Miracle-dz/UniFAR-FTUs huggingface dataset:
Human complement component C3 N-glycome changes in type 1 diabetes complications

Aim Changes in N-glycosylation have been described in numerous diseases and are being considered as biomarkers of ongoing pathological condition. Previous studies demonstrated the interrelation of N-glycosylation and type 1 diabetes (T1D), particularly linking serum N-glycan changes with complications accompanying the disease. Moreover, the role of complement component C3 in diabetic nephropathy and retinopathy has been implicated, and C3 N-glycome was found to be altered in young T1D patients. Therefore, we investigated associations between C3 N-glycan profiles and albuminuria and retinopathy accompanying T1D, as well as glycosylation connection with other known T1D complication risk factors. Research design and methods Complement component C3 N-glycosylation profiles have been analyzed from 189 serum samples of T1D patients (median age 46) recruited at a Croatian hospital centre. Using our recently developed high-throughput method, relative abundances of all six of the C3 glycopeptides have been determined. Assessment of C3 N-glycome interconnection with T1D complications, hypertension, smoking status, estimated glomerular filtration rate (eGFR), glycaemic control and duration of the disease was done using linear modelling. Results Significant changes of C3 N-glycome in severe albuminuria accompanying type 1 diabetes were observed, as well as in T1D subjects with hypertension. All except one of the C3 glycopeptides proved to be associated with measured HbA1c levels. One of the glycoforms was shown to be changed in non-proliferative T1D retinopathy. Smoking and eGFR showed no effect on C3 N-glycome. Furthermore, C3 N-glycosylation profile was shown to be independent of disease duration. Conclusion This study empowered the role of C3 N-glycosylation in T1D, showing value in distinguishing subjects with different diabetic complications. Being independent of the disease duration, these changes may be associated with the disease onset, making C3 N-glycome a potential novel marker of the disease progression and severity.
The Gaussian Network Model

One of the first ENMs developed for the study of protein dynamics is the Gaussian Network Model (GNM) of Bahar and others [1]. This model has its origins in elastic polymer theory, although the exact connection may be a little difficult to see. The early GNM papers refer to the work of Flory [2] as the inspiration for the model. Flory’s paper discusses the elastic properties of bulk polymer materials, such as rubber. Specifically, the paper addresses polymer networks, or random networks of long polymers that cross and connect at certain points. In the Flory model, the nodes of the network are crossings of polymer chains, and its edges are the polymer chains themselves. The elastic properties of a random network of polymers thus arises as the sum of elastic interactions between nodes that are connected by springlike chains. In the GNM, the nodes are the protein residues, each represented by it alpha carbon atom. The edges represent the abstract realization of the net pairwise forces between residues in the folded protein. In the spirit of Flory, we can derive the GNM from the elastic nature of a simple chain molecule. Recall that the mean end-to-end vector h of a freely jointed chain with n edges of length l is given by
The ReInforcement of adherence via self-monitoring app orchestrating biosignals and medication of RivaroXaban in patients with atrial fibrillation and co-morbidities: a study protocol for a randomized controlled trial (RIVOX-AF)

Background Because of the short half-life of non-vitamin K antagonist oral anticoagulants (NOACs), consistent drug adherence is crucial to maintain the effect of anticoagulants for stroke prevention in atrial fibrillation (AF). Considering the low adherence to NOACs in practice, we developed a mobile health platform that provides an alert for drug intake, visual confirmation of drug administration, and a list of medication intake history. This study aims to evaluate whether this smartphone app-based intervention will increase drug adherence compared with usual care in patients with AF requiring NOACs in a large population. Methods This prospective, randomized, open-label, multicenter trial (RIVOX-AF study) will include a total of 1,042 patients (521 patients in the intervention group and 521 patients in the control group) from 13 tertiary hospitals in South Korea. Patients with AF aged ≥19 years with one or more comorbidities, including heart failure, myocardial infarction, stable angina, hypertension, or diabetes mellitus, will be included in this study. Participants will be randomly assigned to either the intervention group (MEDI-app) or the conventional treatment group in a 1:1 ratio using a web-based randomization service. The intervention group will use a smartphone app that includes an alarm for drug intake, visual confirmation of drug administration through a camera check, and presentation of a list of medication intake history. The primary endpoint is adherence to rivaroxaban by pill count measurements at 12 and 24 weeks. The key secondary endpoints are clinical composite endpoints, including systemic embolic events, stroke, major bleeding requiring transfusion or hospitalization, or death during the 24 weeks of follow-up. Discussion This randomized controlled trial will investigate the feasibility and efficacy of smartphone apps and mobile health platforms in improving adherence to NOACs. Trial registration The study design has been registered in ClinicalTrial.gov (NCT05557123).
Causal inference between aggressive extrathyroidal extension and survival in papillary thyroid cancer: a propensity score matching and weighting analysis

Background Extrathyroidal extension is a major risk factor for poor prognosis in papillary thyroid cancer. However, the effect of different degrees of extrathyroidal extension on prognosis remains controversial. We performed a retrospective study to elucidate how the extent of extrathyroidal extension in papillary thyroid cancer affected the clinical prognosis of patients and its covariates. Methods The study included 108,426 patients with papillary thyroid cancer. We categorized the extent of extension into none, capsule, strap muscles, and other organs. Three causal inference methods for retrospective studies, namely, inverse probability of treatment weighting, standardized mortality ratio weighting, and propensity score matching analysis, were used to minimize potential selection bias. Kaplan–Meier analysis and univariate Cox regression analyses were applied to analyze the precise effect of ETE on survival in papillary thyroid cancer patients. Results In the Kaplan–Meier survival analysis, only extrathyroidal extension into or beyond the strap muscles was statistically significant for both overall survival (OS) and thyroid cancer-specific survival (TCSS). In univariate Cox regression analyses before and after matching or weighting based on causal inference, extrathyroidal extension into soft tissues or other organs is a high-risk factor for both overall survival and thyroid cancer-specific survival. Sensitivity analysis revealed that lower overall survival was observed in patients with older age (≥55) and larger tumor size (>2 cm) of papillary thyroid cancer with extrathyroidal extension into or beyond the strap muscles. Conclusions Our study indicates that extrathyroidal extension into soft tissues or other organs is a high-risk factor in all papillary thyroid cancer. Even though invasion into the strap muscles did not seem to be a marker for poor prognosis, it still impaired the overall survival of patients with older age (≥55 years old) or larger tumor size (>2 cm). Further investigation is needed to confirm our results and to clarify further risk factors independent of extrathyroidal extension.
Low Rank Pruning via Output Perturbation

Neural networks have become very widespread due to the mainstream availability of computational devices such as GPUs, and as these devices become more powerful, these networks have become much larger. With the growing demand for fast, efficient networks, weight pruning has become a popular technique for reducing both the speed and computational time of these networks, but they introduce sparse matrices, which can be tedious to implement properly. In this paper, we investigate a different approach to model pruning involving low rank decompositions and output perturbation
Early warning scores to identify the risk of clinical worsening or death in patients hospitalized for COVID-19

Background: identifying patients at risk for negative outcomes is key for performing a timely triage and adapting the care intensity for patients with COVID-19. Early warning scores are rules that alert to the risk of adverse outcomes during hospitalization. We sought to validate the modified NEWS, NEWS-2 and COVID-19 Severity Index (CSI). Methods: a prospective observational multicenter study of patients hospitalized for COVID-19 at three quaternary care hospitals in Bogotá, Colombia, between April and November 2020. The operating characteristics and areas under the ROC curve were calculated. Results: 711 patients were included, in whom the AUC for death was 0.68, 0.58 and 0.68, and for ICU admission was 0.61, 0.63 and 0.66 for mNEWS, NEWS-2 and CSI, respectively. The CSI had the greatest sensitivity for ICU admission or death (87.6 and 90.0%) and NEWS-2 had the greatest specificity (76.8 and 75.5%). Conclusions: the three early warning scores had a low to moderate performance in predicting ICU admission or death in patients hospitalized for COVID-19. (Acta Med Colomb 2022; 47. DOI: https://doi.org/10.36104/amc.2022.2225).
An immersed free-surface boundary treatment for seismic wave simulation

ABSTRACTFinite-difference methods are popular for wave simulation within the seismic exploration community, thanks to their efficiency. However, difficulties arise when encountering complex topography due to the regular grid pattern of the finite-difference schemes. Despite alternatives that can handle the free surface with little effort, such as the spectral element or discontinuous Galerkin’s methods, incorporating a free-surface boundary condition within the finite-difference framework is still appealing, even at the cost of extra algorithm complexity and stronger requirement of computational resources. We present a free-surface boundary treatment within the finite-difference framework, belonging to the family of the immersed-boundary methods. Inherently, the presented boundary treatment is separated from the rest of the wave simulation, which makes it easy to be integrated in existing finite-difference codes. Specifically, we construct an extrapolation operator for each grid point above the free surfa.
Modified method of sea clutter cancellation for sky wave radar

Considering that the times of cancellation can not be determined adaptively by using the conventional sea clutter cancellation of circulation for sky wave radar, this paper puts forward an algorithm,namely a sea clutter cancellation of circulation based on referring to the adjacent cells. This proposed algorithm constructs a reference signal using the echoe signals from other resolution cells in the sub zone where the resolution cells for current sea surface detection are located, and implements the sea clutter cancellation of circulation using the sea clutter's Doppler frequency parameter extracted from the reference signals. By theoretical analysis and test of the measured data, it is proved that this algorithm is of availability.
Asymptotical null structure of an electro-vacuum spacetime with a cosmological constant

Bondi–Sachs (BS) framework is a powerful tool to analyze the asymptotical null structure of a spacetime. Based on Bondi’s outgoing boundary condition, the asymptotical null structure of an electro-vacuum spacetime without a cosmological constant has been constructed clearly. Recently more and more observations imply that the Einstein equation should be modified with an nonzero cosmological constant. It is interesting to investigate the asymptotical null structure of a spacetime with a cosmological constant. In this paper, we extend our previous result from vacuum case to electro-vacuum case. We find that the gravitational sector of the asymptotical null structure depends strongly on the boundary conditions, while the electrical sector is independent of the boundary condition.
Inequalities for the quantum Renyi divergences with applications to compound coding problems

We show two-sided bounds between the conventional quantum R\'enyi divergences and the new notion of R\'enyi divergences introduced recently in M\"uller-Lennert, Dupuis, Szehr, Fehr and Tomamichel, J. Math. Phys. 54, 122203, (2013), and Wilde, Winter, Yang, arXiv:1306.1586. The bounds imply that the two versions can be used interchangeably near alpha=1, and hence one can benefit from the best properties of both when proving coding theorems in the case of asymptotically vanishing error. We illustrate this by giving short and simple proofs of the quantum Stein's lemma with composite null-hypothesis, universal source compression, and the achievability part of the classical capacity of compound quantum channels. Apart from the above interchangeability, we benefit from a weak quasi-concavity property of the new Renyi divergences that we also establish here.
Horizontal Jets in Stagnant Fluid of Other Density

The influence of the density difference between a jet and the surrounding fluid on the diffusion caused by a circular horizontal submerged turbulent jet is studied theoretically on the basis of the similarity principle. A theoretical solution is given on the basis of the assumption that the local variation of density in the jet is small in comparison with the density of the ambient fluid. The theoretical results show how the coordinates of the axis of the jet and the rate of mixing, and the velocity at the axis of the jet depend on the initial density difference between the jet and the stagnant ambient fluid and on the velocity of the jet when it issues from a nozzle. The theoretical solution agrees fairly well with experimental data available in literature. Only three dimensional, circular horizontal jets are considered in this study.
INFLUENCE OF DIFFERENT SHOULDER ABDUCTION ANGLES DURING BASEBALL PlTCHING ON 'THROWING PERFORMANCE AND JOINT KINETICS

The relationships between shoulder abduction angle at ball release and wrist velocity and several injury-related kinetic parameters were investigated. Based on kinematic data of nine overhand and three-quarter-hand pitchers, several pitching motions with different shoulder abduction angles from the original were simulated. The wrist velocity and several injury-related kinetic parameters for the motion with 90 degree shoulder abduction angle at ball release were compared with those for the motions with other shoulder abduction angles. The 90 degree abduction angle maximised wrist velocity and decreased elbow joint kinetics, but did not always decrease shoulder joint kinetics.
Efficacy, biosafety, and metabolic impacts of feeding mice egg yolks enriched with three bioactive nutrients in different combinations

Background: Docosahexaenoic acid (DHA), 25-hydroxyvitamin D3 (25-OH D3), and astaxanthin (AST) are three bioactive and health-promoting nutrients. We previously enriched eggs with DHA alone and in combination with 25-OH D3 and (or) AST as a novel food source of these nutrients by the public. This study was to determine dietary efficacy, biosafety, and metabolic impacts and mechanisms of feeding these egg yolks with four different enrichments of the three nutrients in mice. Methods: Eighty mice (23- to 40-week-old, n = 8, four males and females each) were divided into two experiments and were fed a sucrose-yeast basal diet with control egg yolk (BD) or one of the four types of enriched yolks (BD + DHA, BD + DHA + 25-OH D3, BD + DHA + AST, and BD + DHA + 25-OH D3 + AST) at recommended (1X, Experiment I) and high dose (5X, Experiment II) for 6 weeks. Concentrations of fatty acids, 25-OH D3, AST, and lipids and expression of genes and proteins related to lipid and vitamin D metabolism in the plasma, liver, and (or) heart were determined. Data within each experiment were analyzed by one-way ANOVA. Results: Compared with BD, the four diets with enriched yolks at the 1X level elevated (P < 0.001, up to 61%) hepatic DHA concentrations. Feeding the enriched yolks at either dose did not affect body weights or plasma glucose and triacylglycerol concentrations. In Experiment I, total cholesterol concentrations were 40% higher (P < 0.05) in the liver of BD + DHA than BD and were 1.5-fold higher (P < 0.05) in the heart of BD + DHA + 25-OH D3 + AST than BD + DHA + 25-OH D3. Compared with BD + DHA, BD + DHA + 25-OH D3 upregulated (P < 0.05) hepatic Dgat1 gene expression by 1.4-fold and hepatic DGAT1 protein expression by 1.7-fold. Conclusions: Feeding mice egg yolks enriched with DHA alone or with other nutrients at two doses (1X and 5X) improved hepatic DHA status and exerted moderate impacts on tissue lipid profiles and the related gene expressions. These eggs may be safe for future human trials.
Distinct trajectories of caregiver–toddler physiological attunement during routine vaccinations

Supplemental Digital Content is Available in the Text. Abstract Introduction: Toddlers rely on their caregivers for regulatory support when faced with pain-related distress. The caregiver's ability to support their toddler relies on their capacity to regulate their own distress and respond effectively to the child's need for support. The aim of the current study was to describe patterns of caregiver–toddler physiological co-regulatory patterns, also known as attunement, during routine vaccinations across the second year of life. Methods: Caregiver–toddler dyads (N = 189) were part of a longitudinal cohort observed at either 12-, 18-, or 24-month well-baby vaccinations. Parallel-process growth-mixture modeling was used to examine patterns of dyadic physiological co-regulatory responses, indexed by high-frequency heart rate variability (HF-HRV). Results: Three groups of dyads were discerned. The largest group (approximately 80%) demonstrated physiological attunement, with a stable and parallel regulatory pattern of HF-HRV from baseline to postneedle. The second group (7.9%) had parallel regulatory trajectories but with notably lower (ie, less regulated) HF-HRV values, which indicates independent regulatory responses (ie, a lack of attunement among dyad members). The third group (11.1%) showed diverging regulatory trajectories: Caregivers showed a stable regulatory trajectory, but toddlers demonstrated a steep decrease followed by an increase in HF-HRV values that surpassed their baseline levels by the third minute postneedle. Post hoc analyses with the HF-HRV groupings explored heart rate patterns and potential predictors. Conclusions: These findings elucidate potential adaptive and maladaptive co-regulatory parasympathetic patterns in an acute pain context.
Pharmacotherapeutic Potential of Aloe secundiflora against Colorectal Cancer Growth and Proliferation

Aloe species are widespread and diverse in African ecosystems, and this commonly correlates to their habitual use as reservoirs of herbal medicine. The side effects associated with chemotherapy and the development of antimicrobial resistance to empirically used antimicrobial drugs are substantial, paving the way for novel phytotherapeutic approaches. This comprehensive study aimed to evaluate and present Aloe secundiflora (A. secundiflora) as a compelling alternative with potential benefits in colorectal cancer (CRC) treatment. Important databases were systematically searched for relevant literature, and out of a large collection of 6421 titles and abstracts, only 68 full-text articles met the inclusion criteria. A. secundiflora possesses an abundant presence of bioactive phytoconstituents in the leaves and roots, including anthraquinones, naphthoquinones, phenols, alkaloids, saponins, tannins, and flavonoids, among others. These metabolites have proven diverse efficacy in inhibiting cancer growth. The presence of innumerable biomolecules in A. secundiflora signifies the beneficial effects of incorporating the plant as a potential anti-CRC agent. Nonetheless, we recommend further research to determine the optimal concentrations necessary to elicit beneficial effects in the management of CRC. Furthermore, they should be investigated as potential raw ingredients for making conventional medications.
CELL MODELS FOR FLOW THROUGH A SWARM OF IMPERMEABLE CYLINDERS COVERED WITH POROUS LAYER

This paper concerns a comparative study of flow through aggregate of porous cylindrical particles with impermeable core, using different cell methods. Four known boundary conditions namely Happel’s, Kuwabara’s, Kvashnin’s and Mehta-Morse’s (Cunninghum) boundary conditions are considered on the outer cell and their comparison has been made on the drag force and the flow pattern. Emphasis is given on impact of jump coefficient on the drag force and some new results are reported. Flow through permeable aggregates has always been a topic, frequently used to investigate the problems such as membrane filtration process, sedimentation and flow of underground water and oil etc. Flow through porous media is modeled by Brinkman’s equation (Brinkman 1947) which is modified form of Darcy’s equation. Currently, the cell model technique is very effectively used for investigation of such flows. The basic principle of the cell model technique is to replace a system of chaotically distributed particles by a periodic array of cylinders embedded in identical cylindrical liquid cells. Appropriate boundary conditions on the cell take into account, the effect of surrounding particles on the particle in the center of the cell. Happel (1959) and Kuwabara (1959) proposed cell models in which both particle and outer envelope are spheres/cylinders. The Happel model assumes nil shear stress on the outer envelope, whereas, Kuwabara assumed zero vorticity on the outer envelope. Apart from this, Kvashnin (1979) and Mehta-Morse (Cunninghum) (1975) gave their respective boundary conditions for the outer cell. However, Mehta-Morse (1975) assumed the tangential velocity as a component of the fluid velocity, signifying the homogeneity of the flow on the cell boundary. This paper concerns a brief review of the four boundary conditions applied on the cell surface: Happel’s, Kuwabara’s, Kvashnin’s and Mehta-Morse’s boundary conditions for the Stokes flow through porous circular cylinder-in-cell enclosing an impermeable core with stress jump boundary condition at the fluid-porous interface. Results obtained are of great consequences in the filtration process and in biomechanics to evaluate stress on smooth muscle cells which are assumed to be a periodic array of cylindrical particles (1995).