Miracle-dz/UniFAR-FTUs huggingface dataset:
Statistical optimization of a podoviral anti-MRSA phage CCASU-L10 generated from an under sampled repository: Chicken rinse

Introduction The insurgence of antimicrobial resistance is an imminent health danger globally. A wide range of challenging diseases are attributed to methicillin-resistant Staphylococcus aureus (MRSA) as it is weaponized with a unique array of virulence factors, and most importantly, the resistance it develops to most of the antibiotics used clinically. On that account, the present study targeted the optimization of the production of a bacteriophage active against MRSA, and evaluating some of its characters. Methods and results The bacteriophage originated from a quite peculiar environmental source, raw chicken rinse and was suggested to belong to Podoviridae, order Caudovirales. It withstood a variety of extreme conditions and yield optimization was accomplished via the D-optimal design by response surface methodology (RSM). A reduced quadratic model was generated, and the ideal production conditions recommended were pH 8, glycerol 0.9% v/v, peptone 0.08% w/v, and 107 CFU/ml as the host inoculum size. These conditions led to a two-log fold increase in the phage titer (1.17x10¹² PFU/ml), as compared to the regular conditions. Discussion To conclude, statistical optimization successfully enhanced the output of the podoviral phage titer by two-log fold and therefore, can be regarded as a potential scale-up strategy. The produced phage was able to tolerate extreme environmental condition making it suitable for topical pharmaceutical preparations. Further preclinical and clinical studies are required to ensure its suitability for use in human.
Preoperative inflammatory markers predict postoperative clinical outcomes in patients undergoing heart valve surgery: A large-sample retrospective study

Introduction Preoperative inflammation affects the postoperative outcomes of patients undergoing heart valve surgery. This study aimed to explore the role and predictive effects of preoperative inflammation on the primary outcomes after valvular cardiac surgery. Methods This retrospective study utilized a medical recording system to screen 5075 patients who underwent heart valve surgery. Data on the C-reactive protein (CRP) levels, erythrocyte sedimentation rate (ESR), and neutrophil-to-lymphocyte ratio (NLR) before heart valve surgery were collected from the hospital’s medical system. Postoperative hepatic insufficiency, acute kidney injury, heart failure, and myocardial damage were assessed using blood indicators. Patients with and without prolonged mechanical ventilation, extended intensive care unit stays, prolonged hospital stays, and death within 30 days after surgery (considered the primary outcome in this study) were compared. Group comparisons, receiver operating characteristic (ROC) curve analyses, and logistic analyses were performed to determine the associations between preoperative inflammation and outcomes after heart valve surgery. Results A total of 3249 patients were included in the analysis. Significant differences in CRP level, ESR, and NLR were found between patients with and without postoperative adverse outcomes. ROC analysis showed that CRP levels >5 mg/L effectively predicted postoperative heart failure, and NLR >3.5 had a good predictive effect on all-cause mortality within 30 days after surgery. Patients with CRP levels >5 mg/L had a higher incidence of postoperative heart failure than other patients (20.7% vs. 12.6%, P<0.001), with a relative risk of 1.447 (95% confidence interval: 1.155–1.814). Patients with NLR >3.5 had a higher incidence of death within 30 days after surgery (5.3% vs. 1.2%, P<0.001), with a relative risk of 3.236 (95% confidence interval: 1.773–5.906). Conclusion Preoperative inflammation can affect postoperative outcomes in patients undergoing heart valve surgery. CRP level >5 mg/L and NLR >3.5 can effectively predict postoperative heart failure and death within 30 days after surgery, respectively.
Tunable and nonlinear fishnet metamaterials based on liquid crystal infiltration

We demonstrate the use of liquid crystal infiltration of fishnet structures for the realization of highly tunable and nonlinear optical metamaterials. We show that fishnet metamaterials infiltrated with nematic liquid crystals can exhibit strong nonlinear response at moderate laser powers. We also show that this nonlinear response arises due to the molecular orientation of the liquid crystal molecules and can be therefore be fine-tuned with an electric field, opening new opportunities for electrically tunable nonlinear metamaterials.
Artificial intelligence for clinical decision support for monitoring patients in cardiovascular ICUs: A systematic review

Background Artificial intelligence (AI) and machine learning (ML) models continue to evolve the clinical decision support systems (CDSS). However, challenges arise when it comes to the integration of AI/ML into clinical scenarios. In this systematic review, we followed the Preferred Reporting Items for Systematic reviews and Meta-Analyses (PRISMA), the population, intervention, comparator, outcome, and study design (PICOS), and the medical AI life cycle guidelines to investigate studies and tools which address AI/ML-based approaches towards clinical decision support (CDS) for monitoring cardiovascular patients in intensive care units (ICUs). We further discuss recent advances, pitfalls, and future perspectives towards effective integration of AI into routine practices as were identified and elaborated over an extensive selection process for state-of-the-art manuscripts. Methods Studies with available English full text from PubMed and Google Scholar in the period from January 2018 to August 2022 were considered. The manuscripts were fetched through a combination of the search keywords including AI, ML, reinforcement learning (RL), deep learning, clinical decision support, and cardiovascular critical care and patients monitoring. The manuscripts were analyzed and filtered based on qualitative and quantitative criteria such as target population, proper study design, cross-validation, and risk of bias. Results More than 100 queries over two medical search engines and subjective literature research were developed which identified 89 studies. After extensive assessments of the studies both technically and medically, 21 studies were selected for the final qualitative assessment. Discussion Clinical time series and electronic health records (EHR) data were the most common input modalities, while methods such as gradient boosting, recurrent neural networks (RNNs) and RL were mostly used for the analysis. Seventy-five percent of the selected papers lacked validation against external datasets highlighting the generalizability issue. Also, interpretability of the AI decisions was identified as a central issue towards effective integration of AI in healthcare.
Altered coronary artery function, arteriogenesis and endothelial YAP signaling in postnatal hypertrophic cardiomyopathy

Introduction: Hypertrophic cardiomyopathy (HCM) is a cardiovascular genetic disease caused largely by sarcomere protein mutations. Gaps in our understanding exist as to how maladaptive sarcomeric biophysical signals are transduced to intra- and extracellular compartments leading to HCM progression. To investigate early HCM progression, we focused on the onset of myofilament dysfunction during neonatal development and examined cardiac dynamics, coronary vascular structure and function, and mechano-transduction signaling in mice harboring a thin-filament HCM mutation. Methods: We studied postnatal days 7–28 (P7–P28) in transgenic (TG) TG-cTnT-R92Q and non-transgenic (NTG) mice using skinned fiber mechanics, echocardiography, biochemistry, histology, and immunohistochemistry. Results: At P7, skinned myofiber bundles exhibited an increased Ca2+-sensitivity (pCa50 TG: 5.97 ± 0.04, NTG: 5.84 ± 0.01) resulting from cTnT-R92Q expression on a background of slow skeletal (fetal) troponin I and α/β myosin heavy chain isoform expression. Despite the transition to adult isoform expressions between P7–P14, the increased Ca2+- sensitivity persisted through P28 with no apparent differences in gross morphology among TG and NTG hearts. At P7 significant diastolic dysfunction was accompanied by coronary flow perturbation (mean diastolic velocity, TG: 222.5 ± 18.81 mm/s, NTG: 338.7 ± 28.07 mm/s) along with localized fibrosis (TG: 4.36% ± 0.44%, NTG: 2.53% ± 0.47%). Increased phosphorylation of phospholamban (PLN) was also evident indicating abnormalities in Ca2+ homeostasis. By P14 there was a decline in arteriolar cross-sectional area along with an expansion of fibrosis (TG: 9.72% ± 0.73%, NTG: 2.72% ± 0.2%). In comparing mechano-transduction signaling in the coronary arteries, we uncovered an increase in endothelial YAP expression with a decrease in its nuclear to cytosolic ratio at P14 in TG hearts, which was reversed by P28. Conclusion: We conclude that those early mechanisms that presage hypertrophic remodeling in HCM include defective biophysical signals within the sarcomere that drive diastolic dysfunction, impacting coronary flow dynamics, defective arteriogenesis and fibrosis. Changes in mechano-transduction signaling between the different cellular compartments contribute to the pathogenesis of HCM.
Microalgal polyunsaturated fatty acids: Hotspots and production techniques

Algae play a crucial role in the earth’s primary productivity by producing not only oxygen but also a variety of high-value nutrients. One such nutrient is polyunsaturated fatty acids (PUFAs), which are accumulated in many algae and can be consumed by animals through the food chain and eventually by humans. Omega-3 and omega-6 PUFAs are essential nutrients for human and animal health. However, compared with plants and aquatic sourced PUFA, the production of PUFA-rich oil from microalgae is still in the early stages of exploration. This study has collected recent reports on algae-based PUFA production and analyzed related research hotspots and directions, including algae cultivation, lipids extraction, lipids purification, and PUFA enrichment processes. The entire technological process for the extraction, purification and enrichment of PUFA oils from algae is systemically summarized in this review, providing important guidance and technical reference for scientific research and industrialization of algae-based PUFA production.
Impact of selenium biofortification on production characteristics of forages grown following standard management practices in Oregon

Introduction Low selenium (Se) concentrations in soils and plants pose a health risk for ruminants consuming locally-grown forages. Previous studies have shown that Se concentrations in forages can be increased using soil-applied selenate amendments. However, the effects of foliar selenate amendments applied with traditional nitrogen-phosphorus-potassium-sulfur (NPKS) fertilizers on forage yields, and nutrient contents, and agronomic efficiencies are unknown. Methods Using a split plot design, we determined the effects of springtime sodium selenate foliar amendment rates (0, 45, and 90 g Se ha-1) and NPKS application (none, NPK for grasses/PK for alfalfa, and NPKS/PKS fertilization at amounts adapted to meet local forage and soil requirements) on forage growth and N, S, and Se concentrations, yields, and agronomic efficiencies. This 2-year study was conducted across Oregon on four representative forage fields: orchardgrass (Dactylis glomerata L.) in Terrebonne (central Oregon), grass-clover mixture in Roseburg (southwestern Oregon), and both grass mixture and alfalfa (Medicago sativa L.) fields in Union (eastern Oregon). Results Grasses grew poorly and were low in N content without NPK fertilization. Fertilization with NPK/PK promoted forage growth, increased forage N concentrations, and had to be co-applied with S when plant available S was low. Without Se amendment, forage Se concentrations were low and further decreased with NPKS/PKS fertilization. Selenate amendment linearly increased forage Se concentration without adversely affecting forage yields, N and S concentrations, or N and S agronomic efficiencies. Discussion Importantly, S fertilization did not interfere with Se uptake in Se amended plots. In conclusion, co-application of NPKS/PKS fertilizers and foliar sodium selenate in springtime is an effective strategy to increase forage total Se concentrations, while maintaining optimal growth and quality of Oregon forages.
High order methods for complicated flows interacting with shock waves

We present in this paper numerical simulations of reactive flows interacting with shock waves. We argue that Spectral methods are suitable for these problems and review the recent developments in spectral methods that have made them powerful numerical tools appropriate for long term integrations of complicated flows, even in the presence of shock waves. A spectral code is described in detail, and the theory that leads to each of its components is explained. Results of interactions of hydrogen jets with shock waves are presented and analyzed, and comparisons with ENO finite difference schemes are carried out.
Prevalence, Cardiometabolic Comorbidities and Reporting of Chronic Kidney Disease; A Hungarian Cohort Analysis

Objectives: Chronic kidney disease (CKD) implies increased comorbidity burden, disability, and mortality, becoming a significant public health problem worldwide, however, prevalence data are lacking in Hungary. Methods: We determined CKD prevalence, stage distribution, comorbidities using estimated glomerular filtration rate (eGFR), albuminuria, and international disease codes in a cohort of healthcare utilizing residents within the catchment area of the University of Pécs, in the County Baranya, Hungary, between 2011 and 2019 by database analysis. The number of laboratory-confirmed and diagnosis-coded CKD patients were compared. Results: Of the total 296,781 subjects of the region, 31.3% had eGFR tests and 6.4% had albuminuria measurements, of whom we identified 13,596 CKD patients (14.0%) based on laboratory thresholds. Distribution by eGFR was presented (G3a: 70%, G3b: 22%, G4: 6%, G5: 2%). Amongst all CKD patients 70.2% had hypertension, 41.5% diabetes, 20.5% heart failure, 9.4% myocardial infarction, 10.5% stroke. Only 28.6% of laboratory-confirmed cases were diagnosis-coded for CKD in 2011–2019. Conclusion: CKD prevalence was 14.0% in a Hungarian subpopulation of healthcare-utilizing subjects in 2011–2019, and substantial under-reporting of CKD was also found.
Mitochondrial redox system: A key target of antioxidant therapy to prevent acquired sensorineural hearing loss

Noise (noise-induced hearing loss), and ototoxic drugs (drug-induced ototoxicity), and aging (age-related hearing loss) are the major environmental factors that lead to acquired sensorineural hearing loss. So far, there have been numerous efforts to develop protective or therapeutic agents for acquired hearing loss by investigating the pathological mechanisms of each types of hearing loss, especially in cochlear hair cells and auditory nerves. Although there is still a lack of information on the underlying mechanisms of redox homeostasis and molecular redox networks in hair cells, an imbalance in mitochondrial reactive oxygen species (ROS) levels that enhance oxidative stress has been suggested as a key pathological factor eventually causing acquired sensorineural hearing loss. Thus, various types of antioxidants have been investigated for their abilities to support auditory cells in maintenance of the hearing function against ototoxic stimuli. In this review, we will discuss the scientific possibility of developing drugs that target particular key elements of the mitochondrial redox network in prevention or treatment of noise- and ototoxic drug-induced hearing loss.
Maintenance and recall of memory T cell populations against tuberculosis: Implications for vaccine design

Despite the widespread use of standardised drug regimens, advanced diagnostics, and Mycobacterium bovis Bacille-Calmette-Guérin (BCG) vaccines, the global tuberculosis (TB) epidemic remains uncontrollable. To address this challenge, improved vaccines are urgently required that can elicit persistent immunologic memory, the hallmark of successful vaccines. Nonetheless, the processes underlying the induction and maintenance of immunologic memory are not entirely understood. Clarifying how memory T cells (Tm cells) are created and survive long term may be a crucial step towards the development of effective T cell–targeted vaccines. Here, we review research findings on the memory T cell response, which involves mobilization of several distinct Tm cell subsets that are required for efficient host suppression of M. tuberculosis (Mtb) activity. We also summaries current knowledge related to the T cell response-based host barrier against Mtb infection and discuss advantages and disadvantages of novel TB vaccine candidates.
Exploring the Tropically Excited Arctic Warming Mechanism with Station Data: Links between Tropical Convection and Arctic Downward Infrared Radiation

AbstractThe Tropically Excited Arctic Warming (TEAM) mechanism ascribes warming of the Arctic surface to tropical convection, which excites poleward-propagating Rossby wave trains that transport water vapor and heat into the Arctic. A crucial component of the TEAM mechanism is the increase in downward infrared radiation (IR) that precedes the Arctic warming. Previous studies have examined the downward IR associated with the TEAM mechanism using reanalysis data. To corroborate previous findings, this study examines the linkage between tropical convection, Rossby wave trains, and downward IR with Baseline Surface Radiation Network (BSRN) downward IR station data. The physical processes that drive changes in the downward IR are also investigated by regressing 300-hPa geopotential height, outgoing longwave radiation, water vapor flux, ERA-Interim downward IR, and other key variables against the BSRN downward IR at Barrow, Alaska, and Ny-Alesund, Spitsbergen.Both the Barrow and the Ny-Alesund station downward .
Dust Voids in Magnetized Dusty Plasmas

The emergence of dust voids in magnetized dusty plasmas is investigated theoretically. Using a fully nonlinear gyrokinetic description for ions, a self-consistent stationary solution of the Vlasov–Maxwell system is found in the form of a cylindrically symmetric ion hole, which causes a complete local depletion of negatively charged dust grains. The ion drag force does not play a significant role in the creation of these nonlinear structures. Instead, they are supported by the population of resonant ions, whose guiding centers are trapped in the direction perpendicular to the magnetic field by the combined action of the grad-B, polarization and finite Larmor radius effects.
Cerebellar contribution to the regulation of defensive states

Despite fine tuning voluntary movement as the most prominently studied function of the cerebellum, early human studies suggested cerebellar involvement emotion regulation. Since, the cerebellum has been associated with various mood and anxiety-related conditions. Research in animals provided evidence for cerebellar contributions to fear memory formation and extinction. Fear and anxiety can broadly be referred to as defensive states triggered by threat and characterized by multimodal adaptations such as behavioral and cardiac responses integrated into an intricately orchestrated defense reaction. This is mediated by an evolutionary conserved, highly interconnected network of defense-related structures with functional connections to the cerebellum. Projections from the deep cerebellar nucleus interpositus to the central amygdala interfere with retention of fear memory. Several studies uncovered tight functional connections between cerebellar deep nuclei and pyramis and the midbrain periaqueductal grey. Specifically, the fastigial nucleus sends direct projections to the ventrolateral PAG to mediate fear-evoked innate and learned freezing behavior. The cerebellum also regulates cardiovascular responses such as blood pressure and heart rate-effects dependent on connections with medullary cardiac regulatory structures. Because of the integrated, multimodal nature of defensive states, their adaptive regulation has to be highly dynamic to enable responding to a moving threatening stimulus. In this, predicting threat occurrence are crucial functions of calculating adequate responses. Based on its role in prediction error generation, its connectivity to limbic regions, and previous results on a role in fear learning, this review presents the cerebellum as a regulator of integrated cardio-behavioral defensive states.
Two-photon polymerization of hybrid polymers for applications in micro-optics

Miniaturization and higher integration of opto-electronic components require highly sophisticated optical designs. This creates the demand for freeform technologies like Two-Photon Polymerization (2PP) and new specially adapted materials like hybrid polymers (ORMOCERRs). Recent progress in the fabrication of microoptical structures using 2PP and specially designed hybrid polymers is presented. Among the structures are freeform and aberration-optimized microlenses and multilevel diffractive optical elements. These components are discussed with respect to fabrication process and their resulting optical performance. Furthermore, 2PP-initiated refractive index modification, offering high potential for energy-efficient fabrication of 3D optical interconnects, is discussed.
Spatial Stability of Jets: The Nonaxisymmetric Fundamental and Reflection Modes

A spatial stability analysis of the relativistic dispersion relation governing the growth and propagation of harmonic components comprising a perturbation to the surface of a cylindrical jet is performed. The spatial growth of harmonic components associated with the nonaxisymmetric fundamental solution and reflection solutions of several Fourier modes are analyzed. Approximate analytical expressions describing resonant frequencies and wavelengths, and maximum growth rates at resonance applicable to relativistic jets are found from the dispersion relation, and the nature of the resonances is explored. On transonic jets there is only a fundamental solution for each Fourier mode with no resonance or maximum growth rate. On supersonic jets there is a fundamental solution and reflection solutions for each Fourier mode, and each solution contains a resonance at which the growth rate is a maximum. A numerical analysis of the fundamental and first three reflection solutions of the axisymmetric and first three nonaxisymmetric Fourier modes is performed. The numerical analysis is restricted to nonrelativistic flows but otherwise covers a broad range of Mach numbers and jet densities. The numerical results are used along with the analytical results to obtain accurate expressions for resonant frequencies, wavelengths, and growth rates as a function of Mach numnbermore » and jet density. In all cases the fastest spatial growth rate at a given frequency is of harmonic components associated with the fundamental solution of one of the nonaxisymmetric Fourier modes. The application of these results to jet structure and implication of these results for jet structure in extragalactic radio sources are considered. 23 references. « less
Acoustic streaming jets: A scaling and dimensional analysis

We present our work on acoustic streaming free jets driven by ultrasonic beams in liquids. These jets are steady flows generated far from walls by progressive acoustic waves. As can be seen on figure 1, our set-up, denominated AStrID for Acoustic Streaming Investigation Device, is made of a water tank in which a 29 mm plane source emits continuous ultrasonic waves at typically 2 MHz. Our approach combines an experimental characterization of both the acoustic pressure field (hydrophone) and the obtained acoustic streaming velocity field (PIV visualization) on one hand, with CFD using an incompressible Navier-Stokes solver on the other hand.