Miracle-dz/UniFAR-FTUs huggingface dataset:
Mechanistic and biophysical characterization of polymyxin resistance response regulator PmrA in Acinetobacter baumannii

Introduction Acinetobacter baumannii PmrAB is a crucial two-component regulatory system (TCS) that plays a vital role in conferring resistance to polymyxin. PmrA, a response regulator belonging to the OmpR/PhoB family, is composed of a C-terminal DNA-binding effector domain and an N-terminal receiver domain. The receiver domain can be phosphorylated by PmrB, a transmembrane sensor histidine kinase that interacts with PmrA. Once phosphorylated, PmrA undergoes a conformational change, resulting in the formation of a symmetric dimer in the receiver domain. This conformational change facilitates the recognition of promoter DNA by the DNA-binding domain of PmrA, leading to the activation of adaptive responses. Methods X-ray crystallography was carried out to solve the structure of PmrA receiver domain. Electrophoretic mobility shift assay and Isothermal titration calorimetry were recruited to validate the interaction between the recombinant PmrA protein and target DNA. Field-emission scanning electron microscopy (FE-SEM) was employed to characterize the surface morphology of A. baumannii in both the PmrA knockout and mutation strains. Results The receiver domain of PmrA follows the canonical α5β5 response regulator assembly, which undergoes dimerization upon phosphorylation and activation. Beryllium trifluoride is utilized as an aspartate phosphorylation mimic in this process. Mutations involved in phosphorylation and dimerization significantly affected the expression of downstream pmrC and naxD genes. This impact resulted in an enhanced cell surface smoothness with fewer modifications, ultimately contributing to a decrease in colistin (polymyxin E) and polymyxin B resistance. Additionally, a conservative direct-repeat DNA PmrA binding sequence TTTAAGNNNNNTTTAAG was identified at the promoter region of the pmrC and naxD gene. These findings provide structural insights into the PmrA receiver domain and reveal the mechanism of polymyxin resistance, suggesting that PmrA could be a potential drug target to reverse polymyxin resistance in Acinetobacter baumannii.
A Permittivity Imaging Method: Electrical Capacitance Tomography Based on Electromagnetic Momentum

Electrical capacitance tomography (ECT) is widely used in industrial two-phase flow detection. Noniterative algorithms have fast imaging speed but low image spatial resolution, while iterative algorithms improve image resolution by increasing the computation time. To increase the image resolution, one can either increase the complexity of the imaging algorithms or increase the observation data according to different imaging principles. ECT technique is an imaging technique based on Green’s reciprocity theorem, which detects scalar, i.e., capacitance. Green’s reciprocity theorem is an energy reciprocity theorem. In recent years, the momentum reciprocity theorem has been proposed. The imaging principle corresponding to the momentum reciprocity theorem detects vector, which is expected to obtain higher resolution permittivity images. A permittivity imaging method is proposed to better recognize the boundary of the object and reduce the complexity of the algorithm. The core of this method is ECT based on electromagnetic momentum (ECT-EMM). ECT-EMM is an imaging technique based on the EMM reciprocity theorem, which detects vector, i.e., capacitance gradient. We first obtain the capacitance gradient by the electrodes-moving scheme and the object-moving scheme. According to the principle of ECT-EMM, the permittivity gradient is reconstructed. Then, the permittivity distribution is recovered from the permittivity gradient. In this article, the principle of ECT-EMM is derived, and the object-moving scheme is used. Numerical simulation and experimental demonstration are performed using the Tikhonov regularization algorithm. The reconstructed images and quantitative metrics show that compared to ECT, the proposed method clearly reflects the boundaries of the two-phase flow and performs more stability with noise for certain objects.
Cognitive performance in aged rats is associated with differences in distinctive neuronal populations in the ventral tegmental area and altered synaptic plasticity in the hippocampus

Introduction Deterioration of cognitive functions is commonly associated with aging, although there is wide variation in the onset and manifestation. Albeit heterogeneity in age-related cognitive decline has been studied at the cellular and molecular level, there is poor evidence for electrophysiological correlates. The aim of the current study was to address the electrophysiological basis of heterogeneity of cognitive functions in cognitively Inferior and Superior old (19-20 months) rats in the ventral tegmental area (VTA) and the hippocampus, having Young (12 weeks) rats as a control. The midbrain VTA operates as a hub amidst affective and cognitive facets, processing sensory inputs related to motivated behaviours and hippocampal memory. Increasing evidence shows direct dopaminergic and non-dopaminergic input from the VTA to the hippocampus. Methods Aged Superior and Inferior male rats were selected from a cohort of 88 animals based on their performance in a spatial learning and memory task. Using in vivo single-cell recording in the VTA, we examined the electrical activity of different neuronal populations (putative dopaminergic, glutamatergic and GABAergic neurons). In the same animals, basal synaptic transmission and synaptic plasticity were examined in hippocampal slices. Results Electrophysiological recordings from the VTA and hippocampus showed alterations associated with aging per se, together with differences specifically linked to the cognitive status of aged animals. In particular, the bursting activity of dopamine neurons was lower, while the firing frequency of glutamatergic neurons was higher in VTA of Inferior old rats. The response to high-frequency stimulation in hippocampal slices also discriminated between Superior and Inferior aged animals. Discussion This study provides new insight into electrophysiological information underlying compromised cerebral ageing. Further understanding of brain senescence, possibly related to neurocognitive decline, will help develop new strategies towards the preservation of a high quality of life.
Behaviour of nitriding layers for condition of small amplitude fretting

Purpose: It was explored fretting resistance titanic alloy VT3-1 (Ti-Al6-Cr2-Mo2,5) after low temperature ionic nitriding in unhydrogen environment. Design/methodology/approach: Small amplitude fretting was initiated by the dynamic contact of ball and flat in the regime of the partial slip on edge of spot of contact. A method differs by simplicity and express determination of fretting resistance, namely areas of destruction by action of fretting for part nominally fixed contact - how the functions of cycles of loading. Findings: As a result of fretting the central region of sticking decreasing, and the edge of areas of fretting are increasing. Practical implications: The method of initiation of small amplitude fretting within bounds of preliminary displacement is offered. On the offered method the destruction of titanic alloys is explored at fretting and influencing of ionic nitriding on fretting. By a computation method the work of forces of friction in the area of
Chromium speciation in water using magnetic polyaniline nanoparticles coupled with microsampling injection-flame atomic absorption spectroscopy

The chromium speciation procedure was optimized using magnetic polyaniline nanoparticles (Fe3O4@PANI NPs) solid-phase extraction coupled with microsampling injection-flame atomic absorption spectrometry (MIS-FAAS). Chromium speciation was successfully achieved by Fe3O4@PANI NPs at pH 8.0. The recoveries obtained for Cr(III) and Cr(VI) were above 95% and under 5%, respectively. Recoveries of over 95% for Cr(III) from 40.0 mL of the sample were obtained using 25 mg Fe3O4@PANI NPs and 500 μL of 0.2% (w/v) thiourea (TU) solution prepared in 2 mol L−1 HCl as eluent. Total chromium as Cr(III) was extracted quantitatively after reducing the Cr(VI) to Cr(III). The linear range, detection limit, preconcentration factor, and precision of the optimized method for Cr(III) in aqueous solution were 2.5–94.0 μg L−1, 0.335 μg L−1, 80, and 3.07%, respectively. The validation of the method was controlled using SPS-WW2 Batch 114 wastewater and BCR-715 industrial wastewater as standard reference materials (SRMs) for environmental water, and the obtained results were in close agreement with the certified values.
Use of Monoglycerides and Diglycerides to Mitigate Poultry Production Losses: A Review

Simple Summary This review summarizes the available literature on the impact of monoglycerides and diglycerides on poultry productivity and health. Consumption of poultry meat and eggs continues to increase in all geographies. Monoglycerides and diglycerides are products that producers can use to help fill the demand for their products while meeting the needs of today’s consumers, retailers, and policymakers. Abstract Consumer preference dictates not only what food is consumed but also how that food is produced. Ingredients in livestock feed that are not antibiotics, not genetically modified, and not of animal origin but that are nutrient-like tend to be more acceptable to consumers, retailers, and producers. Mono- and diglycerides (MDG) fit these criteria, are commonly used in food, and are generally recognized as safe. But beyond being emulsifiers and a source of energy, MDG are also known to have antimicrobial, immune, and microbiome modulation and angiogenic activity. MDG in broiler diets have been shown to impact a variety of immune-related functions such as the regulation of circulating antibodies, as well as decreased gene expression or protein concentration of pro-inflammatory cytokines like TNF-α, IL-1β, IL-6, and IFN-γ. In addition, MDG can affect metabolic function and intestinal integrity. Results of this review show that MDG can serve as antimicrobial and growth-supporting alternatives for reducing poultry production losses, improving resource utilization and meeting consumer demand for sustainably produced and safe animal protein.
Therapeutic Effect of Natural Products and Dietary Supplements on Aflatoxin-Induced Nephropathy

Aflatoxins are harmful natural contaminants found in foods and are known to be hepatotoxic. However, recent studies have linked chronic consumption of aflatoxins to nephrotoxicity in both animals and humans. Here, we conducted a systematic review of active compounds, crude extracts, herbal formulations, and probiotics against aflatoxin-induced renal dysfunction, highlighting their mechanisms of action in both in vitro and in vivo studies. The natural products and dietary supplements discussed in this study alleviated aflatoxin-induced renal oxidative stress, inflammation, tissue damage, and markers of renal function, mostly in animal models. Therefore, the information provided in this review may improve the management of kidney disease associated with aflatoxin exposure and potentially aid in animal feed supplementation. However, future research is warranted to translate the outcomes of this study into clinical use in kidney patients.
A comparison of manned and unmanned aerial Lidar systems in the context of sustainable forest management

Sustainable forest management practices support the growing effort to make efficient use of natural resources without a reduction in future yield potential. These efforts require accurate and timely measurement of the world’s forests to monitor volume, biomass, and stored carbon level changes. Historically, these measurements have been effected through manual measurements of individual trees in representative plots, spaced throughout the forest region. Through the process of imputation, the missing values are interpolated, often through a regression model based on the collected reference data. Remote sensing technologies, specifically lidar (light detection and ranging), possess the capability to rapidly capture structural data of entire forests; however, airborne lidar mounted on manned aircraft can be cost prohibitive. The increasing capabilities and reduction of cost associated with small unmanned aerial systems (sUAS), coupled with the decreasing size and mass of lidar sensors, have opened the possibility for these platforms to provide a cost effective method with comparable performance. This study completes a cost comparison of the two platforms using a regression model of above ground live carbon as a method of comparing performance in context of sustainable forestry. The sUAS performed comparably based on our two data sets. The sUAS achieved a R2 of 0.74, and the manned aircraft lidar system achieved an R2 of 0.61, with both models producing RSE(%) within one percent of each other. The sUAS has the capability to be competitive with the manned aircraft at a cost of $8.12/acre for the study area, compared to the manned aircraft’s cost of $8.09/acre. The added benefits of sUAS include rapid deployment and low mobilization costs, while disadvantages include operational considerations, such as the need for line-of-sight operations. However, we concluded that sUAS is a viable alternative to airborne manned sensing platforms for fine-scale, local forest assessments.
A Scalable and Robust Chloroplast Genotyping Solution: Development and Application of SNP and InDel Markers in the Maize Chloroplast Genome

Maize(Zea mays. L) is a globally important crop, and understanding its genetic diversity is crucial for plant breeding phylogenetic analyses and comparative genetics. While nuclear markers have been extensively used for mapping agriculturally important genes, they are limited in recognizing characteristics, such as cytoplasmic male sterility and reciprocal cross hybrids. In this study, we performed next-generation sequencing of 176samples, and the maize cultivars represented five distinct groups. A total of 89 single nucleotide polymorphisms (SNPs) and 11 insertion/deletion polymorphisms (InDels) were identified. To enable high-throughput detection, we successfully amplified and confirmed 49 SNP and InDel markers, which were defined as a Varietal Chloroplast Panel (VCP) using the Kompetitive Allele Specific PCR (KASP). The specific markers provided a valuable tool for identifying chloroplast groups. The verification experiment, focusing on the identification of reciprocal cross hybrids and cytoplasmic male sterility hybrids, demonstrated the significant advantages of VCP markers in maternal inheritance characterization. Furthermore, only a small subset of these markers is needed to provide useful information, showcasing the effectiveness of these markers in elucidating the artificial selection process of elite maize lines.
Extending removal and distance-removal models for abundance estimation by modeling detections in continuous time

In this disseration, we estimate abundance from removal-sampled animal wildlife pointcount surveys, focusing on models to account for heterogeneous detection probabilities. In contrast to many published models, our research treats individual times to detection as continuoustime responses. Adopting this method enables us to ask questions that are impractical under existing discrete-time models. We accomplish our analyses by using a parametric survival analysis approach within the N-mixture class of hierarchical animal abundance models. In Chapter 2, we construct models for removal-sampled data that allow detection rates to change systematically over the course of each observation period. Most studies assume detection rates are constant, but our analysis demonstrates this assumption to be very informative, leading to biased and overly precise estimates. Non-constant models prove less biased with better coverage statistics over a range of simulated datasets. In Chapter 3, we extend the continuoustime modeling approach to distance-removal sampled surveys. We introduce a new model that successfully integrates two subtly different existing mechanisms for modeling distance-removal surveys: one that focuses on detecting available individuals and one that focuses on detecting availability cues (e.g. bird calls). We articulate the distinctions between the two and place them within current terminology for availability and perceptibility. Our new model accurately estimates abundance and detection from datasets simulated via either mechanism, but models that assume only one mechanism are often not robust to misspecification. In Chapter 4, we apply our model from Chapter 3 to six avian species monitored in removaland distance-sampled point-count surveys in Iowa agricultural fields. We articulate several ways in which the model does not match data characteristics, and we identify priorities for developing this model in order to make it more flexible and feasible.
The Uricosuric Effect of SGLT2 Inhibitors Is Maintained in the Long Term in Patients with Chronic Kidney Disease and Type 2 Diabetes Mellitus

(1) Background: Sodium–glucose co-transporter 2 inhibitors (SGLT2is) increase uric acid excretion. The intensity of uricosuria is linked to glycosuria. (2) Methods: We aim to analyze the effect of SGLT2 inhibitors on urinary fractional excretion (FE) of uric acid and glucose in patients with type 2 diabetes mellitus (T2DM) and chronic kidney disease (CKD) in a single-center retrospective study with patients with T2DM and CKD who started on treatment with SGLT2is. Patients on renal replacement therapy or with glucagon-like peptide-1 (GLP1) analogs were excluded. Subgroup analysis was performed according to the estimated glomerular filtration rate (eGFR), the SGLT2i molecule, the main comorbidities, and concomitant treatment. As a secondary objective, the study analyzed the effect of SGLT2 inhibitors on uricemia levels. (3) Results: Seventy-three patients were analyzed, with a mean follow-up of 1.2 years. Uric acid and glucose FE significantly increased after the initiation of SGLT2is. This increase remained stable during the follow-up without differences among eGFR groups. No significant reduction in uricemia was observed. However, a trend towards a decrease was observed. (4) Conclusion: The use of SGLT2is in patients with CKD and T2DM is associated with an increase in uric acid FE, which maintains stability irrespective of glomerular filtration loss at least during 24 months of follow-up.
A Herbal Prescription of Insamyangyeongtang as a Therapeutic Agent for Frailty in Elderly: A Narrative Review

Frailty is a major geriatric syndrome with a multifactorial etiology that induces a decline in multiple physiological and psychological functions. In traditional East Asian medicine (TEAM), qi and blood deficiency clinically represent as fatigue, anemia, anorexia, decreased strength after illness, and weakness, commonly interpretated as frailty. An herbal prescription of Insamyangyeongtang (IYT, Ninjin’yoeito in Japanese, Ren-Shen-Yang-Rong-Tang in Chinese) tonifies qi and blood and has the potential to treat multiple targets caused by qi and blood deficiency. As the population ages and frailty increases, there is an increase in the potential effectiveness of IYT in frailty. This study reviewed relevant clinical trials to provide an updated view on the effect of IYT on frailty. IYT has therapeutic effects on frailty associated with chronic respiratory diseases (e.g., chronic obstructive pulmonary disease) and cognitive impairments (e.g., Alzheimer’s disease) and improves respiratory symptoms and cognition. IYT also has therapeutic effects on weight gain, muscle mass, and strength, and improves nutritional status in frail elderly individuals who have decreased muscle mass and strength, loss of appetite, and weight loss. The same effect has been shown in frailty in elderly individuals with rehabilitation treatment and chronic diseases. IYT also improves frailty associated with symptoms such as intractable dizziness and genitourinary symptoms. The beneficial effects of IYT in several diseases could be important for medication replacement, reduction, and prevention of polypharmacy. Based on the results of this review, we suggest that IYT has the potential to be a therapeutic agent against frailty.
Benchmarking the influence of pre-training on explanation performance in MR image classification

Convolutional Neural Networks (CNNs) are frequently and successfully used in medical prediction tasks. They are often used in combination with transfer learning, leading to improved performance when training data for the task are scarce. The resulting models are highly complex and typically do not provide any insight into their predictive mechanisms, motivating the field of “explainable” artificial intelligence (XAI). However, previous studies have rarely quantitatively evaluated the “explanation performance” of XAI methods against ground-truth data, and transfer learning and its influence on objective measures of explanation performance has not been investigated. Here, we propose a benchmark dataset that allows for quantifying explanation performance in a realistic magnetic resonance imaging (MRI) classification task. We employ this benchmark to understand the influence of transfer learning on the quality of explanations. Experimental results show that popular XAI methods applied to the same underlying model differ vastly in performance, even when considering only correctly classified examples. We further observe that explanation performance strongly depends on the task used for pre-training and the number of CNN layers pre-trained. These results hold after correcting for a substantial correlation between explanation and classification performance.
The Effect of Different Grape Varieties and Adding Different Ratios of Mustard Seeds on the Phenolic Compounds, Antioxidant Capacity, and Bioaccessibility Values of Hardaliye under In Vitro Digestion

Hardaliye, grape-based fermented beverage, rich in antioxidant phenolic compounds. Bioaccessibility and antioxidant capacity of bioactive compounds in hardaliye, produced using varying amounts of mustard seeds (1%, 1.5%, and 2%) with Merlot and Papazkarası grape varieties, were evaluated under in vitro gastrointestinal digestion conditions. After digestion, Merlot and Papazkarası samples with 2% addition of mustard seed showed significantly higher total phenolic compounds (TPC) (358.48±14.73 and 89.01±2.42 mg GAE/L, respectively) compared to other samples (P<0.05). 2% mustard seed added Merlot samples resulted in the highest 1,1-diphenyl-2-picrylhydrazyl (DPPH) and cupric reducing antioxidant capacity (CUPRAC) values (19.06±3.91 and 9.96±1.83 mmol TEAC/L, respectively) which differed significantly from other samples (P<0.05). The Merlot sample with 2% addition of mustard seed showed significantly higher TPC, total flavonoid compounds (TFC), DPPH, and CUPRAC bioaccessibility values compared to other Merlot samples (P<0.05). For Papazkarası samples with 2% mustard seed addition, significant differences were observed only in terms of TPC and TFC bioaccessibility values (15.87±2.30% and 15.27±1.29%, respectively) compared to samples with 1% and 1.5% mustard seed addition (P<0.05). The study demonstrated that the bioaccessibility of bioactive compounds in hardaliye can vary depending on the grape variety and to some extent, the use of mustard seed. This suggests that the food matrix and interaction with other food matrices in the environment can affect the stability and bioavailability of bioactive compounds during simulated digestion.