Miracle-dz/UniFAR-FTUs huggingface dataset:
Experimental Assessment of the Performance of Dual Pneumatic Vitreous Cutters According to Gauge and Cut Rate

Purpose To compare and analyze the performance of dual pneumatic ultra-high-speed vitreous cutters based on their cut rates, vacuum levels, and diameters in terms of flow rate and cutting time. Methods The Constellation Vision System was used to remove egg white for 30 seconds, after which we calculated the flow rate by measuring the change in weight. We then measured the time required to remove 4 mL of egg white. We tested the UltraVit (UV) 7,500 cuts per minute (cpm) probe and the Advanced UltraVit (AUV) 10,000 cpm probe in biased open duty cycle mode, using 23-, 25-, and 27-gauge probes, respectively. Results In biased open duty cycle, the flow rate tended to decrease as the cut rates increased for all three gauges. At the same cut rates, the flow rate increased as the vacuum level increased (p < 0.05), and as the diameter increased (p < 0.05). Among cutters with the same diameter, the AUV cutter showed higher flow rates than the UV cutter, with increases of 0.267 mL/ min (18.5%) at 27 gauge, 0.627 mL/min (20.8%) at 25 gauge, and 1.000 mL/min (20.7%) at 23 gauge (all p < 0.05). The times required to remove 4 mL of egg white took longer with the UV cutter than the AUV cutter for all three gauges (all p < 0.05). Conclusions The use of a smaller gauge vitreous cutter may reduce the flow rate and increase the time required for vitrectomy, but this can be partially compensated for by increasing the vacuum level as well as using a vitreous cutter with a higher maximum cut rate, improved port size, and improved duty cycle.
Qualitative metabolomics-based characterization of a phenolic UDP-xylosyltransferase with a broad substrate spectrum from Lentinus brumalis

Significance Biocatalysts became an attractive alternative to conventional chemical catalysts. Many natural enzymes need to be optimized through protein engineering for being applied as biocatalysts, and promiscuous enzymes are advantageous as a starting point. Here, we employed a mass spectrometry–based untargeted metabolomics analysis to navigate the catalytic activities of wood-decaying fungi against phytochemicals, hypothesizing that there will be enzymes with broad substrate specificity for detoxification of compounds remaining in dead plant bodies. The metabolomics analysis guided us to identify UGT66A1, an enzyme catalyzing O-xylosylation on diverse phenolic compounds including synthetic molecules. This case demonstrates the efficiency of the method described here as a method for enzyme discovery, as well as the potential of wood-decaying fungi as a pool of biocatalysts.
Budding uninhibited by benzimidazoles-1 (BUB1) regulates EGFR signaling by reducing EGFR internalization

EGFR signaling initiates upon ligand binding which leads to activation and internalization of the receptor-ligand complex. Here, we evaluated if BUB1 impacted EGFR signaling by regulating EGFR receptor internalization and activation. BUB1 was ablated genomically (siRNA) or biochemically (2OH-BNPP1) in cells. EGF ligand was used to initiate EGFR signaling while disuccinimidyl suberate (DSS) was used for cross linking cellular proteins. EGFR signaling was measured by western immunoblotting and receptor internalization was evaluated by fluorescent microscopy (pEGFR (pY1068) colocalization with early endosome marker EEA1). siRNA mediated BUB1 depletion led to an overall increase in total EGFR levels and more phospho-EGFR (Y845, Y1092, and Y1173) dimers while the amount of total EGFR (non-phospho) dimers remained unchanged. BUB1 inhibitor (BUB1i) decreased EGF mediated EGFR signaling including pEGFR Y845, pAKT S473 and pERK1/2 in a time dependent manner. Additionally, BUB1i also reduced EGF mediated pEGFR (Y845) dimers (asymmetric dimers) without affecting total EGFR dimers (symmetric dimers) indicating that dimerization of inactive EGFR is not affected by BUB1. Furthermore, BUB1i blocked EGF mediated EGFR degradation (increase in EGFR half-life) without impacting half-lives of HER2 or c-MET. BUB1i also reduced co-localization of pEGFR with EEA1 positive endosomes suggesting that BUB1 might modulate EGFR endocytosis. Our data provide evidence that BUB1 protein and its kinase activity may regulate EGFR activation, endocytosis, degradation, and downstream signaling without affecting other members of the receptor tyrosine kinase family.
Comparison of some parameters in estimating in-hospital mortality risk in patients undergoing open-heart surgery.

OBJECTIVE Despite accumulating evidence showing the importance of various scoring systems in predicting preoperative mortality rates among patients who are undergoing open cardiac surgery, the prediction of in-hospital mortality is still limited. This study aimed to investigate the contributing factors associated with in-hospital mortality in patients who undergo cardiac surgery. PATIENTS AND METHODS All patients, aged 19 to 80 years, who underwent cardiac surgery between February 2019 and November 2020 at our tertiary healthcare institute were analyzed retrospectively. Demographic details, transthoracic echocardiography data, operation-related details, cardiopulmonary bypass time and laboratory measurement results were retrieved from the institutional digital database. RESULTS Data was available for a total of 311 subjects whose median age was 59 (52-67) years, and 65% of which were male. Among these 311 subjects, 296 (95%) were successfully discharged; however, in-hospital mortality was observed in 15 (5%) patients. Multiple logistic regression analysis revealed that low ejection fraction (p=0.049 and p=0.018), emergency surgery (p=0.022), low postoperative platelet (p=0.002) and high postoperative creatinine (p=0.007) were the most significant risk factors of mortality. CONCLUSIONS In conclusion, in a population of subjects undergoing cardiac and thoracic surgery, the in-hospital mortality rate was 4.8%. Left ventricular ejection fraction (LVEF) <40%, emergency surgery, postoperative platelet count and postoperative creatinine were significant risk factors for mortality.
Adequate versus deep response to ursodeoxycholic acid in primary biliary cholangitis: To what extent and under what conditions is normal alkaline phosphatase level associated with complication-free survival gain?

Background and Aims: Normal alkaline phosphatase (ALP) levels in ursodeoxycholic acid (UDCA)-treated patients with primary biliary cholangitis (PBC) are associated with better long-term outcome. However, second-line therapies are currently recommended only when ALP levels remain above 1.5 times the upper limit of normal (×ULN) after 12-month UDCA. We assessed whether, in patients considered good responders to UDCA, normal ALP levels were associated with significant survival gains. Approach and Results: We performed a retrospective cohort study of 1047 patients with PBC who attained an adequate response to UDCA according to Paris-2 criteria. Time to liver-related complications, liver transplantation, or death was assessed using adjusted restricted mean survival time (RMST) analysis. The overall incidence rate of events was 17.0 (95% CI: 13.7–21.1) per 1000 out of 4763.2 patient-years. On the whole population, normal serum ALP values (but not normal gamma-glutamyl transpeptidase (GGT), alanine aminotransferase (ALT), or aspartate aminotransferase (AST); or total bilirubin < 0.6 ×ULN) were associated with a significant absolute complication-free survival gain at 10 years (mean 7.6 months, 95% CI: 2.7 - 12.6 mo.; p = 0.003). In subgroup analysis, this association was significant in patients with a liver stiffness measurement ≥ 10 kPa and/or age ≤ 62 years, with a 10-year absolute complication-free survival gain of 52.8 months (95% CI: 45.7–59.9, p < 0.001) when these 2 conditions were met. Conclusions: PBC patients with an adequate response to UDCA and persistent ALP elevation between 1.1 and 1.5 ×ULN, particularly those with advanced fibrosis and/or who are sufficiently young, remain at risk of poor outcome. Further therapeutic efforts should be considered for these patients.
Stability and Hopf bifurcation of an HIV infection model with saturation incidence and two delays

In this paper, the dynamical behaviors of a viral infection model with cytotoxic T-lymphocyte (CTL) immune response, immune response delay and production delay are investigated. The threshold values for virus infection and immune response are established. By means of Lyapunov functionals methods and LaSalle's invariance principle, sufficient conditions for the global stability of the infection-free and CTL-absent equilibria are established. Global stability of the CTL-present infection equilibrium is also studied when there is no immune delay in the model. Furthermore, to deal with the local stability of the CTL-present infection equilibrium in a general case with two delays being positive, we extend an existing geometric method to treat the associated characteristic equation. When the two delays are positive, we show some conditions for Hopf bifurcation at the CTL-present infection equilibrium by using the immune delay as a bifurcation parameter. Numerical simulations are performed in order to illustrate the dynamical behaviors of the model.
Elucidating interprotein energy transfer dynamics within the antenna network from purple bacteria

Significance Energy transport over long distances with high efficiency is a critical design parameter of photosynthetic light harvesting, where photonic energy travels across multiple antenna proteins to reach the reaction center. Understanding transport requires that energy transfer between proteins be resolved, but this crucial step has been experimentally inaccessible. Here, we used near-native membrane nanodiscs to isolate two antenna proteins from purple bacteria, one of the most ancient and most efficient photosynthetic organisms. By measuring the structural organization and dynamics, we characterized interprotein energy transfer across the physiological range of distances. Simulations revealed that the presence of fast energy transfer steps enhances long-distance transport. These results point to pairwise interactions as a key mediator of energy transport.
Screening for pre‐eclampsia by maternal serum glycosylated fibronectin at 11−13 weeks' gestation

To examine the performance of screening for preterm and term pre‐eclampsia (PE) at 11–13 weeks' gestation by maternal factors and combinations of maternal serum glycosylated fibronectin (GlyFn), mean arterial pressure (MAP), uterine artery pulsatility index (UtA‐PI) and serum placental growth factor (PlGF).
Spatiotemporal profile of atrophy in the first year following moderate‐severe traumatic brain injury

Abstract Traumatic brain injury (TBI) triggers progressive neurodegeneration resulting in brain atrophy that continues months‐to‐years following injury. However, a comprehensive characterization of the spatial and temporal evolution of TBI‐related brain atrophy remains incomplete. Utilizing a sensitive and unbiased morphometry analysis pipeline optimized for detecting longitudinal changes, we analyzed a sample consisting of 37 individuals with moderate‐severe TBI who had primarily high‐velocity and high‐impact injury mechanisms. They were scanned up to three times during the first year after injury (3 months, 6 months, and 12 months post‐injury) and compared with 33 demographically matched controls who were scanned once. Individuals with TBI already showed cortical thinning in frontal and temporal regions and reduced volume in the bilateral thalami at 3 months post‐injury. Longitudinally, only a subset of cortical regions in the parietal and occipital lobes showed continued atrophy from 3 to 12 months post‐injury. Additionally, cortical white matter volume and nearly all deep gray matter structures exhibited progressive atrophy over this period. Finally, we found that disproportionate atrophy of cortex along sulci relative to gyri, an emerging morphometric marker of chronic TBI, was present as early as 3 month post‐injury. In parallel, neurocognitive functioning largely recovered during this period despite this pervasive atrophy. Our findings demonstrate msTBI results in characteristic progressive neurodegeneration patterns that are divergent across regions and scale with the severity of injury. Future clinical research using atrophy during the first year of TBI as a biomarker of neurodegeneration should consider the spatiotemporal profile of atrophy described in this study.
Computer-assisted equilibrium validation for the diblock copolymer model

The diblock copolymer model is a fourth-order parabolic partial differential equation which models phase separation with fine structure. The equation is a gradient flow with respect to an extension of the standard van der Waals free energy functional which involves nonlocal interactions. Thus, the long-term dynamical behavior of the diblock copolymer model is described by its finite-dimensional attractor. However, even on one-dimensional domains, the full structure of the underlying equilibrium set is not fully understood. In this paper, we develop a rigorous computational approach for establishing the existence of equilibrium solutions of the diblock copolymer model. We consider both individual solutions, as well as pieces of solution branches in a parameter-dependent situation. The results are presented for the case of one-dimensional domains, and can easily be implemented using standard interval arithmetic packages.
Altered collagen I and premature pulmonary embryonic differentiation in patients with OI type II

Pulmonary hypoplasia and respiratory failure are primary causes of death in patients with osteogenesis imperfecta (OI) type II. OI is a genetic skeletal disorder caused by pathogenic variants in genes encoding collagen type I. It is still unknown if the collagen defect also affects lung development and structure, causing lung hypoplasia in OI type II. The aim of this study was to investigate the intrinsic characteristics of OI embryonic lung parenchyma and to determine whether altered collagen type I may compromise airway development and lung structure. Lung tissue from nine fetuses with OI type II and six control fetuses, matched by gestational age, was analyzed for TTF‐1 and collagen type I expression by immunohistochemistry, to evaluate the state of lung development and amount of collagen. The differentiation of epithelium into type 2 pneumocytes during embryonic development was premature in OI type II fetuses compared to controls (p < 0.05). Collagen type I showed no significant differences between the two groups. However, the amount of alpha2(I) chains was higher in fetuses with OI and the ratio of alpha1(I) to alpha2(I) lower in OI compared to controls. Cell differentiation during lung embryonic development in patients with OI type II is premature and impaired. This may be the underlying cause of pulmonary hypoplasia. Altered cell differentiation can be secondary to mechanical chest factors or a consequence of disrupted type I collagen synthesis. Our findings suggest that collagen type I is a biochemical regulator of pulmonary cell differentiation, influencing lung development.
SIMULATION OF STAR FORMATIONS IN COSMOLOGICAL VOLUME (240 Mpc/h) 3

In this paper the Lambda Cold Dark Matter ( ΛCDM) model was used for studying star formation inside a box of size (240Mpc/h) 3 by simulating eight million dark matter particles and eight million gas particles together with cosmological density Ω=0.25, dark energy density ΩΛ=0.75, baryon density Ωb=0.04, fluctuation amplitude σ8=0.9 and Hubble constant H0=100h kms -1 Mpc -1 . The gadget-2 code was used for simulating the particles from early Universe, z=30 (450 million years) to z=0 (13.4 billion years). In the box the structures formation were shown including galaxy clusters, voids and filaments which observed clearly at low redshift, z=0. In the temperature-density planes, the thermal processes of cooled gas show the density and temperature values which were different at each redshift, and the gas cooled in the box at nearly 10 4 K caused star formations at certain redshifts. It was also found that stars were formed from z=7.3 which increased with decreasing redshifts. In addition, the total number of star formed in the box was 226217 stars. Sixteen processors of high performance supercomputer of Nottingham University-England were used in the simulation.
Demographic consequences of phenological asynchrony for North American songbirds

Significance Changes in phenology—the timing of seasonal events—are among the most pronounced ecological responses to climate change. Scientists are concerned that differential phenological responses across trophic levels could have negative consequences for animal populations, but widespread evidence is lacking. Here, we present evidence of a link between reproductive productivity and the timing of both bird breeding and the arrival of spring across the North American continent. These findings, which are the broadest yet in extent, in conjunction with evidence that bird phenology is not keeping pace with climate change, suggest that future phenological change will likely result in negative demographic consequences for these birds.
Dental hygienists and dentists as providers of brush biopsies for oral mucosa screening.

BACKGROUND Oral cancer is a severe and potentially fatal disease usually starting in the squamous epithelium lining the oral cavity. Together with oropharyngeal carcinoma, it is the fifth to sixth most common malignancy worldwide. To limit the increase in the global oral cancer incidence over the past two decades, the World Health Assembly adopted a resolution urging member states to integrate preventive measures such as engagement and training of dental personnel in screening, early diagnosis, and treatment into their national cancer control programs. AIM The aim of this study was to investigate if dental hygienists (DHs) and dentists (Ds) in general dental practice care can be entrusted to perform brush sampling of oral potentially malignant disorders (OPMDs), and to evaluate their level of comfort in performing brush biopsies. METHODS Participants were five DHs and five Ds who received one day of theoretical and clinical training in oral pathology to identify OPMDs (leukoplakia [LP], erythroplakia [EP], and oral lichen planus [OLP]), and perform brush sampling for PAP cytology and high-risk human papillomavirus (hrHPV) analysis. RESULTS Out of 222 collected samples, 215 were adequate for morphological assessment and hrHPV analysis. All the participants agreed that sample collection can be incorporated in DHs and Ds routine clinical duties, and most of them reported that sample collection and processing was easy/quite easy. CONCLUSION Dentists and DHs are capable of collecting satisfactory material for cytology and hrHPV analysis. All the participating DHs and Ds were of the opinion that brush sampling could be handled routinely by DHs and Ds in GDP.
Long‐term forecast of thermal mortality with climate warming in riverine amphipods

Forecasting long‐term consequences of global warming requires knowledge on thermal mortality and how heat stress interacts with other environmental stressors on different timescales. Here, we describe a flexible analytical framework to forecast mortality risks by combining laboratory measurements on tolerance and field temperature records. Our framework incorporates physiological acclimation effects, temporal scale differences and the ecological reality of fluctuations in temperature, and other factors such as oxygen. As a proof of concept, we investigated the heat tolerance of amphipods Dikerogammarus villosus and Echinogammarus trichiatus in the river Waal, the Netherlands. These organisms were acclimated to different temperatures and oxygen levels. By integrating experimental data with high‐resolution field data, we derived the daily heat mortality probabilities for each species under different oxygen levels, considering current temperatures as well as 1 and 2°C warming scenarios. By expressing heat stress as a mortality probability rather than a upper critical temperature, these can be used to calculate cumulative annual mortality, allowing the scaling up from individuals to populations. Our findings indicate a substantial increase in annual mortality over the coming decades, driven by projected increases in summer temperatures. Thermal acclimation and adequate oxygenation improved heat tolerance and their effects were magnified on longer timescales. Consequently, acclimation effects appear to be more effective than previously recognized and crucial for persistence under current temperatures. However, even in the best‐case scenario, mortality of D. villosus is expected to approach 100% by 2100, while E. trichiatus appears to be less vulnerable with mortality increasing to 60%. Similarly, mortality risks vary spatially: In southern, warmer rivers, riverine animals will need to shift from the main channel toward the cooler head waters to avoid thermal mortality. Overall, this framework generates high‐resolution forecasts on how rising temperatures, in combination with other environmental stressors such as hypoxia, impact ecological communities.
Congruence between ultraconserved element‐based matrices and phylotranscriptomic datasets in the scorpion Tree of Life

Scorpions are ancient and historically renowned for their potent venom. Traditionally, the systematics of this group of arthropods was supported by morphological characters, until recent phylogenomic analyses (using RNAseq data) revealed most of the higher‐level taxa to be non‐monophyletic. While these phylogenomic hypotheses are stable for almost all lineages, some nodes have been hard to resolve due to minimal taxonomic sampling (e.g. family Chactidae). In the same line, it has been shown that some nodes in the Arachnid Tree of Life show disagreement between hypotheses generated using transcritptomes and other genomic sources such as the ultraconserved elements (UCEs). Here, we compared the phylogenetic signal of transcriptomes vs. UCEs by retrieving UCEs from new and previously published scorpion transcriptomes and genomes, and reconstructed phylogenies using both datasets independently. We reexamined the monophyly and phylogenetic placement of Chactidae, sampling an additional chactid species using both datasets. Our results showed that both sets of genome‐scale datasets recovered highly similar topologies, with Chactidae rendered paraphyletic owing to the placement of Nullibrotheas allenii. As a first step toward redressing the systematics of Chactidae, we establish the family Anuroctonidae (new family) to accommodate the genus Anuroctonus.