Miracle-dz/UniFAR-FTUs huggingface dataset:
Biofilm antimicrobial susceptibility testing: where are we and where could we be going?

SUMMARY Our knowledge about the fundamental aspects of biofilm biology, including the mechanisms behind the reduced antimicrobial susceptibility of biofilms, has increased drastically over the last decades. However, this knowledge has so far not been translated into major changes in clinical practice. While the biofilm concept is increasingly on the radar of clinical microbiologists, physicians, and healthcare professionals in general, the standardized tools to study biofilms in the clinical microbiology laboratory are still lacking; one area in which this is particularly obvious is that of antimicrobial susceptibility testing (AST). It is generally accepted that the biofilm lifestyle has a tremendous impact on antibiotic susceptibility, yet AST is typically still carried out with planktonic cells. On top of that, the microenvironment at the site of infection is an important driver for microbial physiology and hence susceptibility; but this is poorly reflected in current AST methods. The goal of this review is to provide an overview of the state of the art concerning biofilm AST and highlight the knowledge gaps in this area. Subsequently, potential ways to improve biofilm-based AST will be discussed. Finally, bottlenecks currently preventing the use of biofilm AST in clinical practice, as well as the steps needed to get past these bottlenecks, will be discussed.
S‐acylation: an orchestrator of the life cycle and function of membrane proteins

S‐acylation is a covalent post‐translational modification of proteins with fatty acids, achieved by enzymatic attachment via a labile thioester bond. This modification allows for dynamic control of protein properties and functions in association with cell membranes. This lipid modification regulates a substantial portion of the human proteome and plays an increasingly recognized role throughout the lifespan of affected proteins. Recent technical advancements have propelled the S‐acylation field into a ‘molecular era’, unveiling new insights into its mechanistic intricacies and far‐reaching implications. With a striking increase in the number of studies on this modification, new concepts are indeed emerging on the roles of S‐acylation in specific cell biology processes and features. After a brief overview of the enzymes involved in S‐acylation, this viewpoint focuses on the importance of S‐acylation in the homeostasis, function, and coordination of integral membrane proteins. In particular, we put forward the hypotheses that S‐acylation is a gatekeeper of membrane protein folding and turnover and a regulator of the formation and dynamics of membrane contact sites.
Reference area as a factor affecting potential yield estimates of coral reef fishes

A compilation of 48 estimates of Caribbean and Pacific coral reef fish catches, ranging from 0.1 to 23.7 t km super(-2) year super(-1), obtained from coral reef areas ranging from 0.1 to nearly 4-10 super(5) km super(2), are used to show that observed catches, and hence potential yield estimates, depend strongly on the reference area. The implications for coral reef fisheries assessments are discussed.
The latent HIV reservoir: current advances in genetic sequencing approaches

ABSTRACT Multiple cellular HIV reservoirs in diverse anatomical sites can undergo clonal expansion and persist for years despite suppressive antiretroviral therapy, posing a major barrier toward an HIV cure. Commonly adopted assays to assess HIV reservoir size mainly consist of PCR-based measures of cell-associated total proviral DNA, intact proviruses and transcriptionally competent provirus (viral RNA), flow cytometry and microscopy-based methods to measure translationally competent provirus (viral protein), and quantitative viral outgrowth assay, the gold standard to measure replication-competent provirus; yet no assay alone can provide a comprehensive view of the total HIV reservoir or its dynamics. Furthermore, the detection of extant provirus by these measures does not preclude defects affecting replication competence. An accurate measure of the latent reservoir is essential for evaluating the efficacy of HIV cure strategies. Recent approaches have been developed, which generate proviral sequence data to create a more detailed profile of the latent reservoir. These sequencing approaches are valuable tools to understand the complex multicellular processes in a diverse range of tissues and cell types and have provided insights into the mechanisms of HIV establishment and persistence. These advancements over previous sequencing methods have allowed multiplexing and new assays have emerged, which can document transcriptional activity, chromosome accessibility, and in-depth cellular phenotypes harboring latent HIV, enabling the characterization of rare infected cells across restrictive sites such as the brain. In this manuscript, we provide a review of HIV sequencing-based assays adopted to address challenges in quantifying and characterizing the latent HIV reservoir.
Perifoveal Microvascular Changes following Internal Limiting Membrane Peeling Surgery for Epiretinal Membrane and Macular Hole

Introduction: The aim of the study was to evaluate perifoveal microvasculature changes following pars plana vitrectomy with internal limiting membrane peeling for the epiretinal membrane (ERM) and macular hole (MH). Methods: This retrospective study included 59 eyes from 59 patients. Subjects were divided into two groups: an ERM group (n = 43) and an MH group (n = 16) based on the initial diagnosis. Swept-source optical coherence tomography angiography (SS-OCTA) was performed in the macular area, pre- and postoperatively. Perifoveal microvascular changes were calculated using MATLAB from the 6 × 6 mm SS-OCTA images, excluding the foveal avascular zone. Pre- and postoperative perifoveal vessel densities (pfVDs) were separately analyzed in six sectors (superior, superotemporal, inferotemporal, inferior, inferonasal, and superonasal) in the superficial capillary plexus (SCP) and deep capillary plexus (DCP). The baseline characteristics and other clinical factors were compared between the ERM and MH groups. Results: The postoperative best-corrected visual acuity significantly improved in both groups (p < 0.05). One year after surgery, the pfVD in the SCP of the ERM group significantly decreased in the inferotemporal sector (p = 0.049). The postoperative pfVD in the DCP of the MH group significantly decreased in temporal sectors (p < 0.05). The postoperative mean pfVD in the SCP in the MH group was significantly lower than that in the ERM group (p = 0.003). The presence of a dissociated optic nerve fiber layer (DONFL) was 75% in the MH group and 22% in the ERM group (p = 0.018). The correlation between the pfVD and DONFL was not statistically significant. Conclusion: Postoperative pfVD reduction in the temporal sector, a corresponding area in which DONFL is present after MH surgery, was significantly observed. After vitreoretinal surgery in MH patients, OCTA may serve as a useful tool for monitoring perifoveal microvascular changes, especially in temporal sectors.
Draft genome sequences of representative Paenibacillus polymyxa, Bacillus cereus, Fictibacillus sp., and Brevibacillus agri strains isolated from Amazonian dark earth

ABSTRACT Here, we report 10 distinct bacterial genomes from Amazonian dark earths, including six identified as Paenibacillus polymyxa, while the remaining four were unique representatives of Paenibacillus vini, Bacillus cereus, Brevibacillus agri, and Fictibacillus sp. , respectively. Each strain exhibited antagonistic activity against Fusarium oxysporum, underscoring their potential as sustainable agriculture resources.
ClinicalOmicsDB: exploring molecular associations of oncology drug responses in clinical trials

Abstract Matching patients to optimal treatment is challenging, in part due to the limited availability of real-world clinical datasets for predictive biomarker identification. The growing integration of omics profiling into clinical trials presents a new opportunity to tackle this challenge. Here, we introduce ClinicalOmicsDB, a web application for exploring molecular associations of oncology drug responses in clinical trials. This database includes transcriptomic data from 40 clinical trial studies, with 5913 patients spanning 11 cancer types. These studies include 67 treatment arms with a variety of chemotherapy, targeted therapy and immunotherapy drugs, and their combinations, which we organize based on an established ontology for easier navigation. The web application provides users with three options to explore molecular associations of oncology drug responses, focusing on studies, treatments or genes, respectively. Gene set analysis further connects treatment response to pathway activity and tumor microenvironment attributes. The user-friendly web interface of ClinicalOmicsDB streamlines interactive analysis. A Rust-based backend speeds up response time, and application programming interfaces and an R package enable programmatic access. We use three case studies to demonstrate the utility of this resource in human cancer studies. ClinicalOmicsDB is freely available at http://trials.linkedomics. org/.
Berberine ameliorates renal interstitial inflammation and fibrosis in mice with unilateral ureteral obstruction

Berberine acts via multiple pathways to alleviate fibrosis in various tissues and shows renoprotective effects. However, its role and underlying mechanisms in renal fibrosis remain unclear. Herein, we aimed to investigate the protective effects and molecular mechanisms of berberine against unilateral ureteric obstruction‐induced renal fibrosis. The results indicated that berberine treatment (50 mg/kg/day) markedly alleviated histopathological alterations, collagen deposition and inflammatory cell infiltration in kidney tissue and restored mouse renal function. Mechanistically, berberine intervention inhibited NOD‐like receptor family pyrin domain‐containing 3 (NLRP3) inflammasome activation and the levels of the inflammatory cytokine IL‐1β in the kidneys of unilateral ureteric obstruction mice. In addition, berberine relieved unilateral ureteric obstruction‐induced renal injury by activating adenosine monophosphate‐activated protein kinase (AMPK) signalling and promoting fatty acid β‐oxidation. In vitro models showed that berberine treatment prevented the TGF‐β1‐induced profibrotic phenotype of hexokinase 2 (HK‐2) cells, characterized by loss of an epithelial phenotype (alpha smooth muscle actin [α‐SMA]) and acquisition of mesenchymal marker expression (E‐cadherin), by restoring abnormal fatty acid β‐oxidation and upregulating the expression of the fatty acid β‐oxidation related‐key enzymes or regulators (phosphorylated‐AMPK, peroxisome proliferator activated receptor alpha [PPARα] and carnitine palmitoyltransferase 1A [CPT1A]). Collectively, berberine alleviated renal fibrosis by inhibiting NLRP3 inflammasome activation and protected tubular epithelial cells by reversing defective fatty acid β‐oxidation. Our findings might be exploited clinically to provide a potential novel therapeutic strategy for renal fibrosis.
Texture analysis of sidescan sonar data

Describes the use of texture analysis techniques for extracting information from sidescan sonar images of the seafloor. High resolution sidescan images are often highly textured due to the presence of sedimented regions of seafloor (sand ripples, mud, gravel, etc.). Two techniques are presented for the classification of these images into regions of different sediment type. The first of these is based upon the fractal model, however it is demonstrated that calculation of the fractal dimension is not necessary and that consideration of the directionality of the textures is important. The second technique is based upon the theory of spatial processes, and is concerned with the distributions of grey-level values in the textures. Results for both techniques are presented for samples of sidescan data. Another application of texture analysis is presented for the detection of man-made objects in sidescan images of the seafloor. These objects are regarded as being disturbances in the background texture and may be detected by computing probabilities from the texture model. Results are presented for samples of real sidescan data. Finally, a novel technique for compressing sidescan data is presented. This technique uses the information obtained from the sediment classification and object detection schemes to generate an image containing synthetic textures following the original sediment boundaries, with the targets of interest included at the appropriate positions. >
Isolation of Extracellular Vesicles from Phloem Sap by Size Exclusion Chromatography

Extracellular vesicles (EVs) are nanoparticles that are released by cells and participate in the transfer of information. It is now known that EVs from mammalian cells are involved in different physiological and pathophysiological processes (antigen presentation, tissue regeneration, cancer, inflammation, diabetes, etc.). In the past few years, several studies on plants have demonstrated that EVs are also key tools for plant intercellular and cross‐kingdom communications, suggesting that these nanostructures may contribute to distinct aspects of plant physiology such as development, defense, reproduction, symbiotic relationships, etc. These findings are challenging the traditional view of signaling in plants.
Enzyme‐functionalized alginate microparticles enable anaerobic culture under ambient oxygen

Methods for culturing oxygen‐sensitive cells and organisms under anaerobic conditions are vital to biotechnology research. Here, we report a biomaterial‐based platform for anaerobic culture that consists of glucose oxidase (GOX) functionalized alginate microparticles (ALG‐GOX), which are designed to deplete dissolved [O2] through enzymatic activity. ALG‐GOX microparticles were synthesized via a water‐in‐oil emulsion and had a size of 132.0 ± 51.4 µm. Despite having a low storage modulus, the microparticles remained stable under aqueous conditions due to covalent crosslinking through amide bonds. Enzyme activity was tunable based on the loaded GOX concentration, with a maximum activity of 3.6 ± 0.3 units/mg of microparticles being achieved at an initial loading concentration of 5 mg/mL of GOX in alginate precursor solution. High enzyme activity in ALG‐GOX microparticles resulted in rapid oxygen depletion, producing a suitable environment for anaerobic culture. Microparticles loaded with both GOX and catalase (ALG‐GOX‐CAT) to reduce H2O2 buildup exhibited sustained activity for potential long‐term anaerobic culture. ALG‐GOX‐CAT microparticles were highly effective for the anaerobic culture of Bacteroides thetaiotaomicron, with 10 mg/mL of ALG‐GOX‐CAT microparticles supporting the same level of growth in an aerobic environment compared to an anaerobic chamber after 16 h (8.70 ± 0.96 and 10.03 ± 1.03 million CFU, respectively; N.S. p = 0.07). These microparticles could be a valuable tool for research and development in biotechnology.
Cortical networks of parkinsonian gait: a metabolic and functional connectivity study

Objective: Locomotion is an automated voluntary movement sustained by coordinated neural synchronization across a distributed brain network. The cerebral cortex is central for adapting the locomotion pattern to the environment and alterations of cortical network dynamics can lead to gait impairments. Gait problems are a common symptom with a still unclear pathophysiology and represent an unmet therapeutical need in Parkinson's disease. Little is known about the cortical network dynamics of locomotor control in these patients. Methods: We studied the cortical basis of parkinsonian gait by combining metabolic brain imaging with high-density EEG recordings and kinematic measurements performed at rest and during unperturbed overground walking. Results: We found significant changes in functional connectivity between frontal, sensorimotor and visuomotor cortical areas during walking as compared to resting. Specifically, hypokinetic gait was associated with poor information flow from the supplementary motor area (SMA) to precuneus and from calcarine to lingual gyrus as well as high information flow from calcarine to cuneus. Interpretation: Our findings support a role for visuomotor integration processes in PD-related hypokinetic gait and suggest that reinforcing visual information may act as a compensatory strategy to allow SMA-related feedforward locomotor control in PD.
A Synopsis of the Evidence for the Science and Clinical Management of Cardiovascular-Kidney-Metabolic (CKM) Syndrome: A Scientific Statement From the American Heart Association

A growing appreciation of the pathophysiological interrelatedness of metabolic risk factors such as obesity and diabetes, chronic kidney disease, and cardiovascular disease has led to the conceptualization of cardiovascular-kidney-metabolic syndrome. The confluence of metabolic risk factors and chronic kidney disease within cardiovascular-kidney-metabolic syndrome is strongly linked to risk for adverse cardiovascular and kidney outcomes. In addition, there are unique management considerations for individuals with established cardiovascular disease and coexisting metabolic risk factors, chronic kidney disease, or both. An extensive body of literature supports our scientific understanding of, and approach to, prevention and management for individuals with cardiovascular-kidney-metabolic syndrome. However, there are critical gaps in knowledge related to cardiovascular-kidney-metabolic syndrome in terms of mechanisms of disease development, heterogeneity within clinical phenotypes, interplay between social determinants of health and biological risk factors, and accurate assessments of disease incidence in the context of competing risks. There are also key limitations in the data supporting the clinical care for cardiovascular-kidney-metabolic syndrome, particularly in terms of early-life prevention, screening for risk factors, interdisciplinary care models, optimal strategies for supporting lifestyle modification and weight loss, targeting of emerging cardioprotective and kidney-protective therapies, management of patients with both cardiovascular disease and chronic kidney disease, and the impact of systematically assessing and addressing social determinants of health. This scientific statement uses a crosswalk of major guidelines, in addition to a review of the scientific literature, to summarize the evidence and fundamental gaps related to the science, screening, prevention, and management of cardiovascular-kidney-metabolic syndrome.
The elastic properties of carbonates

Although carbonates contain about 60% of the world's oil reserves, the characterization of carbonate reservoirs remains challenging because of their heterogeneity andcomplex microstructure. Central to the seismic characterization of carbonates is an understanding of the effect of porosity on the elastic moduli and seismic-wave velocities. Figure 1 shows the compressional and shear-wave velocities measured by Rafavich et al. (1984) for limestones and dolomites from the Williston Basin, North Dakota, measured on air-saturated samples. It is seen that although the velocities decrease with increasing porosity, there is considerable scatter of the data. In this article, the possible contribution of variations in pore shape to the elastic moduli of carbonates is discussed, the role of microcracks and fractures is assessed, and differences between the static and dynamic moduli are highlighted.
A Comparison of Change Detection Analyses Using Different Band Algebras for Baraila Wetland with Nasa’s Multi-Temporal Landsat Dataset

Wetlands are those landscapes which are saturated with water or covered by water either perennially or for a major part of the year. Due to transforming nature of the wetlands from aquatic to terrestrial, the related physical features are not easy to be monitored. With the recent advancement in Remote sensing technique, the feature extraction of wetland with the help of different satellite derived band algebras including Normalized Difference Vegetation Index (NDVI), Normalized Difference Water Index (NDWI), Modified NDWI (MNDWI), Normalized Difference Moisture Index (NDMI) is being used by experts. The common diagnostic features of wetlands are surface water, swamps and aquatic vegetation. The present study is based on a comparison between these four indices. Baraila wetland of Vaishali district Bihar is selected as a site for the study because the surface water of this “BAT” shaped wetland has decreased rapidly in last half decade which is alarming for the related ecology and biodiversity.
Patient education about breathlessness

Purpose of the review Effective education enables people to modify the distress and impact of breathlessness by integrating evidence-informed breathlessness-related behaviours (knowledge, skill, attitude) into everyday life. This review considers recent studies of educational approaches focussed on chronic breathlessness as a modifiable, noxious and debilitating multidimensional experience. Recent findings Systematic assessments of text-based patient education materials and mobile phone applications specific to breathlessness indicate that while these resources are readily available, issues continue to persist with quality, readability, usefulness and availability of non-English language versions. Various forms of educational interventions for breathlessness have proven feasible and valued by people living with breathlessness and their significant others (uptake/completion, personal benefit, ripple effect on health professionals). Health professional knowledge about the impact of chronic breathlessness and effective management can be altered through structured, educational interventions. Summary Empiric studies of patient education for breathlessness are scarce despite persistent calls for better breathlessness education for people living with or providing care for someone living with this noxious symptom. In clinical practice, it is highly likely that there are effective and ineffective educational practices, both of which, if publicly disseminated, would inform future educational strategies to advance breathlessness self-management.