Broad Diversity Research Articles

Text summarization using modified generative adversarial network1

Text summarizing (TS) takes key information from a source text and condenses it for the user while retaining the primary material. When it comes to text summaries, the most difficult problem is to provide broad topic coverage and diversity in a single summary. Overall, text summarization addresses the fundamental need to distill large volumes of information into more manageable and digestible forms, making it a crucial technology in the era of information abundance. It benefits individuals, businesses, researchers, and various other stakeholders by enhancing efficiency and comprehension in dealing with textual data. In this paper, proposed a novel Modified Generative adversarial network (MGAN) for summarize the text. The proposed model involves three stages namely pre-processing, Extractive summarization, and summary generation. In the first Phase, the Text similarity dataset is pre-processed using Lowering Casing, Tokenization, Lemmatization, and, Stop Word Removal. In the second Phase, the Extractive summarization is done in three steps Generating similarity metrics, Sentence Ranking, and Sentence Extractive. In the third stage, a generative adversarial network (GAN) employs summary generation to jointly train the discriminative model D and the generative model G. To classify texts and annotate their syntax, Generative Model G employs a convolutional neural network called Bidirectional Gated Recursive Unit (CNN-BiGRU). The performance analysis of the proposed MGAN is calculated based on the parameters like accuracy, specificity, Recall, and Precision metrics. The proposed MGAN achieves an accuracy range of 99%. The result shows that the proposed MGAN improves the overall accuracy better than 9%, 6.5% and 5.4% is DRM, LSTM, and CNN respectively.

Modeling the scattering polarization in the solar Ca I 4227Å line with angle-dependent PRD effects and bulk velocities

Context. Modeling the scattering polarization signals of strong chromospheric lines requires solving the radiative transfer problem for polarized radiation, out of local thermodynamic equilibrium, taking partial frequency redistribution (PRD) effects into account. This problem is extremely challenging from a computational standpoint and, so far, most studies have been carried out by either modeling PRD effects under the angle-average approximation or by considering academic models of the solar atmosphere. Thanks to a new solution strategy, applicable to atomic systems that allow for a linearization of the problem, accurate solutions can now be routinely obtained in realistic 1D models, taking angle-dependent (AD) PRD effects into account. Aims. This work is aimed at assessing the suitability and performance of this new approach to handling dynamic scenarios. At the same time, it aims to explore the joint impact of magnetic fields and bulk velocities on the scattering polarization profiles of strong resonance lines, accounting for AD PRD effects and considering more realistic atmospheric models than in previous investigations. Methods. By using a two-level atomic model for neutral calcium, we synthesized the intensity and polarization profiles of the Ca I 4227 Å line. Our calculations were performed in 1D atmospheric models, both semi-empirical and extracted from 3D magnetohydrodynamic simulations, including vertical bulk velocities and magnetic fields of arbitrary strength and orientation, both constant and varying with height. Results. We obtained accurate solutions after only a few iterations across all considered scenarios. Even when formulating the problem in the observer’s reference frame, the frequency and angular grids required for accurate results were easily manageable. The calculated profiles showed the expected signatures of bulk velocities: wavelength shifts, enhancement of the line-core polarization amplitude, and prominent asymmetries in the wing signals. The results obtained in atmospheric models with complex thermal, dynamic, and magnetic structures unveiled the broad diversity of features in the emergent radiation that can be expected from realistic scenarios. Conclusions. The presented results assess the suitability of the proposed solution strategy and its parallel implementation, thus supporting its generalization to the 3D case. Our applications in increasingly realistic atmospheric models showed the difficulty related to precisely establishing the individual weight of bulk velocities and magnetic fields in the shape of the emergent profiles. This highlights the need to account for both these physical ingredients to perform reliable inversions of observed scattering polarization profiles.

Mixed-mode size-exclusion silica resin for polishing human antibodies in flow-through mode

The polishing step in the downstream processing of therapeutic antibodies removes residual impurities from Protein A eluates. Among the various classes of impurities, antibody fragments are especially challenging to remove due to the broad biomolecular diversity generated by a multitude of fragmentation patterns. The current approach to fragment removal relies on ion exchange or mixed-mode adsorbents operated in bind-and-gradient-elution mode. However, fragments that bear strong similarity to the intact product or whose biophysical features deviate from the ensemble average can elude these adsorbents, and the lack of a chromatographic technology enabling robust antibody polishing is recognized as a major gap in downstream bioprocessing. Responding to this challenge, this study introduces size-exclusion mixed-mode (SEMM) silica resins as a novel chromatographic adsorbent for the capture of antibody fragments irrespective of their biomolecular features. The pore diameter of the silica beads features a narrow distribution and is selected to exclude monomeric antibodies, while allowing their fragments to access the pores where they are captured by the mixed-mode ligands. The static and dynamic binding capacity of the adsorbent ranged respectively between 30-45 and 25–33 gs of antibody fragments per liter of resin. Selected SEMM-silica resins also demonstrated the ability to capture antibody aggregates, which adsorb on the outer layer of the beads. Optimization of the SEMM-silica design and operation conditions – namely, pore size (10 nm) and ligand composition (quaternary amine and alkyl chain) as well as the linear velocity (100 cm/h), ionic strength (5.7 mS/cm), and pH (7) of the mobile phase – afforded a significant reduction of both fragments and aggregates, resulting into a final antibody yield up to 80% and monomeric purity above 97%.

Structure and Functions of Endophytic Bacterial Communities Associated with Sphagnum Mosses and Their Drivers in Two Different Nutrient Types of Peatlands

Sphagnum mosses are keystone plant species in the peatland ecosystems that play a crucial role in the formation of peat, which shelters a broad diversity of endophytic bacteria with important ecological functions. In particular, methanotrophic and nitrogen-fixing endophytic bacteria benefit Sphagnum moss hosts by providing both carbon and nitrogen. However, the composition and abundance of endophytic bacteria from different species of Sphagnum moss in peatlands of different nutrient statuses and their drivers remain unclear. This study used 16S rRNA gene amplicon sequencing to examine endophytic bacterial communities in Sphagnum mosses and measured the activity of methanotrophic microbial by the 13C-CH4 oxidation rate. According to the results, the endophytic bacterial community structure varied among Sphagnum moss species and Sphagnum capillifolium had the highest endophytic bacterial alpha diversity. Moreover, chlorophyll, phenol oxidase, carbon contents, and water retention capacity strongly shaped the communities of endophytic bacteria. Finally, Sphagnum palustre in Hani (SP) had a higher methane oxidation rate than S. palustre in Taishanmiao. This result is associated with the higher average relative abundance of Methyloferula an obligate methanotroph in SP. In summary, this work highlights the effects of Sphagnum moss characteristics on the endophytic bacteriome. The endophytic bacteriome is important for Sphagnum moss productivity, as well as for carbon and nitrogen cycles in Sphagnum moss peatlands.

Filling the gap: The unique isotopic niche of medium-sized and large sharks in the northwestern Mediterranean Sea

The Mediterranean Sea is considered a biodiversity hotspot and hosts a broad diversity of shark species. Unfortunately, many shark populations have suffered a long story of overexploitation and their abundance has strongly declined over the last decades. A few studies have addressed the trophic role of sharks in the northwestern Mediterranean Sea, yet little is known about their isotopic niches. In this study, the isotopic niches of six shark species (Alopias vulpinus, Galeorhinus galeus, Hexanchus griseus, Isurus oxyrinchus, Prionace glauca and Squalus acanthias) from the northwestern Mediterranean Sea were determined and compared with those of sympatric predatory teleosts and marine mammals. Overall, δ13C and δ15N values were similar amongst all the shark species except for the three individuals of G. galeus, whose high δ15N values indicate recent immigration from a distinct area with a different isotopic baseline and hence were excluded from further analysis. The mixing models identified cephalopods as the dominant prey of the other five shark species and revealed that the medium-sized and large shark species studied here filled unique isotopic niches. Their trophic positions were similar to those of predatory teleosts and small dolphins but lower than those of larger dolphins, pilot whales and beaked whales. The high contribution of cephalopods to the diet of sharks in the northwestern Mediterranean Sea might be indicative of fish scarcity and deserves further research in the context of potential ontogenetic diet changes.

Real-World Clinical Performance of a DNA-Based Comprehensive Genomic Profiling Assay for Detecting Targetable Fusions in Nonsquamous NSCLC.

Genomic fusions are potent oncogenic drivers across cancer types and many are targetable. We demonstrate the clinical performance of DNA-based comprehensive genomic profiling (CGP) for detecting targetable fusions. We analyzed targetable fusion genes in >450 000 tissue specimens profiled using DNA CGP (FoundationOne CDx, FoundationOne). Using a de-identified nationwide (US-based) non-small cell lung cancer (NSCLC) clinico-genomic database, we assessed outcomes in patients with nonsquamous NSCLC (NonSqNSCLC) who received matched therapy based on a fusion identified using DNA CGP. Lastly, we modeled the added value of RNA CGP for fusion detection in NonSqNSCLC. We observed a broad diversity of fusion partners detected with DNA CGP in conjunction with targetable fusion genes (ALK, BRAF, FGFR2, FGFR3, NTRK1/2/3, RET, and ROS1). In NonSqNSCLC with oncogenic ALK, NTRK, RET, and ROS1 fusions detected by DNA CGP, patients treated with a matched tyrosine kinase inhibitor had better real-world progression-free survival than those receiving alternative treatment regimens and benefit was observed regardless of the results of orthogonal fusion testing. An estimated 1.3% of patients with NonSqNSCLC were predicted to have an oncogenic driver fusion identified by RNA, but not DNA CGP, according to a model that accounts for multiple real-world factors. A well-designed DNA CGP assay is capable of robust fusion detection and these fusion calls are reliable for informing clinical decision-making. While DNA CGP detects most driver fusions, the clinical impact of fusion detection is substantial for individual patients and exhaustive efforts, inclusive of additional RNA-based testing, should be considered when an oncogenic driver is not clearly identified.

The local state of hydrogen atoms and proton transfer in the crystal structure of natural berborite, Be2(BO3)(OH)‧H2O: Low-temperature single crystal X-ray analysis, IR and 1H NMR spectroscopy, and crystal chemistry and structural complexity of beryllium borates

Beryllium borates are mostly water-free, with the natural mineral berborite, Be2(BO3)(OH)‧H2O, being the only known exception. A sample of berborite from the Vevja quarry, Tvedalen, Larvik, Norway was studied by single-crystal X-ray diffraction, variable temperature 1H nuclear magnetic resonance (NMR), and infrared (IR) spectroscopy. The crystal structure is the trigonal 1T-polytype with space group P321 and is based on electroneutral [BeØ2(BΔO3)]-layers formed by BeO3Ø-tetrahedra and BΔO3-triangles. Due to statistical occupancy of the Ø-ligand by hydroxyl groups (50%) and water molecules (50%), berborite-1T and its related polytypes are characterized by complex systems of hydrogen bonds. Accurate analysis shows that in the structure of berborite there are two independent systems of hydrogen bonds involving mobile protons. Lowering of temperature results in the complete stabilization of protons at the critical “freezing-point” of 243 K. The crystal chemistry and complexity of layered beryllium borates are discussed. Despite the broad structural diversity of these compounds, their crystal structures are classified as simple (20–100 bits per unit cell) or intermediately complex (100–500 bits per unit cell). The complexity of berborite polytypes increases in accordance with the quantity of layers from 29.038 (1T) to 78.077 (2H), which is in good agreement with the negative contribution of complexity to the configurational entropy.

Comparative genomics and host range analysis of four Ralstonia pseudosolanacearum strains isolated from sunflower reveals genomic and phenotypic differences.

Bacterial wilt caused by Ralstonia solanacearum species complex (RSSC) is one of the devastating diseases in crop production, seriously reducing the yield of crops. R. pseudosolanacearum, is known for its broad infrasubspecific diversity and comprises 36 sequevars that are currently known. Previous studies found that R. pseudosolanacearum contained four sequevars (13, 14, 17 and 54) isolated from sunflowers sown in the same field. Here, we provided the complete genomes and the results of genome comparison of the four sequevars strains (RS639, RS642, RS647, and RS650). Four strains showed different pathogenicities to the same cultivars and different host ranges. Their genome sizes were about 5.84 ~ 5.94Mb, encoding 5002 ~ 5079 genes and the average G + C content of 66.85% ~ 67%. Among the coding genes, 146 ~ 159 specific gene families (contained 150 ~ 160 genes) were found in the chromosomes and 34 ~ 77specific gene families (contained 34 ~ 78 genes) in the megaplasmids from four strains. The average nucleotide identify (ANI) values between any two strains ranged from 99.05% ~ 99.71%, and the proportion of the total base length of collinear blocks accounts for the total gene length of corresponding genome was all more than 93.82%. Then, we performed a search for genomic islands, prophage sequences, the gene clusters macromolecular secretion systems, type III secreted effectors and other virulence factors in these strains, which provided detailed comparison results of their presence and distinctive features compared to the reference strain GMI1000. Among them, the number and types of T2SS gene clusters were different in the four strains, among which RS650 included all five types. T4SS gene cluster of RS639 and RS647 were missed. In the T6SS gene cluster, several genes were inserted in the RS639, RS647, and RS650, and gene deletion was also detected in the RS642. A total of 78 kinds of type III secreted effectors were found, which included 52 core and 9 specific effectors in four strains. This study not only provided the complete genomes of multiple R. pseudosolanacearum strains isolated from a new host, but also revealed the differences in their genomic levels through comparative genomics. Furthermore, these findings expand human knowledge about the range of hosts that Ralstonia can infect, and potentially contribute to exploring rules and factors of the genetic evolution and analyzing its pathogenic mechanism.

Biocarbon-Enhanced Flexible Nanofiber Mats for Sustainable Energy Generation and Wearable Device Applications

A broad diversity of nanofillers and polymers have been used to prepare polymer nanocomposites having potential applications in transportation, sports materials, aerospace, electronics, communication, energy, environment, and biomedical. Polyvinylidene fluoride (PVDF) finds a remarkable place in energy applications attributed to its highest known piezo- and pyroelectric properties. Like most carbon materials, Biochar has excellent electrical conductivity, since it comprises graphene layers with a great amount of carbon content. This study explores the behavior of composite nanofibers fabricated from rice straw-derived biochar-PVDF as wearable mats to harvest body energy into electricity. The composite nanofiber mats were fabricated using the electrospinning technique to get the benefit of both the piezoelectric properties of PVDF and the excellent electric properties of Biochar. The research found that incorporating 12 wt % of Biochar greatly enhances the piezoelectric content of the nanofiber mats without noteworthy loss in flexibility. In addition, the effects of membrane thickness (0.5, 0.9, and 1 mm) on their output voltages as a performance factor of the nanogenerator were measured. Results indicated that the effect of thickness was most influential in the thickness of 1 mm of PVDF/biochar nanofibers generator. The results of this work imply promising application development of such flexible composite piezoelectric nanofibrous membranes for environmentally sustainable energy generation and wearable self-powered electrical devices.

Integrative analysis of epilepsy-associated genes reveals expression-phenotype correlations

Epilepsy is a highly prevalent neurological disorder characterized by recurrent seizures. Patients exhibit broad genetic, molecular, and clinical diversity involving mild to severe comorbidities. The factors that contribute to this phenotypic diversity remain unclear. Here we used publicly available datasets to systematically interrogate the expression pattern of 230 epilepsy-associated genes across human tissues, developmental stages, and central nervous system (CNS) cellular subtypes. We grouped genes based on their curated phenotypes into 3 broad classes: core epilepsy genes (CEG), where seizures are the dominant phenotype, developmental and epileptic encephalopathy genes (DEEG) that are associated with developmental and epileptic encephalopathy, and seizure-related genes (SRG), which are characterized by the presence of seizures and gross brain malformations. We find that compared to the other two groups of genes, DEEGs are highly expressed within the adult CNS, exhibit the highest and most dynamic expression in various brain regions across development, and are significantly enriched in GABAergic neurons. Our analysis provides an overview of the expression pattern of epilepsy-associated genes with spatiotemporal resolution and establishes a broad expression-phenotype correlation in epilepsy.

Physical-chemical, mechanical and durability characterization of historical adobe buildings from the State of Michoacan, Mexico

Most earthen historical buildings have been abandoned for decades, exposed to the weathering and the passage of time. In Mexico, the low status of earthen constructions has increased these deterioration processes, resulting into the risk of disappearance of this significant architectural heritage. Historical adobes from monumental buildings in the State of Michoacan were sampled and collected in the localities of La Huacana (H) and Santa Cruz de Morelos (SC). The specimens were characterized in the materials laboratory, assessing their physical-chemical, mechanical and durability properties. An interdisciplinary methodology was designed through institutional cooperation and the application of different test methods.The adobes showed totally different compositions and proportions, and stabilizers like vegetal fibers, nevertheless, the mechanical performance of both samples was very similar, achieving respectable values in the context of historical adobe structures. Several correlations were found through the analyses: the physical properties like the density, the color or the electrical resistivity were related with the mechanical and durability ones; the non-destructive testing (NDT) allowed to calculate the dynamic elasticity modulus and infer the mechanical behavior; the chemical characterization enabled to obtain the elemental and mineralogical composition; and the Atterberg limits gave the soil classification.The research showed the broad diversity of earthen solutions and demonstrated how the granulometry is not a limitation to the adobe production, since the local soils can achieve similar mechanical and durability behaviors. Furthermore, H presented very different composition than the guidelines for earthen construction; nevertheless, the samples showed better durability performance and lower capillarity absorption rates. It is hoped that the results obtained with this research can help the further development of the earthen materials characterization and the decision-making process for the restoration and conservation of historical and vernacular constructions.

A generalized model for monitor units determination in ocular proton therapy using machine learning: A proof-of-concept study

Objective. Determining and verifying the number of monitor units is crucial to achieving the desired dose distribution in radiotherapy and maintaining treatment efficacy. However, current commercial treatment planning system(s) dedicated to ocular passive eyelines in proton therapy do not provide the number of monitor units for patient-specific plan delivery. Performing specific pre-treatment field measurements, which is time and resource consuming, is usually gold-standard practice. This proof-of-concept study reports on the development of a multi-institutional-based generalized model for monitor units determination in proton therapy for eye melanoma treatments. Approach. To cope with the small number of patients being treated in proton centers, three European institutes participated in this study. Measurements data were collected to address output factor differences across the institutes, especially as function of field size, spread-out Bragg peak modulation width, residual range, and air gap. A generic model for monitor units prediction using a large number of 3748 patients and broad diversity in tumor patterns, was evaluated using six popular machine learning algorithms: (i) decision tree; (ii) random forest, (iii) extra trees, (iv) K-nearest neighbors, (v) gradient boosting, and (vi) the support vector regression. Features used as inputs into each machine learning pipeline were: Spread-out Bragg peak width, range, air gap, fraction and calibration doses. Performance measure was scored using the mean absolute error, which was the difference between predicted and real monitor units, as collected from institutional gold-standard methods. Main results. Predictions across algorithms were accurate within 3% uncertainty for up to 85.2% of the plans and within 10% uncertainty for up to 98.6% of the plans with the extra trees algorithm. Significance. A proof-of-concept of using machine learning-based generic monitor units determination in ocular proton therapy has been demonstrated. This could trigger the development of an independent monitor units calculation tool for clinical use.

Fuel types misrepresent forest structure and composition in interior British Columbia: a way forward

BackgroundA clear understanding of the connectivity, structure, and composition of wildland fuels is essential for effective wildfire management. However, fuel typing and mapping are challenging owing to a broad diversity of fuel conditions and their spatial and temporal heterogeneity. In Canada, fuel types and potential fire behavior are characterized using the Fire Behavior Prediction (FBP) System, which uses an association approach to categorize vegetation into 16 fuel types based on stand structure and composition. In British Columbia (BC), provincial and national FBP System fuel type maps are derived from remotely sensed forest inventory data and are widely used for wildfire operations, fuel management, and scientific research. Despite their widespread usage, the accuracy and applicability of these fuel type maps have not been formally assessed. To address this knowledge gap, we quantified the agreement between on-site assessments and provincial and national fuel type maps in interior BC.ResultsWe consistently found poor correspondence between field assessment data and both provincial and national fuel types. Mismatches were particularly frequent for (i) dry interior ecosystems, (ii) mixedwood and deciduous fuel types, and (iii) post-harvesting conditions. For 58% of field plots, there was no suitable match to the extant fuel structure and composition. Mismatches were driven by the accuracy and availability of forest inventory data and low applicability of the Canadian FBP System to interior BC fuels.ConclusionsThe fuel typing mismatches we identified can limit scientific research, but also challenge wildfire operations and fuel management decisions. Improving fuel typing accuracy will require a significant effort in fuel inventory data and system upgrades to adequately represent the diversity of extant fuels. To more effectively link conditions to expected fire behavior outcomes, we recommend a fuel classification approach and emphasis on observed fuels and measured fire behavior data for the systems we seek to represent.

Importance of Thymoquinone, Sulforaphane, Phloretin, and Epigallocatechin and their Health Benefits

Abstract: Natural products have a broad diversity of multidimensional chemical formations, which play an important role, and indicate the crucial nature as a golden source for gaining herbal drug discovery. Thymoquinone performs various functions and impacts anticancer, anti-inflammatory, antioxidant, and anti-diabetic. It shows the significant influence on the treatment of different cancer types, such as bone cancer, bladder cancer, lung cancer, breast cancer, prostate cancer, and colon cancer. Sulforaphane has anticancer and antimicrobial properties and anticarcinogenic constituents. Phloretin is a dihydrochalcone flavonoid that indicates a potent antioxidant activity in peroxynitrite scavenging and restraint of lipid peroxidation. The most important health benefits of phloretin are anti-inflammatory and antioxidant activity and its impacts on cancer cells. Its antioxidant activity occurs through a reducer of lipid peroxidation, the scavenger of ROS, and its anti-inflammatory impacts happen through a declined level of cytokines, adhesion molecules, chemokines, suppression of NF-κβ transcription, and decreased expression of COX- 2 and iNOS. Phloretin impacts cancer cells through cytotoxic and apoptotic activity and activation of immune cells against the tumor. Epigallocatechin-3-gallate is the most abundant tea polyphenol, followed by other polyphenols, namely, catechin, epicatechin, epigallocatechin, and epicatechin-3-gallate. This review manuscript mentions some important medical health advantages and pharmaceutical effects of thymoquinone, sulforaphane, phloretin, and epigallocatechin.

Genotyping of Toxoplasma gondii in domestic animals from Campeche, México, reveals virulent genotypes and a recombinant ROP5 allele.

Toxoplasma gondii has at least 318 genotypes distributed worldwide, and tropical regions usually have greater genetic diversity. Campeche is a state located in the southeastern region of México and has favourable climate conditions for the replication and dissemination of this protozoan, similar to those in South American countries where broad genetic diversity has been described. Thus, in this study, 4 T. gondii isolates were obtained from tissues of stray dogs and free-range chickens in Campeche, México, and were genotyped by Mn-PCR-RFLP with 10 typing markers (SAG1, altSAG2, SAG3, BTUB, GRA6, c22-8, c29-2, L358, PK1 and Apico) and 5 virulence markers (CS3, ROP16, ROP17, ROP18 and ROP5) to provide new information about the distribution and virulence prediction of T. gondii genotypes. Two isolates of T. gondii genotype #116 and 2 of genotype #38 were obtained from stray dogs and chickens, respectively. The parasite load found in these species was between <50 and more than 35 000 tachyzoites per mg of tissue. Virulence marker genotyping revealed a recombinant 1&3 ROP5 RFLP pattern in 2 ToxoDB #116 isolates with no prediction of virulence in a murine model, while in the 2 ToxoDB #38 isolates, the ROP18/ROP5 combination predicted high virulence. Considering all the typed markers, there is a predominance of type I and III alleles, as constantly reported for the isolates characterized in various regions of México. It is crucial to determine their phenotype to corroborate the genetic virulence profile of the T. gondii isolates obtained in this study.

The redescription of Malerisaurus robinsonae (Archosauromorpha: Allokotosauria) from the Upper Triassic lower Maleri Formation, Pranhita-Godavari Basin, India.

Allokotosauria, a clade of non-archosauriform archosauromorphs with a broad diversity of body plans, plays a crucial role in better understanding the evolutionary history of early diverging stem-archosaurs. Here we provide a detailed redescription of Malerisaurus robinsonae, a malerisaurine allokotosaur from the middle Carnian-lowermost Norian lower Maleri Formation, Pranhita-Godavari Basin, India. The new anatomical information available from recently discovered and well-preserved skeletons of various allokotosaurs, such as Azendohsaurus madagaskarensis, Shringasaurus indicus, Puercosuchus traverorum, and Malerisaurus-like taxa, and their comparison with Malerisaurus robinsonae enriches our understanding of the anatomy of this species. To reassess the phylogenetic relationships of Malerisaurus robinsonae, we revised its scorings and included eight additional allokotosaurian species to the already most comprehensive phylogenetic dataset focused on Permo-Triassic archosauromorphs. We modified 70 scorings for Malerisaurus robinsonae and the new analysis recovered this species at the base of Malerisaurinae and this group as the earliest branch of Azendohsauridae. Pamelaria dolichotrachela is found as the earliest diverging non-malerisaurine azendohsaurid and sister taxon to the Shringasaurus indicus + Azendohsaurus spp. clade. Trilophosaurid interrelationships are well resolved, with Teraterpeton hrynewichorum, Coelodontognathus ricovi, and Rutiotomodon tytthos as their successive earliest-branching species. The position of Anisodontosaurus greeri as a sister taxon to Variodens inopinatus bolsters long ghost lineages in the Late Triassic trilophosaurid record. A disparity analysis of tooth crown morphology shows that Allokotosauria is the most disparate Permo-Triassic archosauromorph clade, exploring the almost complete range of basic crown morphologies. Trilophosaurids occupy an area of the dental morphospace unique among archosauromorphs.

Membrane vesicles in Acidithiobacillia class extreme acidophiles: influence on collective behaviors of 'Fervidacidithiobacillus caldus'.

Membrane vesicles (MVs) are envelope-derived extracellular sacs that perform a broad diversity of physiological functions in bacteria. While considerably studied in pathogenic microorganisms, the roles, relevance, and biotechnological potential of MVs from environmental bacteria are less well established. Acidithiobacillaceae family bacteria are active players in the sulfur and iron biogeochemical cycles in extremely acidic environments and drivers of the leaching of mineral ores contributing to acid rock/mine drainage (ARD/AMD) and industrial bioleaching. One key aspect of such a role is the ability of these bacteria to tightly interact with the mineral surfaces and extract electrons and nutrients to support their chemolithotrophic metabolism. Despite recent advances in the characterization of acidithiobacilli biofilms and extracellular matrix (ECM) components, our understanding of its architectural and mechanistic aspects remains scant. Using different microscopy techniques and nano-tracking analysis we show that vesiculation is a common phenomenon in distant members of the Acidithiobacillaceae family, and further explore the role of MVs in multicellular colonization behaviors using 'Fervidacidithiobacillus caldus' as a bacterial model. Production of MVs in 'F. caldus' occurred in both planktonic cultures and biofilms formed on sulfur surfaces, where MVs appeared individually or in chains resembling tube-shaped membranous structures (TSMSs) important for microbial communication. Liquid chromatography-mass spectrometry data and bioinformatic analysis of the MV-associated proteome revealed that 'F. caldus' MVs were enriched in proteins involved in cell-cell and cell-surface processes and largely typified the MVs as outer MVs (OMVs). Finally, microbiological assays showed that amendment of 'F. caldus' MVs to cells and/or biofilms affects collective colonizing behaviors relevant to the ecophysiology and applications of these acidophiles, providing grounds for their exploitation in biomining.

Comprehensive Analysis of HIV-1 Integrase Resistance-Related Mutations in African Countries.

The growing emergence of non-nucleoside reverse transcriptase inhibitor (NNRTI) HIV drug resistance in sub-Saharan Africa (SSA) led to the World Health Organization (WHO) recommending, in 2018, a transition to dolutegravir (DTG) as a first-line antiretroviral therapy (ART) in SSA. The broad HIV-1 genetic diversity in SSA could shape DTG effectiveness and the pattern of drug resistance mutations (DRMs) in this region. This study evaluated HIV-1 integrase (IN) DRMs and conserved regions among published groups M, N, O, and P HIV-1 sequences spanning forty years of the HIV epidemic during the transition of DTG-based ART. Overall, we found low levels of integrase strand transfer inhibitor (INSTI)-DRMs (<1%) across HIV groups between the years 1983 and 2023; however, it was unexpected to detect DRMs at statistically significantly higher frequencies in pre-INSTI (1983-2007) than in the INSTI (2008-2023) era. The variability of accessory INSTI-DRMs depended on the HIV subtypes, with implications for susceptibility to DTG. Our findings provide new perspectives on the molecular epidemiology and drug resistance profiles of INSTIs in SSA, emphasizing the need for ongoing surveillance and customized treatment approaches to address the continent's varied HIV subtypes and changing resistance patterns.

Intravesicular Solute Delivery and Surface Area Regulation in Giant Unilamellar Vesicles Driven by Cycles of Osmotic Stresses.

Phospholipid bilayers are dynamic cellular components that undergo constant changes in their topology, facilitating a broad diversity of physiological functions including endo- and exocytosis, cell division, and intracellular trafficking. These shape transformations consume energy, supplied invariably by the activity of proteins. Here, we show that cycles of oppositely directed osmotic stresses─unassisted by any protein activity─can induce well-defined remodeling of giant unilamellar vesicles, minimally recapitulating the phenomenologies of surface area homeostasis and macropinocytosis. We find that a stress cycle consisting of deflationary hypertonic stress followed by an inflationary hypotonic one prompts an elaborate sequence of membrane shape changes ultimately transporting molecular cargo from the outside into the intravesicular milieu. The initial osmotic deflation produces microscopic spherical invaginations. During the subsequent inflation, the first subpopulation contributes area to the swelling membrane, thereby providing a means for surface area regulation and tensional homeostasis. The second subpopulation vesiculates into the lumens of the mother vesicles, producing pinocytic vesicles. Remarkably, the gradients of solute concentrations between the GUV and the daughter pinocytic vesicles create cascades of water current, inducing pulsatory transient poration that enable solute exchange between the buds and the GUV interior. This results in an efficient water-flux-mediated delivery of molecular cargo across the membrane boundary. Our findings suggest a primitive physical mechanism for communication and transport across protocellular compartments driven only by osmotic stresses. They also suggest plausible physical routes for intravesicular, and possibly intracellular, delivery of ions, solutes, and molecular cargo stimulated simply by cycles of osmotic currents of water.

Evolutionary history of the cytochrome P450s from Colletotrichum species and prediction of their putative functional roles during host-pathogen interactions

The genomes of species belonging to the genus Colletotrichum harbor a substantial number of cytochrome P450 monooxygenases (CYPs) encoded by a broad diversity of gene families. However, the biological role of their CYP complement (CYPome) has not been elucidated. Here, we investigated the putative evolutionary scenarios that occurred during the evolution of the CYPome belonging to the Colletotrichum Graminicola species complex (s.c.) and their biological implications. The study revealed that most of the CYPome gene families belonging to the Graminicola s.c. experienced gene contractions. The reductive evolution resulted in species restricted CYPs are predominant in each CYPome of members from the Graminicola s.c., whereas only 18 families are absolutely conserved among these species. However, members of CYP families displayed a notably different phylogenetic relationship at the tertiary structure level, suggesting a putative convergent evolution scenario. Most of the CYP enzymes of the Graminicola s.c. share redundant functions in secondary metabolite biosynthesis and xenobiotic metabolism. Hence, this current work suggests that the presence of a broad CYPome in the genus Colletotrichum plays a critical role in the optimization of the colonization capability and virulence.