Miracle-dz/UniFAR-FTUs huggingface dataset:
Whole‐mitochondrial genomes of Nannizziopsis provide insights in evolution and detection

Abstract Infectious fungal diseases can have devastating effects on wildlife health and a detailed understanding of the evolution of related emerging fungal pathogen along with the ability to detect them in the wild is considered indispensable for effective management strategies. Several fungi from the genera Nannizziopsis and Paranannizziopsis are emerging pathogens of reptiles and have been observed to cause disease in a wide range of taxa. Nannizziopsis barbatae has become a particularly important pathogen of Australian reptiles with an increasing number of herpetofauna being reported with cases of infection from across the country. Here, we present the mitochondrial genome sequences and phylogenetic analysis for seven species in this group of fungi uncovering new information on the evolutionary relationship of these emerging pathogens. From this analysis, we designed a species‐specific qPCR assay for the rapid detection of N. barbatae and demonstrate its application in a wild urban population of a dragon lizard.
Scaling behaviour of the thermopower in a two-component composite near a percolation threshold

An exact relation between the bulk effective Seebeck coefficient alpha e of a composite conductor and the bulk effective electrical and thermal conductivities sigma e and gamma e is used to study the scaling behaviour of alpha e near percolation. The behaviour turns out to be quite rich, as a result of its dependence on three dimensionless small parameters, namely, the electrical and thermal conductivity ratios of the two components sigma I/ sigma M, gamma I/ gamma M, and the distance away from the percolation threshold Delta p identical to pM-pc. The behaviour of the thermoelectric figure of merit Ze in the different parts of the critical region is also discussed.
Characterizing contaminant noise in barcoded perturbation experiments

Bursting cells lead to ambient RNA that contaminates sequencing data. This process is especially problematic in perturbation experiments where transcription factors are implanted into cells to determine their effects. The presence of contaminants makes it difficult to determine whether a factor is truly expressed in the cell. This paper studies the properties of contaminant noise from an analytical perspective, showing that the cell bursting process constrains the form of the noise distribution across factors. These constraints can be leveraged to improve decontamination by removing counts that are more likely the result of noise than expression. In two biological replicates of a perturbation experiment, run across two sequencing protocols, decontaminated counts agree with bulk genomic measurements of the transduction rate and are automatically corrected for differences in sequencing.
Roughness-induced transition and turbulent wedge spreading

Boundary layer transition triggered by a discrete roughness element generates a turbulent wedge that spreads laterally as it proceeds downstream. Historical literature reports the spreading half angle is approximately 6$^{\circ}$ in zero-pressure gradient flows regardless of Reynolds number and roughness shape. Recent simulations and experiments have sought to explain the lateral-spreading mechanism and have observed high- and low-speed streaks along the flanks of the wedge that appear central to the spreading process. To better elucidate the roles of Reynolds number and of streaks, a naphthalene flow-visualization survey and hotwire measurements are conducted over a wider range of Reynolds numbers and longer streamwise domain than previous experiments. The naphthalene results show that, while the mean spreading angle is consistent with the historical literature, there may be a weak dependency on $x$-based Reynolds number, which emerges as a result of the large sample size of the survey. The distance between the roughness element and the wedge origin exhibits a clear trend with the roughness-height-based Reynolds number. The hotwire measurements explain that this difference originates from whether breakdown occurs first in the central lobe or flanking streaks of the turbulent wedge. This observation highlights different transition dynamics at play within the supercritical regime. In agreement with past experiments, the hotwire measurements reveal that breakdown occurs in the wall normal shear layer above low-speed streaks. Due to the elongated streamwise extent of this experiment, secondary streak dynamics are also uncovered. A high-speed streak is produced directly downstream of the initiating low-speed streak. Subsequently, a new low-speed streak is observed outboard of the previous high-speed streak. This self-sustaining process is the driving mechanism of turbulent wedge spreading.
Three-Dimensional Particle-in-Cell Simulation of Fast Oscillation Startup in Strapped Magnetron Using Electrically Primed Electrons

Fast oscillation startup in a strapped magnetron using electrically primed electrons is demonstrated by a three-dimensional particle-in-cell simulation. The electrons are electrically primed by five-fold perturbation of the radial electric field along the azimuthal direction in a 10-vane strapped magnetron, and this leads to fast oscillation startup in the desired π-mode. The start of oscillation is advanced from 62 to 52 ns, and the time at which the steady state is reached from 130 to 85 ns when the radial variation of the protrusion and recession of the central region of the anode is 0.3 mm with an angular width of 0.5 mm.
Prognostic Value of Machine‐Learning‐Based PRAISE Score for Ischemic and Bleeding Events in Patients With Acute Coronary Syndrome Undergoing Percutaneous Coronary Intervention

Background The PRAISE (Prediction of Adverse Events Following an Acute Coronary Syndrome) score is a machine‐learning‐based model for predicting 1‐year all‐cause death, myocardial infarction, and Bleeding Academic Research Consortium (BARC) type 3/5 bleeding. Its utility in an unselected Asian population undergoing percutaneous coronary intervention for acute coronary syndrome remains unknown. We aimed to validate the PRAISE score in a real‐world Asian population. Methods and Results A total of 6412 consecutive patients undergoing percutaneous coronary intervention for acute coronary syndrome were prospectively included. The PRAISE scores were compared with established scoring systems (GRACE [Global Registry of Acute Coronary Events] 2.0, PRECISE‐DAPT (Predicting Bleeding Complications in Patients Undergoing Stent Implantation and Subsequent Dual Antiplatelet Therapy), and PARIS [Patterns of Non‐Adherence to Anti‐Platelet Regimen in Stented Patients]) to evaluate their discrimination, calibration, and reclassification. The risk of all‐cause mortality (hazard ratio [HR], 12.24 [95% CI, 5.32–28.15]) and recurrent acute myocardial infarction (HR, 3.92 [95% CI, 1.76–8.73]) was greater in the high‐risk group than in the low‐risk group. The C‐statistics for death, myocardial infarction, and major bleeding were 0.75 (0.67–0.83), 0.61 (0.52–0.69), and 0.62 (0.46–0.77), respectively. The observed to expected ratio of death, myocardial infarction, and major bleeding was 0.427, 0.260, and 0.106, respectively. Based on the decision curve analysis, the PRAISE score displayed a slightly greater net benefit for the 1‐year risk of death (5%–10%) than the GRACE score did. Conclusions The PRAISE score showed limited potential for risk prediction in our validation cohort with acute coronary syndrome. As a result, new prediction models or model refitting are required with improved discrimination and accuracy in risk prediction.
Dynamic decision modeling of production and marketing in low-carbon supply chains considering delay effects

This article deals with a dynamic decision-making model for a low-carbon supply chain which consists of a manufacturer and a platform retailer. Consideration of delay effects, a delayed differential equation for the effect of low-carbon investment efforts (LIE) in R&D and low-carbon promotional effort (LPE) on low-carbon goodwill (LG) is developed. Moreover, Hamilton's function is applied to solve the decision problem of optimal control. In the model, the differences between the agency selling and reselling patterns are analyzed by comparing LIE, LPE, LG, and net discounted profit. The commission system is a key measure for dynamic decision making on low-carbon products, while the commission rate is also an important reference point for decision making on cooperation patterns. In contrast to the findings of previous studies, this article derives specific thresholds for commissions. Furthermore, this study considers delay effects from a dynamic perspective. The findings show differences in both decentralized and centralized decision-making solutions for supply chains as the delay time changes. The proposed models are analyzed mathematically and numerical examples are illustrated to justify the feasibility of the model in reality. This study provides new insights into the choice of platform sales patterns for firms to develop agency selling and reselling partnership solutions in practice.
ABCB1 and ABCG2 Regulation at the Blood-Brain Barrier: Potential New Targets to Improve Brain Drug Delivery

The drug efflux transporters ABCB1 and ABCG2 at the blood-brain barrier limit the delivery of drugs into the brain. Strategies to overcome ABCB1/ABCG2 have been largely unsuccessful, which poses a tremendous clinical problem to successfully treat central nervous system (CNS) diseases. Understanding basic transporter biology, including intracellular regulation mechanisms that control these transporters, is critical to solving this clinical problem. In this comprehensive review, we summarize current knowledge on signaling pathways that regulate ABCB1/ABCG2 at the blood-brain barrier. In Section I, we give a historical overview on blood-brain barrier research and introduce the role that ABCB1 and ABCG2 play in this context. In Section II, we summarize the most important strategies that have been tested to overcome the ABCB1/ABCG2 efflux system at the blood-brain barrier. In Section III, the main component of this review, we provide detailed information on the signaling pathways that have been identified to control ABCB1/ABCG2 at the blood-brain barrier and their potential clinical relevance. This is followed by Section IV, where we explain the clinical implications of ABCB1/ABCG2 regulation in the context of CNS disease. Lastly, in Section V, we conclude by highlighting examples of how transporter regulation could be targeted for therapeutic purposes in the clinic. Significance Statement The ABCB1/ABCG2 drug efflux system at the blood-brain barrier poses a significant problem to successful drug delivery to the brain. The article reviews signaling pathways that regulate blood-brain barrier ABCB1/ABCG2 and could potentially be targeted for therapeutic purposes.
Mechanical Evaluation of Commercially Available Fibrin Sealants for Cartilage Repair.

OBJECTIVE Fibrin sealants are routinely used for intra-articular surgical fixation of cartilage fragments and implants. However, the mechanical properties of fibrin sealants in the context of cartilage repair are unknown. The purpose of this study was to characterize the adhesive and frictional properties of fibrin sealants using an ex vivo model. DESIGN Native bovine cartilage-bone composites were assembled with a single application of Tisseel or Vistaseal. Composites were tested in tension and lap shear. In addition, the coefficient of friction (COF) was measured in a native cartilage annulus model alone and with minced cartilage. Finally, the effect of a double application of fibrin sealant was evaluated. RESULTS There were no significant differences in tensile modulus, ultimate tensile strength (UTS), shear modulus, or ultimate shear strength (USS) between the 2 fibrin sealants. Both fibrin sealants demonstrated a UTS and USS of <8 and <30 kPa, respectively. There were no differences in COF between the sealants when tested alone or with minced cartilage. A double application of fibrin sealant did not alter the mechanical properties compared with a single application of fibrin sealant. CONCLUSIONS Fibrin sealant adhesive properties are not affected by the sealant type studied or the number of applications in a bovine cartilage-bone model. Fibrin sealant tribological properties are not affected by sealant type or the addition of minced cartilage. The adhesive properties of Tisseel and Vistaseal were less than those desired for the in vivo fixation of cartilage repair implants. These findings motivate the development of an improved cartilage-specific adhesive for cartilage repair applications.
p53 expression in cytology samples may represent a marker of early‐stage cancer

TP53 gene plays a major role in the negative control of cell proliferation and in the regulation of signaling cascades. TP53 mutation may have a relevant role in the malignant transformation of thyroid cells as well as thyroid tumor progression. TP53 mutation has been detected only in few well differentiated thyroid carcinomas and is absent in benign conditions.
Urea Reduction in Acute Kidney Injury and Mortality Risk

Introduction: Urea is a toxin present in acute kidney injury (AKI). We hypothesize that reduction in serum urea levels might improve clinical outcomes. We examined the association between the reduction in urea and mortality. Methods: Patients with AKI admitted to the Hospital Civil de Guadalajara were enrolled in this retrospective cohort study. We create 4 groups of urea reduction ratio (UXR) stratified by their decrease in urea from the highest index value in comparison to the value on day 10 (0%, 1–25%, 26–50%, and >50%), or at the time of death or discharge if prior to 10 days. Our primary endpoint was to observe the association between UXR and mortality. Secondary observations included determination of which types of patients achieved a UXR >50%, whether the modality of kidney replacement therapy (KRT) effected changes in UXR, and if serum creatinine (sCr) value changes were similarly associated with patient mortality. Results: A total of 651 AKI patients were enrolled. The mean age was 54.1 years, and 58.6% were male. AKI 3 was present in 58.5%; the mean admission urea was 154 mg/dL. KRT was started in 32.4%, and 18.9% died. A trend toward decreased risk of death was observed in association with the magnitude of UXR. The best survival (94.3%) was observed in patients with a UXR >50%, and the highest mortality (72.1%) was observed in patients achieving a UXR of 0%. After adjusting for age, sex, diabetes mellitus, CKD, antibiotics, sepsis, hypovolemia, cardio-renal syndrome, shock, and AKI stage, the 10-day mortality was higher in groups that did not achieve a UXR of at least 25% (OR: 1.20). Patients achieving a UXR >50% were most likely initiated on dialysis due to a diagnosis of the uremic syndrome or had a diagnosis of obstructive nephropathy. Percentage change in sCr was also associated with increased mortality risk. Conclusions: In our retrospective cohort of AKI patients, the percent decrease in UXR from admission was associated with a stratified risk of death. Patients with a UXR >25% had the best associated outcomes. Overall, a greater magnitude in UXR was associated with improved patient survival.
Updates in pediatric ultrasound

Purpose of review Point-of-care ultrasound (POCUS) has various diagnostic and therapeutic applications in the pediatric acute care setting that have an impact on clinical outcomes. Recent findings POCUS can improve diagnostic efficiency and expedite management in pediatric patients who present to the emergency department with common complaints such as respiratory distress, abdominal pain, shock, and pain. Summary Rapid advancements in POCUS have allowed it to become a powerful tool in pediatric care. As the clinical applications of ultrasound diversify, research is needed to evaluate impacts on healthcare outcomes, delivery, and costs.
Homogeneous Hypersurfaces in C 3 , Associated withaModel CR-Cubic

The model 4-dimensional CR-cubic in C3 has the following “model” property: it is (essentially) the unique locally homogeneous 4-dimensional CR-manifold in C3 with finite-dimensional infinitesimal automorphism algebra g and non-trivial isotropy subalgebra. We study and classify, up to local biholomorphic equivalence, all g-homogeneous hypersurfaces in C3 and also classify the corresponding local transitive actions of the model algebra g on hypersurfaces in C3.
Robot position servoing using visual gap measurement

A typical robotic work space is rigidly structured. In practice, work pieces may be positioned less than perfectly, requiring special end-effectors and jigs. The introduction of a vision system allows work pieces to be more loosely positioned. In addition, a visual servoing system can make use of dynamic information gathered from the actual workpiece as it is picked up, positioned and worked on. This information can be used, for example, to bring two work pieces into alignment. In particular we describe a system capable of maintaining a steady width gap between a fixed and a movable workpiece. In this paper we use modular feature-based tracking. The application uses a hierarchical feature model. Features may be composed of several other sub-ordinate features. The main feature used in our application is one of a gap measurement type. This feature uses thresholding and moment calculations to determine the width of a gap presented in its region of interest.
Extinction in polycrystalline materials

An expression is given for an extinction factor appropriate to powders composed of spherical perfect crystal grains or subgrains. This factor extrapolates to the dynamical theory value for the plane parallel plate in the symmetric Bragg case. Experimental tests of the theory have been made by nelitron diffraction experiments on polycrystalline specimens of MgO of controlled grain size. Agreement is excellent to an extinction level of y = 0·60.
Climatology of planetary wave type oscillations with periods of 2–20 days derived from O 2 atmospheric and OH(6-2) airglow observations at mid-latitude with SATI

Abstract. The presence of planetary wave type oscillations at mid-latitudes in the mesosphere/lower thermosphere region has been investigated using airglow observations. The observations were taken with a Spectral Airglow Temperature Imager (SATI) installed at Sierra Nevada Observatory (37.06° N, 3.38° W) at 2900 m height. Airglow data of the column emission rate of the O2 Atmospheric (0-1) band and of the OH Meinel (6-2) band and deduced rotational temperatures from 1998 to 2007 have been used in this study. From these observations a climatology of planetary wave type oscillations at this location is inferred. It has been found that the planetary wave type oscillations of 5-day period is predominant in our data throughout the year, with activity greater than 50% during March/April and October/November months. The planetary wave type oscillations of 2-day period is predominant during both solstices, being predominant during winter solstice in O2 while a 10-day oscillation appears throughout the year with activity around 20% and with maximum activity during spring and autumn equinoxes. The 16-day oscillation has maximum occurrence during autumn-winter while its activity is almost disappeared during spring-summer. No clear seasonal dependence of the amplitude of the planetary wave type oscillations was observed in the cases considered in this study. The waves simultaneously detected in the rotational temperatures deduced from both OH and O2 emissions usually show an upward energy propagation and are affected by dissipation processes.
Application and development of noninvasive biomarkers for colorectal cancer screening: a systematic review

Background: Colorectal cancer (CRC) is the second most common cause of cancer-related death (9.4% of the 9.9 million cancer deaths). However, CRC develops slowly, and early detection and intervention can effectively improve the survival rate and quality of life. Although colonoscopy can detect and diagnose CRC, it is unsuitable for CRC screening in average-risk populations. Some commercial kits based on DNA mutation or methylation are approved for screening, but the low sensitivity for advanced adenoma or early-stage CRC would limit the applications. Main results: Recently, researchers have focused on developing noninvasive or minimally invasive, easily accessible biomarkers with higher sensitivity and accuracy for CRC screening. Numerous reports describe advances in biomarkers, including DNA mutations and methylation, mRNA and miRNA, gut microbes, and metabolites, as well as low-throughput multiomics panels. In small cohorts, the specificity and sensitivity improved when fecal immunochemical testing combined with other biomarkers; further verification in large cohorts is expected. In addition, the continuous improvement of laboratory technology has also improved the sensitivity of detection technology, such as PCR, and the application of CRISPR/Cas technology. Besides, artificial intelligence has extensively promoted the mining of biomarkers. Machine learning was performed to construct a diagnosis model for CRC screening based on the cfDNA fragment features from whole-genome sequencing data. In another study, multiomics markers, including cfDNA, epigenetic, and protein signals, were also discovered by machine learning. Finally, advancements in sensor technology promote the applicability of volatile organic compounds in CRC early detection. Conclusion: Here, the authors review advances in early detection and screening of CRC based on different biomarker types. Most studies reported optimistic findings based on preliminary research, and prospective clinical studies are ongoing. These promising biomarkers are expected to more accurately identify early-stage patients with CRC and be applied in the future.