bluuebunny/crossref_metadata_2025_split huggingface dataset:
Potentialities of Medicinal Indigenous taxa for accumulation of macro- and micro elements increasing nearby Abu-Tartur phosphate mining ore, Egypt
Authors: Elshamy Maha , Al-Balawi Siham M. , Ramadan Samah M. 
Published: April 2023

Abstract
Background and Aims
Some wild taxa (Astragalus vogalii, Sesbania sesban, Trigonella hamosa, Melilotus indicus, Senna italica, Bidens pilosa and Conyza bonariensis) growing around Abu-Tartur phosphate mining ore in Egypt, were conducted to identify species accumulation of Fe, Mn, Zn, Cu, Mo, Se, B, Pb, Cr, Cd, Ni, Ag, Si and Na in plants and soils.
Methods
These metals levels were measured by atomic spectroscopy techniques, including flame-AAS, GF-AAS, and ICP-AES.
Results
The bioavailability of trace elements to plants was affected by soil factors such as soil pH, organic matter (OM) content. Soil considered alkali soil (pH range from 7.4- 8.6) with low organic contents (1.26-1.80 %). By comparing the soil content around the phosphate mining area in the Western Desert as part of the extremely dry deserts range with the ideal agricultural soil content of macronutrients, it was found that there were low contents of them. Bioconcentration Factor, Translocation Factor (TF), Biological Accumulation Coefficient (BAC) and element accumulation index (EAI) were calculated for the studied metals associated with phosphate mining process. BF and BAC for all metals are more than unity.
Conclusion
Our study showed that these native plants with a high BF and low (TF) and have the potential for phytostabilization and will be used in phytoremediation of the metallic pollutants in soils after further research in accumulation mechanism of phosphate mining spoils.
Iodine-supported implants in prevention and treatment of surgical site infections for compromised hosts: A prospective study
Authors: Shirai Toshiharu , Tsuchiya Hiroyuki , Terauchi Ryu , Tsuchida Shinji , Shimomura Seiji , Kajino Yoshitomo , Takahashi Kenji 
Published: April 2023

Abstract
Background
Surgical site infection (SSI) is a common complication following orthopedic implantation. We developed an iodine coating for titanium implants to reduce implant-related infectionsand conducted a prospective clinical study to evaluate the efficacy and potential drawbacks of iodine-supported implants.
Patients and Methods
Between July 2008 and July 2017, 653 patients (377 male and 27 female patients; mean age, 48.6) with postoperative infection or a compromised status were treated using iodine-loaded titanium implants. The mean follow-up period was 41.7 months. In 477 patients, iodine-supported implants were used to prevent infection and in 176 patients, to treat active infection (one-stage surgery, 89 patients; two-stage surgery,87 patients). In the limbs and pelvis, the primary diagnoses included the following: 161 tumors, 92 deformities/shortening, 47 pseudarthrosis, 42 fractures, 32 infected TKA, 25 osteoarthritis, 21 pyogenic arthritis, 20 infected THA, and 6 osteomyelitis. In the spinal cases, there were 136 cases of tumors, 36 cases of pyogenic spondylitis, and 35 cases of degeneration. Five modes of implant failure were identified and classified as follows: soft tissue failure(type 1), aseptic loosening (type 2), structural failure (type 3), infection (type 4), and tumor progression (type 5).
Results
The overall failure rate in our series was 26.3% (172/653). There were 101 mechanical failures, including 22 type 1, 20 type 2, and 59 type 3 failures. Non-mechanical causes accounted for 71 failures, including 45 type 4 and 26 type 5 failures. The overall incidence of infections was 6.8%. The mean time to the onset of infection after implantation was 9.1 months. The overall infection rate was 3.7% in the prevention cases and 15.3% in the treatment cases. There was no difference between one-stage replacement (14.6%) and two-stage replacement (16.0%). There were 11 cases of treatment for SSI of spine surgery, and the re-infection rate was 0% using iodine-coated instruments.
Conclusions
The five modes of failure of the iodine-supported implant were satisfactory compared with previous reports. In particular, because the infection rate of iodine-coated implants used for compromised hosts is low compared with other methods, postoperative infection is more easily controlled. It can be considered highly effective for spinal infections that require one-stage revision surgery.
Level of Evidence: IV
Trial registration: prospective, observation study
Reliable Binary Interaction Parameters for SRK EOS for Modeling CO2 and H2 Storage in Depleted Oil and Gas Reservoirs
Authors: Kundu Gaurav , Upadhyay Rajeev , Kumar Ashutosh 
Published: April 2023

Abstract
Modeling Underground Hydrogen (H2) Storage (UHS) and Underground Carbon dioxide (CO2) Storage (UCS) in depleted oil and gas reservoirs requires compositional simulation. Cubic Equation of State (EOS) models for the reservoir fluids have the edge over other models like GERG 2008 and PC SAFT. Soave-Redlich-Kwong (SRK) EOS, a reliable choice of EOS, needs reliable Binary Interaction Parameters (BIPs) for its efficient and reliable application to UHS and UCS modeling. Existing correlations for estimating BIPs for SRK EOS may not be suitable for binaries having long-chain n-alkanes. This exhaustive work presents optimized BIPs and correlations for components relevant to UHS and UCS storages in depleted oil and gas reservoirs. The optimization process uses large amounts of data (3241 P-x data for binary mixtures, 35 critical points data for multicomponent mixtures) and a two-step process. Optimized BIP values are presented in terms of correlations as functions of temperature (T) and carbon number (CN) of the n-alkanes. A comparative analysis shows that the developed correlations are more reliable for compositional phase behavior than Chueh and Prausnitz (1967) and Oellrich et al. (1981) BIP-correlations commonly used in commercial simulators. The BIPs developed for CO2, N2, and n-alkanes mixture have fitting accuracy of 1.3% and 1.9% in terms of Average Absolute Relative Deviations (AARDs) for critical temperature and critical pressure, respectively, for 35 natural gas mixtures with SRK EOS. The correlations proposed are more reliable estimates for developing an EOS model for UHS and UCS in depleted oil and gas reservoirs.
A synergistic effect of fibrous carboxymethyl cellulose with equine collagen improved the hemostatic properties of freeze-dried wound dressings
Authors: Sedlář Marian , Kacvinská Katarína , Fohlerová Zdenka , Izsák David , Chalupová Marta , Suchý Pavel , Dohnalová Marcela , Sopuch Tomáš , Vojtová Lucy 
Published: April 2023

Abstract
Bleeding is one of the most commonly occurring injuries; it can be painful and even life-threatening condition. The hemostats are substances that promote blood clotting and fasten hemostasis. In this paper, we evaluated the hemostatic effect of freeze-dried wound dressings based on equine collagen, porcine collagen, fibrous carboxymethyl cellulose (CMC) and their mixtures. The wound dressings were investigated for their morphological structure, chemical structure, absorption properties, in vitro hemostasis, cytotoxicity assay and lastly, for in vivo hemostasis. We have found out that adding fibrous CMC into collagen-based hemostatic wound dressings creates a strong synergistic effect, which significantly improves absorption capacity by almost doubling it, as well as supports clotting time. Based on the in vivo studies on partial nephrectomy in rats, the time needed for achieving hemostasis was significantly lower due to the synergy of collagen and CMC. Our materials were compared to the commonly used hemostatic sealing patch on the market (Tachosil) during the in vivo testing, and sample of a mixture of equine collagen and CMC showed better hemostatic efficacy.
Genomic variations and mutational analysis of South Indian isolates of BmNPV
Authors: Sathyanarayana Madhuri , Neelagund S. E. , Hegde Rajat , Sajjan Dayanand B 
Published: April 2023

Abstract
BmNPV belongs to the genus AlphaBaculovirus and is an arthropod-specific virus that infects the commercial sericulture insect B. mori. BmNPV was identified in the virus family Baculoviridae and has a large, circular, double-stranded DNA genome of 128.4 kb expressing 143 proteins. Many viruses are studied because of their damaging effects, the study of Baculoviruses was triggered by their potential utility to control insect pests. Later, the utility of Baculoviruses as expression vectors was evidenced, and a new research area emerged. We are attempting to investigate the genomic diversity of BmNPV from different locations in the southern Indian states, as it is one of the leading parts that have embraced sericulture on a large scale. The genome analysis of BmNPV provides additional data that may help to understand Baculovirus evolution and adaptations to their hosts. Here we present a comprehensive analysis of the relationships between the 4 B. mori Baculoviruses. Sequencing of BmNPV's whole genome from different isolates followed by mutational analysis would reveal information about the functional role of important viral genes, which can be demonstrated with the help of In silico bioinformatics models. This resulted in the presence of SNPs and INDELS in the most important genes of BmNPV, which may lead to further changes in the gene products.
Aggregate Query Frameworks for Preserving Privacy Data in Big Data Analytics
Authors: Riyana Surapon , Sasujit Kittikorn , Homdoung Nigran 
Published: April 2023

Abstract
Data utility and data privacy are both serious issues that must be considered when datasets are released to use in big data analytics because they are traded-off issues. That is, high-utility datasets are generally high risks in terms of privacy violation issues. Likewise, datasets are formed to be high security in terms of privacy preservation, they often lead to data utility issues. To address these issues in datasets, several privacy preservation models have been proposed such as k-Anonymity, l-Diversity, t-Closeness, Anatomy, k-Likeness, and (lp1, . . . , lpn)-Privacy, i.e., all users’ explicit identifier values and all unique quasi-identifier values in datasets are removed and distorted respectively. Unfortunately, these privacy preservation models are static data models and still have data utility issues that must be addressed. Thus, they could be insufficient to address privacy violation issues in big data analytics. For this reason, a new efficient and effective privacy preservation model is proposed in this work such that it is based on aggregate query answers that can guarantee the confidence of the range and the minimized number of values that can be re-identified. The aims of the proposed privacy preservation model are that aside from privacy preservation constraints, the complexity and data utility are also maintained as much as possible. Furthermore, we show that the proposed model is a privacy preservation model that is efficient and effective by using extensive experiments.
Exploring the hub genes and mechanisms of Daphne altaica. treating esophageal squamous cell carcinoma based on Network Pharmacology and Bioinformatics Analysis
Authors: Hailati Sendaer , Talihati Ziruo , Abudurousuli Kayisaier , Han Meng , Nuer Muhadaisi , Khan Nawaz , Maihemuti Nulibiya , Simayi Jimilihan , Dilimulati Dilihuma , nueraihemaiti Nuerbiye , Zhou Wenting 
Published: April 2023

Abstract
Purpose Esophageal squamous cell carcinoma (ESCC), is a frequent digestive tract malignant carcinoma with a high fatality rate. Daphne altaica. (D. altaica), a medicinal plant that is frequently employed in Kazakh traditional medicine, and which has traditionally been used to cure cancer and respiratory conditions, but research on the mechanism is lacking. Therefore, we examined and verified the hub genes and mechanism of D. altaica treating ESCC.Methods Active compounds and targets of D. altaica were screened by databases such as TCMSP, and ESCC targets were screened by databases such as GeneCards and constructed the compound-target network and PPI network. Meantime, datasets between tissues and adjacent non-cancerous tissues from GEO database (GSE100942, GPL570) were analyzed to obtain DEGs using the limma package in R. Hub genes were validated using data from the Kaplan-Meier plotter database, TIMER2.0 and GEPIA2 databases. Finally, AutoDock software was used to predict the binding sites through molecular docking.Results In total, 830 compound targets were obtained from TCMSP and other databases. And 17710 disease targets were acquired based on GeneCards and other databases. And we constructed the compound-target network and PPI network. Then, 127 DEGs were observed (82 up-regulated and 45 down-regulated genes). Hub genes were screened including TOP2A, NUF2, CDKN2A, BCHE, and NEK2, and had been validated with the help of several publicly available databases. Finally, molecular docking results showed more stable binding between five hub genes and active compounds .Conclusions In the present study, five hub genes were screened and validated, and potential mechanisms of action were predicted, which could provide a theoretical understanding of the treatment of ESCC with D. altaica.
High prevalence of colistin heteroresistance in specific species and lineages of Enterobacter cloacae complex derived from human clinical specimens
Authors: Fukuzawa Shota , Sato Toyotaka , Aoki Kotaro , Yamamoto Soh , Ogasawara Noriko , Nakajima Chie , Suzuki Yasuhiko , Horiuchi Motohiro , Takahashi Satoshi , Yokota Shin-ichi 
Published: April 2023

Abstract
Background Colistin (CST) is a last-line drug for multidrug-resistant Gram-negative bacterial infections. CST-heteroresistant Enterobacter cloacae complex (ECC) has been isolated. However, integrated analysis of epidemiology and resistance mechanisms based on the complete ECC species identification has not been performed.
Methods Clinical isolates identified as “E. cloacae complex” by MALDI-TOF MS Biotyper Compass in a university hospital in Japan were analyzed. Minimum inhibitory concentrations of CST were determined by the broth microdilution method. The population analysis profiling (PAP) was performed for detecting the heteroresistant phenotype. The heat shock protein 60 (hsp60) cluster was determined from its partial nucleotide sequence. From the data of whole-genome sequencing, average nucleotide identity (ANI) for determining ECC species, multilocus sequence type, core genome SNPs-based phylogenetic analysis were performed. phoPQ-, eptA-, and arnT-deleted mutants were established to evaluate the mechanism underlying colistin heteroresistance. The arnT mRNA expression levels were determined by reverse transcription quantitative PCR.
Results Thirty-eight CST-resistant isolates, all of which exhibited the heteroresistant phenotype by PAP, were found from 138 ECC clinical isolates (27.5%). The prevalence of CST-resistant isolates did not significantly differ among the origin of specimens (29.0%, 27.8%, and 20.2% for respiratory, urine, and blood specimens, respectively). hsp60clusters, core genome phylogeny, and ANI revealed that the CST-heteroresistant isolates were found in all or most of Enterobacter roggenkampii (hsp60 cluster IV), Enterobacter kobei (cluster II), Enterobacter chuandaensis (clusters III and IX), and Enterobacter cloacaesubspecies (cluster XI and XII). No heteroresistant isolates were found in Enterobacter hormaechei subspecies (cluster VIII, VI, and III) and Enterobacter ludwigii (cluster V). Upregulation of arnT, which encodes 4-amino-4-deoxy-L-arabinose transferase, mRNA induced by CST was observed in the CST-heteroresistant isolates, and it is mediated by phoPQ pathway. Isolates possessing mcr-9- and mcr-10 (3.6% and 5.6% of total ECC isolates, respectively) exhibited similar CST susceptibility and PAP compared with mcr-negative isolates.
Conclusions Significant prevalence (approximately 28%) of CST heteroresistance is observed in ECC clinical isolates, and theyare accumulated in specific species and lineages. Heteroresistance is occurred by upregulation of arnT mRNA induced by CST. Acquisition of mcr genes contributes less to CST resistance in ECC.
Pseudorange Bias from Inter-Signal Interference: the QZSS L5-L5S Case
Authors: Sleewaegen Jean-Marie , Montenbruck Oliver , Steigenberger Peter 
Published: April 2023

Abstract
Analysis of the bias between Quasi-Zenith Satellite System (QZSS) L5-Q and L5-I pseudoranges reveals decimeter-level variations over the satellite passes, a phenomenon that is not observed on any other GNSS signal. The paper provides a study of this QZSS peculiarity. It is shown that the bias depends on the orientation of the line-of-sight vector with respect to the transmit antenna panel of the QZSS satellite, and that the amplitude of its variation is satellite dependent. The cause of the L5 bias is identified as interference from the L5S signal transmitted by QZSS satellites at the same frequency and from a different antenna. The interference introduces a distortion of the correlation peak dependent on the primary and secondary code selected for the L5 and L5S signals and on the relative delay and phase between the received L5 and L5S signals. This distortion induces tracking biases affecting pseudoranges produced using the pilot signal component. A theoretical model of the interference is provided, and it is shown that the bias variation can be accurately modelled and compensated for if L5 and L5S measurements are available.
How to preserve narrow endemics in view of climate change? The Nuratau Mountains as the case
Authors: Volis Sergei , Beshko Natalya 
Published: April 2023

Abstract
Endemic species usually have higher risk of extinction than widespread species and therefore for endemics negative effects of climate change can be especially dramatic. The Nuratau Mountains, located in Uzbekistan, are rich in endemic species and are a part of the Mountains of Central Asia Global Biodiversity Hotspot and one of Key Biodiversity Areas. To understand consequences of the climate change for a group of endemic plant species found in this region we conducted species distribution modelling (SDM) and produced species maps of habitat suitability, as well as maps of predicted endemic species richness under current and expected future climatic conditions. From the obtained information we assessed i) how well the existing in the region protected area (Nuratau Nature Reserve) protects the local endemics, and ii) what should be done to preserve these species under the expected future warming. Among 27 studied species, 14 appear to be the true narrow endemics because their predicted range is mostly or totally confined to the Nuratau Mountains. The remaining species have a wide predicted range of which the Nuratau Mountains are only a small part. Majority of the Nuratau endemics will have no climatically suitable habitat under the Rcp85 scenario in the Nuratau Mountains or surrounding ranges. Only seven species will have suitable habitats within the Nuratau Mountains and only five of them will have suitable habitat within the protected territory of the Nuratau Nature Reserve. For six species there will be no suitable area in the whole study area. Surprisingly, 13 species will have a suitable habitat in the Kugitang Range where Surkhan Nature Reserve is located. We suggest as the most appropriate climate change adaptation strategy for these Nuratau endemics the artificial increasing their dispersal capacity via in situ introduction trials and the creation of new populations in Surkhan Nature Reserve.
The composition and functionality of bacterial membrane vesicles (bMVs) in Escherichia coli – a time course comparison study in different media
Authors: Yu Mia S. C. , Chiang Dapi Menglin , Reithmair Marlene , Meidert Agnes , Brandes Florian , Schelling Gustav , Ludwig Christina , Meng Chen , Kirchner Benedikt , Zenner Christian , Muller Laurent , Pfaffl Michael W. 
Published: April 2023

Abstract
Background
Bacteria inhabit the in- and outside of the human body, such as skin, gut or the oral cavity where they play an innoxious, beneficial, e.g. as probiotic bacteria, or even pathogenic role, e.g. during a sepsis. Recent studies have shown that bacteria can secrete membrane vesicles (MVs) like eukaryotic cells with extracellular vesicles (EVs). Several studies indicate that bacterial membrane vesicles (bMVs) play a crucial role in microbiome-host interactions. However, the composition of such bMVs and their functionality under different culture conditions are still largely unknown.
Methods
To get more insights into bMVs, we investigated the composition and functionality of E. coli (DSM 105380) bMVs from the culture media Lysogeny broth (LB) and RPMI 1640 throughout the different phases of growth (lag-, log- and stationary-phase). bMVs from 3 time points from 2 media (LB_8h, LB_54h, LB_168h, RPMI_8h, RPMI_54h and RPMI_168h) were isolated by ultracentrifugation and analyzed using nanoparticle tracking analysis (NTA), EV flow-cytometry, cryogenic electron microscopy (Cryo-EM), conventional transmission electron microscopy (TEM) and mass spectrometry-based proteomics (LC-MS/MS). Furthermore, we examined pro-inflammatory cytokines IL-1 and IL-8 in the human monocyte cell line THP-1 by treatment with bMVs.
Results
Particle numbers increased with inoculation periods. The bMV morphologies in Cryo-EM/TEM were similar at each time point and condition. EV flow-cytometry showed a similarity of the common bMV markers OmpA+ GroEL- and OmpA- GroEL+ in each group. We found 140 proteins to be consistently expressed in the 6 groups with LC-MS/MS proteomics while we could also observe unique proteins throughout these treatments. Treatment of THP-1 cells with bMVs of all 6 groups lead to significantly high IL-1 and IL-8 expressions.
Conclusions
Our study showed that the choice of medium and the duration of culturing significantly influences E.coli bMV protein composition. Moreover, our flow-cytometry results indicate that different bMV subpopulations may be shed. Irrespective of the medium used, we observed an accumulation of E. coli bMVs over time, possibly due to increase of bacterial cells. Our cell culture experiments/functional assays imply that bMVs isolated from the 6 groups by ultracentrifugation retain their function and lead to comparable cytokine induction.