Predominance of blaNDM- and blaIMP-Harboring Escherichia coli Belonging to Clonal Complexes 131 and 23 in a Major University Hospital.

Background and Objectives: Carbapenem resistance is a growing global challenge for healthcare, and, therefore, monitoring its prevalence and patterns is crucial for implementing targeted interventions to mitigate its impact on patient outcomes and public health. This study aimed to determine the prevalence of carbapenem resistance among Escherichia coli (E. coli) strains in the largest tertiary care hospital of the capital territory of Pakistan and to characterize the isolates for the presence of antimicrobial resistance genes. Additionally, the most prevalent sequence types were analyzed. Materials and Methods: A total of 15,467 clinical samples were collected from November 2020 to May 2022, underwent antimicrobial susceptibility testing, and were analyzed for antimicrobial resistance genes through conventional PCR and sequence typing using MLST. Results: In carbapenem-resistant E. coli (CR-EC), 74.19% of isolates harbored the blaNDM gene, with blaNDM-1 (66.96%), blaNDM-5 (12.17%), and blaNDM-7 (20.87%) variants detected. Additionally, blaIMP was found in 25.81% and blaOXA-48 in 35.48% of isolates. The presence of blaCTX-M15 and blaTEM was identified in 83.87% and 73.55% of CR-EC isolates, respectively, while armA and rmtB were detected in 40% and 65.16% of isolates, respectively. Colistin and tigecycline were the most effective drugs against CR-EC isolates, with both showing an MIC50 of 0.5 µg/mL. The MIC90 for colistin was 1 µg/mL, while for tigecycline, it was 2 µg/mL. MLST analysis revealed that the CR-EC isolates belonged to ST131 (24.52%), ST2279 (23.87%), ST3499 (16.13%), ST8051 (15.48%), ST8900 (9.68%), ST3329 (7.10%), ST88 (1.94%), and ST6293 (1.29%). The ST131 complex (70.97%) was the most prevalent, harboring 95.65% of the blaNDM gene, while the ST23 complex (18.06%) harbored 62.50% of the blaIMP gene. Conclusions: Implementing large-scale surveillance studies to monitor the spread of specific pathogens, along with active infection control policies, is crucial for the effective containment and prevention of future epidemics.

Dynamic Behavior of Above-Room-Temperature Robust Skyrmions in 2D Van der Waals Magnet.

Magnetic skyrmions are swirl-like spin configurations that present topological properties, which have great potential as information carriers for future high-density and low-energy-consumption devices. The optimization of skyrmion-hosting materials that can be integrated with semiconductor-based circuits is the primary challenge for their industrialization. Two-dimensional van der Waals ferromagnets are emerging materials that have excellent carrier mobility and compatibility with integrated circuits, making them an ideal candidate for spintronic devices. Here, we report the realization of skyrmions at above room temperature in the 2D ferromagnet Fe3GaTe2. The thickness tunability of their skyrmion size and the formation of the skyrmion lattice are revealed. Furthermore, we demonstrate that the skyrmions can be moved by a low-density current at room temperature, together with an apparent skyrmion Hall effect, which is consistent with our quantitative micromagnetic simulation. Our work offers a promising 2D material platform for harnessing magnetic skyrmions in practical device applications.

Functional genomics and taxonomic insights into heavy metal tolerant novel bacterium Brevibacterium metallidurans sp. nov. NCCP-602T isolated from tannery effluent in Pakistan.

The strain designated NCCP-602T was isolated from tannery effluent, and displayed aerobic, gram-positive, rod-shaped cells that were characterized by oxidase negative, catalase positive, and non-motile features. The most favourable growth conditions were observed at a temperature of 30°C, pH 7.0, and NaCl concentration of 1% (w/v). It tolerated heavy metals at high concentrations of chromium (3600 ppm), copper (3300 ppm), cadmium (3000 ppm), arsenic (1200 ppm) and lead (1500 ppm). The results of phylogenetic analysis, derived from sequences of the 16S rRNA gene, indicated the position of strain NCCP-602T within genus Brevibacterium and showed that it was closely related to Brevibacterium ammoniilyticum JCM 17537T. Strain NCCP-602 T formed a robust branch that was clearly separate from closely related taxa. A comparison of 16S rRNA gene sequence similarity and dDDH values between the closely related type strains and strain NCCP-602T provided additional evidence supporting the classification of strain NCCP-602T as a distinct novel genospecies. The polar lipid profile included diphosphatidylglycerol, glycolipid, phospholipids and amino lipids. MK-7 and MK-8 were found as the respiratory quinones, while anteiso-C15:0, iso-C15:0, iso-C16:0, iso-C17:0, and anteiso-C17:0 were identified as the predominant cellular fatty acids (> 10%). Considering the convergence of phylogenetic, phenotypic, chemotaxonomic, and genotypic traits, it is suggested that strain NCCP-602 T be classified as a distinct species Brevibacterium metallidurans sp. nov. within genus Brevibacterium with type strain NCCP-602T (JCM 18882T = CGMCC1.62055T).

Modelling and optimization of an existing onshore gas gathering network using PIPESIM.

Pakistan has limited natural gas reserves, and most are found onshore. This article reports on the problems of an onshore gas gathering network (GGN) analysed through steady-state simulation modelling using PIPESIM software. The research methodology incorporates a comprehensive steady-state hydraulic analysis considering fluid flowing velocity limitations, liquid holdup and slugging along with other issues faced by gas gathering networks. The steady-state hydraulic analysis has led us to pinpoint specific GGN pipelines facing critically low gas velocities and consequent liquid holdup. Addressing these issues involved application of PIPESIM software for modelling, considering various operating schemes of gas-producing wells and their associated pipelines. To select an optimal operating scheme, the study utilized the Analytic Hierarchy Process (AHP) for operational optimization, to identify the most effective solution for reduced liquid holdup, improving production, and ensuring the safe operation among available alternatives. Findings from our hydraulic analysis highlight the importance of reducing GGN outlet pressure to mitigate challenges associated with liquid holdup which causes slugging and back pressure effect at source leading to low production and poor performance of the GGN. Study of three alternative cases reveals that decreasing outlet pressure lowers the liquid holdup, improve gas flowing velocities, and enhanced overall production. These findings validate our hypothesis that reducing GGN outlet pressure is a viable strategy to lower the liquid holdup in pipelines. This research offers significant value by providing a comprehensive solution to GGN liquid holdup, low flowing velocities, back pressure and low production challenges. The integration of steady-state hydraulic analysis, simulation modelling with PIPESIM, and the application of AHP for optimization contributes novel insights into the optimization of operation of gas gathering networks. Emphasizing the reduction of liquid holdup and enhancing production through outlet pressure adjustments offers a practical framework for optimizing the functionality of gas gathering networks.

Phylogenomic analyses and comparative genomic studies of Thermus strains isolated from Tengchong and Tibet Hot Springs, China.

Genus Thermus is the main focus of researcher among the thermophiles. Members of this genus are the inhabitants of both natural and artificial thermal environments. We performed phylogenomic analyses and comparative genomic studies to unravel the genomic diversity among the strains belonging to the genus Thermus in geographically different thermal springs. Sixteen Thermus strains were isolated and sequenced from hot springs, Qucai hot springs in Tibet and Tengchong hot springs in Yunnan, China. 16S rRNA gene based phylogeny and phylogenomic analyses based on concatenated set of 971 Orthologous Protein Families (supermatrix and gene content methods) revealed a mixed distribution of the Thermus strains. Whole genome based phylogenetic analysis showed, all 16 Thermus strains belong to five species; Thermus oshimai (YIM QC-2-109, YIM 1640, YIM 1627, 77359, 77923, 77838), Thermus antranikianii (YIM 73052, 77412, 77311, 71206), Thermus brokianus (YIM 73518, 71318, 72351), Thermus hydrothermalis (YIM 730264 and 77927) and one potential novel species 77420 forming clade with Thermus thalpophilus SYSU G00506T. Although the genomes of different strains of Thermus of same species were highly similar in their metabolic pathways, but subtle differences were found. CRISPR loci were detected through genome-wide screening, which showed that Thermus isolates from two different thermal locations had well developed defense system against viruses and adopt similar strategy for survival. Additionally, comparative genome analysis screened competence loci across all the Thermus genomes which could be helpful to acquire DNA from environment. In the present study it was found that Thermus isolates use two mechanism of incomplete denitrification pathway, some Thermus strains produces nitric oxide while others nitrious oxide (dinitrogen oxide), which show the heterotrophic lifestyle of Thermus genus. All isolated organisms encoded complete pathways for glycolysis, tricarboxylic acid and pentose phosphate. Calvin Benson Bassham cycle genes were identified in genomes of T. oshimai and T. antranikianii strains, while genomes of all T. brokianus strains and organism 77420 were lacking. Arsenic, cadmium and cobalt-zinc-cadmium resistant genes were detected in genomes of all sequenced Thermus strains. Strains 77,420, 77,311, 73,518, 77,412 and 72,351 genomes were found harboring genes for siderophores production. Sox gene clusters were identified in all sequenced genomes, except strain YIM 730264, suggesting a mode of chemolithotrophy. Through the comparative genomic analysis, we also identified 77420 as the genome type species and its validity as novel organism was confirmed by whole genome sequences comparison. Although isolate 77420 had 99.0% 16S rRNA gene sequence similarity with T. thalpophilus SYSU G00506T but based on ANI 95.86% (Jspecies) and digital DDH 68.80% (GGDC) values differentiate it as a potential novel species. Similarly, in the phylogenomic tree, the novel isolate 77,420 forming a separate branch with their closest reference type strain T. thalpophilus SYSU G00506T.

Advancements in prokaryotic systematics and the role of Bergey's International Society for Microbial Systematicsin addressing challenges in the meta-data era.

Prokaryotes are ubiquitous in the biosphere, important for human health and drive diverse biological and environmental processes. Systematics of prokaryotes, whose origins can be traced to the discovery of microorganisms in the 17th century, has transitioned from a phenotype-based classification to a more comprehensive polyphasic taxonomy and eventually to the current genome-based taxonomic approach. This transition aligns with a foundational shift from studies focused on phenotypic traits that have limited comparative value to those using genome sequences. In this context, Bergey's Manual of Systematics of Archaea and Bacteria (BMSAB) and Bergey's International Society for Microbial Systematics (BISMiS) play a pivotal role in guiding prokaryotic systematics. This review focuses on the historical development of prokaryotic systematics with a focus on the roles of BMSAB and BISMiS. We also explore significant contributions and achievements by microbiologists, highlight the latest progress in the field and anticipate challenges and opportunities within prokaryotic systematics. Additionally, we outline five focal points of BISMiS that are aimed at addressing these challenges. In conclusion, our collaborative effort seeks to enhance ongoing advancements in prokaryotic systematics, ensuring its continued relevance and innovative characters in the contemporary landscape of genomics and bioinformatics.

Analysis of processed natural gas injection on hydrate formation in high pressure refrigerated condensate lines.

Natural gas and condensate are exposed to hydrates formation at high pressure and low temperature in the presence of traces of water. Hydrates formation results in blockage of pipelines and equipment leading to plant shutdown and production losses. This study intends to find a novel hydrate prevention process for high pressure refrigerated condensate (HPRC) lines. HPRC is utilised as lean oil for enhanced liquified petroleum gas recovery in absorption process. This research was conducted by performing fifteen tests in which various processed natural gas (PNG) samples were injected into different HPRC samples using Aspen HYSYS software. The results showed lowering of the hydrates formation temperature in the HPRC at constant pressure. By capitalizing on in-house resources and reducing dependence on traditional hydrate inhibitors, this innovative approach offers cost-effectiveness and readily available hydrate inhibitor for HPRC lines in gas processing facilities. Moreover, it has been found that PNG samples with a relatively higher percentage of methane are more effective in lowering the hydrate formation temperature when injected into the HPRC lines. This study will enable hydrates researchers in reducing hydrates management costs in HPRC lines and invite hydrates prevention research in all areas capitalizing on in-house resources and reducing external dependence.

The germination response of Zea mays L. to osmotic potentials across optimal temperatures via halo-thermal time model.

The maize (Zea mays L.) is a monocot that is a member of the Poaceae family and a valuable feed for livestock, human food, and raw material for various industries. The halothermal time model determines how plants respond to salt (NaCl) stress under sub-optimal conditions. This model examines the relation between NaClb (g), GR, GP, salinity and temperature stress on germination of seeds dynamics in various crops. Five constant temperatures i.e. 20, 25, 30, 35, and 40 °C and five ψ levels (NaCl concentrations converted to ψ - 0, - 0.2, - 0.4, - 0.6, and - 0.8 MPa) were used in this experiment. In light of the results, the maximum halo-thermal time constant value was recorded at 35 °C temperature, while maximum germination percentage was detected at 30 °C in the controlled condition. Moreover, the lowermost value was recorded at 20 °C at - 0.8 MPa osmotic potential. The highest CAT, APX, and GPX activities were recorded at 15 °C at - 0.8 MPa, while the lowest values were observed for 0 MPa at 30 °C temperature. In conclusion, by employing the halo thermal time model, the germination of maize variety (var.30W52) was accurately predicted for the first time under varying levels of temperature and osmotic potentials.

Probing the microbial diversity and probiotic candidates from Pakistani foods: isolation, characterization, and functional profiling.

Probiotics represent beneficial living microorganisms that confer physiological, nutritional, and functional advantages to human health, holding significant potential for development of functional foods. This research aimed to isolate, identify, and characterize potential probiotic bacterial strains sourced from fermented and non-fermented foods from Pakistan. A total of 341 bacterial strains were isolated from diverse food samples (81) collected from various regions of Pakistan. Strains were identified using 16S rRNA gene sequencing and phylogenetic analysis. The identified strains belonged to genera Bacillus, Staphylococcus, Microbacterium, Shigella, Micrococcus, Enterococcus, Sporosarcina, Paenibacillus, Limosilactobacillus, Kosakonia, Dietzia, Leclercia, Lacticaseibacillus, Levilactobacillus, Kluyvera, Providencia, Enterobacter, Neisseria, Streptococcus, Acinetobacter, Corynebacterium, Pantoea, Mammaliicoccus, Pseudomonas, Burkholderia, and Alkalihalobacillus. Selected strains were chosen for probiotic assessment, employing existing literature as a guideline. Among these selections, six strains exhibited hemolytic activity, and seven strains displayed resistance to multiple antibiotics, prompting their exclusion from subsequent evaluations. The remaining strains demonstrated auto-aggregation capacities spanning 3.39-79.7%, and displayed coaggregation capabilities with reported food-borne pathogens. Furthermore, nine strains exhibited antimicrobial properties against food-borne pathogens. The assessment encompassed diverse characteristics such as cell surface hydrophobicity, survival rates under varying conditions, cholesterol reduction ability, casein digestion capability, and antioxidant activity. Phylogenomic analysis, digital-DNA DNA hybridization (digi-DDH), and average nucleotide identity (ANI) calculations unveiled novel species potentially belonging to the genera Sporosarcina and Dietzia. Based on these findings, we advocate for the consideration of Staphylococcus cohnii subsp. cohnii NCCP-2414, Lacticaseibacillus rhamnosus NCCP-2569 and Levilactobacillus brevis NCCP-2574 as prime probiotic candidates with the potential for integration into formulation of functional foods. Supplementary Information: The online version contains supplementary material available at 10.1007/s13205-023-03903-6.

Survival Rates and Patient-Reported Outcomes Support the Use of Custom Cement-Over Megaprosthesis (CCOM) in Complex Revision Lower Limb Arthroplasty.

BACKGROUND: Patients presenting with periprosthetic osteolysis or fracture between ipsilateral hip and knee arthroplasties are challenging to treat successfully. Long-stem implants, osteopenic bones, and patient comorbidities all represent considerable surgical challenges. Poor results of fracture fixation in this group, coupled with the desire to retain well-performing implants and minimize soft-tissue trauma led to the developmentof the custom cement-over megaprostheses (CCOM). The aims of the study were to evaluate implant survivals, complications, and patient outcomes in those undergoing CCOM within our institution. METHODS: A retrospective analysis of patients undergoing CCOM between 2002 and 2022 was performed. We studied 34 cases, 33 patients, one patient underwent staged bilateral surgery with 26 women and 8 men. INDICATIONS: trauma (16), failure of implants /aseptic loosening (9), or joint pathology. The mean Charlson comorbidity index was 3.5 (range, 0 to 8). All patients were followed up (mean 75 months [range, 9 to 170]) at 6 weeks, 6 months, 1 year, and annually thereafter. The VAS, EuroQol-5D-3L and MSTS scores were collected at 1 year. RESULTS: Implant survival defined by the primary outcome (all-cause revision of the implant at any time point) at 12 months of 97% (32 of 33). In surviving patients, implant survival was 90% (18 of 20) and all 7 survived at 5 and 10 years, respectively. Implant survival including those in the primary outcome group and those free of infection at 12 months was 84.8% (28 of 33) and in surviving patients, implant survival was 70% (14 of 20) and 7 out of 7 at 5 and 10 years, respectively. CONCLUSIONS: The CCOM technique demonstrates good implant survivorships and satisfactory patient-reported outcomes in complex, often frail patients who have compromised bone stock. This series confirms the technique as an established alternative to total femoral replacement in these cases.

Synthesis of Silver Nanoparticles from Ganoderma Species and Their Activity against Multi Drug Resistant Pathogens.

The widespread and indiscriminate use of broad-spectrum antibiotics leads to microbial resistance, which causes major problems in the treatment of infectious diseases. However, advances in nanotechnology using mushrooms have opened up new domains for the synthesis and use of nanoparticles against multidrug-resistant pathogens. Mushooms have recently attracted attention and are exploited for food and medicinal purposes. The current study focuses on the molecular identification, characterization of biologically synthesized silver nanoparticles by X-ray diffraction (XRD) spectroscopy, Fourier Transform Infrared Spectroscopy (FTIR), UV-Vis spectroscopy and scanning electron microscopy (SEM) and antibacterial analysis of extract and silver nanoparticles (AgNPs) synthesis from Ganoderma resinaceum against multidrug resistant microbes. Accurate identification of mushrooms is key in utilizing them for the benefit of humans. However, morphological identification of mushrooms is time consuming, tedious and may be prone to error. Molecular techniques are quick and reliable tools that are useful in mushroom taxonomy. Blast results showed that G. resinaceum (GU451247) obtained from Pakistan was 97 % same to the recognized G. resinaceum (GU451247) obtained from China as well as G. resinaceum (GU451247) obtained from India. The antimicrobial potential of mushroom composite and AgNPs showed high efficacy against pathogenic Staphylococcus aureus (ZOI 23 mm) K. pneumonia (ZOI 20 mm), Pseudomonas aeruginosa (ZOI 24 mm) and E. fecalis and A. baumannii (ZOI 10 mm), and multidrug resistant (MDR) A. baumannii (ZOI 24 mm). XRD evaluation revealed the crystalline composition of synthesized NPs with diameter of 45 nm. UV-Vis spectroscopy obsorption peaked of 589 nm confirmed the presence of AgNPs. SEM results showed the cubic morphology of AgNPs. The FTIR analysis of NPs obtained from G. resinaceum containing C=O as well as (O=C-H) stretching revealed presence of hydrogen, carbonyl and amide groups. The synthesized extract and AgNPs showed promising minimum inhibitory concentration (MIC) at 2 mg concentration against the MDR strains. AgNPs are observed to be efficient as they need less quantities to prevent bacterial growth. In the view of challenges for developing antimicrobial NPs of variable shape and size by various other methods, tuning nanoparticles synthesized via mushrooms can be a wonderful approach to resolve existing hurdles.

Assessment of Salivary MMP-8 and IL-1ß for the Diagnosis of Periodontal Diseases in Pakistani Population.

OBJECTIVE: Clinical methods use the subjective diagnosis of periodontal diseases by visual observation that could result in differences and variability of diagnosis. The addition of specific markers could aid in the accurate diagnosis of the local population. The objective of the study was to target two of the major proteins for possible significance in such an approach. MATERIALS AND METHODS: Unstimulated saliva samples were collected from 60 participants aged between 18 and 70 years. Three groups each with twenty participants were recruited into periodontitis, gingivitis, and healthy control. STATISTICAL ANALYSIS: The samples were analyzed using human enzyme-linked immunosorbent assay kits for matrix metalloproteinase-8 (MMP-8) and interleukin-1ß (IL-1ß). RESULTS: SPSS version 20 was used to analyze the result. Posthoc analysis by Tukey's test revealed that MMP-8 levels were higher in gingivitis and periodontitis groups as compared with healthy controls. The test also revealed that IL-1ß levels were higher in the periodontitis group compared with the healthy control and gingivitis group. Additionally, one-way analysis of variance analysis showed a significant effect on probing depth in gingivitis and periodontitis patients. The mean age of periodontitis group was significantly higher than other groups. CONCLUSION: Salivary biomarkers may provide useful diagnostic information and could be utilized as tests for periodontal disease screening, prognosis, and prediction.

Identification of Four Novel Candidate Genes for Non-syndromic Intellectual Disability in Pakistani Families.

Intellectual disability, a genetically and clinically varied disorder and is a significant health problem, particularly in less developed countries due to larger family size and high ratio of consanguineous marriages. In the current genetic study, we investigate and find the novel disease causative factors in the four Pakistani families with severe type of non-syndromic intellectual disability. For genetic analysis whole-exome sequencing (WES) and Sanger sequencing was performed. I-TASSER and Cluspro tools were used for Protein modeling and Protein-protein docking. Sanger sequencing confirms the segregation of novel homozygous variants in all the families i.e., c.245 T > C; p.Leu82Pro in SLC50A1 gene in family 1, missense variant c.1037G > A; p.Arg346His in TARS2 gene in family 2, in family 3 and 4, nonsense mutation c.234G > A; p.Trp78Term and missense mutation c.2200G > A; p.Asp734Asn in TBC1D3 and ANAPC2 gene, respectively. In silico functional studies have found the drastic effect of these mutations on protein structure and its interaction properties. Substituted amino acids were highly conserved and present on highly conserved region throughout the species. The discovery of pathogenic variants in SLC50A1, TARS2, TBC1D1 and ANAPC2 shows that the specific pathways connected with these genes may be important in cognitive impairment. The decisive role of pathogenic variants in these genes cannot be determined with certainty due to lack of functional data. However, exome sequencing and segregation analysis of all filtered variants revealed that the currently reported variants were the only variations from the respective families that segregated with the phenotype in the family.

Plant growth-promoting rhizobacteria and biochar as bioeffectors and bioalleviators of drought stress in faba bean (Vicia faba L.).

Plants are subjected to a variety of abiotic stressors, including drought stress, that are fatal to their growth and ability to produce under natural conditions. Therefore, the present study was intended to investigate the drought tolerance potential of faba bean (Vicia faba L.) plants under the co-application of biochar and rhizobacteria, Cellulomonas pakistanensis (National Culture Collection of Pakistan (NCCP)11) and Sphingobacterium pakistanensis (NCCP246). The experiment was initiated by sowing the inoculated seeds with the aforementioned rhizobacterial strains in earthen pots filled with 3 kg of sand-mixed soil and 5% biochar. The morphology of biochar was observed with highly porous nature, along with the detection of various essential elements. The biochemical and physiological data showed that phenolic compounds and osmolytes were adversely affected by the induction of drought stress. However, the application of biochar and rhizobacteria boosted the level of flavonoids on average by 52.03%, total phenols by 50.67%, soluble sugar by 82.85%, proline by 76.81%, glycine betaine by 107.25%, and total protein contents by 89.18% in all co-treatments of biochar and rhizobacteria. In addition, stress indicator compounds, including malondialdehyde (MDA) contents and H2O2, were remarkably alleviated by 54.21% and 47.03%, respectively. Similarly, the amplitude of antioxidant enzymes including catalase, peroxidase, superoxide dismutase, ascorbate peroxidase, and guaiacol peroxidase was also enhanced by 63.80%, 80.95%, 37.87%, and 58.20%, respectively, in all co-treatments of rhizobacteria and biochar. Conclusively, biochar and rhizobacteria have a magnificent role in enhancing the drought tolerance potential of crop plants by boosting the physio-biochemical traits and enhancing the level of antioxidant enzymes.

EasyCGTree: a pipeline for prokaryotic phylogenomic analysis based on core gene sets.

BACKGROUND: Genome-scale phylogenetic analysis based on core gene sets is routinely used in microbiological research. However, the techniques are still not approachable for individuals with little bioinformatics experience. Here, we present EasyCGTree, a user-friendly and cross-platform pipeline to reconstruct genome-scale maximum-likehood (ML) phylogenetic tree using supermatrix (SM) and supertree (ST) approaches. RESULTS: EasyCGTree was implemented in Perl programming languages and was built using a collection of published reputable programs. All the programs were precompiled as standalone executable files and contained in the EasyCGTree package. It can run after installing Perl language environment. Several profile hidden Markov models (HMMs) of core gene sets were prepared in advance to construct a profile HMM database (PHD) that was enclosed in the package and available for homolog searching. Customized gene sets can also be used to build profile HMM and added to the PHD via EasyCGTree. Taking 43 genomes of the genus Paracoccus as the testing data set, consensus (a variant of the typical SM), SM, and ST trees were inferred via EasyCGTree successfully, and the SM trees were compared with those inferred via the pipelines UBCG and bcgTree, using the metrics of cophenetic correlation coefficients (CCC) and Robinson-Foulds distance (topological distance). The results suggested that EasyCGTree can infer SM trees with nearly identical topology (distance < 0.1) and accuracy (CCC > 0.99) to those of trees inferred with the two pipelines. CONCLUSIONS: EasyCGTree is an all-in-one automatic pipeline from input data to phylogenomic tree with guaranteed accuracy, and is much easier to install and use than the reference pipelines. In addition, ST is implemented in EasyCGTree conveniently and can be used to explore prokaryotic evolutionary signals from a different perspective. The EasyCGTree version 4 is freely available for Linux and Windows users at Github ( https://github.com/zdf1987/EasyCGTree4 ).

Rare renaissance: Quadruple synchronous renal cell tumors in one kidney - A case report.

Multifocality in renal tumors is a rare occurrence, but not unheard of. Commonly the different foci correspond to the same histological pathology, however co-existence with other renal lesions, including both malignant and benign tumors, have also been reported. Here we present a 57-year-old male, ex-smoker who exhibited four distinct histological tumors in an ipsilateral kidney; multilocular cystic clear cell renal cell carcinoma (RCC) of low malignant potential, clear cell papillary RCC, renal oncocytoma, and renomedullary interstitial cell tumor. To our knowledge this is the first time these four tumors were found in the same patient, let alone the same kidney.

Multi-Walled CNTs/BiVO4 Heterostructures for Solar-Driven Evaporation System and Efficient Photocatalytic Activity against Oxytetracycline.

Developing a sustainable environment requires addressing primitive water scarcity and water contamination. Antibiotics such as oxytetracycline (OTC) may accumulate in the environment and in the human body, increasing the risks to the ecosystem. The treatment of polluted water and the production of potable water can be achieved in a variety of ways, including photodegradation, solar distillation, and filtration. Freshwater supplies can be increased by implementing energy-efficient technologies for the production of clean water. Solar water evaporation combined with photocatalytic degradation and sterilization offers a promising avenue for integration into the clean water and energy production fields. The present study reports the synthesis of a 3D solar steam generator comprised of BiVO4 and carbon nanotubes (CNT) nanocomposite decorated over a cigarette filter as the light-to-heat conversion layer for solar steam generation. The BiVO4@CNT-based 3D solar evaporator over the hydrophilic cellulosic fibers of the cigarette filter endowed excellent evaporation rates (2.36 kg m-2 h-1) under 1 kW m-2 solar irradiation, owing to its superior hydrophilicity and broadband solar absorption (96%) equipped with localized heating at microscale thermal confinement optimized by the minimum thermal conductivity of the overall system. Furthermore, the BiVO4@CNT composite exhibited a heightened photo activity up to 83% of the photodegradation of oxytetracycline (OTC) antibiotic due to the inhibition of charge recombination from the industrial effluents. This approach transforms the water-energy nexus into a synergistic bond that offers opportunities to meet expected demand, rather than being competitive.