calcium oxalate stones (P=0.01) with more MetS traits.

Conclusions

Stone-forming patients with MetS have a defined pattern of metabolic and dietary risk factors that contribute to an increased risk of stone formation, including higher acid excretion, largely the result of greater protein intake, and lower urine pH.
Boron removal from aqueous solutions by polyethyleneimine-Fe3+ attached column adsorbents
Authors: Akpınar Şahin , Koçyiğit Hasan , Gürbüz Fatma , Odabaşı Mehmet
Published: November 2021

Although, boron (B) is an essential micronutrient for plants, animals and human beings; at high concentration of boron in water resources may be hazardous for living being. Hence the boron concentration has to be reduced down to suggested level by the World Health Organization for safe use of water for irrigation and drinking. The present study examines boron pollution level in groundwater and suggests an alternative sorbent to remove it from water sources used for irrigation and drinking. The poly-2-Hydroxyethyl methacrylate (HEMA)-co- glycidyl methacrylate (GMA)- polyethyleneimine (PEI)- Fe3+ columns were synthesized to adsorb the boron compounds from a real groundwater samples and synthetic solution. Boron was removed 78.2% by poly (HEMA-co-GMA)-PEI- Fe3+ column at an amount of 54.42 mg/g, pH 8. However, the lower adsorption ratio was recorded as between 35.8–58.1% of real groundwater where adsorbed amount of boron and its derivates were found as 9–28.67 mg/g due to other chemical ions in real groundwater samples. Boron-loaded columns were regenerated by 0.01 M NaOH treatment for industrial practice. Regeneration cycles were performed successfully 15-times with only a loss of 5% in adsorption capacity of columns.
Pengembangan Aplikasi Penjualan Mobil dengan Framework Scrum pada PT XYZ
Authors: Suryantara I Gusti Ngurah
Published: November 2021

Suatu perusahaan perlu merencanakan pengembangan aplikasi yang terintegrasi dengan baik. Untuk itu diperlukan perencanaan yang matang sehingga dalam berinvestasi teknologi informasi tepat sasaran dan memberikan keuntungan untuk menunjang jalannya proses bisnis. Banyak perusahaan sekarang ini mengembangkan cetak biru enterprise architecture (arsitektur enterprise) untuk keselarasan teknologi informasi dalam perusahaanya. Setelah memiliki cetak biru arsitektur enterprise perlu diimplementasikan sehingga aplikasi yang sudah tersusun dalam cetak biru dapat terwujud guna menunjang proses bisnis pada perusahaan, untuk itu diperlukan kerangka kerja pengembangan sistem. Dalam implementasi cetak biru arsitektur enterprise dapat menggunakan kerangka kerja Scrum. Kerangka kerja Scrum dapat digunakan untuk pengembangan sistem yang cepat, karena kerangka kerja Scrum merupakan salah satu dari kerangka kerja Agile. Sehingga kerangka kerja Scrum, sangat tepat sebagai kerangka kerja dalam pengembangan sistem pada suatu perusahaan.  Dengan adanya aplikasi yang terintegrasi yang dipetakan dengan cetak biru arsitektur enterprise, dan diimplementasikan dengan kerangka kerja Scrum, maka terjadi kesinergian antara pemangku kebijakan pada perusahaan dengan proses bisnis yang memerlukan dukungan investasi teknologi informasi pada perusahaan.
Analisis Frequency Rate dan Severity Rate dalam Kecelakaan Kerja di PT XYZ
Authors: Fitri Rika Ainil , Efelina Vita
Published: November 2021

Program keselamatan dan kesehatan kerja (K3) merupakan salah satu bagian penting yang perlu diterapkan dalam pelaksanaan kerja. Risiko kecelakaan serta penyakit akibat kerja sering terjadi karena pihak perusahaan tidak menerapkan program K3 dengan baik. Hal ini dapat berdampak pada tingkat produktivitas pekerja. Dengan adanya implementasi program K3 diharapkan dapat meningkatkan produktivitas kerja karyawan. Untuk mengetahui bagaimana pengaruh implementasi program K3 terhadap produktivitas kerja serta seberapa besar hubungan antara keduanya maka dilakukanlah penelitian terhadap karyawan pada PT XYZ. Penelitian ini bertujuan untuk menganalisis frequency rate dan severity rate dalam kecelakaan kerja di PT XYZ. Keselamatan kerja berkaitan dengan mesin, alat kerja, dan proses pengolahannya, landasan tempat kerja dan lingkungan serta cara-cara melakukan pekerjaan. PT XYZ yang mengelola karet mentah menjadi crumb rubber Sir 20 memiliki 308 orang tenaga kerja, sehingga wajib untuk menerapkan Sistem Manajemen Keselamatan dan Kesehatan Kerja (SMK3). Faktor yang menyebabkan kecelakaan adalah kurang berhati-hatinya karyawan saat bekerja dan kurangnya pemahaman karyawan terhadap program K3 yang sudah ditentukan oleh perusahaan. Berdasarkan analisis yang telah dilakukan, diketahui bahwa frekuensi kecelakaan kerja yang terjadi pada saat produksi dalam satu tahun kerja yaitu sebesar 4,24 kecelakaan per 1.000.000 jam kerja dan tingkat keparahan kecelakaan kerja sebesar 5,29 per 1.000.000 jam kerja.
Usulan Penerapan Metode Shared Storage pada Tata Letak Stock di Gudang PT XYZ
Authors: Prasetyo Rendy Adi , Herwanto Dene , Nugraha Asep Erik
Published: November 2021

Penelitian ini bertujuan untuk menerapkan metode shared storage dalam mengevaluasi tata letak gudang sehingga diperoleh alternatif tata letak yang lebih efisien. Data yang digunakan pada penelitian ini adalah layout saat ini, jumlah permintaan produk, dan frekuensi aktivitas yang terjadi dalam gudang pada masing-masing produk. Berdasarkan penerapan metode shared storage dapat diusulkan tata letak gudang yang lebih baik. Dari hasil yang didapatkan, dilakukan perbaikan rak penyimpanan dari empat slot menjadi enam slot sehingga lebih menghemat penggunaan area karena produk disimpan pada rak bertingkat. Dari hasil perhitungan didapatkan penurunan kebutuhan luas lantai, yaitu untuk produk homeware 16,06%, health & beauty 15,6%, dan electronic 16,32%. Dari hasil tersebut diketahui produk homeware memiliki kebutuhan tertinggi berdasarkan jumlah permintaannya dan produk electronic mengalami penurunan luas terbesar. Oleh karena itu, penempatan produk pada gudang harus mempertimbangkan frekuensi tersebut agar terciptanya efisiensi saat transportasi.